# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 00:56:14 2022
#   Inital geometry file: a 120 line input string
#   Ligand name: 1,3-dimethyl-5-[1-(oxan-4-ylmethyl)benzimidazol-2-yl]pyridin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C=C(C=C(C)C1=O)c2nc3ccccc3n2CC4CCOCC4
#
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
 NUB  NUB  1,3-dimethyl-5-[1-(oxan-4-ylmethyl)benzimidazol-2-yl]pyridin-2-one  ligand  48  25  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NUB
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
 NUB  C20  C  CR56  0   0.135   2.4527   1.8460   0.5131
 NUB  C21  C  CR16  0  -0.342   3.5944   2.4712   1.0143
 NUB  C01  C  CH3   0  -0.710  -3.8430   1.0035  -2.6112
 NUB  C05  C  CR6   0  -0.127  -3.0606   1.0925  -1.3415
 NUB  C06  C  CR16  0  -0.187  -1.7026   1.1182  -1.3121
 NUB  C08  C  CR6   0  -0.138  -0.9884   1.2106  -0.0891
 NUB  C09  C  CR16  0   0.034  -1.7120   1.2975   1.0599
 NUB  N11  N  NR6   0  -0.507  -3.0617   1.2735   1.0556
 NUB  C12  C  CH3   0  -0.518  -3.7918   1.3561   2.3137
 NUB  C16  C  CR6   0   0.561  -3.8134   1.1636  -0.1078
 NUB  O17  O  O     0  -0.496  -5.0384   1.1398  -0.0457
 NUB  C18  C  CR5   0   0.425   0.4710   1.2603  -0.0111
 NUB  N19  N  N     0  -0.472   1.1269   2.1552   0.6817
 NUB  C23  C  CR16  0  -0.272   4.8256   1.9436   0.6687
 NUB  C25  C  CR16  0  -0.278   4.9313   0.8154  -0.1592
 NUB  C27  C  CR16  0  -0.311   3.8097   0.1841  -0.6689
 NUB  C29  C  CR56  0   0.337   2.5767   0.7239  -0.3191
 NUB  N30  N  NR5   0  -0.540   1.2912   0.3683  -0.6469
 NUB  C31  C  CH2   0  -0.323   0.9419  -0.8698  -1.3177
 NUB  C34  C  CH1   0  -0.262   1.0305  -2.0920  -0.4081
 NUB  C36  C  CH2   0  -0.446   0.7212  -3.3576  -1.2059
 NUB  C39  C  CH2   0  -0.180   0.7181  -4.5750  -0.2944
 NUB  O42  O  O2    0  -0.484  -0.1841  -4.4290   0.7801
 NUB  C43  C  CH2   0  -0.175   0.1234  -3.3092   1.5807
 NUB  C46  C  CH2   0  -0.448   0.0881  -2.0107   0.7902
 NUB  H1   H  HCR6  0   0.254   3.5153   3.3407   1.6542
 NUB  H2   H  HCH3  0   0.246  -4.5201   1.8519  -2.7227
 NUB  H3   H  HCH3  0   0.244  -3.1805   0.9824  -3.4749
 NUB  H4   H  HCH3  0   0.247  -4.4582   0.1023  -2.6350
 NUB  H6   H  HCR6  0   0.308  -1.2363   1.3803   2.0268
 NUB  H7   H  HCH3  0   0.263  -4.4261   2.2397   2.3292
 NUB  H8   H  HCH3  0   0.263  -4.4140   0.4745   2.4511
 NUB  H9   H  HCH3  0   0.259  -3.0810   1.4175   3.1315
 NUB  H10  H  HCR6  0   0.253   5.7291   2.4081   1.0416
 NUB  H11  H  HCR6  0   0.256   5.9122   0.4294  -0.4030
 NUB  H12  H  HCR6  0   0.266   3.8991  -0.6852  -1.3080
 NUB  H13  H  HCH2  0   0.271  -0.0632  -0.7824  -1.7275
 NUB  H14  H  HCH2  0   0.276   1.6142  -0.9848  -2.1703
 NUB  H15  H  HCH1  0   0.240   2.0582  -2.1727  -0.0319
 NUB  H16  H  HCH2  0   0.227  -0.2561  -3.2619  -1.6913
 NUB  H17  H  HCH2  0   0.242   1.4605  -3.5051  -1.9975
 NUB  H18  H  HCH2  0   0.236   0.4162  -5.4676  -0.8449
 NUB  H19  H  HCH2  0   0.196   1.7364  -4.7506   0.0835
 NUB  H20  H  HCH2  0   0.237  -0.6083  -3.2858   2.3897
 NUB  H21  H  HCH2  0   0.196   1.1167  -3.4290   2.0391
 NUB  H22  H  HCH2  0   0.241   0.3661  -1.1941   1.4614
 NUB  H23  H  HCH2  0   0.226  -0.9332  -1.8120   0.4475
 NUB  H5   H  HCR6  0   0.276  -1.1548   1.0944  -2.2471

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
 NUB  C43  O42  single    1.410  0.020  1.410
 NUB  C43  C46  single    1.521  0.020  1.521
 NUB  O42  C39  single    1.411  0.020  1.411
 NUB  C46  C34  single    1.527  0.020  1.527
 NUB  C39  C36  single    1.521  0.020  1.521
 NUB  C34  C36  single    1.528  0.020  1.528
 NUB  C34  C31  single    1.526  0.020  1.526
 NUB  C31  N30  single    1.451  0.020  1.451
 NUB  C27  C25  aromatic  1.384  0.020  1.384
 NUB  C27  C29  aromatic  1.391  0.020  1.391
 NUB  N30  C29  aromatic  1.373  0.020  1.373
 NUB  N30  C18  aromatic  1.368  0.020  1.368
 NUB  C01  C05  single    1.494  0.020  1.494
 NUB  C25  C23  aromatic  1.403  0.020  1.403
 NUB  C29  C20  aromatic  1.403  0.020  1.403
 NUB  C06  C05  double    1.359  0.020  1.359
 NUB  C06  C08  single    1.419  0.020  1.419
 NUB  C05  C16  single    1.447  0.020  1.447
 NUB  C18  C08  single    1.462  0.020  1.462
 NUB  C18  N19  aromatic  1.308  0.020  1.308
 NUB  C08  C09  double    1.361  0.020  1.361
 NUB  C16  O17  double    1.227  0.020  1.227
 NUB  C16  N11  single    1.389  0.020  1.389
 NUB  C23  C21  aromatic  1.383  0.020  1.383
 NUB  C20  N19  aromatic  1.372  0.020  1.372
 NUB  C20  C21  aromatic  1.395  0.020  1.395
 NUB  C09  N11  single    1.350  0.020  1.350
 NUB  N11  C12  single    1.457  0.020  1.457
 NUB  C21  H1   single    0.930  0.020  1.080
 NUB  C01  H2   single    0.970  0.020  1.090
 NUB  C01  H3   single    0.970  0.020  1.090
 NUB  C01  H4   single    0.970  0.020  1.090
 NUB  C06  H5   single    0.930  0.020  1.080
 NUB  C09  H6   single    0.930  0.020  1.080
 NUB  C12  H7   single    0.970  0.020  1.090
 NUB  C12  H8   single    0.970  0.020  1.090
 NUB  C12  H9   single    0.970  0.020  1.090
 NUB  C23  H10  single    0.930  0.020  1.080
 NUB  C25  H11  single    0.930  0.020  1.080
 NUB  C27  H12  single    0.930  0.020  1.080
 NUB  C31  H13  single    0.970  0.020  1.090
 NUB  C31  H14  single    0.970  0.020  1.090
 NUB  C34  H15  single    0.970  0.020  1.090
 NUB  C36  H16  single    0.970  0.020  1.090
 NUB  C36  H17  single    0.970  0.020  1.090
 NUB  C39  H18  single    0.970  0.020  1.090
 NUB  C39  H19  single    0.970  0.020  1.090
 NUB  C43  H20  single    0.970  0.020  1.090
 NUB  C43  H21  single    0.970  0.020  1.090
 NUB  C46  H22  single    0.970  0.020  1.090
 NUB  C46  H23  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
 NUB  C29  C20  N19  109.80  3.000
 NUB  N19  C20  C21  130.23  3.000
 NUB  C29  C20  C21  119.97  3.000
 NUB  H1   C21  C23  121.27  3.000
 NUB  H1   C21  C20  120.84  3.000
 NUB  C23  C21  C20  117.89  3.000
 NUB  H4   C01  H3   108.04  3.000
 NUB  H4   C01  H2   106.86  3.000
 NUB  H3   C01  H2   108.15  3.000
 NUB  H4   C01  C05  111.28  3.000
 NUB  H3   C01  C05  110.90  3.000
 NUB  H2   C01  C05  111.44  3.000
 NUB  C16  C05  C06  120.04  3.000
 NUB  C16  C05  C01  117.07  3.000
 NUB  C06  C05  C01  122.89  3.000
 NUB  H5   C06  C08  119.37  3.000
 NUB  H5   C06  C05  119.08  3.000
 NUB  C08  C06  C05  121.52  3.000
 NUB  C18  C08  C09  118.92  3.000
 NUB  C09  C08  C06  117.66  3.000
 NUB  C18  C08  C06  123.39  3.000
 NUB  H6   C09  N11  116.37  3.000
 NUB  H6   C09  C08  121.76  3.000
 NUB  N11  C09  C08  121.87  3.000
 NUB  C16  N11  C12  117.16  3.000
 NUB  C12  N11  C09  119.83  3.000
 NUB  C16  N11  C09  123.02  3.000
 NUB  H9   C12  H8   108.98  3.000
 NUB  H9   C12  H7   108.97  3.000
 NUB  H8   C12  H7   108.85  3.000
 NUB  H9   C12  N11  109.01  3.000
 NUB  H8   C12  N11  110.48  3.000
 NUB  H7   C12  N11  110.52  3.000
 NUB  O17  C16  N11  119.96  3.000
 NUB  N11  C16  C05  115.87  3.000
 NUB  O17  C16  C05  124.17  3.000
 NUB  N30  C18  N19  113.05  3.000
 NUB  N19  C18  C08  123.50  3.000
 NUB  N30  C18  C08  123.45  3.000
 NUB  C18  N19  C20  105.38  3.000
 NUB  H10  C23  C25  119.04  3.000
 NUB  H10  C23  C21  119.56  3.000
 NUB  C25  C23  C21  121.40  3.000
 NUB  H11  C25  C27  119.27  3.000
 NUB  H11  C25  C23  119.21  3.000
 NUB  C27  C25  C23  121.53  3.000
 NUB  H12  C27  C29  122.23  3.000
 NUB  H12  C27  C25  121.11  3.000
 NUB  C29  C27  C25  116.66  3.000
 NUB  N30  C29  C27  132.02  3.000
 NUB  N30  C29  C20  105.43  3.000
 NUB  C27  C29  C20  122.56  3.000
 NUB  C31  N30  C29  123.82  3.000
 NUB  C29  N30  C18  106.34  3.000
 NUB  C31  N30  C18  128.81  3.000
 NUB  H14  C31  H13  106.44  3.000
 NUB  H14  C31  C34  110.20  3.000
 NUB  H13  C31  C34  110.00  3.000
 NUB  H14  C31  N30  107.62  3.000
 NUB  H13  C31  N30  109.13  3.000
 NUB  C34  C31  N30  113.19  3.000
 NUB  H15  C34  C46  108.24  3.000
 NUB  H15  C34  C36  107.92  3.000
 NUB  C46  C34  C36  109.22  3.000
 NUB  H15  C34  C31  108.51  3.000
 NUB  C36  C34  C31  109.90  3.000
 NUB  C46  C34  C31  112.91  3.000
 NUB  H17  C36  H16  107.11  3.000
 NUB  H17  C36  C39  109.11  3.000
 NUB  H16  C36  C39  109.49  3.000
 NUB  H17  C36  C34  110.68  3.000
 NUB  H16  C36  C34  109.86  3.000
 NUB  C39  C36  C34  110.52  3.000
 NUB  H19  C39  H18  107.38  3.000
 NUB  H19  C39  O42  110.29  3.000
 NUB  H18  C39  O42  106.97  3.000
 NUB  H19  C39  C36  109.37  3.000
 NUB  H18  C39  C36  110.67  3.000
 NUB  O42  C39  C36  112.03  3.000
 NUB  C43  O42  C39  112.03  3.000
 NUB  H21  C43  H20  107.38  3.000
 NUB  H21  C43  C46  109.30  3.000
 NUB  H20  C43  C46  110.58  3.000
 NUB  H21  C43  O42  110.29  3.000
 NUB  H20  C43  O42  106.96  3.000
 NUB  C46  C43  O42  112.20  3.000
 NUB  H23  C46  H22  107.08  3.000
 NUB  H23  C46  C43  109.83  3.000
 NUB  H22  C46  C43  108.23  3.000
 NUB  H23  C46  C34  109.86  3.000
 NUB  H22  C46  C34  111.40  3.000
 NUB  C43  C46  C34  110.37  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
 NUB  CONST_01  C25  C27  C29  C20     0.00   0.0  0
 NUB  CONST_02  C18  N30  C29  C20     0.00   0.0  0
 NUB  CONST_03  N30  C18  N19  C20     0.00   0.0  0
 NUB  CONST_04  C25  C23  C21  C20     0.00   0.0  0
 NUB  CONST_05  C27  C25  C23  C21     0.00   0.0  0
 NUB  CONST_06  C27  C29  C20  C21     0.00   0.0  0
 NUB  CONST_07  N30  C29  C20  C21   180.00   0.0  0
 NUB  CONST_08  C18  N19  C20  C21   180.00   0.0  0
 NUB  CONST_09  C27  C29  N30  C18   180.00   0.0  0
 NUB  CONST_10  C29  C20  N19  C18     0.00   0.0  0
 NUB  CONST_11  C29  N30  C18  N19     0.00   0.0  0
 NUB  CONST_12  C27  C29  C20  N19   180.00   0.0  0
 NUB  CONST_13  N30  C29  C20  N19     0.00   0.0  0
 NUB  CONST_14  C23  C21  C20  N19   180.00   0.0  0
 NUB  CONST_15  C29  C27  C25  C23     0.00   0.0  0
 NUB  CONST_16  C29  C20  C21  C23     0.00   0.0  0
 NUB  CONST_17  N30  C29  C27  C25   180.00   0.0  0
 NUB  CONST_18  C08  C18  N19  C20   180.00   0.0  0
 NUB  CONST_19  C29  N30  C18  C08   180.00   0.0  0
 NUB  CONST_20  C09  N11  C16  C05     0.00   0.0  0
 NUB  CONST_21  C31  N30  C29  C20   180.00   0.0  0
 NUB  CONST_22  C31  N30  C18  C08     0.00   0.0  0
 NUB  CONST_23  C31  N30  C18  N19   180.00   0.0  0
 NUB  CONST_24  C31  N30  C29  C27     0.00   0.0  0
 NUB  CONST_25  C12  N11  C16  C05   180.00   0.0  0
 NUB  CONST_26  O17  C16  N11  C09   180.00   0.0  0
 NUB  CONST_27  H12  C27  C29  C20   180.00   0.0  0
 NUB  CONST_28  H10  C23  C21  C20   180.00   0.0  0
 NUB  CONST_29  H11  C25  C23  C21   180.00   0.0  0
 NUB  CONST_30  H1   C21  C20  N19     0.00   0.0  0
 NUB  CONST_31  O17  C16  N11  C12     0.00   0.0  0
 NUB  Var_01    N30  C18  C08  C06   -50.35  30.0  2
 NUB  Var_02    O42  C43  C46  C34   -56.05  30.0  1
 NUB  Var_03    O42  C39  C36  C34    55.99  30.0  1
 NUB  Var_04    C46  C43  O42  C39    59.59  30.0  1
 NUB  Var_05    C34  C31  N30  C18   -92.65  30.0  2
 NUB  Var_06    H2   C01  C05  C06  -121.58  30.0  3
 NUB  Var_07    H7   C12  N11  C09   119.02  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
 NUB  chir_01  C34  C46  C36  C31  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
 NUB  plan-1  C01  0.020
 NUB  plan-1  C05  0.020
 NUB  plan-1  C06  0.020
 NUB  plan-1  C08  0.020
 NUB  plan-1  C09  0.020
 NUB  plan-1  N11  0.020
 NUB  plan-1  C12  0.020
 NUB  plan-1  C16  0.020
 NUB  plan-1  O17  0.020
 NUB  plan-1  C18  0.020
 NUB  plan-1  H6   0.020
 NUB  plan-1  H5   0.020
 NUB  plan-2  C20  0.020
 NUB  plan-2  C21  0.020
 NUB  plan-2  C08  0.020
 NUB  plan-2  C18  0.020
 NUB  plan-2  N19  0.020
 NUB  plan-2  C23  0.020
 NUB  plan-2  C25  0.020
 NUB  plan-2  C27  0.020
 NUB  plan-2  C29  0.020
 NUB  plan-2  N30  0.020
 NUB  plan-2  C31  0.020
 NUB  plan-2  H1   0.020
 NUB  plan-2  H10  0.020
 NUB  plan-2  H11  0.020
 NUB  plan-2  H12  0.020

