# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 22:30:06 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: (1R,2R,3S)-2-(methylcarbamoyl)-3-[4-(phosphonooxy)phenyl]cyclopropanecarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)[C@H]1[C@@H]([C@H]1c2ccc(O[P](O)(O)=O)cc2)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
 AY0  AY0  '(1R,2R,3S)-2-(methylcarbamoyl)-3-[4-(phosphonooxy)phenyl]cyclopropanecarboxylic acid'  peptide  32  21  .  2022-03-11  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_AY0
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
 AY0  C1   C  CH3    0  -0.512   3.1193   3.9257  -0.3480
 AY0  O2   O  O      0  -0.504   2.3956   1.7943   1.2730
 AY0  O    O  O      0  -0.607   4.6245  -2.4029  -0.4390
 AY0  O4   O  O      0  -0.879  -4.3480  -1.4109   0.4933
 AY0  O5   O  OP    -1  -0.876  -4.2928  -0.4245  -1.8714
 AY0  O6   O  OP    -1  -0.884  -5.6923   0.7185  -0.0415
 AY0  C2   C  CR16   0  -0.344  -1.2643  -0.1241   1.0577
 AY0  C3   C  CR16   0  -0.336  -1.2574   0.5006  -1.2539
 AY0  C4   C  CR16   0  -0.306   0.0648  -0.5107   0.9542
 AY0  C5   C  CR16   0  -0.297   0.0685   0.1090  -1.3460
 AY0  N    N  NH1    0  -0.640   3.3803   2.5313  -0.6086
 AY0  C6   C  C      0   0.591   2.9867   1.5551   0.2270
 AY0  C    C  C      0   0.439   4.1440  -2.1100   0.6744
 AY0  C8   C  CR6    0   0.380  -1.9418   0.4093  -0.0389
 AY0  C9   C  CR6    0   0.112   0.7582  -0.3994  -0.2455
 AY0  C10  C  CH1    0  -0.388   3.3113   0.1783  -0.2348
 AY0  C11  C  CH1    0  -0.411   3.1390  -0.9726   0.7174
 AY0  C12  C  CH1    0  -0.269   2.1783  -0.8081  -0.4128
 AY0  P1   P  P      0   1.203  -4.5221  -0.1859  -0.3878
 AY0  OXT  O  OC    -1  -0.613   4.3984  -2.6592   1.7647
 AY0  H15  H  HCH3   0   0.234   2.0504   4.1313  -0.2745
 AY0  H3   H  HCH3   0   0.233   3.5934   4.2606   0.5757
 AY0  H6   H  HCR6   0   0.234  -1.7821  -0.2195   2.0042
 AY0  H7   H  HCR6   0   0.235  -1.7694   0.8951  -2.1214
 AY0  H8   H  HCR6   0   0.229   0.5633  -0.9125   1.8277
 AY0  H9   H  HCR6   0   0.232   0.5824   0.2015  -2.2969
 AY0  H10  H  HCH1   0   0.265   4.1148   0.0920  -0.9579
 AY0  H11  H  HCH1   0   0.244   2.7785  -0.6938   1.7011
 AY0  H12  H  HCH1   0   0.264   2.3492  -1.4832  -1.2458
 AY0  H13  H  HCH3   0   0.246   3.5227   4.5116  -1.1692
 AY0  H2   H  HNH1   0   0.400   3.8455   2.2842  -1.4650
 AY0  O7   O  O2     0  -0.674  -3.1988   0.8565   0.0855

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
 AY0  C1   H15  single    0.970  0.020  1.090
 AY0  C1   H3   single    0.970  0.020  1.090
 AY0  C1   H13  single    0.970  0.020  1.090
 AY0  O    C    deloc     1.231  0.020  1.231
 AY0  O4   P1   deloc     1.519  0.020  1.519
 AY0  O5   P1   deloc     1.520  0.020  1.520
 AY0  C2   C4   aromatic  1.388  0.020  1.388
 AY0  C2   H6   single    0.930  0.020  1.080
 AY0  C3   C5   aromatic  1.386  0.020  1.386
 AY0  C3   C8   aromatic  1.397  0.020  1.397
 AY0  C3   H7   single    0.930  0.020  1.080
 AY0  C4   H8   single    0.930  0.020  1.080
 AY0  C5   C9   aromatic  1.395  0.020  1.395
 AY0  C5   H9   single    0.930  0.020  1.080
 AY0  N    C1   single    1.442  0.020  1.442
 AY0  N    C6   single    1.344  0.020  1.344
 AY0  N    H2   single    0.860  0.020  1.020
 AY0  O7   C8   single    1.340  0.020  1.340
 AY0  O7   P1   single    1.750  0.020  1.750
 AY0  C6   O2   double    1.225  0.020  1.225
 AY0  C    OXT  deloc     1.247  0.020  1.247
 AY0  C8   C2   aromatic  1.395  0.020  1.395
 AY0  C9   C4   aromatic  1.390  0.020  1.390
 AY0  C9   C12  single    1.487  0.020  1.487
 AY0  C10  C6   single    1.488  0.020  1.488
 AY0  C10  C11  single    1.504  0.020  1.504
 AY0  C10  H10  single    0.970  0.020  1.090
 AY0  C11  C    single    1.518  0.020  1.518
 AY0  C11  H11  single    0.970  0.020  1.090
 AY0  C12  C10  single    1.513  0.020  1.513
 AY0  C12  C11  single    1.492  0.020  1.492
 AY0  C12  H12  single    0.970  0.020  1.090
 AY0  P1   O6   deloc     1.519  0.020  1.519

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
 AY0  H13  C1   H3   108.24  3.000
 AY0  H13  C1   H15  108.25  3.000
 AY0  H3   C1   H15  108.12  3.000
 AY0  H13  C1   N    108.51  3.000
 AY0  H3   C1   N    111.78  3.000
 AY0  H15  C1   N    111.82  3.000
 AY0  H6   C2   C8   119.24  3.000
 AY0  C8   C2   C4   120.86  3.000
 AY0  H6   C2   C4   119.89  3.000
 AY0  H7   C3   C8   119.29  3.000
 AY0  H7   C3   C5   120.18  3.000
 AY0  C8   C3   C5   120.53  3.000
 AY0  H8   C4   C9   119.75  3.000
 AY0  C9   C4   C2   121.31  3.000
 AY0  H8   C4   C2   118.94  3.000
 AY0  H9   C5   C9   119.24  3.000
 AY0  H9   C5   C3   119.17  3.000
 AY0  C9   C5   C3   121.59  3.000
 AY0  H2   N    C6   119.11  3.000
 AY0  H2   N    C1   118.38  3.000
 AY0  C6   N    C1   122.47  3.000
 AY0  C10  C6   N    114.54  3.000
 AY0  C10  C6   O2   123.43  3.000
 AY0  N    C6   O2   122.03  3.000
 AY0  OXT  C    C11  116.12  3.000
 AY0  C11  C    O    117.14  3.000
 AY0  OXT  C    O    126.74  3.000
 AY0  O7   C8   C3   121.22  3.000
 AY0  O7   C8   C2   120.68  3.000
 AY0  C3   C8   C2   118.07  3.000
 AY0  C12  C9   C5   118.92  3.000
 AY0  C12  C9   C4   123.46  3.000
 AY0  C5   C9   C4   117.61  3.000
 AY0  H10  C10  C12  115.12  3.000
 AY0  C12  C10  C11   59.31  3.000
 AY0  H10  C10  C11  116.50  3.000
 AY0  C12  C10  C6   118.45  3.000
 AY0  H10  C10  C6   116.24  3.000
 AY0  C11  C10  C6   119.12  3.000
 AY0  H11  C11  C12  116.41  3.000
 AY0  C12  C11  C10   60.65  3.000
 AY0  H11  C11  C10  114.57  3.000
 AY0  C12  C11  C    119.16  3.000
 AY0  H11  C11  C    116.00  3.000
 AY0  C10  C11  C    118.66  3.000
 AY0  H12  C12  C11  114.27  3.000
 AY0  H12  C12  C10  112.20  3.000
 AY0  C11  C12  C10   60.05  3.000
 AY0  H12  C12  C9   114.04  3.000
 AY0  C11  C12  C9   124.04  3.000
 AY0  C10  C12  C9   121.52  3.000
 AY0  O7   P1   O6    99.57  3.000
 AY0  O6   P1   O5   115.61  3.000
 AY0  O7   P1   O5   104.09  3.000
 AY0  O6   P1   O4   115.86  3.000
 AY0  O7   P1   O4   103.70  3.000
 AY0  O5   P1   O4   114.98  3.000
 AY0  P1   O7   C8   119.05  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
 AY0  CONST_01  C5   C9   C4   C2     0.00   0.0  0
 AY0  CONST_02  C5   C3   C8   C2     0.00   0.0  0
 AY0  CONST_03  C4   C9   C5   C3     0.00   0.0  0
 AY0  CONST_04  C4   C2   C8   C3     0.00   0.0  0
 AY0  CONST_05  C9   C5   C3   C8     0.00   0.0  0
 AY0  CONST_06  C9   C4   C2   C8     0.00   0.0  0
 AY0  CONST_07  C12  C9   C4   C2   180.00   0.0  0
 AY0  CONST_08  C12  C9   C5   C3   180.00   0.0  0
 AY0  CONST_09  O7   C8   C2   C4   180.00   0.0  0
 AY0  CONST_10  O7   C8   C3   C5   180.00   0.0  0
 AY0  CONST_11  H7   C3   C8   C2   180.00   0.0  0
 AY0  CONST_12  H6   C2   C8   C3   180.00   0.0  0
 AY0  CONST_13  H9   C5   C9   C4   180.00   0.0  0
 AY0  CONST_14  H8   C4   C9   C5   180.00   0.0  0
 AY0  CONST_15  C10  C6   N    C1   180.00   0.0  0
 AY0  CONST_16  H2   N    C6   C10    0.00   0.0  0
 AY0  CONST_17  O2   C6   N    C1     0.00   0.0  0
 AY0  Var_01    C10  C12  C9   C4   -92.90  30.0  2
 AY0  Var_02    C11  C10  C12  C9   113.86  30.0  1
 AY0  Var_03    C12  C11  C10  C6   107.67  30.0  1
 AY0  Var_04    H15  C1   N    C6   -60.01  30.0  3

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
 AY0  chir_01  C10  C6   C11  C12  both
 AY0  chir_02  C11  C12  C    C10  both
 AY0  chir_03  C12  C9   C10  C11  both

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
 AY0  plan-1  C2   0.020
 AY0  plan-1  C3   0.020
 AY0  plan-1  C4   0.020
 AY0  plan-1  C5   0.020
 AY0  plan-1  C8   0.020
 AY0  plan-1  C9   0.020
 AY0  plan-1  C12  0.020
 AY0  plan-1  H6   0.020
 AY0  plan-1  H7   0.020
 AY0  plan-1  H8   0.020
 AY0  plan-1  H9   0.020
 AY0  plan-1  O7   0.020
 AY0  plan-2  C1   0.020
 AY0  plan-2  O2   0.020
 AY0  plan-2  N    0.020
 AY0  plan-2  C6   0.020
 AY0  plan-2  C10  0.020
 AY0  plan-2  H2   0.020
 AY0  plan-3  O    0.020
 AY0  plan-3  C    0.020
 AY0  plan-3  C11  0.020
 AY0  plan-3  OXT  0.020

