# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 16:45:44 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: (2~{S})-~{N}-[(1~{R},2~{R})-1-(aminomethyl)-2-[4-[4-(trifluoromethyl)phenyl]phenyl]cyclopropyl]-2-azanyl-butanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H](N)C(=O)N[C@]1(CN)C[C@@H]1c2ccc(cc2)c3ccc(cc3)C(F)(F)F
#
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
 H9B  H9B  (2~{S})-~{N}-[(1~{R},2~{R})-1-(aminomethyl)-2-[4-[4-(trifluoromethyl)phenyl]phenyl]cyclopropyl]-2-azanyl-butanamide  ligand  52  28  .  2022-07-25  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_H9B
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
 H9B  C5   C  CR6   0   0.209  -1.9106   1.8371   0.0340
 H9B  C6   C  CR16  0  -0.319  -1.3004   1.2747  -1.0849
 H9B  C7   C  CR16  0  -0.285   0.0459   0.9463  -1.0741
 H9B  C8   C  CR6   0   0.072   0.8377   1.1826   0.0486
 H9B  C10  C  CR16  0  -0.297  -1.1154   2.0769   1.1544
 H9B  C15  C  CH2   0  -0.431  -4.3680  -3.2790  -0.2718
 H9B  C17  C  CR6   0   0.102   2.2707   0.8363   0.0578
 H9B  C20  C  CR6   0  -0.215   4.9951   0.1818   0.0723
 H9B  C21  C  CR16  0  -0.256   4.0848  -0.6244  -0.6028
 H9B  C22  C  CR16  0  -0.302   2.7402  -0.2982  -0.6074
 H9B  C25  C  CT    0   1.051   6.4387  -0.2029   0.1088
 H9B  F26  F  F     0  -0.310   6.8503  -0.7275  -1.0527
 H9B  F27  F  F     0  -0.306   7.2384   0.8354   0.3753
 H9B  C19  C  CR16  0  -0.261   4.5445   1.3111   0.7444
 H9B  C18  C  CR16  0  -0.302   3.1975   1.6323   0.7322
 H9B  C9   C  CR16  0  -0.299   0.2315   1.7633   1.1637
 H9B  C2   C  CH1   0  -0.349  -3.3501   2.1712   0.1039
 H9B  C3   C  CH2   0  -0.501  -4.2540   2.2064  -1.0949
 H9B  C1   C  CT    0   0.205  -4.4223   1.1177  -0.0926
 H9B  C23  C  CH2   0  -0.297  -5.6152   1.1405   0.8331
 H9B  N24  N  NH2   0  -0.798  -6.7752   0.5415   0.1907
 H9B  N4   N  NH1   0  -0.676  -4.0044  -0.1786  -0.5196
 H9B  C11  C  C     0   0.580  -3.3846  -1.0671   0.2856
 H9B  O13  O  O     0  -0.480  -3.1312  -0.8389   1.4554
 H9B  C12  C  CH1   0  -0.226  -3.0956  -2.4147  -0.3616
 H9B  N14  N  NH2   0  -0.775  -1.9129  -2.9871   0.2467
 H9B  H1   H  HCR6  0   0.240  -1.8661   1.0962  -1.9899
 H9B  H2   H  HCR6  0   0.251   0.4872   0.5235  -1.9681
 H9B  H3   H  HCR6  0   0.248  -1.5629   2.5087   2.0415
 H9B  H4   H  HCH2  0   0.227  -4.6330  -3.4121   0.7820
 H9B  H5   H  HCH2  0   0.224  -5.2020  -2.7452  -0.7369
 H9B  H6   H  HCR6  0   0.275   4.4090  -1.5154  -1.1244
 H9B  H7   H  HCR6  0   0.263   2.0471  -0.9498  -1.1238
 H9B  H8   H  HCR6  0   0.273   5.2312   1.9578   1.2736
 H9B  H9   H  HCR6  0   0.264   2.8719   2.5314   1.2388
 H9B  H10  H  HCR6  0   0.252   0.8086   1.9518   2.0606
 H9B  H11  H  HCH1  0   0.263  -3.5838   2.8895   0.8837
 H9B  H12  H  HCH2  0   0.269  -5.0077   2.9823  -1.1380
 H9B  H13  H  HCH2  0   0.267  -3.8352   1.9481  -2.0610
 H9B  H14  H  HCH2  0   0.215  -5.3360   0.6634   1.7805
 H9B  H15  H  HCH2  0   0.224  -5.8476   2.1814   1.0680
 H9B  H16  H  HNH2  0   0.336  -6.6187  -0.4532   0.0818
 H9B  H17  H  HNH2  0   0.351  -7.5705   0.6179   0.8123
 H9B  H19  H  HNH1  0   0.399  -4.1761  -0.4373  -1.4782
 H9B  H20  H  HCH1  0   0.245  -2.8745  -2.2543  -1.4227
 H9B  H21  H  HNH2  0   0.338  -2.1098  -3.2384   1.2082
 H9B  H22  H  HNH2  0   0.350  -1.6750  -3.8484  -0.2277
 H9B  H24  H  HCH3  0   0.218  -3.4479  -5.2451  -0.4483
 H9B  H25  H  HCH3  0   0.238  -5.1421  -5.1990  -0.9030
 H9B  H26  H  HCH3  0   0.223  -3.9269  -4.5316  -1.9888
 H9B  C16  C  CH3   0  -0.672  -4.2088  -4.6371  -0.9395
 H9B  F28  F  F     0  -0.316   6.6826  -1.1286   1.0513

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
 H9B  F26  C25  single    1.339  0.020  1.339
 H9B  C21  C22  aromatic  1.384  0.020  1.384
 H9B  C21  C20  aromatic  1.391  0.020  1.391
 H9B  F27  C25  single    1.337  0.020  1.337
 H9B  C22  C17  aromatic  1.396  0.020  1.396
 H9B  C7   C6   aromatic  1.386  0.020  1.386
 H9B  C7   C8   aromatic  1.394  0.020  1.394
 H9B  C25  C20  single    1.494  0.020  1.494
 H9B  C25  F28  single    1.343  0.020  1.343
 H9B  C6   C5   aromatic  1.393  0.020  1.393
 H9B  C20  C19  aromatic  1.389  0.020  1.389
 H9B  C17  C8   single    1.474  0.020  1.474
 H9B  C17  C18  aromatic  1.395  0.020  1.395
 H9B  C8   C9   aromatic  1.396  0.020  1.396
 H9B  C19  C18  aromatic  1.385  0.020  1.385
 H9B  C5   C2   single    1.479  0.020  1.479
 H9B  C5   C10  aromatic  1.395  0.020  1.395
 H9B  C2   C3   single    1.502  0.020  1.502
 H9B  C2   C1   single    1.516  0.020  1.516
 H9B  N24  C23  single    1.455  0.020  1.455
 H9B  C9   C10  aromatic  1.383  0.020  1.383
 H9B  C3   C1   single    1.489  0.020  1.489
 H9B  C1   C23  single    1.510  0.020  1.510
 H9B  C1   N4   single    1.427  0.020  1.427
 H9B  O13  C11  double    1.219  0.020  1.219
 H9B  N4   C11  single    1.350  0.020  1.350
 H9B  C11  C12  single    1.523  0.020  1.523
 H9B  N14  C12  single    1.448  0.020  1.448
 H9B  C12  C15  single    1.541  0.020  1.541
 H9B  C15  C16  single    1.522  0.020  1.522
 H9B  C6   H1   single    0.930  0.020  1.080
 H9B  C7   H2   single    0.930  0.020  1.080
 H9B  C10  H3   single    0.930  0.020  1.080
 H9B  C15  H4   single    0.970  0.020  1.090
 H9B  C15  H5   single    0.970  0.020  1.090
 H9B  C21  H6   single    0.930  0.020  1.080
 H9B  C22  H7   single    0.930  0.020  1.080
 H9B  C19  H8   single    0.930  0.020  1.080
 H9B  C18  H9   single    0.930  0.020  1.080
 H9B  C9   H10  single    0.930  0.020  1.080
 H9B  C2   H11  single    0.970  0.020  1.090
 H9B  C3   H12  single    0.970  0.020  1.090
 H9B  C3   H13  single    0.970  0.020  1.090
 H9B  C23  H14  single    0.970  0.020  1.090
 H9B  C23  H15  single    0.970  0.020  1.090
 H9B  N24  H16  single    0.890  0.020  1.040
 H9B  N24  H17  single    0.890  0.020  1.040
 H9B  N4   H19  single    0.860  0.020  1.020
 H9B  C12  H20  single    0.970  0.020  1.090
 H9B  N14  H21  single    0.890  0.020  1.040
 H9B  N14  H22  single    0.890  0.020  1.040
 H9B  C16  H24  single    0.970  0.020  1.090
 H9B  C16  H25  single    0.970  0.020  1.090
 H9B  C16  H26  single    0.970  0.020  1.090

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
 H9B  C2   C5   C10  118.55  3.000
 H9B  C10  C5   C6   117.70  3.000
 H9B  C2   C5   C6   123.74  3.000
 H9B  H1   C6   C7   118.38  3.000
 H9B  H1   C6   C5   120.62  3.000
 H9B  C7   C6   C5   121.00  3.000
 H9B  H2   C7   C8   119.97  3.000
 H9B  H2   C7   C6   118.82  3.000
 H9B  C8   C7   C6   121.19  3.000
 H9B  C9   C8   C17  120.99  3.000
 H9B  C9   C8   C7   117.86  3.000
 H9B  C17  C8   C7   121.15  3.000
 H9B  H3   C10  C9   119.15  3.000
 H9B  H3   C10  C5   119.40  3.000
 H9B  C9   C10  C5   121.45  3.000
 H9B  H5   C15  H4   106.50  3.000
 H9B  H5   C15  C16  109.19  3.000
 H9B  H4   C15  C16  109.83  3.000
 H9B  H5   C15  C12  109.33  3.000
 H9B  H4   C15  C12  108.91  3.000
 H9B  C16  C15  C12  112.87  3.000
 H9B  C18  C17  C22  118.06  3.000
 H9B  C18  C17  C8   120.97  3.000
 H9B  C22  C17  C8   120.97  3.000
 H9B  C19  C20  C25  120.71  3.000
 H9B  C19  C20  C21  119.59  3.000
 H9B  C25  C20  C21  119.66  3.000
 H9B  H6   C21  C22  118.93  3.000
 H9B  H6   C21  C20  121.00  3.000
 H9B  C22  C21  C20  120.07  3.000
 H9B  H7   C22  C21  118.81  3.000
 H9B  H7   C22  C17  120.07  3.000
 H9B  C21  C22  C17  121.11  3.000
 H9B  F27  C25  F26  107.05  3.000
 H9B  F27  C25  F28  106.66  3.000
 H9B  F26  C25  F28  106.43  3.000
 H9B  F28  C25  C20  111.71  3.000
 H9B  F27  C25  C20  112.49  3.000
 H9B  F26  C25  C20  112.12  3.000
 H9B  H8   C19  C18  118.89  3.000
 H9B  H8   C19  C20  121.12  3.000
 H9B  C18  C19  C20  119.98  3.000
 H9B  H9   C18  C19  118.76  3.000
 H9B  H9   C18  C17  120.03  3.000
 H9B  C19  C18  C17  121.19  3.000
 H9B  H10  C9   C10  119.02  3.000
 H9B  H10  C9   C8   120.17  3.000
 H9B  C10  C9   C8   120.79  3.000
 H9B  H11  C2   C1   113.62  3.000
 H9B  H11  C2   C3   115.36  3.000
 H9B  C1   C2   C3    59.15  3.000
 H9B  H11  C2   C5   113.13  3.000
 H9B  C1   C2   C5   121.67  3.000
 H9B  C3   C2   C5   123.59  3.000
 H9B  H13  C3   H12  113.84  3.000
 H9B  H13  C3   C1   117.98  3.000
 H9B  H12  C3   C1   118.17  3.000
 H9B  H13  C3   C2   118.25  3.000
 H9B  H12  C3   C2   117.88  3.000
 H9B  C1   C3   C2    60.90  3.000
 H9B  N4   C1   C23  115.36  3.000
 H9B  N4   C1   C3   115.44  3.000
 H9B  C23  C1   C3   119.39  3.000
 H9B  N4   C1   C2   117.57  3.000
 H9B  C23  C1   C2   117.95  3.000
 H9B  C3   C1   C2    59.95  3.000
 H9B  H15  C23  H14  106.44  3.000
 H9B  H15  C23  N24  108.52  3.000
 H9B  H14  C23  N24  113.90  3.000
 H9B  H15  C23  C1   108.32  3.000
 H9B  H14  C23  C1   108.78  3.000
 H9B  N24  C23  C1   110.66  3.000
 H9B  H17  N24  H16  105.16  3.000
 H9B  H17  N24  C23  108.92  3.000
 H9B  H16  N24  C23  109.18  3.000
 H9B  H19  N4   C11  118.47  3.000
 H9B  H19  N4   C1   117.90  3.000
 H9B  C11  N4   C1   123.63  3.000
 H9B  C12  C11  O13  122.30  3.000
 H9B  C12  C11  N4   114.60  3.000
 H9B  O13  C11  N4   123.01  3.000
 H9B  H20  C12  N14  107.45  3.000
 H9B  H20  C12  C11  108.68  3.000
 H9B  N14  C12  C11  109.05  3.000
 H9B  H20  C12  C15  107.77  3.000
 H9B  N14  C12  C15  115.36  3.000
 H9B  C11  C12  C15  108.36  3.000
 H9B  H22  N14  H21  106.24  3.000
 H9B  H22  N14  C12  109.37  3.000
 H9B  H21  N14  C12  109.76  3.000
 H9B  H26  C16  H25  107.64  3.000
 H9B  H26  C16  H24  107.85  3.000
 H9B  H25  C16  H24  107.15  3.000
 H9B  H26  C16  C15  111.26  3.000
 H9B  H25  C16  C15  110.85  3.000
 H9B  H24  C16  C15  111.89  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
 H9B  CONST_01  C8   C7   C6   C5     0.00   0.0  0
 H9B  CONST_02  C8   C9   C10  C5     0.00   0.0  0
 H9B  CONST_03  C17  C8   C7   C6   180.00   0.0  0
 H9B  CONST_04  C9   C8   C7   C6     0.00   0.0  0
 H9B  CONST_05  C9   C10  C5   C6     0.00   0.0  0
 H9B  CONST_06  C10  C5   C6   C7     0.00   0.0  0
 H9B  CONST_09  C10  C9   C8   C7     0.00   0.0  0
 H9B  CONST_10  C21  C22  C17  C8   180.00   0.0  0
 H9B  CONST_11  C19  C18  C17  C8   180.00   0.0  0
 H9B  CONST_12  C17  C8   C9   C10  180.00   0.0  0
 H9B  CONST_13  C20  C21  C22  C17    0.00   0.0  0
 H9B  CONST_14  C20  C19  C18  C17    0.00   0.0  0
 H9B  CONST_15  C18  C17  C22  C21    0.00   0.0  0
 H9B  CONST_16  C18  C19  C20  C21    0.00   0.0  0
 H9B  CONST_17  C19  C20  C21  C22    0.00   0.0  0
 H9B  CONST_19  C19  C18  C17  C22    0.00   0.0  0
 H9B  CONST_21  C2   C5   C6   C7   180.00   0.0  0
 H9B  CONST_22  C2   C5   C10  C9   180.00   0.0  0
 H9B  CONST_23  C25  C20  C21  C22  180.00   0.0  0
 H9B  CONST_24  C18  C19  C20  C25  180.00   0.0  0
 H9B  CONST_25  H2   C7   C6   C5   180.00   0.0  0
 H9B  CONST_26  H10  C9   C10  C5   180.00   0.0  0
 H9B  CONST_27  H3   C10  C5   C6   180.00   0.0  0
 H9B  CONST_28  H1   C6   C7   C8   180.00   0.0  0
 H9B  CONST_29  H7   C22  C17  C8     0.00   0.0  0
 H9B  CONST_30  H9   C18  C17  C8     0.00   0.0  0
 H9B  CONST_31  H6   C21  C22  C17  180.00   0.0  0
 H9B  CONST_32  H8   C19  C18  C17  180.00   0.0  0
 H9B  CONST_33  O13  C11  N4   C1     0.00   0.0  0
 H9B  CONST_34  C12  C11  N4   C1   180.00   0.0  0
 H9B  CONST_35  H19  N4   C11  O13  180.00   0.0  0
 H9B  Var_01    C1   C3   C2   C5   109.73  30.0  1
 H9B  Var_02    C3   C2   C5   C6   -12.91  30.0  2
 H9B  Var_03    F26  C25  C20  C21   38.14  30.0  3
 H9B  Var_04    N24  C23  C1   C2   153.83  30.0  3
 H9B  Var_05    C11  N4   C1   C2    74.20  30.0  3
 H9B  Var_06    H16  N24  C23  C1    68.86  30.0  3
 H9B  Var_07    H24  C16  C15  C12   63.45  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
 H9B  chir_03  C12  C11  N14  C15  negativ
 H9B  chir_04  C2   C5   C3   C1   both
 H9B  chir_05  C1   C23  C3   C2   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
 H9B  plan-1  C5   0.020
 H9B  plan-1  C6   0.020
 H9B  plan-1  C7   0.020
 H9B  plan-1  C8   0.020
 H9B  plan-1  C10  0.020
 H9B  plan-1  C17  0.020
 H9B  plan-1  C9   0.020
 H9B  plan-1  C2   0.020
 H9B  plan-1  H1   0.020
 H9B  plan-1  H2   0.020
 H9B  plan-1  H3   0.020
 H9B  plan-1  H10  0.020
 H9B  plan-2  C8   0.020
 H9B  plan-2  C17  0.020
 H9B  plan-2  C20  0.020
 H9B  plan-2  C21  0.020
 H9B  plan-2  C22  0.020
 H9B  plan-2  C25  0.020
 H9B  plan-2  C19  0.020
 H9B  plan-2  C18  0.020
 H9B  plan-2  H6   0.020
 H9B  plan-2  H7   0.020
 H9B  plan-2  H8   0.020
 H9B  plan-2  H9   0.020
 H9B  plan-3  C1   0.020
 H9B  plan-3  N4   0.020
 H9B  plan-3  C11  0.020
 H9B  plan-3  O13  0.020
 H9B  plan-3  C12  0.020
 H9B  plan-3  H19  0.020

