# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 12:11:44 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: 2-fluoranyl-5-[2-[(4~{R})-4-methyl-2-oxidanylidene-4-phenyl-pyrrolidin-1-yl]ethoxy]benzenecarbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@]1(CN(CCOc2ccc(F)c(c2)C#N)C(=O)C1)c3ccccc3
#
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
 7BK  7BK  2-fluoranyl-5-[2-[(4~{R})-4-methyl-2-oxidanylidene-4-phenyl-pyrrolidin-1-yl]ethoxy]benzenecarbonitrile  ligand  44  25  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7BK
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
 7BK  C1   C  CH3   0  -0.682  -1.4282   1.1980   0.1399
 7BK  C2   C  CT    0  -0.217  -2.5180   0.1304   0.2430
 7BK  C3   C  CH2   0  -0.237  -2.1351  -1.0433  -0.6866
 7BK  N4   N  NT    0  -0.447  -1.2705  -1.8624   0.1367
 7BK  C5   C  CH2   0  -0.334  -0.3741  -2.8353  -0.4276
 7BK  C6   C  CH2   0  -0.203   0.8302  -2.1936  -1.0875
 7BK  C8   C  CR6   0   0.414   2.5236  -0.6415  -0.4660
 7BK  C10  C  CR16  0  -0.388   4.1345   0.2501  -2.0339
 7BK  C11  C  CR6   0   0.548   4.6429   1.0551  -1.0425
 7BK  C13  C  CR6   0  -0.164   4.1095   1.0270   0.2412
 7BK  C14  C  CSP   0   0.075   4.6568   1.8710   1.2496
 7BK  C16  C  CR16  0  -0.332   3.0468   0.1784   0.5297
 7BK  C19  C  CH2   0  -0.554  -2.4224  -0.5297   1.6298
 7BK  C21  C  CR16  0  -0.337  -4.1468   2.0082  -0.3296
 7BK  C22  C  CR16  0  -0.232  -5.4341   2.4735  -0.5780
 7BK  C23  C  CR16  0  -0.274  -6.5113   1.6025  -0.5568
 7BK  C24  C  CR16  0  -0.239  -6.2891   0.2582  -0.2827
 7BK  C25  C  CR16  0  -0.320  -5.0050  -0.1995  -0.0344
 7BK  O7   O  O2    0  -0.464   1.5010  -1.4304  -0.1021
 7BK  C9   C  CR16  0  -0.345   3.0751  -0.6012  -1.7465
 7BK  F12  F  F     0  -0.290   5.6623   1.8807  -1.2925
 7BK  N15  N  NS    0  -0.238   5.0966   2.5519   2.0674
 7BK  C17  C  C     0   0.528  -1.3919  -1.6225   1.4577
 7BK  O18  O  O     0  -0.494  -0.8038  -2.2104   2.3497
 7BK  C20  C  CR6   0   0.211  -3.9070   0.6652  -0.0531
 7BK  H27  H  HCH3  0   0.243  -1.3973   1.6492  -0.8524
 7BK  H28  H  HCH3  0   0.244  -1.5742   1.9919   0.8733
 7BK  H26  H  HCH3  0   0.249  -0.4484   0.7548   0.3270
 7BK  H29  H  HCH2  0   0.258  -3.0029  -1.6190  -1.0218
 7BK  H30  H  HCH2  0   0.258  -1.6167  -0.6907  -1.5812
 7BK  H32  H  HCH2  0   0.268  -0.0552  -3.5158   0.3612
 7BK  H31  H  HCH2  0   0.267  -0.8977  -3.4319  -1.1786
 7BK  H34  H  HCH2  0   0.251   1.4800  -2.9765  -1.4930
 7BK  H33  H  HCH2  0   0.235   0.5179  -1.5568  -1.9229
 7BK  H36  H  HCR6  0   0.302   4.5569   0.2782  -3.0292
 7BK  H37  H  HCR6  0   0.300   2.6271   0.1549   1.5267
 7BK  H38  H  HCH2  0   0.279  -2.1387   0.1697   2.4169
 7BK  H39  H  HCH2  0   0.285  -3.3622  -0.9948   1.9403
 7BK  H40  H  HCR6  0   0.255  -3.3322   2.7184  -0.3523
 7BK  H41  H  HCR6  0   0.255  -5.5892   3.5245  -0.7859
 7BK  H42  H  HCR6  0   0.255  -7.5129   1.9639  -0.7500
 7BK  H43  H  HCR6  0   0.255  -7.1181  -0.4373  -0.2600
 7BK  H44  H  HCR6  0   0.251  -4.8639  -1.2529   0.1787
 7BK  H35  H  HCR6  0   0.305   2.6979  -1.2304  -2.5404

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
 7BK  F12  C11  single    1.335  0.020  1.335
 7BK  C23  C22  aromatic  1.385  0.020  1.385
 7BK  C23  C24  aromatic  1.390  0.020  1.390
 7BK  C10  C11  aromatic  1.375  0.020  1.375
 7BK  C10  C9   aromatic  1.389  0.020  1.389
 7BK  C22  C21  aromatic  1.391  0.020  1.391
 7BK  C11  C13  aromatic  1.390  0.020  1.390
 7BK  C24  C25  aromatic  1.386  0.020  1.386
 7BK  C9   C8   aromatic  1.395  0.020  1.395
 7BK  C21  C20  aromatic  1.392  0.020  1.392
 7BK  C25  C20  aromatic  1.398  0.020  1.398
 7BK  C13  C14  single    1.424  0.020  1.424
 7BK  C13  C16  aromatic  1.390  0.020  1.390
 7BK  C20  C2   single    1.518  0.020  1.518
 7BK  C8   C16  aromatic  1.392  0.020  1.392
 7BK  C8   O7   single    1.342  0.020  1.342
 7BK  C14  N15  triple    1.151  0.020  1.151
 7BK  C6   O7   single    1.415  0.020  1.415
 7BK  C6   C5   single    1.516  0.020  1.516
 7BK  C19  C2   single    1.539  0.020  1.539
 7BK  C19  C17  single    1.512  0.020  1.512
 7BK  O18  C17  double    1.220  0.020  1.220
 7BK  C2   C3   single    1.545  0.020  1.545
 7BK  C2   C1   single    1.529  0.020  1.529
 7BK  C17  N4   single    1.348  0.020  1.348
 7BK  C3   N4   single    1.448  0.020  1.448
 7BK  N4   C5   single    1.438  0.020  1.438
 7BK  C1   H27  single    0.970  0.020  1.090
 7BK  C1   H28  single    0.970  0.020  1.090
 7BK  C1   H26  single    0.970  0.020  1.090
 7BK  C3   H29  single    0.970  0.020  1.090
 7BK  C3   H30  single    0.970  0.020  1.090
 7BK  C5   H32  single    0.970  0.020  1.090
 7BK  C5   H31  single    0.970  0.020  1.090
 7BK  C6   H34  single    0.970  0.020  1.090
 7BK  C6   H33  single    0.970  0.020  1.090
 7BK  C10  H36  single    0.930  0.020  1.080
 7BK  C16  H37  single    0.930  0.020  1.080
 7BK  C19  H38  single    0.970  0.020  1.090
 7BK  C19  H39  single    0.970  0.020  1.090
 7BK  C21  H40  single    0.930  0.020  1.080
 7BK  C22  H41  single    0.930  0.020  1.080
 7BK  C23  H42  single    0.930  0.020  1.080
 7BK  C24  H43  single    0.930  0.020  1.080
 7BK  C25  H44  single    0.930  0.020  1.080
 7BK  C9   H35  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
 7BK  H26  C1   H28  107.49  3.000
 7BK  H26  C1   H27  107.37  3.000
 7BK  H28  C1   H27  108.34  3.000
 7BK  H26  C1   C2   110.16  3.000
 7BK  H28  C1   C2   111.56  3.000
 7BK  H27  C1   C2   111.74  3.000
 7BK  C20  C2   C19  112.57  3.000
 7BK  C19  C2   C3   101.59  3.000
 7BK  C20  C2   C3   112.15  3.000
 7BK  C3   C2   C1   108.25  3.000
 7BK  C19  C2   C1   108.42  3.000
 7BK  C20  C2   C1   113.15  3.000
 7BK  H30  C3   H29  107.18  3.000
 7BK  H30  C3   N4   111.40  3.000
 7BK  H29  C3   N4   110.50  3.000
 7BK  H30  C3   C2   111.41  3.000
 7BK  H29  C3   C2   112.79  3.000
 7BK  N4   C3   C2   103.63  3.000
 7BK  C17  N4   C5   124.12  3.000
 7BK  C5   N4   C3   122.13  3.000
 7BK  C17  N4   C3   113.75  3.000
 7BK  H31  C5   H32  107.27  3.000
 7BK  H31  C5   C6   108.22  3.000
 7BK  H32  C5   C6   110.31  3.000
 7BK  H31  C5   N4   109.90  3.000
 7BK  H32  C5   N4   108.72  3.000
 7BK  C6   C5   N4   112.31  3.000
 7BK  H33  C6   H34  107.59  3.000
 7BK  H33  C6   O7   110.64  3.000
 7BK  H34  C6   O7   111.22  3.000
 7BK  H33  C6   C5   110.57  3.000
 7BK  H34  C6   C5   109.27  3.000
 7BK  O7   C6   C5   107.56  3.000
 7BK  C9   C8   O7   124.56  3.000
 7BK  O7   C8   C16  116.02  3.000
 7BK  C9   C8   C16  119.41  3.000
 7BK  H36  C10  C9   120.28  3.000
 7BK  H36  C10  C11  120.27  3.000
 7BK  C9   C10  C11  119.45  3.000
 7BK  F12  C11  C13  118.57  3.000
 7BK  C13  C11  C10  120.81  3.000
 7BK  F12  C11  C10  120.62  3.000
 7BK  C16  C13  C14  120.56  3.000
 7BK  C16  C13  C11  119.82  3.000
 7BK  C14  C13  C11  119.62  3.000
 7BK  N15  C14  C13  180.00  3.000
 7BK  H37  C16  C13  120.06  3.000
 7BK  H37  C16  C8   120.04  3.000
 7BK  C13  C16  C8   119.89  3.000
 7BK  H39  C19  H38  106.94  3.000
 7BK  H39  C19  C17  108.10  3.000
 7BK  H38  C19  C17  111.62  3.000
 7BK  H39  C19  C2   112.64  3.000
 7BK  H38  C19  C2   113.04  3.000
 7BK  C17  C19  C2   104.47  3.000
 7BK  H40  C21  C20  120.54  3.000
 7BK  H40  C21  C22  118.29  3.000
 7BK  C20  C21  C22  121.17  3.000
 7BK  H41  C22  C23  120.13  3.000
 7BK  H41  C22  C21  119.44  3.000
 7BK  C23  C22  C21  120.43  3.000
 7BK  H42  C23  C24  120.41  3.000
 7BK  H42  C23  C22  120.46  3.000
 7BK  C24  C23  C22  119.13  3.000
 7BK  H43  C24  C25  119.59  3.000
 7BK  H43  C24  C23  120.21  3.000
 7BK  C25  C24  C23  120.20  3.000
 7BK  H44  C25  C20  120.11  3.000
 7BK  H44  C25  C24  118.48  3.000
 7BK  C20  C25  C24  121.42  3.000
 7BK  C8   O7   C6   119.30  3.000
 7BK  H35  C9   C10  118.09  3.000
 7BK  H35  C9   C8   121.30  3.000
 7BK  C10  C9   C8   120.61  3.000
 7BK  O18  C17  C19  126.43  3.000
 7BK  O18  C17  N4   125.98  3.000
 7BK  C19  C17  N4   107.55  3.000
 7BK  C25  C20  C21  117.66  3.000
 7BK  C25  C20  C2   119.90  3.000
 7BK  C21  C20  C2   122.44  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
 7BK  CONST_01  C11  C10  C9   C8     0.00   0.0  0
 7BK  CONST_02  C11  C13  C16  C8     0.00   0.0  0
 7BK  CONST_03  C16  C13  C11  C10    0.00   0.0  0
 7BK  CONST_04  C16  C8   C9   C10    0.00   0.0  0
 7BK  CONST_05  C9   C10  C11  C13    0.00   0.0  0
 7BK  CONST_06  C9   C8   C16  C13    0.00   0.0  0
 7BK  CONST_07  C24  C23  C22  C21    0.00   0.0  0
 7BK  CONST_08  C24  C25  C20  C21    0.00   0.0  0
 7BK  CONST_09  C25  C24  C23  C22    0.00   0.0  0
 7BK  CONST_10  C25  C20  C21  C22    0.00   0.0  0
 7BK  CONST_11  C20  C21  C22  C23    0.00   0.0  0
 7BK  CONST_12  C20  C25  C24  C23    0.00   0.0  0
 7BK  CONST_13  C22  C21  C20  C2   180.00   0.0  0
 7BK  CONST_14  C24  C25  C20  C2   180.00   0.0  0
 7BK  CONST_15  C19  C17  N4   C3     0.00   0.0  0
 7BK  CONST_16  C14  C13  C16  C8   180.00   0.0  0
 7BK  CONST_17  C14  C13  C11  C10  180.00   0.0  0
 7BK  CONST_18  O7   C8   C9   C10  180.00   0.0  0
 7BK  CONST_19  O7   C8   C16  C13  180.00   0.0  0
 7BK  CONST_20  F12  C11  C13  C16  180.00   0.0  0
 7BK  CONST_21  F12  C11  C10  C9   180.00   0.0  0
 7BK  CONST_22  O18  C17  N4   C3   180.00   0.0  0
 7BK  CONST_23  C19  C17  N4   C5   180.00   0.0  0
 7BK  CONST_24  H40  C21  C20  C2     0.00   0.0  0
 7BK  CONST_25  H44  C25  C20  C2     0.00   0.0  0
 7BK  CONST_26  H36  C10  C9   C8   180.00   0.0  0
 7BK  CONST_27  H35  C9   C10  C11  180.00   0.0  0
 7BK  CONST_28  H37  C16  C13  C11  180.00   0.0  0
 7BK  CONST_29  H42  C23  C22  C21  180.00   0.0  0
 7BK  CONST_30  H43  C24  C23  C22  180.00   0.0  0
 7BK  CONST_31  H41  C22  C23  C24  180.00   0.0  0
 7BK  CONST_32  O18  C17  N4   C5     0.00   0.0  0
 7BK  Var_01    N4   C17  C19  C2   -18.31  30.0  1
 7BK  Var_02    C17  N4   C3   C2    18.86  30.0  1
 7BK  Var_03    C6   C5   N4   C3    74.11  30.0  3
 7BK  Var_04    C9   C8   O7   C6    -6.34  30.0  3
 7BK  Var_05    O7   C6   C5   N4    58.79  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
 7BK  chir_01  C2  C19  C3  C20  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
 7BK  plan-1  C8   0.020
 7BK  plan-1  C10  0.020
 7BK  plan-1  C11  0.020
 7BK  plan-1  C13  0.020
 7BK  plan-1  C14  0.020
 7BK  plan-1  C16  0.020
 7BK  plan-1  O7   0.020
 7BK  plan-1  C9   0.020
 7BK  plan-1  F12  0.020
 7BK  plan-1  N15  0.020
 7BK  plan-1  H36  0.020
 7BK  plan-1  H37  0.020
 7BK  plan-1  H35  0.020
 7BK  plan-2  C2   0.020
 7BK  plan-2  C21  0.020
 7BK  plan-2  C22  0.020
 7BK  plan-2  C23  0.020
 7BK  plan-2  C24  0.020
 7BK  plan-2  C25  0.020
 7BK  plan-2  C20  0.020
 7BK  plan-2  H40  0.020
 7BK  plan-2  H41  0.020
 7BK  plan-2  H42  0.020
 7BK  plan-2  H43  0.020
 7BK  plan-2  H44  0.020
 7BK  plan-3  C3   0.020
 7BK  plan-3  N4   0.020
 7BK  plan-3  C5   0.020
 7BK  plan-3  C19  0.020
 7BK  plan-3  C17  0.020
 7BK  plan-3  O18  0.020

