# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 21:58:27 2022
#   Inital geometry file: a 71 line input string
#   Ligand name: (2S)-3-(1H-imidazol-5-yl)-2-(1H-pyrrol-1-yl)propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@H](Cc1[nH]cnc1)n2cccc2
#
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
 8YI  8YI  "(2S)-3-(1H-imidazol-5-yl)-2-(1H-pyrrol-1-yl)propanoic acid"  ligand  25  15  .  2022-09-16  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_8YI
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
 8YI  C10  C  CR5    0   0.315  -3.5786  -14.2408  14.4289
 8YI  N12  N  N      0  -0.441  -1.9738  -13.3376  15.7287
 8YI  C13  C  CR15   0   0.071  -2.0426  -12.6759  14.6041
 8YI  C02  C  C      0   0.426  -5.8797  -15.5212  16.0398
 8YI  C03  C  CH1    0  -0.201  -5.1937  -16.1139  14.7731
 8YI  C05  C  CR15   0  -0.061  -7.3484  -16.6247  13.5916
 8YI  C06  C  CR15   0  -0.370  -7.9194  -17.7236  12.9969
 8YI  C07  C  CR15   0  -0.373  -7.0071  -18.7985  13.1422
 8YI  C08  C  CR15   0  -0.063  -5.9162  -18.3068  13.8170
 8YI  C09  C  CH2    0  -0.503  -4.6681  -15.0509  13.8165
 8YI  C11  C  CR15   0  -0.264  -2.9263  -14.3159  15.6309
 8YI  N04  N  NR5    0  -0.412  -6.1317  -16.9893  14.0859
 8YI  N14  N  NR15   0  -0.615  -2.9932  -13.1828  13.7910
 8YI  H2   H  HCR5   0   0.270  -1.4359  -11.8283  14.3238
 8YI  H3   H  HCH1   0   0.243  -4.3647  -16.7517  15.0859
 8YI  H4   H  HCR5   0   0.264  -7.7174  -15.6191  13.7049
 8YI  H5   H  HCR5   0   0.231  -8.8855  -17.7509  12.5171
 8YI  H6   H  HCR5   0   0.232  -7.1329  -19.8125  12.7963
 8YI  H7   H  HCR5   0   0.266  -5.0036  -18.7915  14.1264
 8YI  H8   H  HCH2   0   0.251  -5.4902  -14.3992  13.5107
 8YI  H9   H  HCH2   0   0.253  -4.2995  -15.5390  12.9085
 8YI  H10  H  HCR5   0   0.243  -3.1039  -15.0171  16.4322
 8YI  H11  H  HNR5   0   0.413  -3.2309  -12.8384  12.8735
 8YI  O01  O  OC    -1  -0.591  -5.6843  -16.1425  17.0986
 8YI  O15  O  O      0  -0.585  -6.5767  -14.5060  15.8639

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
 8YI  C06  C05  aromatic  1.374  0.020  1.374
 8YI  C06  C07  aromatic  1.417  0.020  1.417
 8YI  C05  N04  aromatic  1.363  0.020  1.363
 8YI  C07  C08  aromatic  1.374  0.020  1.374
 8YI  C09  C10  single    1.489  0.020  1.489
 8YI  C09  C03  single    1.524  0.020  1.524
 8YI  N04  C08  aromatic  1.362  0.020  1.362
 8YI  N04  C03  single    1.455  0.020  1.455
 8YI  N14  C10  aromatic  1.367  0.020  1.367
 8YI  N14  C13  aromatic  1.350  0.020  1.350
 8YI  C10  C11  aromatic  1.370  0.020  1.370
 8YI  C03  C02  single    1.558  0.020  1.558
 8YI  C13  N12  aromatic  1.307  0.020  1.307
 8YI  C11  N12  aromatic  1.369  0.020  1.369
 8YI  C02  O15  deloc     1.244  0.020  1.244
 8YI  C02  O01  deloc     1.243  0.020  1.243
 8YI  C13  H2   single    0.930  0.020  1.080
 8YI  C03  H3   single    0.970  0.020  1.090
 8YI  C05  H4   single    0.930  0.020  1.080
 8YI  C06  H5   single    0.930  0.020  1.080
 8YI  C07  H6   single    0.930  0.020  1.080
 8YI  C08  H7   single    0.930  0.020  1.080
 8YI  C09  H8   single    0.970  0.020  1.090
 8YI  C09  H9   single    0.970  0.020  1.090
 8YI  C11  H10  single    0.930  0.020  1.080
 8YI  N14  H11  single    0.860  0.020  1.020

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
 8YI  N14  C10  C11  104.36  3.000
 8YI  C11  C10  C09  132.80  3.000
 8YI  N14  C10  C09  122.84  3.000
 8YI  C11  N12  C13  105.30  3.000
 8YI  H2   C13  N14  122.30  3.000
 8YI  H2   C13  N12  126.27  3.000
 8YI  N14  C13  N12  111.43  3.000
 8YI  O15  C02  O01  128.05  3.000
 8YI  O01  C02  C03  115.68  3.000
 8YI  O15  C02  C03  116.25  3.000
 8YI  H3   C03  N04  105.86  3.000
 8YI  H3   C03  C09  109.00  3.000
 8YI  N04  C03  C09  110.21  3.000
 8YI  H3   C03  C02  108.89  3.000
 8YI  N04  C03  C02  109.21  3.000
 8YI  C09  C03  C02  113.40  3.000
 8YI  H4   C05  N04  121.16  3.000
 8YI  H4   C05  C06  130.54  3.000
 8YI  N04  C05  C06  108.31  3.000
 8YI  H5   C06  C07  127.07  3.000
 8YI  H5   C06  C05  125.79  3.000
 8YI  C07  C06  C05  107.14  3.000
 8YI  H6   C07  C08  125.91  3.000
 8YI  H6   C07  C06  127.22  3.000
 8YI  C08  C07  C06  106.87  3.000
 8YI  H7   C08  N04  120.79  3.000
 8YI  H7   C08  C07  130.69  3.000
 8YI  N04  C08  C07  108.52  3.000
 8YI  H9   C09  H8   106.69  3.000
 8YI  H9   C09  C03  109.01  3.000
 8YI  H8   C09  C03  109.40  3.000
 8YI  H9   C09  C10  109.71  3.000
 8YI  H8   C09  C10  109.94  3.000
 8YI  C03  C09  C10  111.94  3.000
 8YI  H10  C11  N12  121.72  3.000
 8YI  H10  C11  C10  127.49  3.000
 8YI  N12  C11  C10  110.79  3.000
 8YI  C08  N04  C05  109.17  3.000
 8YI  C08  N04  C03  124.97  3.000
 8YI  C05  N04  C03  125.85  3.000
 8YI  H11  N14  C13  125.86  3.000
 8YI  H11  N14  C10  126.01  3.000
 8YI  C13  N14  C10  108.13  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
 8YI  CONST_01  N12  C13  N14  C10     0.00   0.0  0
 8YI  CONST_02  C13  N12  C11  C10     0.00   0.0  0
 8YI  CONST_03  N14  C10  C11  N12     0.00   0.0  0
 8YI  CONST_04  C11  C10  N14  C13     0.00   0.0  0
 8YI  CONST_05  C08  C07  C06  C05     0.00   0.0  0
 8YI  CONST_06  C07  C08  N04  C05     0.00   0.0  0
 8YI  CONST_07  C08  N04  C05  C06     0.00   0.0  0
 8YI  CONST_08  N04  C08  C07  C06     0.00   0.0  0
 8YI  CONST_09  N04  C05  C06  C07     0.00   0.0  0
 8YI  CONST_10  N14  C13  N12  C11     0.00   0.0  0
 8YI  CONST_11  C09  C10  C11  N12   180.00   0.0  0
 8YI  CONST_12  C09  C10  N14  C13   180.00   0.0  0
 8YI  CONST_13  C06  C05  N04  C03   180.00   0.0  0
 8YI  CONST_14  C07  C08  N04  C03   180.00   0.0  0
 8YI  CONST_15  H2   C13  N14  C10   180.00   0.0  0
 8YI  CONST_16  H11  N14  C13  N12   180.00   0.0  0
 8YI  CONST_17  H10  C11  N12  C13   180.00   0.0  0
 8YI  CONST_18  H6   C07  C06  C05   180.00   0.0  0
 8YI  CONST_19  H7   C08  N04  C05   180.00   0.0  0
 8YI  CONST_20  H7   C08  C07  C06   180.00   0.0  0
 8YI  CONST_21  H4   C05  C06  C07   180.00   0.0  0
 8YI  CONST_22  H5   C06  C07  C08   180.00   0.0  0
 8YI  CONST_23  H4   C05  N04  C08   180.00   0.0  0
 8YI  CONST_24  H11  N14  C10  C11   180.00   0.0  0
 8YI  CONST_25  H2   C13  N12  C11   180.00   0.0  0
 8YI  CONST_26  H5   C06  C05  N04   180.00   0.0  0
 8YI  CONST_27  H6   C07  C08  N04   180.00   0.0  0
 8YI  CONST_28  H10  C11  C10  N14   180.00   0.0  0
 8YI  Var_01    N14  C10  C09  C03  -176.65  30.0  2
 8YI  Var_02    C11  C10  C09  C03     4.13  30.0  2
 8YI  Var_03    H8   C09  C10  C11   125.95  30.0  2
 8YI  Var_04    H9   C09  C10  C11  -117.03  30.0  2
 8YI  Var_05    H8   C09  C10  N14   -54.84  30.0  2
 8YI  Var_06    H9   C09  C10  N14    62.19  30.0  2

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
 8YI  chir_01  C03  C09  N04  C02  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
 8YI  plan-1  C03  0.020
 8YI  plan-1  C05  0.020
 8YI  plan-1  C06  0.020
 8YI  plan-1  C07  0.020
 8YI  plan-1  C08  0.020
 8YI  plan-1  N04  0.020
 8YI  plan-1  H4   0.020
 8YI  plan-1  H5   0.020
 8YI  plan-1  H6   0.020
 8YI  plan-1  H7   0.020
 8YI  plan-2  C10  0.020
 8YI  plan-2  N12  0.020
 8YI  plan-2  C13  0.020
 8YI  plan-2  C09  0.020
 8YI  plan-2  C11  0.020
 8YI  plan-2  N14  0.020
 8YI  plan-2  H2   0.020
 8YI  plan-2  H10  0.020
 8YI  plan-2  H11  0.020
 8YI  plan-3  C02  0.020
 8YI  plan-3  C03  0.020
 8YI  plan-3  O01  0.020
 8YI  plan-3  O15  0.020

