# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 03:36:18 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: (1R,2R)-N-(3,4-dichlorobenzyl)-2-(4,6-dimethoxypyrimidin-2-yl)cyclohexanecarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(OC)nc(n1)[C@@H]2CCCC[C@H]2C(=O)NCc3ccc(Cl)c(Cl)c3
#
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
 2W5  2W5  (1R,2R)-N-(3,4-dichlorobenzyl)-2-(4,6-dimethoxypyrimidin-2-yl)cyclohexanecarboxamide  ligand  51  28  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_2W5
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
 2W5  C1   C   CH3   0  -0.418   0.8147   2.1876  -1.6812
 2W5  C3   C   CR6   0   0.561   2.8666   1.8616  -0.5558
 2W5  C7   C   CH3   0  -0.419   6.8225   0.9621   1.8269
 2W5  C9   C   CR6   0   0.409   3.3522  -0.1965   0.2435
 2W5  C11  C   CH1   0  -0.294   2.9965  -1.6510   0.3838
 2W5  C13  C   CH2   0  -0.426   3.9074  -2.5019  -0.5131
 2W5  C14  C   CH2   0  -0.435   3.6029  -3.9874  -0.3597
 2W5  C15  C   CH2   0  -0.435   2.1333  -4.2862  -0.6298
 2W5  C16  C   CH2   0  -0.419   1.2264  -3.4322   0.2481
 2W5  C19  C   C     0   0.598   0.6154  -1.1326   0.9742
 2W5  C22  C   CH2   0  -0.328  -1.4868   0.1177   1.1049
 2W5  C24  C   CR16  0  -0.281  -3.4686  -1.0189   0.0479
 2W5  C30  C   CR16  0  -0.275  -3.3148   1.3678  -0.0729
 2W5  O2   O   O2    0  -0.463   2.0535   2.6916  -1.1949
 2W5  C4   C   CR16  0  -0.500   4.0581   2.3693  -0.0611
 2W5  C5   C   CR6   0   0.553   4.8555   1.4498   0.6102
 2W5  O6   O   O2    0  -0.465   6.0062   1.8803   1.1073
 2W5  N8   N   N     0  -0.486   4.5095   0.1820   0.7702
 2W5  N10  N   N     0  -0.488   2.5161   0.5902  -0.4135
 2W5  C17  C   CH1   0  -0.372   1.5287  -1.9376   0.0718
 2W5  O20  O   O     0  -0.500   0.8546  -0.9636   2.1622
 2W5  N21  N   NH1   0  -0.640  -0.5094  -0.6771   0.3948
 2W5  C23  C   CR6   0   0.073  -2.7827   0.1570   0.3444
 2W5  C25  C   CR16  0  -0.200  -4.6632  -0.9831  -0.6471
 2W5  C26  C   CR6   0  -0.018  -5.1925   0.2329  -1.0590
 2W5  CL7  CL  CL    0  -0.096  -6.6813   0.2634  -1.9229
 2W5  C28  C   CR6   0   0.026  -4.5156   1.4097  -0.7686
 2W5  CL9  CL  CL    0  -0.095  -5.1452   2.9323  -1.2701
 2W5  H1   H   HCH3  0   0.236   0.9605   1.4088  -2.4298
 2W5  H2   H   HCH3  0   0.225   0.2016   1.7875  -0.8738
 2W5  H3   H   HCH3  0   0.252   0.3070   3.0352  -2.1327
 2W5  H4   H   HCH3  0   0.234   6.3220   0.5993   2.7246
 2W5  H5   H   HCH3  0   0.235   7.1103   0.1081   1.2140
 2W5  H6   H   HCH3  0   0.249   7.7115   1.5190   2.1100
 2W5  H7   H   HCH1  0   0.253   3.1955  -1.9360   1.4226
 2W5  H8   H   HCH2  0   0.224   3.7694  -2.2016  -1.5581
 2W5  H9   H   HCH2  0   0.244   4.9508  -2.3017  -0.2621
 2W5  H10  H   HCH2  0   0.235   4.2380  -4.5652  -1.0349
 2W5  H11  H   HCH2  0   0.217   3.8571  -4.3058   0.6567
 2W5  H12  H   HCH2  0   0.216   1.9077  -4.0917  -1.6837
 2W5  H13  H   HCH2  0   0.235   1.9236  -5.3442  -0.4575
 2W5  H14  H   HCH2  0   0.241   0.1785  -3.6240   0.0056
 2W5  H15  H   HCH2  0   0.225   1.3641  -3.7088   1.2987
 2W5  H16  H   HCH2  0   0.274  -1.6522  -0.3229   2.0899
 2W5  H17  H   HCH2  0   0.256  -1.1216   1.1356   1.2728
 2W5  H19  H   HCR6  0   0.287  -2.7968   2.2934   0.1427
 2W5  H20  H   HCR6  0   0.281   4.3432   3.4048  -0.1821
 2W5  H21  H   HCH1  0   0.250   1.3335  -1.6685  -0.9718
 2W5  H22  H   HNH1  0   0.400  -0.5832  -0.7287  -0.6083
 2W5  H23  H   HCR6  0   0.290  -5.1919  -1.8997  -0.8701
 2W5  H18  H   HCR6  0   0.272  -3.0718  -1.9758   0.3623

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
 2W5  C1   O2   single    1.423  0.020  1.423
 2W5  O2   C3   single    1.326  0.020  1.326
 2W5  C4   C3   aromatic  1.386  0.020  1.386
 2W5  C4   C5   aromatic  1.390  0.020  1.390
 2W5  C3   N10  aromatic  1.327  0.020  1.327
 2W5  O6   C5   single    1.325  0.020  1.325
 2W5  O6   C7   single    1.424  0.020  1.424
 2W5  C5   N8   aromatic  1.324  0.020  1.324
 2W5  N10  C9   aromatic  1.323  0.020  1.323
 2W5  N8   C9   aromatic  1.327  0.020  1.327
 2W5  C13  C11  single    1.536  0.020  1.536
 2W5  C13  C14  single    1.524  0.020  1.524
 2W5  C9   C11  single    1.504  0.020  1.504
 2W5  C11  C17  single    1.528  0.020  1.528
 2W5  C14  C15  single    1.524  0.020  1.524
 2W5  C15  C16  single    1.524  0.020  1.524
 2W5  C25  C24  aromatic  1.383  0.020  1.383
 2W5  C25  C26  aromatic  1.389  0.020  1.389
 2W5  C24  C23  aromatic  1.393  0.020  1.393
 2W5  C17  C16  single    1.535  0.020  1.535
 2W5  C17  C19  single    1.515  0.020  1.515
 2W5  N21  C19  single    1.345  0.020  1.345
 2W5  N21  C22  single    1.446  0.020  1.446
 2W5  C19  O20  double    1.224  0.020  1.224
 2W5  CL7  C26  single    1.722  0.020  1.722
 2W5  C26  C28  aromatic  1.388  0.020  1.388
 2W5  C23  C22  single    1.503  0.020  1.503
 2W5  C23  C30  aromatic  1.387  0.020  1.387
 2W5  C28  C30  aromatic  1.388  0.020  1.388
 2W5  C28  CL9  single    1.722  0.020  1.722
 2W5  C1   H1   single    0.970  0.020  1.090
 2W5  C1   H2   single    0.970  0.020  1.090
 2W5  C1   H3   single    0.970  0.020  1.090
 2W5  C7   H4   single    0.970  0.020  1.090
 2W5  C7   H5   single    0.970  0.020  1.090
 2W5  C7   H6   single    0.970  0.020  1.090
 2W5  C11  H7   single    0.970  0.020  1.090
 2W5  C13  H8   single    0.970  0.020  1.090
 2W5  C13  H9   single    0.970  0.020  1.090
 2W5  C14  H10  single    0.970  0.020  1.090
 2W5  C14  H11  single    0.970  0.020  1.090
 2W5  C15  H12  single    0.970  0.020  1.090
 2W5  C15  H13  single    0.970  0.020  1.090
 2W5  C16  H14  single    0.970  0.020  1.090
 2W5  C16  H15  single    0.970  0.020  1.090
 2W5  C22  H16  single    0.970  0.020  1.090
 2W5  C22  H17  single    0.970  0.020  1.090
 2W5  C24  H18  single    0.930  0.020  1.080
 2W5  C30  H19  single    0.930  0.020  1.080
 2W5  C4   H20  single    0.930  0.020  1.080
 2W5  C17  H21  single    0.970  0.020  1.090
 2W5  N21  H22  single    0.860  0.020  1.020
 2W5  C25  H23  single    0.930  0.020  1.080

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
 2W5  H3   C1   H2   109.36  3.000
 2W5  H3   C1   H1   109.54  3.000
 2W5  H2   C1   H1   108.77  3.000
 2W5  H3   C1   O2   105.81  3.000
 2W5  H2   C1   O2   111.50  3.000
 2W5  H1   C1   O2   111.80  3.000
 2W5  N10  C3   C4   122.67  3.000
 2W5  N10  C3   O2   119.31  3.000
 2W5  C4   C3   O2   118.02  3.000
 2W5  H6   C7   H5   109.40  3.000
 2W5  H6   C7   H4   109.37  3.000
 2W5  H5   C7   H4   108.88  3.000
 2W5  H6   C7   O6   105.68  3.000
 2W5  H5   C7   O6   111.87  3.000
 2W5  H4   C7   O6   111.57  3.000
 2W5  N10  C9   N8   125.38  3.000
 2W5  N8   C9   C11  116.43  3.000
 2W5  N10  C9   C11  118.17  3.000
 2W5  H7   C11  C17  108.63  3.000
 2W5  H7   C11  C13  107.58  3.000
 2W5  C17  C11  C13  110.28  3.000
 2W5  H7   C11  C9   107.29  3.000
 2W5  C17  C11  C9   112.93  3.000
 2W5  C13  C11  C9   109.94  3.000
 2W5  H9   C13  H8   106.81  3.000
 2W5  H9   C13  C14  110.28  3.000
 2W5  H8   C13  C14  109.75  3.000
 2W5  H9   C13  C11  109.33  3.000
 2W5  H8   C13  C11  109.29  3.000
 2W5  C14  C13  C11  111.27  3.000
 2W5  H11  C14  H10  106.56  3.000
 2W5  H11  C14  C15  109.35  3.000
 2W5  H10  C14  C15  110.33  3.000
 2W5  H11  C14  C13  109.30  3.000
 2W5  H10  C14  C13  109.71  3.000
 2W5  C15  C14  C13  111.46  3.000
 2W5  H13  C15  H12  106.52  3.000
 2W5  H13  C15  C16  109.73  3.000
 2W5  H12  C15  C16  109.41  3.000
 2W5  H13  C15  C14  110.31  3.000
 2W5  H12  C15  C14  109.54  3.000
 2W5  C16  C15  C14  111.22  3.000
 2W5  H15  C16  H14  106.81  3.000
 2W5  H15  C16  C17  109.35  3.000
 2W5  H14  C16  C17  109.53  3.000
 2W5  H15  C16  C15  109.65  3.000
 2W5  H14  C16  C15  110.15  3.000
 2W5  C17  C16  C15  111.24  3.000
 2W5  N21  C19  O20  122.35  3.000
 2W5  O20  C19  C17  122.26  3.000
 2W5  N21  C19  C17  115.31  3.000
 2W5  H17  C22  H16  106.71  3.000
 2W5  H17  C22  C23  109.94  3.000
 2W5  H16  C22  C23  109.66  3.000
 2W5  H17  C22  N21  111.16  3.000
 2W5  H16  C22  N21  108.88  3.000
 2W5  C23  C22  N21  110.41  3.000
 2W5  H18  C24  C25  119.05  3.000
 2W5  H18  C24  C23  120.25  3.000
 2W5  C25  C24  C23  120.70  3.000
 2W5  H19  C30  C28  119.20  3.000
 2W5  H19  C30  C23  120.20  3.000
 2W5  C28  C30  C23  120.60  3.000
 2W5  C3   O2   C1   118.48  3.000
 2W5  H20  C4   C5   122.45  3.000
 2W5  H20  C4   C3   122.52  3.000
 2W5  C5   C4   C3   115.03  3.000
 2W5  N8   C5   O6   119.51  3.000
 2W5  N8   C5   C4   122.82  3.000
 2W5  O6   C5   C4   117.67  3.000
 2W5  C5   O6   C7   118.55  3.000
 2W5  C5   N8   C9   116.95  3.000
 2W5  C9   N10  C3   117.15  3.000
 2W5  H21  C17  C19  109.24  3.000
 2W5  H21  C17  C16  108.27  3.000
 2W5  C19  C17  C16  109.27  3.000
 2W5  H21  C17  C11  108.65  3.000
 2W5  C19  C17  C11  110.97  3.000
 2W5  C16  C17  C11  110.39  3.000
 2W5  H22  N21  C22  117.88  3.000
 2W5  H22  N21  C19  118.23  3.000
 2W5  C22  N21  C19  122.68  3.000
 2W5  C30  C23  C24  118.94  3.000
 2W5  C30  C23  C22  120.39  3.000
 2W5  C24  C23  C22  120.67  3.000
 2W5  H23  C25  C26  119.65  3.000
 2W5  H23  C25  C24  120.27  3.000
 2W5  C26  C25  C24  120.07  3.000
 2W5  C28  C26  CL7  120.77  3.000
 2W5  C28  C26  C25  119.63  3.000
 2W5  CL7  C26  C25  119.60  3.000
 2W5  CL9  C28  C26  120.68  3.000
 2W5  CL9  C28  C30  119.26  3.000
 2W5  C26  C28  C30  120.06  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
 2W5  CONST_01  N8   C5   C4   C3      0.00   0.0  0
 2W5  CONST_02  N8   C9   N10  C3      0.00   0.0  0
 2W5  CONST_03  C4   C3   N10  C9      0.00   0.0  0
 2W5  CONST_04  C4   C5   N8   C9      0.00   0.0  0
 2W5  CONST_05  C28  C26  C25  C24     0.00   0.0  0
 2W5  CONST_06  C28  C30  C23  C24     0.00   0.0  0
 2W5  CONST_07  C25  C24  C23  C30     0.00   0.0  0
 2W5  CONST_08  C25  C26  C28  C30     0.00   0.0  0
 2W5  CONST_09  N10  C3   C4   C5      0.00   0.0  0
 2W5  CONST_10  N10  C9   N8   C5      0.00   0.0  0
 2W5  CONST_11  C26  C25  C24  C23     0.00   0.0  0
 2W5  CONST_12  C26  C28  C30  C23     0.00   0.0  0
 2W5  CONST_13  C11  C9   N10  C3    180.00   0.0  0
 2W5  CONST_14  C5   N8   C9   C11   180.00   0.0  0
 2W5  CONST_15  O6   C5   C4   C3    180.00   0.0  0
 2W5  CONST_16  O2   C3   N10  C9    180.00   0.0  0
 2W5  CONST_17  O6   C5   N8   C9    180.00   0.0  0
 2W5  CONST_18  C25  C24  C23  C22   180.00   0.0  0
 2W5  CONST_19  C28  C30  C23  C22   180.00   0.0  0
 2W5  CONST_20  CL7  C26  C25  C24   180.00   0.0  0
 2W5  CONST_21  CL7  C26  C28  C30   180.00   0.0  0
 2W5  CONST_22  C5   C4   C3   O2    180.00   0.0  0
 2W5  CONST_23  CL9  C28  C30  C23   180.00   0.0  0
 2W5  CONST_24  CL9  C28  C26  C25   180.00   0.0  0
 2W5  CONST_25  H19  C30  C23  C24   180.00   0.0  0
 2W5  CONST_26  H18  C24  C23  C30   180.00   0.0  0
 2W5  CONST_27  H20  C4   C5   N8    180.00   0.0  0
 2W5  CONST_28  H23  C25  C24  C23   180.00   0.0  0
 2W5  CONST_29  C17  C19  N21  C22   180.00   0.0  0
 2W5  CONST_30  H22  N21  C19  C17     0.00   0.0  0
 2W5  CONST_31  O20  C19  N21  C22     0.00   0.0  0
 2W5  Var_01    C15  C14  C13  C11    55.39  30.0  1
 2W5  Var_02    C16  C15  C14  C13   -54.67  30.0  1
 2W5  Var_03    C17  C16  C15  C14    55.54  30.0  1
 2W5  Var_04    C4   C3   O2   C1   -178.65  30.0  2
 2W5  Var_05    C4   C5   O6   C7    178.49  30.0  2
 2W5  Var_06    N21  C22  C23  C24    59.14  30.0  2
 2W5  Var_07    C23  C22  N21  C19  -164.38  30.0  3
 2W5  Var_08    H1   C1   O2   C3    -62.63  30.0  3
 2W5  Var_09    H4   C7   O6   C5    -62.79  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
 2W5  chir_01  C11  C13  C9   C17  negativ
 2W5  chir_02  C17  C11  C16  C19  negativ

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
 2W5  plan-1  C3   0.020
 2W5  plan-1  C9   0.020
 2W5  plan-1  C11  0.020
 2W5  plan-1  O2   0.020
 2W5  plan-1  C4   0.020
 2W5  plan-1  C5   0.020
 2W5  plan-1  O6   0.020
 2W5  plan-1  N8   0.020
 2W5  plan-1  N10  0.020
 2W5  plan-1  H20  0.020
 2W5  plan-2  C22  0.020
 2W5  plan-2  C24  0.020
 2W5  plan-2  C30  0.020
 2W5  plan-2  C23  0.020
 2W5  plan-2  C25  0.020
 2W5  plan-2  C26  0.020
 2W5  plan-2  CL7  0.020
 2W5  plan-2  C28  0.020
 2W5  plan-2  CL9  0.020
 2W5  plan-2  H19  0.020
 2W5  plan-2  H23  0.020
 2W5  plan-2  H18  0.020
 2W5  plan-3  C19  0.020
 2W5  plan-3  C22  0.020
 2W5  plan-3  C17  0.020
 2W5  plan-3  O20  0.020
 2W5  plan-3  N21  0.020
 2W5  plan-3  H22  0.020

