* AMBER Cornell et al. (parm94) force field conversion * See: JACS (1995) 117, 5179-5197. * nucleic acid part converted by tec3, march 1997 * protein part converted by tec3, february 1999 * 23 1 ! ! WARNING! Please read through all the comments here in order to ! properly understand how to set up a CHARMM run with this force ! field and to properly understand the limitations and potential ! errors... ! ! NOTE: the charges here are un-scaled and represent the ! exact AMBER charges. See the comment on the electrostatics below. ! ! Standard CHARMM residue names are utilized: ! ! ADE, THY, GUA, CYT, URA. ! ! ALA, ARG, ASN, ASP, CYS, CYM, CYX, GLN, GLU, GLH, ! GLY, HID, HIE, HIP, ILE, LEU, LYS, MET, PHE, PRO, ! SER, THR, TRP, TYR, VAL, ACE, NME ! ! ! Atom type names conform to the AMBER Cornell et. al. 1995, ! parm94.dat, all_nuc94.in, and all_amino* naming conventions ! where possible. Exceptions to this rule include types with "*" ! in the name (i.e. N*->NS, C*->CS). CHARMM atom names are utilized. ! To build the residues, the BILD arrays from the top_all22_na.inp were ! utilized (since these are actually probably more trustworthy then ! those supplied in AMBER) and modified where necessary (i.e. THY). ! They may not be reliable in all cases. BONDS were also copied from ! top_all22_na.inp and all angles and dihedrals autogenerated. ! The impropers were taken straight from the AMBER residue topology ! files (and placed in proper order). All this was done by hand editing. ! ! Results were checked by comparing energies and forces for all the ! residues defined herein. In general, in simulations performing a ! single energy and force evaluation with a cutoff large enough to ! span the entire system the energies and forces agree ! to within ~0.00005 using both CHARMM and AMBER. The AMBER energies ! and forces were calculated using AMBER 4.1/5.0_alpha sander ! (minimization or dynamics) and CHARMM c25n3 (ener). Note that ! differences in the forces may be apparent if the coordinates do not ! match exactly or in cases where different constants are used between ! AMBER and CHARMM. These points require a little more elaboration. ! ! Differences in the coordinates: ! ! (*) incorrect mapping between AMBER and CHARMM coordinates ! (i.e. not 1-to-1). This is possible with hand editting of the ! AMBER names to convert to CHARMM if the correct mapping isn't ! followed. The only case that was readily apparent in this ! analysis was incorrect mapping of H2' and H2'' in the DNA ! residues of ADE, GUA and CYT. The rename command can be used ! to swap names and alleviate this problem (which is not a real ! problem except when comparing forces). ! ! (*) parm coordinate precision. If the parm coordinates were ! created from a PDB file using the link-edit-parm path, improper ! conversion from text->binary->text in edit/parm leads to ! differences in the parm coordinates from the PDB file. ! Therefore, the coordinates will be different than those ! generated by CHARMM using the same PDB coordinates. Therefore, ! prior to comparing forces, the PDB should be converted directly ! to the parm coordinates (which can be done using carnal). ! ! Differences in the electrostatic energies: ! ! (*) The conversion from charge units to kcal/mol in CHARMM is based ! on the value 332.0716 whereas AMBER uses 18.2223**2 or 332.0522173. ! The actual value is somewhat lower than both these values ! (~331.843)! To convert the charges to "CHARMM", they should be ! multiplied by 1.000058372. This was not done within this file. ! [When this is done, the charges are not rounded and therefore ! non-integral charges for the residues are apparent.] To get around ! this problem either the charges can be scaled within CHARMM (which ! will still lead to non-integral charge) or in versions of CHARMM ! beyond c25n3, and through the application of the "AMBER" keyword in ! pref.dat, the AMBER constant can be used. By default, the "fast" ! routines cannot be used with the AMBER-style impropers. In the ! later versions of CHARMM, the AMBER keyword circumvents this ! problem. ! ! BUILDING NUCLEIC ACID STRUCTURES: ! ! To build residues, use the standard naming conventions. By default ! the 5ter and 3ter patchs are applied which convert the first ! residue to a 5'-hydroxyl (no terminal phosphate) and the last ! residue to a 3'-hydroxyl. ! ! NOTE that in the case of case of ADE, GUA and CYT, by default the ! system is RIBONUCLEIC acid. To convert to deoxyribose, use the ! following patchs: ! ! patch DOA5 segid residue <-- 5'-terminal ADE ! patch DOA segid residue <-- standard ADE ! patch DOA3 segid residue <-- 3'-terminal ADE ! patch DOC5 segid residue <-- 5'-terminal CYT ! patch DOC segid residue <-- standard CYT ! patch DOC3 segid residue <-- 3'-terminal CYT ! patch DOG5 segid residue <-- 5'-terminal GUA ! patch DOG segid residue <-- standard GUA ! patch DOG3 segid residue <-- 3'-terminal GUA ! ! ...where "segid" is the current segment and "residue" is the ! residue number ! ! As an example, let's build a single stranded DNA, d[CATG]. We need ! to apply 5' and 3' terminal patches and also patches to turn the ! RNA into DNA for each residue (except THY which is DNA). ! ! read sequence card ! 4 ! CYT ADE THY GUA ! generate s1 setup ! patch doc5 s1 1 ! patch doa s1 2 ! patch dog3 s1 4 ! ! ! PROTEIN PARAMETERS: ! ! note: isolated amino acids have not been tested, only tri-peptides ! with the same amino acids in the chain, i.e. ala-ala-ala, etc. ! have been tested with charged terminii (i.e. nala-ala-cala). ! The patches to the terminii (for each residue append N for the ! N-terminal or C for the C terminal) are applied automatically ! to the first/last residues. In general the energy/force comparison ! is as good as with the nucleic acid parameters, but do note that as ! the energy increases (such as with large van der Waals overlap) the ! absolute agreement no longer is as good. This may relate to (1) ! slight coordinate differences between AMBER/CHARMM and (2) ! numerical differences due to differing operations in the ! calculation. In any event, equivalent parameters are used and ! there is an equivalent number of bonds/angles/dihedrals, etc ! between the CHARMM PSF files and AMBER prmtop files. ! ! PROTEIN CONVERSION NOTES: ! ! (1) there are no terminal CYM (negatively charged CYS) residues ! within the Cornell et al. force field. The CYM and CYX ! residues were not tested for reliability. Use at own risk. ! (2) GLH, or neutral glutamic acid isn't available as a C- or N- ! terminal residue. This has not been tested for reliability; ! use at own risk. Note also that the IC table was not modified ! to include the extra hydrogen... ! (3) The atom order is different for HIP, HID and HIE (all the ! histidine residues so force comparisons were only cursorly ! done, hence use these parameters at own risk. The energies ! agreed though! ! (4) TRP: the impropers on "CD1 CD2 CG CB" are giving a slight ! energy and force error that I do not understand at present. ! Use at own risk. ! ! Any problems? Let me know... ! cheatham@helix.nih.gov, cheatham@cgl.ucsf.edu ! ! ! AMBER atom types and masses (from all_nuc94.in) ! MASS 1 BR 79.90 ! bromine MASS 2 C 12.01 ! sp2 C carbonyl group MASS 3 CA 12.01 ! sp2 C pure aromatic (benzene) MASS 4 CB 12.01 ! sp2 aromatic C, 5&6 membered ring junction MASS 5 CC 12.01 ! sp2 aromatic C, 5 memb. ring HIS MASS 6 CK 12.01 ! sp2 C 5 memb.ring in purines MASS 7 CM 12.01 ! sp2 C pyrimidines in pos. 5 & 6 MASS 8 CN 12.01 ! sp2 C aromatic 5&6 memb.ring junct.(TRP) MASS 9 CQ 12.01 ! sp2 C in 5 mem.ring of purines between 2 N MASS 10 CR 12.01 ! sp2 arom as CQ but in HIS MASS 11 CT 12.01 ! sp3 aliphatic C MASS 12 CV 12.01 ! sp2 arom. 5 memb.ring w/1 N and 1 H (HIS) MASS 13 CW 12.01 ! sp2 arom. 5 memb.ring w/1 N-H and 1 H (HIS) MASS 14 CS 12.01 ! sp2 arom. 5 memb.ring w/1 subst. (TRP) MASS 15 C0 40.08 ! calcium MASS 16 H 1.008 ! H bonded to nitrogen atoms MASS 17 HC 1.008 ! H aliph. bond. to C without electrwd.group MASS 18 H1 1.008 ! H aliph. bond. to C with 1 electrwd. group MASS 19 H2 1.008 ! H aliph. bond. to C with 2 electrwd.groups MASS 20 H3 1.008 ! H aliph. bond. to C with 3 eletrwd.groups MASS 21 HA 1.008 ! H arom. bond. to C without elctrwd. groups MASS 22 H4 1.008 ! H arom. bond. to C with 1 electrwd. group MASS 23 H5 1.008 ! H arom. bond. to C with 2 electrwd. groups MASS 24 HO 1.008 ! hydroxyl group MASS 25 HS 1.008 ! hydrogen bonded to sulphur MASS 26 HW 1.008 ! H in TIP3P water MASS 27 HP 1.008 ! H bonded to C next to positively charged gr MASS 28 F 19.00 ! fluorine MASS 29 I 126.9 ! iodine MASS 30 IM 35.45 ! assumed to be Cl- MASS 31 IP 22.99 ! assumed to be Na+ MASS 32 IB 131.0 ! 'big ion w/ waters' for vacuum (Na+, 6H2O) MASS 33 MG 24.305 ! magnesium MASS 34 N 14.01 ! sp2 nitrogen in amide groups MASS 35 NA 14.01 ! sp2 N in 5 memb.ring w/H atom (HIS) MASS 36 NB 14.01 ! sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA) MASS 37 NC 14.01 ! sp2 N in 6 memb.ring w/LP (ADE,GUA) MASS 38 N2 14.01 ! sp2 N in amino groups MASS 39 N3 14.01 ! sp3 N for charged amino groups (Lys, etc) MASS 40 NS 14.01 ! sp2 N; note N* --> NS to avoid confusion with wildcard MASS 41 O 16.00 ! carbonyl group oxygen MASS 42 OW 16.00 ! oxygen in TIP3P water MASS 43 OH 16.00 ! oxygen in hydroxyl group MASS 44 OS 16.00 ! ether and ester oxygen MASS 45 O2 16.00 ! carboxyl and phosphate group oxygen MASS 46 P 30.97 ! phosphate MASS 47 S 32.06 ! sulphur in disulfide linkage MASS 48 SH 32.06 ! sulphur in cystine MASS 49 CU 63.55 ! copper MASS 50 FE 55.00 ! iron MASS 51 Li 6.94 ! lithium MASS 52 K 39.10 ! potassium MASS 53 Rb 85.47 ! rubidium DECL -CA ! proteins DECL -C DECL -O DECL +N DECL +H DECL +CA DECL +P ! nucleic acids DECL +O1P DECL +O2P DECL +O5' DECL -O3' DEFAULT FIRST NTER LAST CTER AUTOGENERATE ANGLES DIHEDRAL RESIDUE ADE -1.0 ! note: this is RNA (RA); patches to make GROUP ! terminal or deoxyribose are required ATOM P P 1.1662 ATOM O1P O2 -0.7760 ATOM O2P O2 -0.7760 ATOM O5' OS -0.4989 ATOM C5' CT 0.0558 ATOM H5' H1 0.0679 ! note: type is H5'1 --> this should be checked ATOM H5'' H1 0.0679 ! note: type is H5'2 ATOM C4' CT 0.1065 ATOM H4' H1 0.1174 ATOM O4' OS -0.3548 ATOM C1' CT 0.0394 ATOM H1' H2 0.2007 ATOM N9 NS -0.0251 ! note: type is N* ATOM C8 CK 0.2006 ATOM H8 H5 0.1553 ATOM N7 NB -0.6073 ATOM C5 CB 0.0515 ATOM C6 CA 0.7009 ATOM N6 N2 -0.9019 ATOM H61 H 0.4115 ATOM H62 H 0.4115 ATOM N1 NC -0.7615 ATOM C2 CQ 0.5875 ATOM H2 H5 0.0473 ATOM N3 NC -0.6997 ATOM C4 CB 0.3053 ATOM C3' CT 0.2022 ATOM H3' H1 0.0615 ATOM C2' CT 0.0670 ATOM H2'' H1 0.0972 ! note: this is H2'1 ATOM O2' OH -0.6139 ATOM H2' HO 0.4186 ! note: this is HO'2 ATOM O3' OS -0.5246 ! using charmm bond lists (top_all22_na.inp) BOND P O1P P O2P P O5' BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 BOND C4 C5 N3 C2 C2 N1 N1 C6 C6 N6 BOND N6 H61 N6 H62 C6 C5 C5 N7 N7 C8 BOND C2' C3' C2' O2' O2' H2' C3' O3' O3' +P BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' BOND C5' H5'' C8 H8 C2 H2 IMPROPER C8 C4 N9 C1' IMPROPER C6 H61 N6 H62 IMPROPER N7 N9 C8 H8 IMPROPER N1 N3 C2 H2 IMPROPER C5 N1 C6 N6 DONO H61 N6 DONO H62 N6 DONO H2' O2' ACCE N3 ACCE N7 ACCE N1 ACCE O1P P ACCE O2P P ACCE O2' ACCE O3' ACCE O4' ACCE O5' ! using charmm geometry (top_all22_na.inp) IC -O3' P O5' C5' 1.6001 101.45 -39.25 119.00 1.4401 IC -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 IC -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 IC P O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 IC O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 IC C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 IC C4' C3' O3' +P 1.5284 111.92 159.13 119.05 1.6001 IC C3' O3' +P +O5' 1.4212 119.05 -98.86 101.45 1.5996 IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 IC C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 IC C3' C2' C1' N9 1.5284 101.97 144.39 113.71 1.4896 IC O4' C1' N9 C4 1.5251 113.71 -96.00 125.97 1.3703 IC C1' C4 *N9 C8 1.4896 125.97 -179.94 106.0 1.367 IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 IC N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 IC H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 IC N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 IC H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 PATCH FIRST ADE5 LAST ADE3 RESIDUE URA -1.0 ! note: this is RNA (RA); patches to make GROUP ! terminal are required. ATOM P P 1.1662 ATOM O1P O2 -0.7760 ATOM O2P O2 -0.7760 ATOM O5' OS -0.4989 ATOM C5' CT 0.0558 ATOM H5' H1 0.0679 ! note: name is H5'1 ATOM H5'' H1 0.0679 ! note: name is H5'2 ATOM C4' CT 0.1065 ATOM H4' H1 0.1174 ATOM O4' OS -0.3548 ATOM C1' CT 0.0674 ATOM H1' H2 0.1824 ATOM N1 NS 0.0418 ! note: type is N* ATOM C6 CM -0.1126 ATOM H6 H4 0.2188 ATOM C5 CM -0.3635 ATOM H5 HA 0.1811 ATOM C4 C 0.5952 ATOM O4 O -0.5761 ATOM N3 NA -0.3549 ATOM H3 H 0.3154 ATOM C2 C 0.4687 ATOM O2 O -0.5477 ATOM C3' CT 0.2022 ATOM H3' H1 0.0615 ATOM C2' CT 0.0670 ATOM H2'' H1 0.0972 ! note: name is H2'1 ATOM O2' OH -0.6139 ATOM H2' HO 0.4186 ! note: name is HO'2 ATOM O3' OS -0.5246 ! bonds from charmm (top_all22_na.inp) BOND P O1P P O2P P O5' BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' N1 C1' C2' N1 C2 N1 C6 C2 O2 BOND C2 N3 N3 H3 N3 C4 C4 O4 C4 C5 BOND C5 C6 C2' C3' C3' O3' O3' +P BOND C2' O2' O2' H2' BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' BOND C5' H5'' C5 H5 C6 H6 IMPROPER C6 C2 N1 C1' IMPROPER C4 C6 C5 H5 IMPROPER N1 N3 C2 O2 IMPROPER C5 N3 C4 O4 IMPROPER C2 C4 N3 H3 IMPROPER N1 C5 C6 H6 DONO H3 N3 DONO H2' O2' ACCE O2 C2 ACCE O4 C4 ACCE O1P P ACCE O2P P ACCE O2' ACCE O3' ACCE O4' ACCE O5' ! build from charmm (top_all22_na.inp) IC -O3' P O5' C5' 1.6001 101.45 -39.25 119.00 1.4401 IC -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 IC -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 IC P O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 IC O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 IC C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 IC C4' C3' O3' +P 1.5284 111.92 159.13 119.05 1.6001 IC C3' O3' +P +O5' 1.4212 119.05 -98.86 101.45 1.5996 IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 IC C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 IC C3' C2' C1' N1 1.5284 101.97 144.39 113.71 1.4896 IC O4' C1' N1 C2 1.5251 113.71 -96.0 117.06 1.3746 IC C1' C2 *N1 C6 1.4896 117.06 -180.0 121.3 1.379 IC C2 N1 C6 C5 1.379 121.3 0.0 122.8 1.338 IC C6 N1 C2 N3 1.380 121.3 0.0 114.8 1.373 IC N1 N3 *C2 O2 1.379 114.8 -180.0 122.0 1.218 IC N1 C2 N3 C4 1.379 114.8 0.0 127.0 1.383 IC C5 N3 *C4 O4 1.440 114.7 180.0 119.8 1.227 IC C2 C4 *N3 H3 1.373 127.0 180.0 116.5 1.03 IC C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 PATCH FIRST URA5 LAST URA3 RESIDUE THY -1.0 ! note: this is DNA (DT); patches to make GROUP ! terminal are required ATOM P P 1.1659 ATOM O1P O2 -0.7761 ATOM O2P O2 -0.7761 ATOM O5' OS -0.4954 ATOM C5' CT -0.0069 ATOM H5' H1 0.0754 ! this is H5'1 ATOM H5'' H1 0.0754 ! this is H5'2 ATOM C4' CT 0.1629 ATOM H4' H1 0.1176 ATOM O4' OS -0.3691 ATOM C1' CT 0.0680 ATOM H1' H2 0.1804 ATOM N1 NS -0.0239 ! this is atom type N* ATOM C6 CM -0.2209 ATOM H6 H4 0.2607 ATOM C5 CM 0.0025 ATOM C7 CT -0.2269 ATOM H71 HC 0.0770 ATOM H72 HC 0.0770 ATOM H73 HC 0.0770 ATOM C4 C 0.5194 ATOM O4 O -0.5563 ATOM N3 NA -0.4340 ATOM H3 H 0.3420 ATOM C2 C 0.5677 ATOM O2 O -0.5881 ATOM C3' CT 0.0713 ATOM H3' H1 0.0985 ATOM C2' CT -0.0854 ATOM H2' HC 0.0718 ! this is H2'1 ATOM H2'' HC 0.0718 ! this is H2'2 ATOM O3' OS -0.5232 ! bonds from charmm (top_all22_na.inp) ! swapped C5M with C7 ! swapped H5? with H7? BOND P O1P P O2P P O5' BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' N1 C1' C2' N1 C2 N1 C6 C2 O2 BOND C2 N3 N3 H3 N3 C4 C4 O4 C4 C5 BOND C5 C7 C5 C6 C2' C3' C3' O3' O3' +P BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' BOND C5' H5'' C6 H6 C7 H71 C7 H72 C7 H73 BOND C2' H2' IMPROPER C6 C2 N1 C1' IMPROPER C4 C6 C5 C7 IMPROPER N1 N3 C2 O2 IMPROPER C5 N3 C4 O4 IMPROPER C2 C4 N3 H3 IMPROPER N1 C5 C6 H6 DONO H3 N3 ACCE O2 C2 ACCE O4 C4 ACCE O1P P ACCE O2P P ACCE O3' ACCE O4' ACCE O5' ! build from charmm (top_all22_na.inp) ! name swapping as above, delete references to O2' IC -O3' P O5' C5' 1.6001 101.45 -39.25 119.00 1.4401 IC -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 IC -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 IC P O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 IC O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 IC C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 IC C4' C3' O3' +P 1.5284 111.92 159.13 119.05 1.6001 IC C3' O3' +P +O5' 1.4212 119.05 -98.86 101.45 1.5996 IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 IC C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 IC C3' C2' C1' N1 1.5284 101.97 144.39 113.71 1.4896 IC O4' C1' N1 C2 1.5251 113.71 -96.0 117.06 1.3746 IC C1' C2 *N1 C6 1.4896 117.06 -179.96 122.08 1.3704 IC C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3432 IC C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813 IC N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191 IC N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795 IC C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327 IC C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900 IC C4 C6 *C5 C7 1.4439 120.78 -179.94 121.63 1.5000 IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 IC C6 C5 C7 H71 0.0 0.0 0.0 0.0 0.0 IC C5 H71 *C7 H72 0.0 0.0 115.0 0.0 0.0 IC H71 H72 *C7 H73 0.0 0.0 -115.0 0.0 0.0 IC C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 PATCH FIRST THY5 LAST THY3 RESI CYT -1.0 ! note: this is RNA (RC); patches to make GROUP ! terminal or deoxyribose are required ATOM P P 1.1662 ATOM O1P O2 -0.7760 ATOM O2P O2 -0.7760 ATOM O5' OS -0.4989 ATOM C5' CT 0.0558 ATOM H5' H1 0.0679 ! this is H5'1 ATOM H5'' H1 0.0679 ! this is H5'2 ATOM C4' CT 0.1065 ATOM H4' H1 0.1174 ATOM O4' OS -0.3548 ATOM C1' CT 0.0066 ATOM H1' H2 0.2029 ATOM N1 NS -0.0484 ! this is type N* ATOM C6 CM 0.0053 ATOM H6 H4 0.1958 ATOM C5 CM -0.5215 ATOM H5 HA 0.1928 ATOM C4 CA 0.8185 ATOM N4 N2 -0.9530 ATOM H41 H 0.4234 ATOM H42 H 0.4234 ATOM N3 NC -0.7584 ATOM C2 C 0.7538 ATOM O2 O -0.6252 ATOM C3' CT 0.2022 ATOM H3' H1 0.0615 ATOM C2' CT 0.0670 ATOM H2'' H1 0.0972 ! this is H2'1 ATOM O2' OH -0.6139 ATOM H2' HO 0.4186 ! this is HO'2 ATOM O3' OS -0.5246 BOND P O1P P O2P P O5' BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' N1 C1' C2' N1 C2 N1 C6 C2 O2 BOND C2 N3 N3 C4 C4 N4 N4 H41 N4 H42 BOND C4 C5 C5 C6 C2' C3' C3' O3' O3' +P BOND C2' O2' O2' H2' BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' BOND C5' H5'' C5 H5 C6 H6 IMPROPER C6 C2 N1 C1' IMPROPER N1 N3 C2 O2 IMPROPER C4 H41 N4 H42 IMPROPER N1 C5 C6 H6 IMPROPER C6 C4 C5 H5 IMPROPER N3 C5 C4 N4 DONO H42 N4 DONO H2' O2' DONO H41 N4 ACCE O2 C2 ACCE N3 ACCE O1P P ACCE O2P P ACCE O2' ACCE O3' ACCE O4' ACCE O5' IC -O3' P O5' C5' 1.6001 101.45 -39.25 119.00 1.4401 IC -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 IC -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 IC P O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 IC O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 IC C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 IC C4' C3' O3' +P 1.5284 111.92 159.13 119.05 1.6001 IC C3' O3' +P +O5' 1.4212 119.05 -98.86 101.45 1.5996 IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 IC C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 IC C3' C2' C1' N1 1.5284 101.97 144.39 113.71 1.4896 IC O4' C1' N1 C2 1.5251 113.71 -96.0 117.79 1.399 IC C1' C2 *N1 C6 1.4896 117.79 -180.00 120.6 1.364 IC C2 N1 C6 C5 1.399 120.6 0.0 121.0 1.337 IC C6 N1 C2 N3 1.364 120.6 0.0 118.9 1.356 IC N1 N3 *C2 O2 1.399 118.9 180.0 121.9 1.237 IC N1 C2 N3 C4 1.399 118.9 0.0 120.0 1.334 IC C5 N3 *C4 N4 1.426 121.8 180.00 118.9 1.337 IC N3 C4 N4 H41 1.337 117.9 0.00 118.9 1.01 IC H41 C4 *N4 H42 1.01 118.9 180.00 120.7 1.01 IC C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 PATCH FIRST CYT5 LAST CYT3 RESI GUA -1.0 ! note: this is GUA (RG); patches to make GROUP ! terminal or deoxyribose are required ATOM P P 1.1662 ATOM O1P O2 -0.7760 ATOM O2P O2 -0.7760 ATOM O5' OS -0.4989 ATOM C5' CT 0.0558 ATOM H5' H1 0.0679 ! this is H5'1 ATOM H5'' H1 0.0679 ! this is H5'2 ATOM C4' CT 0.1065 ATOM H4' H1 0.1174 ATOM O4' OS -0.3548 ATOM C1' CT 0.0191 ATOM H1' H2 0.2006 ATOM N9 NS 0.0492 ! this is type N* ATOM C8 CK 0.1374 ATOM H8 H5 0.1640 ATOM N7 NB -0.5709 ATOM C5 CB 0.1744 ATOM C6 C 0.4770 ATOM O6 O -0.5597 ATOM N1 NA -0.4787 ATOM H1 H 0.3424 ATOM C2 CA 0.7657 ATOM N2 N2 -0.9672 ATOM H21 H 0.4364 ATOM H22 H 0.4364 ATOM N3 NC -0.6323 ATOM C4 CB 0.1222 ATOM C3' CT 0.2022 ATOM H3' H1 0.0615 ATOM C2' CT 0.0670 ATOM H2'' H1 0.0972 ! this is H2'1 ATOM O2' OH -0.6139 ATOM H2' HO 0.4186 ! this is HO'2 ATOM O3' OS -0.5246 ! bonds from charmm (top_all22_na.inp) BOND P O1P P O2P P O5' BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 BOND C4 C5 N3 C2 C2 N2 C2 N1 N2 H21 BOND N2 H22 N1 H1 N1 C6 C6 O6 C6 C5 BOND C5 N7 N7 C8 C2' C3' C3' O3' O3' +P BOND C2' O2' O2' H2' BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' BOND C5' H5'' C8 H8 IMPROPER C8 C4 N9 C1' IMPROPER C5 N1 C6 O6 IMPROPER C6 C2 N1 H1 IMPROPER C2 H21 N2 H22 IMPROPER N7 N9 C8 H8 IMPROPER N1 N3 C2 N2 DONO H21 N2 DONO H22 N2 DONO H1 N1 DONO H2' O2' ACCE O6 C6 ACCE N3 ACCE N7 ACCE O1P P ACCE O2P P ACCE O2' ACCE O3' ACCE O4' ACCE O5' ! build array from charmm (top_all22_na.inp) IC -O3' P O5' C5' 1.6001 101.45 -39.25 119.00 1.4401 IC -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 IC -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 IC P O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 IC O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 IC C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 IC C4' C3' O3' +P 1.5284 111.92 159.13 119.05 1.6001 IC C3' O3' +P +O5' 1.4212 119.05 -98.86 101.45 1.5996 IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 IC C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 IC C3' C2' C1' N9 1.5284 101.97 144.39 113.71 1.4896 IC O4' C1' N9 C4 1.5251 113.71 -96.0 125.59 1.3783 IC C1' C4 *N9 C8 1.4896 125.59 -179.99 106.0 1.374 IC C4 N9 C8 N7 1.377 106.0 0.0 113.5 1.304 IC C8 N9 C4 C5 1.374 106.0 0.0 105.6 1.377 IC N9 C5 *C4 N3 1.377 105.6 180.0 128.4 1.355 IC C5 C4 N3 C2 1.377 128.4 0.0 111.8 1.327 IC C4 N3 C2 N1 1.355 111.8 0.0 124.0 1.375 IC N1 N3 *C2 N2 1.375 124.0 180.0 119.7 1.341 IC N3 C2 N2 H21 1.327 119.7 180.0 127.0 1.01 IC H21 C2 *N2 H22 1.01 127.0 -180.0 116.5 1.01 IC N3 C2 N1 C6 1.327 124.0 0.0 124.9 1.393 IC C6 C2 *N1 H1 1.393 124.9 180.00 117.4 1.03 IC C5 N1 *C6 O6 1.415 111.7 180.0 120.0 1.239 IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 PATCH FIRST GUA5 LAST GUA3 ! ! PROTEIN RESIDUES ! RESI ALA 0.00 GROUP ATOM N N -0.41570 ! | ATOM HN H 0.27190 ! HN-N ATOM CA CT 0.03370 ! | HB1 ATOM HA H1 0.08230 ! | / ATOM CB CT -0.18250 ! HA-CA--CB-HB2 ALANINE ATOM HB1 HC 0.06030 ! | \ ATOM HB2 HC 0.06030 ! | HB2 ATOM HB3 HC 0.06030 ! O=C ATOM C C 0.59730 ! | ATOM O O -0.56790 BOND CB CA N HN N CA C CA C +N BOND CA HA CB HB1 CB HB2 CB HB3 C O IMPROPER -C CA N HN IMPROPER CA +N C O DONOR HN N ACCEPTOR O C IC -C CA *N HN 1.3551 126.4900 180.0000 115.4200 0.9996 IC -C N CA C 1.3551 126.4900 180.0000 114.4400 1.5390 IC N CA C +N 1.4592 114.4400 180.0000 116.8400 1.3558 IC +N CA *C O 1.3558 116.8400 180.0000 122.5200 1.2297 IC CA C +N +CA 1.5390 116.8400 180.0000 126.7700 1.4613 IC N C *CA CB 1.4592 114.4400 123.2300 111.0900 1.5461 IC N C *CA HA 1.4592 114.4400 -120.4500 106.3900 1.0840 IC C CA CB HB1 1.5390 111.0900 177.2500 109.6000 1.1109 IC HB1 CA *CB HB2 1.1109 109.6000 119.1300 111.0500 1.1119 IC HB1 CA *CB HB3 1.1109 109.6000 -119.5800 111.6100 1.1114 PATCH FIRST NALA LAST CALA RESI ARG 1.00 GROUP ATOM N N -0.34790 ! | HH11 ATOM HN H 0.27470 ! HN-N | ATOM CA CT -0.26370 ! | HB1 HG1 HD1 HE NH1-HH12 ATOM HA H1 0.15600 ! | | | | | //(+) ATOM CB CT -0.00070 ! HA-CA--CB--CG--CD--NE--CZ ATOM HB1 HC 0.03270 ! | | | | \ ATOM HB2 HC 0.03270 ! | HB2 HG2 HD2 NH2-HH22 ATOM CG CT 0.03900 ! O=C | ATOM HG1 HC 0.02850 ! | HH21 ATOM HG2 HC 0.02850 ATOM CD CT 0.04860 ATOM HD1 H1 0.06870 ATOM HD2 H1 0.06870 ATOM NE N2 -0.52950 ATOM HE H 0.34560 ATOM CZ CA 0.80760 ATOM NH1 N2 -0.86270 ATOM HH11 H 0.44780 ATOM HH12 H 0.44780 ATOM NH2 N2 -0.86270 ATOM HH21 H 0.44780 ATOM HH22 H 0.44780 ATOM C C 0.73410 ATOM O O -0.58940 BOND CB CA CG CB CD CG NE CD CZ NE BOND NH2 CZ N HN N CA BOND C CA C +N CA HA CB HB1 BOND CB HB2 CG HG1 CG HG2 CD HD1 CD HD2 BOND NE HE NH1 HH11 NH1 HH12 NH2 HH21 NH2 HH22 BOND O C CZ NH1 IMPROPER -C CA N HN IMPROPER CA +N C O IMPROPER NE NH1 CZ NH2 IMPROPER CD CZ NE HE IMPROPER CZ HH11 NH1 HH12 IMPROPER CZ HH21 NH2 HH22 DONOR HN N DONOR HE NE DONOR HH11 NH1 DONOR HH12 NH1 DONOR HH21 NH2 DONOR HH22 NH2 ACCEPTOR O C IC -C CA *N HN 1.3496 122.4500 180.0000 116.6700 0.9973 IC -C N CA C 1.3496 122.4500 180.0000 109.8600 1.5227 IC N CA C +N 1.4544 109.8600 180.0000 117.1200 1.3511 IC +N CA *C O 1.3511 117.1200 180.0000 121.4000 1.2271 IC CA C +N +CA 1.5227 117.1200 180.0000 124.6700 1.4565 IC N C *CA CB 1.4544 109.8600 123.6400 112.2600 1.5552 IC N C *CA HA 1.4544 109.8600 -117.9300 106.6100 1.0836 IC N CA CB CG 1.4544 110.7000 180.0000 115.9500 1.5475 IC CG CA *CB HB1 1.5475 115.9500 120.0500 106.4000 1.1163 IC CG CA *CB HB2 1.5475 115.9500 -125.8100 109.5500 1.1124 IC CA CB CG CD 1.5552 115.9500 180.0000 114.0100 1.5384 IC CD CB *CG HG1 1.5384 114.0100 125.2000 108.5500 1.1121 IC CD CB *CG HG2 1.5384 114.0100 -120.3000 108.9600 1.1143 IC CB CG CD NE 1.5475 114.0100 180.0000 107.0900 1.5034 IC NE CG *CD HD1 1.5034 107.0900 120.6900 109.4100 1.1143 IC NE CG *CD HD2 1.5034 107.0900 -119.0400 111.5200 1.1150 IC CG CD NE CZ 1.5384 107.0900 180.0000 123.0500 1.3401 IC CZ CD *NE HE 1.3401 123.0500 180.0000 113.1400 1.0065 IC CD NE CZ NH1 1.5034 123.0500 180.0000 118.0600 1.3311 IC NE CZ NH1 HH11 1.3401 118.0600 -178.2800 120.6100 0.9903 IC HH11 CZ *NH1 HH12 0.9903 120.6100 171.1900 116.2900 1.0023 IC NH1 NE *CZ NH2 1.3311 118.0600 178.6400 122.1400 1.3292 IC NE CZ NH2 HH21 1.3401 122.1400 -174.1400 119.9100 0.9899 IC HH21 CZ *NH2 HH22 0.9899 119.9100 166.1600 116.8800 0.9914 PATCH FIRST NARG LAST CARG RESI ASN 0.00 GROUP ATOM N N -0.41570 ! | ATOM HN H 0.27190 ! HN-N ATOM CA CT 0.01430 ! | HB1 OD1 HD21 (cis to OD1) ATOM HA H1 0.10480 ! | | || / ATOM CB CT -0.20410 ! HA-CA--CB--CG--ND2 ATOM HB1 HC 0.07970 ! | | \ ATOM HB2 HC 0.07970 ! | HB2 HD22 (trans to OD1) ATOM CG C 0.71300 ! O=C ATOM OD1 O -0.59310 ! | ATOM ND2 N -0.91910 ATOM HD21 H 0.41960 ATOM HD22 H 0.41960 ATOM C C 0.59730 ATOM O O -0.56790 BOND CB CA CG CB ND2 CG BOND N HN N CA C CA C +N BOND CA HA CB HB1 CB HB2 ND2 HD21 ND2 HD22 BOND C O CG OD1 IMPROPER -C CA N HN IMPROPER CA +N C O IMPROPER CB ND2 CG OD1 IMPROPER CG HD21 ND2 HD22 DONOR HN N DONOR HD21 ND2 DONOR HD22 ND2 ACCEPTOR OD1 CG ACCEPTOR O C IC -C CA *N HN 1.3480 124.0500 180.0000 114.4900 0.9992 IC -C N CA C 1.3480 124.0500 180.0000 105.2300 1.5245 IC N CA C +N 1.4510 105.2300 180.0000 117.3800 1.3467 IC +N CA *C O 1.3467 117.3800 180.0000 120.3200 1.2282 IC CA C +N +CA 1.5245 117.3800 180.0000 124.8800 1.4528 IC N C *CA CB 1.4510 105.2300 121.1800 113.0400 1.5627 IC N C *CA HA 1.4510 105.2300 -115.5200 107.6300 1.0848 IC N CA CB CG 1.4510 110.9100 180.0000 114.3000 1.5319 IC CG CA *CB HB1 1.5319 114.3000 119.1700 107.8200 1.1120 IC CG CA *CB HB2 1.5319 114.3000 -123.7400 110.3400 1.1091 IC CA CB CG OD1 1.5627 114.3000 180.0000 122.5600 1.2323 IC OD1 CB *CG ND2 1.2323 122.5600 -179.1900 116.1500 1.3521 IC CB CG ND2 HD21 1.5319 116.1500 -179.2600 117.3500 0.9963 IC HD21 CG *ND2 HD22 0.9963 117.3500 178.0200 120.0500 0.9951 PATCH FIRST NASN LAST CASN RESI ASP -1.00 GROUP ATOM N N -0.51630 ! | ATOM HN H 0.29360 ! HN-N ATOM CA CT 0.03810 ! | HB1 OD1 ATOM HA H1 0.08800 ! | | // ATOM CB CT -0.03030 ! HA-CA--CB--CG ATOM HB1 HC -0.01220 ! | | \ ATOM HB2 HC -0.01220 ! | HB2 OD2(-) ATOM CG C 0.79940 ! O=C ATOM OD1 O2 -0.80140 ! | ATOM OD2 O2 -0.80140 ATOM C C 0.53660 ATOM O O -0.58190 BOND CB CA CG CB OD2 CG BOND N HN N CA C CA C +N BOND CA HA CB HB1 CB HB2 BOND O C CG OD1 IMPROPER -C CA N HN IMPROPER CA +N C O IMPROPER CB OD1 CG OD2 DONOR HN N ACCEPTOR OD1 CG ACCEPTOR OD2 CG ACCEPTOR O C IC -C CA *N HN 1.3465 125.3100 180.0000 112.9400 0.9966 IC -C N CA C 1.3465 125.3100 180.0000 105.6300 1.5315 IC N CA C +N 1.4490 105.6300 180.0000 117.0600 1.3478 IC +N CA *C O 1.3478 117.0600 180.0000 120.7100 1.2330 IC CA C +N +CA 1.5315 117.0600 180.0000 125.3900 1.4484 IC N C *CA CB 1.4490 105.6300 122.3300 114.1000 1.5619 IC N C *CA HA 1.4490 105.6300 -116.4000 106.7700 1.0841 IC N CA CB CG 1.4490 111.1000 180.0000 112.6000 1.5218 IC CG CA *CB HB1 1.5218 112.6000 119.2200 109.2300 1.1086 IC CG CA *CB HB2 1.5218 112.6000 -121.6100 110.6400 1.1080 IC CA CB CG OD1 1.5619 112.6000 180.0000 117.9900 1.2565 IC OD1 CB *CG OD2 1.2565 117.9900 -170.2300 117.7000 1.2541 PATCH FIRST NASP LAST CASP RESI CYS 0.00 GROUP ATOM N N -0.41570 ! | ATOM HN H 0.27190 ! HN-N ATOM CA CT 0.02130 ! | HB1 ATOM HA H1 0.11240 ! | | ATOM CB CT -0.12310 ! HA-CA--CB--SG ATOM HB1 H1 0.11120 ! | | \ ATOM HB2 H1 0.11120 ! | HB2 HG1 ATOM SG SH -0.31190 ! O=C ATOM HG1 HS 0.19330 ! | ATOM C C 0.59730 ATOM O O -0.56790 BOND CB CA SG CB N HN N CA BOND C CA C +N CA HA CB HB1 BOND CB HB2 SG HG1 BOND O C IMPROPER -C CA N HN IMPROPER CA +N C O DONOR HN N DONOR HG1 SG ACCEPTOR O C IC -C CA *N HN 1.3479 123.9300 180.0000 114.7700 0.9982 IC -C N CA C 1.3479 123.9300 180.0000 105.8900 1.5202 IC N CA C +N 1.4533 105.8900 180.0000 118.3000 1.3498 IC +N CA *C O 1.3498 118.3000 180.0000 120.5900 1.2306 IC CA C +N +CA 1.5202 118.3000 180.0000 124.5000 1.4548 IC N C *CA CB 1.4533 105.8900 121.7900 111.9800 1.5584 IC N C *CA HA 1.4533 105.8900 -116.3400 107.7100 1.0837 IC N CA CB SG 1.4533 111.5600 180.0000 113.8700 1.8359 IC SG CA *CB HB1 1.8359 113.8700 119.9100 107.2400 1.1134 IC SG CA *CB HB2 1.8359 113.8700 -125.3200 109.8200 1.1124 IC CA CB SG HG1 1.5584 113.8700 176.9600 97.1500 1.3341 PATCH FIRST NCYS LAST CCYS RESI CYM -1.00 ! NOTE: there is no terminal negative CYS GROUP ! residues within Cornell et al.!!! ATOM N N -0.41570 ! | ATOM HN H 0.27190 ! HN-N ATOM CA CT -0.03510 ! | HB1 ATOM HA H1 0.05080 ! | | ATOM CB CT -0.24130 ! HA-CA--CB--SG ATOM HB1 H1 0.11220 ! | | (-) ATOM HB2 H1 0.11220 ! | HB2 ATOM SG SH -0.88440 ! O=C ATOM C C 0.59730 ! | ATOM O O -0.56790 BOND CB CA SG CB N HN N CA BOND C CA C +N CA HA CB HB1 BOND CB HB2 BOND O C IMPROPER -C CA N HN IMPROPER CA +N C O DONOR HN N ACCEPTOR O C IC -C CA *N HN 1.3479 123.9300 180.0000 114.7700 0.9982 IC -C N CA C 1.3479 123.9300 180.0000 105.8900 1.5202 IC N CA C +N 1.4533 105.8900 180.0000 118.3000 1.3498 IC +N CA *C O 1.3498 118.3000 180.0000 120.5900 1.2306 IC CA C +N +CA 1.5202 118.3000 180.0000 124.5000 1.4548 IC N C *CA CB 1.4533 105.8900 121.7900 111.9800 1.5584 IC N C *CA HA 1.4533 105.8900 -116.3400 107.7100 1.0837 IC N CA CB SG 1.4533 111.5600 180.0000 113.8700 1.8359 IC SG CA *CB HB1 1.8359 113.8700 119.9100 107.2400 1.1134 IC SG CA *CB HB2 1.8359 113.8700 -125.3200 109.8200 1.1124 PATCH FIRST NONE LAST NONE RESI CYX 0.00 GROUP ATOM N N -0.41570 ! | ATOM HN H 0.27190 ! HN-N ATOM CA CT 0.04290 ! | HB1 ATOM HA H1 0.07660 ! | | ATOM CB CT -0.07900 ! HA-CA--CB--SG ATOM HB1 H1 0.09100 ! | | (-) ATOM HB2 H1 0.09100 ! | HB2 ATOM SG SH -0.10810 ! O=C ATOM C C 0.59730 ! | ATOM O O -0.56790 BOND CB CA SG CB N HN N CA BOND C CA C +N CA HA CB HB1 BOND CB HB2 BOND O C IMPROPER -C CA N HN IMPROPER CA +N C O DONOR HN N ACCEPTOR O C IC -C CA *N HN 1.3479 123.9300 180.0000 114.7700 0.9982 IC -C N CA C 1.3479 123.9300 180.0000 105.8900 1.5202 IC N CA C +N 1.4533 105.8900 180.0000 118.3000 1.3498 IC +N CA *C O 1.3498 118.3000 180.0000 120.5900 1.2306 IC CA C +N +CA 1.5202 118.3000 180.0000 124.5000 1.4548 IC N C *CA CB 1.4533 105.8900 121.7900 111.9800 1.5584 IC N C *CA HA 1.4533 105.8900 -116.3400 107.7100 1.0837 IC N CA CB SG 1.4533 111.5600 180.0000 113.8700 1.8359 IC SG CA *CB HB1 1.8359 113.8700 119.9100 107.2400 1.1134 IC SG CA *CB HB2 1.8359 113.8700 -125.3200 109.8200 1.1124 PATCH FIRST NCYX LAST CCYX RESI GLN 0.00 GROUP ATOM N N -0.41570 ! | ATOM HN H 0.27190 ! HN-N ATOM CA CT -0.00310 ! | HB1 HG1 OE1 HE21 (cis to OE1) ATOM HA H1 0.08500 ! | | | || / ATOM CB CT -0.00360 ! HA-CA--CB--CG--CD--NE2 ATOM HB1 HC 0.01710 ! | | | \ ATOM HB2 HC 0.01710 ! | HB2 HG2 HE22 (trans to OE1) ATOM CG CT -0.06450 ! O=C ATOM HG1 HC 0.03520 ! | ATOM HG2 HC 0.03520 ATOM CD C 0.69510 ATOM OE1 O -0.60860 ATOM NE2 N -0.94070 ATOM HE21 H 0.42510 ATOM HE22 H 0.42510 ATOM C C 0.59730 ATOM O O -0.56790 BOND CB CA CG CB CD CG NE2 CD BOND N HN N CA C CA BOND C +N CA HA CB HB1 CB HB2 CG HG1 BOND CG HG2 NE2 HE21 NE2 HE22 BOND O C CD OE1 IMPROPER -C CA N HN IMPROPER CA +N C O IMPROPER CG NE2 CD OE1 IMPROPER CD HE21 NE2 HE22 DONOR HN N DONOR HE21 NE2 DONOR HE22 NE2 ACCEPTOR OE1 CD ACCEPTOR O C IC -C CA *N HN 1.3477 123.9300 180.0000 114.4500 0.9984 IC -C N CA C 1.3477 123.9300 180.0000 106.5700 1.5180 IC N CA C +N 1.4506 106.5700 180.0000 117.7200 1.3463 IC +N CA *C O 1.3463 117.7200 180.0000 120.5900 1.2291 IC CA C +N +CA 1.5180 117.7200 180.0000 124.3500 1.4461 IC N C *CA CB 1.4506 106.5700 121.9100 111.6800 1.5538 IC N C *CA HA 1.4506 106.5700 -116.8200 107.5300 1.0832 IC N CA CB CG 1.4506 111.4400 180.0000 115.5200 1.5534 IC CG CA *CB HB1 1.5534 115.5200 120.9300 106.8000 1.1147 IC CG CA *CB HB2 1.5534 115.5200 -124.5800 109.3400 1.1140 IC CA CB CG CD 1.5538 115.5200 180.0000 112.5000 1.5320 IC CD CB *CG HG1 1.5320 112.5000 118.6900 110.4100 1.1112 IC CD CB *CG HG2 1.5320 112.5000 -121.9100 110.7400 1.1094 IC CB CG CD OE1 1.5534 112.5000 180.0000 121.5200 1.2294 IC OE1 CG *CD NE2 1.2294 121.5200 179.5700 116.8400 1.3530 IC CG CD NE2 HE21 1.5320 116.8400 -179.7200 116.8600 0.9959 IC HE21 CD *NE2 HE22 0.9959 116.8600 -178.9100 119.8300 0.9943 PATCH FIRST NGLN LAST CGLN RESI GLU -1.00 ATOM N N -0.51630 ! | ATOM HN H 0.29360 ! HN-N ATOM CA CT 0.03970 ! | HB1 HG1 OE1 ATOM HA H1 0.11050 ! | | | // ATOM CB CT 0.05600 ! HA-CA--CB--CG--CD ATOM HB1 HC -0.01730 ! | | | \ ATOM HB2 HC -0.01730 ! | HB2 HG2 OE2(-) ATOM CG CT 0.01360 ! O=C ATOM HG1 HC -0.04250 ! | ATOM HG2 HC -0.04250 ATOM CD C 0.80540 ATOM OE1 O2 -0.81880 ATOM OE2 O2 -0.81880 ATOM C C 0.53660 ATOM O O -0.58190 BOND CB CA CG CB CD CG OE2 CD BOND N HN N CA C CA BOND C +N CA HA CB HB1 CB HB2 CG HG1 BOND CG HG2 O C CD OE1 IMPROPER -C CA N HN IMPROPER CA +N C O IMPROPER CG OE1 CD OE2 DONOR HN N ACCEPTOR OE1 CD ACCEPTOR OE2 CD ACCEPTOR O C IC -C CA *N HN 1.3471 124.4500 180.0000 113.9900 0.9961 IC -C N CA C 1.3471 124.4500 180.0000 107.2700 1.5216 IC N CA C +N 1.4512 107.2700 180.0000 117.2500 1.3501 IC +N CA *C O 1.3501 117.2500 180.0000 121.0700 1.2306 IC CA C +N +CA 1.5216 117.2500 180.0000 124.3000 1.4530 IC N C *CA CB 1.4512 107.2700 121.9000 111.7100 1.5516 IC N C *CA HA 1.4512 107.2700 -118.0600 107.2600 1.0828 IC N CA CB CG 1.4512 111.0400 180.0000 115.6900 1.5557 IC CG CA *CB HB1 1.5557 115.6900 121.2200 108.1600 1.1145 IC CG CA *CB HB2 1.5557 115.6900 -123.6500 109.8100 1.1131 IC CA CB CG CD 1.5516 115.6900 180.0000 115.7300 1.5307 IC CD CB *CG HG1 1.5307 115.7300 117.3800 109.5000 1.1053 IC CD CB *CG HG2 1.5307 115.7300 -121.9600 111.0000 1.1081 IC CB CG CD OE1 1.5557 115.7300 180.0000 114.9900 1.2590 IC OE1 CG *CD OE2 1.2590 114.9900 -179.1000 120.0800 1.2532 PATCH FIRST NGLU LAST CGLU RESI GLH 0.00 ATOM N N -0.41570 ! | ATOM HN H 0.27190 ! HN-N ATOM CA CT 0.01450 ! | HB1 HG1 OE1 ATOM HA H1 0.07790 ! | | | // ATOM CB CT -0.00710 ! HA-CA--CB--CG--CD ATOM HB1 HC 0.02560 ! | | | \ ATOM HB2 HC 0.02560 ! | HB2 HG2 OE2(-) ATOM CG CT -0.01740 ! O=C ATOM HG1 HC 0.04300 ! | ATOM HG2 HC 0.04300 ATOM CD C 0.68010 ATOM OE1 O -0.58380 ATOM OE2 OH -0.65110 ATOM HE2 HO 0.46410 ATOM C C 0.59730 ATOM O O -0.56790 BOND CB CA CG CB CD CG OE2 CD BOND N HN N CA C CA BOND C +N CA HA CB HB1 CB HB2 CG HG1 BOND CG HG2 O C CD OE1 OE2 HE2 IMPROPER -C CA N HN IMPROPER CA +N C O IMPROPER CG OE1 CD OE2 DONOR HN N DONOR HE2 OE2 ACCEPTOR OE1 CD ACCEPTOR OE2 CD ACCEPTOR O C IC -C CA *N HN 1.3471 124.4500 180.0000 113.9900 0.9961 IC -C N CA C 1.3471 124.4500 180.0000 107.2700 1.5216 IC N CA C +N 1.4512 107.2700 180.0000 117.2500 1.3501 IC +N CA *C O 1.3501 117.2500 180.0000 121.0700 1.2306 IC CA C +N +CA 1.5216 117.2500 180.0000 124.3000 1.4530 IC N C *CA CB 1.4512 107.2700 121.9000 111.7100 1.5516 IC N C *CA HA 1.4512 107.2700 -118.0600 107.2600 1.0828 IC N CA CB CG 1.4512 111.0400 180.0000 115.6900 1.5557 IC CG CA *CB HB1 1.5557 115.6900 121.2200 108.1600 1.1145 IC CG CA *CB HB2 1.5557 115.6900 -123.6500 109.8100 1.1131 IC CA CB CG CD 1.5516 115.6900 180.0000 115.7300 1.5307 IC CD CB *CG HG1 1.5307 115.7300 117.3800 109.5000 1.1053 IC CD CB *CG HG2 1.5307 115.7300 -121.9600 111.0000 1.1081 IC CB CG CD OE1 1.5557 115.7300 180.0000 114.9900 1.2590 IC OE1 CG *CD OE2 1.2590 114.9900 -179.1000 120.0800 1.2532 PATCH FIRST NONE LAST NONE RESI GLY 0.00 GROUP ! | ATOM N N -0.41570 ! N-H ATOM HN H 0.27190 ! | ATOM CA CT -0.02520 ! | ATOM HA1 H1 0.06980 ! HA1-CA-HA2 ATOM HA2 H1 0.06980 ! | ATOM C C 0.59730 ! | ATOM O O -0.56790 ! C=O ! | BOND N HN N CA C CA BOND C +N CA HA1 CA HA2 BOND O C IMPROPER -C CA N HN IMPROPER CA +N C O DONOR HN N ACCEPTOR O C IC -C CA *N HN 1.3475 122.8200 180.0000 115.6200 0.9992 IC -C N CA C 1.3475 122.8200 180.0000 108.9400 1.4971 IC N CA C +N 1.4553 108.9400 180.0000 117.6000 1.3479 IC +N CA *C O 1.3479 117.6000 180.0000 120.8500 1.2289 IC CA C +N +CA 1.4971 117.6000 180.0000 124.0800 1.4560 IC N C *CA HA1 1.4553 108.9400 117.8600 108.0300 1.0814 IC N C *CA HA2 1.4553 108.9400 -118.1200 107.9500 1.0817 PATCH FIRST NGLY LAST CGLY RESI HID 0.00 ! neutral HIS, proton on ND1 GROUP ATOM N N -0.41570 ! | HD1 HE1 ATOM HN H 0.27190 ! HN-N | / ATOM CA CT 0.01880 ! | HB1 ND1--CE1 ATOM HA H1 0.08810 ! | | / || ATOM ND1 NA -0.38110 ! HA-CA--CB--CG || ATOM HD1 H 0.36490 ! | | \\ || ATOM CG CC -0.02660 ! | HB2 CD2--NE2 ATOM CB CT -0.04620 ! O=C | ATOM HB1 HC 0.04020 ! | HD2 ATOM HB2 HC 0.04020 ATOM NE2 NB -0.57270 ATOM CD2 CV 0.12920 ATOM HD2 H4 0.11470 ATOM CE1 CR 0.20570 ATOM HE1 H5 0.13920 ATOM C C 0.59730 ATOM O O -0.56790 BOND CB CA CG CB ND1 CG CE1 ND1 BOND NE2 CD2 N HN N CA BOND C CA C +N CA HA CB HB1 BOND CB HB2 ND1 HD1 CD2 HD2 CE1 HE1 BOND O C CG CD2 CE1 NE2 IMPROPER -C CA N HN IMPROPER CA +N C O IMPROPER CG CE1 ND1 HD1 IMPROPER CG NE2 CD2 HD2 IMPROPER ND1 NE2 CE1 HE1 IMPROPER ND1 CD2 CG CB DONOR HN N DONOR HD1 ND1 ACCEPTOR NE2 ACCEPTOR O C IC -C CA *N HN 1.3475 123.2700 180.0000 115.2100 0.9988 IC -C N CA C 1.3475 123.2700 180.0000 107.7000 1.5166 IC N CA C +N 1.4521 107.7000 180.0000 117.5700 1.3509 IC +N CA *C O 1.3509 117.5700 180.0000 120.2400 1.2273 IC CA C +N +CA 1.5166 117.5700 180.0000 123.7200 1.4545 IC N C *CA CB 1.4521 107.7000 122.4600 109.9900 1.5519 IC N C *CA HA 1.4521 107.7000 -117.4900 107.3700 1.0830 IC N CA CB CG 1.4521 112.1200 180.0000 114.0500 1.5041 IC CG CA *CB HB1 1.5041 114.0500 121.1700 109.0100 1.1118 IC CG CA *CB HB2 1.5041 114.0500 -122.3600 109.5300 1.1121 IC CA CB CG ND1 1.5519 114.0500 90.0000 124.1000 1.3783 IC ND1 CB *CG CD2 1.3783 124.1000 -171.2900 129.6000 1.3597 IC CB CG ND1 CE1 1.5041 124.1000 -173.2100 107.0300 1.3549 IC CB CG CD2 NE2 1.5041 129.6000 171.9900 110.0300 1.3817 IC NE2 ND1 *CE1 HE1 1.3166 111.6300 -179.6300 123.8900 1.0932 IC CE1 CG *ND1 HD1 1.3549 107.0300 -174.6500 126.2600 1.0005 IC NE2 CG *CD2 HD2 1.3817 110.0300 -177.8500 129.6300 1.0834 PATCH FIRST NHID LAST CHID RESI HIE 0.00 ! neutral His, proton on NE2 GROUP ATOM N N -0.41570 ! | HE1 ATOM HN H 0.27190 ! HN-N __ / ATOM CA CT -0.05810 ! | HB1 ND1--CE1 ATOM HA H1 0.13600 ! | | / | ATOM NE2 NA -0.27950 ! HA-CA--CB--CG | ATOM HE2 H 0.33390 ! | | \\ | ATOM CD2 CW -0.22070 ! | HB2 CD2--NE2 ATOM HD2 H4 0.18620 ! O=C | \ ATOM ND1 NB -0.54320 ! | HD2 HE2 ATOM CG CC 0.18680 ATOM CE1 CR 0.16350 ATOM HE1 H5 0.14350 ATOM CB CT -0.00740 ATOM HB1 HC 0.03670 ATOM HB2 HC 0.03670 ATOM C C 0.59730 ATOM O O -0.56790 BOND CB CA CG CB ND1 CG BOND NE2 CD2 N HN N CA BOND C CA C +N NE2 CE1 CA HA CB HB1 BOND CB HB2 NE2 HE2 CD2 HD2 CE1 HE1 BOND O C CD2 CG CE1 ND1 IMPROPER -C CA N HN IMPROPER CA +N C O IMPROPER CE1 CD2 NE2 HE2 IMPROPER CG NE2 CD2 HD2 IMPROPER ND1 NE2 CE1 HE1 IMPROPER ND1 CD2 CG CB DONOR HN N DONOR HE2 NE2 ACCEPTOR ND1 ACCEPTOR O C IC -C CA *N HN 1.3472 124.1600 180.0000 114.3600 0.9991 IC -C N CA C 1.3472 124.1600 180.0000 106.4300 1.5166 IC N CA C +N 1.4532 106.4300 180.0000 116.9700 1.3446 IC +N CA *C O 1.3446 116.9700 180.0000 120.6800 1.2290 IC CA C +N +CA 1.5166 116.9700 180.0000 124.9500 1.4505 IC N C *CA CB 1.4532 106.4300 123.5200 111.6700 1.5578 IC N C *CA HA 1.4532 106.4300 -116.4900 107.0800 1.0833 IC N CA CB CG 1.4532 112.8200 180.0000 116.9400 1.5109 IC CG CA *CB HB1 1.5109 116.9400 119.8000 107.9100 1.1114 IC CG CA *CB HB2 1.5109 116.9400 -124.0400 109.5000 1.1101 IC CA CB CG ND1 1.5578 116.9400 90.0000 120.1700 1.3859 IC ND1 CB *CG CD2 1.3859 120.1700 -178.2600 129.7100 1.3596 IC CB CG ND1 CE1 1.5109 120.1700 -179.2000 105.2000 1.3170 IC CB CG CD2 NE2 1.5109 129.7100 178.6600 105.8000 1.3782 IC NE2 ND1 *CE1 HE1 1.3539 111.7600 179.6900 124.5800 1.0929 IC CE1 CD2 *NE2 HE2 1.3539 107.1500 -178.6900 125.8600 0.9996 IC NE2 CG *CD2 HD2 1.3782 105.8000 -179.3500 129.8900 1.0809 PATCH FIRST NHIE LAST CHIE RESI HIP 1.00 ! Protonated His GROUP ATOM N N -0.34790 ! | HD1 HE1 ATOM HN H 0.27470 ! HN-N | / ATOM CA CT -0.13540 ! | HB1 ND1--CE1 ATOM HA H1 0.12120 ! | | / || ATOM ND1 NA -0.15130 ! HA-CA--CB--CG || ATOM HD1 H 0.38660 ! | | \\ || ATOM NE2 NA -0.17180 ! | HB2 CD2--NE2(+) ATOM HE2 H 0.39110 ! O=C | \ ATOM CE1 CR -0.01700 ! | HD2 HE2 ATOM HE1 H5 0.26810 ATOM CD2 CW -0.11410 ATOM HD2 H4 0.23170 ATOM CG CC -0.00120 ATOM CB CT -0.04140 ATOM HB1 HC 0.08100 ATOM HB2 HC 0.08100 ATOM C C 0.73410 ATOM O O -0.58940 BOND CB CA CG CB ND1 CG CE1 ND1 BOND NE2 CD2 N HN N CA BOND C CA C +N CA HA CB HB1 BOND CB HB2 ND1 HD1 NE2 HE2 CD2 HD2 CE1 HE1 BOND O C CD2 CG NE2 CE1 IMPROPER -C CA N HN IMPROPER CA +N C O IMPROPER CG CE1 ND1 HD1 IMPROPER CE1 CD2 NE2 HE2 IMPROPER CG NE2 CD2 HD2 IMPROPER ND1 NE2 CE1 HE1 IMPROPER ND1 CD2 CG CB DONOR HN N DONOR HD1 ND1 DONOR HE2 NE2 ACCEPTOR O C IC -C CA *N HN 1.3489 123.9300 180.0000 118.8000 1.0041 IC -C N CA C 1.3489 123.9300 180.0000 112.0300 1.5225 IC N CA C +N 1.4548 112.0300 180.0000 116.4900 1.3464 IC +N CA *C O 1.3464 116.4900 180.0000 121.2000 1.2284 IC CA C +N +CA 1.5225 116.4900 180.0000 124.2400 1.4521 IC N C *CA CB 1.4548 112.0300 125.1300 109.3800 1.5533 IC N C *CA HA 1.4548 112.0300 -119.2000 106.7200 1.0832 IC N CA CB CG 1.4548 112.2500 180.0000 114.1800 1.5168 IC CG CA *CB HB1 1.5168 114.1800 122.5000 108.9900 1.1116 IC CG CA *CB HB2 1.5168 114.1800 -121.5100 108.9700 1.1132 IC CA CB CG ND1 1.5533 114.1800 90.0000 122.9400 1.3718 IC ND1 CB *CG CD2 1.3718 122.9400 -165.2600 128.9300 1.3549 IC CB CG ND1 CE1 1.5168 122.9400 -167.6200 108.9000 1.3262 IC CB CG CD2 NE2 1.5168 128.9300 167.1300 106.9300 1.3727 IC NE2 ND1 *CE1 HE1 1.3256 108.5000 178.3900 125.7600 1.0799 IC CE1 CD2 *NE2 HE2 1.3256 108.8200 -172.9400 125.5200 1.0020 IC CE1 CG *ND1 HD1 1.3262 108.9000 171.4900 126.0900 1.0018 IC NE2 CG *CD2 HD2 1.3727 106.9300 -174.4900 128.4100 1.0867 PATCH FIRST NHIP LAST CHIP RESI ILE 0.00 GROUP ATOM N N -0.41570 ! | HG21 HG22 ATOM HN H 0.27190 ! HN-N | / ATOM CA CT -0.05970 ! | CG2--HG23 ATOM HA H1 0.08690 ! | / ATOM CB CT 0.13030 ! HA-CA--CB-HB HD1 ATOM HB HC 0.01870 ! | \ / ATOM CG2 CT -0.32040 ! | CG1--CD--HD2 ATOM HG21 HC 0.08820 ! O=C / \ \ ATOM HG22 HC 0.08820 ! | HG11 HG12 HD3 ATOM HG23 HC 0.08820 ATOM CG1 CT -0.04300 ATOM HG11 HC 0.02360 ATOM HG12 HC 0.02360 ATOM CD CT -0.06600 ATOM HD1 HC 0.01860 ATOM HD2 HC 0.01860 ATOM HD3 HC 0.01860 ATOM C C 0.59730 ATOM O O -0.56790 BOND CB CA CG1 CB CG2 CB CD CG1 BOND N HN N CA C CA C +N BOND CA HA CB HB CG1 HG11 CG1 HG12 CG2 HG21 BOND CG2 HG22 CG2 HG23 CD HD1 CD HD2 CD HD3 BOND O C IMPROPER -C CA N HN IMPROPER CA +N C O DONOR HN N ACCEPTOR O C IC -C CA *N HN 1.3470 124.1600 180.0000 114.1900 0.9978 IC -C N CA C 1.3470 124.1600 180.0000 106.3500 1.5190 IC N CA C +N 1.4542 106.3500 180.0000 117.9700 1.3465 IC +N CA *C O 1.3465 117.9700 180.0000 120.5900 1.2300 IC CA C +N +CA 1.5190 117.9700 180.0000 124.2100 1.4467 IC N C *CA CB 1.4542 106.3500 124.2200 112.9300 1.5681 IC N C *CA HA 1.4542 106.3500 -115.6300 106.8100 1.0826 IC N CA CB CG1 1.4542 112.7900 180.0000 113.6300 1.5498 IC CG1 CA *CB HB 1.5498 113.6300 114.5500 104.4800 1.1195 IC CG1 CA *CB CG2 1.5498 113.6300 -130.0400 113.9300 1.5452 IC CA CB CG2 HG21 1.5681 113.9300 -171.3000 110.6100 1.1100 IC HG21 CB *CG2 HG22 1.1100 110.6100 119.3500 110.9000 1.1102 IC HG21 CB *CG2 HG23 1.1100 110.6100 -120.0900 110.9700 1.1105 IC CA CB CG1 CD 1.5681 113.6300 180.0000 114.0900 1.5381 IC CD CB *CG1 HG11 1.5381 114.0900 122.3600 109.7800 1.1130 IC CD CB *CG1 HG12 1.5381 114.0900 -120.5900 108.8900 1.1141 IC CB CG1 CD HD1 1.5498 114.0900 -176.7800 110.3100 1.1115 IC HD1 CG1 *CD HD2 1.1115 110.3100 119.7500 110.6500 1.1113 IC HD1 CG1 *CD HD3 1.1115 110.3100 -119.7000 111.0200 1.1103 PATCH FIRST NILE LAST CILE RESI LEU 0.00 GROUP ATOM N N -0.41570 ! | HD11 HD12 ATOM HN H 0.27190 ! HN-N | / ATOM CA CT -0.05180 ! | HB1 CD1--HD13 ATOM HA H1 0.09220 ! | | / ATOM CB CT -0.11020 ! HA-CA--CB--CG-HG ATOM HB1 HC 0.04570 ! | | \ ATOM HB2 HC 0.04570 ! | HB2 CD2--HD23 ATOM CG CT 0.35310 ! O=C | \ ATOM HG HC -0.03610 ! | HD21 HD22 ATOM CD1 CT -0.41210 ATOM HD11 HC 0.10000 ATOM HD12 HC 0.10000 ATOM HD13 HC 0.10000 ATOM CD2 CT -0.41210 ATOM HD21 HC 0.10000 ATOM HD22 HC 0.10000 ATOM HD23 HC 0.10000 ATOM C C 0.59730 ATOM O O -0.56790 BOND CB CA CG CB CD1 CG CD2 CG BOND N HN N CA C CA C +N BOND CA HA CB HB1 CB HB2 CG HG CD1 HD11 BOND CD1 HD12 CD1 HD13 CD2 HD21 CD2 HD22 CD2 HD23 BOND O C IMPROPER -C CA N HN IMPROPER CA +N C O DONOR HN N ACCEPTOR O C IC -C CA *N HN 1.3474 124.3100 180.0000 114.2600 0.9979 IC -C N CA C 1.3474 124.3100 180.0000 106.0500 1.5184 IC N CA C +N 1.4508 106.0500 180.0000 117.9300 1.3463 IC +N CA *C O 1.3463 117.9300 180.0000 120.5600 1.2299 IC CA C +N +CA 1.5184 117.9300 180.0000 124.2600 1.4467 IC N C *CA CB 1.4508 106.0500 121.5200 112.1200 1.5543 IC N C *CA HA 1.4508 106.0500 -116.5000 107.5700 1.0824 IC N CA CB CG 1.4508 111.1900 180.0000 117.4600 1.5472 IC CG CA *CB HB1 1.5472 117.4600 120.9800 107.1700 1.1145 IC CG CA *CB HB2 1.5472 117.4600 -124.6700 108.9800 1.1126 IC CA CB CG CD1 1.5543 117.4600 180.0000 110.4800 1.5361 IC CD1 CB *CG CD2 1.5361 110.4800 -123.7500 112.5700 1.5360 IC CD1 CD2 *CG HG 1.5361 110.2600 -116.6300 108.0200 1.1168 IC CB CG CD1 HD11 1.5472 110.4800 177.3300 110.5400 1.1111 IC HD11 CG *CD1 HD12 1.1111 110.5400 119.9600 110.6200 1.1112 IC HD11 CG *CD1 HD13 1.1111 110.5400 -119.8500 110.6900 1.1108 IC CB CG CD2 HD21 1.5472 112.5700 178.9600 110.3200 1.1116 IC HD21 CG *CD2 HD22 1.1116 110.3200 119.7100 111.6900 1.1086 IC HD21 CG *CD2 HD23 1.1116 110.3200 -119.6100 110.4900 1.1115 PATCH FIRST NLEU LAST CLEU RESI LYS 1.00 GROUP ATOM N N -0.34790 ! | ATOM HN H 0.27470 ! HN-N ATOM CA CT -0.24000 ! | HB1 HG1 HD1 HE1 HZ1 ATOM HA H1 0.14260 ! | | | | | / ATOM CB CT -0.00940 ! HA-CA--CB--CG--CD--CE--NZ--HZ2 ATOM HB1 HC 0.03620 ! | | | | | \ ATOM HB2 HC 0.03620 ! | HB2 HG2 HD2 HE2 HZ3 ATOM CG CT 0.01870 ! O=C ATOM HG1 HC 0.01030 ! | ATOM HG2 HC 0.01030 ATOM CD CT -0.04790 ATOM HD1 HC 0.06210 ATOM HD2 HC 0.06210 ATOM CE CT -0.01430 ATOM HE1 HP 0.11350 ATOM HE2 HP 0.11350 ATOM NZ N3 -0.38540 ATOM HZ1 H 0.34000 ATOM HZ2 H 0.34000 ATOM HZ3 H 0.34000 ATOM C C 0.73410 ATOM O O -0.58940 BOND CB CA CG CB CD CG CE CD NZ CE BOND N HN N CA C CA BOND C +N CA HA CB HB1 CB HB2 CG HG1 BOND CG HG2 CD HD1 CD HD2 CE HE1 CE HE2 BOND O C BOND NZ HZ1 NZ HZ2 NZ HZ3 IMPROPER -C CA N HN IMPROPER CA +N C O DONOR HN N DONOR HZ1 NZ DONOR HZ2 NZ DONOR HZ3 NZ ACCEPTOR O C IC -C CA *N HN 1.3482 123.5700 180.0000 115.1100 0.9988 IC -C N CA C 1.3482 123.5700 180.0000 107.2900 1.5187 IC N CA C +N 1.4504 107.2900 180.0000 117.2700 1.3478 IC +N CA *C O 1.3478 117.2700 180.0000 120.7900 1.2277 IC CA C +N +CA 1.5187 117.2700 180.0000 124.9100 1.4487 IC N C *CA CB 1.4504 107.2900 122.2300 111.3600 1.5568 IC N C *CA HA 1.4504 107.2900 -116.8800 107.3600 1.0833 IC N CA CB CG 1.4504 111.4700 180.0000 115.7600 1.5435 IC CG CA *CB HB1 1.5435 115.7600 120.9000 107.1100 1.1146 IC CG CA *CB HB2 1.5435 115.7600 -124.4800 108.9900 1.1131 IC CA CB CG CD 1.5568 115.7600 180.0000 113.2800 1.5397 IC CD CB *CG HG1 1.5397 113.2800 120.7400 109.1000 1.1138 IC CD CB *CG HG2 1.5397 113.2800 -122.3400 108.9900 1.1143 IC CB CG CD CE 1.5435 113.2800 180.0000 112.3300 1.5350 IC CE CG *CD HD1 1.5350 112.3300 122.2500 108.4100 1.1141 IC CE CG *CD HD2 1.5350 112.3300 -121.5900 108.1300 1.1146 IC CG CD CE NZ 1.5397 112.3300 180.0000 110.4600 1.4604 IC NZ CD *CE HE1 1.4604 110.4600 119.9100 110.5100 1.1128 IC NZ CD *CE HE2 1.4604 110.4600 -120.0200 110.5700 1.1123 IC CD CE NZ HZ1 1.5350 110.4600 179.9200 110.0200 1.0404 IC HZ1 CE *NZ HZ2 1.0404 110.0200 120.2700 109.5000 1.0402 IC HZ1 CE *NZ HZ3 1.0404 110.0200 -120.1300 109.4000 1.0401 PATCH FIRST NLYS LAST CLYS RESI MET 0.00 GROUP ATOM N N -0.41570 ! | ATOM HN H 0.27190 ! HN-N ATOM CA CT -0.02370 ! | HB1 HG1 HE1 ATOM HA H1 0.08800 ! | | | | ATOM CB CT 0.03420 ! HA-CA--CB--CG--SD--CE--HE3 ATOM HB1 HC 0.02410 ! | | | | ATOM HB2 HC 0.02410 ! | HB2 HG2 HE2 ATOM CG CT 0.00180 ! O=C ATOM HG1 H1 0.04400 ! | ATOM HG2 H1 0.04400 ATOM SD S -0.27370 ATOM CE CT -0.05360 ATOM HE1 H1 0.06840 ATOM HE2 H1 0.06840 ATOM HE3 H1 0.06840 ATOM C C 0.59730 ATOM O O -0.56790 BOND CB CA CG CB SD CG CE SD BOND N HN N CA C CA C +N BOND CA HA CB HB1 CB HB2 CG HG1 CG HG2 BOND CE HE1 CE HE2 CE HE3 BOND O C IMPROPER -C CA N HN IMPROPER CA +N C O DONOR HN N ACCEPTOR O C IC -C CA *N HN 1.3478 124.2100 180.0000 114.3900 0.9978 IC -C N CA C 1.3478 124.2100 180.0000 106.3100 1.5195 IC N CA C +N 1.4510 106.3100 180.0000 117.7400 1.3471 IC +N CA *C O 1.3471 117.7400 180.0000 120.6400 1.2288 IC CA C +N +CA 1.5195 117.7400 180.0000 124.5200 1.4471 IC N C *CA CB 1.4510 106.3100 121.6200 111.8800 1.5546 IC N C *CA HA 1.4510 106.3100 -116.9800 107.5700 1.0832 IC N CA CB CG 1.4510 111.2500 180.0000 115.9200 1.5460 IC CG CA *CB HB1 1.5460 115.9200 120.5600 106.9000 1.1153 IC CG CA *CB HB2 1.5460 115.9200 -124.8000 109.3800 1.1129 IC CA CB CG SD 1.5546 115.9200 180.0000 110.2800 1.8219 IC SD CB *CG HG1 1.8219 110.2800 120.5000 110.3400 1.1106 IC SD CB *CG HG2 1.8219 110.2800 -121.1600 109.6400 1.1119 IC CB CG SD CE 1.5460 110.2800 180.0000 98.9400 1.8206 IC CG SD CE HE1 1.8219 98.9400 -179.4200 110.9100 1.1111 IC HE1 SD *CE HE2 1.1111 110.9100 119.9500 111.0300 1.1115 IC HE1 SD *CE HE3 1.1111 110.9100 -119.9500 111.0900 1.1112 PATCH FIRST NMET LAST CMET RESI PHE 0.00 GROUP ATOM N N -0.41570 ! | HD1 HE1 ATOM HN H 0.27190 ! HN-N | | ATOM CA CT -0.00240 ! | HB1 CD1--CE1 ATOM HA H1 0.09780 ! | | // \\ ATOM CB CT -0.03430 ! HA-CA--CB--CG CZ--HZ ATOM HB1 HC 0.02950 ! | | \ __ / ATOM HB2 HC 0.02950 ! | HB2 CD2--CE2 ATOM CG CA 0.01180 ! O=C | | ATOM CD1 CA -0.12560 ! | HD2 HE2 ATOM HD1 HA 0.13300 ATOM CE1 CA -0.17040 ATOM HE1 HA 0.14300 ATOM CZ CA -0.10720 ATOM HZ HA 0.12970 ATOM CE2 CA -0.17040 ATOM HE2 HA 0.14300 ATOM CD2 CA -0.12560 ATOM HD2 HA 0.13300 ATOM C C 0.59730 ATOM O O -0.56790 BOND CB CA CG CB CD2 CG CE1 CD1 BOND CZ CE2 N HN BOND N CA C CA C +N CA HA BOND CB HB1 CB HB2 CD1 HD1 CD2 HD2 CE1 HE1 BOND O C CD1 CG CZ CE1 CE2 CD2 BOND CE2 HE2 CZ HZ IMPROPER -C CA N HN IMPROPER CA +N C O IMPROPER CG CE2 CD2 HD2 !IMPROPER CD2 CZ CE2 HE2 IMPROPER CZ CD2 CE2 HE2 IMPROPER CE1 CE2 CZ HZ IMPROPER CD1 CZ CE1 HE1 IMPROPER CG CE1 CD1 HD1 IMPROPER CD1 CD2 CG CB DONOR HN N ACCEPTOR O C IC -C CA *N HN 1.3476 123.8900 180.0000 114.4700 0.9987 IC -C N CA C 1.3476 123.8900 180.0000 106.3800 1.5229 IC N CA C +N 1.4504 106.3800 180.0000 117.6500 1.3483 IC +N CA *C O 1.3483 117.6500 180.0000 120.4900 1.2287 IC CA C +N +CA 1.5229 117.6500 180.0000 124.1000 1.4523 IC N C *CA CB 1.4504 106.3800 122.4900 112.4500 1.5594 IC N C *CA HA 1.4504 106.3800 -115.6300 107.0500 1.0832 IC N CA CB CG 1.4504 111.6300 180.0000 112.7600 1.5109 IC CG CA *CB HB1 1.5109 112.7600 118.2700 109.1000 1.1119 IC CG CA *CB HB2 1.5109 112.7600 -123.8300 111.1100 1.1113 IC CA CB CG CD1 1.5594 112.7600 90.0000 120.3200 1.4059 IC CD1 CB *CG CD2 1.4059 120.3200 -177.9600 120.7600 1.4062 IC CB CG CD1 CE1 1.5109 120.3200 -177.3700 120.6300 1.4006 IC CE1 CG *CD1 HD1 1.4006 120.6300 179.7000 119.6500 1.0814 IC CB CG CD2 CE2 1.5109 120.7600 177.2000 120.6200 1.4002 IC CE2 CG *CD2 HD2 1.4002 120.6200 -178.6900 119.9900 1.0811 IC CG CD1 CE1 CZ 1.4059 120.6300 -0.1200 119.9300 1.4004 IC CZ CD1 *CE1 HE1 1.4004 119.9300 -179.6900 120.0100 1.0808 IC CZ CD2 *CE2 HE2 1.4000 119.9600 -179.9300 119.8700 1.0811 IC CE1 CE2 *CZ HZ 1.4004 119.9800 179.5100 119.9700 1.0807 PATCH FIRST NPHE LAST CPHE RESI PRO 0.00 GROUP ATOM N N -0.25480 ! HD1 HD2 ATOM CD CT 0.01920 ! | \ / ATOM HD1 H1 0.03910 ! N---CD HG1 ATOM HD2 H1 0.03910 ! | \ / ATOM CG CT 0.01890 ! | CG ATOM HG1 HC 0.02130 ! | / \ ATOM HG2 HC 0.02130 ! HA-CA--CB HG2 ATOM CB CT -0.00700 ! | / \ ATOM HB1 HC 0.02530 ! | HB1 HB2 ATOM HB2 HC 0.02530 ! O=C ATOM CA CT -0.02660 ! | ATOM HA H1 0.06410 ATOM C C 0.58960 ATOM O O -0.57480 BOND C CA C +N BOND N CA CA CB CB CG CG CD N CD BOND HA CA HG1 CG HG2 CG HD1 CD HD2 CD HB1 CB HB2 CB BOND O C IMPROPER -C CD N CA IMPROPER CA +N C O ACCEPTOR O C IC -C CA *N CD 1.3366 122.9400 178.5100 112.7500 1.4624 IC -C N CA C 1.3366 122.9400 -76.1200 110.8600 1.5399 IC N CA C +N 1.4585 110.8600 180.0000 114.7500 1.3569 IC +N CA *C O 1.3569 114.7500 177.1500 120.4600 1.2316 IC CA C +N +CA 1.5399 116.1200 180.0000 124.8900 1.4517 IC N C *CA CB 1.4585 110.8600 113.7400 111.7400 1.5399 IC N C *CA HA 1.4585 110.8600 -122.4000 109.0900 1.0837 IC N CA CB CG 1.4585 102.5600 31.6100 104.3900 1.5322 IC CA CB CG CD 1.5399 104.3900 -34.5900 103.2100 1.5317 IC N CA CB HB1 1.4585 102.5600 -84.9400 109.0200 1.1131 IC N CA CB HB2 1.4585 102.5600 153.9300 112.7400 1.1088 IC CA CB CG HG1 1.5399 104.3900 -156.7200 112.9500 1.1077 IC CA CB CG HG2 1.5399 104.3900 81.2600 109.2200 1.1143 IC CB CG CD HD1 1.5322 103.2100 -93.5500 110.0300 1.1137 IC CB CG CD HD2 1.5322 103.2100 144.5200 110.0000 1.1144 PATCH FIRST NPRO LAST CPRO RESI SER 0.00 GROUP ATOM N N -0.41570 ! | ATOM HN H 0.27190 ! HN-N ATOM CA CT -0.02490 ! | HB1 ATOM HA H1 0.08430 ! | | ATOM CB CT 0.21170 ! HA-CA--CB--OG ATOM HB1 H1 0.03520 ! | | \ ATOM HB2 H1 0.03520 ! | HB2 HG1 ATOM OG OH -0.65460 ! O=C ATOM HG1 HO 0.42750 ! | ATOM C C 0.59730 ATOM O O -0.56790 BOND CB CA OG CB N HN N CA BOND C CA C +N CA HA CB HB1 BOND CB HB2 OG HG1 BOND O C IMPROPER -C CA N HN IMPROPER CA +N C O DONOR HN N DONOR HG1 OG ACCEPTOR OG ACCEPTOR O C IC -C CA *N HN 1.3474 124.3700 180.0000 114.1800 0.9999 IC -C N CA C 1.3474 124.3700 180.0000 105.8100 1.5166 IC N CA C +N 1.4579 105.8100 180.0000 117.7200 1.3448 IC +N CA *C O 1.3448 117.7200 180.0000 120.2500 1.2290 IC CA C +N +CA 1.5166 117.7200 180.0000 124.6300 1.4529 IC N C *CA CB 1.4579 105.8100 124.7500 111.4000 1.5585 IC N C *CA HA 1.4579 105.8100 -115.5600 107.3000 1.0821 IC N CA CB OG 1.4579 114.2800 180.0000 112.4500 1.4341 IC OG CA *CB HB1 1.4341 112.4500 119.3200 108.1000 1.1140 IC OG CA *CB HB2 1.4341 112.4500 -123.8600 110.3800 1.1136 IC CA CB OG HG1 1.5585 112.4500 165.9600 107.0800 0.9655 PATCH FIRST NSER LAST CSER RESI THR 0.00 GROUP ATOM N N -0.41570 ! | ATOM HN H 0.27190 ! HN-N ATOM CA CT -0.03890 ! | OG1--HG1 ATOM HA H1 0.10070 ! | / ATOM CB CT 0.36540 ! HA-CA--CB-HB ATOM HB H1 0.00430 ! | \ ATOM CG2 CT -0.24380 ! | CG2--HG21 ATOM HG21 HC 0.06420 ! O=C / \ ATOM HG22 HC 0.06420 ! | HG21 HG22 ATOM HG23 HC 0.06420 ATOM OG1 OH -0.67610 ATOM HG1 HO 0.41020 ATOM C C 0.59730 ATOM O O -0.56790 BOND CB CA OG1 CB CG2 CB N HN BOND N CA C CA C +N CA HA BOND CB HB OG1 HG1 CG2 HG21 CG2 HG22 CG2 HG23 BOND O C IMPROPER -C CA N HN IMPROPER CA +N C O DONOR HN N DONOR HG1 OG1 ACCEPTOR OG1 ACCEPTOR O C IC -C CA *N HN 1.3471 124.1200 180.0000 114.2600 0.9995 IC -C N CA C 1.3471 124.1200 180.0000 106.0900 1.5162 IC N CA C +N 1.4607 106.0900 180.0000 117.6900 1.3449 IC +N CA *C O 1.3449 117.6900 180.0000 120.3000 1.2294 IC CA C +N +CA 1.5162 117.6900 180.0000 124.6600 1.4525 IC N C *CA CB 1.4607 106.0900 126.4600 112.7400 1.5693 IC N C *CA HA 1.4607 106.0900 -114.9200 106.5300 1.0817 IC N CA CB OG1 1.4607 114.8100 180.0000 112.1600 1.4252 IC OG1 CA *CB HB 1.4252 112.1600 116.3900 106.1100 1.1174 IC OG1 CA *CB CG2 1.4252 112.1600 -124.1300 115.9100 1.5324 IC CA CB OG1 HG1 1.5693 112.1600 -179.2800 105.4500 0.9633 IC CA CB CG2 HG21 1.5693 115.9100 -173.6500 110.8500 1.1104 IC HG21 CB *CG2 HG22 1.1104 110.8500 119.5100 110.4100 1.1109 IC HG21 CB *CG2 HG23 1.1104 110.8500 -120.3900 111.1100 1.1113 PATCH FIRST NTHR LAST CTHR RESI TRP 0.00 GROUP ATOM N N -0.41570 ! | HE3 ATOM HN H 0.27190 ! HN-N | ATOM CA CT -0.02750 ! | HB1 CE3 ATOM HA H1 0.11230 ! | | / \\ ATOM CB CT -0.00500 ! HA-CA--CB---CG-----CD2 CZ3-HZ3 ATOM HB1 HC 0.03390 ! | | || || | ATOM HB2 HC 0.03390 ! | HB2 CD1 CE2 CH2-HH2 ATOM CG CS -0.14150 ! O=C / \ / \ // ATOM CD1 CW -0.16380 ! | HD1 NE1 CZ2 ATOM HD1 H4 0.20620 ! | | ATOM NE1 NA -0.34180 ! HE1 HZ2 ATOM HE1 H 0.34120 ATOM CE2 CN 0.13800 ATOM CZ2 CA -0.26010 ATOM HZ2 HA 0.15720 ATOM CH2 CA -0.11340 ATOM HH2 HA 0.14170 ATOM CZ3 CA -0.19720 ATOM HZ3 HA 0.14470 ATOM CE3 CA -0.23870 ATOM HE3 HA 0.17000 ATOM CD2 CB 0.12430 ATOM C C 0.59730 ATOM O O -0.56790 BOND CB CA CG CB CD2 CG NE1 CD1 BOND CZ2 CE2 BOND N HN N CA C CA C +N BOND CZ3 CH2 CD2 CE3 NE1 CE2 CA HA CB HB1 BOND CB HB2 CD1 HD1 NE1 HE1 CE3 HE3 CZ2 HZ2 BOND CZ3 HZ3 CH2 HH2 BOND O C CD1 CG CE2 CD2 CZ3 CE3 CH2 CZ2 IMPROPER -C CA N HN IMPROPER CA +N C O IMPROPER CD1 CE2 NE1 HE1 IMPROPER CE2 CH2 CZ2 HZ2 IMPROPER CZ2 CZ3 CH2 HH2 IMPROPER CH2 CE3 CZ3 HZ3 IMPROPER CZ3 CD2 CE3 HE3 IMPROPER CG NE1 CD1 HD1 IMPROPER CD1 CD2 CG CB DONOR HN N DONOR HE1 NE1 ACCEPTOR O C IC -C CA *N HN 1.3482 123.5100 180.0000 115.0200 0.9972 IC -C N CA C 1.3482 123.5100 180.0000 107.6900 1.5202 IC N CA C +N 1.4507 107.6900 180.0000 117.5700 1.3505 IC +N CA *C O 1.3505 117.5700 180.0000 121.0800 1.2304 IC CA C +N +CA 1.5202 117.5700 180.0000 124.8800 1.4526 IC N C *CA CB 1.4507 107.6900 122.6800 111.2300 1.5560 IC N C *CA HA 1.4507 107.6900 -117.0200 106.9200 1.0835 IC N CA CB CG 1.4507 111.6800 180.0000 115.1400 1.5233 IC CG CA *CB HB1 1.5233 115.1400 119.1700 107.8400 1.1127 IC CG CA *CB HB2 1.5233 115.1400 -124.7300 109.8700 1.1118 IC CA CB CG CD2 1.5560 115.1400 90.0000 123.9500 1.4407 IC CD2 CB *CG CD1 1.4407 123.9500 -172.8100 129.1800 1.3679 IC CD1 CG CD2 CE2 1.3679 106.5700 -0.0800 106.6500 1.4126 IC CG CD2 CE2 NE1 1.4407 106.6500 0.1400 107.8700 1.3746 IC CE2 CG *CD2 CE3 1.4126 106.6500 179.2100 132.5400 1.4011 IC CE2 CD2 CE3 CZ3 1.4126 120.8000 -0.2000 118.1600 1.4017 IC CD2 CE3 CZ3 CH2 1.4011 118.1600 0.1000 120.9700 1.4019 IC CE3 CZ3 CH2 CZ2 1.4017 120.9700 0.0100 120.8700 1.4030 IC CZ3 CD2 *CE3 HE3 1.4017 118.1600 -179.6200 121.8400 1.0815 IC CH2 CE3 *CZ3 HZ3 1.4019 120.9700 -179.8200 119.4500 1.0811 IC CZ2 CZ3 *CH2 HH2 1.4030 120.8700 -179.9200 119.5700 1.0811 IC CE2 CH2 *CZ2 HZ2 1.3939 118.4200 179.8700 120.0800 1.0790 IC CD1 CE2 *NE1 HE1 1.3752 108.8100 177.7800 124.6800 0.9767 IC CG NE1 *CD1 HD1 1.3679 110.1000 178.1000 125.4300 1.0820 PATCH FIRST NTRP LAST CTRP RESI TYR 0.00 GROUP ATOM N N -0.41570 ! | HD1 HE1 ATOM HN H 0.27190 ! HN-N | | ATOM CA CT -0.00140 ! | HB1 CD1--CE1 ATOM HA H1 0.08760 ! | | // \\ ATOM CB CT -0.01520 ! HA-CA--CB--CG CZ--OH ATOM HB1 HC 0.02950 ! | | \ __ / \ ATOM HB2 HC 0.02950 ! | HB2 CD2--CE2 HH ATOM CG CA -0.00110 ! O=C | | ATOM CD1 CA -0.19060 ! | HD2 HE2 ATOM HD1 HA 0.16990 ATOM CE1 CA -0.23410 ATOM HE1 HA 0.16560 ATOM CZ C 0.32260 ATOM OH OH -0.55790 ATOM HH HO 0.39920 ATOM CE2 CA -0.23410 ATOM HE2 HA 0.16560 ATOM CD2 CA -0.19060 ATOM HD2 HA 0.16990 ATOM C C 0.59730 ATOM O O -0.56790 BOND CB CA CG CB CD2 CG CE1 CD1 BOND CZ CE2 OH CZ BOND N HN N CA C CA C +N BOND CA HA CB HB1 CB HB2 CD1 HD1 CD2 HD2 BOND CE1 HE1 CE2 HE2 OH HH BOND O C CD1 CG CE1 CZ CE2 CD2 IMPROPER -C CA N HN IMPROPER CA +N C O IMPROPER CG CE2 CD2 HD2 !IMPROPER CD2 CZ CE2 HE2 IMPROPER CZ CD2 CE2 HE2 IMPROPER CD1 CZ CE1 HE1 IMPROPER CG CE1 CD1 HD1 IMPROPER CD1 CD2 CG CB IMPROPER CE1 CE2 CZ OH DONOR HN N DONOR HH OH ACCEPTOR OH ACCEPTOR O C IC -C CA *N HN 1.3476 123.8100 180.0000 114.5400 0.9986 IC -C N CA C 1.3476 123.8100 180.0000 106.5200 1.5232 IC N CA C +N 1.4501 106.5200 180.0000 117.3300 1.3484 IC +N CA *C O 1.3484 117.3300 180.0000 120.6700 1.2287 IC CA C +N +CA 1.5232 117.3300 180.0000 124.3100 1.4513 IC N C *CA CB 1.4501 106.5200 122.2700 112.3400 1.5606 IC N C *CA HA 1.4501 106.5200 -116.0400 107.1500 1.0833 IC N CA CB CG 1.4501 111.4300 180.0000 112.9400 1.5113 IC CG CA *CB HB1 1.5113 112.9400 118.8900 109.1200 1.1119 IC CG CA *CB HB2 1.5113 112.9400 -123.3600 110.7000 1.1115 IC CA CB CG CD1 1.5606 112.9400 90.0000 120.4900 1.4064 IC CD1 CB *CG CD2 1.4064 120.4900 -176.4600 120.4600 1.4068 IC CB CG CD1 CE1 1.5113 120.4900 -175.4900 120.4000 1.4026 IC CE1 CG *CD1 HD1 1.4026 120.4000 178.9400 119.8000 1.0814 IC CB CG CD2 CE2 1.5113 120.4600 175.3200 120.5600 1.4022 IC CE2 CG *CD2 HD2 1.4022 120.5600 -177.5700 119.9800 1.0813 IC CG CD1 CE1 CZ 1.4064 120.4000 -0.1900 120.0900 1.3978 IC CZ CD1 *CE1 HE1 1.3978 120.0900 179.6400 120.5800 1.0799 IC CZ CD2 *CE2 HE2 1.3979 119.9200 -178.6900 119.7600 1.0798 IC CE1 CE2 *CZ OH 1.3978 120.0500 -178.9800 120.2500 1.4063 IC CE1 CZ OH HH 1.3978 119.6800 175.4500 107.4700 0.9594 PATCH FIRST NTYR LAST CTYR RESI VAL 0.00 GROUP ATOM N N -0.41570 ! | HG11 HG12 ATOM HN H 0.27190 ! HN-N | / ATOM CA CT -0.08750 ! | CG1--HG13 ATOM HA H1 0.09690 ! | / ATOM CB CT 0.29850 ! HA-CA--CB-HB ATOM HB HC -0.02970 ! | \ ATOM CG1 CT -0.31920 ! | CG2--HG21 ATOM HG11 HC 0.07910 ! O=C / \ ATOM HG12 HC 0.07910 ! | HG21 HG22 ATOM HG13 HC 0.07910 ATOM CG2 CT -0.31920 ATOM HG21 HC 0.07910 ATOM HG22 HC 0.07910 ATOM HG23 HC 0.07910 ATOM C C 0.59730 ATOM O O -0.56790 BOND CB CA CG1 CB CG2 CB N HN BOND N CA C CA C +N CA HA BOND CB HB CG1 HG11 CG1 HG12 CG1 HG13 CG2 HG21 BOND CG2 HG22 CG2 HG23 BOND O C IMPROPER -C CA N HN IMPROPER CA +N C O DONOR HN N ACCEPTOR O C IC -C CA *N HN 1.3482 124.5700 180.0000 114.4100 0.9966 IC -C N CA C 1.3482 124.5700 180.0000 105.5400 1.5180 IC N CA C +N 1.4570 105.5400 180.0000 117.8300 1.3471 IC +N CA *C O 1.3471 117.8300 180.0000 120.7000 1.2297 IC CA C +N +CA 1.5180 117.8300 180.0000 124.0800 1.4471 IC N C *CA CB 1.4570 105.5400 122.9500 111.2300 1.5660 IC N C *CA HA 1.4570 105.5400 -117.2400 107.4600 1.0828 IC N CA CB CG1 1.4570 113.0500 180.0000 113.9700 1.5441 IC CG1 CA *CB CG2 1.5441 113.9700 123.9900 112.1700 1.5414 IC CG1 CA *CB HB 1.5441 113.9700 -119.1700 107.5700 1.1178 IC CA CB CG1 HG11 1.5660 113.9700 177.8300 110.3000 1.1114 IC HG11 CB *CG1 HG12 1.1114 110.3000 119.2500 111.6700 1.1097 IC HG11 CB *CG1 HG13 1.1114 110.3000 -119.4900 110.7000 1.1110 IC CA CB CG2 HG21 1.5660 112.1700 -177.7800 110.7100 1.1108 IC HG21 CB *CG2 HG22 1.1108 110.7100 120.0800 110.5600 1.1115 IC HG21 CB *CG2 HG23 1.1108 110.7100 -119.5500 111.2300 1.1098 PATCH FIRST NVAL LAST CVAL RESI ACE 0.00 ! acetylated N-terminus GROUP ! ATOM HY1 HC 0.11230 ! HY1 HY2 HY3 ATOM CAY CT -0.36620 ! \ | / ATOM HY2 HC 0.11230 ! CAY ATOM HY3 HC 0.11230 ! | ATOM C C 0.59720 ! C=O ATOM O O -0.56790 ! | BOND C CAY C +N CAY HY1 CAY HY2 CAY HY3 BOND O C IMPROPER CAY +N C O ACCEPTOR O C IC C N CA C 0.0000 0.0000 -60.0000 0.0000 0.0000 IC C CA *N HN 0.0000 0.0000 180.0000 0.0000 0.0000 IC CAY C N CA 0.0000 0.0000 180.0000 0.0000 0.0000 IC N CAY *C O 0.0000 0.0000 180.0000 0.0000 0.0000 IC O C CAY HY1 0.0000 0.0000 180.0000 0.0000 0.0000 IC O C CAY HY2 0.0000 0.0000 60.0000 0.0000 0.0000 IC O C CAY HY3 0.0000 0.0000 -60.0000 0.0000 0.0000 PATCH FIRST NONE LAST NONE RESI NME 0.00 ! N-Methylamide C-terminus GROUP ATOM N N -0.41570 ! | ATOM HN H 0.27190 ! N-HN ATOM CAT CT -0.14900 ! | ATOM HT1 H1 0.09760 ! HT1-CAT-HT3 ATOM HT2 H1 0.09760 ! | ATOM HT3 H1 0.09760 ! HT2 BOND N HN N CAT CAT HT1 CAT HT2 CAT HT3 IMPROPER -C CAT N HN DONOR HN N IC N CA -C -O 0.0000 0.0000 180.0000 0.0000 0.0000 IC -C CAT *N HN 0.0000 0.0000 180.0000 0.0000 0.0000 IC C N CAT HT1 0.0000 0.0000 60.0000 0.0000 0.0000 IC C N CAT HT2 0.0000 0.0000 180.0000 0.0000 0.0000 IC C N CAT HT3 0.0000 0.0000 -60.0000 0.0000 0.0000 PATCH FIRST NONE LAST NONE RESI WAT 0.00 ! TIPS3P WATER MODEL ! GENERATE USING NOANGLE NODIHEDRAL GROUP ATOM OH2 OW -0.834 ATOM H1 HW 0.417 ATOM H2 HW 0.417 BOND OH2 H1 OH2 H2 H1 H2 ! THE LAST BOND IS NEEDED FOR SHAKE ANGLE H1 OH2 H2 ! REQUIRED PATCHING FIRS NONE LAST NONE RESI CIP 1.00 ! Sodium Ion GROUP ATOM NA IP 1.00 PATCHING FIRST NONE LAST NONE ! ! Definition of patch residues ! ! ! 5'-terminal adenine, replace phosphate by hydroxyl ! PRES ADE5 -0.1928 ATOM H5T HO 0.4295 ATOM O5' OH -0.6223 DELETE ATOM P DELETE ATOM O1P DELETE ATOM O2P BOND H5T O5' IC H5T O5' C5' C4' 0.0000 0.00 180.00 0.00 0.0000 ! ! 5'-terminal uracil, replace phosphate by hydroxyl ! PRES URA5 -0.1928 ATOM H5T HO 0.4295 ATOM O5' OH -0.6223 DELETE ATOM P DELETE ATOM O1P DELETE ATOM O2P BOND H5T O5' DONO H5T O5' IC H5T O5' C5' C4' 0.0000 0.00 180.00 0.00 0.0000 ! ! 5'-terminal thymine, replace phosphate by hydroxyl ! PRES THY5 -0.1896 ATOM H5T HO 0.4422 ATOM O5' OH -0.6318 DELETE ATOM P DELETE ATOM O1P DELETE ATOM O2P BOND H5T O5' DONO H5T O5' IC H5T O5' C5' C4' 0.0000 0.00 180.00 0.00 0.0000 ! ! 5'-terminal cytosine, replace phosphate by hydroxyl ! PRES CYT5 -0.1928 ATOM H5T HO 0.4295 ATOM O5' OH -0.6223 DELETE ATOM P DELETE ATOM O1P DELETE ATOM O2P BOND H5T O5' DONO H5T O5' IC H5T O5' C5' C4' 0.0000 0.00 180.00 0.00 0.0000 ! ! 5'-terminal guanine, replace phosphate by hydroxyl ! PRES GUA5 -0.1928 ATOM H5T HO 0.4295 ATOM O5' OH -0.6223 DELETE ATOM P DELETE ATOM O1P DELETE ATOM O2P BOND H5T O5' DONO H5T O5' IC H5T O5' C5' C4' 0.0000 0.00 180.00 0.00 0.0000 ! ! 3'-terminal adenine, add terminal hydrogen ! PRES ADE3 -0.2165 ATOM O3' OH -0.6541 ATOM H3T HO 0.4376 BOND O3' H3T DONO H3T O3' IC H3T O3' C3' C4' 0.9600 114.97 148.63 111.92 1.5284 ! ! 3'-terminal uracil, add terminal hydrogen ! PRES URA3 -0.2165 ATOM O3' OH -0.6541 ATOM H3T HO 0.4376 BOND O3' H3T DONO H3T O3' IC H3T O3' C3' C4' 0.9600 114.97 148.63 111.92 1.5284 ! ! 3'-terminal thymine, add terminal hydrogen ! PRES THY3 -0.2153 ATOM O3' OH -0.6549 ATOM H3T HO 0.4396 BOND O3' H3T DONO H3T O3' IC H3T O3' C3' C4' 0.9600 114.97 148.63 111.92 1.5284 ! ! 3'-terminal cytosine, add terminal hydrogen ! PRES CYT3 -0.2165 ATOM O3' OH -0.6541 ATOM H3T HO 0.4376 BOND O3' H3T DONO H3T O3' IC H3T O3' C3' C4' 0.9600 114.97 148.63 111.92 1.5284 ! ! 3'-terminal guanine, add terminal hydrogen ! PRES GUA3 -0.2165 ATOM O3' OH -0.6541 ATOM H3T HO 0.4376 BOND O3' H3T DONO H3T O3' IC H3T O3' C3' C4' 0.9600 114.97 148.63 111.92 1.5284 ! ! DEOXYRIBOSE PATCHES, NOTE: these are made extra tricky by the fact ! that all the charges change upon conversion from RNA to DNA and ! some atom types change as well. This requires special patches for ! 5'-terminal, standard and 3'-terminal residues. ! ! ! deoxyribose patch for adenine 5'-terminal ! PRES DOA5 -0.3079 DELETE ATOM O2' ATOM H5T HO 0.4422 ATOM O5' OH -0.6318 ATOM C5' CT -0.0069 ATOM H5' H1 0.0754 ! note: type is H5'1 --> this should be checked ATOM H5'' H1 0.0754 ! note: type is H5'2 ATOM C4' CT 0.1629 ATOM H4' H1 0.1176 ATOM O4' OS -0.3691 ATOM C1' CT 0.0431 ATOM H1' H2 0.1838 ATOM N9 NS -0.0268 ! note: type is N* ATOM C8 CK 0.1607 ATOM H8 H5 0.1877 ATOM N7 NB -0.6175 ATOM C5 CB 0.0725 ATOM C6 CA 0.6897 ATOM N6 N2 -0.9123 ATOM H61 H 0.4167 ATOM H62 H 0.4167 ATOM N1 NC -0.7624 ATOM C2 CQ 0.5716 ATOM H2 H5 0.0598 ATOM N3 NC -0.7417 ATOM C4 CB 0.3800 ATOM C3' CT 0.0713 ATOM H3' H1 0.0985 ATOM C2' CT -0.0854 ATOM H2'' HC 0.0718 ! note: this is H2'2 ATOM H2' HC 0.0718 ! note: this is H2'1 ATOM O3' OS -0.5232 BOND C2' H2' THET C1' C2' H2' C3' C2' H2' H2' C2' H2'' DIHE H2' C2' C1' O4' H2' C2' C1' N9 H2' C2' C1' H1' DIHE H2' C2' C3' C4' H2' C2' C3' O3' H2' C2' C3' H3' IC C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 ! ! deoxyribose patch for adenine ! PRES DOA -1.0 DELETE ATOM O2' ATOM P P 1.1659 ATOM O1P O2 -0.7761 ATOM O2P O2 -0.7761 ATOM O5' OS -0.4954 ATOM C5' CT -0.0069 ATOM H5' H1 0.0754 ! note: type is H5'1 --> this should be checked ATOM H5'' H1 0.0754 ! note: type is H5'2 ATOM C4' CT 0.1629 ATOM H4' H1 0.1176 ATOM O4' OS -0.3691 ATOM C1' CT 0.0431 ATOM H1' H2 0.1838 ATOM N9 NS -0.0268 ! note: type is N* ATOM C8 CK 0.1607 ATOM H8 H5 0.1877 ATOM N7 NB -0.6175 ATOM C5 CB 0.0725 ATOM C6 CA 0.6897 ATOM N6 N2 -0.9123 ATOM H61 H 0.4167 ATOM H62 H 0.4167 ATOM N1 NC -0.7624 ATOM C2 CQ 0.5716 ATOM H2 H5 0.0598 ATOM N3 NC -0.7417 ATOM C4 CB 0.3800 ATOM C3' CT 0.0713 ATOM H3' H1 0.0985 ATOM C2' CT -0.0854 ATOM H2' HC 0.0718 ! note: this is H2'1 ATOM H2'' HC 0.0718 ! note: this is H2'2 ATOM O3' OS -0.5232 BOND C2' H2' THET C1' C2' H2' C3' C2' H2' H2' C2' H2'' DIHE H2' C2' C1' O4' H2' C2' C1' N9 H2' C2' C1' H1' DIHE H2' C2' C3' C4' H2' C2' C3' O3' H2' C2' C3' H3' IC C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 ! ! deoxyribose patch for 3'-terminal adenine ! PRES DOA3 -0.6921 DELETE ATOM O2' ATOM P P 1.1659 ATOM O1P O2 -0.7761 ATOM O2P O2 -0.7761 ATOM O5' OS -0.4954 ATOM C5' CT -0.0069 ATOM H5' H1 0.0754 ! note: type is H5'1 --> this should be checked ATOM H5'' H1 0.0754 ! note: type is H5'2 ATOM C4' CT 0.1629 ATOM H4' H1 0.1176 ATOM O4' OS -0.3691 ATOM C1' CT 0.0431 ATOM H1' H2 0.1838 ATOM N9 NS -0.0268 ! note: type is N* ATOM C8 CK 0.1607 ATOM H8 H5 0.1877 ATOM N7 NB -0.6175 ATOM C5 CB 0.0725 ATOM C6 CA 0.6897 ATOM N6 N2 -0.9123 ATOM H61 H 0.4167 ATOM H62 H 0.4167 ATOM N1 NC -0.7624 ATOM C2 CQ 0.5716 ATOM H2 H5 0.0598 ATOM N3 NC -0.7417 ATOM C4 CB 0.3800 ATOM C3' CT 0.0713 ATOM H3' H1 0.0985 ATOM C2' CT -0.0854 ATOM H2' HC 0.0718 ! note: this is H2'1 ATOM H2'' HC 0.0718 ! note: this is H2'2 ATOM O3' OH -0.6549 ATOM H3T HO 0.4396 BOND C2' H2' THET C1' C2' H2' C3' C2' H2' H2' C2' H2'' DIHE H2' C2' C1' O4' H2' C2' C1' N9 H2' C2' C1' H1' DIHE H2' C2' C3' C4' H2' C2' C3' O3' H2' C2' C3' H3' IC C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 ! ! deoxyribose patch for 5'-terminal cytosine ! PRES DOC5 -0.3079 DELETE ATOM O2' ATOM H5T HO 0.4422 ATOM O5' OH -0.6318 ATOM C5' CT -0.0069 ATOM H5' H1 0.0754 ! this is H5'1 ATOM H5'' H1 0.0754 ! this is H5'2 ATOM C4' CT 0.1629 ATOM H4' H1 0.1176 ATOM O4' OS -0.3691 ATOM C1' CT -0.0116 ATOM H1' H2 0.1963 ATOM N1 NS -0.0339 ! this is type N* ATOM C6 CM -0.0183 ATOM H6 H4 0.2293 ATOM C5 CM -0.5222 ATOM H5 HA 0.1863 ATOM C4 CA 0.8439 ATOM N4 N2 -0.9773 ATOM H41 H 0.4314 ATOM H42 H 0.4314 ATOM N3 NC -0.7748 ATOM C2 C 0.7959 ATOM O2 O -0.6548 ATOM C3' CT 0.0713 ATOM H3' H1 0.0985 ATOM C2' CT -0.0854 ATOM H2'' HC 0.0718 ! this is H2'1 ATOM H2' HC 0.0718 ! this is HO'2 ATOM O3' OS -0.5232 BOND C2' H2' THET C1' C2' H2' C3' C2' H2' H2' C2' H2'' DIHE H2' C2' C1' O4' H2' C2' C1' N1 H2' C2' C1' H1' DIHE H2' C2' C3' C4' H2' C2' C3' O3' H2' C2' C3' H3' IC C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 ! ! deoxyribose patch for cytosine ! PRES DOC -1.00 DELETE ATOM O2' ATOM P P 1.1659 ATOM O1P O2 -0.7761 ATOM O2P O2 -0.7761 ATOM O5' OS -0.4954 ATOM C5' CT -0.0069 ATOM H5' H1 0.0754 ! this is H5'1 ATOM H5'' H1 0.0754 ! this is H5'2 ATOM C4' CT 0.1629 ATOM H4' H1 0.1176 ATOM O4' OS -0.3691 ATOM C1' CT -0.0116 ATOM H1' H2 0.1963 ATOM N1 NS -0.0339 ! this is type N* ATOM C6 CM -0.0183 ATOM H6 H4 0.2293 ATOM C5 CM -0.5222 ATOM H5 HA 0.1863 ATOM C4 CA 0.8439 ATOM N4 N2 -0.9773 ATOM H41 H 0.4314 ATOM H42 H 0.4314 ATOM N3 NC -0.7748 ATOM C2 C 0.7959 ATOM O2 O -0.6548 ATOM C3' CT 0.0713 ATOM H3' H1 0.0985 ATOM C2' CT -0.0854 ATOM H2'' HC 0.0718 ! this is H2'2 ATOM H2' HC 0.0718 ! this is H2'1 ATOM O3' OS -0.5232 BOND C2' H2' THET C1' C2' H2' C3' C2' H2' H2' C2' H2'' DIHE H2' C2' C1' O4' H2' C2' C1' N1 H2' C2' C1' H1' DIHE H2' C2' C3' C4' H2' C2' C3' O3' H2' C2' C3' H3' IC C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 ! ! deoxyribose patch for 3'-terminal cytosine ! PRES DOC3 -0.6921 DELETE ATOM O2' ATOM P P 1.1659 ATOM O1P O2 -0.7761 ATOM O2P O2 -0.7761 ATOM O5' OS -0.4954 ATOM C5' CT -0.0069 ATOM H5' H1 0.0754 ! this is H5'1 ATOM H5'' H1 0.0754 ! this is H5'2 ATOM C4' CT 0.1629 ATOM H4' H1 0.1176 ATOM O4' OS -0.3691 ATOM C1' CT -0.0116 ATOM H1' H2 0.1963 ATOM N1 NS -0.0339 ! this is type N* ATOM C6 CM -0.0183 ATOM H6 H4 0.2293 ATOM C5 CM -0.5222 ATOM H5 HA 0.1863 ATOM C4 CA 0.8439 ATOM N4 N2 -0.9773 ATOM H41 H 0.4314 ATOM H42 H 0.4314 ATOM N3 NC -0.7748 ATOM C2 C 0.7959 ATOM O2 O -0.6548 ATOM C3' CT 0.0713 ATOM H3' H1 0.0985 ATOM C2' CT -0.0854 ATOM H2'' HC 0.0718 ! this is H2'2 ATOM H2' HC 0.0718 ! this is H2'1 ATOM O3' OH -0.6549 ATOM H3T HO 0.4396 BOND C2' H2' THET C1' C2' H2' C3' C2' H2' H2' C2' H2'' DIHE H2' C2' C1' O4' H2' C2' C1' N1 H2' C2' C1' H1' DIHE H2' C2' C3' C4' H2' C2' C3' O3' H2' C2' C3' H3' IC C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 ! ! deoxyribose patch for 5'-terminal guanine ! PRES DOG5 -0.3079 DELETE ATOM O2' ATOM H5T HO 0.4422 ATOM O5' OH -0.6318 ATOM C5' CT -0.0069 ATOM H5' H1 0.0754 ! this is H5'1 ATOM H5'' H1 0.0754 ! this is H5'2 ATOM C4' CT 0.1629 ATOM H4' H1 0.1176 ATOM O4' OS -0.3691 ATOM C1' CT 0.0358 ATOM H1' H2 0.1746 ATOM N9 NS 0.0577 ! this is type N* ATOM C8 CK 0.0736 ATOM H8 H5 0.1997 ATOM N7 NB -0.5725 ATOM C5 CB 0.1991 ATOM C6 C 0.4918 ATOM O6 O -0.5699 ATOM N1 NA -0.5053 ATOM H1 H 0.3520 ATOM C2 CA 0.7432 ATOM N2 N2 -0.9230 ATOM H21 H 0.4235 ATOM H22 H 0.4235 ATOM N3 NC -0.6636 ATOM C4 CB 0.1814 ATOM C3' CT 0.0713 ATOM H3' H1 0.0985 ATOM C2' CT -0.0854 ATOM H2'' HC 0.0718 ! this is H2'2 ATOM H2' HC 0.0718 ! this is H2'1 ATOM O3' OS -0.5232 BOND C2' H2' THET C1' C2' H2' C3' C2' H2' H2' C2' H2'' DIHE H2' C2' C1' O4' H2' C2' C1' N9 H2' C2' C1' H1' DIHE H2' C2' C3' C4' H2' C2' C3' O3' H2' C2' C3' H3' IC C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 ! ! deoxyribose patch for guanine ! PRES DOG -1.00 DELETE ATOM O2' ATOM P P 1.1659 ATOM O1P O2 -0.7761 ATOM O2P O2 -0.7761 ATOM O5' OS -0.4954 ATOM C5' CT -0.0069 ATOM H5' H1 0.0754 ! this is H5'1 ATOM H5'' H1 0.0754 ! this is H5'2 ATOM C4' CT 0.1629 ATOM H4' H1 0.1176 ATOM O4' OS -0.3691 ATOM C1' CT 0.0358 ATOM H1' H2 0.1746 ATOM N9 NS 0.0577 ! this is type N* ATOM C8 CK 0.0736 ATOM H8 H5 0.1997 ATOM N7 NB -0.5725 ATOM C5 CB 0.1991 ATOM C6 C 0.4918 ATOM O6 O -0.5699 ATOM N1 NA -0.5053 ATOM H1 H 0.3520 ATOM C2 CA 0.7432 ATOM N2 N2 -0.9230 ATOM H21 H 0.4235 ATOM H22 H 0.4235 ATOM N3 NC -0.6636 ATOM C4 CB 0.1814 ATOM C3' CT 0.0713 ATOM H3' H1 0.0985 ATOM C2' CT -0.0854 ATOM H2'' HC 0.0718 ! this is H2'2 ATOM H2' HC 0.0718 ! this is H2'1 ATOM O3' OS -0.5232 BOND C2' H2' THET C1' C2' H2' C3' C2' H2' H2' C2' H2'' DIHE H2' C2' C1' O4' H2' C2' C1' N9 H2' C2' C1' H1' DIHE H2' C2' C3' C4' H2' C2' C3' O3' H2' C2' C3' H3' IC C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 ! ! deoxyribose patch for 3'-terminal guanine ! PRES DOG3 -0.6921 DELETE ATOM O2' ATOM P P 1.1659 ATOM O1P O2 -0.7761 ATOM O2P O2 -0.7761 ATOM O5' OS -0.4954 ATOM C5' CT -0.0069 ATOM H5' H1 0.0754 ! this is H5'1 ATOM H5'' H1 0.0754 ! this is H5'2 ATOM C4' CT 0.1629 ATOM H4' H1 0.1176 ATOM O4' OS -0.3691 ATOM C1' CT 0.0358 ATOM H1' H2 0.1746 ATOM N9 NS 0.0577 ! this is type N* ATOM C8 CK 0.0736 ATOM H8 H5 0.1997 ATOM N7 NB -0.5725 ATOM C5 CB 0.1991 ATOM C6 C 0.4918 ATOM O6 O -0.5699 ATOM N1 NA -0.5053 ATOM H1 H 0.3520 ATOM C2 CA 0.7432 ATOM N2 N2 -0.9230 ATOM H21 H 0.4235 ATOM H22 H 0.4235 ATOM N3 NC -0.6636 ATOM C4 CB 0.1814 ATOM C3' CT 0.0713 ATOM H3' H1 0.0985 ATOM C2' CT -0.0854 ATOM H2'' HC 0.0718 ! this is H2'2 ATOM H2' HC 0.0718 ! this is H2'1 ATOM O3' OH -0.6549 ATOM H3T HO 0.4396 BOND C2' H2' THET C1' C2' H2' C3' C2' H2' H2' C2' H2'' DIHE H2' C2' C1' O4' H2' C2' C1' N9 H2' C2' C1' H1' DIHE H2' C2' C3' C4' H2' C2' C3' O3' H2' C2' C3' H3' IC C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 PRES NALA 1.0 DELETE ATOM HN ATOM N N3 0.14140 ! ATOM HT1 H 0.19970 ! HT2 ATOM HT2 H 0.19970 ! |(+) ATOM HT3 H 0.19970 ! HT1-N-HT3 ATOM CA CT 0.09620 ! | HB1 ATOM HA HP 0.08890 ! | / ATOM CB CT -0.05970 ! HA-CA--CB-HB2 ALANINE ATOM HB1 HC 0.03000 ! | \ ATOM HB2 HC 0.03000 ! | HB2 ATOM HB3 HC 0.03000 ! O=C ATOM C C 0.61630 ! | ATOM O O -0.57220 BOND HT1 N HT2 N HT3 N DONOR HT1 N DONOR HT2 N DONOR HT3 N IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 PRES CALA -1.0 DELETE ATOM O ATOM N N -0.38210 ! | ATOM HN H 0.26810 ! HN-N ATOM CA CT -0.17470 ! | HB1 ATOM HA H1 0.10670 ! | / ATOM CB CT -0.20930 ! HA-CA--CB-HB2 ALANINE ATOM HB1 HC 0.07640 ! | \ ATOM HB2 HC 0.07640 ! | HB2 ATOM HB3 HC 0.07640 ! OT1=C ATOM C C 0.77310 ! | ATOM OT1 O2 -0.80550 ! OT2 ATOM OT2 O2 -0.80550 BOND C OT2 BOND C OT1 IMPROPER CA OT2 C OT1 ACCEPTOR OT1 C ACCEPTOR OT2 C IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 PRES NARG 2.0 DELETE ATOM HN ATOM N N3 0.13050 ATOM HT1 H 0.20830 ATOM HT2 H 0.20830 ! HT2 ATOM HT3 H 0.20830 ! |(+) HH11 ATOM CA CT -0.02230 ! HT1-N-HT3 | ATOM HA HP 0.12420 ! | HB1 HG1 HD1 HE NH1-HH12 ATOM CB CT 0.01180 ! | | | | | //(+) ATOM HB1 HC 0.02260 ! HA-CA--CB--CG--CD--NE--CZ ATOM HB2 HC 0.02260 ! | | | | \ ATOM CG CT 0.02360 ! | HB2 HG2 HD2 NH2-HH22 ATOM HG1 HC 0.03090 ! O=C | ATOM HG2 HC 0.03090 ! | HH21 ATOM CD CT 0.09350 ATOM HD1 H1 0.05270 ATOM HD2 H1 0.05270 ATOM NE N2 -0.56500 ATOM HE H 0.35920 ATOM CZ CA 0.82810 ATOM NH1 N2 -0.86930 ATOM HH11 H 0.44940 ATOM HH12 H 0.44940 ATOM NH2 N2 -0.86930 ATOM HH21 H 0.44940 ATOM HH22 H 0.44940 ATOM C C 0.72140 ATOM O O -0.60130 BOND HT1 N HT2 N HT3 N DONOR HT1 N DONOR HT2 N DONOR HT3 N IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 PRES CARG 0.0 DELETE ATOM O ATOM N N -0.34810 ! | HH11 ATOM HN H 0.27640 ! HN-N | ATOM CA CT -0.30680 ! | HB1 HG1 HD1 HE NH1-HH12 ATOM HA H1 0.14470 ! | | | | | //(+) ATOM CB CT -0.03740 ! HA-CA--CB--CG--CD--NE--CZ ATOM HB1 HC 0.03710 ! | | | | \ ATOM HB2 HC 0.03710 ! | HB2 HG2 HD2 NH2-HH22 ATOM CG CT 0.07440 ! OT1=C | ATOM HG1 HC 0.01850 ! | HH21 ATOM HG2 HC 0.01850 ! OT2 ATOM CD CT 0.11140 ATOM HD1 H1 0.04680 ATOM HD2 H1 0.04680 ATOM NE N2 -0.55640 ATOM HE H 0.34790 ATOM CZ CA 0.83680 ATOM NH1 N2 -0.87370 ATOM HH11 H 0.44930 ATOM HH12 H 0.44930 ATOM NH2 N2 -0.87370 ATOM HH21 H 0.44930 ATOM HH22 H 0.44930 ATOM C C 0.85570 ATOM OT1 O2 -0.82660 ATOM OT2 O2 -0.82660 BOND C OT2 BOND C OT1 IMPROPER CA OT2 C OT1 ACCEPTOR OT1 C ACCEPTOR OT2 C IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 PRES NASN 1.0 DELETE ATOM HN ATOM N N3 0.18010 ATOM HT1 H 0.19210 ATOM HT2 H 0.19210 ATOM HT3 H 0.19210 ATOM CA CT 0.03680 ATOM HA HP 0.12310 ATOM CB CT -0.02830 ATOM HB1 HC 0.05150 ATOM HB2 HC 0.05150 ATOM CG C 0.58330 ATOM OD1 O -0.57440 ATOM ND2 N -0.86340 ATOM HD21 H 0.40970 ATOM HD22 H 0.40970 ATOM C C 0.61630 ATOM O O -0.57220 BOND HT1 N HT2 N HT3 N DONOR HT1 N DONOR HT2 N DONOR HT3 N IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 PRES CASN -1.0 DELETE ATOM O ATOM N N -0.38210 ATOM HN H 0.26810 ATOM CA CT -0.20800 ATOM HA H1 0.13580 ATOM CB CT -0.22990 ATOM HB1 HC 0.10230 ATOM HB2 HC 0.10230 ATOM CG C 0.71530 ATOM OD1 O -0.60100 ATOM ND2 N -0.90840 ATOM HD21 H 0.41500 ATOM HD22 H 0.41500 ATOM C C 0.80500 ATOM OT1 O2 -0.81470 ATOM OT2 O2 -0.81470 BOND C OT2 BOND C OT1 IMPROPER CA OT2 C OT1 ACCEPTOR OT1 C ACCEPTOR OT2 C IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 PRES NASP 0.0 DELETE ATOM HN ATOM N N3 0.07820 ATOM HT1 H 0.22000 ATOM HT2 H 0.22000 ATOM HT3 H 0.22000 ATOM CA CT 0.02920 ATOM HA HP 0.11410 ATOM CB CT -0.02350 ATOM HB1 HC -0.01690 ATOM HB2 HC -0.01690 ATOM CG C 0.81940 ATOM OD1 O2 -0.80840 ATOM OD2 O2 -0.80840 ATOM C C 0.56210 ATOM O O -0.58890 BOND HT1 N HT2 N HT3 N DONOR HT1 N DONOR HT2 N DONOR HT3 N IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 PRES CASP -2.0 DELETE ATOM O ATOM N N -0.51920 ATOM HN H 0.30550 ATOM CA CT -0.18170 ATOM HA H1 0.10460 ATOM CB CT -0.06770 ATOM HB1 HC -0.02120 ATOM HB2 HC -0.02120 ATOM CG C 0.88510 ATOM OD1 O2 -0.81620 ATOM OD2 O2 -0.81620 ATOM C C 0.72560 ATOM OT1 O2 -0.78870 ATOM OT2 O2 -0.78870 BOND C OT2 BOND C OT1 IMPROPER CA OT2 C OT1 ACCEPTOR OT1 C ACCEPTOR OT2 C IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 PRES NCYS 1.0 DELETE ATOM HN ATOM N N3 0.13250 ATOM HT1 H 0.20230 ATOM HT2 H 0.20230 ATOM HT3 H 0.20230 ATOM CA CT 0.09270 ATOM HA HP 0.14110 ATOM CB CT -0.11950 ATOM HB1 H1 0.11880 ATOM HB2 H1 0.11880 ATOM SG SH -0.32980 ATOM HG1 HS 0.19750 ATOM C C 0.61230 ATOM O O -0.57130 BOND HT1 N HT2 N HT3 N DONOR HT1 N DONOR HT2 N DONOR HT3 N IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 PRES CCYS -1.0 DELETE ATOM O ATOM N N -0.38210 ATOM HN H 0.26810 ATOM CA CT -0.16350 ATOM HA H1 0.13960 ATOM CB CT -0.19960 ATOM HB1 H1 0.14370 ATOM HB2 H1 0.14370 ATOM SG SH -0.31020 ATOM HG1 HS 0.20680 ATOM C C 0.74970 ATOM OT1 O2 -0.79810 ATOM OT2 O2 -0.79810 BOND C OT2 BOND C OT1 IMPROPER CA OT2 C OT1 ACCEPTOR OT1 C ACCEPTOR OT2 C IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 PRES NCYX 1.0 DELETE ATOM HN ATOM N N3 0.20690 ATOM HT1 H 0.18150 ATOM HT2 H 0.18150 ATOM HT3 H 0.18150 ATOM CA CT 0.10550 ATOM HA HP 0.09220 ATOM CB CT -0.02770 ATOM HB1 H1 0.06800 ATOM HB2 H1 0.06800 ATOM SG SH -0.09840 ATOM C C 0.61230 ATOM O O -0.57130 BOND HT1 N HT2 N HT3 N DONOR HT1 N DONOR HT2 N DONOR HT3 N IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 PRES CCYX -1.0 DELETE ATOM O ATOM N N -0.38210 ATOM HN H 0.26810 ATOM CA CT -0.13180 ATOM HA H1 0.09380 ATOM CB CT -0.19430 ATOM HB1 H1 0.12280 ATOM HB2 H1 0.12280 ATOM SG SH -0.05290 ATOM C C 0.76180 ATOM OT1 O2 -0.80410 ATOM OT2 O2 -0.80410 BOND C OT2 BOND C OT1 IMPROPER CA OT2 C OT1 ACCEPTOR OT1 C ACCEPTOR OT2 C IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 PRES NGLN +1.0 DELETE ATOM HN ATOM N N3 0.14930 ATOM HT1 H 0.19960 ATOM HT2 H 0.19960 ATOM HT3 H 0.19960 ATOM CA CT 0.05360 ATOM HA HP 0.10150 ATOM CB CT 0.06510 ATOM HB1 HC 0.00500 ATOM HB2 HC 0.00500 ATOM CG CT -0.09030 ATOM HG1 HC 0.03310 ATOM HG2 HC 0.03310 ATOM CD C 0.73540 ATOM OE1 O -0.61330 ATOM NE2 N -1.00310 ATOM HE21 H 0.44290 ATOM HE22 H 0.44290 ATOM C C 0.61230 ATOM O O -0.57130 BOND HT1 N HT2 N HT3 N DONOR HT1 N DONOR HT2 N DONOR HT3 N IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 PRES CGLN -1.0 DELETE ATOM O ATOM N N -0.38210 ATOM HN H 0.26810 ATOM CA CT -0.22480 ATOM HA H1 0.12320 ATOM CB CT -0.06640 ATOM HB1 HC 0.04520 ATOM HB2 HC 0.04520 ATOM CG CT -0.02100 ATOM HG1 HC 0.02030 ATOM HG2 HC 0.02030 ATOM CD C 0.70930 ATOM OE1 O -0.60980 ATOM NE2 N -0.95740 ATOM HE21 H 0.43040 ATOM HE22 H 0.43040 ATOM C C 0.77750 ATOM OT1 O2 -0.80420 ATOM OT2 O2 -0.80420 BOND C OT2 BOND C OT1 IMPROPER CA OT2 C OT1 ACCEPTOR OT1 C ACCEPTOR OT2 C IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 PRES NGLU 0.0 DELETE ATOM HN ATOM N N3 0.00170 ATOM HT1 H 0.23910 ATOM HT2 H 0.23910 ATOM HT3 H 0.23910 ATOM CA CT 0.05880 ATOM HA HP 0.12020 ATOM CB CT 0.09090 ATOM HB1 HC -0.02320 ATOM HB2 HC -0.02320 ATOM CG CT -0.02360 ATOM HG1 HC -0.03150 ATOM HG2 HC -0.03150 ATOM CD C 0.80870 ATOM OE1 O2 -0.81890 ATOM OE2 O2 -0.81890 ATOM C C 0.56210 ATOM O O -0.58890 BOND HT1 N HT2 N HT3 N DONOR HT1 N DONOR HT2 N DONOR HT3 N IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 PRES CGLU -2.0 DELETE ATOM O ATOM N N -0.51920 ATOM HN H 0.30550 ATOM CA CT -0.20590 ATOM HA H1 0.13990 ATOM CB CT 0.00710 ATOM HB1 HC -0.00780 ATOM HB2 HC -0.00780 ATOM CG CT 0.06750 ATOM HG1 HC -0.05480 ATOM HG2 HC -0.05480 ATOM CD C 0.81830 ATOM OE1 O2 -0.82200 ATOM OE2 O2 -0.82200 ATOM C C 0.74200 ATOM OT1 O2 -0.79300 ATOM OT2 O2 -0.79300 BOND C OT2 BOND C OT1 IMPROPER CA OT2 C OT1 ACCEPTOR OT1 C ACCEPTOR OT2 C IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 PRES NGLY 1.0 DELETE ATOM HN ATOM N N3 0.29430 ATOM HT1 H 0.16420 ATOM HT2 H 0.16420 ATOM HT3 H 0.16420 ATOM CA CT -0.01000 ATOM HA1 HP 0.08950 ATOM HA2 HP 0.08950 ATOM C C 0.61630 ATOM O O -0.57220 BOND HT1 N HT2 N HT3 N DONOR HT1 N DONOR HT2 N DONOR HT3 N IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 PRES CGLY -1.0 DELETE ATOM O ATOM N N -0.38210 ATOM HN H 0.26810 ATOM CA CT -0.24930 ATOM HA1 H1 0.10560 ATOM HA2 H1 0.10560 ATOM C C 0.72310 ATOM OT1 O2 -0.78550 ATOM OT2 O2 -0.78550 BOND C OT2 BOND C OT1 IMPROPER CA OT2 C OT1 ACCEPTOR OT1 C ACCEPTOR OT2 C IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 PRES NHID 1.0 DELETE ATOM HN ATOM N N3 0.15420 ATOM HT1 H 0.19630 ATOM HT2 H 0.19630 ATOM HT3 H 0.19630 ATOM CA CT 0.09640 ATOM HA HP 0.09580 ATOM ND1 NA -0.38190 ATOM HD1 H 0.36320 ATOM CG CC -0.03990 ATOM CB CT 0.02590 ATOM HB1 HC 0.02090 ATOM HB2 HC 0.02090 ATOM NE2 NB -0.57110 ATOM CD2 CV 0.10460 ATOM HD2 H4 0.12990 ATOM CE1 CR 0.21270 ATOM HE1 H5 0.13850 ATOM C C 0.61230 ATOM O O -0.57130 BOND HT1 N HT2 N HT3 N DONOR HT1 N DONOR HT2 N DONOR HT3 N IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 PRES CHID -1.0 DELETE ATOM O ATOM N N -0.38210 ATOM HN H 0.26810 ATOM CA CT -0.17390 ATOM HA H1 0.11000 ATOM ND1 NA -0.38920 ATOM HD1 H 0.37550 ATOM CG CC 0.02930 ATOM CB CT -0.10460 ATOM HB1 HC 0.05650 ATOM HB2 HC 0.05650 ATOM NE2 NB -0.56290 ATOM CD2 CV 0.10010 ATOM HD2 H4 0.12410 ATOM CE1 CR 0.19250 ATOM HE1 H5 0.14180 ATOM C C 0.76150 ATOM OT1 O2 -0.80160 ATOM OT2 O2 -0.80160 BOND C OT2 BOND C OT1 IMPROPER CA OT2 C OT1 ACCEPTOR OT1 C ACCEPTOR OT2 C IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 PRES NHIE 1.0 DELETE ATOM HN ATOM N N3 0.14720 ATOM HT1 H 0.20160 ATOM HT2 H 0.20160 ATOM HT3 H 0.20160 ATOM CA CT 0.02360 ATOM HA HP 0.13800 ATOM NE2 NA -0.27810 ATOM HE2 H 0.33240 ATOM CD2 CW -0.23490 ATOM HD2 H4 0.19630 ATOM ND1 NB -0.55790 ATOM CG CC 0.17400 ATOM CE1 CR 0.18040 ATOM HE1 H5 0.13970 ATOM CB CT 0.04890 ATOM HB1 HC 0.02230 ATOM HB2 HC 0.02230 ATOM C C 0.61230 ATOM O O -0.57130 BOND HT1 N HT2 N HT3 N DONOR HT1 N DONOR HT2 N DONOR HT3 N IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 PRES CHIE -1.0 DELETE ATOM O ATOM N N -0.38210 ATOM HN H 0.26810 ATOM CA CT -0.26990 ATOM HA H1 0.16500 ATOM NE2 NA -0.26700 ATOM HE2 H 0.33190 ATOM CD2 CW -0.25880 ATOM HD2 H4 0.19570 ATOM ND1 NB -0.55170 ATOM CG CC 0.27240 ATOM CE1 CR 0.15580 ATOM HE1 H5 0.14480 ATOM CB CT -0.10680 ATOM HB1 HC 0.06200 ATOM HB2 HC 0.06200 ATOM C C 0.79160 ATOM OT1 O2 -0.80650 ATOM OT2 O2 -0.80650 BOND C OT2 BOND C OT1 IMPROPER CA OT2 C OT1 ACCEPTOR OT1 C ACCEPTOR OT2 C IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 PRES NHIP 2.0 DELETE ATOM HN ATOM N N3 0.25600 ATOM HT1 H 0.17040 ATOM HT2 H 0.17040 ATOM HT3 H 0.17040 ATOM CA CT 0.05810 ATOM HA HP 0.10470 ATOM ND1 NA -0.15100 ATOM HD1 H 0.38210 ATOM NE2 NA -0.17390 ATOM HE2 H 0.39210 ATOM CE1 CR -0.00110 ATOM HE1 H5 0.26450 ATOM CD2 CW -0.14330 ATOM HD2 H4 0.24950 ATOM CG CC -0.02360 ATOM CB CT 0.04840 ATOM HB1 HC 0.05310 ATOM HB2 HC 0.05310 ATOM C C 0.72140 ATOM O O -0.60130 BOND HT1 N HT2 N HT3 N DONOR HT1 N DONOR HT2 N DONOR HT3 N IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 PRES CHIP 0.0 DELETE ATOM O ATOM N N -0.34810 ATOM HN H 0.27640 ATOM CA CT -0.14450 ATOM HA H1 0.11150 ATOM ND1 NA -0.15010 ATOM HD1 H 0.38830 ATOM NE2 NA -0.16830 ATOM HE2 H 0.39130 ATOM CE1 CR -0.02510 ATOM HE1 H5 0.26940 ATOM CD2 CW -0.12560 ATOM HD2 H4 0.23360 ATOM CG CC 0.02980 ATOM CB CT -0.08000 ATOM HB1 HC 0.08680 ATOM HB2 HC 0.08680 ATOM C C 0.80320 ATOM OT1 O2 -0.81770 ATOM OT2 O2 -0.81770 BOND C OT2 BOND C OT1 IMPROPER CA OT2 C OT1 ACCEPTOR OT1 C ACCEPTOR OT2 C IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 PRES NILE 1.0 DELETE ATOM HN ATOM N N3 0.03110 ATOM HT1 H 0.23290 ATOM HT2 H 0.23290 ATOM HT3 H 0.23290 ATOM CA CT 0.02570 ATOM HA HP 0.10310 ATOM CB CT 0.18850 ATOM HB HC 0.02130 ATOM CG2 CT -0.37200 ATOM HG21 HC 0.09470 ATOM HG22 HC 0.09470 ATOM HG23 HC 0.09470 ATOM CG1 CT -0.03870 ATOM HG11 HC 0.02010 ATOM HG12 HC 0.02010 ATOM CD CT -0.09080 ATOM HD1 HC 0.02260 ATOM HD2 HC 0.02260 ATOM HD3 HC 0.02260 ATOM C C 0.61230 ATOM O O -0.57130 BOND HT1 N HT2 N HT3 N DONOR HT1 N DONOR HT2 N DONOR HT3 N IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 PRES CILE -1.0 DELETE ATOM O ATOM N N -0.38210 ATOM HN H 0.26810 ATOM CA CT -0.31000 ATOM HA H1 0.13750 ATOM CB CT 0.03630 ATOM HB HC 0.07660 ATOM CG2 CT -0.34980 ATOM HG21 HC 0.10210 ATOM HG22 HC 0.10210 ATOM HG23 HC 0.10210 ATOM CG1 CT -0.03230 ATOM HG11 HC 0.03210 ATOM HG12 HC 0.03210 ATOM CD CT -0.06990 ATOM HD1 HC 0.01960 ATOM HD2 HC 0.01960 ATOM HD3 HC 0.01960 ATOM C C 0.83430 ATOM OT1 O2 -0.81900 ATOM OT2 O2 -0.81900 BOND C OT2 BOND C OT1 IMPROPER CA OT2 C OT1 ACCEPTOR OT1 C ACCEPTOR OT2 C IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 PRES NLEU 1.0 DELETE ATOM HN ATOM N N3 0.10100 ATOM HT1 H 0.21480 ATOM HT2 H 0.21480 ATOM HT3 H 0.21480 ATOM CA CT 0.01040 ATOM HA HP 0.10530 ATOM CB CT -0.02440 ATOM HB1 HC 0.02560 ATOM HB2 HC 0.02560 ATOM CG CT 0.34210 ATOM HG HC -0.03800 ATOM CD1 CT -0.41060 ATOM HD11 HC 0.09800 ATOM HD12 HC 0.09800 ATOM HD13 HC 0.09800 ATOM CD2 CT -0.41040 ATOM HD21 HC 0.09800 ATOM HD22 HC 0.09800 ATOM HD23 HC 0.09800 ATOM C C 0.61230 ATOM O O -0.57130 BOND HT1 N HT2 N HT3 N DONOR HT1 N DONOR HT2 N DONOR HT3 N IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 PRES CLEU -1.0 DELETE ATOM O ATOM N N -0.38210 ATOM HN H 0.26810 ATOM CA CT -0.28470 ATOM HA H1 0.13460 ATOM CB CT -0.24690 ATOM HB1 HC 0.09740 ATOM HB2 HC 0.09740 ATOM CG CT 0.37060 ATOM HG HC -0.03740 ATOM CD1 CT -0.41630 ATOM HD11 HC 0.10380 ATOM HD12 HC 0.10380 ATOM HD13 HC 0.10380 ATOM CD2 CT -0.41630 ATOM HD21 HC 0.10380 ATOM HD22 HC 0.10380 ATOM HD23 HC 0.10380 ATOM C C 0.83260 ATOM OT1 O2 -0.81990 ATOM OT2 O2 -0.81990 BOND C OT2 BOND C OT1 IMPROPER CA OT2 C OT1 ACCEPTOR OT1 C ACCEPTOR OT2 C IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 PRES NLYS 2.0 DELETE ATOM HN ATOM N N3 0.09660 ATOM HT1 H 0.21650 ATOM HT2 H 0.21650 ATOM HT3 H 0.21650 ATOM CA CT -0.00150 ATOM HA HP 0.11800 ATOM CB CT 0.02120 ATOM HB1 HC 0.02830 ATOM HB2 HC 0.02830 ATOM CG CT -0.00480 ATOM HG1 HC 0.01210 ATOM HG2 HC 0.01210 ATOM CD CT -0.06080 ATOM HD1 HC 0.06330 ATOM HD2 HC 0.06330 ATOM CE CT -0.01810 ATOM HE1 HP 0.11710 ATOM HE2 HP 0.11710 ATOM NZ N3 -0.37640 ATOM HZ1 H 0.33820 ATOM HZ2 H 0.33820 ATOM HZ3 H 0.33820 ATOM C C 0.72140 ATOM O O -0.60130 BOND HT1 N HT2 N HT3 N DONOR HT1 N DONOR HT2 N DONOR HT3 N IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 PRES CLYS 0.0 DELETE ATOM O ATOM N N -0.34810 ATOM HN H 0.27640 ATOM CA CT -0.29030 ATOM HA H1 0.14380 ATOM CB CT -0.05380 ATOM HB1 HC 0.04820 ATOM HB2 HC 0.04820 ATOM CG CT 0.02270 ATOM HG1 HC 0.01340 ATOM HG2 HC 0.01340 ATOM CD CT -0.03920 ATOM HD1 HC 0.06110 ATOM HD2 HC 0.06110 ATOM CE CT -0.01760 ATOM HE1 HP 0.11210 ATOM HE2 HP 0.11210 ATOM NZ N3 -0.37410 ATOM HZ1 H 0.33740 ATOM HZ2 H 0.33740 ATOM HZ3 H 0.33740 ATOM C C 0.84880 ATOM OT1 O2 -0.82520 ATOM OT2 O2 -0.82520 BOND C OT2 BOND C OT1 IMPROPER CA OT2 C OT1 ACCEPTOR OT1 C ACCEPTOR OT2 C IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 PRES NMET 1.0 DELETE ATOM HN ATOM N N3 0.15920 ATOM HT1 H 0.19840 ATOM HT2 H 0.19840 ATOM HT3 H 0.19840 ATOM CA CT 0.02210 ATOM HA HP 0.11160 ATOM CB CT 0.08650 ATOM HB1 HC 0.01250 ATOM HB2 HC 0.01250 ATOM CG CT 0.03340 ATOM HG1 H1 0.02920 ATOM HG2 H1 0.02920 ATOM SD S -0.27740 ATOM CE CT -0.03410 ATOM HE1 H1 0.05970 ATOM HE2 H1 0.05970 ATOM HE3 H1 0.05970 ATOM C C 0.61230 ATOM O O -0.57130 BOND HT1 N HT2 N HT3 N DONOR HT1 N DONOR HT2 N DONOR HT3 N IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 PRES CMET -1.0 DELETE ATOM O ATOM N N -0.38210 ATOM HN H 0.26810 ATOM CA CT -0.25970 ATOM HA H1 0.12770 ATOM CB CT -0.02360 ATOM HB1 HC 0.04800 ATOM HB2 HC 0.04800 ATOM CG CT 0.04920 ATOM HG1 H1 0.03170 ATOM HG2 H1 0.03170 ATOM SD S -0.26920 ATOM CE CT -0.03760 ATOM HE1 H1 0.06250 ATOM HE2 H1 0.06250 ATOM HE3 H1 0.06250 ATOM C C 0.80130 ATOM OT1 O2 -0.81050 ATOM OT2 O2 -0.81050 BOND C OT2 BOND C OT1 IMPROPER CA OT2 C OT1 ACCEPTOR OT1 C ACCEPTOR OT2 C IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 PRES NPHE 1.0 DELETE ATOM HN ATOM N N3 0.17370 ATOM HT1 H 0.19210 ATOM HT2 H 0.19210 ATOM HT3 H 0.19210 ATOM CA CT 0.07330 ATOM HA HP 0.10410 ATOM CB CT 0.03300 ATOM HB1 HC 0.01040 ATOM HB2 HC 0.01040 ATOM CG CA 0.00310 ATOM CD1 CA -0.13920 ATOM HD1 HA 0.13740 ATOM CE1 CA -0.16020 ATOM HE1 HA 0.14330 ATOM CZ CA -0.12080 ATOM HZ HA 0.13290 ATOM CE2 CA -0.16030 ATOM HE2 HA 0.14330 ATOM CD2 CA -0.13910 ATOM HD2 HA 0.13740 ATOM C C 0.61230 ATOM O O -0.57130 BOND HT1 N HT2 N HT3 N DONOR HT1 N DONOR HT2 N DONOR HT3 N IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 PRES CPHE -1.0 DELETE ATOM O ATOM N N -0.38210 ATOM HN H 0.26810 ATOM CA CT -0.18250 ATOM HA H1 0.10980 ATOM CB CT -0.09590 ATOM HB1 HC 0.04430 ATOM HB2 HC 0.04430 ATOM CG CA 0.05520 ATOM CD1 CA -0.13000 ATOM HD1 HA 0.14080 ATOM CE1 CA -0.18470 ATOM HE1 HA 0.14610 ATOM CZ CA -0.09440 ATOM HZ HA 0.12800 ATOM CE2 CA -0.18470 ATOM HE2 HA 0.14610 ATOM CD2 CA -0.13000 ATOM HD2 HA 0.14080 ATOM C C 0.76600 ATOM OT1 O2 -0.80260 ATOM OT2 O2 -0.80260 BOND C OT2 BOND C OT1 !IMPROPER CA OT2 C OT1 IMPROPER CA OT1 C OT2 ACCEPTOR OT1 C ACCEPTOR OT2 C IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 PRES NPRO 1.0 ATOM N N3 -0.20200 ATOM HN1 H 0.31200 ATOM HN2 H 0.31200 ATOM CD CT -0.01200 ATOM HD1 HP 0.10000 ATOM HD2 HP 0.10000 ATOM CG CT -0.12100 ATOM HG1 HC 0.10000 ATOM HG2 HC 0.10000 ATOM CB CT -0.11500 ATOM HB1 HC 0.10000 ATOM HB2 HC 0.10000 ATOM CA CT 0.10000 ATOM HA HP 0.10000 ATOM C C 0.52600 ATOM O O -0.50000 BOND HN1 N HN2 N ! HD1 HD2 DONOR HN1 N DONOR HN2 N IC HN1 CA *N CD 0.0000 0.0000 120.0000 0.0000 0.0000 IC HN2 CA *N HN1 0.0000 0.0000 120.0000 0.0000 0.0000 PRES CPRO -1.0 DELETE ATOM O ATOM N N -0.28020 ATOM CD CT 0.04340 ATOM HD1 H1 0.03310 ATOM HD2 H1 0.03310 ATOM CG CT 0.04660 ATOM HG1 HC 0.01720 ATOM HG2 HC 0.01720 ATOM CB CT -0.05430 ATOM HB1 HC 0.03810 ATOM HB2 HC 0.03810 ATOM CA CT -0.13360 ATOM HA H1 0.07760 ATOM C C 0.66310 ATOM OT1 O2 -0.76970 ATOM OT2 O2 -0.76970 BOND C OT2 BOND C OT1 IMPROPER CA OT2 C OT1 ACCEPTOR OT1 C ACCEPTOR OT2 C IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 PRES NSER 1.0 DELETE ATOM HN ATOM N N3 0.18490 ATOM HT1 H 0.18980 ATOM HT2 H 0.18980 ATOM HT3 H 0.18980 ATOM CA CT 0.05670 ATOM HA HP 0.07820 ATOM CB CT 0.25960 ATOM HB1 H1 0.02730 ATOM HB2 H1 0.02730 ATOM OG OH -0.67140 ATOM HG1 HO 0.42390 ATOM C C 0.61630 ATOM O O -0.57220 BOND HT1 N HT2 N HT3 N DONOR HT1 N DONOR HT2 N DONOR HT3 N IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 PRES CSER -1.0 DELETE ATOM O ATOM N N -0.38210 ATOM HN H 0.26810 ATOM CA CT -0.27220 ATOM HA H1 0.13040 ATOM CB CT 0.11230 ATOM HB1 H1 0.08130 ATOM HB2 H1 0.08130 ATOM OG OH -0.65140 ATOM HG1 HO 0.44740 ATOM C C 0.81130 ATOM OT1 O2 -0.81320 ATOM OT2 O2 -0.81320 BOND C OT2 BOND C OT1 IMPROPER CA OT2 C OT1 ACCEPTOR OT1 C ACCEPTOR OT2 C IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 PRES NTHR 1.0 DELETE ATOM HN ATOM N N3 0.18120 ATOM HT1 H 0.19340 ATOM HT2 H 0.19340 ATOM HT3 H 0.19340 ATOM CA CT 0.00340 ATOM HA HP 0.10870 ATOM CB CT 0.45140 ATOM HB H1 -0.03230 ATOM CG2 CT -0.25540 ATOM HG21 HC 0.06270 ATOM HG22 HC 0.06270 ATOM HG23 HC 0.06270 ATOM OG1 OH -0.67640 ATOM HG1 HO 0.40700 ATOM C C 0.61630 ATOM O O -0.57220 BOND HT1 N HT2 N HT3 N DONOR HT1 N DONOR HT2 N DONOR HT3 N IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 PRES CTHR -1.0 DELETE ATOM O ATOM N N -0.38210 ATOM HN H 0.26810 ATOM CA CT -0.24200 ATOM HA H1 0.12070 ATOM CB CT 0.30250 ATOM HB H1 0.00780 ATOM CG2 CT -0.18530 ATOM HG21 HC 0.05860 ATOM HG22 HC 0.05860 ATOM HG23 HC 0.05860 ATOM OG1 OH -0.64960 ATOM HG1 HO 0.41190 ATOM C C 0.78100 ATOM OT1 O2 -0.80440 ATOM OT2 O2 -0.80440 BOND C OT2 BOND C OT1 IMPROPER CA OT1 C OT2 ACCEPTOR OT1 C ACCEPTOR OT2 C IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 PRES NTRP 1.0 DELETE ATOM HN ATOM N N3 0.19130 ATOM HT1 H 0.18880 ATOM HT2 H 0.18880 ATOM HT3 H 0.18880 ATOM CA CT 0.04210 ATOM HA HP 0.11620 ATOM CB CT 0.05430 ATOM HB1 HC 0.02220 ATOM HB2 HC 0.02220 ATOM CG CS -0.16540 ATOM CD1 CW -0.17880 ATOM HD1 H4 0.21950 ATOM NE1 NA -0.34440 ATOM HE1 H 0.34120 ATOM CE2 CN 0.15750 ATOM CZ2 CA -0.27100 ATOM HZ2 HA 0.15890 ATOM CH2 CA -0.10800 ATOM HH2 HA 0.14110 ATOM CZ3 CA -0.20340 ATOM HZ3 HA 0.14580 ATOM CE3 CA -0.22650 ATOM HE3 HA 0.16460 ATOM CD2 CB 0.11320 ATOM C C 0.61230 ATOM O O -0.57130 BOND HT1 N HT2 N HT3 N DONOR HT1 N DONOR HT2 N DONOR HT3 N IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 PRES CTRP -1.0 DELETE ATOM O ATOM N N -0.38210 ATOM HN H 0.26810 ATOM CA CT -0.20840 ATOM HA H1 0.12720 ATOM CB CT -0.07420 ATOM HB1 HC 0.04970 ATOM HB2 HC 0.04970 ATOM CG CS -0.07960 ATOM CD1 CW -0.18080 ATOM HD1 H4 0.20430 ATOM NE1 NA -0.33160 ATOM HE1 H 0.34130 ATOM CE2 CN 0.12220 ATOM CZ2 CA -0.25940 ATOM HZ2 HA 0.15670 ATOM CH2 CA -0.10200 ATOM HH2 HA 0.14010 ATOM CZ3 CA -0.22870 ATOM HZ3 HA 0.15070 ATOM CE3 CA -0.18370 ATOM HE3 HA 0.14910 ATOM CD2 CB 0.10780 ATOM C C 0.76580 ATOM OT1 O2 -0.80110 ATOM OT2 O2 -0.80110 BOND C OT2 BOND C OT1 IMPROPER CA OT1 C OT2 ACCEPTOR OT1 C ACCEPTOR OT2 C IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 PRES NTYR 1.0 DELETE ATOM HN ATOM N N3 0.19400 ATOM HT1 H 0.18730 ATOM HT2 H 0.18730 ATOM HT3 H 0.18730 ATOM CA CT 0.05700 ATOM HA HP 0.09830 ATOM CB CT 0.06590 ATOM HB1 HC 0.01020 ATOM HB2 HC 0.01020 ATOM CG CA -0.02050 ATOM CD1 CA -0.20020 ATOM HD1 HA 0.17200 ATOM CE1 CA -0.22390 ATOM HE1 HA 0.16500 ATOM CZ C 0.31390 ATOM OH OH -0.55780 ATOM HH HO 0.40010 ATOM CE2 CA -0.22390 ATOM HE2 HA 0.16500 ATOM CD2 CA -0.20020 ATOM HD2 HA 0.17200 ATOM C C 0.61230 ATOM O O -0.57130 BOND HT1 N HT2 N HT3 N DONOR HT1 N DONOR HT2 N DONOR HT3 N IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 PRES CTYR -1.0 DELETE ATOM O ATOM N N -0.38210 ATOM HN H 0.26810 ATOM CA CT -0.20150 ATOM HA H1 0.10920 ATOM CB CT -0.07520 ATOM HB1 HC 0.04900 ATOM HB2 HC 0.04900 ATOM CG CA 0.02430 ATOM CD1 CA -0.19220 ATOM HD1 HA 0.17800 ATOM CE1 CA -0.24580 ATOM HE1 HA 0.16730 ATOM CZ C 0.33950 ATOM OH OH -0.56430 ATOM HH HO 0.40170 ATOM CE2 CA -0.24580 ATOM HE2 HA 0.16730 ATOM CD2 CA -0.19220 ATOM HD2 HA 0.17800 ATOM C C 0.78170 ATOM OT1 O2 -0.80700 ATOM OT2 O2 -0.80700 BOND C OT2 BOND C OT1 IMPROPER CA OT1 C OT2 ACCEPTOR OT1 C ACCEPTOR OT2 C IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 PRES NVAL 1.0 DELETE ATOM HN ATOM N N3 0.05770 ATOM HT1 H 0.22720 ATOM HT2 H 0.22720 ATOM HT3 H 0.22720 ATOM CA CT -0.00540 ATOM HA HP 0.10930 ATOM CB CT 0.31960 ATOM HB HC -0.02210 ATOM CG1 CT -0.31290 ATOM HG11 HC 0.07350 ATOM HG12 HC 0.07350 ATOM HG13 HC 0.07350 ATOM CG2 CT -0.31290 ATOM HG21 HC 0.07350 ATOM HG22 HC 0.07350 ATOM HG23 HC 0.07350 ATOM C C 0.61630 ATOM O O -0.57220 BOND HT1 N HT2 N HT3 N DONOR HT1 N DONOR HT2 N DONOR HT3 N IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 PRES CVAL -1.0 DELETE ATOM O ATOM N N -0.38210 ATOM HN H 0.26810 ATOM CA CT -0.34380 ATOM HA H1 0.14380 ATOM CB CT 0.19400 ATOM HB HC 0.03080 ATOM CG1 CT -0.30640 ATOM HG11 HC 0.08360 ATOM HG12 HC 0.08360 ATOM HG13 HC 0.08360 ATOM CG2 CT -0.30640 ATOM HG21 HC 0.08360 ATOM HG22 HC 0.08360 ATOM HG23 HC 0.08360 ATOM C C 0.83500 ATOM OT1 O2 -0.81730 ATOM OT2 O2 -0.81730 BOND C OT2 BOND C OT1 IMPROPER CA OT2 C OT1 ACCEPTOR OT1 C ACCEPTOR OT2 C IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 END