# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar  7 20:19:57 2022
#   Inital geometry file: a 110 line input string
#   Ligand name: ~{N}-[(2-chlorophenyl)methyl]-3-[(2-chlorophenyl)methylamino]pyrazine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccccc1CNC(=O)c2nccnc2NCc3ccccc3Cl
#
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
 0W4  0W4  ~{N}-[(2-chlorophenyl)methyl]-3-[(2-chlorophenyl)methylamino]pyrazine-2-carboxamide  ligand  42  26  .  2022-08-09  2022-08-09
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_0W4
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
 0W4  C19  C   CH2   0  -0.358   6.3263  40.6429  26.4961
 0W4  C20  C   CR6   0   0.187   7.3223  41.6351  27.0351
 0W4  N1   N   N     0  -0.375   7.2492  36.9222  27.9072
 0W4  C2   C   CR6   0  -0.003   6.0006  37.2725  28.1479
 0W4  C7   C   C     0   0.575   5.5529  38.6025  27.6346
 0W4  C6   C   CR16  0  -0.158   7.6952  35.7510  28.3307
 0W4  C5   C   CR16  0  -0.082   6.8448  34.9015  29.0235
 0W4  C3   C   CR6   0   0.520   5.1336  36.4014  28.8669
 0W4  C11  C   CH2   0  -0.333   3.0031  35.8714  29.9406
 0W4  C12  C   CR6   0   0.158   2.3621  34.7394  29.1677
 0W4  C17  C   CR16  0  -0.308   2.4777  34.6314  27.7857
 0W4  C16  C   CR16  0  -0.229   1.8743  33.5944  27.0881
 0W4  C15  C   CR16  0  -0.277   1.1374  32.6354  27.7665
 0W4  C14  C   CR16  0  -0.199   1.0010  32.7212  29.1440
 0W4  C13  C   CR6   0  -0.101   1.6089  33.7669  29.8207
 0W4  C21  C   CR6   0  -0.105   7.2808  42.0985  28.3482
 0W4  C22  C   CR16  0  -0.198   8.2089  43.0065  28.8331
 0W4  C23  C   CR16  0  -0.273   9.2115  43.4697  27.9934
 0W4  C24  C   CR16  0  -0.228   9.2767  43.0263  26.6813
 0W4  C25  C   CR16  0  -0.315   8.3379  42.1174  26.2153
 0W4  N10  N   NH1   0  -0.688   3.8615  36.7162  29.1605
 0W4  N4   N   N     0  -0.417   5.5915  35.2174  29.2852
 0W4  N9   N   NH1   0  -0.629   6.5197  39.3312  27.0662
 0W4  O8   O   O     0  -0.496   4.3848  38.9714  27.7337
 0W4  CL1  CL  CL    0  -0.128   1.4066  33.8585  31.5459
 0W4  CL2  CL  CL    0  -0.123   6.0319  41.5475  29.4180
 0W4  H1   H   HCH2  0   0.271   5.3068  40.9650  26.7042
 0W4  H2   H   HCH2  0   0.273   6.4299  40.5939  25.4096
 0W4  H3   H   HCR6  0   0.270   8.7224  35.4857  28.1194
 0W4  H4   H   HCR6  0   0.275   7.1926  33.9354  29.3715
 0W4  H5   H   HCH2  0   0.281   2.2216  36.5059  30.3628
 0W4  H6   H   HCH2  0   0.261   3.5592  35.4642  30.7868
 0W4  H7   H   HCR6  0   0.257   3.0469  35.3759  27.2445
 0W4  H8   H   HCR6  0   0.259   1.9824  33.5378  26.0131
 0W4  H9   H   HCR6  0   0.264   0.6663  31.8216  27.2313
 0W4  H10  H   HCR6  0   0.277   0.4267  31.9828  29.6873
 0W4  H11  H   HCR6  0   0.278   8.1483  43.3516  29.8565
 0W4  H12  H   HCR6  0   0.267   9.9370  44.1780  28.3705
 0W4  H13  H   HCR6  0   0.262  10.0551  43.3850  26.0213
 0W4  H14  H   HCR6  0   0.263   8.3876  41.7698  25.1905
 0W4  H15  H   HNH1  0   0.417   3.5172  37.5931  28.7976
 0W4  H16  H   HNH1  0   0.407   7.4377  38.9137  27.0107

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
 0W4  C25  C24  aromatic  1.387  0.020  1.387
 0W4  C25  C20  aromatic  1.391  0.020  1.391
 0W4  C24  C23  aromatic  1.387  0.020  1.387
 0W4  C19  C20  single    1.506  0.020  1.506
 0W4  C19  N9   single    1.443  0.020  1.443
 0W4  C16  C15  aromatic  1.387  0.020  1.387
 0W4  C16  C17  aromatic  1.388  0.020  1.388
 0W4  C20  C21  aromatic  1.393  0.020  1.393
 0W4  N9   C7   single    1.338  0.020  1.338
 0W4  C15  C14  aromatic  1.387  0.020  1.387
 0W4  C23  C22  aromatic  1.387  0.020  1.387
 0W4  C17  C12  aromatic  1.391  0.020  1.391
 0W4  C7   O8   double    1.229  0.020  1.229
 0W4  C7   C2   single    1.494  0.020  1.494
 0W4  C21  C22  aromatic  1.386  0.020  1.386
 0W4  C21  CL2  single    1.734  0.020  1.734
 0W4  N1   C2   aromatic  1.319  0.020  1.319
 0W4  N1   C6   aromatic  1.323  0.020  1.323
 0W4  C2   C3   aromatic  1.424  0.020  1.424
 0W4  C14  C13  aromatic  1.386  0.020  1.386
 0W4  C12  C13  aromatic  1.393  0.020  1.393
 0W4  C12  C11  single    1.513  0.020  1.513
 0W4  N10  C3   single    1.343  0.020  1.343
 0W4  N10  C11  single    1.435  0.020  1.435
 0W4  C6   C5   aromatic  1.387  0.020  1.387
 0W4  C3   N4   aromatic  1.337  0.020  1.337
 0W4  C13  CL1  single    1.739  0.020  1.739
 0W4  C5   N4   aromatic  1.319  0.020  1.319
 0W4  C19  H1   single    0.970  0.020  1.090
 0W4  C19  H2   single    0.970  0.020  1.090
 0W4  C6   H3   single    0.930  0.020  1.080
 0W4  C5   H4   single    0.930  0.020  1.080
 0W4  C11  H5   single    0.970  0.020  1.090
 0W4  C11  H6   single    0.970  0.020  1.090
 0W4  C17  H7   single    0.930  0.020  1.080
 0W4  C16  H8   single    0.930  0.020  1.080
 0W4  C15  H9   single    0.930  0.020  1.080
 0W4  C14  H10  single    0.930  0.020  1.080
 0W4  C22  H11  single    0.930  0.020  1.080
 0W4  C23  H12  single    0.930  0.020  1.080
 0W4  C24  H13  single    0.930  0.020  1.080
 0W4  C25  H14  single    0.930  0.020  1.080
 0W4  N10  H15  single    0.860  0.020  1.020
 0W4  N9   H16  single    0.860  0.020  1.020

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
 0W4  H2   C19  H1   106.98  3.000
 0W4  H2   C19  N9   109.84  3.000
 0W4  H1   C19  N9   108.58  3.000
 0W4  H2   C19  C20  108.84  3.000
 0W4  H1   C19  C20  110.85  3.000
 0W4  N9   C19  C20  111.64  3.000
 0W4  C25  C20  C21  117.51  3.000
 0W4  C21  C20  C19  122.47  3.000
 0W4  C25  C20  C19  120.02  3.000
 0W4  C6   N1   C2   119.73  3.000
 0W4  C3   C2   C7   122.38  3.000
 0W4  C3   C2   N1   120.40  3.000
 0W4  C7   C2   N1   117.22  3.000
 0W4  O8   C7   N9   123.90  3.000
 0W4  O8   C7   C2   121.62  3.000
 0W4  N9   C7   C2   114.48  3.000
 0W4  H3   C6   C5   121.96  3.000
 0W4  H3   C6   N1   118.35  3.000
 0W4  C5   C6   N1   119.69  3.000
 0W4  H4   C5   N4   117.04  3.000
 0W4  H4   C5   C6   120.62  3.000
 0W4  N4   C5   C6   122.34  3.000
 0W4  N4   C3   N10  117.63  3.000
 0W4  N4   C3   C2   119.43  3.000
 0W4  N10  C3   C2   122.94  3.000
 0W4  H6   C11  H5   106.36  3.000
 0W4  H6   C11  N10  109.66  3.000
 0W4  H5   C11  N10  107.24  3.000
 0W4  H6   C11  C12  109.44  3.000
 0W4  H5   C11  C12  109.21  3.000
 0W4  N10  C11  C12  114.59  3.000
 0W4  C13  C12  C17  117.16  3.000
 0W4  C13  C12  C11  120.80  3.000
 0W4  C17  C12  C11  122.03  3.000
 0W4  H7   C17  C16  119.43  3.000
 0W4  H7   C17  C12  119.15  3.000
 0W4  C16  C17  C12  121.42  3.000
 0W4  H8   C16  C15  120.19  3.000
 0W4  H8   C16  C17  119.68  3.000
 0W4  C15  C16  C17  120.12  3.000
 0W4  H9   C15  C14  119.67  3.000
 0W4  H9   C15  C16  120.63  3.000
 0W4  C14  C15  C16  119.69  3.000
 0W4  H10  C14  C13  120.18  3.000
 0W4  H10  C14  C15  120.58  3.000
 0W4  C13  C14  C15  119.24  3.000
 0W4  CL1  C13  C14  118.23  3.000
 0W4  CL1  C13  C12  119.42  3.000
 0W4  C14  C13  C12  122.35  3.000
 0W4  CL2  C21  C22  118.33  3.000
 0W4  CL2  C21  C20  119.82  3.000
 0W4  C22  C21  C20  121.85  3.000
 0W4  H11  C22  C23  120.44  3.000
 0W4  H11  C22  C21  120.16  3.000
 0W4  C23  C22  C21  119.40  3.000
 0W4  H12  C23  C24  120.51  3.000
 0W4  H12  C23  C22  119.49  3.000
 0W4  C24  C23  C22  120.00  3.000
 0W4  H13  C24  C25  119.95  3.000
 0W4  H13  C24  C23  120.34  3.000
 0W4  C25  C24  C23  119.71  3.000
 0W4  H14  C25  C24  119.80  3.000
 0W4  H14  C25  C20  118.66  3.000
 0W4  C24  C25  C20  121.54  3.000
 0W4  H15  N10  C11  120.18  3.000
 0W4  H15  N10  C3   116.62  3.000
 0W4  C11  N10  C3   123.19  3.000
 0W4  C3   N4   C5   118.40  3.000
 0W4  H16  N9   C7   117.07  3.000
 0W4  H16  N9   C19  118.41  3.000
 0W4  C7   N9   C19  124.48  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
 0W4  CONST_01  C23  C24  C25  C20    0.00   0.0  0
 0W4  CONST_02  C23  C22  C21  C20    0.00   0.0  0
 0W4  CONST_03  N4   C3   C2   N1     0.00   0.0  0
 0W4  CONST_04  N4   C5   C6   N1     0.00   0.0  0
 0W4  CONST_05  C5   C6   N1   C2     0.00   0.0  0
 0W4  CONST_06  C5   N4   C3   C2     0.00   0.0  0
 0W4  CONST_07  C3   C2   N1   C6     0.00   0.0  0
 0W4  CONST_08  C3   N4   C5   C6     0.00   0.0  0
 0W4  CONST_09  C15  C16  C17  C12    0.00   0.0  0
 0W4  CONST_10  C15  C14  C13  C12    0.00   0.0  0
 0W4  CONST_11  C14  C15  C16  C17    0.00   0.0  0
 0W4  CONST_12  C14  C13  C12  C17    0.00   0.0  0
 0W4  CONST_13  C13  C14  C15  C16    0.00   0.0  0
 0W4  CONST_14  C13  C12  C17  C16    0.00   0.0  0
 0W4  CONST_15  C24  C25  C20  C21    0.00   0.0  0
 0W4  CONST_16  C24  C23  C22  C21    0.00   0.0  0
 0W4  CONST_17  C25  C24  C23  C22    0.00   0.0  0
 0W4  CONST_18  C25  C20  C21  C22    0.00   0.0  0
 0W4  CONST_19  C24  C25  C20  C19  180.00   0.0  0
 0W4  CONST_20  C22  C21  C20  C19  180.00   0.0  0
 0W4  CONST_21  N10  C3   C2   N1   180.00   0.0  0
 0W4  CONST_22  C6   N1   C2   C7   180.00   0.0  0
 0W4  CONST_23  N4   C3   C2   C7   180.00   0.0  0
 0W4  CONST_24  N10  C3   N4   C5   180.00   0.0  0
 0W4  CONST_25  C16  C17  C12  C11  180.00   0.0  0
 0W4  CONST_26  C14  C13  C12  C11  180.00   0.0  0
 0W4  CONST_27  CL1  C13  C12  C17  180.00   0.0  0
 0W4  CONST_28  CL1  C13  C14  C15  180.00   0.0  0
 0W4  CONST_29  CL2  C21  C22  C23  180.00   0.0  0
 0W4  CONST_30  CL2  C21  C20  C25  180.00   0.0  0
 0W4  CONST_31  H13  C24  C25  C20  180.00   0.0  0
 0W4  CONST_32  H11  C22  C21  C20  180.00   0.0  0
 0W4  CONST_33  H4   C5   C6   N1   180.00   0.0  0
 0W4  CONST_34  H3   C6   N1   C2   180.00   0.0  0
 0W4  CONST_35  H8   C16  C17  C12  180.00   0.0  0
 0W4  CONST_36  H10  C14  C13  C12  180.00   0.0  0
 0W4  CONST_37  H9   C15  C16  C17  180.00   0.0  0
 0W4  CONST_38  H7   C17  C16  C15  180.00   0.0  0
 0W4  CONST_39  H14  C25  C20  C21  180.00   0.0  0
 0W4  CONST_40  H12  C23  C22  C21  180.00   0.0  0
 0W4  CONST_41  C11  N10  C3   C2   180.00   0.0  0
 0W4  CONST_42  N4   C3   N10  C11    0.00   0.0  0
 0W4  CONST_43  H15  N10  C3   C2     0.00   0.0  0
 0W4  CONST_44  C2   C7   N9   C19  180.00   0.0  0
 0W4  CONST_45  H16  N9   C7   C2     0.00   0.0  0
 0W4  CONST_46  O8   C7   N9   C19    0.00   0.0  0
 0W4  Var_01    N9   C7   C2   N1    -4.68  30.0  2
 0W4  Var_02    C12  C11  N10  C3   -81.42  30.0  3
 0W4  Var_03    N10  C11  C12  C17   -7.18  30.0  2
 0W4  Var_04    N9   C19  C20  C21  -70.33  30.0  2
 0W4  Var_05    C7   N9   C19  C20  128.43  30.0  3

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
 0W4  plan-1  N1   0.020
 0W4  plan-1  C2   0.020
 0W4  plan-1  C7   0.020
 0W4  plan-1  C6   0.020
 0W4  plan-1  C5   0.020
 0W4  plan-1  C3   0.020
 0W4  plan-1  N10  0.020
 0W4  plan-1  N4   0.020
 0W4  plan-1  H3   0.020
 0W4  plan-1  H4   0.020
 0W4  plan-2  C11  0.020
 0W4  plan-2  C12  0.020
 0W4  plan-2  C17  0.020
 0W4  plan-2  C16  0.020
 0W4  plan-2  C15  0.020
 0W4  plan-2  C14  0.020
 0W4  plan-2  C13  0.020
 0W4  plan-2  CL1  0.020
 0W4  plan-2  H7   0.020
 0W4  plan-2  H8   0.020
 0W4  plan-2  H9   0.020
 0W4  plan-2  H10  0.020
 0W4  plan-3  C19  0.020
 0W4  plan-3  C20  0.020
 0W4  plan-3  C21  0.020
 0W4  plan-3  C22  0.020
 0W4  plan-3  C23  0.020
 0W4  plan-3  C24  0.020
 0W4  plan-3  C25  0.020
 0W4  plan-3  CL2  0.020
 0W4  plan-3  H11  0.020
 0W4  plan-3  H12  0.020
 0W4  plan-3  H13  0.020
 0W4  plan-3  H14  0.020
 0W4  plan-4  C19  0.020
 0W4  plan-4  C2   0.020
 0W4  plan-4  C7   0.020
 0W4  plan-4  N9   0.020
 0W4  plan-4  O8   0.020
 0W4  plan-4  H16  0.020
 0W4  plan-5  C3   0.020
 0W4  plan-5  C11  0.020
 0W4  plan-5  N10  0.020
 0W4  plan-5  H15  0.020

