# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 09:43:12 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: (2R,3S,4R)-3-(4'-chloro-2',6'-difluoro[1,1'-biphenyl]-4-yl)-4-(fluoromethyl)azetidine-2-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC[C@@H]1N[C@@H](C#N)[C@@H]1c2ccc(cc2)c3c(F)cc(Cl)cc3F
#
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
 H9V  H9V  (2R,3S,4R)-3-(4'-chloro-2',6'-difluoro[1,1'-biphenyl]-4-yl)-4-(fluoromethyl)azetidine-2-carbonitrile  ligand  35  23  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_H9V
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
 H9V  C1   C   CR16  0  -0.304  -1.5040  -0.0426   0.8582
 H9V  N2   N   NS    0  -0.259  -6.4589  -2.4249   0.3838
 H9V  C3   C   CR16  0  -0.302  -1.3158  -0.8158  -1.3977
 H9V  C4   C   CR16  0  -0.267   0.0657  -0.7290  -1.3178
 H9V  C5   C   CR6   0   0.099   0.6767  -0.2945  -0.1459
 H9V  C6   C   CR16  0  -0.266  -0.1245   0.0449   0.9423
 H9V  C8   C   CR6   0   0.560   2.7899   1.0199   0.1732
 H9V  C9   C   CR16  0  -0.381   4.1613   1.1570   0.2567
 H9V  C10  C   CR6   0  -0.015   4.9311   0.0163   0.0992
 H9V  C11  C   CR16  0  -0.381   4.3591  -1.2237  -0.1342
 H9V  C12  C   CR6   0   0.559   2.9819  -1.2896  -0.2067
 H9V  C13  C   C     0  -0.419  -3.6114  -0.5425  -0.4605
 H9V  C14  C   C     0  -0.095  -4.3867   0.8018  -0.3948
 H9V  C15  C   C     0  -0.152  -4.3889  -0.8936   0.8383
 H9V  C16  C   CH2   0   0.005  -3.6302   2.0745  -0.6505
 H9V  C17  C   CSP   0   0.132  -5.5412  -1.7583   0.5778
 H9V  C2   C   CR6   0   0.181  -2.1209  -0.4707  -0.3165
 H9V  C7   C   CR6   0  -0.372   2.1477  -0.1893  -0.0588
 H9V  F2   F   F     0  -0.292   2.0391   2.1153   0.3116
 H9V  F3   F   F     0  -0.379  -4.5006   3.1555  -0.5157
 H9V  N1   N   N     0  -0.587  -4.7126   0.5186   1.0068
 H9V  CL1  CL  CL    0  -0.099   6.6485   0.1432   0.1957
 H9V  H1   H   HCR6  0   0.267  -2.0992   0.2419   1.7177
 H9V  H2   H   HCR6  0   0.261  -1.7719  -1.1568  -2.3190
 H9V  H3   H   HCR6  0   0.260   0.6650  -0.9896  -2.1806
 H9V  H4   H   HCR6  0   0.260   0.3292   0.3716   1.8690
 H9V  H5   H   HCR6  0   0.307   4.6074   2.1259   0.4337
 H9V  H6   H   HCR6  0   0.307   4.9603  -2.1143  -0.2536
 H9V  H7   H   H     0   0.294  -3.8703  -1.1539  -1.3230
 H9V  H8   H   H     0   0.264  -5.2549   0.7625  -1.0632
 H9V  H9   H   H     0   0.312  -3.8106  -1.3406   1.6512
 H9V  H10  H   HCH2  0   0.208  -2.8156   2.2083   0.0605
 H9V  H11  H   HCH2  0   0.213  -3.2258   2.0787  -1.6651
 H9V  H12  H   H     0   0.370  -5.6486   0.7437   1.3185
 H9V  F1   F   F     0  -0.292   2.4185  -2.4811  -0.4205

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
 H9V  F2   C8   single    1.335  0.020  1.335
 H9V  C9   C8   aromatic  1.381  0.020  1.381
 H9V  C9   C10  aromatic  1.385  0.020  1.385
 H9V  CL1  C10  single    1.725  0.020  1.725
 H9V  C8   C7   aromatic  1.389  0.020  1.389
 H9V  N2   C17  triple    1.151  0.020  1.151
 H9V  C10  C11  aromatic  1.385  0.020  1.385
 H9V  C4   C3   aromatic  1.387  0.020  1.387
 H9V  C4   C5   aromatic  1.391  0.020  1.391
 H9V  C17  C15  single    1.464  0.020  1.464
 H9V  C3   C2   aromatic  1.391  0.020  1.391
 H9V  C7   C5   single    1.477  0.020  1.477
 H9V  C7   C12  aromatic  1.389  0.020  1.389
 H9V  C11  C12  aromatic  1.381  0.020  1.381
 H9V  C5   C6   aromatic  1.393  0.020  1.393
 H9V  C15  C13  single    1.554  0.020  1.554
 H9V  C15  N1   single    1.459  0.020  1.459
 H9V  C12  F1   single    1.335  0.020  1.335
 H9V  C2   C13  single    1.499  0.020  1.499
 H9V  C2   C1   aromatic  1.394  0.020  1.394
 H9V  C13  C14  single    1.553  0.020  1.553
 H9V  C6   C1   aromatic  1.385  0.020  1.385
 H9V  N1   C14  single    1.467  0.020  1.467
 H9V  C14  C16  single    1.502  0.020  1.502
 H9V  F3   C16  single    1.394  0.020  1.394
 H9V  C1   H1   single    0.930  0.020  1.080
 H9V  C3   H2   single    0.930  0.020  1.080
 H9V  C4   H3   single    0.930  0.020  1.080
 H9V  C6   H4   single    0.930  0.020  1.080
 H9V  C9   H5   single    0.930  0.020  1.080
 H9V  C11  H6   single    0.930  0.020  1.080
 H9V  C13  H7   single    0.970  0.020  1.090
 H9V  C14  H8   single    0.970  0.020  1.090
 H9V  C15  H9   single    0.970  0.020  1.090
 H9V  C16  H10  single    0.970  0.020  1.090
 H9V  C16  H11  single    0.970  0.020  1.090
 H9V  N1   H12  single    0.890  0.020  1.040

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
 H9V  H1   C1   C2   120.40  3.000
 H9V  H1   C1   C6   118.84  3.000
 H9V  C2   C1   C6   120.75  3.000
 H9V  H2   C3   C2   119.69  3.000
 H9V  H2   C3   C4   119.23  3.000
 H9V  C2   C3   C4   121.07  3.000
 H9V  H3   C4   C5   120.23  3.000
 H9V  H3   C4   C3   119.38  3.000
 H9V  C5   C4   C3   120.38  3.000
 H9V  C7   C5   C6   120.61  3.000
 H9V  C6   C5   C4   118.78  3.000
 H9V  C7   C5   C4   120.61  3.000
 H9V  H4   C6   C5   120.08  3.000
 H9V  H4   C6   C1   119.25  3.000
 H9V  C5   C6   C1   120.67  3.000
 H9V  F2   C8   C7   118.14  3.000
 H9V  C7   C8   C9   123.77  3.000
 H9V  F2   C8   C9   118.09  3.000
 H9V  H5   C9   C10  121.82  3.000
 H9V  H5   C9   C8   120.57  3.000
 H9V  C10  C9   C8   117.61  3.000
 H9V  CL1  C10  C11  119.10  3.000
 H9V  C11  C10  C9   121.79  3.000
 H9V  CL1  C10  C9   119.11  3.000
 H9V  H6   C11  C12  120.64  3.000
 H9V  H6   C11  C10  121.76  3.000
 H9V  C12  C11  C10  117.60  3.000
 H9V  F1   C12  C7   118.08  3.000
 H9V  F1   C12  C11  118.15  3.000
 H9V  C7   C12  C11  123.77  3.000
 H9V  H7   C13  C2   109.85  3.000
 H9V  H7   C13  C15  114.60  3.000
 H9V  C2   C13  C15  115.34  3.000
 H9V  H7   C13  C14  113.63  3.000
 H9V  C2   C13  C14  116.79  3.000
 H9V  C15  C13  C14   84.86  3.000
 H9V  H8   C14  N1   113.56  3.000
 H9V  H8   C14  C16  108.98  3.000
 H9V  N1   C14  C16  115.98  3.000
 H9V  H8   C14  C13  109.78  3.000
 H9V  C16  C14  C13  118.33  3.000
 H9V  N1   C14  C13   89.09  3.000
 H9V  H9   C15  N1   115.30  3.000
 H9V  H9   C15  C17  107.89  3.000
 H9V  N1   C15  C17  114.70  3.000
 H9V  H9   C15  C13  116.69  3.000
 H9V  N1   C15  C13   89.36  3.000
 H9V  C17  C15  C13  112.25  3.000
 H9V  H11  C16  H10  109.20  3.000
 H9V  H11  C16  F3   108.54  3.000
 H9V  H10  C16  F3   107.96  3.000
 H9V  H11  C16  C14  110.36  3.000
 H9V  H10  C16  C14  111.68  3.000
 H9V  F3   C16  C14  109.03  3.000
 H9V  C15  C17  N2   180.00  3.000
 H9V  C13  C2   C3   119.26  3.000
 H9V  C13  C2   C1   122.38  3.000
 H9V  C3   C2   C1   118.35  3.000
 H9V  C12  C7   C8   115.47  3.000
 H9V  C12  C7   C5   122.37  3.000
 H9V  C8   C7   C5   122.16  3.000
 H9V  H12  N1   C15  117.14  3.000
 H9V  H12  N1   C14  117.19  3.000
 H9V  C15  N1   C14   91.56  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
 H9V  CONST_01  C4   C3   C2   C1     0.00  0.0  0
 H9V  CONST_02  C4   C5   C6   C1     0.00  0.0  0
 H9V  CONST_03  C7   C5   C6   C1   180.00  0.0  0
 H9V  CONST_04  C7   C5   C4   C3   180.00  0.0  0
 H9V  CONST_05  C6   C5   C4   C3     0.00  0.0  0
 H9V  CONST_06  C6   C1   C2   C3     0.00  0.0  0
 H9V  CONST_09  C2   C3   C4   C5     0.00  0.0  0
 H9V  CONST_10  C9   C8   C7   C5   180.00  0.0  0
 H9V  CONST_11  C11  C12  C7   C5   180.00  0.0  0
 H9V  CONST_12  C2   C1   C6   C5     0.00  0.0  0
 H9V  CONST_15  C11  C10  C9   C8     0.00  0.0  0
 H9V  CONST_16  C11  C12  C7   C8     0.00  0.0  0
 H9V  CONST_17  C12  C7   C8   C9     0.00  0.0  0
 H9V  CONST_18  C12  C11  C10  C9     0.00  0.0  0
 H9V  CONST_19  C7   C8   C9   C10    0.00  0.0  0
 H9V  CONST_20  C7   C12  C11  C10    0.00  0.0  0
 H9V  CONST_21  C13  C2   C3   C4   180.00  0.0  0
 H9V  CONST_22  C13  C2   C1   C6   180.00  0.0  0
 H9V  CONST_23  F2   C8   C7   C5     0.00  0.0  0
 H9V  CONST_24  F1   C12  C7   C5     0.00  0.0  0
 H9V  CONST_25  CL1  C10  C9   C8   180.00  0.0  0
 H9V  CONST_26  F1   C12  C7   C8   180.00  0.0  0
 H9V  CONST_27  F2   C8   C9   C10  180.00  0.0  0
 H9V  CONST_28  F1   C12  C11  C10  180.00  0.0  0
 H9V  CONST_29  F2   C8   C7   C12  180.00  0.0  0
 H9V  CONST_30  CL1  C10  C11  C12  180.00  0.0  0
 H9V  CONST_31  H2   C3   C2   C1   180.00  0.0  0
 H9V  CONST_32  H1   C1   C2   C3   180.00  0.0  0
 H9V  CONST_33  H4   C6   C5   C4   180.00  0.0  0
 H9V  CONST_34  H3   C4   C5   C6   180.00  0.0  0
 H9V  CONST_35  H6   C11  C10  C9   180.00  0.0  0
 H9V  CONST_36  H5   C9   C10  C11  180.00  0.0  0

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
 H9V  chir_01  C13  C15  C2   C14  positiv
 H9V  chir_02  C14  N1   C13  C16  positiv
 H9V  chir_03  C15  N1   C13  C17  positiv

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
 H9V  plan-1  C1   0.020
 H9V  plan-1  C3   0.020
 H9V  plan-1  C4   0.020
 H9V  plan-1  C5   0.020
 H9V  plan-1  C6   0.020
 H9V  plan-1  C13  0.020
 H9V  plan-1  C2   0.020
 H9V  plan-1  C7   0.020
 H9V  plan-1  H1   0.020
 H9V  plan-1  H2   0.020
 H9V  plan-1  H3   0.020
 H9V  plan-1  H4   0.020
 H9V  plan-2  C5   0.020
 H9V  plan-2  C8   0.020
 H9V  plan-2  C9   0.020
 H9V  plan-2  C10  0.020
 H9V  plan-2  C11  0.020
 H9V  plan-2  C12  0.020
 H9V  plan-2  C7   0.020
 H9V  plan-2  F2   0.020
 H9V  plan-2  CL1  0.020
 H9V  plan-2  H5   0.020
 H9V  plan-2  H6   0.020
 H9V  plan-2  F1   0.020

