# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 01:04:28 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  35  21  .  2022-03-11  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.514   3.1152   3.9295  -0.6798
 AY0  O2   O  O     0  -0.492   2.3373   1.8831   1.0426
 AY0  O    O  O     0  -0.449   4.6472  -2.4364  -0.2677
 AY0  O4   O  O     0  -0.689  -4.3982  -1.7633   0.5084
 AY0  O5   O  OH1   0  -0.732  -4.3412  -0.5326  -1.6811
 AY0  O6   O  OH1   0  -0.724  -5.6261   0.5540   0.2789
 AY0  C2   C  CR16  0  -0.294  -1.3038  -0.6010   1.1003
 AY0  C3   C  CR16  0  -0.303  -1.2415   0.6941  -0.9328
 AY0  C4   C  CR16  0  -0.303   0.0349  -0.9225   0.9253
 AY0  C5   C  CR16  0  -0.284   0.0945   0.3629  -1.0930
 AY0  N    N  NH1   0  -0.640   3.3706   2.5193  -0.8548
 AY0  C6   C  C     0   0.603   2.9518   1.6002   0.0241
 AY0  C    C  C     0   0.587   4.1688  -1.9438   0.7257
 AY0  C8   C  CR6   0   0.338  -1.9295   0.2109   0.1691
 AY0  C9   C  CR6   0   0.112   0.7480  -0.4462  -0.1678
 AY0  C10  C  CH1   0  -0.386   3.2741   0.1905  -0.3558
 AY0  C11  C  CH1   0  -0.411   3.1607  -0.8583   0.7220
 AY0  C12  C  CH1   0  -0.249   2.1694  -0.8220  -0.3995
 AY0  P1   P  P     0   1.438  -4.4270  -0.4202  -0.0934
 AY0  OXT  O  OH1   0  -0.592   4.4878  -2.3174   1.9568
 AY0  HXT  H  HOH1  0   0.484   5.1438  -3.0305   1.9292
 AY0  H15  H  HCH3  0   0.238   2.0465   4.1459  -0.6613
 AY0  H3   H  HCH3  0   0.239   3.5570   4.3057   0.2432
 AY0  H4   H  HOH1  0   0.499  -4.4684   0.2866  -2.1784
 AY0  H5   H  HOH1  0   0.509  -6.4965   0.1324   0.2733
 AY0  H6   H  HCR6  0   0.276  -1.8473  -0.9697   1.9599
 AY0  H7   H  HCR6  0   0.273  -1.7383   1.3334  -1.6512
 AY0  H8   H  HCR6  0   0.259   0.5254  -1.5536   1.6558
 AY0  H9   H  HCR6  0   0.258   0.6349   0.7464  -1.9498
 AY0  H10  H  HCH1  0   0.298   4.0631   0.0544  -1.0867
 AY0  H11  H  HCH1  0   0.302   2.8257  -0.5029   1.6891
 AY0  H12  H  HCH1  0   0.306   2.3118  -1.5825  -1.1612
 AY0  H13  H  HCH3  0   0.251   3.5583   4.4646  -1.5146
 AY0  H2   H  HNH1  0   0.407   3.8640   2.2232  -1.6799
 AY0  O7   O  O2    0  -0.615  -3.2477   0.5829   0.3541

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  OXT  HXT  single    0.850  0.020  0.980
 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    double    1.231  0.020  1.231
 AY0  O4   P1   double    1.472  0.020  1.472
 AY0  O5   P1   single    1.594  0.020  1.594
 AY0  O5   H4   single    0.850  0.020  0.980
 AY0  O6   H5   single    0.850  0.020  0.980
 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  1.386  0.020  1.386
 AY0  C3   H7   single    0.930  0.020  1.080
 AY0  C4   H8   single    0.930  0.020  1.080
 AY0  C5   C9   aromatic  1.392  0.020  1.392
 AY0  C5   H9   single    0.930  0.020  1.080
 AY0  N    C1   single    1.444  0.020  1.444
 AY0  N    C6   single    1.339  0.020  1.339
 AY0  N    H2   single    0.860  0.020  1.020
 AY0  O7   C8   single    1.382  0.020  1.382
 AY0  O7   P1   single    1.612  0.020  1.612
 AY0  C6   O2   double    1.223  0.020  1.223
 AY0  C    OXT  single    1.326  0.020  1.326
 AY0  C8   C2   aromatic  1.385  0.020  1.385
 AY0  C9   C4   aromatic  1.389  0.020  1.389
 AY0  C9   C12  single    1.488  0.020  1.488
 AY0  C10  C6   single    1.495  0.020  1.495
 AY0  C10  C11  single    1.508  0.020  1.508
 AY0  C10  H10  single    0.970  0.020  1.090
 AY0  C11  C    single    1.481  0.020  1.481
 AY0  C11  H11  single    0.970  0.020  1.090
 AY0  C12  C10  single    1.499  0.020  1.499
 AY0  C12  C11  single    1.497  0.020  1.497
 AY0  C12  H12  single    0.970  0.020  1.090
 AY0  P1   O6   single    1.589  0.020  1.589

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   108.39  3.000
 AY0  H13  C1   H15  108.36  3.000
 AY0  H3   C1   H15  108.32  3.000
 AY0  H13  C1   N    108.42  3.000
 AY0  H3   C1   N    111.59  3.000
 AY0  H15  C1   N    111.66  3.000
 AY0  H4   O5   P1   116.46  3.000
 AY0  H5   O6   P1   114.23  3.000
 AY0  H6   C2   C8   120.47  3.000
 AY0  C8   C2   C4   119.13  3.000
 AY0  H6   C2   C4   120.39  3.000
 AY0  H7   C3   C8   120.38  3.000
 AY0  H7   C3   C5   120.46  3.000
 AY0  C8   C3   C5   119.16  3.000
 AY0  H8   C4   C9   119.87  3.000
 AY0  C9   C4   C2   121.00  3.000
 AY0  H8   C4   C2   119.13  3.000
 AY0  H9   C5   C9   119.82  3.000
 AY0  H9   C5   C3   119.20  3.000
 AY0  C9   C5   C3   120.97  3.000
 AY0  H2   N    C6   119.32  3.000
 AY0  H2   N    C1   118.28  3.000
 AY0  C6   N    C1   122.39  3.000
 AY0  C10  C6   N    114.40  3.000
 AY0  C10  C6   O2   122.56  3.000
 AY0  N    C6   O2   123.03  3.000
 AY0  OXT  C    C11  111.88  3.000
 AY0  C11  C    O    124.50  3.000
 AY0  OXT  C    O    123.62  3.000
 AY0  O7   C8   C3   119.08  3.000
 AY0  O7   C8   C2   119.92  3.000
 AY0  C3   C8   C2   120.97  3.000
 AY0  C12  C9   C5   119.44  3.000
 AY0  C12  C9   C4   121.75  3.000
 AY0  C5   C9   C4   118.76  3.000
 AY0  H10  C10  C12  115.59  3.000
 AY0  C12  C10  C11   59.72  3.000
 AY0  H10  C10  C11  116.69  3.000
 AY0  C12  C10  C6   119.03  3.000
 AY0  H10  C10  C6   116.53  3.000
 AY0  C11  C10  C6   117.25  3.000
 AY0  H11  C11  C12  117.12  3.000
 AY0  C12  C11  C10   59.84  3.000
 AY0  H11  C11  C10  115.66  3.000
 AY0  C12  C11  C    118.05  3.000
 AY0  H11  C11  C    116.65  3.000
 AY0  C10  C11  C    117.40  3.000
 AY0  H12  C12  C11  114.93  3.000
 AY0  H12  C12  C10  113.38  3.000
 AY0  C11  C12  C10   60.44  3.000
 AY0  H12  C12  C9   114.29  3.000
 AY0  C11  C12  C9   121.45  3.000
 AY0  C10  C12  C9   121.92  3.000
 AY0  O7   P1   O6    96.06  3.000
 AY0  O6   P1   O5   108.49  3.000
 AY0  O7   P1   O5   106.32  3.000
 AY0  O6   P1   O4   118.58  3.000
 AY0  O7   P1   O4   116.11  3.000
 AY0  O5   P1   O4   109.99  3.000
 AY0  HXT  OXT  C    110.11  3.000
 AY0  P1   O7   C8   119.55  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  HXT  OXT  C    C11   180.00   0.0  0
 AY0  CONST_18  O2   C6   N    C1      0.00   0.0  0
 AY0  Var_01    C10  C12  C9   C4   -115.32  30.0  2
 AY0  Var_02    C11  C10  C12  C9    110.70  30.0  1
 AY0  Var_03    C12  C11  C10  C6    109.35  30.0  1
 AY0  Var_04    H15  C1   N    C6    -61.11  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
 AY0  plan-3  HXT  0.020

