# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 12:20:53 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: 6-[[2-(2-chlorophenyl)-5-(4-pyrimidin-5-yloxyphenyl)pyrrol-1-yl]methyl]pyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cccc(Cn2c(ccc2c3ccccc3Cl)c4ccc(Oc5cncnc5)cc4)n1
#
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
 879  879  6-[[2-(2-chlorophenyl)-5-(4-pyrimidin-5-yloxyphenyl)pyrrol-1-yl]methyl]pyridin-2-amine  ligand  53  33  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_879
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
 879  C1    C   CR16  0  -0.222  -5.7240   0.8079  -0.3574
 879  N1    N   N     0  -0.374   6.7958  -3.0593   0.3451
 879  O1    O   O2    0  -0.499   5.3722   0.2737   0.2196
 879  CL1   CL  CL    0  -0.127  -3.0540  -2.1402   1.7383
 879  C2    C   CR16  0  -0.270  -6.1374   0.2032   0.8212
 879  N2    N   N     0  -0.377   8.2413  -1.5113   1.3794
 879  C3    C   CR16  0  -0.142  -3.4711   3.5289   1.4197
 879  N3    N   N     0  -0.451  -1.6619   2.5378  -0.4186
 879  C4    C   CR16  0  -0.278  -4.4702   0.5262  -0.8725
 879  N4    N   NR5   0  -0.491  -1.1182  -0.2327  -0.1910
 879  C5    C   CR16  0  -0.300   2.2159   0.2257  -1.5929
 879  N5    N   NH2   0  -0.838  -2.1351   4.2302  -1.8985
 879  C6    C   CR16  0  -0.299   1.8624  -0.6775   0.5996
 879  C7    C   CR16  0  -0.296   3.5630   0.3962  -1.3119
 879  C8    C   CR16  0  -0.288   3.2015  -0.4916   0.8999
 879  C9    C   CR16  0  -0.198  -5.3049  -0.6962   1.4700
 879  C10   C   CR15  0  -0.392  -0.5513  -1.1528  -2.1325
 879  C11   C   CR15  0  -0.395  -1.9568  -1.1952  -2.0110
 879  C12   C   CR16  0  -0.352  -2.7679   2.3575   1.6901
 879  C13   C   CR16  0  -0.384  -3.2707   4.1872   0.2284
 879  C14   C   CR16  0  -0.098   5.9285  -2.0896   0.0863
 879  C15   C   CR16  0  -0.084   7.3814  -0.5387   1.1285
 879  C16   C   CR16  0   0.038   7.9084  -2.7300   0.9784
 879  C17   C   CR6   0   0.029   1.3450  -0.3179  -0.6481
 879  C18   C   CR6   0   0.092  -3.6043  -0.3614  -0.2336
 879  C19   C   CR6   0   0.293   4.0452   0.0427  -0.0632
 879  C20   C   CR6   0   0.255   6.1812  -0.7791   0.4693
 879  C21   C   CR6   0  -0.111  -4.0574  -0.9740   0.9341
 879  C22   C   CR5   0   0.329  -0.0561  -0.5463  -1.0000
 879  C23   C   CR5   0   0.337  -2.2788  -0.6189  -0.8070
 879  C24   C   CR6   0   0.249  -1.8799   1.9085   0.7310
 879  C25   C   CR6   0   0.433  -2.3429   3.6478  -0.6817
 879  H1    H   HCR6  0   0.260  -6.3719   1.5076  -0.8678
 879  H2    H   HCR6  0   0.266  -7.1119   0.4220   1.2373
 879  H3    H   HCR6  0   0.262  -4.1811   3.9186   2.1379
 879  H4    H   HCR6  0   0.254  -4.1339   1.0134  -1.7782
 879  H5    H   HCR6  0   0.260   1.8363   0.5245  -2.5613
 879  HN5   H   HNH2  0   0.379  -1.2913   3.9629  -2.3783
 879  HN5A  H   HNH2  0   0.388  -2.3740   5.2026  -1.9974
 879  H6    H   HCR6  0   0.271   1.2191  -1.1275   1.3454
 879  H7    H   HCR6  0   0.277   4.2292   0.8171  -2.0541
 879  H8    H   HCR6  0   0.286   3.5819  -0.7711   1.8745
 879  H9    H   HCR6  0   0.279  -5.6269  -1.1852   2.3794
 879  H10   H   HCR5  0   0.247   0.0443  -1.5612  -2.9342
 879  H11   H   HCR5  0   0.246  -2.6598  -1.6244  -2.7078
 879  H12   H   HCR6  0   0.249  -2.9251   1.8037   2.6056
 879  H13   H   HCR6  0   0.262  -3.8099   5.0948  -0.0102
 879  H14   H   HCR6  0   0.294   5.0197  -2.3677  -0.4360
 879  H15   H   HCR6  0   0.292   7.6407   0.4647   1.4501
 879  H16   H   HCR6  0   0.267   8.6113  -3.5272   1.1885
 879  H26   H   HCH2  0   0.267  -1.4509   0.1279   1.8455
 879  H26A  H   HCH2  0   0.289  -0.0472   0.9111   1.1581
 879  C26   C   CH2   0  -0.386  -1.0854   0.6476   0.9594

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
 879  C1   C2    aromatic  1.388  0.020  1.388
 879  C1   C4    aromatic  1.385  0.020  1.385
 879  N1   C14   aromatic  1.326  0.020  1.326
 879  N1   C16   aromatic  1.322  0.020  1.322
 879  O1   C19   single    1.376  0.020  1.376
 879  O1   C20   single    1.351  0.020  1.351
 879  CL1  C21   single    1.736  0.020  1.736
 879  C2   C9    aromatic  1.387  0.020  1.387
 879  N2   C15   aromatic  1.322  0.020  1.322
 879  N2   C16   aromatic  1.325  0.020  1.325
 879  C3   C12   aromatic  1.393  0.020  1.393
 879  C3   C13   aromatic  1.376  0.020  1.376
 879  N3   C24   aromatic  1.329  0.020  1.329
 879  N3   C25   aromatic  1.329  0.020  1.329
 879  C4   C18   aromatic  1.395  0.020  1.395
 879  N4   C22   aromatic  1.371  0.020  1.371
 879  N4   C23   aromatic  1.370  0.020  1.370
 879  N4   C26   single    1.449  0.020  1.449
 879  C5   C7    aromatic  1.387  0.020  1.387
 879  C5   C17   aromatic  1.395  0.020  1.395
 879  N5   C25   single    1.365  0.020  1.365
 879  C6   C8    aromatic  1.385  0.020  1.385
 879  C6   C17   aromatic  1.398  0.020  1.398
 879  C7   C19   aromatic  1.384  0.020  1.384
 879  C8   C19   aromatic  1.387  0.020  1.387
 879  C9   C21   aromatic  1.386  0.020  1.386
 879  C10  C11   aromatic  1.411  0.020  1.411
 879  C10  C22   aromatic  1.377  0.020  1.377
 879  C11  C23   aromatic  1.373  0.020  1.373
 879  C12  C24   aromatic  1.382  0.020  1.382
 879  C13  C25   aromatic  1.407  0.020  1.407
 879  C14  C20   aromatic  1.389  0.020  1.389
 879  C15  C20   aromatic  1.390  0.020  1.390
 879  C17  C22   single    1.463  0.020  1.463
 879  C18  C21   aromatic  1.394  0.020  1.394
 879  C18  C23   single    1.467  0.020  1.467
 879  C24  C26   single    1.508  0.020  1.508
 879  C1   H1    single    0.930  0.020  1.080
 879  C2   H2    single    0.930  0.020  1.080
 879  C3   H3    single    0.930  0.020  1.080
 879  C4   H4    single    0.930  0.020  1.080
 879  C5   H5    single    0.930  0.020  1.080
 879  N5   HN5   single    0.890  0.020  1.040
 879  N5   HN5A  single    0.890  0.020  1.040
 879  C6   H6    single    0.930  0.020  1.080
 879  C7   H7    single    0.930  0.020  1.080
 879  C8   H8    single    0.930  0.020  1.080
 879  C9   H9    single    0.930  0.020  1.080
 879  C10  H10   single    0.930  0.020  1.080
 879  C11  H11   single    0.930  0.020  1.080
 879  C12  H12   single    0.930  0.020  1.080
 879  C13  H13   single    0.930  0.020  1.080
 879  C14  H14   single    0.930  0.020  1.080
 879  C15  H15   single    0.930  0.020  1.080
 879  C16  H16   single    0.930  0.020  1.080
 879  C26  H26   single    0.970  0.020  1.090
 879  C26  H26A  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
 879  H1    C1   C4   119.90  3.000
 879  H1    C1   C2   120.28  3.000
 879  C4    C1   C2   119.81  3.000
 879  C16   N1   C14  117.49  3.000
 879  C20   O1   C19  118.99  3.000
 879  H2    C2   C9   119.47  3.000
 879  H2    C2   C1   120.46  3.000
 879  C9    C2   C1   120.07  3.000
 879  C16   N2   C15  117.10  3.000
 879  H3    C3   C13  119.85  3.000
 879  H3    C3   C12  120.34  3.000
 879  C13   C3   C12  119.80  3.000
 879  C25   N3   C24  118.88  3.000
 879  H4    C4   C18  118.49  3.000
 879  H4    C4   C1   120.08  3.000
 879  C18   C4   C1   121.41  3.000
 879  C26   N4   C23  123.20  3.000
 879  C26   N4   C22  126.14  3.000
 879  C23   N4   C22  109.05  3.000
 879  H5    C5   C17  119.64  3.000
 879  H5    C5   C7   119.22  3.000
 879  C17   C5   C7   121.14  3.000
 879  HN5A  N5   HN5  114.12  3.000
 879  HN5A  N5   C25  117.64  3.000
 879  HN5   N5   C25  116.05  3.000
 879  H6    C6   C17  120.12  3.000
 879  H6    C6   C8   118.75  3.000
 879  C17   C6   C8   121.13  3.000
 879  H7    C7   C19  120.23  3.000
 879  H7    C7   C5   120.45  3.000
 879  C19   C7   C5   119.32  3.000
 879  H8    C8   C19  120.70  3.000
 879  H8    C8   C6   120.02  3.000
 879  C19   C8   C6   119.28  3.000
 879  H9    C9   C21  120.17  3.000
 879  H9    C9   C2   120.52  3.000
 879  C21   C9   C2   119.31  3.000
 879  H10   C10  C22  125.41  3.000
 879  H10   C10  C11  127.03  3.000
 879  C22   C10  C11  107.49  3.000
 879  H11   C11  C23  125.49  3.000
 879  H11   C11  C10  127.24  3.000
 879  C23   C11  C10  107.24  3.000
 879  H12   C12  C24  120.96  3.000
 879  H12   C12  C3   121.45  3.000
 879  C24   C12  C3   117.58  3.000
 879  H13   C13  C25  120.49  3.000
 879  H13   C13  C3   121.31  3.000
 879  C25   C13  C3   118.21  3.000
 879  H14   C14  C20  121.83  3.000
 879  H14   C14  N1   117.03  3.000
 879  C20   C14  N1   121.14  3.000
 879  H15   C15  C20  120.45  3.000
 879  H15   C15  N2   117.94  3.000
 879  C20   C15  N2   121.62  3.000
 879  H16   C16  N2   117.06  3.000
 879  H16   C16  N1   117.11  3.000
 879  N2    C16  N1   125.84  3.000
 879  C22   C17  C6   121.95  3.000
 879  C22   C17  C5   119.73  3.000
 879  C6    C17  C5   118.27  3.000
 879  C23   C18  C21  122.95  3.000
 879  C23   C18  C4   119.57  3.000
 879  C21   C18  C4   117.48  3.000
 879  C8    C19  C7   120.84  3.000
 879  C8    C19  O1   120.55  3.000
 879  C7    C19  O1   118.57  3.000
 879  C15   C20  C14  116.81  3.000
 879  C15   C20  O1   118.03  3.000
 879  C14   C20  O1   125.13  3.000
 879  C18   C21  C9   121.89  3.000
 879  C18   C21  CL1  119.69  3.000
 879  C9    C21  CL1  118.42  3.000
 879  C17   C22  C10  127.67  3.000
 879  C17   C22  N4   124.35  3.000
 879  C10   C22  N4   107.91  3.000
 879  C18   C23  C11  128.92  3.000
 879  C18   C23  N4   122.71  3.000
 879  C11   C23  N4   108.30  3.000
 879  C26   C24  C12  120.34  3.000
 879  C26   C24  N3   116.15  3.000
 879  C12   C24  N3   123.51  3.000
 879  C13   C25  N5   120.89  3.000
 879  C13   C25  N3   122.02  3.000
 879  N5    C25  N3   117.07  3.000
 879  H26A  C26  H26  106.65  3.000
 879  H26A  C26  C24  109.12  3.000
 879  H26   C26  C24  110.18  3.000
 879  H26A  C26  N4   108.26  3.000
 879  H26   C26  N4   110.37  3.000
 879  C24   C26  N4   112.08  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
 879  CONST_01  C21  C9   C2   C1     0.00   0.0  0
 879  CONST_02  C21  C18  C4   C1     0.00   0.0  0
 879  CONST_03  C23  C18  C4   C1   180.00   0.0  0
 879  CONST_04  C15  C20  C14  N1     0.00   0.0  0
 879  CONST_05  C15  N2   C16  N1     0.00   0.0  0
 879  CONST_06  C18  C4   C1   C2     0.00   0.0  0
 879  CONST_07  C18  C21  C9   C2     0.00   0.0  0
 879  CONST_08  C14  C20  C15  N2     0.00   0.0  0
 879  CONST_09  C14  N1   C16  N2     0.00   0.0  0
 879  CONST_10  N3   C24  C12  C3     0.00   0.0  0
 879  CONST_11  N3   C25  C13  C3     0.00   0.0  0
 879  CONST_12  C9   C2   C1   C4     0.00   0.0  0
 879  CONST_13  C9   C21  C18  C4     0.00   0.0  0
 879  CONST_16  C11  C10  C22  N4     0.00   0.0  0
 879  CONST_19  C10  C11  C23  N4     0.00   0.0  0
 879  CONST_21  C8   C19  C7   C5     0.00   0.0  0
 879  CONST_22  C8   C6   C17  C5     0.00   0.0  0
 879  CONST_24  C7   C19  C8   C6     0.00   0.0  0
 879  CONST_25  C7   C5   C17  C6     0.00   0.0  0
 879  CONST_27  C22  C17  C5   C7   180.00   0.0  0
 879  CONST_28  C22  C17  C6   C8   180.00   0.0  0
 879  CONST_29  C23  C18  C21  C9   180.00   0.0  0
 879  CONST_30  C18  C23  C11  C10  180.00   0.0  0
 879  CONST_31  C23  N4   C22  C10    0.00   0.0  0
 879  CONST_32  C17  C22  C10  C11  180.00   0.0  0
 879  CONST_33  C22  N4   C23  C11    0.00   0.0  0
 879  CONST_35  C25  C13  C3   C12    0.00   0.0  0
 879  CONST_36  C25  N3   C24  C12    0.00   0.0  0
 879  CONST_37  C24  C12  C3   C13    0.00   0.0  0
 879  CONST_38  C24  N3   C25  C13    0.00   0.0  0
 879  CONST_39  C20  C14  N1   C16    0.00   0.0  0
 879  CONST_40  C20  C15  N2   C16    0.00   0.0  0
 879  CONST_41  C19  C7   C5   C17    0.00   0.0  0
 879  CONST_42  C19  C8   C6   C17    0.00   0.0  0
 879  CONST_43  C23  N4   C22  C17  180.00   0.0  0
 879  CONST_44  C22  N4   C23  C18  180.00   0.0  0
 879  CONST_45  C23  C11  C10  C22    0.00   0.0  0
 879  CONST_46  O1   C20  C14  N1   180.00   0.0  0
 879  CONST_47  C5   C7   C19  O1   180.00   0.0  0
 879  CONST_48  C6   C8   C19  O1   180.00   0.0  0
 879  CONST_49  N2   C15  C20  O1   180.00   0.0  0
 879  CONST_50  C2   C9   C21  CL1  180.00   0.0  0
 879  CONST_51  C4   C18  C21  CL1  180.00   0.0  0
 879  CONST_52  C23  C18  C21  CL1    0.00   0.0  0
 879  CONST_53  C26  C24  C12  C3   180.00   0.0  0
 879  CONST_54  N5   C25  C13  C3   180.00   0.0  0
 879  CONST_55  C24  N3   C25  N5   180.00   0.0  0
 879  CONST_56  C26  N4   C22  C10  180.00   0.0  0
 879  CONST_57  C26  N4   C23  C11  180.00   0.0  0
 879  CONST_59  C26  N4   C23  C18    0.00   0.0  0
 879  CONST_60  C26  C24  N3   C25  180.00   0.0  0
 879  CONST_61  H9   C9   C2   C1   180.00   0.0  0
 879  CONST_62  H4   C4   C1   C2   180.00   0.0  0
 879  CONST_63  H12  C12  C24  N3   180.00   0.0  0
 879  CONST_64  H13  C13  C25  N3   180.00   0.0  0
 879  CONST_65  H2   C2   C1   C4   180.00   0.0  0
 879  CONST_66  H10  C10  C22  N4   180.00   0.0  0
 879  CONST_67  H11  C11  C23  N4   180.00   0.0  0
 879  CONST_68  H6   C6   C17  C5   180.00   0.0  0
 879  CONST_69  H5   C5   C17  C6   180.00   0.0  0
 879  CONST_70  H8   C8   C19  C7   180.00   0.0  0
 879  CONST_71  H7   C7   C19  C8   180.00   0.0  0
 879  CONST_72  H1   C1   C2   C9   180.00   0.0  0
 879  CONST_73  H16  C16  N1   C14  180.00   0.0  0
 879  CONST_74  H15  C15  C20  C14  180.00   0.0  0
 879  CONST_75  H14  C14  C20  C15  180.00   0.0  0
 879  CONST_76  H3   C3   C12  C24  180.00   0.0  0
 879  Var_01    N4   C26  C24  N3   -47.57  30.0  2
 879  Var_02    C24  C26  N4   C22  112.66  30.0  2

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
 879  plan-1  N4    0.020
 879  plan-1  C10   0.020
 879  plan-1  C11   0.020
 879  plan-1  C17   0.020
 879  plan-1  C18   0.020
 879  plan-1  C22   0.020
 879  plan-1  C23   0.020
 879  plan-1  H10   0.020
 879  plan-1  H11   0.020
 879  plan-1  C26   0.020
 879  plan-2  C1    0.020
 879  plan-2  CL1   0.020
 879  plan-2  C2    0.020
 879  plan-2  C4    0.020
 879  plan-2  C9    0.020
 879  plan-2  C18   0.020
 879  plan-2  C21   0.020
 879  plan-2  C23   0.020
 879  plan-2  H1    0.020
 879  plan-2  H2    0.020
 879  plan-2  H4    0.020
 879  plan-2  H9    0.020
 879  plan-3  N1    0.020
 879  plan-3  O1    0.020
 879  plan-3  N2    0.020
 879  plan-3  C14   0.020
 879  plan-3  C15   0.020
 879  plan-3  C16   0.020
 879  plan-3  C20   0.020
 879  plan-3  H14   0.020
 879  plan-3  H15   0.020
 879  plan-3  H16   0.020
 879  plan-4  C3    0.020
 879  plan-4  N3    0.020
 879  plan-4  N5    0.020
 879  plan-4  C12   0.020
 879  plan-4  C13   0.020
 879  plan-4  C24   0.020
 879  plan-4  C25   0.020
 879  plan-4  H3    0.020
 879  plan-4  H12   0.020
 879  plan-4  H13   0.020
 879  plan-4  C26   0.020
 879  plan-5  O1    0.020
 879  plan-5  C5    0.020
 879  plan-5  C6    0.020
 879  plan-5  C7    0.020
 879  plan-5  C8    0.020
 879  plan-5  C17   0.020
 879  plan-5  C19   0.020
 879  plan-5  C22   0.020
 879  plan-5  H5    0.020
 879  plan-5  H6    0.020
 879  plan-5  H7    0.020
 879  plan-5  H8    0.020
 879  plan-6  N5    0.020
 879  plan-6  C25   0.020
 879  plan-6  HN5   0.020
 879  plan-6  HN5A  0.020

