# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 07:31:06 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: (4-amino-1,2,5-oxadiazol-3-yl)[3-(1H-benzimidazol-2-ylmethoxy)phenyl]methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nonc1C(=O)c2cccc(OCc3[nH]c4ccccc4n3)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
 1VE  1VE  (4-amino-1,2,5-oxadiazol-3-yl)[3-(1H-benzimidazol-2-ylmethoxy)phenyl]methanone  ligand  38  25  .  2021-08-03  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_1VE
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
 1VE  C2   C  CR5   0   0.389  -5.8894  -1.3596  -0.0648
 1VE  C6   C  CR5   0   0.033  -4.7197  -0.5822   0.2429
 1VE  C7   C  C     0   0.372  -3.3832  -0.6917  -0.3729
 1VE  C10  C  CR16  0  -0.284  -2.7592   1.7272  -0.0440
 1VE  C11  C  CR16  0  -0.225  -1.7730   2.6922   0.0552
 1VE  C12  C  CR16  0  -0.367  -0.4270   2.3505   0.0290
 1VE  C13  C  CR6   0   0.420  -0.0599   1.0147  -0.1145
 1VE  C15  C  CH2   0  -0.277   2.2612   1.5178  -0.0194
 1VE  C16  C  CR5   0   0.424   3.5452   0.7660  -0.0413
 1VE  C19  C  CR16  0  -0.335   6.8865   0.0905  -0.8242
 1VE  C21  C  CR16  0  -0.277   7.0834  -1.9245   0.5209
 1VE  C22  C  CR16  0  -0.308   5.7719  -1.8383   0.9535
 1VE  C23  C  CR56  0   0.340   5.0299  -0.7621   0.4797
 1VE  C26  C  CR16  0  -0.372  -1.0431   0.0385  -0.2370
 1VE  N1   N  NH2   0  -0.838  -6.0491  -2.2593  -1.0530
 1VE  N3   N  N     0  -0.189  -6.8311  -0.9848   0.7546
 1VE  O4   O  O     0  -0.203  -6.2750  -0.0226   1.5398
 1VE  N5   N  N     0  -0.091  -5.0163   0.2055   1.2284
 1VE  O8   O  O     0  -0.374  -3.1325  -1.6946  -1.0098
 1VE  C9   C  CR6   0   0.017  -2.3877   0.3893  -0.1905
 1VE  N17  N  N     0  -0.470   4.6038   1.1341  -0.7062
 1VE  C18  C  CR56  0   0.135   5.5627   0.1970  -0.3977
 1VE  C20  C  CR16  0  -0.272   7.6330  -0.9750  -0.3553
 1VE  N24  N  NR15  0  -0.688   3.7378  -0.3615   0.6878
 1VE  H29  H  HCR6  0   0.268  -3.7973   2.0243  -0.0370
 1VE  H30  H  HCR6  0   0.274  -2.0483   3.7335   0.1533
 1VE  H31  H  HCR6  0   0.298   0.3108   3.1360   0.1144
 1VE  H33  H  HCH2  0   0.265   2.1699   2.0661   0.9259
 1VE  H32  H  HCH2  0   0.266   2.2689   2.2463  -0.8345
 1VE  H34  H  HCR6  0   0.256   7.3133   0.8203  -1.5001
 1VE  H36  H  HCR6  0   0.256   7.7016  -2.7423   0.8677
 1VE  H37  H  HCR6  0   0.267   5.3487  -2.5710   1.6279
 1VE  H38  H  HCR6  0   0.278  -0.7479  -0.9965  -0.3571
 1VE  H28  H  HNH2  0   0.405  -6.8788  -2.8295  -1.0259
 1VE  H27  H  HNH2  0   0.408  -5.2227  -2.7284  -1.3831
 1VE  H35  H  HCR6  0   0.254   8.6632  -1.0834  -0.6680
 1VE  H25  H  HNR5  0   0.422   3.0572  -0.8144   1.2778
 1VE  O14  O  O2    0  -0.477   1.2149   0.5766  -0.1571

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
 1VE  C21  C20  aromatic  1.404  0.020  1.404
 1VE  C21  C22  aromatic  1.384  0.020  1.384
 1VE  C20  C19  aromatic  1.383  0.020  1.383
 1VE  C22  C23  aromatic  1.390  0.020  1.390
 1VE  C19  C18  aromatic  1.395  0.020  1.395
 1VE  C23  C18  aromatic  1.405  0.020  1.405
 1VE  C23  N24  aromatic  1.369  0.020  1.369
 1VE  C18  N17  aromatic  1.376  0.020  1.376
 1VE  N24  C16  aromatic  1.356  0.020  1.356
 1VE  N17  C16  aromatic  1.303  0.020  1.303
 1VE  C16  C15  single    1.488  0.020  1.488
 1VE  C15  O14  single    1.414  0.020  1.414
 1VE  O14  C13  single    1.349  0.020  1.349
 1VE  O8   C7   double    1.214  0.020  1.214
 1VE  C26  C13  aromatic  1.391  0.020  1.391
 1VE  C26  C9   aromatic  1.390  0.020  1.390
 1VE  C13  C12  aromatic  1.393  0.020  1.393
 1VE  C7   C9   single    1.481  0.020  1.481
 1VE  C7   C6   single    1.476  0.020  1.476
 1VE  C9   C10  aromatic  1.396  0.020  1.396
 1VE  N1   C2   single    1.346  0.020  1.346
 1VE  C6   C2   aromatic  1.438  0.020  1.438
 1VE  C6   N5   aromatic  1.296  0.020  1.296
 1VE  C2   N3   aromatic  1.303  0.020  1.303
 1VE  N5   O4   aromatic  1.316  0.020  1.316
 1VE  C12  C11  aromatic  1.389  0.020  1.389
 1VE  N3   O4   aromatic  1.361  0.020  1.361
 1VE  C10  C11  aromatic  1.383  0.020  1.383
 1VE  C10  H29  single    0.930  0.020  1.080
 1VE  C11  H30  single    0.930  0.020  1.080
 1VE  C12  H31  single    0.930  0.020  1.080
 1VE  C15  H33  single    0.970  0.020  1.090
 1VE  C15  H32  single    0.970  0.020  1.090
 1VE  C19  H34  single    0.930  0.020  1.080
 1VE  C21  H36  single    0.930  0.020  1.080
 1VE  C22  H37  single    0.930  0.020  1.080
 1VE  C26  H38  single    0.930  0.020  1.080
 1VE  N1   H28  single    0.890  0.020  1.040
 1VE  N1   H27  single    0.890  0.020  1.040
 1VE  C20  H35  single    0.930  0.020  1.080
 1VE  N24  H25  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
 1VE  N3   C2   N1   124.62  3.000
 1VE  N3   C2   C6   107.32  3.000
 1VE  N1   C2   C6   127.96  3.000
 1VE  N5   C6   C7   124.73  3.000
 1VE  N5   C6   C2   107.77  3.000
 1VE  C7   C6   C2   127.40  3.000
 1VE  C9   C7   O8   121.92  3.000
 1VE  C9   C7   C6   120.22  3.000
 1VE  O8   C7   C6   117.86  3.000
 1VE  H29  C10  C9   121.34  3.000
 1VE  H29  C10  C11  119.53  3.000
 1VE  C9   C10  C11  119.10  3.000
 1VE  H30  C11  C12  119.03  3.000
 1VE  H30  C11  C10  119.78  3.000
 1VE  C12  C11  C10  121.19  3.000
 1VE  H31  C12  C13  121.68  3.000
 1VE  H31  C12  C11  118.77  3.000
 1VE  C13  C12  C11  119.56  3.000
 1VE  O14  C13  C26  115.94  3.000
 1VE  C26  C13  C12  119.73  3.000
 1VE  O14  C13  C12  124.33  3.000
 1VE  H32  C15  H33  108.07  3.000
 1VE  H32  C15  O14  112.09  3.000
 1VE  H33  C15  O14  110.80  3.000
 1VE  H32  C15  C16  108.64  3.000
 1VE  H33  C15  C16  109.70  3.000
 1VE  O14  C15  C16  107.51  3.000
 1VE  N24  C16  N17  113.19  3.000
 1VE  N17  C16  C15  124.46  3.000
 1VE  N24  C16  C15  122.31  3.000
 1VE  H34  C19  C20  121.23  3.000
 1VE  H34  C19  C18  120.90  3.000
 1VE  C20  C19  C18  117.87  3.000
 1VE  H36  C21  C20  119.17  3.000
 1VE  H36  C21  C22  119.23  3.000
 1VE  C20  C21  C22  121.60  3.000
 1VE  H37  C22  C23  121.85  3.000
 1VE  H37  C22  C21  121.56  3.000
 1VE  C23  C22  C21  116.58  3.000
 1VE  N24  C23  C18  104.66  3.000
 1VE  N24  C23  C22  132.73  3.000
 1VE  C18  C23  C22  122.60  3.000
 1VE  H38  C26  C9   120.56  3.000
 1VE  H38  C26  C13  119.20  3.000
 1VE  C9   C26  C13  120.24  3.000
 1VE  H27  N1   H28  114.93  3.000
 1VE  H27  N1   C2   117.08  3.000
 1VE  H28  N1   C2   117.16  3.000
 1VE  O4   N3   C2   105.71  3.000
 1VE  N5   O4   N3   112.13  3.000
 1VE  O4   N5   C6   107.06  3.000
 1VE  C26  C9   C10  120.17  3.000
 1VE  C10  C9   C7   122.25  3.000
 1VE  C26  C9   C7   117.51  3.000
 1VE  C18  N17  C16  105.04  3.000
 1VE  N17  C18  C23  109.92  3.000
 1VE  N17  C18  C19  130.16  3.000
 1VE  C23  C18  C19  119.92  3.000
 1VE  H35  C20  C21  119.03  3.000
 1VE  H35  C20  C19  119.54  3.000
 1VE  C21  C20  C19  121.42  3.000
 1VE  H25  N24  C23  126.50  3.000
 1VE  H25  N24  C16  126.31  3.000
 1VE  C23  N24  C16  107.19  3.000
 1VE  C15  O14  C13  118.70  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
 1VE  CONST_01  O4   N5   C6   C2      0.00   0.0  0
 1VE  CONST_02  N5   O4   N3   C2      0.00   0.0  0
 1VE  CONST_03  O4   N3   C2   C6      0.00   0.0  0
 1VE  CONST_04  N3   O4   N5   C6      0.00   0.0  0
 1VE  CONST_05  C13  C26  C9   C10     0.00   0.0  0
 1VE  CONST_06  C13  C12  C11  C10     0.00   0.0  0
 1VE  CONST_07  C26  C13  C12  C11     0.00   0.0  0
 1VE  CONST_08  C26  C9   C10  C11     0.00   0.0  0
 1VE  CONST_09  C9   C26  C13  C12     0.00   0.0  0
 1VE  CONST_10  C9   C10  C11  C12     0.00   0.0  0
 1VE  CONST_11  C22  C23  N24  C16   180.00   0.0  0
 1VE  CONST_12  C18  C23  N24  C16     0.00   0.0  0
 1VE  CONST_13  C19  C18  N17  C16   180.00   0.0  0
 1VE  CONST_14  C23  C18  N17  C16     0.00   0.0  0
 1VE  CONST_15  C22  C21  C20  C19     0.00   0.0  0
 1VE  CONST_16  C22  C23  C18  C19     0.00   0.0  0
 1VE  CONST_17  N24  C23  C18  C19   180.00   0.0  0
 1VE  CONST_18  C18  C19  C20  C21     0.00   0.0  0
 1VE  CONST_19  C18  C23  C22  C21     0.00   0.0  0
 1VE  CONST_20  N24  C23  C22  C21   180.00   0.0  0
 1VE  CONST_21  N17  C18  C23  C22   180.00   0.0  0
 1VE  CONST_22  C20  C21  C22  C23     0.00   0.0  0
 1VE  CONST_23  C20  C19  C18  C23     0.00   0.0  0
 1VE  CONST_24  N17  C16  N24  C23     0.00   0.0  0
 1VE  CONST_25  N5   C6   C2   N3      0.00   0.0  0
 1VE  CONST_26  C20  C19  C18  N17   180.00   0.0  0
 1VE  CONST_27  N24  C23  C18  N17     0.00   0.0  0
 1VE  CONST_28  N24  C16  N17  C18     0.00   0.0  0
 1VE  CONST_29  C13  C26  C9   C7    180.00   0.0  0
 1VE  CONST_30  C11  C10  C9   C7    180.00   0.0  0
 1VE  CONST_31  N3   C2   C6   C7    180.00   0.0  0
 1VE  CONST_32  O4   N5   C6   C7    180.00   0.0  0
 1VE  CONST_33  O14  C13  C12  C11   180.00   0.0  0
 1VE  CONST_34  C23  N24  C16  C15   180.00   0.0  0
 1VE  CONST_35  C18  N17  C16  C15   180.00   0.0  0
 1VE  CONST_36  N5   C6   C2   N1    180.00   0.0  0
 1VE  CONST_37  O4   N3   C2   N1    180.00   0.0  0
 1VE  CONST_38  O14  C13  C26  C9    180.00   0.0  0
 1VE  CONST_39  H38  C26  C9   C10   180.00   0.0  0
 1VE  CONST_40  H31  C12  C11  C10   180.00   0.0  0
 1VE  CONST_41  H29  C10  C11  C12   180.00   0.0  0
 1VE  CONST_42  H30  C11  C12  C13   180.00   0.0  0
 1VE  CONST_43  H36  C21  C20  C19   180.00   0.0  0
 1VE  CONST_44  H34  C19  C20  C21   180.00   0.0  0
 1VE  CONST_45  H35  C20  C21  C22   180.00   0.0  0
 1VE  CONST_46  H25  N24  C23  C22     0.00   0.0  0
 1VE  CONST_47  H37  C22  C23  C18   180.00   0.0  0
 1VE  CONST_48  H28  N1   C2   C6    180.00   0.0  0
 1VE  Var_01    C9   C7   C6   C2    164.75  30.0  2
 1VE  Var_02    C26  C9   C7   C6    151.91  30.0  2
 1VE  Var_03    C16  C15  O14  C13   177.51  30.0  1
 1VE  Var_04    C26  C13  O14  C15  -179.14  30.0  2
 1VE  Var_05    N24  C16  C15  O14   -46.32  30.0  1

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
 1VE  plan-1  C2   0.020
 1VE  plan-1  C6   0.020
 1VE  plan-1  C7   0.020
 1VE  plan-1  N1   0.020
 1VE  plan-1  N3   0.020
 1VE  plan-1  O4   0.020
 1VE  plan-1  N5   0.020
 1VE  plan-2  C7   0.020
 1VE  plan-2  C10  0.020
 1VE  plan-2  C11  0.020
 1VE  plan-2  C12  0.020
 1VE  plan-2  C13  0.020
 1VE  plan-2  C26  0.020
 1VE  plan-2  C9   0.020
 1VE  plan-2  H29  0.020
 1VE  plan-2  H30  0.020
 1VE  plan-2  H31  0.020
 1VE  plan-2  H38  0.020
 1VE  plan-2  O14  0.020
 1VE  plan-3  C15  0.020
 1VE  plan-3  C16  0.020
 1VE  plan-3  C19  0.020
 1VE  plan-3  C21  0.020
 1VE  plan-3  C22  0.020
 1VE  plan-3  C23  0.020
 1VE  plan-3  N17  0.020
 1VE  plan-3  C18  0.020
 1VE  plan-3  C20  0.020
 1VE  plan-3  N24  0.020
 1VE  plan-3  H34  0.020
 1VE  plan-3  H36  0.020
 1VE  plan-3  H37  0.020
 1VE  plan-3  H35  0.020
 1VE  plan-3  H25  0.020
 1VE  plan-4  C2   0.020
 1VE  plan-4  N1   0.020
 1VE  plan-4  H28  0.020
 1VE  plan-4  H27  0.020
 1VE  plan-5  C6   0.020
 1VE  plan-5  C7   0.020
 1VE  plan-5  O8   0.020
 1VE  plan-5  C9   0.020

