# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 17:47:25 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: (1S,2S,3S)-1-fluoranyl-2-[4-(5-fluoranylpyrimidin-2-yl)phenyl]-N-oxidanyl-3-phenyl-cyclopropane-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ONC(=O)[C@]1(F)[C@@H]([C@H]1c2ccc(cc2)c3ncc(F)cn3)c4ccccc4
#
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
 OTF  OTF  (1S,2S,3S)-1-fluoranyl-2-[4-(5-fluoranylpyrimidin-2-yl)phenyl]-N-oxidanyl-3-phenyl-cyclopropane-1-carboxamide  ligand  42  27  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_OTF
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
 OTF  C1   C  C     0   0.484   3.3416  -1.6892   0.0095
 OTF  C2   C  CT    0   0.325   2.2394  -0.8479  -0.5505
 OTF  C3   C  CH1   0  -0.421   1.4481   0.0460   0.3645
 OTF  C4   C  CH1   0  -0.337   2.3713   0.6373  -0.6579
 OTF  F5   F  F     0  -0.333   1.5446  -1.4534  -1.5636
 OTF  O6   O  O     0  -0.456   3.9395  -1.3559   1.0140
 OTF  N7   N  NH1   0  -0.385   3.5801  -2.8154  -0.6826
 OTF  O8   O  OH1   0  -0.536   4.6679  -3.5680  -0.3644
 OTF  C9   C  CR6   0   0.130   3.6144   1.3660  -0.2835
 OTF  C10  C  CR16  0  -0.293   4.7452   1.2575  -1.0886
 OTF  C11  C  CR16  0  -0.243   5.8984   1.9652  -0.7838
 OTF  C12  C  CR16  0  -0.266   5.9317   2.7967   0.3292
 OTF  C13  C  CR16  0  -0.241   4.8056   2.9134   1.1325
 OTF  C14  C  CR16  0  -0.308   3.6530   2.2012   0.8262
 OTF  C15  C  CR6   0   0.208  -0.0319   0.0912   0.2631
 OTF  C16  C  CR16  0  -0.286  -0.7827  -0.4208   1.3206
 OTF  C17  C  CR16  0  -0.268  -2.1654  -0.4305   1.2790
 OTF  C18  C  CR6   0  -0.021  -2.8440   0.0740   0.1699
 OTF  C19  C  CR16  0  -0.256  -2.0959   0.5936  -0.8855
 OTF  C20  C  CR16  0  -0.319  -0.7121   0.6010  -0.8392
 OTF  C21  C  CR6   0   0.405  -4.3192   0.0579   0.1134
 OTF  N22  N  N     0  -0.407  -4.9031   0.5628  -0.9699
 OTF  C23  C  CR16  0  -0.147  -6.2232   0.5441  -1.0319
 OTF  C24  C  CR6   0   0.396  -6.9659   0.0136   0.0035
 OTF  C25  C  CR16  0  -0.147  -6.2945  -0.4906   1.0990
 OTF  N26  N  N     0  -0.407  -4.9737  -0.4648   1.1466
 OTF  F27  F  F     0  -0.288  -8.2968  -0.0120  -0.0542
 OTF  H7   H  HNH1  0   0.421   3.1818  -3.0059  -1.5905
 OTF  H3   H  HCH1  0   0.298   1.8215   0.0462   1.3838
 OTF  H4   H  HCH1  0   0.321   1.8909   1.0239  -1.5538
 OTF  H8   H  HOH1  0   0.482   4.3402  -4.3000   0.1747
 OTF  H10  H  HCR6  0   0.250   4.7258   0.6114  -1.9588
 OTF  H14  H  HCR6  0   0.252   2.7779   2.2981   1.4574
 OTF  H11  H  HCR6  0   0.256   6.7720   1.8675  -1.4153
 OTF  H12  H  HCR6  0   0.255   6.8301   3.3517   0.5671
 OTF  H13  H  HCR6  0   0.256   4.8220   3.5607   1.9998
 OTF  H16  H  HCR6  0   0.258  -0.2768  -0.8189   2.1915
 OTF  H20  H  HCR6  0   0.254  -0.1724   1.0255  -1.6750
 OTF  H17  H  HCR6  0   0.257  -2.7202  -0.8352   2.1140
 OTF  H19  H  HCR6  0   0.258  -2.5987   0.9969  -1.7533
 OTF  H23  H  HCR6  0   0.300  -6.6997   0.9552  -1.9151
 OTF  H25  H  HCR6  0   0.300  -6.8283  -0.9184   1.9406

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
 OTF  C1   C2   single    1.495  0.020  1.495
 OTF  C1   O6   double    1.216  0.020  1.216
 OTF  C1   N7   single    1.343  0.020  1.343
 OTF  C2   C3   single    1.504  0.020  1.504
 OTF  C2   C4   single    1.495  0.020  1.495
 OTF  C2   F5   single    1.370  0.020  1.370
 OTF  C3   C4   single    1.499  0.020  1.499
 OTF  C3   C15  single    1.484  0.020  1.484
 OTF  C4   C9   single    1.489  0.020  1.489
 OTF  N7   O8   single    1.361  0.020  1.361
 OTF  C9   C10  aromatic  1.392  0.020  1.392
 OTF  C9   C14  aromatic  1.389  0.020  1.389
 OTF  C10  C11  aromatic  1.387  0.020  1.387
 OTF  C11  C12  aromatic  1.390  0.020  1.390
 OTF  C12  C13  aromatic  1.388  0.020  1.388
 OTF  C13  C14  aromatic  1.389  0.020  1.389
 OTF  C15  C16  aromatic  1.394  0.020  1.394
 OTF  C15  C20  aromatic  1.392  0.020  1.392
 OTF  C16  C17  aromatic  1.383  0.020  1.383
 OTF  C17  C18  aromatic  1.395  0.020  1.395
 OTF  C18  C19  aromatic  1.394  0.020  1.394
 OTF  C18  C21  single    1.476  0.020  1.476
 OTF  C19  C20  aromatic  1.385  0.020  1.385
 OTF  C21  N22  aromatic  1.330  0.020  1.330
 OTF  C21  N26  aromatic  1.330  0.020  1.330
 OTF  N22  C23  aromatic  1.322  0.020  1.322
 OTF  C23  C24  aromatic  1.380  0.020  1.380
 OTF  C24  C25  aromatic  1.380  0.020  1.380
 OTF  C24  F27  single    1.332  0.020  1.332
 OTF  C25  N26  aromatic  1.322  0.020  1.322
 OTF  N7   H7   single    0.860  0.020  1.020
 OTF  C3   H3   single    0.970  0.020  1.090
 OTF  C4   H4   single    0.970  0.020  1.090
 OTF  O8   H8   single    0.850  0.020  0.980
 OTF  C10  H10  single    0.930  0.020  1.080
 OTF  C14  H14  single    0.930  0.020  1.080
 OTF  C11  H11  single    0.930  0.020  1.080
 OTF  C12  H12  single    0.930  0.020  1.080
 OTF  C13  H13  single    0.930  0.020  1.080
 OTF  C16  H16  single    0.930  0.020  1.080
 OTF  C20  H20  single    0.930  0.020  1.080
 OTF  C17  H17  single    0.930  0.020  1.080
 OTF  C19  H19  single    0.930  0.020  1.080
 OTF  C23  H23  single    0.930  0.020  1.080
 OTF  C25  H25  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
 OTF  N7   C1   O6   124.64  3.000
 OTF  N7   C1   C2   114.18  3.000
 OTF  O6   C1   C2   121.18  3.000
 OTF  F5   C2   C4   115.52  3.000
 OTF  F5   C2   C3   116.47  3.000
 OTF  C4   C2   C3    59.98  3.000
 OTF  F5   C2   C1   113.72  3.000
 OTF  C4   C2   C1   121.39  3.000
 OTF  C3   C2   C1   119.63  3.000
 OTF  H3   C3   C15  114.03  3.000
 OTF  H3   C3   C4   115.37  3.000
 OTF  C15  C3   C4   123.75  3.000
 OTF  H3   C3   C2   112.98  3.000
 OTF  C15  C3   C2   120.08  3.000
 OTF  C4   C3   C2    59.71  3.000
 OTF  H4   C4   C9   113.71  3.000
 OTF  H4   C4   C3   115.46  3.000
 OTF  C9   C4   C3   122.40  3.000
 OTF  H4   C4   C2   111.92  3.000
 OTF  C9   C4   C2   122.81  3.000
 OTF  C3   C4   C2    60.31  3.000
 OTF  H7   N7   O8   114.92  3.000
 OTF  H7   N7   C1   123.48  3.000
 OTF  O8   N7   C1   119.03  3.000
 OTF  H8   O8   N7   106.16  3.000
 OTF  C14  C9   C10  119.08  3.000
 OTF  C14  C9   C4   121.22  3.000
 OTF  C10  C9   C4   119.64  3.000
 OTF  H10  C10  C11  119.70  3.000
 OTF  H10  C10  C9   119.74  3.000
 OTF  C11  C10  C9   120.56  3.000
 OTF  H11  C11  C12  120.12  3.000
 OTF  H11  C11  C10  119.79  3.000
 OTF  C12  C11  C10  120.08  3.000
 OTF  H12  C12  C13  120.20  3.000
 OTF  H12  C12  C11  120.18  3.000
 OTF  C13  C12  C11  119.62  3.000
 OTF  H13  C13  C14  119.73  3.000
 OTF  H13  C13  C12  120.11  3.000
 OTF  C14  C13  C12  120.16  3.000
 OTF  H14  C14  C13  119.73  3.000
 OTF  H14  C14  C9   119.78  3.000
 OTF  C13  C14  C9   120.49  3.000
 OTF  C20  C15  C16  118.16  3.000
 OTF  C20  C15  C3   123.54  3.000
 OTF  C16  C15  C3   118.29  3.000
 OTF  H16  C16  C17  119.25  3.000
 OTF  H16  C16  C15  119.56  3.000
 OTF  C17  C16  C15  121.20  3.000
 OTF  H17  C17  C18  120.00  3.000
 OTF  H17  C17  C16  119.49  3.000
 OTF  C18  C17  C16  120.51  3.000
 OTF  C21  C18  C19  120.75  3.000
 OTF  C21  C18  C17  120.84  3.000
 OTF  C19  C18  C17  118.41  3.000
 OTF  H19  C19  C20  119.33  3.000
 OTF  H19  C19  C18  119.81  3.000
 OTF  C20  C19  C18  120.86  3.000
 OTF  H20  C20  C19  118.35  3.000
 OTF  H20  C20  C15  120.78  3.000
 OTF  C19  C20  C15  120.86  3.000
 OTF  N26  C21  N22  124.46  3.000
 OTF  N26  C21  C18  117.79  3.000
 OTF  N22  C21  C18  117.75  3.000
 OTF  C23  N22  C21  118.11  3.000
 OTF  H23  C23  C24  121.35  3.000
 OTF  H23  C23  N22  118.14  3.000
 OTF  C24  C23  N22  120.51  3.000
 OTF  F27  C24  C25  120.88  3.000
 OTF  F27  C24  C23  120.82  3.000
 OTF  C25  C24  C23  118.30  3.000
 OTF  H25  C25  N26  118.13  3.000
 OTF  H25  C25  C24  121.37  3.000
 OTF  N26  C25  C24  120.50  3.000
 OTF  C25  N26  C21  118.12  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
 OTF  CONST_01  C12  C11  C10  C9      0.00   0.0  0
 OTF  CONST_02  C12  C13  C14  C9      0.00   0.0  0
 OTF  CONST_03  C13  C14  C9   C10     0.00   0.0  0
 OTF  CONST_04  C13  C12  C11  C10     0.00   0.0  0
 OTF  CONST_05  C14  C9   C10  C11     0.00   0.0  0
 OTF  CONST_06  C14  C13  C12  C11     0.00   0.0  0
 OTF  CONST_07  C18  C17  C16  C15     0.00   0.0  0
 OTF  CONST_08  C18  C19  C20  C15     0.00   0.0  0
 OTF  CONST_09  C19  C20  C15  C16     0.00   0.0  0
 OTF  CONST_10  C19  C18  C17  C16     0.00   0.0  0
 OTF  CONST_11  C21  C18  C17  C16   180.00   0.0  0
 OTF  CONST_12  C20  C15  C16  C17     0.00   0.0  0
 OTF  CONST_13  C20  C19  C18  C17     0.00   0.0  0
 OTF  CONST_14  N22  C21  C18  C17   180.00   0.0  0
 OTF  CONST_15  N26  C21  C18  C17     0.00   0.0  0
 OTF  CONST_16  C23  N22  C21  C18   180.00   0.0  0
 OTF  CONST_17  C25  N26  C21  C18   180.00   0.0  0
 OTF  CONST_18  N22  C21  C18  C19     0.00   0.0  0
 OTF  CONST_19  N26  C21  C18  C19   180.00   0.0  0
 OTF  CONST_20  C21  C18  C19  C20   180.00   0.0  0
 OTF  CONST_21  C24  C23  N22  C21     0.00   0.0  0
 OTF  CONST_22  C24  C25  N26  C21     0.00   0.0  0
 OTF  CONST_23  C25  N26  C21  N22     0.00   0.0  0
 OTF  CONST_24  C25  C24  C23  N22     0.00   0.0  0
 OTF  CONST_25  N26  C21  N22  C23     0.00   0.0  0
 OTF  CONST_26  N26  C25  C24  C23     0.00   0.0  0
 OTF  CONST_27  C17  C16  C15  C3    180.00   0.0  0
 OTF  CONST_28  C19  C20  C15  C3    180.00   0.0  0
 OTF  CONST_29  C11  C10  C9   C4    180.00   0.0  0
 OTF  CONST_30  C13  C14  C9   C4    180.00   0.0  0
 OTF  CONST_31  F27  C24  C23  N22   180.00   0.0  0
 OTF  CONST_32  F27  C24  C25  N26   180.00   0.0  0
 OTF  CONST_33  H16  C16  C15  C3      0.00   0.0  0
 OTF  CONST_34  H20  C20  C15  C3      0.00   0.0  0
 OTF  CONST_35  H10  C10  C9   C4      0.00   0.0  0
 OTF  CONST_36  H14  C14  C9   C4      0.00   0.0  0
 OTF  CONST_37  H11  C11  C10  C9    180.00   0.0  0
 OTF  CONST_38  H13  C13  C14  C9    180.00   0.0  0
 OTF  CONST_39  H12  C12  C11  C10   180.00   0.0  0
 OTF  CONST_40  H17  C17  C16  C15   180.00   0.0  0
 OTF  CONST_41  H19  C19  C20  C15   180.00   0.0  0
 OTF  CONST_42  H23  C23  N22  C21   180.00   0.0  0
 OTF  CONST_43  H25  C25  N26  C21   180.00   0.0  0
 OTF  CONST_44  O8   N7   C1   C2    180.00   0.0  0
 OTF  CONST_45  H7   N7   C1   C2      0.00   0.0  0
 OTF  CONST_46  O8   N7   C1   O6      0.00   0.0  0
 OTF  Var_01    C9   C4   C3   C2   -112.15  30.0  1
 OTF  Var_02    C16  C15  C3   C2    112.28  30.0  2
 OTF  Var_03    C10  C9   C4   C2     71.47  30.0  2
 OTF  Var_04    O6   C1   C2   C3    -26.98  30.0  1

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
 OTF  chir_01  C2  C3   C4  F5  both
 OTF  chir_02  C3  C15  C4  C2  both
 OTF  chir_03  C4  C2   C3  C9  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
 OTF  plan-1  C4   0.020
 OTF  plan-1  C9   0.020
 OTF  plan-1  C10  0.020
 OTF  plan-1  C11  0.020
 OTF  plan-1  C12  0.020
 OTF  plan-1  C13  0.020
 OTF  plan-1  C14  0.020
 OTF  plan-1  H10  0.020
 OTF  plan-1  H14  0.020
 OTF  plan-1  H11  0.020
 OTF  plan-1  H12  0.020
 OTF  plan-1  H13  0.020
 OTF  plan-2  C3   0.020
 OTF  plan-2  C15  0.020
 OTF  plan-2  C16  0.020
 OTF  plan-2  C17  0.020
 OTF  plan-2  C18  0.020
 OTF  plan-2  C19  0.020
 OTF  plan-2  C20  0.020
 OTF  plan-2  C21  0.020
 OTF  plan-2  H16  0.020
 OTF  plan-2  H20  0.020
 OTF  plan-2  H17  0.020
 OTF  plan-2  H19  0.020
 OTF  plan-3  C18  0.020
 OTF  plan-3  C21  0.020
 OTF  plan-3  N22  0.020
 OTF  plan-3  C23  0.020
 OTF  plan-3  C24  0.020
 OTF  plan-3  C25  0.020
 OTF  plan-3  N26  0.020
 OTF  plan-3  F27  0.020
 OTF  plan-3  H23  0.020
 OTF  plan-3  H25  0.020
 OTF  plan-4  C1   0.020
 OTF  plan-4  C2   0.020
 OTF  plan-4  O6   0.020
 OTF  plan-4  N7   0.020
 OTF  plan-4  O8   0.020
 OTF  plan-4  H7   0.020

