# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Nov 23 18:21:27 2022
#   Inital geometry file: a 114 line input string
#   Ligand name: 4-(fluoromethyl)-3-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(CNc2cc(ccc2CF)C(O)=O)c1O
#
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
 YCD  YCD  "(4~{R})-4-(fluoranylmethyl)-3-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]cyclohexene-1-carboxylic acid"  ligand  45  27  .  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_YCD
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
 YCD  C10  C  CR16  0  -0.285  -6.7725  -62.4616  -24.6304
 YCD  C11  C  CR16  0  -0.259  -7.3496  -61.2247  -24.4057
 YCD  C12  C  CR6   0   0.272  -1.7374  -60.3688  -28.3280
 YCD  C13  C  CR6   0   0.139  -0.6805  -60.2427  -29.2428
 YCD  C15  C  CR16  0  -0.140   0.7911  -61.0891  -27.7101
 YCD  C16  C  CR6   0  -0.024  -0.1803  -61.2371  -26.7334
 YCD  C17  C  CR6   0   0.035  -1.4881  -60.8570  -27.0452
 YCD  C20  C  CH3   0  -0.720  -0.9285  -59.6872  -30.6107
 YCD  C21  C  CH2   0  -0.090  -5.0062  -63.9636  -25.5401
 YCD  O33  O  O     0  -0.686  -0.7796  -65.2995  -24.1166
 YCD  O34  O  OH1   0  -0.741   0.8893  -63.5659  -23.0570
 YCD  O35  O  OH1   0  -0.744  -1.4273  -63.0219  -22.9763
 YCD  C01  C  CR16  0  -0.296  -5.5654  -60.2105  -25.6590
 YCD  C02  C  CR6   0  -0.084  -6.7336  -60.0867  -24.9183
 YCD  C03  C  C     0   0.533  -7.2913  -58.7226  -24.7216
 YCD  C06  C  CR6   0   0.346  -4.9841  -61.4526  -25.8851
 YCD  C08  C  CR6   0  -0.013  -5.5935  -62.5991  -25.3563
 YCD  C09  C  CH2   0  -0.357  -2.6164  -60.9058  -26.0501
 YCD  F30  F  F     0  -0.372  -3.7308  -64.0254  -24.9626
 YCD  N07  N  NH1   0  -0.758  -3.8077  -61.5071  -26.6614
 YCD  N14  N  N     0  -0.406   0.5528  -60.5984  -28.9198
 YCD  O04  O  O     0  -0.425  -6.7666  -57.7182  -25.1354
 YCD  O05  O  OH1   0  -0.591  -8.4300  -58.7263  -24.0434
 YCD  O19  O  OH1   0  -0.637  -2.9626  -59.9899  -28.7235
 YCD  O31  O  O2    0  -0.582  -0.3061  -63.1256  -25.2891
 YCD  P32  P  P     0   1.462  -0.4372  -63.8856  -23.8854
 YCD  H1   H  HCR6  0   0.270  -7.2453  -63.3463  -24.2221
 YCD  H3   H  HCR6  0   0.269  -8.2624  -61.1609  -23.8313
 YCD  H5   H  HCR6  0   0.256   1.8157  -61.3792  -27.4998
 YCD  H6   H  HCH2  0   0.270   1.2985  -61.8155  -25.3143
 YCD  H7   H  HCH2  0   0.255  -0.1641  -61.1611  -24.5839
 YCD  H8   H  HCH3  0   0.247  -0.0046  -59.6863  -31.1849
 YCD  H9   H  HCH3  0   0.247  -1.6721  -60.2727  -31.1538
 YCD  H10  H  HCH3  0   0.247  -1.3036  -58.6630  -30.5651
 YCD  H11  H  HCH2  0   0.235  -4.8978  -64.2299  -26.5931
 YCD  H12  H  HCH2  0   0.250  -5.6289  -64.7175  -25.0599
 YCD  H13  H  HOH1  0   0.500   1.6649  -64.0671  -23.3446
 YCD  H14  H  HOH1  0   0.492  -2.3619  -63.1432  -23.1951
 YCD  H15  H  HCR6  0   0.275  -5.1057  -59.3281  -26.0860
 YCD  H18  H  HCH2  0   0.264  -2.3347  -61.4342  -25.1399
 YCD  H19  H  HCH2  0   0.286  -2.8622  -59.8835  -25.7535
 YCD  H20  H  HNH1  0   0.395  -3.5885  -62.4470  -26.9658
 YCD  H22  H  HOH1  0   0.487  -8.7544  -57.8195  -23.9345
 YCD  H23  H  HOH1  0   0.483  -3.6142  -60.4286  -28.1288
 YCD  C18  C  CH2   0  -0.304   0.2100  -61.7891  -25.3962

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
 YCD  C20  C13  single    1.497  0.020  1.497
 YCD  C13  N14  aromatic  1.324  0.020  1.324
 YCD  C13  C12  aromatic  1.403  0.020  1.403
 YCD  N14  C15  aromatic  1.327  0.020  1.327
 YCD  O19  C12  single    1.342  0.020  1.342
 YCD  C12  C17  aromatic  1.395  0.020  1.395
 YCD  C15  C16  aromatic  1.385  0.020  1.385
 YCD  C17  C16  aromatic  1.397  0.020  1.397
 YCD  C17  C09  single    1.505  0.020  1.505
 YCD  O04  C03  double    1.206  0.020  1.206
 YCD  C16  C18  single    1.498  0.020  1.498
 YCD  N07  C06  single    1.410  0.020  1.410
 YCD  N07  C09  single    1.468  0.020  1.468
 YCD  C01  C06  aromatic  1.390  0.020  1.390
 YCD  C01  C02  aromatic  1.389  0.020  1.389
 YCD  C06  C08  aromatic  1.402  0.020  1.402
 YCD  C03  C02  single    1.487  0.020  1.487
 YCD  C03  O05  single    1.325  0.020  1.325
 YCD  O31  C18  single    1.437  0.020  1.437
 YCD  O31  P32  single    1.602  0.020  1.602
 YCD  F30  C21  single    1.401  0.020  1.401
 YCD  C02  C11  aromatic  1.392  0.020  1.392
 YCD  C08  C21  single    1.497  0.020  1.497
 YCD  C08  C10  aromatic  1.391  0.020  1.391
 YCD  O33  P32  double    1.473  0.020  1.473
 YCD  P32  O35  single    1.598  0.020  1.598
 YCD  P32  O34  single    1.596  0.020  1.596
 YCD  C11  C10  aromatic  1.383  0.020  1.383
 YCD  C10  H1   single    0.930  0.020  1.080
 YCD  C11  H3   single    0.930  0.020  1.080
 YCD  C15  H5   single    0.930  0.020  1.080
 YCD  C18  H6   single    0.970  0.020  1.090
 YCD  C18  H7   single    0.970  0.020  1.090
 YCD  C20  H8   single    0.970  0.020  1.090
 YCD  C20  H9   single    0.970  0.020  1.090
 YCD  C20  H10  single    0.970  0.020  1.090
 YCD  C21  H11  single    0.970  0.020  1.090
 YCD  C21  H12  single    0.970  0.020  1.090
 YCD  O34  H13  single    0.850  0.020  0.980
 YCD  O35  H14  single    0.850  0.020  0.980
 YCD  C01  H15  single    0.930  0.020  1.080
 YCD  C09  H18  single    0.970  0.020  1.090
 YCD  C09  H19  single    0.970  0.020  1.090
 YCD  N07  H20  single    0.890  0.020  1.040
 YCD  O05  H22  single    0.850  0.020  0.980
 YCD  O19  H23  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
 YCD  H1   C10  C08  119.07  3.000
 YCD  H1   C10  C11  119.15  3.000
 YCD  C08  C10  C11  121.78  3.000
 YCD  H3   C11  C02  121.43  3.000
 YCD  H3   C11  C10  119.44  3.000
 YCD  C02  C11  C10  119.12  3.000
 YCD  O19  C12  C17  122.20  3.000
 YCD  C17  C12  C13  119.75  3.000
 YCD  O19  C12  C13  118.04  3.000
 YCD  N14  C13  C20  118.49  3.000
 YCD  N14  C13  C12  121.23  3.000
 YCD  C20  C13  C12  120.28  3.000
 YCD  H5   C15  N14  116.42  3.000
 YCD  H5   C15  C16  119.78  3.000
 YCD  N14  C15  C16  123.80  3.000
 YCD  C18  C16  C17  122.90  3.000
 YCD  C18  C16  C15  119.07  3.000
 YCD  C17  C16  C15  118.03  3.000
 YCD  C09  C17  C16  123.05  3.000
 YCD  C09  C17  C12  119.04  3.000
 YCD  C16  C17  C12  117.88  3.000
 YCD  H10  C20  H9   106.86  3.000
 YCD  H10  C20  H8   108.25  3.000
 YCD  H9   C20  H8   108.45  3.000
 YCD  H10  C20  C13  111.52  3.000
 YCD  H9   C20  C13  111.62  3.000
 YCD  H8   C20  C13  110.00  3.000
 YCD  H12  C21  H11  108.25  3.000
 YCD  H12  C21  F30  107.94  3.000
 YCD  H11  C21  F30  107.24  3.000
 YCD  H12  C21  C08  110.64  3.000
 YCD  H11  C21  C08  112.32  3.000
 YCD  F30  C21  C08  110.28  3.000
 YCD  H13  O34  P32  114.10  3.000
 YCD  H14  O35  P32  113.72  3.000
 YCD  H15  C01  C06  119.11  3.000
 YCD  H15  C01  C02  119.66  3.000
 YCD  C06  C01  C02  121.22  3.000
 YCD  C03  C02  C01  117.90  3.000
 YCD  C03  C02  C11  122.37  3.000
 YCD  C01  C02  C11  119.72  3.000
 YCD  O05  C03  O04  123.47  3.000
 YCD  O05  C03  C02  112.80  3.000
 YCD  O04  C03  C02  123.73  3.000
 YCD  N07  C06  C08  122.58  3.000
 YCD  C08  C06  C01  119.18  3.000
 YCD  N07  C06  C01  118.22  3.000
 YCD  C06  C08  C21  121.91  3.000
 YCD  C21  C08  C10  119.12  3.000
 YCD  C06  C08  C10  118.97  3.000
 YCD  H19  C09  H18  106.57  3.000
 YCD  H19  C09  N07  108.29  3.000
 YCD  H18  C09  N07  111.05  3.000
 YCD  H19  C09  C17  108.53  3.000
 YCD  H18  C09  C17  111.98  3.000
 YCD  N07  C09  C17  110.26  3.000
 YCD  H20  N07  C09  109.27  3.000
 YCD  H20  N07  C06  112.46  3.000
 YCD  C09  N07  C06  115.59  3.000
 YCD  C15  N14  C13  119.29  3.000
 YCD  H22  O05  C03  110.03  3.000
 YCD  H23  O19  C12  107.47  3.000
 YCD  P32  O31  C18  122.42  3.000
 YCD  O31  P32  O35  107.03  3.000
 YCD  O35  P32  O34   96.40  3.000
 YCD  O31  P32  O34  106.96  3.000
 YCD  O34  P32  O33  117.83  3.000
 YCD  O35  P32  O33  117.66  3.000
 YCD  O31  P32  O33  109.69  3.000
 YCD  H7   C18  H6   107.43  3.000
 YCD  H7   C18  O31  110.87  3.000
 YCD  H6   C18  O31  109.27  3.000
 YCD  H7   C18  C16  111.25  3.000
 YCD  H6   C18  C16  109.60  3.000
 YCD  O31  C18  C16  108.40  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
 YCD  CONST_01  C01  C06  C08  C10     0.00   0.0  0
 YCD  CONST_02  C01  C02  C11  C10     0.00   0.0  0
 YCD  CONST_03  C06  C01  C02  C11     0.00   0.0  0
 YCD  CONST_04  C06  C08  C10  C11     0.00   0.0  0
 YCD  CONST_05  C15  N14  C13  C12     0.00   0.0  0
 YCD  CONST_06  C15  C16  C17  C12     0.00   0.0  0
 YCD  CONST_07  C16  C15  N14  C13     0.00   0.0  0
 YCD  CONST_08  C16  C17  C12  C13     0.00   0.0  0
 YCD  CONST_09  N14  C13  C12  C17     0.00   0.0  0
 YCD  CONST_10  N14  C15  C16  C17     0.00   0.0  0
 YCD  CONST_11  C08  C06  C01  C02     0.00   0.0  0
 YCD  CONST_12  C08  C10  C11  C02     0.00   0.0  0
 YCD  CONST_13  N07  C06  C08  C10   180.00   0.0  0
 YCD  CONST_14  C03  C02  C11  C10   180.00   0.0  0
 YCD  CONST_15  C21  C08  C10  C11   180.00   0.0  0
 YCD  CONST_16  C18  C16  C17  C12   180.00   0.0  0
 YCD  CONST_17  C09  C17  C12  C13   180.00   0.0  0
 YCD  CONST_18  C20  C13  N14  C15   180.00   0.0  0
 YCD  CONST_19  C09  C17  C16  C15   180.00   0.0  0
 YCD  CONST_20  O19  C12  C17  C16   180.00   0.0  0
 YCD  CONST_21  C20  C13  C12  C17   180.00   0.0  0
 YCD  CONST_22  N14  C15  C16  C18   180.00   0.0  0
 YCD  CONST_23  C01  C06  C08  C21   180.00   0.0  0
 YCD  CONST_24  N07  C06  C01  C02   180.00   0.0  0
 YCD  CONST_25  C06  C01  C02  C03   180.00   0.0  0
 YCD  CONST_26  O19  C12  C13  N14   180.00   0.0  0
 YCD  CONST_27  H15  C01  C02  C11   180.00   0.0  0
 YCD  CONST_28  H5   C15  N14  C13   180.00   0.0  0
 YCD  CONST_29  H5   C15  C16  C17   180.00   0.0  0
 YCD  CONST_30  H3   C11  C02  C01   180.00   0.0  0
 YCD  CONST_31  H1   C10  C11  C02   180.00   0.0  0
 YCD  CONST_32  H1   C10  C08  C06   180.00   0.0  0
 YCD  CONST_33  H15  C01  C06  C08   180.00   0.0  0
 YCD  CONST_34  H3   C11  C10  C08   180.00   0.0  0
 YCD  CONST_37  H20  N07  C06  C01   180.00   0.0  0
 YCD  CONST_38  H20  N07  C06  C08     0.00   0.0  0
 YCD  CONST_39  H22  O05  C03  C02   180.00   0.0  0
 YCD  CONST_40  H22  O05  C03  O04     0.00   0.0  0
 YCD  Var_01    F30  C21  C08  C10  -118.57  30.0  2
 YCD  Var_02    O04  C03  C02  C11   178.72  30.0  3
 YCD  Var_03    O05  C03  C02  C11    -1.38  30.0  3
 YCD  Var_04    N07  C09  C17  C12    47.63  30.0  2
 YCD  Var_05    O31  C18  C16  C15  -107.58  30.0  2
 YCD  Var_06    N07  C09  C17  C16  -134.62  30.0  2
 YCD  Var_07    O31  C18  C16  C17    72.62  30.0  2
 YCD  Var_08    C06  N07  C09  C17  -172.16  30.0  1
 YCD  Var_09    O04  C03  C02  C01    -2.21  30.0  3
 YCD  Var_10    O05  C03  C02  C01   177.70  30.0  3
 YCD  Var_11    F30  C21  C08  C06    60.89  30.0  2
 YCD  Var_12    H11  C21  C08  C10   121.87  30.0  2
 YCD  Var_13    H12  C21  C08  C10     0.78  30.0  2
 YCD  Var_14    H8   C20  C13  C12  -178.66  30.0  2
 YCD  Var_15    H9   C20  C13  C12   -58.22  30.0  2
 YCD  Var_16    H10  C20  C13  C12    61.22  30.0  2
 YCD  Var_17    H18  C09  C17  C12   171.81  30.0  2
 YCD  Var_18    H19  C09  C17  C12   -70.83  30.0  2
 YCD  Var_19    H6   C18  C16  C15    11.61  30.0  2
 YCD  Var_20    H7   C18  C16  C15   130.27  30.0  2
 YCD  Var_21    H18  C09  C17  C16   -10.45  30.0  2
 YCD  Var_22    H19  C09  C17  C16   106.92  30.0  2
 YCD  Var_23    H6   C18  C16  C17  -168.20  30.0  2
 YCD  Var_24    H7   C18  C16  C17   -49.53  30.0  2
 YCD  Var_25    H11  C21  C08  C06   -58.67  30.0  2
 YCD  Var_26    H12  C21  C08  C06  -179.76  30.0  2
 YCD  Var_27    H8   C20  C13  N14     1.86  30.0  2
 YCD  Var_28    H9   C20  C13  N14   122.29  30.0  2
 YCD  Var_29    H10  C20  C13  N14  -118.26  30.0  2
 YCD  Var_30    P32  O31  C18  C16  -163.10  30.0  1
 YCD  Var_31    H20  N07  C09  C17    59.81  30.0  1
 YCD  Var_32    H18  C09  N07  C06    63.13  30.0  3
 YCD  Var_33    H19  C09  N07  C06   -53.55  30.0  3
 YCD  Var_34    O33  P32  O31  C18  -170.60  30.0  3
 YCD  Var_35    O35  P32  O31  C18    60.70  30.0  3
 YCD  Var_36    O34  P32  O31  C18   -41.73  30.0  3
 YCD  Var_37    H6   C18  O31  P32    77.50  30.0  3
 YCD  Var_38    H7   C18  O31  P32   -40.72  30.0  3

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
 YCD  plan-1  C12  0.020
 YCD  plan-1  C13  0.020
 YCD  plan-1  C15  0.020
 YCD  plan-1  C16  0.020
 YCD  plan-1  C17  0.020
 YCD  plan-1  C20  0.020
 YCD  plan-1  C09  0.020
 YCD  plan-1  N14  0.020
 YCD  plan-1  O19  0.020
 YCD  plan-1  H5   0.020
 YCD  plan-1  C18  0.020
 YCD  plan-2  C10  0.020
 YCD  plan-2  C11  0.020
 YCD  plan-2  C21  0.020
 YCD  plan-2  C01  0.020
 YCD  plan-2  C02  0.020
 YCD  plan-2  C03  0.020
 YCD  plan-2  C06  0.020
 YCD  plan-2  C08  0.020
 YCD  plan-2  N07  0.020
 YCD  plan-2  H1   0.020
 YCD  plan-2  H3   0.020
 YCD  plan-2  H15  0.020
 YCD  plan-3  C06  0.020
 YCD  plan-3  C09  0.020
 YCD  plan-3  N07  0.020
 YCD  plan-3  H20  0.020
 YCD  plan-4  C02  0.020
 YCD  plan-4  C03  0.020
 YCD  plan-4  O04  0.020
 YCD  plan-4  O05  0.020
 YCD  plan-4  H22  0.020

