# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 02:02:43 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: 4-{[(2R)-2-(2-methylphenyl)pyrrolidin-1-yl]carbonyl}benzene-1,3-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccccc1[C@H]2CCCN2C(=O)c3ccc(O)cc3O
#
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
 PY9  PY9  4-{[(2R)-2-(2-methylphenyl)pyrrolidin-1-yl]carbonyl}benzene-1,3-diol  ligand  41  22  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PY9
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
 PY9  N1    N  NR5   0  -0.493   0.3488  -1.0938  -0.0492
 PY9  C4    C  CR6   0   0.384  -4.5090   0.4498   0.5462
 PY9  C5    C  CR16  0  -0.481  -3.9890   1.0314  -0.6009
 PY9  C6    C  CR6   0   0.373  -2.6410   0.8803  -0.9167
 PY9  C7    C  C     0   0.610  -0.3889  -0.0648  -0.4946
 PY9  C8    C  CR15  0  -0.123   1.7694  -1.1437  -0.4197
 PY9  C10   C  CH2   0  -0.469   0.9178  -3.3608  -0.1052
 PY9  C13   C  CR16  0  -0.294   2.3543   0.2820   1.5543
 PY9  C15   C  CR16  0  -0.257   4.0931   1.9296   1.4871
 PY9  C17   C  CR6   0   0.051   3.5755   0.6288  -0.4959
 PY9  C14   C  CR16  0  -0.263   3.1013   1.2614   2.1910
 PY9  C2    C  CR16  0  -0.255  -2.3566  -0.4570   1.0625
 PY9  C16   C  CR16  0  -0.298   4.3222   1.6084   0.1573
 PY9  C3    C  CR16  0  -0.359  -3.6801  -0.2858   1.3998
 PY9  C1    C  CR6   0  -0.226  -1.8054   0.0797  -0.1057
 PY9  C12   C  CR6   0   0.122   2.5766  -0.0417   0.2190
 PY9  C9    C  CH2   0  -0.470   2.1975  -2.5477   0.0203
 PY9  C11   C  CH2   0  -0.305  -0.1345  -2.3945   0.4194
 PY9  C18   C  CH3   0  -0.758   3.8503   0.3236  -1.9416
 PY9  O3    O  O     0  -0.541   0.1259   0.7827  -1.2469
 PY9  O1    O  OH1   0  -0.634  -2.1842   1.5091  -1.9982
 PY9  H5    H  HCR6  0   0.279  -4.6150   1.6348  -1.2489
 PY9  H8    H  HCR5  0   0.272   1.8442  -1.0748  -1.5072
 PY9  H10   H  HCH2  0   0.244   0.7158  -3.6070  -1.1496
 PY9  H10A  H  HCH2  0   0.258   0.9392  -4.2884   0.4656
 PY9  H13   H  HCR6  0   0.243   1.5791  -0.2357   2.1078
 PY9  H15   H  HCR6  0   0.251   4.6846   2.6972   1.9695
 PY9  H14   H  HCR6  0   0.251   2.9095   1.4999   3.2292
 PY9  H2    H  HCR6  0   0.270  -1.7318  -1.0065   1.7516
 PY9  H16   H  HCR6  0   0.244   5.0952   2.1325  -0.3926
 PY9  H3    H  HCR6  0   0.267  -4.0753  -0.7071   2.3143
 PY9  H9    H  HCH2  0   0.263   3.0187  -2.9219  -0.5904
 PY9  H9A   H  HCH2  0   0.244   2.5359  -2.5353   1.0590
 PY9  H11   H  HCH2  0   0.249  -0.1700  -2.4334   1.5115
 PY9  H11A  H  HCH2  0   0.272  -1.1325  -2.6031   0.0382
 PY9  H18   H  HCH3  0   0.245   4.1530  -0.7141  -2.0935
 PY9  H18A  H  HCH3  0   0.248   2.9657   0.4931  -2.5585
 PY9  H18B  H  HCH3  0   0.253   4.6486   0.9558  -2.3273
 PY9  HO2   H  HOH1  0   0.479  -6.2737   1.1147   0.2492
 PY9  HO1   H  HOH1  0   0.475  -1.1986   1.4172  -1.9741
 PY9  O2    O  OH1   0  -0.622  -5.7961   0.5808   0.8951

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
 PY9  C7   N1    single    1.342  0.020  1.342
 PY9  N1   C11   single    1.465  0.020  1.465
 PY9  N1   C8    single    1.469  0.020  1.469
 PY9  C5   C4    aromatic  1.387  0.020  1.387
 PY9  O2   C4    single    1.340  0.020  1.340
 PY9  C4   C3    aromatic  1.399  0.020  1.399
 PY9  C5   C6    aromatic  1.393  0.020  1.393
 PY9  C5   H5    single    0.930  0.020  1.080
 PY9  O1   C6    single    1.332  0.020  1.332
 PY9  C6   C1    aromatic  1.413  0.020  1.413
 PY9  O3   C7    double    1.245  0.020  1.245
 PY9  C1   C7    single    1.476  0.020  1.476
 PY9  C8   C12   single    1.508  0.020  1.508
 PY9  C8   C9    single    1.532  0.020  1.532
 PY9  C8   H8    single    0.970  0.020  1.090
 PY9  C11  C10   single    1.522  0.020  1.522
 PY9  C10  C9    single    1.521  0.020  1.521
 PY9  C10  H10   single    0.970  0.020  1.090
 PY9  C10  H10A  single    0.970  0.020  1.090
 PY9  C13  C12   aromatic  1.392  0.020  1.392
 PY9  C13  C14   aromatic  1.387  0.020  1.387
 PY9  C13  H13   single    0.930  0.020  1.080
 PY9  C14  C15   aromatic  1.388  0.020  1.388
 PY9  C15  C16   aromatic  1.387  0.020  1.387
 PY9  C15  H15   single    0.930  0.020  1.080
 PY9  C12  C17   aromatic  1.399  0.020  1.399
 PY9  C17  C16   aromatic  1.394  0.020  1.394
 PY9  C17  C18   single    1.503  0.020  1.503
 PY9  C14  H14   single    0.930  0.020  1.080
 PY9  C1   C2    aromatic  1.399  0.020  1.399
 PY9  C3   C2    aromatic  1.377  0.020  1.377
 PY9  C2   H2    single    0.930  0.020  1.080
 PY9  C16  H16   single    0.930  0.020  1.080
 PY9  C3   H3    single    0.930  0.020  1.080
 PY9  C9   H9    single    0.970  0.020  1.090
 PY9  C9   H9A   single    0.970  0.020  1.090
 PY9  C11  H11   single    0.970  0.020  1.090
 PY9  C11  H11A  single    0.970  0.020  1.090
 PY9  C18  H18   single    0.970  0.020  1.090
 PY9  C18  H18A  single    0.970  0.020  1.090
 PY9  C18  H18B  single    0.970  0.020  1.090
 PY9  O2   HO2   single    0.850  0.020  0.980
 PY9  O1   HO1   single    0.850  0.020  0.980

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
 PY9  C11   N1   C8    111.69  3.000
 PY9  C8    N1   C7    118.29  3.000
 PY9  C11   N1   C7    127.28  3.000
 PY9  O2    C4   C3    117.49  3.000
 PY9  C3    C4   C5    120.20  3.000
 PY9  O2    C4   C5    122.30  3.000
 PY9  H5    C5   C6    118.92  3.000
 PY9  H5    C5   C4    120.74  3.000
 PY9  C6    C5   C4    120.32  3.000
 PY9  O1    C6   C1    122.06  3.000
 PY9  C1    C6   C5    120.24  3.000
 PY9  O1    C6   C5    117.70  3.000
 PY9  O3    C7   C1    119.31  3.000
 PY9  C1    C7   N1    121.00  3.000
 PY9  O3    C7   N1    119.69  3.000
 PY9  H8    C8   C9    108.93  3.000
 PY9  H8    C8   C12   109.82  3.000
 PY9  C9    C8   C12   113.48  3.000
 PY9  H8    C8   N1    108.37  3.000
 PY9  C9    C8   N1    103.24  3.000
 PY9  C12   C8   N1    112.71  3.000
 PY9  H10A  C10  H10   108.23  3.000
 PY9  H10A  C10  C11   111.94  3.000
 PY9  H10   C10  C11   110.18  3.000
 PY9  H10A  C10  C9    113.29  3.000
 PY9  H10   C10  C9    110.79  3.000
 PY9  C11   C10  C9    102.34  3.000
 PY9  H13   C13  C12   119.54  3.000
 PY9  H13   C13  C14   119.21  3.000
 PY9  C12   C13  C14   121.25  3.000
 PY9  H15   C15  C16   120.08  3.000
 PY9  H15   C15  C14   120.40  3.000
 PY9  C16   C15  C14   119.53  3.000
 PY9  C18   C17  C12   121.65  3.000
 PY9  C18   C17  C16   119.69  3.000
 PY9  C12   C17  C16   118.66  3.000
 PY9  H14   C14  C15   120.47  3.000
 PY9  H14   C14  C13   120.04  3.000
 PY9  C15   C14  C13   119.49  3.000
 PY9  H2    C2   C1    120.00  3.000
 PY9  H2    C2   C3    117.58  3.000
 PY9  C1    C2   C3    122.40  3.000
 PY9  H16   C16  C17   118.95  3.000
 PY9  H16   C16  C15   119.49  3.000
 PY9  C17   C16  C15   121.56  3.000
 PY9  H3    C3   C2    120.67  3.000
 PY9  H3    C3   C4    120.28  3.000
 PY9  C2    C3   C4    119.05  3.000
 PY9  C2    C1   C7    124.10  3.000
 PY9  C2    C1   C6    117.62  3.000
 PY9  C7    C1   C6    118.14  3.000
 PY9  C17   C12  C13   119.52  3.000
 PY9  C17   C12  C8    121.05  3.000
 PY9  C13   C12  C8    119.40  3.000
 PY9  H9A   C9   H9    107.66  3.000
 PY9  H9A   C9   C10   110.18  3.000
 PY9  H9    C9   C10   113.84  3.000
 PY9  H9A   C9   C8    110.43  3.000
 PY9  H9    C9   C8    111.37  3.000
 PY9  C10   C9   C8    103.36  3.000
 PY9  H11A  C11  H11   108.25  3.000
 PY9  H11A  C11  C10   113.05  3.000
 PY9  H11   C11  C10   110.13  3.000
 PY9  H11A  C11  N1    111.14  3.000
 PY9  H11   C11  N1    111.22  3.000
 PY9  C10   C11  N1    103.03  3.000
 PY9  H18B  C18  H18A  107.69  3.000
 PY9  H18B  C18  H18   107.42  3.000
 PY9  H18A  C18  H18   107.07  3.000
 PY9  H18B  C18  C17   110.91  3.000
 PY9  H18A  C18  C17   111.33  3.000
 PY9  H18   C18  C17   112.18  3.000
 PY9  HO1   O1   C6    106.13  3.000
 PY9  HO2   O2   C4    110.82  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
 PY9  CONST_01  C1   C6   C5   C4      0.00   0.0  0
 PY9  CONST_02  C1   C2   C3   C4      0.00   0.0  0
 PY9  CONST_03  C2   C3   C4   C5      0.00   0.0  0
 PY9  CONST_04  C2   C1   C6   C5      0.00   0.0  0
 PY9  CONST_05  C3   C4   C5   C6      0.00   0.0  0
 PY9  CONST_06  C3   C2   C1   C6      0.00   0.0  0
 PY9  CONST_07  C16  C17  C12  C13     0.00   0.0  0
 PY9  CONST_08  C16  C15  C14  C13     0.00   0.0  0
 PY9  CONST_09  C12  C13  C14  C15     0.00   0.0  0
 PY9  CONST_10  C12  C17  C16  C15     0.00   0.0  0
 PY9  CONST_11  C14  C13  C12  C17     0.00   0.0  0
 PY9  CONST_12  C14  C15  C16  C17     0.00   0.0  0
 PY9  CONST_13  C14  C13  C12  C8    180.00   0.0  0
 PY9  CONST_14  C16  C17  C12  C8    180.00   0.0  0
 PY9  CONST_15  O1   C6   C5   C4    180.00   0.0  0
 PY9  CONST_16  C7   C1   C6   C5    180.00   0.0  0
 PY9  CONST_17  O2   C4   C5   C6    180.00   0.0  0
 PY9  CONST_18  C3   C2   C1   C7    180.00   0.0  0
 PY9  CONST_19  C18  C17  C12  C8      0.00   0.0  0
 PY9  CONST_20  C18  C17  C12  C13   180.00   0.0  0
 PY9  CONST_21  C18  C17  C16  C15   180.00   0.0  0
 PY9  CONST_22  O1   C6   C1   C2    180.00   0.0  0
 PY9  CONST_23  O2   C4   C3   C2    180.00   0.0  0
 PY9  CONST_24  C1   C7   N1   C8    180.00   0.0  0
 PY9  CONST_26  H2   C2   C3   C4    180.00   0.0  0
 PY9  CONST_27  H3   C3   C4   C5    180.00   0.0  0
 PY9  CONST_28  H13  C13  C12  C8      0.00   0.0  0
 PY9  CONST_29  H15  C15  C14  C13   180.00   0.0  0
 PY9  CONST_30  H16  C16  C15  C14   180.00   0.0  0
 PY9  CONST_31  H14  C14  C15  C16   180.00   0.0  0
 PY9  CONST_32  H5   C5   C4   C3    180.00   0.0  0
 PY9  CONST_33  O3   C7   N1   C8      0.00   0.0  0
 PY9  Var_01    C9   C10  C11  N1     35.58  30.0  1
 PY9  Var_02    C10  C11  N1   C8    -18.10  30.0  1
 PY9  Var_03    C11  C10  C9   C8    -40.26  30.0  1
 PY9  Var_04    C6   C1   C7   N1   -159.27  30.0  3
 PY9  Var_05    H18  C18  C17  C16   119.62  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
 PY9  chir_01  C8  N1  C12  C9  negativ

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
 PY9  plan-1  C4   0.020
 PY9  plan-1  C5   0.020
 PY9  plan-1  C6   0.020
 PY9  plan-1  C7   0.020
 PY9  plan-1  C2   0.020
 PY9  plan-1  C3   0.020
 PY9  plan-1  C1   0.020
 PY9  plan-1  O1   0.020
 PY9  plan-1  H5   0.020
 PY9  plan-1  H2   0.020
 PY9  plan-1  H3   0.020
 PY9  plan-1  O2   0.020
 PY9  plan-2  C8   0.020
 PY9  plan-2  C13  0.020
 PY9  plan-2  C15  0.020
 PY9  plan-2  C17  0.020
 PY9  plan-2  C14  0.020
 PY9  plan-2  C16  0.020
 PY9  plan-2  C12  0.020
 PY9  plan-2  C18  0.020
 PY9  plan-2  H13  0.020
 PY9  plan-2  H15  0.020
 PY9  plan-2  H14  0.020
 PY9  plan-2  H16  0.020
 PY9  plan-3  N1   0.020
 PY9  plan-3  C7   0.020
 PY9  plan-3  C8   0.020
 PY9  plan-3  C1   0.020
 PY9  plan-3  C11  0.020
 PY9  plan-3  O3   0.020

