# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 09:18:51 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: 2-fluoranyl-5-[2-[(4~{S})-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
 7K4  7K4  2-fluoranyl-5-[2-[(4~{S})-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_7K4
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
 7K4  C1   C  CH3   0  -0.678   4.4201   1.7135   0.1461
 7K4  C2   C  CT    0  -0.213   3.2259   0.7629   0.2260
 7K4  C3   C  CH2   0  -0.236   2.1929   1.1776  -0.8479
 7K4  N4   N  NT    0  -0.447   1.3871   2.1786  -0.1841
 7K4  C5   C  CH2   0  -0.335   0.4227   2.9666  -0.9030
 7K4  C6   C  CH2   0  -0.209  -0.7296   2.1351  -1.4335
 7K4  C8   C  CR6   0   0.414  -2.2893   0.5726  -0.5482
 7K4  C10  C  CR16  0  -0.388  -3.8702  -0.6346  -1.9240
 7K4  C11  C  CR6   0   0.548  -4.2924  -1.3296  -0.8158
 7K4  C13  C  CR6   0  -0.164  -3.7295  -1.0895   0.4327
 7K4  C14  C  CSP   0   0.076  -4.1855  -1.8252   1.5639
 7K4  C16  C  CR16  0  -0.331  -2.7247  -0.1380   0.5666
 7K4  C19  C  CH2   0  -0.558   2.4578   1.0523   1.5279
 7K4  C21  C  CR16  0  -0.312   2.6250  -1.6873   0.1316
 7K4  C22  C  CR16  0  -0.240   2.9422  -3.0314   0.0219
 7K4  C23  C  CR16  0  -0.274   4.2661  -3.4268  -0.1307
 7K4  C24  C  CR16  0  -0.232   5.2583  -2.4610  -0.1721
 7K4  C25  C  CR16  0  -0.338   4.9337  -1.1126  -0.0621
 7K4  O7   O  O2    0  -0.462  -1.3222   1.4764  -0.3299
 7K4  C9   C  CR16  0  -0.348  -2.8684   0.3185  -1.7915
 7K4  F12  F  F     0  -0.290  -5.2539  -2.2510  -0.9159
 7K4  N15  N  NS    0  -0.238  -4.5491  -2.4164   2.4827
 7K4  C17  C  C     0   0.531   1.4662   2.1326   1.1622
 7K4  O18  O  O     0  -0.493   0.8393   2.8310   1.9401
 7K4  C20  C  CR6   0   0.211   3.6137  -0.6995   0.0921
 7K4  H28  H  HCH3  0   0.243   5.1270   1.5373   0.9577
 7K4  H26  H  HCH3  0   0.243   4.9545   1.6197  -0.8000
 7K4  H27  H  HCH3  0   0.249   4.0828   2.7479   0.2272
 7K4  H29  H  HCH2  0   0.260   2.6776   1.5945  -1.7343
 7K4  H30  H  HCH2  0   0.252   1.5819   0.3328  -1.1792
 7K4  H32  H  HCH2  0   0.268   0.0513   3.7506  -0.2440
 7K4  H31  H  HCH2  0   0.268   0.9046   3.4561  -1.7529
 7K4  H34  H  HCH2  0   0.252  -1.4454   2.7946  -1.9353
 7K4  H33  H  HCH2  0   0.239  -0.3745   1.4064  -2.1707
 7K4  H36  H  HCR6  0   0.302  -4.3167  -0.8262  -2.8904
 7K4  H37  H  HCR6  0   0.300  -2.2815   0.0491   1.5357
 7K4  H38  H  HCH2  0   0.283   1.8945   0.1855   1.8842
 7K4  H39  H  HCH2  0   0.281   3.1059   1.3655   2.3473
 7K4  H40  H  HCR6  0   0.241   1.5834  -1.4110   0.2505
 7K4  H41  H  HCR6  0   0.256   2.1537  -3.7719   0.0553
 7K4  H42  H  HCR6  0   0.255   4.5168  -4.4761  -0.2167
 7K4  H43  H  HCR6  0   0.254   6.2946  -2.7503  -0.2916
 7K4  H44  H  HCR6  0   0.256   5.7344  -0.3874  -0.0979
 7K4  H35  H  HCR6  0   0.305  -2.5580   0.8578  -2.6759

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
 7K4  F12  C11  single    1.335  0.020  1.335
 7K4  C10  C11  aromatic  1.375  0.020  1.375
 7K4  C10  C9   aromatic  1.389  0.020  1.389
 7K4  C11  C13  aromatic  1.390  0.020  1.390
 7K4  C9   C8   aromatic  1.395  0.020  1.395
 7K4  C1   C2   single    1.528  0.020  1.528
 7K4  C13  C14  single    1.424  0.020  1.424
 7K4  C13  C16  aromatic  1.390  0.020  1.390
 7K4  C8   C16  aromatic  1.392  0.020  1.392
 7K4  C8   O7   single    1.342  0.020  1.342
 7K4  C14  N15  triple    1.152  0.020  1.152
 7K4  C6   O7   single    1.415  0.020  1.415
 7K4  C6   C5   single    1.517  0.020  1.517
 7K4  C2   C19  single    1.539  0.020  1.539
 7K4  C2   C20  single    1.519  0.020  1.519
 7K4  C2   C3   single    1.547  0.020  1.547
 7K4  C19  C17  single    1.511  0.020  1.511
 7K4  C20  C21  aromatic  1.398  0.020  1.398
 7K4  C20  C25  aromatic  1.392  0.020  1.392
 7K4  O18  C17  double    1.219  0.020  1.219
 7K4  C17  N4   single    1.349  0.020  1.349
 7K4  C21  C22  aromatic  1.385  0.020  1.385
 7K4  C25  C24  aromatic  1.391  0.020  1.391
 7K4  N4   C3   single    1.446  0.020  1.446
 7K4  N4   C5   single    1.438  0.020  1.438
 7K4  C22  C23  aromatic  1.390  0.020  1.390
 7K4  C24  C23  aromatic  1.385  0.020  1.385
 7K4  C1   H28  single    0.970  0.020  1.090
 7K4  C1   H26  single    0.970  0.020  1.090
 7K4  C1   H27  single    0.970  0.020  1.090
 7K4  C3   H29  single    0.970  0.020  1.090
 7K4  C3   H30  single    0.970  0.020  1.090
 7K4  C5   H32  single    0.970  0.020  1.090
 7K4  C5   H31  single    0.970  0.020  1.090
 7K4  C6   H34  single    0.970  0.020  1.090
 7K4  C6   H33  single    0.970  0.020  1.090
 7K4  C10  H36  single    0.930  0.020  1.080
 7K4  C16  H37  single    0.930  0.020  1.080
 7K4  C19  H38  single    0.970  0.020  1.090
 7K4  C19  H39  single    0.970  0.020  1.090
 7K4  C21  H40  single    0.930  0.020  1.080
 7K4  C22  H41  single    0.930  0.020  1.080
 7K4  C23  H42  single    0.930  0.020  1.080
 7K4  C24  H43  single    0.930  0.020  1.080
 7K4  C25  H44  single    0.930  0.020  1.080
 7K4  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
 7K4  H27  C1   H26  107.31  3.000
 7K4  H27  C1   H28  107.35  3.000
 7K4  H26  C1   H28  108.30  3.000
 7K4  H27  C1   C2   110.14  3.000
 7K4  H26  C1   C2   112.00  3.000
 7K4  H28  C1   C2   111.53  3.000
 7K4  C20  C2   C19  112.53  3.000
 7K4  C20  C2   C3   111.56  3.000
 7K4  C19  C2   C3   101.75  3.000
 7K4  C3   C2   C1   108.58  3.000
 7K4  C20  C2   C1   113.25  3.000
 7K4  C19  C2   C1   108.49  3.000
 7K4  H30  C3   H29  107.26  3.000
 7K4  H30  C3   N4   111.24  3.000
 7K4  H29  C3   N4   110.82  3.000
 7K4  H30  C3   C2   112.10  3.000
 7K4  H29  C3   C2   111.67  3.000
 7K4  N4   C3   C2   103.82  3.000
 7K4  C17  N4   C5   123.84  3.000
 7K4  C5   N4   C3   121.56  3.000
 7K4  C17  N4   C3   113.68  3.000
 7K4  H31  C5   H32  107.37  3.000
 7K4  H31  C5   C6   107.97  3.000
 7K4  H32  C5   C6   110.31  3.000
 7K4  H31  C5   N4   109.79  3.000
 7K4  H32  C5   N4   108.69  3.000
 7K4  C6   C5   N4   112.58  3.000
 7K4  H33  C6   H34  107.70  3.000
 7K4  H33  C6   O7   110.54  3.000
 7K4  H34  C6   O7   111.34  3.000
 7K4  H33  C6   C5   110.71  3.000
 7K4  H34  C6   C5   109.07  3.000
 7K4  O7   C6   C5   107.49  3.000
 7K4  C9   C8   O7   124.55  3.000
 7K4  O7   C8   C16  116.04  3.000
 7K4  C9   C8   C16  119.41  3.000
 7K4  H36  C10  C9   120.29  3.000
 7K4  H36  C10  C11  120.26  3.000
 7K4  C9   C10  C11  119.44  3.000
 7K4  F12  C11  C13  118.55  3.000
 7K4  C13  C11  C10  120.81  3.000
 7K4  F12  C11  C10  120.64  3.000
 7K4  C16  C13  C14  120.55  3.000
 7K4  C16  C13  C11  119.82  3.000
 7K4  C14  C13  C11  119.63  3.000
 7K4  N15  C14  C13  180.00  3.000
 7K4  H37  C16  C13  120.05  3.000
 7K4  H37  C16  C8   120.06  3.000
 7K4  C13  C16  C8   119.89  3.000
 7K4  H39  C19  H38  106.80  3.000
 7K4  H39  C19  C17  111.50  3.000
 7K4  H38  C19  C17  107.91  3.000
 7K4  H39  C19  C2   113.13  3.000
 7K4  H38  C19  C2   112.56  3.000
 7K4  C17  C19  C2   104.90  3.000
 7K4  H40  C21  C20  120.16  3.000
 7K4  H40  C21  C22  118.42  3.000
 7K4  C20  C21  C22  121.42  3.000
 7K4  H41  C22  C23  120.17  3.000
 7K4  H41  C22  C21  119.64  3.000
 7K4  C23  C22  C21  120.18  3.000
 7K4  H42  C23  C24  120.50  3.000
 7K4  H42  C23  C22  120.34  3.000
 7K4  C24  C23  C22  119.15  3.000
 7K4  H43  C24  C25  119.41  3.000
 7K4  H43  C24  C23  120.18  3.000
 7K4  C25  C24  C23  120.41  3.000
 7K4  H44  C25  C20  120.48  3.000
 7K4  H44  C25  C24  118.35  3.000
 7K4  C20  C25  C24  121.18  3.000
 7K4  C8   O7   C6   119.24  3.000
 7K4  H35  C9   C10  118.11  3.000
 7K4  H35  C9   C8   121.26  3.000
 7K4  C10  C9   C8   120.62  3.000
 7K4  O18  C17  C19  126.34  3.000
 7K4  O18  C17  N4   125.95  3.000
 7K4  C19  C17  N4   107.71  3.000
 7K4  C25  C20  C21  117.66  3.000
 7K4  C25  C20  C2   122.53  3.000
 7K4  C21  C20  C2   119.81  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
 7K4  CONST_01  C11  C10  C9   C8     0.00   0.0  0
 7K4  CONST_02  C11  C13  C16  C8     0.00   0.0  0
 7K4  CONST_03  C16  C13  C11  C10    0.00   0.0  0
 7K4  CONST_04  C16  C8   C9   C10    0.00   0.0  0
 7K4  CONST_05  C9   C10  C11  C13    0.00   0.0  0
 7K4  CONST_06  C9   C8   C16  C13    0.00   0.0  0
 7K4  CONST_07  C24  C25  C20  C21    0.00   0.0  0
 7K4  CONST_08  C24  C23  C22  C21    0.00   0.0  0
 7K4  CONST_09  C25  C20  C21  C22    0.00   0.0  0
 7K4  CONST_10  C25  C24  C23  C22    0.00   0.0  0
 7K4  CONST_11  C20  C21  C22  C23    0.00   0.0  0
 7K4  CONST_12  C20  C25  C24  C23    0.00   0.0  0
 7K4  CONST_13  C22  C21  C20  C2   180.00   0.0  0
 7K4  CONST_14  C24  C25  C20  C2   180.00   0.0  0
 7K4  CONST_15  C19  C17  N4   C3     0.00   0.0  0
 7K4  CONST_16  C14  C13  C16  C8   180.00   0.0  0
 7K4  CONST_17  C14  C13  C11  C10  180.00   0.0  0
 7K4  CONST_18  O7   C8   C9   C10  180.00   0.0  0
 7K4  CONST_19  O7   C8   C16  C13  180.00   0.0  0
 7K4  CONST_20  F12  C11  C13  C16  180.00   0.0  0
 7K4  CONST_21  F12  C11  C10  C9   180.00   0.0  0
 7K4  CONST_22  O18  C17  N4   C3   180.00   0.0  0
 7K4  CONST_23  C19  C17  N4   C5   180.00   0.0  0
 7K4  CONST_24  H40  C21  C20  C2     0.00   0.0  0
 7K4  CONST_25  H44  C25  C20  C2     0.00   0.0  0
 7K4  CONST_26  H36  C10  C9   C8   180.00   0.0  0
 7K4  CONST_27  H35  C9   C10  C11  180.00   0.0  0
 7K4  CONST_28  H37  C16  C13  C11  180.00   0.0  0
 7K4  CONST_29  H42  C23  C22  C21  180.00   0.0  0
 7K4  CONST_30  H43  C24  C23  C22  180.00   0.0  0
 7K4  CONST_31  H41  C22  C23  C24  180.00   0.0  0
 7K4  CONST_32  O18  C17  N4   C5     0.00   0.0  0
 7K4  Var_01    N4   C17  C19  C2    15.62  30.0  1
 7K4  Var_02    C17  N4   C3   C2   -19.74  30.0  1
 7K4  Var_03    C6   C5   N4   C3    66.19  30.0  3
 7K4  Var_04    C9   C8   O7   C6    -6.97  30.0  3
 7K4  Var_05    O7   C6   C5   N4    57.01  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
 7K4  chir_01  C2  C19  C20  C3  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
 7K4  plan-1  C8   0.020
 7K4  plan-1  C10  0.020
 7K4  plan-1  C11  0.020
 7K4  plan-1  C13  0.020
 7K4  plan-1  C14  0.020
 7K4  plan-1  C16  0.020
 7K4  plan-1  O7   0.020
 7K4  plan-1  C9   0.020
 7K4  plan-1  F12  0.020
 7K4  plan-1  N15  0.020
 7K4  plan-1  H36  0.020
 7K4  plan-1  H37  0.020
 7K4  plan-1  H35  0.020
 7K4  plan-2  C2   0.020
 7K4  plan-2  C21  0.020
 7K4  plan-2  C22  0.020
 7K4  plan-2  C23  0.020
 7K4  plan-2  C24  0.020
 7K4  plan-2  C25  0.020
 7K4  plan-2  C20  0.020
 7K4  plan-2  H40  0.020
 7K4  plan-2  H41  0.020
 7K4  plan-2  H42  0.020
 7K4  plan-2  H43  0.020
 7K4  plan-2  H44  0.020
 7K4  plan-3  C3   0.020
 7K4  plan-3  N4   0.020
 7K4  plan-3  C5   0.020
 7K4  plan-3  C19  0.020
 7K4  plan-3  C17  0.020
 7K4  plan-3  O18  0.020

