# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 24 10:43:21 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: {5-hydroxy-6-methyl-4-[(E)-{[({[2-(trifluoromethyl)phenyl]carbonyl}amino)acetyl]hydrazono}methyl]pyridin-3-yl}methyl dihydrogen phosphate (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(\C=N\NC(=O)CNC(=O)c2ccccc2C(F)(F)F)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
 P3F  P3F  '{5-hydroxy-6-methyl-4-[(E)-{[({[2-(trifluoromethyl)phenyl]carbonyl}amino)acetyl]hydrazono}methyl]pyridin-3-yl}methyl dihydrogen phosphate (non-preferred name)'  ligand  51  33  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_P3F
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
 P3F  O4    O  OH1   0  -0.753   -4.6340  10.8426  47.5723
 P3F  P1    P  P     0   1.456   -5.8907  11.1196  48.5241
 P3F  O2    O  OH1   0  -0.796   -6.9112   9.9973  48.0784
 P3F  O3    O  O     0  -0.713   -6.3929  12.5084  48.5558
 P3F  O1    O  O2    0  -0.586   -5.3008  10.7040  49.9490
 P3F  C5    C  CH2   0  -0.275   -5.0227   9.3444  50.2947
 P3F  C4    C  CR6   0   0.001   -4.7602   9.2930  51.7652
 P3F  C3    C  CR16  0  -0.139   -3.4475   9.1775  52.1852
 P3F  N1    N  N     0  -0.399   -3.0707   9.1430  53.4573
 P3F  C2    C  CR6   0   0.140   -3.9890   9.2200  54.4028
 P3F  C1    C  CH3   0  -0.790   -3.5455   9.1912  55.8336
 P3F  C17   C  CR6   0   0.259   -5.3525   9.3283  54.0843
 P3F  O9    O  OH1   0  -0.615   -6.2901   9.4022  55.0407
 P3F  C6    C  CR6   0   0.060   -5.7633   9.3716  52.7462
 P3F  C7    C  C1    0  -0.068   -7.2011   9.4578  52.4967
 P3F  N2    N  N     0  -0.191   -7.7171   9.6856  51.3541
 P3F  N3    N  NH1   0  -0.499   -9.0657   9.7161  51.3317
 P3F  C8    C  C     0   0.613   -9.7545   9.9784  50.2089
 P3F  O5    O  O     0  -0.496   -9.2569  10.1471  49.1056
 P3F  C9    C  CH2   0  -0.432  -11.2524  10.1057  50.4238
 P3F  N4    N  NH1   0  -0.607  -11.9852   9.8052  49.2316
 P3F  C10   C  C     0   0.467  -11.9519   8.5702  48.7098
 P3F  O6    O  O     0  -0.458  -11.3377   7.6523  49.2254
 P3F  C11   C  CR6   0  -0.012  -12.6743   8.3985  47.4055
 P3F  C16   C  CR6   0  -0.205  -14.0625   8.4466  47.2619
 P3F  C18   C  CT    0   1.062  -14.9562   8.7101  48.4387
 P3F  F2    F  F     0  -0.311  -14.5227   8.0955  49.5466
 P3F  F1    F  F     0  -0.299  -16.2054   8.2896  48.2263
 P3F  F3    F  F     0  -0.313  -15.0353  10.0186  48.7246
 P3F  C12   C  CR16  0  -0.270  -11.8832   8.1351  46.2933
 P3F  C13   C  CR16  0  -0.233  -12.4569   7.9527  45.0449
 P3F  C14   C  CR16  0  -0.238  -13.8343   8.0141  44.9033
 P3F  C15   C  CR16  0  -0.281  -14.6345   8.2541  46.0093
 P3F  HO4   H  HOH1  0   0.496   -4.7432  11.1561  46.6653
 P3F  HO2   H  HOH1  0   0.508   -7.7962  10.0272  48.5475
 P3F  H51   H  HCH2  0   0.262   -4.1334   9.0045  49.7586
 P3F  H52   H  HCH2  0   0.254   -5.8519   8.6939  50.0176
 P3F  H3    H  HCR6  0   0.266   -2.6554   9.1103  51.4472
 P3F  H11   H  HCH3  0   0.263   -3.9441   8.3256  56.3694
 P3F  H12A  H  HCH3  0   0.264   -3.8571  10.0874  56.3762
 P3F  H13A  H  HCH3  0   0.278   -2.4608   9.1357  55.8822
 P3F  HO9   H  HOH1  0   0.496   -5.9055   9.3282  55.9216
 P3F  H7    H  H     0   0.271   -7.8429   9.3140  53.3656
 P3F  HN3   H  HNH1  0   0.424   -9.5797   9.5648  52.1944
 P3F  H91   H  HCH2  0   0.327  -11.4633  11.1392  50.7026
 P3F  H92   H  HCH2  0   0.290  -11.5814   9.4799  51.2559
 P3F  HN4   H  HNH1  0   0.419  -12.3834  10.5659  48.7064
 P3F  H12   H  HCR6  0   0.276  -10.8077   8.0837  46.4025
 P3F  H13   H  HCR6  0   0.276  -11.8273   7.7587  44.1871
 P3F  H14   H  HCR6  0   0.276  -14.2914   7.8670  43.9343
 P3F  H15   H  HCR6  0   0.280  -15.7078   8.2827  45.8832

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
 P3F  O4   P1    single    1.601  0.020  1.601
 P3F  O4   HO4   single    0.850  0.020  0.980
 P3F  P1   O2    single    1.581  0.020  1.581
 P3F  P1   O3    double    1.477  0.020  1.477
 P3F  P1   O1    single    1.597  0.020  1.597
 P3F  O2   HO2   single    0.850  0.020  0.980
 P3F  O1   C5    single    1.430  0.020  1.430
 P3F  C5   C4    single    1.495  0.020  1.495
 P3F  C5   H51   single    0.970  0.020  1.090
 P3F  C5   H52   single    0.970  0.020  1.090
 P3F  C4   C3    aromatic  1.383  0.020  1.383
 P3F  C4   C6    aromatic  1.405  0.020  1.405
 P3F  C3   N1    aromatic  1.327  0.020  1.327
 P3F  C3   H3    single    0.930  0.020  1.080
 P3F  N1   C2    aromatic  1.320  0.020  1.320
 P3F  C2   C1    single    1.498  0.020  1.498
 P3F  C2   C17   aromatic  1.404  0.020  1.404
 P3F  C1   H11   single    0.970  0.020  1.090
 P3F  C1   H12A  single    0.970  0.020  1.090
 P3F  C1   H13A  single    0.970  0.020  1.090
 P3F  C17  O9    single    1.341  0.020  1.341
 P3F  C17  C6    aromatic  1.400  0.020  1.400
 P3F  O9   HO9   single    0.850  0.020  0.980
 P3F  C6   C7    single    1.462  0.020  1.462
 P3F  C7   N2    double    1.274  0.020  1.274
 P3F  C7   H7    single    0.930  0.020  1.080
 P3F  N2   N3    single    1.349  0.020  1.349
 P3F  N3   C8    single    1.343  0.020  1.343
 P3F  N3   HN3   single    0.860  0.020  1.020
 P3F  C8   O5    double    1.222  0.020  1.222
 P3F  C8   C9    single    1.519  0.020  1.519
 P3F  C9   N4    single    1.431  0.020  1.431
 P3F  C9   H91   single    0.970  0.020  1.090
 P3F  C9   H92   single    0.970  0.020  1.090
 P3F  N4   C10   single    1.341  0.020  1.341
 P3F  N4   HN4   single    0.860  0.020  1.020
 P3F  C10  O6    double    1.219  0.020  1.219
 P3F  C10  C11   single    1.501  0.020  1.501
 P3F  C11  C16   aromatic  1.396  0.020  1.396
 P3F  C11  C12   aromatic  1.390  0.020  1.390
 P3F  C16  C18   single    1.501  0.020  1.501
 P3F  C16  C15   aromatic  1.390  0.020  1.390
 P3F  C18  F2    single    1.339  0.020  1.339
 P3F  C18  F1    single    1.335  0.020  1.335
 P3F  C18  F3    single    1.342  0.020  1.342
 P3F  C12  C13   aromatic  1.386  0.020  1.386
 P3F  C12  H12   single    0.930  0.020  1.080
 P3F  C13  C14   aromatic  1.386  0.020  1.386
 P3F  C13  H13   single    0.930  0.020  1.080
 P3F  C14  C15   aromatic  1.386  0.020  1.386
 P3F  C14  H14   single    0.930  0.020  1.080
 P3F  C15  H15   single    0.930  0.020  1.080

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
 P3F  HO4   O4   P1    114.43  3.000
 P3F  O1    P1   O3    110.56  3.000
 P3F  O1    P1   O2    107.77  3.000
 P3F  O3    P1   O2    117.00  3.000
 P3F  O1    P1   O4    101.27  3.000
 P3F  O3    P1   O4    116.25  3.000
 P3F  O2    P1   O4    102.49  3.000
 P3F  HO2   O2   P1    114.64  3.000
 P3F  C5    O1   P1    122.33  3.000
 P3F  H52   C5   H51   107.99  3.000
 P3F  H52   C5   C4    111.30  3.000
 P3F  H51   C5   C4    109.22  3.000
 P3F  H52   C5   O1    110.98  3.000
 P3F  H51   C5   O1    109.60  3.000
 P3F  C4    C5   O1    107.74  3.000
 P3F  C6    C4   C3    118.04  3.000
 P3F  C6    C4   C5    124.03  3.000
 P3F  C3    C4   C5    117.93  3.000
 P3F  H3    C3   N1    116.31  3.000
 P3F  H3    C3   C4    119.45  3.000
 P3F  N1    C3   C4    124.24  3.000
 P3F  C2    N1   C3    119.17  3.000
 P3F  C17   C2   C1    120.36  3.000
 P3F  C17   C2   N1    121.16  3.000
 P3F  C1    C2   N1    118.48  3.000
 P3F  H13A  C1   H12A  107.71  3.000
 P3F  H13A  C1   H11   107.55  3.000
 P3F  H12A  C1   H11   107.58  3.000
 P3F  H13A  C1   C2    109.81  3.000
 P3F  H12A  C1   C2    111.96  3.000
 P3F  H11   C1   C2    112.04  3.000
 P3F  C6    C17  O9    118.33  3.000
 P3F  C6    C17  C2    120.26  3.000
 P3F  O9    C17  C2    121.41  3.000
 P3F  HO9   O9   C17   111.62  3.000
 P3F  C7    C6   C17   116.97  3.000
 P3F  C7    C6   C4    125.89  3.000
 P3F  C17   C6   C4    117.12  3.000
 P3F  H7    C7   N2    120.00  3.000
 P3F  H7    C7   C6    115.81  3.000
 P3F  N2    C7   C6    124.19  3.000
 P3F  N3    N2   C7    115.07  3.000
 P3F  HN3   N3   C8    118.67  3.000
 P3F  HN3   N3   N2    119.24  3.000
 P3F  C8    N3   N2    122.06  3.000
 P3F  C9    C8   O5    121.19  3.000
 P3F  C9    C8   N3    113.82  3.000
 P3F  O5    C8   N3    124.96  3.000
 P3F  H92   C9   H91   106.86  3.000
 P3F  H92   C9   N4    111.11  3.000
 P3F  H91   C9   N4    108.23  3.000
 P3F  H92   C9   C8    110.92  3.000
 P3F  H91   C9   C8    107.83  3.000
 P3F  N4    C9   C8    111.68  3.000
 P3F  HN4   N4   C10   120.18  3.000
 P3F  HN4   N4   C9    118.59  3.000
 P3F  C10   N4   C9    120.31  3.000
 P3F  C11   C10  O6    121.61  3.000
 P3F  C11   C10  N4    115.56  3.000
 P3F  O6    C10  N4    122.78  3.000
 P3F  C12   C11  C16   119.34  3.000
 P3F  C12   C11  C10   116.30  3.000
 P3F  C16   C11  C10   124.33  3.000
 P3F  C15   C16  C18   119.06  3.000
 P3F  C15   C16  C11   119.79  3.000
 P3F  C18   C16  C11   121.16  3.000
 P3F  F3    C18  F1    106.61  3.000
 P3F  F3    C18  F2    106.88  3.000
 P3F  F1    C18  F2    106.86  3.000
 P3F  F3    C18  C16   111.92  3.000
 P3F  F1    C18  C16   112.16  3.000
 P3F  F2    C18  C16   112.04  3.000
 P3F  H12   C12  C13   119.74  3.000
 P3F  H12   C12  C11   119.59  3.000
 P3F  C13   C12  C11   120.67  3.000
 P3F  H13   C13  C14   120.35  3.000
 P3F  H13   C13  C12   119.81  3.000
 P3F  C14   C13  C12   119.84  3.000
 P3F  H14   C14  C15   119.64  3.000
 P3F  H14   C14  C13   120.37  3.000
 P3F  C15   C14  C13   119.99  3.000
 P3F  H15   C15  C14   118.99  3.000
 P3F  H15   C15  C16   120.66  3.000
 P3F  C14   C15  C16   120.35  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
 P3F  CONST_01  C2   N1   C3   C4      0.00   0.0  0
 P3F  CONST_02  C2   C17  C6   C4      0.00   0.0  0
 P3F  CONST_03  C17  C6   C4   C3      0.00   0.0  0
 P3F  CONST_04  C17  C2   N1   C3      0.00   0.0  0
 P3F  CONST_05  C6   C4   C3   N1      0.00   0.0  0
 P3F  CONST_06  C6   C17  C2   N1      0.00   0.0  0
 P3F  CONST_07  C14  C15  C16  C11     0.00   0.0  0
 P3F  CONST_08  C14  C13  C12  C11     0.00   0.0  0
 P3F  CONST_09  C13  C12  C11  C16     0.00   0.0  0
 P3F  CONST_10  C13  C14  C15  C16     0.00   0.0  0
 P3F  CONST_11  C15  C16  C11  C12     0.00   0.0  0
 P3F  CONST_12  C15  C14  C13  C12     0.00   0.0  0
 P3F  CONST_13  N1   C3   C4   C5    180.00   0.0  0
 P3F  CONST_14  C17  C6   C4   C5    180.00   0.0  0
 P3F  CONST_15  O9   C17  C6   C4    180.00   0.0  0
 P3F  CONST_16  C7   C6   C4   C3    180.00   0.0  0
 P3F  CONST_17  C1   C2   N1   C3    180.00   0.0  0
 P3F  CONST_18  O9   C17  C2   N1    180.00   0.0  0
 P3F  CONST_19  C7   C6   C17  C2    180.00   0.0  0
 P3F  CONST_20  C6   C17  C2   C1    180.00   0.0  0
 P3F  CONST_21  C15  C16  C11  C10   180.00   0.0  0
 P3F  CONST_22  C13  C12  C11  C10   180.00   0.0  0
 P3F  CONST_23  C12  C11  C16  C18   180.00   0.0  0
 P3F  CONST_24  C14  C15  C16  C18   180.00   0.0  0
 P3F  CONST_25  H3   C3   N1   C2    180.00   0.0  0
 P3F  CONST_26  H15  C15  C16  C11   180.00   0.0  0
 P3F  CONST_27  H13  C13  C12  C11   180.00   0.0  0
 P3F  CONST_28  H12  C12  C11  C16   180.00   0.0  0
 P3F  CONST_29  H14  C14  C15  C16   180.00   0.0  0
 P3F  CONST_30  C11  C10  N4   C9    180.00   0.0  0
 P3F  CONST_31  HN4  N4   C10  C11     0.00   0.0  0
 P3F  CONST_32  O5   C8   N3   N2      0.00   0.0  0
 P3F  CONST_33  C9   C8   N3   N2    180.00   0.0  0
 P3F  CONST_34  O6   C10  N4   C9      0.00   0.0  0
 P3F  CONST_35  HN3  N3   C8   O5    180.00   0.0  0
 P3F  Var_01    C3   C4   C5   O1   -103.38  30.0  2
 P3F  Var_02    N2   C7   C6   C4    -11.67  30.0  2
 P3F  Var_03    C16  C11  C10  N4    -69.59  30.0  2
 P3F  Var_04    F2   C18  C16  C11   -38.95  30.0  2
 P3F  Var_05    H11  C1   C2   N1   -117.75  30.0  2
 P3F  Var_06    C4   C5   O1   P1   -168.49  30.0  3
 P3F  Var_07    C8   N3   N2   C7    178.27  30.0  3
 P3F  Var_08    N4   C9   C8   N3   -154.72  30.0  3
 P3F  Var_09    C10  N4   C9   C8     64.66  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
 P3F  plan-1  C5   0.020
 P3F  plan-1  C4   0.020
 P3F  plan-1  C3   0.020
 P3F  plan-1  N1   0.020
 P3F  plan-1  C2   0.020
 P3F  plan-1  C1   0.020
 P3F  plan-1  C17  0.020
 P3F  plan-1  O9   0.020
 P3F  plan-1  C6   0.020
 P3F  plan-1  C7   0.020
 P3F  plan-1  H3   0.020
 P3F  plan-2  C10  0.020
 P3F  plan-2  C11  0.020
 P3F  plan-2  C16  0.020
 P3F  plan-2  C18  0.020
 P3F  plan-2  C12  0.020
 P3F  plan-2  C13  0.020
 P3F  plan-2  C14  0.020
 P3F  plan-2  C15  0.020
 P3F  plan-2  H12  0.020
 P3F  plan-2  H13  0.020
 P3F  plan-2  H14  0.020
 P3F  plan-2  H15  0.020
 P3F  plan-3  N2   0.020
 P3F  plan-3  N3   0.020
 P3F  plan-3  C8   0.020
 P3F  plan-3  O5   0.020
 P3F  plan-3  C9   0.020
 P3F  plan-3  HN3  0.020
 P3F  plan-4  C9   0.020
 P3F  plan-4  N4   0.020
 P3F  plan-4  C10  0.020
 P3F  plan-4  O6   0.020
 P3F  plan-4  C11  0.020
 P3F  plan-4  HN4  0.020
 P3F  plan-5  C6   0.020
 P3F  plan-5  C7   0.020
 P3F  plan-5  N2   0.020
 P3F  plan-5  N3   0.020
 P3F  plan-5  H7   0.020

