# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 11:54:37 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: (2R)-2-(3-carbamimidamidophenyl)-3-sulfanylpropanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)Nc1cccc(c1)[C@@H](CS)C(O)=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 L98  L98  '(2R)-2-(3-carbamimidamidophenyl)-3-sulfanylpropanoic acid'  ligand  28  16  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_L98
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 L98  S     S  S2     0  -0.252  -3.8258  -1.4936   0.7342
 L98  C1    C  CH2    0  -0.536  -2.2346  -0.6633   1.0839
 L98  C2    C  CH1    0  -0.427  -1.5836  -0.1455  -0.1910
 L98  C3    C  CR6    0   0.176  -0.2952   0.5654   0.1439
 L98  C4    C  CR16   0  -0.400   0.9292   0.0122  -0.2128
 L98  C5    C  CR6    0   0.358   2.1298   0.6455   0.1192
 L98  C6    C  CR16   0  -0.318  -0.3203   1.7845   0.8205
 L98  C7    C  CR16   0  -0.232   0.8663   2.4303   1.1298
 L98  C8    C  CR16   0  -0.350   2.0869   1.8663   0.7920
 L98  N9    N  NH1    0  -0.746   3.3771   0.1405  -0.2572
 L98  C10   C  C      0   0.524   3.8215  -1.1664  -0.2874
 L98  N11   N  N      0  -0.707   4.9551  -1.5194  -0.7676
 L98  N12   N  NH2    0  -0.811   2.9612  -2.1101   0.2069
 L98  C13   C  C      0   0.428  -2.5098   0.8008  -0.9934
 L98  O14   O  O      0  -0.604  -2.1194   1.1054  -2.1354
 L98  O15   O  OC    -1  -0.590  -3.5485   1.1874  -0.4242
 L98  HS    H  HSH1   0   0.195  -3.5202  -2.6787   1.2770
 L98  H11A  H  HCH2   0   0.271  -1.5850  -1.3843   1.5793
 L98  H12   H  HCH2   0   0.260  -2.4200   0.1498   1.7845
 L98  H2    H  HCH1   0   0.244  -1.3436  -1.0044  -0.8258
 L98  H4    H  HCR6   0   0.263   0.9443  -0.9176  -0.7661
 L98  H6    H  HCR6   0   0.243  -1.2681   2.2354   1.0882
 L98  H7    H  HCR6   0   0.253   0.8460   3.3810   1.6475
 L98  H8    H  HCR6   0   0.261   3.0101   2.3719   1.0486
 L98  HN9   H  HNH1   0   0.401   4.1067   0.8285  -0.3557
 L98  H11   H  H      0   0.318   5.4346  -0.7345  -1.1929
 L98  H121  H  HNH2   0   0.387   3.3870  -3.0163   0.3171
 L98  H122  H  HNH2   0   0.391   2.3846  -1.8496   0.9918

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 L98  S    C1    single    1.829  0.020  1.829
 L98  S    HS    single    1.200  0.020  1.300
 L98  C1   C2    single    1.522  0.020  1.522
 L98  C1   H11A  single    0.970  0.020  1.090
 L98  C1   H12   single    0.970  0.020  1.090
 L98  C2   C3    single    1.509  0.020  1.509
 L98  C2   C13   single    1.548  0.020  1.548
 L98  C2   H2    single    0.970  0.020  1.090
 L98  C3   C4    aromatic  1.390  0.020  1.390
 L98  C3   C6    aromatic  1.394  0.020  1.394
 L98  C4   C5    aromatic  1.397  0.020  1.397
 L98  C4   H4    single    0.930  0.020  1.080
 L98  C5   C8    aromatic  1.395  0.020  1.395
 L98  C5   N9    single    1.397  0.020  1.397
 L98  C6   C7    aromatic  1.386  0.020  1.386
 L98  C6   H6    single    0.930  0.020  1.080
 L98  C7   C8    aromatic  1.386  0.020  1.386
 L98  C7   H7    single    0.930  0.020  1.080
 L98  C8   H8    single    0.930  0.020  1.080
 L98  N9   C10   single    1.381  0.020  1.381
 L98  N9   HN9   single    0.860  0.020  1.020
 L98  C10  N11   double    1.281  0.020  1.281
 L98  C10  N12   single    1.369  0.020  1.369
 L98  N11  H11   single    0.890  0.020  1.040
 L98  N12  H121  single    0.890  0.020  1.040
 L98  N12  H122  single    0.890  0.020  1.040
 L98  C13  O14   deloc     1.245  0.020  1.245
 L98  C13  O15   deloc     1.246  0.020  1.246

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 L98  HS    S    C1     97.23  3.000
 L98  H12   C1   H11A  107.64  3.000
 L98  H12   C1   C2    110.95  3.000
 L98  H11A  C1   C2    110.54  3.000
 L98  H12   C1   S     108.29  3.000
 L98  H11A  C1   S     107.77  3.000
 L98  C2    C1   S     111.49  3.000
 L98  H2    C2   C13   108.07  3.000
 L98  H2    C2   C3    108.13  3.000
 L98  C13   C2   C3    109.75  3.000
 L98  H2    C2   C1    108.21  3.000
 L98  C13   C2   C1    112.71  3.000
 L98  C3    C2   C1    109.84  3.000
 L98  C6    C3   C4    119.23  3.000
 L98  C6    C3   C2    120.27  3.000
 L98  C4    C3   C2    120.50  3.000
 L98  H4    C4   C5    119.92  3.000
 L98  H4    C4   C3    119.04  3.000
 L98  C5    C4   C3    121.03  3.000
 L98  N9    C5   C8    118.28  3.000
 L98  N9    C5   C4    122.63  3.000
 L98  C8    C5   C4    119.01  3.000
 L98  H6    C6   C7    120.00  3.000
 L98  H6    C6   C3    119.98  3.000
 L98  C7    C6   C3    120.01  3.000
 L98  H7    C7   C8    119.36  3.000
 L98  H7    C7   C6    119.99  3.000
 L98  C8    C7   C6    120.65  3.000
 L98  H8    C8   C7    120.18  3.000
 L98  H8    C8   C5    119.77  3.000
 L98  C7    C8   C5    120.05  3.000
 L98  HN9   N9   C10   114.27  3.000
 L98  HN9   N9   C5    115.21  3.000
 L98  C10   N9   C5    129.44  3.000
 L98  N12   C10  N11   120.10  3.000
 L98  N12   C10  N9    116.25  3.000
 L98  N11   C10  N9    123.64  3.000
 L98  H11   N11  C10   111.27  3.000
 L98  H122  N12  H121  112.89  3.000
 L98  H122  N12  C10   117.54  3.000
 L98  H121  N12  C10   113.20  3.000
 L98  O15   C13  O14   127.21  3.000
 L98  O15   C13  C2    116.85  3.000
 L98  O14   C13  C2    115.94  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 L98  CONST_01  C8    C5   C4   C3    0.00  0.0  0
 L98  CONST_02  C8    C7   C6   C3    0.00  0.0  0
 L98  CONST_03  C7    C6   C3   C4    0.00  0.0  0
 L98  CONST_04  C7    C8   C5   C4    0.00  0.0  0
 L98  CONST_05  C6    C3   C4   C5    0.00  0.0  0
 L98  CONST_06  C6    C7   C8   C5    0.00  0.0  0
 L98  CONST_07  C5    C4   C3   C2  180.00  0.0  0
 L98  CONST_08  C7    C6   C3   C2  180.00  0.0  0
 L98  CONST_09  N9    C5   C4   C3  180.00  0.0  0
 L98  CONST_10  N9    C5   C8   C7  180.00  0.0  0
 L98  CONST_11  H7    C7   C6   C3  180.00  0.0  0
 L98  CONST_12  H6    C6   C3   C4  180.00  0.0  0
 L98  CONST_13  H8    C8   C5   C4  180.00  0.0  0
 L98  CONST_14  H4    C4   C3   C6  180.00  0.0  0
 L98  CONST_18  N11   C10  N9   C5  180.00  0.0  0
 L98  CONST_19  N12   C10  N9   C5    0.00  0.0  0
 L98  CONST_20  H11   N11  C10  N9    0.00  0.0  0
 L98  CONST_21  H121  N12  C10  N9  180.00  0.0  0

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 L98  chir_01  C2  C1  C3  C13  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 L98  plan-1  C2    0.020
 L98  plan-1  C3    0.020
 L98  plan-1  C4    0.020
 L98  plan-1  C5    0.020
 L98  plan-1  C6    0.020
 L98  plan-1  C7    0.020
 L98  plan-1  C8    0.020
 L98  plan-1  N9    0.020
 L98  plan-1  H4    0.020
 L98  plan-1  H6    0.020
 L98  plan-1  H7    0.020
 L98  plan-1  H8    0.020
 L98  plan-2  C5    0.020
 L98  plan-2  N9    0.020
 L98  plan-2  C10   0.020
 L98  plan-2  N11   0.020
 L98  plan-2  N12   0.020
 L98  plan-2  HN9   0.020
 L98  plan-2  H11   0.020
 L98  plan-2  H121  0.020
 L98  plan-2  H122  0.020
 L98  plan-3  C2    0.020
 L98  plan-3  C13   0.020
 L98  plan-3  O14   0.020
 L98  plan-3  O15   0.020

