# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 18 06:06:57 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 2,6-dichloro-N-{2-[(cyclopropylcarbonyl)amino]pyridin-4-yl}benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cccc(Cl)c1C(=O)Nc2ccnc(NC(=O)C3CC3)c2
#
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
 0X5  0X5  2,6-dichloro-N-{2-[(cyclopropylcarbonyl)amino]pyridin-4-yl}benzamide  ligand  36  23  .  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_0X5
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
 0X5  C4   C   CR6   0   0.088   3.1232  -0.4003  -0.1571
 0X5  C5   C   CR6   0  -0.083   3.8835   0.4453  -0.9552
 0X5  C6   C   CR16  0  -0.190   5.2674   0.4149  -0.9291
 0X5  C11  C   CR6   0   0.487  -0.3105   0.6795   0.8616
 0X5  C8   C   C     0   0.476   1.6230  -0.3977  -0.2483
 0X5  C12  C   CR16  0  -0.426  -0.6453   1.5493   1.9061
 0X5  C13  C   CR16  0  -0.058  -1.9760   1.8220   2.1232
 0X5  C3   C   CR6   0  -0.081   3.7892  -1.2904   0.6752
 0X5  C1   C   CR16  0  -0.273   5.9026  -0.4856  -0.0878
 0X5  C2   C   CR16  0  -0.190   5.1722  -1.3428   0.7211
 0X5  CL1  CL  CL    0  -0.097   3.0739   1.5679  -1.9900
 0X5  O9   O   O     0  -0.409   1.0415  -1.0729  -1.0679
 0X5  N10  N   NH1   0  -0.714   1.0401   0.4226   0.6591
 0X5  N14  N   N     0  -0.434  -2.9757   1.3164   1.4043
 0X5  C15  C   CR6   0   0.542  -2.6514   0.4965   0.4219
 0X5  C16  C   CR16  0  -0.482  -1.3354   0.1384   0.1024
 0X5  N17  N   NH1   0  -0.750  -3.6487  -0.0553  -0.3735
 0X5  C18  C   C     0   0.587  -5.0100   0.0290  -0.2548
 0X5  O19  O   O     0  -0.453  -5.5878   0.6232   0.6323
 0X5  C20  C   CH1   0  -0.443  -5.7333  -0.6944  -1.3351
 0X5  C21  C   CH2   0  -0.463  -7.0375  -1.3614  -0.9786
 0X5  C22  C   CH2   0  -0.463  -7.0509  -0.1242  -1.7955
 0X5  CL2  CL  CL    0  -0.097   2.8603  -2.3467   1.6799
 0X5  H1   H   HCR6  0   0.294   5.8411   1.0833  -1.5554
 0X5  H2   H   HCR6  0   0.286   0.1157   1.9984   2.5306
 0X5  H3   H   HCR6  0   0.269  -2.2590   2.4922   2.9269
 0X5  H4   H   HCR6  0   0.288   6.9831  -0.5187  -0.0608
 0X5  H5   H   HCR6  0   0.294   5.6718  -2.0420   1.3768
 0X5  H6   H   HNH1  0   0.433   1.6672   0.9109   1.2827
 0X5  H7   H   HCR6  0   0.303  -1.1459  -0.5394  -0.7140
 0X5  H8   H   HNH1  0   0.422  -3.3115  -0.6103  -1.1447
 0X5  H9   H   HCH1  0   0.285  -5.1291  -1.1851  -2.0894
 0X5  H10  H   HCH2  0   0.266  -7.2459  -2.3062  -1.4624
 0X5  H11  H   HCH2  0   0.260  -7.3605  -1.2973   0.0523
 0X5  H12  H   HCH2  0   0.260  -7.3798   0.7936  -1.3268
 0X5  H13  H   HCH2  0   0.266  -7.2685  -0.1997  -2.8523

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
 0X5  C21  C22  single    1.483  0.020  1.483
 0X5  C21  C20  single    1.508  0.020  1.508
 0X5  C22  C20  single    1.508  0.020  1.508
 0X5  C20  C18  single    1.488  0.020  1.488
 0X5  C18  O19  double    1.214  0.020  1.214
 0X5  C18  N17  single    1.369  0.020  1.369
 0X5  N17  C15  single    1.390  0.020  1.390
 0X5  C15  C16  aromatic  1.401  0.020  1.401
 0X5  C15  N14  aromatic  1.320  0.020  1.320
 0X5  C16  C11  aromatic  1.385  0.020  1.385
 0X5  N14  C13  aromatic  1.331  0.020  1.331
 0X5  N10  C11  single    1.390  0.020  1.390
 0X5  N10  C8   single    1.355  0.020  1.355
 0X5  C11  C12  aromatic  1.400  0.020  1.400
 0X5  C1   C2   aromatic  1.387  0.020  1.387
 0X5  C1   C6   aromatic  1.386  0.020  1.386
 0X5  C2   C3   aromatic  1.385  0.020  1.385
 0X5  C6   C5   aromatic  1.384  0.020  1.384
 0X5  C3   CL2  single    1.729  0.020  1.729
 0X5  C3   C4   aromatic  1.389  0.020  1.389
 0X5  C5   C4   aromatic  1.389  0.020  1.389
 0X5  C5   CL1  single    1.728  0.020  1.728
 0X5  C4   C8   single    1.503  0.020  1.503
 0X5  C8   O9   double    1.211  0.020  1.211
 0X5  C13  C12  aromatic  1.376  0.020  1.376
 0X5  C6   H1   single    0.930  0.020  1.080
 0X5  C12  H2   single    0.930  0.020  1.080
 0X5  C13  H3   single    0.930  0.020  1.080
 0X5  C1   H4   single    0.930  0.020  1.080
 0X5  C2   H5   single    0.930  0.020  1.080
 0X5  N10  H6   single    0.860  0.020  1.020
 0X5  C16  H7   single    0.930  0.020  1.080
 0X5  N17  H8   single    0.860  0.020  1.020
 0X5  C20  H9   single    0.970  0.020  1.090
 0X5  C21  H10  single    0.970  0.020  1.090
 0X5  C21  H11  single    0.970  0.020  1.090
 0X5  C22  H12  single    0.970  0.020  1.090
 0X5  C22  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
 0X5  C3   C4   C8   121.07  3.000
 0X5  C8   C4   C5   120.69  3.000
 0X5  C3   C4   C5   118.17  3.000
 0X5  CL1  C5   C6   119.59  3.000
 0X5  CL1  C5   C4   118.88  3.000
 0X5  C6   C5   C4   121.52  3.000
 0X5  H1   C6   C1   120.67  3.000
 0X5  H1   C6   C5   120.40  3.000
 0X5  C1   C6   C5   118.93  3.000
 0X5  C16  C11  N10  124.54  3.000
 0X5  N10  C11  C12  117.13  3.000
 0X5  C16  C11  C12  118.33  3.000
 0X5  N10  C8   O9   125.76  3.000
 0X5  O9   C8   C4   121.30  3.000
 0X5  N10  C8   C4   112.94  3.000
 0X5  H2   C12  C13  120.46  3.000
 0X5  H2   C12  C11  121.36  3.000
 0X5  C13  C12  C11  118.18  3.000
 0X5  H3   C13  N14  116.05  3.000
 0X5  H3   C13  C12  119.48  3.000
 0X5  N14  C13  C12  124.47  3.000
 0X5  CL2  C3   C2   119.62  3.000
 0X5  CL2  C3   C4   118.84  3.000
 0X5  C2   C3   C4   121.54  3.000
 0X5  H4   C1   C2   119.53  3.000
 0X5  H4   C1   C6   119.53  3.000
 0X5  C2   C1   C6   120.94  3.000
 0X5  H5   C2   C1   120.69  3.000
 0X5  H5   C2   C3   120.41  3.000
 0X5  C1   C2   C3   118.91  3.000
 0X5  H6   N10  C8   116.03  3.000
 0X5  H6   N10  C11  115.09  3.000
 0X5  C8   N10  C11  128.87  3.000
 0X5  C15  N14  C13  116.96  3.000
 0X5  N17  C15  C16  116.24  3.000
 0X5  C16  C15  N14  124.01  3.000
 0X5  N17  C15  N14  119.75  3.000
 0X5  H7   C16  C15  119.91  3.000
 0X5  H7   C16  C11  122.04  3.000
 0X5  C15  C16  C11  118.05  3.000
 0X5  H8   N17  C18  115.65  3.000
 0X5  H8   N17  C15  114.60  3.000
 0X5  C18  N17  C15  129.75  3.000
 0X5  C20  C18  O19  122.49  3.000
 0X5  O19  C18  N17  124.52  3.000
 0X5  C20  C18  N17  112.99  3.000
 0X5  H9   C20  C22  116.48  3.000
 0X5  H9   C20  C21  116.52  3.000
 0X5  C22  C20  C21   58.91  3.000
 0X5  H9   C20  C18  117.03  3.000
 0X5  C22  C20  C18  117.56  3.000
 0X5  C21  C20  C18  117.64  3.000
 0X5  H11  C21  H10  114.85  3.000
 0X5  H11  C21  C22  118.21  3.000
 0X5  H10  C21  C22  118.73  3.000
 0X5  H11  C21  C20  117.21  3.000
 0X5  H10  C21  C20  116.57  3.000
 0X5  C22  C21  C20   60.55  3.000
 0X5  H13  C22  H12  114.93  3.000
 0X5  H13  C22  C21  118.81  3.000
 0X5  H12  C22  C21  118.17  3.000
 0X5  H13  C22  C20  116.59  3.000
 0X5  H12  C22  C20  117.02  3.000
 0X5  C21  C22  C20   60.54  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
 0X5  CONST_01  C1   C2   C3   C4      0.00   0.0  0
 0X5  CONST_02  C1   C6   C5   C4      0.00   0.0  0
 0X5  CONST_03  C2   C1   C6   C5      0.00   0.0  0
 0X5  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 0X5  CONST_05  C3   C2   C1   C6      0.00   0.0  0
 0X5  CONST_06  C3   C4   C5   C6      0.00   0.0  0
 0X5  CONST_07  N14  C15  C16  C11     0.00   0.0  0
 0X5  CONST_08  N14  C13  C12  C11     0.00   0.0  0
 0X5  CONST_09  C15  C16  C11  C12     0.00   0.0  0
 0X5  CONST_10  C15  N14  C13  C12     0.00   0.0  0
 0X5  CONST_11  C16  C15  N14  C13     0.00   0.0  0
 0X5  CONST_12  C16  C11  C12  C13     0.00   0.0  0
 0X5  CONST_13  CL2  C3   C4   C5    180.00   0.0  0
 0X5  CONST_14  C8   C4   C5   C6    180.00   0.0  0
 0X5  CONST_15  N17  C15  C16  C11   180.00   0.0  0
 0X5  CONST_16  C2   C3   C4   C8    180.00   0.0  0
 0X5  CONST_17  N17  C15  N14  C13   180.00   0.0  0
 0X5  CONST_18  N10  C11  C12  C13   180.00   0.0  0
 0X5  CONST_19  CL1  C5   C4   C3    180.00   0.0  0
 0X5  CONST_20  CL2  C3   C2   C1    180.00   0.0  0
 0X5  CONST_21  CL1  C5   C6   C1    180.00   0.0  0
 0X5  CONST_22  C15  C16  C11  N10   180.00   0.0  0
 0X5  CONST_23  H5   C2   C3   C4    180.00   0.0  0
 0X5  CONST_24  H1   C6   C5   C4    180.00   0.0  0
 0X5  CONST_25  H4   C1   C6   C5    180.00   0.0  0
 0X5  CONST_26  H3   C13  C12  C11   180.00   0.0  0
 0X5  CONST_27  H7   C16  C11  C12   180.00   0.0  0
 0X5  CONST_28  H2   C12  C13  N14   180.00   0.0  0
 0X5  CONST_29  C11  N10  C8   C4    180.00   0.0  0
 0X5  CONST_30  C20  C18  N17  C15   180.00   0.0  0
 0X5  CONST_31  C16  C11  N10  C8      0.00   0.0  0
 0X5  CONST_32  C12  C11  N10  C8    180.00   0.0  0
 0X5  CONST_33  C18  N17  C15  N14     0.00   0.0  0
 0X5  CONST_34  C18  N17  C15  C16   180.00   0.0  0
 0X5  CONST_35  H6   N10  C11  C12     0.00   0.0  0
 0X5  CONST_36  H8   N17  C15  N14   180.00   0.0  0
 0X5  CONST_37  O9   C8   N10  C11     0.00   0.0  0
 0X5  CONST_38  O19  C18  N17  C15     0.00   0.0  0
 0X5  Var_01    C22  C21  C20  C18   107.10  30.0  1
 0X5  Var_02    H12  C22  C21  C20  -106.82  30.0  1
 0X5  Var_03    N10  C8   C4   C5    -93.81  30.0  2
 0X5  Var_04    C21  C20  C18  N17   145.52  30.0  1

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
 0X5  chir_01  C20  C21  C22  C18  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
 0X5  plan-1  C4   0.020
 0X5  plan-1  C5   0.020
 0X5  plan-1  C6   0.020
 0X5  plan-1  C8   0.020
 0X5  plan-1  C3   0.020
 0X5  plan-1  C1   0.020
 0X5  plan-1  C2   0.020
 0X5  plan-1  CL1  0.020
 0X5  plan-1  CL2  0.020
 0X5  plan-1  H1   0.020
 0X5  plan-1  H4   0.020
 0X5  plan-1  H5   0.020
 0X5  plan-2  C11  0.020
 0X5  plan-2  C12  0.020
 0X5  plan-2  C13  0.020
 0X5  plan-2  N10  0.020
 0X5  plan-2  N14  0.020
 0X5  plan-2  C15  0.020
 0X5  plan-2  C16  0.020
 0X5  plan-2  N17  0.020
 0X5  plan-2  H2   0.020
 0X5  plan-2  H3   0.020
 0X5  plan-2  H7   0.020
 0X5  plan-3  C15  0.020
 0X5  plan-3  N17  0.020
 0X5  plan-3  C18  0.020
 0X5  plan-3  O19  0.020
 0X5  plan-3  C20  0.020
 0X5  plan-3  H8   0.020
 0X5  plan-4  C4   0.020
 0X5  plan-4  C11  0.020
 0X5  plan-4  C8   0.020
 0X5  plan-4  O9   0.020
 0X5  plan-4  N10  0.020
 0X5  plan-4  H6   0.020

