# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 01:15:58 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: 4-cyano-N-[(1S,2R)-2-phenylcyclopropyl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(N[C@H]1C[C@@H]1c2ccccc2)c3ccc(cc3)C#N
#
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
 S38  S38  4-cyano-N-[(1S,2R)-2-phenylcyclopropyl]benzamide  ligand  34  20  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_S38
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
 S38  C1    C  CR16  0  -0.222  -4.0830   0.7413  -0.8637
 S38  C2    C  CR6   0   0.005  -4.7991   0.2011   0.2020
 S38  C3    C  CR16  0  -0.226  -4.1427  -0.4927   1.2181
 S38  C4    C  CR16  0  -0.257  -2.7700  -0.6420   1.1612
 S38  C5    C  CR6   0  -0.020  -2.0454  -0.1228   0.0909
 S38  C6    C  CR16  0  -0.279  -2.7101   0.5750  -0.9149
 S38  C7    C  C     0   0.541  -0.5583  -0.3089   0.0955
 S38  N8    N  NH1   0  -0.663   0.0424  -0.2952  -1.1087
 S38  C9    C  CH1   0  -0.051   1.4473  -0.4777  -1.2439
 S38  C10   C  CH1   0  -0.364   2.3670   0.6464  -0.8501
 S38  C11   C  CH2   0  -0.506   2.1561   0.2981  -2.2973
 S38  C12   C  CR6   0   0.228   3.6379   0.3646  -0.1424
 S38  C13   C  CR16  0  -0.322   4.0032   1.1578   0.9449
 S38  C14   C  CR16  0  -0.240   5.1797   0.9191   1.6419
 S38  C15   C  CR16  0  -0.276   6.0153  -0.1234   1.2647
 S38  C16   C  CR16  0  -0.236   5.6617  -0.9215   0.1841
 S38  C17   C  CR16  0  -0.355   4.4868  -0.6791  -0.5134
 S38  O18   O  O     0  -0.465   0.0518  -0.4629   1.1405
 S38  C19   C  CSP   0   0.062  -6.2166   0.3639   0.2567
 S38  N20   N  NS    0  -0.244  -7.3604   0.4931   0.3004
 S38  H1    H  HCR6  0   0.290  -4.5939   1.2893  -1.6431
 S38  H3    H  HCR6  0   0.288  -4.7023  -0.9077   2.0449
 S38  H4    H  HCR6  0   0.277  -2.2591  -1.1716   1.9531
 S38  H6    H  HCR6  0   0.276  -2.1687   1.0192  -1.7394
 S38  HN8   H  HNH1  0   0.411  -0.5175  -0.3415  -1.9451
 S38  H9    H  HCH1  0   0.276   1.8078  -1.4826  -1.0393
 S38  H10   H  HCH1  0   0.271   1.8635   1.5472  -0.5174
 S38  H11   H  HCH2  0   0.267   2.9542  -0.1954  -2.8374
 S38  H11A  H  HCH2  0   0.275   1.5778   0.9949  -2.8913
 S38  H13   H  HCR6  0   0.249   3.3566   1.9718   1.2515
 S38  H14   H  HCR6  0   0.254   5.4431   1.5496   2.4817
 S38  H15   H  HCR6  0   0.254   6.9346  -0.3111   1.8041
 S38  H16   H  HCR6  0   0.255   6.3062  -1.7352  -0.1233
 S38  H17   H  HCR6  0   0.249   4.2412  -1.3141  -1.3570

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
 S38  C1   C2    aromatic  1.393  0.020  1.393
 S38  C1   C6    aromatic  1.384  0.020  1.384
 S38  C2   C3    aromatic  1.395  0.020  1.395
 S38  C2   C19   single    1.428  0.020  1.428
 S38  C3   C4    aromatic  1.382  0.020  1.382
 S38  C4   C5    aromatic  1.393  0.020  1.393
 S38  C5   C6    aromatic  1.393  0.020  1.393
 S38  C5   C7    single    1.499  0.020  1.499
 S38  C7   N8    single    1.346  0.020  1.346
 S38  C7   O18   double    1.220  0.020  1.220
 S38  N8   C9    single    1.423  0.020  1.423
 S38  C9   C10   single    1.505  0.020  1.505
 S38  C9   C11   single    1.488  0.020  1.488
 S38  C10  C11   single    1.503  0.020  1.503
 S38  C10  C12   single    1.482  0.020  1.482
 S38  C12  C13   aromatic  1.394  0.020  1.394
 S38  C12  C17   aromatic  1.396  0.020  1.396
 S38  C13  C14   aromatic  1.388  0.020  1.388
 S38  C14  C15   aromatic  1.388  0.020  1.388
 S38  C15  C16   aromatic  1.389  0.020  1.389
 S38  C16  C17   aromatic  1.388  0.020  1.388
 S38  C19  N20   triple    1.152  0.020  1.152
 S38  C1   H1    single    0.930  0.020  1.080
 S38  C3   H3    single    0.930  0.020  1.080
 S38  C4   H4    single    0.930  0.020  1.080
 S38  C6   H6    single    0.930  0.020  1.080
 S38  N8   HN8   single    0.860  0.020  1.020
 S38  C9   H9    single    0.970  0.020  1.090
 S38  C10  H10   single    0.970  0.020  1.090
 S38  C11  H11   single    0.970  0.020  1.090
 S38  C11  H11A  single    0.970  0.020  1.090
 S38  C13  H13   single    0.930  0.020  1.080
 S38  C14  H14   single    0.930  0.020  1.080
 S38  C15  H15   single    0.930  0.020  1.080
 S38  C16  H16   single    0.930  0.020  1.080
 S38  C17  H17   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
 S38  H1    C1   C6   120.20  3.000
 S38  H1    C1   C2   120.34  3.000
 S38  C6    C1   C2   119.45  3.000
 S38  C19   C2   C3   119.74  3.000
 S38  C19   C2   C1   119.70  3.000
 S38  C3    C2   C1   120.56  3.000
 S38  H3    C3   C4   120.27  3.000
 S38  H3    C3   C2   120.31  3.000
 S38  C4    C3   C2   119.42  3.000
 S38  H4    C4   C5   119.97  3.000
 S38  H4    C4   C3   119.49  3.000
 S38  C5    C4   C3   120.53  3.000
 S38  C7    C5   C6   122.54  3.000
 S38  C7    C5   C4   117.87  3.000
 S38  C6    C5   C4   119.56  3.000
 S38  H6    C6   C5   121.15  3.000
 S38  H6    C6   C1   118.38  3.000
 S38  C5    C6   C1   120.46  3.000
 S38  O18   C7   N8   122.99  3.000
 S38  O18   C7   C5   120.97  3.000
 S38  N8    C7   C5   116.03  3.000
 S38  HN8   N8   C9   117.63  3.000
 S38  HN8   N8   C7   119.62  3.000
 S38  C9    N8   C7   121.62  3.000
 S38  H9    C9   C11  117.21  3.000
 S38  H9    C9   C10  116.02  3.000
 S38  C11   C9   C10   60.31  3.000
 S38  H9    C9   N8   115.34  3.000
 S38  C11   C9   N8   118.08  3.000
 S38  C10   C9   N8   118.86  3.000
 S38  H10   C10  C12  114.18  3.000
 S38  H10   C10  C11  115.01  3.000
 S38  C12   C10  C11  122.42  3.000
 S38  H10   C10  C9   114.65  3.000
 S38  C12   C10  C9   120.48  3.000
 S38  C11   C10  C9    59.29  3.000
 S38  H11A  C11  H11  114.42  3.000
 S38  H11A  C11  C10  116.99  3.000
 S38  H11   C11  C10  118.84  3.000
 S38  H11A  C11  C9   118.00  3.000
 S38  H11   C11  C9   117.81  3.000
 S38  C10   C11  C9    60.40  3.000
 S38  C17   C12  C13  118.25  3.000
 S38  C17   C12  C10  122.48  3.000
 S38  C13   C12  C10  119.27  3.000
 S38  H13   C13  C14  119.51  3.000
 S38  H13   C13  C12  119.44  3.000
 S38  C14   C13  C12  121.04  3.000
 S38  H14   C14  C15  120.11  3.000
 S38  H14   C14  C13  119.70  3.000
 S38  C15   C14  C13  120.19  3.000
 S38  H15   C15  C16  120.28  3.000
 S38  H15   C15  C14  120.41  3.000
 S38  C16   C15  C14  119.31  3.000
 S38  H16   C16  C17  119.51  3.000
 S38  H16   C16  C15  120.08  3.000
 S38  C17   C16  C15  120.41  3.000
 S38  H17   C17  C16  118.73  3.000
 S38  H17   C17  C12  120.48  3.000
 S38  C16   C17  C12  120.80  3.000
 S38  N20   C19  C2   180.00  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
 S38  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 S38  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 S38  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 S38  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 S38  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 S38  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 S38  CONST_07  C15  C14  C13  C12     0.00   0.0  0
 S38  CONST_08  C15  C16  C17  C12     0.00   0.0  0
 S38  CONST_09  C16  C17  C12  C13     0.00   0.0  0
 S38  CONST_10  C16  C15  C14  C13     0.00   0.0  0
 S38  CONST_11  C17  C12  C13  C14     0.00   0.0  0
 S38  CONST_12  C17  C16  C15  C14     0.00   0.0  0
 S38  CONST_13  C14  C13  C12  C10   180.00   0.0  0
 S38  CONST_14  C16  C17  C12  C10   180.00   0.0  0
 S38  CONST_15  C7   C5   C6   C1    180.00   0.0  0
 S38  CONST_16  C7   C5   C4   C3    180.00   0.0  0
 S38  CONST_17  C19  C2   C3   C4    180.00   0.0  0
 S38  CONST_18  C19  C2   C1   C6    180.00   0.0  0
 S38  CONST_19  H3   C3   C2   C1    180.00   0.0  0
 S38  CONST_20  H6   C6   C1   C2    180.00   0.0  0
 S38  CONST_21  H4   C4   C3   C2    180.00   0.0  0
 S38  CONST_22  H1   C1   C2   C3    180.00   0.0  0
 S38  CONST_23  H13  C13  C12  C10     0.00   0.0  0
 S38  CONST_24  H17  C17  C12  C10     0.00   0.0  0
 S38  CONST_25  H14  C14  C13  C12   180.00   0.0  0
 S38  CONST_26  H16  C16  C17  C12   180.00   0.0  0
 S38  CONST_27  H15  C15  C14  C13   180.00   0.0  0
 S38  CONST_28  C9   N8   C7   C5    180.00   0.0  0
 S38  CONST_29  O18  C7   N8   C9      0.00   0.0  0
 S38  CONST_30  HN8  N8   C7   C5      0.00   0.0  0
 S38  Var_01    C13  C12  C10  C9   -136.03  30.0  2
 S38  Var_02    C12  C10  C11  C9    108.76  30.0  1
 S38  Var_03    N8   C7   C5   C4    154.74  30.0  2
 S38  Var_04    C10  C9   N8   C7    -73.89  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
 S38  chir_01  C9   N8  C10  C11  both
 S38  chir_02  C10  C9  C11  C12  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
 S38  plan-1  C1   0.020
 S38  plan-1  C2   0.020
 S38  plan-1  C3   0.020
 S38  plan-1  C4   0.020
 S38  plan-1  C5   0.020
 S38  plan-1  C6   0.020
 S38  plan-1  C7   0.020
 S38  plan-1  C19  0.020
 S38  plan-1  N20  0.020
 S38  plan-1  H1   0.020
 S38  plan-1  H3   0.020
 S38  plan-1  H4   0.020
 S38  plan-1  H6   0.020
 S38  plan-2  C10  0.020
 S38  plan-2  C12  0.020
 S38  plan-2  C13  0.020
 S38  plan-2  C14  0.020
 S38  plan-2  C15  0.020
 S38  plan-2  C16  0.020
 S38  plan-2  C17  0.020
 S38  plan-2  H13  0.020
 S38  plan-2  H14  0.020
 S38  plan-2  H15  0.020
 S38  plan-2  H16  0.020
 S38  plan-2  H17  0.020
 S38  plan-3  C5   0.020
 S38  plan-3  C7   0.020
 S38  plan-3  N8   0.020
 S38  plan-3  C9   0.020
 S38  plan-3  O18  0.020
 S38  plan-3  HN8  0.020

