# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 12:42:25 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: N-[2-(2,6-dichlorophenyl)-1H-imidazo[4,5-c]pyridin-4-yl]cyclopropanecarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cccc(Cl)c1c2[nH]c3ccnc(NC(=O)C4CC4)c3n2
#
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
 9ZS  9ZS  N-[2-(2,6-dichlorophenyl)-1H-imidazo[4,5-c]pyridin-4-yl]cyclopropanecarboxamide  ligand  35  23  .  2022-09-16  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_9ZS
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
 9ZS  C4    C   CR6   0   0.164  -2.4626  -0.4903   0.1040
 9ZS  C5    C   CR6   0  -0.113  -2.9117  -1.2658   1.1697
 9ZS  C6    C   CR16  0  -0.186  -4.0502  -2.0476   1.0702
 9ZS  C11   C   CR56  0   0.443  -0.0026   2.0957   0.5745
 9ZS  C8    C   CR5   0   0.410  -1.2413   0.3228   0.2164
 9ZS  C12   C   CR16  0  -0.379   0.5937   3.3268   0.8464
 9ZS  C13   C   CR16  0  -0.095   1.9667   3.3326   0.7410
 9ZS  C3    C   CR6   0  -0.112  -3.2013  -0.5184  -1.0758
 9ZS  C1    C   CR16  0  -0.275  -4.7587  -2.0542  -0.1212
 9ZS  C2    C   CR16  0  -0.186  -4.3427  -1.2919  -1.2016
 9ZS  CL7   CL  CL    0  -0.101  -2.0293  -1.2425   2.6532
 9ZS  N9    N   NR15  0  -0.672  -1.2846   1.6398   0.5585
 9ZS  N14   N   N     0  -0.437   2.7318   2.2774   0.4093
 9ZS  C15   C   CR6   0   0.443   2.1597   1.1221   0.1564
 9ZS  C16   C   CR56  0  -0.013   0.7639   0.9846   0.2282
 9ZS  N17   N   N     0  -0.429  -0.0311  -0.1088   0.0101
 9ZS  N18   N   NH1   0  -0.740   2.8879  -0.0053  -0.1814
 9ZS  C19   C   C     0   0.592   4.2390  -0.1514  -0.3449
 9ZS  O20   O   O     0  -0.453   5.0419   0.7509  -0.2226
 9ZS  C21   C   CH1   0  -0.447   4.6378  -1.5410  -0.6915
 9ZS  C22   C   CH2   0  -0.463   5.8221  -1.7226  -1.6061
 9ZS  C23   C   CH2   0  -0.463   5.9598  -2.0388  -0.1641
 9ZS  CL24  CL  CL    0  -0.100  -2.6742   0.4368  -2.4140
 9ZS  H1    H   HCR6  0   0.294  -4.3793  -2.6433   1.9097
 9ZS  H2    H   HCR6  0   0.280   0.0394   4.2122   1.1215
 9ZS  H3    H   HCR6  0   0.263   2.5084   4.2501   0.9384
 9ZS  H4    H   HCR6  0   0.288  -5.6485  -2.6622  -0.2083
 9ZS  H5    H   HCR6  0   0.294  -4.8977  -1.3014  -2.1290
 9ZS  H6    H   HNR5  0   0.433  -2.1168   2.1720   0.7643
 9ZS  H8    H   HNH1  0   0.421   2.3265  -0.8314  -0.3298
 9ZS  H9    H   HCH1  0   0.285   3.8424  -2.2725  -0.7739
 9ZS  H10   H   HCH2  0   0.266   5.7656  -2.5379  -2.3142
 9ZS  H11   H   HCH2  0   0.260   6.2982  -0.8262  -1.9813
 9ZS  H12   H   HCH2  0   0.260   6.5299  -1.3605   0.4569
 9ZS  H13   H   HCH2  0   0.266   5.9995  -3.0763   0.1393

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
 9ZS  C12   C13  aromatic  1.377  0.020  1.377
 9ZS  C12   C11  aromatic  1.395  0.020  1.395
 9ZS  N9    C11  aromatic  1.361  0.020  1.361
 9ZS  N9    C8   aromatic  1.361  0.020  1.361
 9ZS  C13   N14  aromatic  1.345  0.020  1.345
 9ZS  C11   C16  aromatic  1.394  0.020  1.394
 9ZS  C8    C4   single    1.471  0.020  1.471
 9ZS  C8    N17  aromatic  1.301  0.020  1.301
 9ZS  CL24  C3   single    1.727  0.020  1.727
 9ZS  C3    C4   aromatic  1.392  0.020  1.392
 9ZS  C3    C2   aromatic  1.385  0.020  1.385
 9ZS  C4    C5   aromatic  1.392  0.020  1.392
 9ZS  N14   C15  aromatic  1.314  0.020  1.314
 9ZS  CL7   C5   single    1.726  0.020  1.726
 9ZS  C5    C6   aromatic  1.385  0.020  1.385
 9ZS  C2    C1   aromatic  1.386  0.020  1.386
 9ZS  C1    C6   aromatic  1.386  0.020  1.386
 9ZS  C16   N17  aromatic  1.369  0.020  1.369
 9ZS  C16   C15  aromatic  1.404  0.020  1.404
 9ZS  C15   N18  single    1.384  0.020  1.384
 9ZS  N18   C19  single    1.369  0.020  1.369
 9ZS  O20   C19  double    1.214  0.020  1.214
 9ZS  C19   C21  single    1.487  0.020  1.487
 9ZS  C21   C23  single    1.508  0.020  1.508
 9ZS  C21   C22  single    1.507  0.020  1.507
 9ZS  C23   C22  single    1.483  0.020  1.483
 9ZS  C6    H1   single    0.930  0.020  1.080
 9ZS  C12   H2   single    0.930  0.020  1.080
 9ZS  C13   H3   single    0.930  0.020  1.080
 9ZS  C1    H4   single    0.930  0.020  1.080
 9ZS  C2    H5   single    0.930  0.020  1.080
 9ZS  N9    H6   single    0.860  0.020  1.020
 9ZS  N18   H8   single    0.860  0.020  1.020
 9ZS  C21   H9   single    0.970  0.020  1.090
 9ZS  C22   H10  single    0.970  0.020  1.090
 9ZS  C22   H11  single    0.970  0.020  1.090
 9ZS  C23   H12  single    0.970  0.020  1.090
 9ZS  C23   H13  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
 9ZS  C3    C4   C8   121.08  3.000
 9ZS  C3    C4   C5   117.79  3.000
 9ZS  C8    C4   C5   121.14  3.000
 9ZS  CL7   C5   C6   119.32  3.000
 9ZS  C6    C5   C4   121.65  3.000
 9ZS  CL7   C5   C4   119.03  3.000
 9ZS  H1    C6   C1   120.63  3.000
 9ZS  H1    C6   C5   120.38  3.000
 9ZS  C1    C6   C5   118.99  3.000
 9ZS  C16   C11  N9   104.37  3.000
 9ZS  C16   C11  C12  121.13  3.000
 9ZS  N9    C11  C12  134.50  3.000
 9ZS  N17   C8   N9   112.97  3.000
 9ZS  N17   C8   C4   125.20  3.000
 9ZS  N9    C8   C4   121.83  3.000
 9ZS  H2    C12  C13  121.85  3.000
 9ZS  H2    C12  C11  123.62  3.000
 9ZS  C13   C12  C11  114.53  3.000
 9ZS  H3    C13  N14  115.14  3.000
 9ZS  H3    C13  C12  119.21  3.000
 9ZS  N14   C13  C12  125.65  3.000
 9ZS  CL24  C3   C2   119.36  3.000
 9ZS  C2    C3   C4   121.71  3.000
 9ZS  CL24  C3   C4   118.93  3.000
 9ZS  H4    C1   C2   119.57  3.000
 9ZS  H4    C1   C6   119.51  3.000
 9ZS  C2    C1   C6   120.93  3.000
 9ZS  H5    C2   C1   120.65  3.000
 9ZS  H5    C2   C3   120.41  3.000
 9ZS  C1    C2   C3   118.93  3.000
 9ZS  H6    N9   C8   126.00  3.000
 9ZS  H6    N9   C11  126.72  3.000
 9ZS  C8    N9   C11  107.29  3.000
 9ZS  C15   N14  C13  119.32  3.000
 9ZS  N18   C15  C16  117.10  3.000
 9ZS  N18   C15  N14  122.29  3.000
 9ZS  C16   C15  N14  120.61  3.000
 9ZS  N17   C16  C15  130.32  3.000
 9ZS  C15   C16  C11  118.77  3.000
 9ZS  N17   C16  C11  110.91  3.000
 9ZS  C16   N17  C8   104.47  3.000
 9ZS  H8    N18  C19  116.35  3.000
 9ZS  H8    N18  C15  114.20  3.000
 9ZS  C19   N18  C15  129.45  3.000
 9ZS  C21   C19  O20  122.74  3.000
 9ZS  C21   C19  N18  113.10  3.000
 9ZS  O20   C19  N18  124.16  3.000
 9ZS  H9    C21  C23  116.56  3.000
 9ZS  H9    C21  C22  116.69  3.000
 9ZS  C23   C21  C22   58.91  3.000
 9ZS  H9    C21  C19  116.86  3.000
 9ZS  C22   C21  C19  117.70  3.000
 9ZS  C23   C21  C19  117.53  3.000
 9ZS  H11   C22  H10  114.87  3.000
 9ZS  H11   C22  C23  118.23  3.000
 9ZS  H10   C22  C23  118.74  3.000
 9ZS  H11   C22  C21  117.15  3.000
 9ZS  H10   C22  C21  116.56  3.000
 9ZS  C23   C22  C21   60.56  3.000
 9ZS  H13   C23  H12  114.90  3.000
 9ZS  H13   C23  C22  118.74  3.000
 9ZS  H12   C23  C22  118.25  3.000
 9ZS  H13   C23  C21  116.55  3.000
 9ZS  H12   C23  C21  117.10  3.000
 9ZS  C22   C23  C21   60.53  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
 9ZS  CONST_01  C11   N9   C8   C4    180.00   0.0  0
 9ZS  CONST_02  C16   N17  C8   C4    180.00   0.0  0
 9ZS  CONST_03  C1    C2   C3   C4      0.00   0.0  0
 9ZS  CONST_04  C1    C6   C5   C4      0.00   0.0  0
 9ZS  CONST_07  C2    C3   C4   C5      0.00   0.0  0
 9ZS  CONST_08  C2    C1   C6   C5      0.00   0.0  0
 9ZS  CONST_09  C8    C4   C5   C6    180.00   0.0  0
 9ZS  CONST_10  C3    C4   C5   C6      0.00   0.0  0
 9ZS  CONST_11  C3    C2   C1   C6      0.00   0.0  0
 9ZS  CONST_12  N14   C13  C12  C11     0.00   0.0  0
 9ZS  CONST_13  N17   C8   N9   C11     0.00   0.0  0
 9ZS  CONST_14  C8    N17  C16  C11     0.00   0.0  0
 9ZS  CONST_15  N14   C15  C16  C11     0.00   0.0  0
 9ZS  CONST_16  C12   C11  N9   C8    180.00   0.0  0
 9ZS  CONST_17  C16   C11  N9   C8      0.00   0.0  0
 9ZS  CONST_18  C2    C3   C4   C8    180.00   0.0  0
 9ZS  CONST_19  C15   C16  N17  C8    180.00   0.0  0
 9ZS  CONST_20  C15   N14  C13  C12     0.00   0.0  0
 9ZS  CONST_21  N17   C16  C11  C12   180.00   0.0  0
 9ZS  CONST_22  C15   C16  C11  C12     0.00   0.0  0
 9ZS  CONST_23  N9    C11  C12  C13   180.00   0.0  0
 9ZS  CONST_24  C16   C11  C12  C13     0.00   0.0  0
 9ZS  CONST_25  C16   C15  N14  C13     0.00   0.0  0
 9ZS  CONST_28  N17   C16  C11  N9      0.00   0.0  0
 9ZS  CONST_29  C15   C16  C11  N9    180.00   0.0  0
 9ZS  CONST_30  C16   N17  C8   N9      0.00   0.0  0
 9ZS  CONST_31  N17   C16  C15  N14   180.00   0.0  0
 9ZS  CONST_32  CL24  C3   C4   C5    180.00   0.0  0
 9ZS  CONST_33  N18   C15  C16  C11   180.00   0.0  0
 9ZS  CONST_34  CL24  C3   C4   C8      0.00   0.0  0
 9ZS  CONST_35  CL7   C5   C4   C8      0.00   0.0  0
 9ZS  CONST_36  N18   C15  N14  C13   180.00   0.0  0
 9ZS  CONST_37  CL7   C5   C4   C3    180.00   0.0  0
 9ZS  CONST_38  CL24  C3   C2   C1    180.00   0.0  0
 9ZS  CONST_39  CL7   C5   C6   C1    180.00   0.0  0
 9ZS  CONST_40  N18   C15  C16  N17     0.00   0.0  0
 9ZS  CONST_41  H6    N9   C8   C4      0.00   0.0  0
 9ZS  CONST_42  H5    C2   C3   C4    180.00   0.0  0
 9ZS  CONST_43  H1    C6   C5   C4    180.00   0.0  0
 9ZS  CONST_44  H4    C1   C6   C5    180.00   0.0  0
 9ZS  CONST_45  H3    C13  C12  C11   180.00   0.0  0
 9ZS  CONST_46  H2    C12  C11  N9      0.00   0.0  0
 9ZS  CONST_47  C21   C19  N18  C15   180.00   0.0  0
 9ZS  CONST_48  C19   N18  C15  N14     0.00   0.0  0
 9ZS  CONST_49  C19   N18  C15  C16   180.00   0.0  0
 9ZS  CONST_50  H8    N18  C15  N14   180.00   0.0  0
 9ZS  CONST_51  O20   C19  N18  C15     0.00   0.0  0
 9ZS  Var_01    C22   C23  C21  C19  -107.32  30.0  1
 9ZS  Var_02    H10   C22  C23  C21  -106.02  30.0  1
 9ZS  Var_03    C23   C21  C19  N18  -146.17  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
 9ZS  chir_01  C21  C19  C23  C22  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
 9ZS  plan-1  C4    0.020
 9ZS  plan-1  C5    0.020
 9ZS  plan-1  C6    0.020
 9ZS  plan-1  C8    0.020
 9ZS  plan-1  C3    0.020
 9ZS  plan-1  C1    0.020
 9ZS  plan-1  C2    0.020
 9ZS  plan-1  CL7   0.020
 9ZS  plan-1  CL24  0.020
 9ZS  plan-1  H1    0.020
 9ZS  plan-1  H4    0.020
 9ZS  plan-1  H5    0.020
 9ZS  plan-2  C4    0.020
 9ZS  plan-2  C11   0.020
 9ZS  plan-2  C8    0.020
 9ZS  plan-2  C12   0.020
 9ZS  plan-2  C13   0.020
 9ZS  plan-2  N9    0.020
 9ZS  plan-2  N14   0.020
 9ZS  plan-2  C15   0.020
 9ZS  plan-2  C16   0.020
 9ZS  plan-2  N17   0.020
 9ZS  plan-2  N18   0.020
 9ZS  plan-2  H2    0.020
 9ZS  plan-2  H3    0.020
 9ZS  plan-2  H6    0.020
 9ZS  plan-3  C15   0.020
 9ZS  plan-3  N18   0.020
 9ZS  plan-3  C19   0.020
 9ZS  plan-3  O20   0.020
 9ZS  plan-3  C21   0.020
 9ZS  plan-3  H8    0.020

