# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 13:59:17 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 5-[2-[(4~{S})-4-~{tert}-butyl-2-oxidanylidene-pyrrolidin-1-yl]ethoxy]-2-fluoranyl-benzenecarbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)[C@H]1CN(CCOc2ccc(F)c(c2)C#N)C(=O)C1
#
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
 7BP  7BP  5-[2-[(4~{S})-4-~{tert}-butyl-2-oxidanylidene-pyrrolidin-1-yl]ethoxy]-2-fluoranyl-benzenecarbonitrile  ligand  43  22  .  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_7BP
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
 7BP  C1   C  CH3   0  -0.653  -2.7621  -2.1500   1.0294
 7BP  C2   C  CT    0  -0.099  -4.0106  -1.3144   0.7373
 7BP  C3   C  CH3   0  -0.644  -4.6048  -0.8331   2.0636
 7BP  C5   C  CH1   0  -0.239  -3.7165  -0.0894  -0.1469
 7BP  C7   C  CH2   0  -0.243  -2.7317   0.9298   0.4424
 7BP  C10  C  CH2   0  -0.213  -0.0541   2.4595   0.1713
 7BP  C12  C  CR6   0   0.411   1.7079   0.8649   0.1432
 7BP  C13  C  CR16  0  -0.347   2.3134   1.3952   1.2826
 7BP  C14  C  CR16  0  -0.388   3.4322   0.7871   1.8374
 7BP  C15  C  CR6   0   0.548   3.9455  -0.3463   1.2538
 7BP  C21  C  C     0   0.546  -2.3184   0.8555  -1.8628
 7BP  C23  C  CH2   0  -0.594  -3.1378  -0.3710  -1.5339
 7BP  C4   C  CH3   0  -0.643  -5.0380  -2.1902   0.0177
 7BP  N8   N  NT    0  -0.457  -2.1631   1.5669  -0.7270
 7BP  C9   C  CH2   0  -0.331  -1.3206   2.7268  -0.6173
 7BP  O11  O  O2    0  -0.461   0.6282   1.3897  -0.4566
 7BP  F16  F  F     0  -0.290   5.0182  -0.9509   1.7706
 7BP  C17  C  CR6   0  -0.165   3.3593  -0.8885   0.1155
 7BP  C18  C  CSP   0   0.076   3.9106  -2.0650  -0.4683
 7BP  N19  N  NS    0  -0.238   4.3530  -3.0165  -0.9426
 7BP  C20  C  CR16  0  -0.329   2.2374  -0.2829  -0.4396
 7BP  O22  O  O     0  -0.501  -1.8717   1.1535  -2.9585
 7BP  H24  H  HCH3  0   0.232  -3.0314  -3.0161   1.6366
 7BP  H25  H  HCH3  0   0.226  -2.2911  -2.5311   0.1218
 7BP  H26  H  HCH3  0   0.226  -2.0085  -1.5904   1.5856
 7BP  H29  H  HCH3  0   0.229  -3.8834  -0.2565   2.6466
 7BP  H27  H  HCH3  0   0.224  -5.4824  -0.2033   1.9005
 7BP  H28  H  HCH3  0   0.229  -4.9154  -1.6800   2.6791
 7BP  H6   H  HCH1  0   0.253  -4.6694   0.4329  -0.2905
 7BP  H33  H  HCH2  0   0.251  -3.2253   1.6661   1.0788
 7BP  H34  H  HCH2  0   0.233  -1.9513   0.4482   1.0414
 7BP  H38  H  HCH2  0   0.253   0.5560   3.3687   0.1827
 7BP  H37  H  HCH2  0   0.238  -0.2912   2.2048   1.2101
 7BP  H39  H  HCR6  0   0.305   1.9354   2.2888   1.7593
 7BP  H40  H  HCR6  0   0.302   3.8975   1.2033   2.7205
 7BP  H42  H  HCH2  0   0.267  -2.4699  -1.2383  -1.5432
 7BP  H43  H  HCH2  0   0.275  -3.8950  -0.5447  -2.2982
 7BP  H30  H  HCH3  0   0.228  -5.3107  -3.0538   0.6276
 7BP  H31  H  HCH3  0   0.223  -5.9528  -1.6327  -0.1959
 7BP  H32  H  HCH3  0   0.231  -4.6511  -2.5702  -0.9305
 7BP  H36  H  HCH2  0   0.264  -1.8609   3.5333  -0.1145
 7BP  H35  H  HCH2  0   0.266  -1.0768   3.0751  -1.6202
 7BP  H41  H  HCR6  0   0.299   1.7755  -0.7038  -1.3229

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
 7BP  F16  C15  single    1.335  0.020  1.335
 7BP  C14  C15  aromatic  1.374  0.020  1.374
 7BP  C14  C13  aromatic  1.389  0.020  1.389
 7BP  C15  C17  aromatic  1.390  0.020  1.390
 7BP  C13  C12  aromatic  1.395  0.020  1.395
 7BP  C17  C18  single    1.424  0.020  1.424
 7BP  C17  C20  aromatic  1.390  0.020  1.390
 7BP  C4   C2   single    1.530  0.020  1.530
 7BP  C12  C20  aromatic  1.392  0.020  1.392
 7BP  C12  O11  single    1.342  0.020  1.342
 7BP  C1   C2   single    1.530  0.020  1.530
 7BP  C5   C23  single    1.529  0.020  1.529
 7BP  C5   C2   single    1.539  0.020  1.539
 7BP  C5   C7   single    1.535  0.020  1.535
 7BP  C18  N19  triple    1.151  0.020  1.151
 7BP  C10  O11  single    1.416  0.020  1.416
 7BP  C10  C9   single    1.516  0.020  1.516
 7BP  C23  C21  single    1.511  0.020  1.511
 7BP  C2   C3   single    1.531  0.020  1.531
 7BP  O22  C21  double    1.220  0.020  1.220
 7BP  C21  N8   single    1.349  0.020  1.349
 7BP  C7   N8   single    1.448  0.020  1.448
 7BP  N8   C9   single    1.438  0.020  1.438
 7BP  C1   H24  single    0.970  0.020  1.090
 7BP  C1   H25  single    0.970  0.020  1.090
 7BP  C1   H26  single    0.970  0.020  1.090
 7BP  C3   H29  single    0.970  0.020  1.090
 7BP  C3   H27  single    0.970  0.020  1.090
 7BP  C3   H28  single    0.970  0.020  1.090
 7BP  C5   H6   single    0.970  0.020  1.090
 7BP  C7   H33  single    0.970  0.020  1.090
 7BP  C7   H34  single    0.970  0.020  1.090
 7BP  C10  H38  single    0.970  0.020  1.090
 7BP  C10  H37  single    0.970  0.020  1.090
 7BP  C13  H39  single    0.930  0.020  1.080
 7BP  C14  H40  single    0.930  0.020  1.080
 7BP  C23  H42  single    0.970  0.020  1.090
 7BP  C23  H43  single    0.970  0.020  1.090
 7BP  C4   H30  single    0.970  0.020  1.090
 7BP  C4   H31  single    0.970  0.020  1.090
 7BP  C4   H32  single    0.970  0.020  1.090
 7BP  C9   H36  single    0.970  0.020  1.090
 7BP  C9   H35  single    0.970  0.020  1.090
 7BP  C20  H41  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
 7BP  H26  C1   H25  107.76  3.000
 7BP  H26  C1   H24  107.09  3.000
 7BP  H25  C1   H24  106.98  3.000
 7BP  H26  C1   C2   112.37  3.000
 7BP  H25  C1   C2   112.58  3.000
 7BP  H24  C1   C2   109.77  3.000
 7BP  C4   C2   C5   108.28  3.000
 7BP  C5   C2   C3   108.76  3.000
 7BP  C4   C2   C3   109.08  3.000
 7BP  C3   C2   C1   108.84  3.000
 7BP  C5   C2   C1   112.85  3.000
 7BP  C4   C2   C1   108.97  3.000
 7BP  H28  C3   H27  107.62  3.000
 7BP  H28  C3   H29  107.24  3.000
 7BP  H27  C3   H29  107.82  3.000
 7BP  H28  C3   C2   110.79  3.000
 7BP  H27  C3   C2   111.33  3.000
 7BP  H29  C3   C2   111.84  3.000
 7BP  H6   C5   C23  107.33  3.000
 7BP  H6   C5   C7   106.96  3.000
 7BP  C23  C5   C7   103.17  3.000
 7BP  H6   C5   C2   106.76  3.000
 7BP  C7   C5   C2   115.50  3.000
 7BP  C23  C5   C2   116.54  3.000
 7BP  H34  C7   H33  107.46  3.000
 7BP  H34  C7   N8   110.82  3.000
 7BP  H33  C7   N8   110.59  3.000
 7BP  H34  C7   C5   112.04  3.000
 7BP  H33  C7   C5   112.44  3.000
 7BP  N8   C7   C5   103.53  3.000
 7BP  H37  C10  H38  107.69  3.000
 7BP  H37  C10  O11  110.43  3.000
 7BP  H38  C10  O11  111.32  3.000
 7BP  H37  C10  C9   110.70  3.000
 7BP  H38  C10  C9   108.94  3.000
 7BP  O11  C10  C9   107.77  3.000
 7BP  C20  C12  O11  116.19  3.000
 7BP  O11  C12  C13  124.45  3.000
 7BP  C20  C12  C13  119.36  3.000
 7BP  H39  C13  C14  117.87  3.000
 7BP  H39  C13  C12  121.51  3.000
 7BP  C14  C13  C12  120.62  3.000
 7BP  H40  C14  C15  120.23  3.000
 7BP  H40  C14  C13  120.28  3.000
 7BP  C15  C14  C13  119.49  3.000
 7BP  C17  C15  F16  118.62  3.000
 7BP  C17  C15  C14  120.78  3.000
 7BP  F16  C15  C14  120.60  3.000
 7BP  O22  C21  N8   125.81  3.000
 7BP  N8   C21  C23  107.89  3.000
 7BP  O22  C21  C23  126.30  3.000
 7BP  H43  C23  H42  106.96  3.000
 7BP  H43  C23  C21  110.70  3.000
 7BP  H42  C23  C21  108.08  3.000
 7BP  H43  C23  C5   113.74  3.000
 7BP  H42  C23  C5   112.61  3.000
 7BP  C21  C23  C5   104.66  3.000
 7BP  H32  C4   H31  107.72  3.000
 7BP  H32  C4   H30  107.35  3.000
 7BP  H31  C4   H30  107.68  3.000
 7BP  H32  C4   C2   111.69  3.000
 7BP  H31  C4   C2   111.23  3.000
 7BP  H30  C4   C2   110.96  3.000
 7BP  C9   N8   C21  123.85  3.000
 7BP  C9   N8   C7   121.56  3.000
 7BP  C21  N8   C7   113.75  3.000
 7BP  H35  C9   H36  107.35  3.000
 7BP  H35  C9   N8   108.59  3.000
 7BP  H36  C9   N8   109.92  3.000
 7BP  H35  C9   C10  110.39  3.000
 7BP  H36  C9   C10  107.68  3.000
 7BP  N8   C9   C10  112.77  3.000
 7BP  C12  O11  C10  119.01  3.000
 7BP  C20  C17  C18  120.56  3.000
 7BP  C20  C17  C15  119.81  3.000
 7BP  C18  C17  C15  119.63  3.000
 7BP  N19  C18  C17  180.00  3.000
 7BP  H41  C20  C17  120.06  3.000
 7BP  H41  C20  C12  120.01  3.000
 7BP  C17  C20  C12  119.93  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
 7BP  CONST_01  C15  C14  C13  C12     0.00   0.0  0
 7BP  CONST_02  C15  C17  C20  C12     0.00   0.0  0
 7BP  CONST_03  C17  C15  C14  C13     0.00   0.0  0
 7BP  CONST_04  C17  C20  C12  C13     0.00   0.0  0
 7BP  CONST_05  C20  C17  C15  C14     0.00   0.0  0
 7BP  CONST_06  C20  C12  C13  C14     0.00   0.0  0
 7BP  CONST_07  C23  C21  N8   C7      0.00   0.0  0
 7BP  CONST_08  C18  C17  C20  C12   180.00   0.0  0
 7BP  CONST_09  F16  C15  C14  C13   180.00   0.0  0
 7BP  CONST_10  C18  C17  C15  C14   180.00   0.0  0
 7BP  CONST_11  O11  C12  C13  C14   180.00   0.0  0
 7BP  CONST_12  C17  C20  C12  O11   180.00   0.0  0
 7BP  CONST_13  C20  C17  C15  F16   180.00   0.0  0
 7BP  CONST_14  O22  C21  N8   C7    180.00   0.0  0
 7BP  CONST_15  C9   N8   C21  C23   180.00   0.0  0
 7BP  CONST_16  H40  C14  C13  C12   180.00   0.0  0
 7BP  CONST_17  H41  C20  C12  C13   180.00   0.0  0
 7BP  CONST_18  H39  C13  C14  C15   180.00   0.0  0
 7BP  CONST_19  O22  C21  N8   C9      0.00   0.0  0
 7BP  Var_01    N8   C21  C23  C5     13.57  30.0  1
 7BP  Var_02    C21  N8   C7   C5    -19.00  30.0  1
 7BP  Var_03    C10  C9   N8   C7     61.71  30.0  3
 7BP  Var_04    C13  C12  O11  C10    -7.70  30.0  2
 7BP  Var_05    C9   C10  O11  C12  -172.55  30.0  2
 7BP  Var_06    O11  C10  C9   N8     56.92  30.0  2
 7BP  Var_07    H30  C4   C2   C5   -177.61  30.0  3
 7BP  Var_08    H24  C1   C2   C5   -178.58  30.0  3
 7BP  Var_09    H29  C3   C2   C5    -65.86  30.0  3

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
 7BP  chir_01  C5  C23  C2  C7  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
 7BP  plan-1  C12  0.020
 7BP  plan-1  C13  0.020
 7BP  plan-1  C14  0.020
 7BP  plan-1  C15  0.020
 7BP  plan-1  O11  0.020
 7BP  plan-1  F16  0.020
 7BP  plan-1  C17  0.020
 7BP  plan-1  C18  0.020
 7BP  plan-1  N19  0.020
 7BP  plan-1  C20  0.020
 7BP  plan-1  H39  0.020
 7BP  plan-1  H40  0.020
 7BP  plan-1  H41  0.020
 7BP  plan-2  C7   0.020
 7BP  plan-2  C21  0.020
 7BP  plan-2  C23  0.020
 7BP  plan-2  N8   0.020
 7BP  plan-2  C9   0.020
 7BP  plan-2  O22  0.020

