# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jun  9 04:11:09 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: 4-[1-(cyclopropylmethyl)-1H-benzimidazol-2-yl]-1,2,5-oxadiazol-3-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nonc1c2nc3ccccc3n2CC4CC4
#
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
 ZO9  ZO9  4-[1-(cyclopropylmethyl)-1H-benzimidazol-2-yl]-1,2,5-oxadiazol-3-amine  ligand  32  19  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_ZO9
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
 ZO9  C     C  CR16  0  -0.270  -3.8673   1.7517  -0.1295
 ZO9  N     N  N     0  -0.516  -0.1759   1.6614  -0.2532
 ZO9  O     O  O     0  -0.217   3.8187  -0.3229   0.1399
 ZO9  C1    C  CR16  0  -0.270  -4.0532   0.4343   0.3238
 ZO9  N1    N  NR5   0  -0.550  -0.4604  -0.4342   0.4665
 ZO9  C2    C  CR16  0  -0.314  -2.9864  -0.4115   0.5609
 ZO9  N2    N  N     0  -0.127   2.5402  -0.6467   0.2741
 ZO9  C3    C  CR56  0   0.338  -1.7142   0.1050   0.3278
 ZO9  N3    N  N     0  -0.192   3.9798   0.9936  -0.1623
 ZO9  C4    C  CR56  0   0.173  -1.5142   1.4206  -0.1203
 ZO9  N4    N  NH2   0  -0.851   2.4892   2.7916  -0.4290
 ZO9  C5    C  CR16  0  -0.329  -2.6046   2.2609  -0.3550
 ZO9  C6    C  CR5   0   0.538   0.4116   0.5442   0.0971
 ZO9  C7    C  CH2   0  -0.354  -0.1725  -1.8052   0.8641
 ZO9  C8    C  CH1   0  -0.250   0.0641  -2.7113  -0.3118
 ZO9  C9    C  CH2   0  -0.489  -0.2889  -4.1610  -0.1875
 ZO9  C10   C  CH2   0  -0.483  -1.0968  -3.2655  -1.0771
 ZO9  C11   C  CR5   0   0.092   1.8537   0.4319   0.0708
 ZO9  C12   C  CR5   0   0.356   2.7805   1.4979  -0.2100
 ZO9  H     H  HCR6  0   0.258  -4.7346   2.3750  -0.3020
 ZO9  H1    H  HCR6  0   0.262  -5.0586   0.0720   0.4915
 ZO9  H2    H  HCR6  0   0.270  -3.1503  -1.4219   0.9117
 ZO9  HN4   H  HNH2  0   0.403   3.2009   3.3785  -0.8309
 ZO9  HN4A  H  HNH2  0   0.414   1.5325   3.0021  -0.6674
 ZO9  H5    H  HCR6  0   0.261  -2.4572   3.2760  -0.7001
 ZO9  H7    H  HCH2  0   0.288   0.6876  -1.8007   1.5317
 ZO9  H7A   H  HCH2  0   0.278  -1.0213  -2.1549   1.4524
 ZO9  H8    H  HCH1  0   0.270   0.9570  -2.4855  -0.8835
 ZO9  H9    H  HCH2  0   0.258   0.3729  -4.8847  -0.6451
 ZO9  H9A   H  HCH2  0   0.250  -0.7410  -4.4965   0.7382
 ZO9  H10   H  HCH2  0   0.248  -2.0965  -3.0021  -0.7546
 ZO9  H10A  H  HCH2  0   0.257  -0.9926  -3.3726  -2.1489

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
 ZO9  C    C1    aromatic  1.406  0.020  1.406
 ZO9  C    C5    aromatic  1.380  0.020  1.380
 ZO9  N    C4    aromatic  1.366  0.020  1.366
 ZO9  N    C6    aromatic  1.310  0.020  1.310
 ZO9  O    N2    aromatic  1.326  0.020  1.326
 ZO9  O    N3    aromatic  1.360  0.020  1.360
 ZO9  C1   C2    aromatic  1.382  0.020  1.382
 ZO9  N1   C3    aromatic  1.372  0.020  1.372
 ZO9  N1   C6    aromatic  1.362  0.020  1.362
 ZO9  N1   C7    single    1.456  0.020  1.456
 ZO9  C2   C3    aromatic  1.393  0.020  1.393
 ZO9  N2   C11   aromatic  1.295  0.020  1.295
 ZO9  C3   C4    aromatic  1.404  0.020  1.404
 ZO9  N3   C12   aromatic  1.302  0.020  1.302
 ZO9  C4   C5    aromatic  1.397  0.020  1.397
 ZO9  N4   C12   single    1.344  0.020  1.344
 ZO9  C6   C11   single    1.447  0.020  1.447
 ZO9  C7   C8    single    1.503  0.020  1.503
 ZO9  C8   C9    single    1.497  0.020  1.497
 ZO9  C8   C10   single    1.497  0.020  1.497
 ZO9  C9   C10   single    1.499  0.020  1.499
 ZO9  C11  C12   aromatic  1.440  0.020  1.440
 ZO9  C    H     single    0.930  0.020  1.080
 ZO9  C1   H1    single    0.930  0.020  1.080
 ZO9  C2   H2    single    0.930  0.020  1.080
 ZO9  N4   HN4   single    0.890  0.020  1.040
 ZO9  N4   HN4A  single    0.890  0.020  1.040
 ZO9  C5   H5    single    0.930  0.020  1.080
 ZO9  C7   H7    single    0.970  0.020  1.090
 ZO9  C7   H7A   single    0.970  0.020  1.090
 ZO9  C8   H8    single    0.970  0.020  1.090
 ZO9  C9   H9    single    0.970  0.020  1.090
 ZO9  C9   H9A   single    0.970  0.020  1.090
 ZO9  C10  H10   single    0.970  0.020  1.090
 ZO9  C10  H10A  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
 ZO9  H     C    C5   119.66  3.000
 ZO9  H     C    C1   119.04  3.000
 ZO9  C5    C    C1   121.30  3.000
 ZO9  C6    N    C4   105.24  3.000
 ZO9  N3    O    N2   111.91  3.000
 ZO9  H1    C1   C2   119.07  3.000
 ZO9  H1    C1   C    119.13  3.000
 ZO9  C2    C1   C    121.80  3.000
 ZO9  C7    N1   C6   128.61  3.000
 ZO9  C7    N1   C3   125.33  3.000
 ZO9  C6    N1   C3   105.98  3.000
 ZO9  H2    C2   C3   122.61  3.000
 ZO9  H2    C2   C1   120.68  3.000
 ZO9  C3    C2   C1   116.71  3.000
 ZO9  C11   N2   O    106.98  3.000
 ZO9  C4    C3   C2   122.07  3.000
 ZO9  C4    C3   N1   105.69  3.000
 ZO9  C2    C3   N1   132.23  3.000
 ZO9  C12   N3   O    105.90  3.000
 ZO9  C5    C4   C3   120.41  3.000
 ZO9  C5    C4   N    129.97  3.000
 ZO9  C3    C4   N    109.61  3.000
 ZO9  HN4A  N4   HN4  117.06  3.000
 ZO9  HN4A  N4   C12  116.43  3.000
 ZO9  HN4   N4   C12  118.24  3.000
 ZO9  H5    C5   C4   120.77  3.000
 ZO9  H5    C5   C    121.52  3.000
 ZO9  C4    C5   C    117.71  3.000
 ZO9  C11   C6   N1   125.98  3.000
 ZO9  C11   C6   N    120.56  3.000
 ZO9  N1    C6   N    113.47  3.000
 ZO9  H7A   C7   H7   106.58  3.000
 ZO9  H7A   C7   C8   110.57  3.000
 ZO9  H7    C7   C8   110.96  3.000
 ZO9  H7A   C7   N1   107.18  3.000
 ZO9  H7    C7   N1   108.64  3.000
 ZO9  C8    C7   N1   112.65  3.000
 ZO9  H8    C8   C10  116.51  3.000
 ZO9  H8    C8   C9   116.08  3.000
 ZO9  C10   C8   C9    60.07  3.000
 ZO9  H8    C8   C7   114.62  3.000
 ZO9  C10   C8   C7   120.07  3.000
 ZO9  C9    C8   C7   118.79  3.000
 ZO9  H9A   C9   H9   114.17  3.000
 ZO9  H9A   C9   C10  117.86  3.000
 ZO9  H9    C9   C10  118.57  3.000
 ZO9  H9A   C9   C8   117.98  3.000
 ZO9  H9    C9   C8   117.92  3.000
 ZO9  C10   C9   C8    59.95  3.000
 ZO9  H10A  C10  H10  114.07  3.000
 ZO9  H10A  C10  C9   118.48  3.000
 ZO9  H10   C10  C9   117.79  3.000
 ZO9  H10A  C10  C8   117.93  3.000
 ZO9  H10   C10  C8   118.27  3.000
 ZO9  C9    C10  C8    59.98  3.000
 ZO9  C12   C11  C6   125.98  3.000
 ZO9  C12   C11  N2   107.82  3.000
 ZO9  C6    C11  N2   126.19  3.000
 ZO9  C11   C12  N4   127.21  3.000
 ZO9  C11   C12  N3   107.39  3.000
 ZO9  N4    C12  N3   125.34  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
 ZO9  CONST_01  C3    C2   C1   C      0.00   0.0  0
 ZO9  CONST_02  N     C4   C5   C    180.00   0.0  0
 ZO9  CONST_03  C3    C4   C5   C      0.00   0.0  0
 ZO9  CONST_04  N1    C3   C4   N      0.00   0.0  0
 ZO9  CONST_05  C2    C3   C4   N    180.00   0.0  0
 ZO9  CONST_06  C3    N1   C6   N      0.00   0.0  0
 ZO9  CONST_07  N2    C11  C6   N    180.00   0.0  0
 ZO9  CONST_08  C12   C11  C6   N      0.00   0.0  0
 ZO9  CONST_09  C6    C11  N2   O    180.00   0.0  0
 ZO9  CONST_10  C12   C11  N2   O      0.00   0.0  0
 ZO9  CONST_11  C11   C12  N3   O      0.00   0.0  0
 ZO9  CONST_12  C4    C5   C    C1     0.00   0.0  0
 ZO9  CONST_13  N1    C3   C2   C1   180.00   0.0  0
 ZO9  CONST_14  C4    C3   C2   C1     0.00   0.0  0
 ZO9  CONST_15  C5    C4   C3   N1   180.00   0.0  0
 ZO9  CONST_16  C4    N    C6   N1     0.00   0.0  0
 ZO9  CONST_17  N2    C11  C6   N1     0.00   0.0  0
 ZO9  CONST_18  C12   C11  C6   N1   180.00   0.0  0
 ZO9  CONST_19  C5    C    C1   C2     0.00   0.0  0
 ZO9  CONST_20  C6    N1   C3   C2   180.00   0.0  0
 ZO9  CONST_21  C5    C4   C3   C2     0.00   0.0  0
 ZO9  CONST_22  C12   N3   O    N2     0.00   0.0  0
 ZO9  CONST_23  N3    C12  C11  N2     0.00   0.0  0
 ZO9  CONST_24  C11   C6   N1   C3   180.00   0.0  0
 ZO9  CONST_25  C6    N    C4   C3     0.00   0.0  0
 ZO9  CONST_26  C11   N2   O    N3     0.00   0.0  0
 ZO9  CONST_27  C6    C11  C12  N3   180.00   0.0  0
 ZO9  CONST_28  C11   C6   N    C4   180.00   0.0  0
 ZO9  CONST_29  C6    N1   C3   C4     0.00   0.0  0
 ZO9  CONST_30  C6    N    C4   C5   180.00   0.0  0
 ZO9  CONST_31  C7    N1   C6   N    180.00   0.0  0
 ZO9  CONST_32  N4    C12  N3   O    180.00   0.0  0
 ZO9  CONST_33  C7    N1   C3   C2     0.00   0.0  0
 ZO9  CONST_34  N4    C12  C11  N2   180.00   0.0  0
 ZO9  CONST_35  C7    N1   C3   C4   180.00   0.0  0
 ZO9  CONST_36  C6    C11  C12  N4     0.00   0.0  0
 ZO9  CONST_37  C11   C6   N1   C7     0.00   0.0  0
 ZO9  CONST_38  H2    C2   C1   C    180.00   0.0  0
 ZO9  CONST_39  H5    C5   C4   N      0.00   0.0  0
 ZO9  CONST_40  H     C    C1   C2   180.00   0.0  0
 ZO9  CONST_41  H1    C1   C2   C3   180.00   0.0  0
 ZO9  CONST_43  HN4A  N4   C12  N3   180.00   0.0  0
 ZO9  Var_01    C9    C8   C7   N1  -150.25  30.0  3
 ZO9  Var_02    C8    C7   N1   C3    96.03  30.0  2
 ZO9  Var_03    C10   C9   C8   C7   110.08  30.0  1
 ZO9  Var_04    H10   C10  C9   C8  -108.28  30.0  1

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
 ZO9  chir_01  C8  C7  C9  C10  both

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
 ZO9  plan-1  O     0.020
 ZO9  plan-1  N2    0.020
 ZO9  plan-1  N3    0.020
 ZO9  plan-1  N4    0.020
 ZO9  plan-1  C6    0.020
 ZO9  plan-1  C11   0.020
 ZO9  plan-1  C12   0.020
 ZO9  plan-2  C     0.020
 ZO9  plan-2  N     0.020
 ZO9  plan-2  C1    0.020
 ZO9  plan-2  N1    0.020
 ZO9  plan-2  C2    0.020
 ZO9  plan-2  C3    0.020
 ZO9  plan-2  C4    0.020
 ZO9  plan-2  C5    0.020
 ZO9  plan-2  C6    0.020
 ZO9  plan-2  C7    0.020
 ZO9  plan-2  C11   0.020
 ZO9  plan-2  H     0.020
 ZO9  plan-2  H1    0.020
 ZO9  plan-2  H2    0.020
 ZO9  plan-2  H5    0.020
 ZO9  plan-3  N4    0.020
 ZO9  plan-3  C12   0.020
 ZO9  plan-3  HN4   0.020
 ZO9  plan-3  HN4A  0.020

