# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 18 14:18:46 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: 2,6-dichloro-4-cyano-N-{2-[(cyclopropylcarbonyl)amino]pyridin-4-yl}benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cc(cc(Cl)c1C(=O)Nc2ccnc(NC(=O)C3CC3)c2)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
 0X6  0X6  2,6-dichloro-4-cyano-N-{2-[(cyclopropylcarbonyl)amino]pyridin-4-yl}benzamide  ligand  37  25  .  2022-09-22  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_0X6
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
 0X6  C4   C   CR6   0   0.548   3.3130   0.4014   0.3065
 0X6  C14  C   CR16  0  -0.175  -4.3428  -1.5273   0.1252
 0X6  C5   C   CR16  0  -0.520   1.9884   0.1046  -0.0142
 0X6  C6   C   CR6   0   0.498   0.9687   0.7811   0.6397
 0X6  C11  C   CR6   0  -0.075  -3.3862   0.8985  -0.8343
 0X6  C8   C   C     0   0.486  -1.4967   0.8835   0.8277
 0X6  C10  C   CR6   0   0.093  -2.7059   0.2518   0.1901
 0X6  C12  C   CR16  0  -0.175  -4.5274   0.3565  -1.3959
 0X6  C13  C   CR6   0  -0.011  -4.9962  -0.8573  -0.9039
 0X6  N3   N   N     0  -0.429   3.6502   1.3077   1.2081
 0X6  C1   C   CR16  0  -0.389   1.3134   1.7382   1.5971
 0X6  C2   C   CR16  0  -0.064   2.6606   1.9439   1.8240
 0X6  N7   N   NH1   0  -0.718  -0.3355   0.4488   0.2855
 0X6  O9   O   O     0  -0.400  -1.6143   1.6846   1.7254
 0X6  C15  C   CR6   0  -0.070  -3.2017  -0.9584   0.6594
 0X6  CL1  CL  CL    0  -0.072  -2.3698  -1.7688   1.9310
 0X6  C17  C   CSP   0   0.073  -6.1776  -1.4288  -1.4684
 0X6  N18  N   NS    0  -0.229  -7.1304  -1.8876  -1.9226
 0X6  N20  N   NH1   0  -0.751   4.2991  -0.3011  -0.3742
 0X6  C21  C   C     0   0.589   5.6564  -0.3078  -0.1865
 0X6  O22  O   O     0  -0.450   6.2391   0.3557   0.6456
 0X6  C23  C   CH1   0  -0.444   6.3648  -1.2291  -1.1155
 0X6  C24  C   CH2   0  -0.463   7.7351  -0.8229  -1.5958
 0X6  C25  C   CH2   0  -0.464   7.6041  -1.9179  -0.6045
 0X6  H1   H   HCR6  0   0.317  -4.7167  -2.4706   0.4969
 0X6  H2   H   HCR6  0   0.295   1.7610  -0.6489  -0.7589
 0X6  H3   H   HCR6  0   0.317  -5.0465   0.8671  -2.1946
 0X6  H4   H   HCR6  0   0.294   0.5853   2.3084   2.1475
 0X6  H5   H   HCR6  0   0.268   2.9598   2.6829   2.5590
 0X6  H6   H   HNH1  0   0.434  -0.4193  -0.2324  -0.4561
 0X6  H7   H   HNH1  0   0.420   3.9536  -0.9218  -1.0897
 0X6  H8   H   HCH1  0   0.283   5.7542  -1.7870  -1.8156
 0X6  H9   H   HCH2  0   0.266   7.9816  -1.0754  -2.6182
 0X6  H10  H   HCH2  0   0.261   8.1157   0.1317  -1.2566
 0X6  H11  H   HCH2  0   0.260   7.8925  -1.7162   0.4188
 0X6  H12  H   HCH2  0   0.268   7.7622  -2.9370  -0.9311
 0X6  CL2  CL  CL    0  -0.070  -2.7879   2.4017  -1.4220

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
 0X6  C24  C25  single    1.483  0.020  1.483
 0X6  C24  C23  single    1.508  0.020  1.508
 0X6  C25  C23  single    1.507  0.020  1.507
 0X6  C23  C21  single    1.488  0.020  1.488
 0X6  C21  O22  double    1.213  0.020  1.213
 0X6  C21  N20  single    1.370  0.020  1.370
 0X6  N20  C4   single    1.389  0.020  1.389
 0X6  C4   C5   aromatic  1.395  0.020  1.395
 0X6  C4   N3   aromatic  1.322  0.020  1.322
 0X6  C5   C6   aromatic  1.387  0.020  1.387
 0X6  N18  C17  triple    1.151  0.020  1.151
 0X6  C17  C13  single    1.429  0.020  1.429
 0X6  N3   C2   aromatic  1.328  0.020  1.328
 0X6  C14  C13  aromatic  1.391  0.020  1.391
 0X6  C14  C15  aromatic  1.382  0.020  1.382
 0X6  C13  C12  aromatic  1.391  0.020  1.391
 0X6  N7   C6   single    1.392  0.020  1.392
 0X6  N7   C8   single    1.353  0.020  1.353
 0X6  C6   C1   aromatic  1.397  0.020  1.397
 0X6  CL1  C15  single    1.722  0.020  1.722
 0X6  C15  C10  aromatic  1.389  0.020  1.389
 0X6  C12  C11  aromatic  1.383  0.020  1.383
 0X6  C11  C10  aromatic  1.389  0.020  1.389
 0X6  C11  CL2  single    1.721  0.020  1.721
 0X6  C10  C8   single    1.506  0.020  1.506
 0X6  C8   O9   double    1.209  0.020  1.209
 0X6  C2   C1   aromatic  1.382  0.020  1.382
 0X6  C14  H1   single    0.930  0.020  1.080
 0X6  C5   H2   single    0.930  0.020  1.080
 0X6  C12  H3   single    0.930  0.020  1.080
 0X6  C1   H4   single    0.930  0.020  1.080
 0X6  C2   H5   single    0.930  0.020  1.080
 0X6  N7   H6   single    0.860  0.020  1.020
 0X6  N20  H7   single    0.860  0.020  1.020
 0X6  C23  H8   single    0.970  0.020  1.090
 0X6  C24  H9   single    0.970  0.020  1.090
 0X6  C24  H10  single    0.970  0.020  1.090
 0X6  C25  H11  single    0.970  0.020  1.090
 0X6  C25  H12  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
 0X6  N20  C4   N3   119.99  3.000
 0X6  N3   C4   C5   123.01  3.000
 0X6  N20  C4   C5   117.00  3.000
 0X6  H1   C14  C15  120.79  3.000
 0X6  H1   C14  C13  120.83  3.000
 0X6  C15  C14  C13  118.38  3.000
 0X6  H2   C5   C6   120.58  3.000
 0X6  H2   C5   C4   120.35  3.000
 0X6  C6   C5   C4   119.07  3.000
 0X6  N7   C6   C1   124.70  3.000
 0X6  C1   C6   C5   118.40  3.000
 0X6  N7   C6   C5   116.90  3.000
 0X6  CL2  C11  C12  119.38  3.000
 0X6  CL2  C11  C10  119.21  3.000
 0X6  C12  C11  C10  121.41  3.000
 0X6  O9   C8   N7   126.43  3.000
 0X6  O9   C8   C10  120.95  3.000
 0X6  N7   C8   C10  112.62  3.000
 0X6  C15  C10  C8   120.59  3.000
 0X6  C8   C10  C11  120.67  3.000
 0X6  C15  C10  C11  118.66  3.000
 0X6  H3   C12  C13  120.78  3.000
 0X6  H3   C12  C11  120.76  3.000
 0X6  C13  C12  C11  118.46  3.000
 0X6  C17  C13  C12  119.20  3.000
 0X6  C12  C13  C14  121.58  3.000
 0X6  C17  C13  C14  119.22  3.000
 0X6  C2   N3   C4   117.04  3.000
 0X6  H4   C1   C2   119.79  3.000
 0X6  H4   C1   C6   123.13  3.000
 0X6  C2   C1   C6   117.08  3.000
 0X6  H5   C2   C1   118.81  3.000
 0X6  H5   C2   N3   115.80  3.000
 0X6  C1   C2   N3   125.39  3.000
 0X6  H6   N7   C8   116.07  3.000
 0X6  H6   N7   C6   115.18  3.000
 0X6  C8   N7   C6   128.72  3.000
 0X6  CL1  C15  C10  119.13  3.000
 0X6  C10  C15  C14  121.50  3.000
 0X6  CL1  C15  C14  119.37  3.000
 0X6  N18  C17  C13  180.00  3.000
 0X6  H7   N20  C21  115.70  3.000
 0X6  H7   N20  C4   114.57  3.000
 0X6  C21  N20  C4   129.69  3.000
 0X6  C23  C21  O22  122.56  3.000
 0X6  O22  C21  N20  124.54  3.000
 0X6  C23  C21  N20  112.90  3.000
 0X6  H8   C23  C25  116.55  3.000
 0X6  H8   C23  C24  116.42  3.000
 0X6  C25  C23  C24   58.92  3.000
 0X6  H8   C23  C21  117.00  3.000
 0X6  C25  C23  C21  117.57  3.000
 0X6  C24  C23  C21  117.70  3.000
 0X6  H10  C24  H9   114.96  3.000
 0X6  H10  C24  C25  118.22  3.000
 0X6  H9   C24  C25  118.67  3.000
 0X6  H10  C24  C23  117.22  3.000
 0X6  H9   C24  C23  116.45  3.000
 0X6  C25  C24  C23   60.52  3.000
 0X6  H12  C25  H11  114.97  3.000
 0X6  H12  C25  C24  118.75  3.000
 0X6  H11  C25  C24  118.10  3.000
 0X6  H12  C25  C23  116.64  3.000
 0X6  H11  C25  C23  117.04  3.000
 0X6  C24  C25  C23   60.56  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
 0X6  CONST_01  C1   C6   C5   C4      0.00   0.0  0
 0X6  CONST_02  C1   C2   N3   C4      0.00   0.0  0
 0X6  CONST_03  C11  C12  C13  C14     0.00   0.0  0
 0X6  CONST_04  C11  C10  C15  C14     0.00   0.0  0
 0X6  CONST_05  C2   N3   C4   C5      0.00   0.0  0
 0X6  CONST_06  C2   C1   C6   C5      0.00   0.0  0
 0X6  CONST_07  N3   C4   C5   C6      0.00   0.0  0
 0X6  CONST_08  N3   C2   C1   C6      0.00   0.0  0
 0X6  CONST_09  C13  C14  C15  C10     0.00   0.0  0
 0X6  CONST_10  C13  C12  C11  C10     0.00   0.0  0
 0X6  CONST_11  C15  C14  C13  C12     0.00   0.0  0
 0X6  CONST_12  C15  C10  C11  C12     0.00   0.0  0
 0X6  CONST_13  N7   C6   C5   C4    180.00   0.0  0
 0X6  CONST_14  C8   C10  C15  C14   180.00   0.0  0
 0X6  CONST_15  N20  C4   C5   C6    180.00   0.0  0
 0X6  CONST_16  C17  C13  C12  C11   180.00   0.0  0
 0X6  CONST_17  CL1  C15  C10  C11   180.00   0.0  0
 0X6  CONST_18  C12  C11  C10  C8    180.00   0.0  0
 0X6  CONST_19  CL1  C15  C14  C13   180.00   0.0  0
 0X6  CONST_20  CL2  C11  C12  C13   180.00   0.0  0
 0X6  CONST_21  N20  C4   N3   C2    180.00   0.0  0
 0X6  CONST_22  N7   C6   C1   C2    180.00   0.0  0
 0X6  CONST_23  C17  C13  C14  C15   180.00   0.0  0
 0X6  CONST_24  CL2  C11  C10  C15   180.00   0.0  0
 0X6  CONST_25  H5   C2   N3   C4    180.00   0.0  0
 0X6  CONST_26  H3   C12  C13  C14   180.00   0.0  0
 0X6  CONST_27  H4   C1   C6   C5    180.00   0.0  0
 0X6  CONST_28  H1   C14  C15  C10   180.00   0.0  0
 0X6  CONST_29  H2   C5   C4   N3    180.00   0.0  0
 0X6  CONST_30  C23  C21  N20  C4    180.00   0.0  0
 0X6  CONST_31  C10  C8   N7   C6    180.00   0.0  0
 0X6  CONST_32  C21  N20  C4   C5    180.00   0.0  0
 0X6  CONST_33  C8   N7   C6   C5    180.00   0.0  0
 0X6  CONST_34  C1   C6   N7   C8      0.00   0.0  0
 0X6  CONST_35  C21  N20  C4   N3      0.00   0.0  0
 0X6  CONST_36  H7   N20  C4   C5      0.00   0.0  0
 0X6  CONST_37  H6   N7   C6   C5      0.00   0.0  0
 0X6  CONST_38  O22  C21  N20  C4      0.00   0.0  0
 0X6  CONST_39  O9   C8   N7   C6      0.00   0.0  0
 0X6  Var_01    C25  C24  C23  C21   107.09  30.0  1
 0X6  Var_02    H11  C25  C24  C23  -106.88  30.0  1
 0X6  Var_03    N7   C8   C10  C11   -95.65  30.0  2
 0X6  Var_04    C24  C23  C21  N20   145.78  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
 0X6  chir_01  C23  C24  C25  C21  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
 0X6  plan-1  C4   0.020
 0X6  plan-1  C5   0.020
 0X6  plan-1  C6   0.020
 0X6  plan-1  N3   0.020
 0X6  plan-1  C1   0.020
 0X6  plan-1  C2   0.020
 0X6  plan-1  N7   0.020
 0X6  plan-1  N20  0.020
 0X6  plan-1  H2   0.020
 0X6  plan-1  H4   0.020
 0X6  plan-1  H5   0.020
 0X6  plan-2  C14  0.020
 0X6  plan-2  C11  0.020
 0X6  plan-2  C8   0.020
 0X6  plan-2  C10  0.020
 0X6  plan-2  C12  0.020
 0X6  plan-2  C13  0.020
 0X6  plan-2  C15  0.020
 0X6  plan-2  CL1  0.020
 0X6  plan-2  C17  0.020
 0X6  plan-2  N18  0.020
 0X6  plan-2  H1   0.020
 0X6  plan-2  H3   0.020
 0X6  plan-2  CL2  0.020
 0X6  plan-3  C4   0.020
 0X6  plan-3  N20  0.020
 0X6  plan-3  C21  0.020
 0X6  plan-3  O22  0.020
 0X6  plan-3  C23  0.020
 0X6  plan-3  H7   0.020
 0X6  plan-4  C6   0.020
 0X6  plan-4  C8   0.020
 0X6  plan-4  C10  0.020
 0X6  plan-4  N7   0.020
 0X6  plan-4  O9   0.020
 0X6  plan-4  H6   0.020

