# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 17:41:51 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: (2R,3S,4R)-3-(2',6'-difluoro-4'-methyl[1,1'-biphenyl]-4-yl)-4-(fluoromethyl)azetidine-2-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(F)c(c(F)c1)c2ccc(cc2)[C@@H]3[C@H](CF)N[C@H]3C#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
 HDJ  HDJ  (2R,3S,4R)-3-(2',6'-difluoro-4'-methyl[1,1'-biphenyl]-4-yl)-4-(fluoromethyl)azetidine-2-carbonitrile  ligand  38  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_HDJ
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
 HDJ  C11  C  CR16  0  -0.448   4.7903   1.1517   0.0560
 HDJ  C12  C  CR6   0   0.571   3.4169   1.2379   0.1549
 HDJ  C13  C  C     0  -0.409  -3.1883   0.5472   0.4829
 HDJ  C14  C  C     0  -0.090  -3.9731  -0.7886   0.3850
 HDJ  C16  C  CH2   0   0.027  -3.2400  -2.0786   0.6251
 HDJ  C17  C  CSP   0   0.095  -5.1232   1.7883  -0.5205
 HDJ  C1   C  CR16  0  -0.286  -0.8764   0.8076   1.3922
 HDJ  C10  C  CR6   0   0.132   5.3815  -0.0798  -0.2055
 HDJ  C15  C  C     0  -0.138  -3.9667   0.9365  -0.8044
 HDJ  C2   C  CR6   0   0.188  -1.7001   0.4648   0.3252
 HDJ  C3   C  CR16  0  -0.295  -1.1018   0.0293  -0.8562
 HDJ  C35  C  CH3   0  -0.693   6.8716  -0.2121  -0.2881
 HDJ  C4   C  CR16  0  -0.250   0.2752  -0.0660  -0.9592
 HDJ  C5   C  CR6   0   0.106   1.0968   0.2698   0.1149
 HDJ  C6   C  CR16  0  -0.254   0.5030   0.7107   1.2929
 HDJ  C7   C  CR6   0  -0.384   2.5651   0.1522   0.0065
 HDJ  C8   C  CR6   0   0.569   3.1963  -1.0571  -0.2537
 HDJ  C9   C  CR16  0  -0.462   4.5641  -1.1954  -0.3632
 HDJ  F1   F  F     0  -0.303   2.8689   2.4375   0.3938
 HDJ  F2   F  F     0  -0.301   2.4321  -2.1481  -0.3984
 HDJ  F3   F  F     0  -0.361  -4.1233  -3.1373   0.4732
 HDJ  N1   N  N     0  -0.565  -4.2792  -0.4722  -1.0119
 HDJ  H1   H  HCR6  0   0.254   5.3932   2.0421   0.1779
 HDJ  H2   H  H     0   0.274  -3.4394   1.1407   1.3602
 HDJ  H3   H  H     0   0.250  -4.8472  -0.7518   1.0470
 HDJ  H4   H  HCH2  0   0.198  -2.4215  -2.2106  -0.0823
 HDJ  H5   H  HCH2  0   0.193  -2.8377  -2.0989   1.6413
 HDJ  H6   H  HCR6  0   0.235  -1.3137   1.1540   2.3204
 HDJ  H7   H  H     0   0.291  -3.3846   1.4059  -1.6020
 HDJ  H8   H  HCR6  0   0.260  -1.7123  -0.2572  -1.7043
 HDJ  H9   H  HCH3  0   0.253   7.2847  -0.5132   0.6758
 HDJ  H10  H  HCH3  0   0.239   7.1668  -0.9653  -1.0167
 HDJ  H11  H  HCH3  0   0.240   7.3426   0.7288  -0.5661
 HDJ  H12  H  HCR6  0   0.235   0.7112  -0.3967  -1.8926
 HDJ  H13  H  HCR6  0   0.238   1.1137   0.9683   2.1483
 HDJ  H14  H  HCR6  0   0.250   4.9891  -2.1705  -0.5656
 HDJ  H15  H  H     0   0.347  -5.2032  -0.7016  -1.3526
 HDJ  N2   N  NS    0  -0.204  -6.0451   2.4416  -0.3037

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
 HDJ  F2   C8   single    1.340  0.020  1.340
 HDJ  C9   C8   aromatic  1.379  0.020  1.379
 HDJ  C9   C10  aromatic  1.392  0.020  1.392
 HDJ  C8   C7   aromatic  1.389  0.020  1.389
 HDJ  C35  C10  single    1.498  0.020  1.498
 HDJ  N2   C17  triple    1.151  0.020  1.151
 HDJ  C10  C11  aromatic  1.391  0.020  1.391
 HDJ  C4   C3   aromatic  1.384  0.020  1.384
 HDJ  C4   C5   aromatic  1.393  0.020  1.393
 HDJ  C17  C15  single    1.464  0.020  1.464
 HDJ  C3   C2   aromatic  1.394  0.020  1.394
 HDJ  C7   C5   single    1.477  0.020  1.477
 HDJ  C7   C12  aromatic  1.388  0.020  1.388
 HDJ  C5   C6   aromatic  1.391  0.020  1.391
 HDJ  C11  C12  aromatic  1.380  0.020  1.380
 HDJ  C15  C13  single    1.554  0.020  1.554
 HDJ  C15  N1   single    1.458  0.020  1.458
 HDJ  C12  F1   single    1.340  0.020  1.340
 HDJ  C2   C13  single    1.499  0.020  1.499
 HDJ  C2   C1   aromatic  1.391  0.020  1.391
 HDJ  C13  C14  single    1.552  0.020  1.552
 HDJ  C6   C1   aromatic  1.386  0.020  1.386
 HDJ  N1   C14  single    1.465  0.020  1.465
 HDJ  F3   C16  single    1.387  0.020  1.387
 HDJ  C14  C16  single    1.503  0.020  1.503
 HDJ  C11  H1   single    0.930  0.020  1.080
 HDJ  C13  H2   single    0.970  0.020  1.090
 HDJ  C14  H3   single    0.970  0.020  1.090
 HDJ  C16  H4   single    0.970  0.020  1.090
 HDJ  C16  H5   single    0.970  0.020  1.090
 HDJ  C1   H6   single    0.930  0.020  1.080
 HDJ  C15  H7   single    0.970  0.020  1.090
 HDJ  C3   H8   single    0.930  0.020  1.080
 HDJ  C35  H9   single    0.970  0.020  1.090
 HDJ  C35  H10  single    0.970  0.020  1.090
 HDJ  C35  H11  single    0.970  0.020  1.090
 HDJ  C4   H12  single    0.930  0.020  1.080
 HDJ  C6   H13  single    0.930  0.020  1.080
 HDJ  C9   H14  single    0.930  0.020  1.080
 HDJ  N1   H15  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
 HDJ  H1   C11  C10  120.86  3.000
 HDJ  H1   C11  C12  119.67  3.000
 HDJ  C10  C11  C12  119.47  3.000
 HDJ  F1   C12  C7   117.92  3.000
 HDJ  F1   C12  C11  118.41  3.000
 HDJ  C7   C12  C11  123.67  3.000
 HDJ  H2   C13  C2   110.11  3.000
 HDJ  H2   C13  C15  114.55  3.000
 HDJ  C2   C13  C15  115.09  3.000
 HDJ  H2   C13  C14  113.79  3.000
 HDJ  C2   C13  C14  116.62  3.000
 HDJ  C15  C13  C14   84.84  3.000
 HDJ  H3   C14  N1   113.69  3.000
 HDJ  H3   C14  C16  108.72  3.000
 HDJ  N1   C14  C16  116.09  3.000
 HDJ  H3   C14  C13  109.62  3.000
 HDJ  C16  C14  C13  118.81  3.000
 HDJ  N1   C14  C13   88.85  3.000
 HDJ  H5   C16  H4   108.95  3.000
 HDJ  H5   C16  F3   108.79  3.000
 HDJ  H4   C16  F3   108.34  3.000
 HDJ  H5   C16  C14  110.12  3.000
 HDJ  H4   C16  C14  111.50  3.000
 HDJ  F3   C16  C14  109.08  3.000
 HDJ  N2   C17  C15  180.00  3.000
 HDJ  H6   C1   C6   119.05  3.000
 HDJ  H6   C1   C2   119.82  3.000
 HDJ  C6   C1   C2   121.14  3.000
 HDJ  C9   C10  C35  120.47  3.000
 HDJ  C35  C10  C11  120.75  3.000
 HDJ  C9   C10  C11  118.77  3.000
 HDJ  H7   C15  N1   115.16  3.000
 HDJ  H7   C15  C17  108.20  3.000
 HDJ  N1   C15  C17  114.86  3.000
 HDJ  H7   C15  C13  116.44  3.000
 HDJ  N1   C15  C13   89.04  3.000
 HDJ  C17  C15  C13  112.38  3.000
 HDJ  C3   C2   C1   118.23  3.000
 HDJ  C1   C2   C13  119.59  3.000
 HDJ  C3   C2   C13  122.17  3.000
 HDJ  H8   C3   C4   118.95  3.000
 HDJ  H8   C3   C2   120.27  3.000
 HDJ  C4   C3   C2   120.76  3.000
 HDJ  H11  C35  H10  108.05  3.000
 HDJ  H11  C35  H9   107.48  3.000
 HDJ  H10  C35  H9   107.31  3.000
 HDJ  H11  C35  C10  111.61  3.000
 HDJ  H10  C35  C10  111.57  3.000
 HDJ  H9   C35  C10  110.62  3.000
 HDJ  H12  C4   C5   120.07  3.000
 HDJ  H12  C4   C3   119.09  3.000
 HDJ  C5   C4   C3   120.84  3.000
 HDJ  C7   C5   C6   120.79  3.000
 HDJ  C6   C5   C4   118.52  3.000
 HDJ  C7   C5   C4   120.69  3.000
 HDJ  H13  C6   C5   120.26  3.000
 HDJ  H13  C6   C1   119.23  3.000
 HDJ  C5   C6   C1   120.50  3.000
 HDJ  C8   C7   C5   122.34  3.000
 HDJ  C5   C7   C12  122.68  3.000
 HDJ  C8   C7   C12  114.98  3.000
 HDJ  F2   C8   C9   118.39  3.000
 HDJ  C9   C8   C7   123.58  3.000
 HDJ  F2   C8   C7   118.04  3.000
 HDJ  H14  C9   C8   119.64  3.000
 HDJ  H14  C9   C10  120.82  3.000
 HDJ  C8   C9   C10  119.54  3.000
 HDJ  H15  N1   C15  117.58  3.000
 HDJ  H15  N1   C14  117.60  3.000
 HDJ  C15  N1   C14   91.62  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
 HDJ  CONST_01  C8   C9   C10  C11    0.00   0.0  0
 HDJ  CONST_02  C8   C7   C12  C11    0.00   0.0  0
 HDJ  CONST_03  C5   C7   C12  C11  180.00   0.0  0
 HDJ  CONST_04  C9   C8   C7   C12    0.00   0.0  0
 HDJ  CONST_07  C9   C10  C11  C12    0.00   0.0  0
 HDJ  CONST_08  C4   C3   C2   C1     0.00   0.0  0
 HDJ  CONST_09  C4   C5   C6   C1     0.00   0.0  0
 HDJ  CONST_10  C7   C5   C6   C1   180.00   0.0  0
 HDJ  CONST_11  C7   C8   C9   C10    0.00   0.0  0
 HDJ  CONST_12  C7   C12  C11  C10    0.00   0.0  0
 HDJ  CONST_13  C5   C4   C3   C2     0.00   0.0  0
 HDJ  CONST_14  C5   C6   C1   C2     0.00   0.0  0
 HDJ  CONST_15  C7   C5   C4   C3   180.00   0.0  0
 HDJ  CONST_16  C6   C5   C4   C3     0.00   0.0  0
 HDJ  CONST_17  C6   C1   C2   C3     0.00   0.0  0
 HDJ  CONST_19  C9   C8   C7   C5   180.00   0.0  0
 HDJ  CONST_21  C4   C3   C2   C13  180.00   0.0  0
 HDJ  CONST_22  C6   C1   C2   C13  180.00   0.0  0
 HDJ  CONST_23  F2   C8   C7   C12  180.00   0.0  0
 HDJ  CONST_24  C35  C10  C11  C12  180.00   0.0  0
 HDJ  CONST_25  F2   C8   C9   C10  180.00   0.0  0
 HDJ  CONST_26  F1   C12  C11  C10  180.00   0.0  0
 HDJ  CONST_27  C8   C9   C10  C35  180.00   0.0  0
 HDJ  CONST_28  F2   C8   C7   C5     0.00   0.0  0
 HDJ  CONST_29  F1   C12  C7   C5     0.00   0.0  0
 HDJ  CONST_30  F1   C12  C7   C8   180.00   0.0  0
 HDJ  CONST_31  H14  C9   C10  C11  180.00   0.0  0
 HDJ  CONST_32  H8   C3   C2   C13    0.00   0.0  0
 HDJ  CONST_33  H6   C1   C2   C13    0.00   0.0  0
 HDJ  CONST_34  H12  C4   C3   C2   180.00   0.0  0
 HDJ  CONST_35  H13  C6   C1   C2   180.00   0.0  0
 HDJ  CONST_36  H1   C11  C12  C7   180.00   0.0  0
 HDJ  Var_01    H9   C35  C10  C11   94.22  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
 HDJ  chir_01  C13  C15  C2   C14  positiv
 HDJ  chir_02  C14  N1   C13  C16  positiv
 HDJ  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
 HDJ  plan-1  C13  0.020
 HDJ  plan-1  C1   0.020
 HDJ  plan-1  C2   0.020
 HDJ  plan-1  C3   0.020
 HDJ  plan-1  C4   0.020
 HDJ  plan-1  C5   0.020
 HDJ  plan-1  C6   0.020
 HDJ  plan-1  C7   0.020
 HDJ  plan-1  H6   0.020
 HDJ  plan-1  H8   0.020
 HDJ  plan-1  H12  0.020
 HDJ  plan-1  H13  0.020
 HDJ  plan-2  C11  0.020
 HDJ  plan-2  C12  0.020
 HDJ  plan-2  C10  0.020
 HDJ  plan-2  C35  0.020
 HDJ  plan-2  C5   0.020
 HDJ  plan-2  C7   0.020
 HDJ  plan-2  C8   0.020
 HDJ  plan-2  C9   0.020
 HDJ  plan-2  F1   0.020
 HDJ  plan-2  F2   0.020
 HDJ  plan-2  H1   0.020
 HDJ  plan-2  H14  0.020

