# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Nov 24 08:05:13 2022
#   Inital geometry file: a 120 line input string
#   Ligand name: (1R,3R,4S)-3-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]-4-methylcyclohexane-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1CC[C@H](C[C@H]1NCc2c(O)c(C)ncc2CO[P](O)(O)=O)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
 Y8P  Y8P  "(3~{S},4~{S})-4-methyl-3-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]cyclohexene-1-carboxylic acid"  ligand  51  26  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_Y8P
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
 Y8P  C18  C  CH2   0  -0.283  -2.0100  -54.4939  -77.7218
 Y8P  C17  C  CR6   0   0.128  -2.0770  -52.2266  -76.5932
 Y8P  C16  C  CR6   0  -0.028  -2.2638  -53.6093  -76.5434
 Y8P  C13  C  CR6   0   0.127  -2.6808  -52.1814  -74.2466
 Y8P  C12  C  CR6   0   0.263  -2.2832  -51.5135  -75.4128
 Y8P  C11  C  CH2   0  -0.415  -1.1963  -48.0579  -79.8455
 Y8P  C01  C  CH2   0  -0.411   0.2803  -48.8460  -77.9674
 Y8P  C02  C  CH1   0  -0.405  -1.0189  -48.1056  -78.3335
 Y8P  C03  C  C     0   0.565  -0.9898  -46.7255  -77.7255
 Y8P  C06  C  CH1   0  -0.095   0.4299  -50.2383  -78.5966
 Y8P  C08  C  CH1   0  -0.228   0.1323  -50.1887  -80.1095
 Y8P  O40  O  O2    0  -0.585  -0.5836  -54.5879  -77.8844
 Y8P  O42  O  O     0  -0.703  -0.6183  -55.2033  -80.4151
 Y8P  O43  O  OH1   0  -0.732   0.0033  -56.8980  -78.5291
 Y8P  O44  O  OH1   0  -0.730   1.5788  -55.0422  -78.9978
 Y8P  P41  P  P     0   1.460   0.0321  -55.4122  -79.1069
 Y8P  C10  C  CH2   0  -0.434  -1.1691  -49.4601  -80.4426
 Y8P  C15  C  CR16  0  -0.134  -2.6561  -54.1848  -75.3436
 Y8P  C20  C  CH3   0  -0.781  -2.9139  -51.4270  -72.9720
 Y8P  C21  C  CH3   0  -0.679   0.2113  -51.5630  -80.7587
 Y8P  N07  N  NH1   0  -0.599  -0.2007  -51.2861  -77.7997
 Y8P  N14  N  N     0  -0.407  -2.8634  -53.4948  -74.2335
 Y8P  O04  O  OH1   0  -0.595  -1.2000  -46.7557  -76.4111
 Y8P  O05  O  O     0  -0.435  -0.7827  -45.7016  -78.3284
 Y8P  O19  O  OH1   0  -0.616  -2.0956  -50.1807  -75.4466
 Y8P  H1   H  HCH2  0   0.258  -2.4636  -54.1005  -78.6333
 Y8P  H2   H  HCH2  0   0.266  -2.4306  -55.4859  -77.5405
 Y8P  H4   H  HCH2  0   0.237  -2.1336  -47.5591  -80.1023
 Y8P  H5   H  HCH2  0   0.231   1.1195  -48.2357  -78.3169
 Y8P  H6   H  HCH1  0   0.238   1.4954  -50.4759  -78.5120
 Y8P  H7   H  HCH1  0   0.217   0.9393  -49.5790  -80.5382
 Y8P  H10  H  HOH1  0   0.498   0.0820  -57.5898  -79.2001
 Y8P  H11  H  HOH1  0   0.501   1.8387  -54.2547  -79.4952
 Y8P  H12  H  HCH2  0   0.222  -2.0369  -50.0301  -80.0986
 Y8P  H13  H  HCH2  0   0.232  -1.2704  -49.3893  -81.5291
 Y8P  H14  H  HCR6  0   0.255  -2.8099  -55.2578  -75.2840
 Y8P  H15  H  HCH3  0   0.270  -3.2095  -52.1151  -72.1839
 Y8P  H16  H  HCH3  0   0.258  -2.0154  -50.9024  -72.6373
 Y8P  H17  H  HCH3  0   0.256  -3.7072  -50.6819  -73.0764
 Y8P  H18  H  HCH3  0   0.225   1.1629  -52.0508  -80.5373
 Y8P  H19  H  HCH3  0   0.222  -0.5865  -52.2238  -80.4182
 Y8P  H20  H  HCH3  0   0.229   0.1285  -51.4839  -81.8438
 Y8P  H21  H  HNH1  0   0.352   0.2605  -52.1657  -77.9865
 Y8P  H23  H  HOH1  0   0.475  -1.1384  -45.8594  -76.0474
 Y8P  H24  H  HOH1  0   0.485  -2.3247  -49.7650  -74.6080
 Y8P  H22  H  HCH2  0   0.242   0.3825  -48.9402  -76.8856
 Y8P  H25  H  HCH1  0   0.270  -1.8684  -48.6290  -77.8876
 Y8P  C09  C  CH2   0  -0.400  -1.6379  -51.4976  -77.8386
 Y8P  H3   H  HCH2  0   0.219  -0.3905  -47.4651  -80.2879
 Y8P  H8   H  HCH2  0   0.264  -2.1513  -50.5404  -77.8687
 Y8P  H9   H  HCH2  0   0.232  -1.9827  -52.0390  -78.7274

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
 Y8P  C10  C11  single    1.524  0.020  1.524
 Y8P  C10  C08  single    1.528  0.020  1.528
 Y8P  C11  C02  single    1.523  0.020  1.523
 Y8P  O42  P41  double    1.476  0.020  1.476
 Y8P  O05  C03  double    1.206  0.020  1.206
 Y8P  O43  P41  single    1.594  0.020  1.594
 Y8P  O44  P41  single    1.594  0.020  1.594
 Y8P  P41  O40  single    1.598  0.020  1.598
 Y8P  C21  C08  single    1.522  0.020  1.522
 Y8P  C08  C06  single    1.543  0.020  1.543
 Y8P  C02  C03  single    1.508  0.020  1.508
 Y8P  C02  C01  single    1.540  0.020  1.540
 Y8P  C03  O04  single    1.331  0.020  1.331
 Y8P  C06  C01  single    1.535  0.020  1.535
 Y8P  C06  N07  single    1.460  0.020  1.460
 Y8P  O40  C18  single    1.439  0.020  1.439
 Y8P  C18  C16  single    1.495  0.020  1.495
 Y8P  C09  N07  single    1.453  0.020  1.453
 Y8P  C09  C17  single    1.508  0.020  1.508
 Y8P  C16  C17  aromatic  1.396  0.020  1.396
 Y8P  C16  C15  aromatic  1.387  0.020  1.387
 Y8P  C17  C12  aromatic  1.394  0.020  1.394
 Y8P  C15  N14  aromatic  1.323  0.020  1.323
 Y8P  C12  O19  single    1.346  0.020  1.346
 Y8P  C12  C13  aromatic  1.401  0.020  1.401
 Y8P  N14  C13  aromatic  1.326  0.020  1.326
 Y8P  C13  C20  single    1.499  0.020  1.499
 Y8P  C18  H1   single    0.970  0.020  1.090
 Y8P  C18  H2   single    0.970  0.020  1.090
 Y8P  C11  H3   single    0.970  0.020  1.090
 Y8P  C11  H4   single    0.970  0.020  1.090
 Y8P  C01  H5   single    0.970  0.020  1.090
 Y8P  C06  H6   single    0.970  0.020  1.090
 Y8P  C08  H7   single    0.970  0.020  1.090
 Y8P  C09  H8   single    0.970  0.020  1.090
 Y8P  C09  H9   single    0.970  0.020  1.090
 Y8P  O43  H10  single    0.850  0.020  0.980
 Y8P  O44  H11  single    0.850  0.020  0.980
 Y8P  C10  H12  single    0.970  0.020  1.090
 Y8P  C10  H13  single    0.970  0.020  1.090
 Y8P  C15  H14  single    0.930  0.020  1.080
 Y8P  C20  H15  single    0.970  0.020  1.090
 Y8P  C20  H16  single    0.970  0.020  1.090
 Y8P  C20  H17  single    0.970  0.020  1.090
 Y8P  C21  H18  single    0.970  0.020  1.090
 Y8P  C21  H19  single    0.970  0.020  1.090
 Y8P  C21  H20  single    0.970  0.020  1.090
 Y8P  N07  H21  single    0.890  0.020  1.040
 Y8P  O04  H23  single    0.850  0.020  0.980
 Y8P  O19  H24  single    0.850  0.020  0.980
 Y8P  C01  H22  single    0.970  0.020  1.090
 Y8P  C02  H25  single    0.970  0.020  1.090

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
 Y8P  H2   C18  H1   107.81  3.000
 Y8P  H2   C18  O40  109.94  3.000
 Y8P  H1   C18  O40  109.95  3.000
 Y8P  H2   C18  C16  109.94  3.000
 Y8P  H1   C18  C16  111.99  3.000
 Y8P  O40  C18  C16  107.22  3.000
 Y8P  C09  C17  C12  119.66  3.000
 Y8P  C12  C17  C16  117.16  3.000
 Y8P  C09  C17  C16  123.17  3.000
 Y8P  C15  C16  C17  118.66  3.000
 Y8P  C15  C16  C18  118.96  3.000
 Y8P  C17  C16  C18  122.35  3.000
 Y8P  N14  C13  C20  117.94  3.000
 Y8P  C20  C13  C12  120.78  3.000
 Y8P  N14  C13  C12  121.28  3.000
 Y8P  O19  C12  C13  122.15  3.000
 Y8P  C13  C12  C17  120.18  3.000
 Y8P  O19  C12  C17  117.67  3.000
 Y8P  H4   C11  H3   106.83  3.000
 Y8P  H4   C11  C10  110.07  3.000
 Y8P  H3   C11  C10  109.08  3.000
 Y8P  H4   C11  C02  110.34  3.000
 Y8P  H3   C11  C02  109.43  3.000
 Y8P  C10  C11  C02  110.98  3.000
 Y8P  H22  C01  H5   107.02  3.000
 Y8P  H22  C01  C06  108.61  3.000
 Y8P  H5   C01  C06  107.46  3.000
 Y8P  H22  C01  C02  110.89  3.000
 Y8P  H5   C01  C02  107.63  3.000
 Y8P  C06  C01  C02  114.90  3.000
 Y8P  H25  C02  C03  106.78  3.000
 Y8P  H25  C02  C01  109.18  3.000
 Y8P  C03  C02  C01  109.14  3.000
 Y8P  H25  C02  C11  109.24  3.000
 Y8P  C01  C02  C11  110.45  3.000
 Y8P  C03  C02  C11  111.95  3.000
 Y8P  O05  C03  O04  122.68  3.000
 Y8P  O04  C03  C02  111.97  3.000
 Y8P  O05  C03  C02  125.34  3.000
 Y8P  H6   C06  N07  102.86  3.000
 Y8P  H6   C06  C08  105.70  3.000
 Y8P  N07  C06  C08  118.37  3.000
 Y8P  H6   C06  C01  105.07  3.000
 Y8P  N07  C06  C01  112.65  3.000
 Y8P  C08  C06  C01  110.73  3.000
 Y8P  H7   C08  C21  107.25  3.000
 Y8P  H7   C08  C10  106.02  3.000
 Y8P  C21  C08  C10  112.44  3.000
 Y8P  H7   C08  C06  105.00  3.000
 Y8P  C21  C08  C06  112.29  3.000
 Y8P  C10  C08  C06  113.17  3.000
 Y8P  P41  O40  C18  120.14  3.000
 Y8P  H10  O43  P41  114.44  3.000
 Y8P  H11  O44  P41  114.50  3.000
 Y8P  O44  P41  O43  102.06  3.000
 Y8P  O44  P41  O42  117.09  3.000
 Y8P  O43  P41  O42  116.44  3.000
 Y8P  O44  P41  O40  101.64  3.000
 Y8P  O43  P41  O40  101.34  3.000
 Y8P  O42  P41  O40  115.81  3.000
 Y8P  H13  C10  H12  105.83  3.000
 Y8P  H13  C10  C08  109.04  3.000
 Y8P  H12  C10  C08  111.02  3.000
 Y8P  H13  C10  C11  109.15  3.000
 Y8P  H12  C10  C11  110.00  3.000
 Y8P  C08  C10  C11  111.61  3.000
 Y8P  H14  C15  N14  116.55  3.000
 Y8P  H14  C15  C16  119.84  3.000
 Y8P  N14  C15  C16  123.61  3.000
 Y8P  H17  C20  H16  107.38  3.000
 Y8P  H17  C20  H15  107.66  3.000
 Y8P  H16  C20  H15  107.78  3.000
 Y8P  H17  C20  C13  111.99  3.000
 Y8P  H16  C20  C13  111.96  3.000
 Y8P  H15  C20  C13  109.88  3.000
 Y8P  H20  C21  H19  107.40  3.000
 Y8P  H20  C21  H18  107.47  3.000
 Y8P  H19  C21  H18  107.67  3.000
 Y8P  H20  C21  C08  110.78  3.000
 Y8P  H19  C21  C08  112.08  3.000
 Y8P  H18  C21  C08  111.23  3.000
 Y8P  H21  N07  C09  108.65  3.000
 Y8P  H21  N07  C06  109.07  3.000
 Y8P  C09  N07  C06  121.14  3.000
 Y8P  C15  N14  C13  119.11  3.000
 Y8P  H23  O04  C03  109.85  3.000
 Y8P  H24  O19  C12  111.84  3.000
 Y8P  H9   C09  H8   105.31  3.000
 Y8P  H9   C09  N07  113.87  3.000
 Y8P  H8   C09  N07  109.86  3.000
 Y8P  H9   C09  C17  109.82  3.000
 Y8P  H8   C09  C17  108.12  3.000
 Y8P  N07  C09  C17  109.64  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
 Y8P  CONST_01  N14  C15  C16  C17     0.00   0.0  0
 Y8P  CONST_02  N14  C13  C12  C17     0.00   0.0  0
 Y8P  CONST_03  C13  C12  C17  C16     0.00   0.0  0
 Y8P  CONST_04  C13  N14  C15  C16     0.00   0.0  0
 Y8P  CONST_05  C15  C16  C17  C12     0.00   0.0  0
 Y8P  CONST_06  C15  N14  C13  C12     0.00   0.0  0
 Y8P  CONST_07  C12  C17  C16  C18   180.00   0.0  0
 Y8P  CONST_08  N14  C15  C16  C18   180.00   0.0  0
 Y8P  CONST_09  C20  C13  C12  C17   180.00   0.0  0
 Y8P  CONST_10  O19  C12  C17  C16   180.00   0.0  0
 Y8P  CONST_11  C09  C17  C12  C13   180.00   0.0  0
 Y8P  CONST_12  C15  C16  C17  C09   180.00   0.0  0
 Y8P  CONST_13  C20  C13  N14  C15   180.00   0.0  0
 Y8P  CONST_14  O19  C12  C13  N14   180.00   0.0  0
 Y8P  CONST_15  H14  C15  C16  C17   180.00   0.0  0
 Y8P  CONST_16  H14  C15  N14  C13   180.00   0.0  0
 Y8P  CONST_17  H23  O04  C03  C02   180.00   0.0  0
 Y8P  CONST_18  H23  O04  C03  O05     0.00   0.0  0
 Y8P  Var_01    C08  C10  C11  C02   -57.82  30.0  1
 Y8P  Var_02    H12  C10  C11  C02    65.88  30.0  1
 Y8P  Var_03    H13  C10  C11  C02  -178.42  30.0  1
 Y8P  Var_04    H3   C11  C10  C08    62.83  30.0  1
 Y8P  Var_05    H4   C11  C10  C08   179.74  30.0  1
 Y8P  Var_06    C06  N07  C09  C17  -158.43  30.0  3
 Y8P  Var_07    O40  C18  C16  C17    73.41  30.0  1
 Y8P  Var_08    N07  C09  C17  C16   -96.67  30.0  3
 Y8P  Var_09    N07  C09  C17  C12    81.77  30.0  3
 Y8P  Var_10    C15  C16  C18  O40  -104.39  30.0  2
 Y8P  Var_11    H1   C18  C16  C17   -47.27  30.0  1
 Y8P  Var_12    H2   C18  C16  C17  -167.10  30.0  1
 Y8P  Var_13    H8   C09  C17  C16   143.56  30.0  3
 Y8P  Var_14    H9   C09  C17  C16    29.15  30.0  3
 Y8P  Var_15    H8   C09  C17  C12   -38.00  30.0  3
 Y8P  Var_16    H9   C09  C17  C12  -152.41  30.0  3
 Y8P  Var_17    H15  C20  C13  C12  -179.72  30.0  2
 Y8P  Var_18    H16  C20  C13  C12   -59.99  30.0  2
 Y8P  Var_19    H17  C20  C13  C12    60.68  30.0  2
 Y8P  Var_20    H1   C18  C16  C15   134.93  30.0  1
 Y8P  Var_21    H2   C18  C16  C15    15.10  30.0  1
 Y8P  Var_22    H15  C20  C13  N14     0.33  30.0  2
 Y8P  Var_23    H16  C20  C13  N14   120.05  30.0  2
 Y8P  Var_24    H17  C20  C13  N14  -119.27  30.0  2
 Y8P  Var_25    P41  O40  C18  C16  -177.15  30.0  2
 Y8P  Var_26    H21  N07  C09  C17    74.22  30.0  3
 Y8P  Var_27    H8   C09  N07  C06   -39.73  30.0  2
 Y8P  Var_28    H9   C09  N07  C06    78.10  30.0  2
 Y8P  Var_29    O42  P41  O40  C18    43.51  30.0  1
 Y8P  Var_30    O43  P41  O40  C18   -83.45  30.0  1
 Y8P  Var_31    O44  P41  O40  C18   171.54  30.0  1
 Y8P  Var_32    H1   C18  O40  P41   -55.18  30.0  3
 Y8P  Var_33    H2   C18  O40  P41    63.36  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
 Y8P  chir_01  C02  C11  C03  C01  positiv
 Y8P  chir_02  C06  N07  C08  C01  negativ
 Y8P  chir_03  C08  C06  C21  C10  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
 Y8P  plan-1  C18  0.020
 Y8P  plan-1  C17  0.020
 Y8P  plan-1  C16  0.020
 Y8P  plan-1  C13  0.020
 Y8P  plan-1  C12  0.020
 Y8P  plan-1  C15  0.020
 Y8P  plan-1  C20  0.020
 Y8P  plan-1  N14  0.020
 Y8P  plan-1  O19  0.020
 Y8P  plan-1  H14  0.020
 Y8P  plan-1  C09  0.020
 Y8P  plan-2  C02  0.020
 Y8P  plan-2  C03  0.020
 Y8P  plan-2  O04  0.020
 Y8P  plan-2  O05  0.020
 Y8P  plan-2  H23  0.020

