# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 06:21:24 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: 2-(5,7-dimethyl-[1,2,4]triazolo[1,5-a]pyrimidin-2-yl)-1-[(2~{S})-2-methyl-1,2-dihydroimidazo[1,2-a]benzimidazol-3-yl]ethanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1Cn2c3ccccc3nc2N1C(=O)Cc4nn5c(C)cc(C)nc5n4
#
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
 D7C  D7C  2-(5,7-dimethyl-[1,2,4]triazolo[1,5-a]pyrimidin-2-yl)-1-[(2~{S})-2-methyl-1,2-dihydroimidazo[1,2-a]benzimidazol-3-yl]ethanone  ligand  46  27  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D7C
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
 D7C  C10  C  CR16  0  -0.271   5.9253   2.5032  -0.4212
 D7C  C11  C  CR16  0  -0.280   6.6542   1.3828  -0.0075
 D7C  C9   C  CR16  0  -0.343   4.5468   2.4570  -0.5713
 D7C  C12  C  CR16  0  -0.305   6.0294   0.1743   0.2672
 D7C  C8   C  CR56  0   0.155   3.8979   1.2585  -0.2971
 D7C  C7   C  CR56  0   0.352   4.6528   0.1378   0.1149
 D7C  C16  C  CR5   0   0.383  -1.8177   0.3620  -0.0180
 D7C  C19  C  CR56  0   0.574  -3.7428   0.4464   0.7906
 D7C  C5   C  CR55  0   0.785   2.5195  -0.2984  -0.0092
 D7C  C22  C  CR16  0  -0.436  -6.1017   0.4266  -0.4774
 D7C  C21  C  CR6   0   0.451  -4.9826   0.3588  -1.2553
 D7C  C23  C  CR6   0   0.270  -5.9918   0.5056   0.9342
 D7C  C1   C  CH2   0  -0.299   3.6156  -2.1923   0.7908
 D7C  C2   C  CR15  0  -0.133   2.1694  -2.5605   0.3871
 D7C  C25  C  CH3   0  -0.718  -4.9499   0.2774  -2.7352
 D7C  C26  C  CH3   0  -0.736  -7.2348   0.5794   1.7583
 D7C  C27  C  CH3   0  -0.658   2.1236  -3.4061  -0.8741
 D7C  C15  C  CH2   0  -0.709  -0.3358   0.3235  -0.1093
 D7C  N6   N  N     0  -0.507   2.5493   0.9479  -0.3665
 D7C  N18  N  N     0  -0.495  -2.4722   0.4442   1.1518
 D7C  N17  N  N     0  -0.286  -2.5754   0.3185  -1.0964
 D7C  N24  N  N     0  -0.464  -4.8332   0.5153   1.5535
 D7C  N4   N  N     0  -0.591   3.7170  -0.8503   0.2717
 D7C  N20  N  N     0  -0.398  -3.8085   0.3694  -0.5781
 D7C  N3   N  NR5   0  -0.618   1.5338  -1.2405   0.1708
 D7C  O14  O  O     0  -0.444  -0.5595  -2.0219   0.3261
 D7C  H1   H  HCR6  0   0.253   6.4504   3.4261  -0.6302
 D7C  H2   H  HCR6  0   0.255   7.7282   1.4589   0.0988
 D7C  H3   H  HCR6  0   0.255   3.9903   3.3281  -0.8922
 D7C  H4   H  HCR6  0   0.270   6.5925  -0.6938   0.5838
 D7C  H5   H  HCR6  0   0.287  -7.0759   0.4217  -0.9446
 D7C  H6   H  HCH2  0   0.284   3.7597  -2.2010   1.8724
 D7C  H7   H  HCH2  0   0.283   4.3435  -2.8609   0.3338
 D7C  H8   H  HCR5  0   0.294   1.6628  -3.0687   1.2054
 D7C  H9   H  HCH3  0   0.276  -4.4436  -0.6321  -3.0602
 D7C  H10  H  HCH3  0   0.270  -5.9607   0.2789  -3.1334
 D7C  H11  H  HCH3  0   0.276  -4.4038   1.1226  -3.1556
 D7C  H12  H  HCH3  0   0.265  -7.8302  -0.3267   1.6342
 D7C  H13  H  HCH3  0   0.260  -6.9975   0.6983   2.8125
 D7C  H14  H  HCH3  0   0.262  -7.8588   1.4147   1.4388
 D7C  H15  H  HCH3  0   0.250   2.6105  -4.3636  -0.6885
 D7C  H16  H  HCH3  0   0.253   1.0989  -3.6048  -1.1823
 D7C  H17  H  HCH3  0   0.237   2.6448  -2.9136  -1.6963
 D7C  H18  H  HCH2  0   0.313  -0.0072   0.6556  -1.0958
 D7C  H19  H  HCH2  0   0.310   0.1013   1.0187   0.6096
 D7C  C13  C  C     0   0.568   0.1786  -1.0760   0.1471

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
 D7C  C1   C2   single    1.546  0.020  1.546
 D7C  C1   N4   single    1.442  0.020  1.442
 D7C  C12  C11  aromatic  1.388  0.020  1.388
 D7C  C12  C7   aromatic  1.385  0.020  1.385
 D7C  C11  C10  aromatic  1.399  0.020  1.399
 D7C  C2   C27  single    1.519  0.020  1.519
 D7C  C2   N3   single    1.481  0.020  1.481
 D7C  N4   C7   aromatic  1.370  0.020  1.370
 D7C  N4   C5   aromatic  1.348  0.020  1.348
 D7C  C7   C8   aromatic  1.413  0.020  1.413
 D7C  C10  C9   aromatic  1.387  0.020  1.387
 D7C  N3   C5   single    1.375  0.020  1.375
 D7C  N3   C13  single    1.365  0.020  1.365
 D7C  C5   N6   aromatic  1.297  0.020  1.297
 D7C  C8   C9   aromatic  1.390  0.020  1.390
 D7C  C8   N6   aromatic  1.386  0.020  1.386
 D7C  O14  C13  double    1.213  0.020  1.213
 D7C  C13  C15  single    1.513  0.020  1.513
 D7C  C25  C21  single    1.483  0.020  1.483
 D7C  C15  C16  single    1.485  0.020  1.485
 D7C  N17  C16  aromatic  1.319  0.020  1.319
 D7C  N17  N20  aromatic  1.339  0.020  1.339
 D7C  C16  N18  aromatic  1.343  0.020  1.343
 D7C  C21  N20  aromatic  1.355  0.020  1.355
 D7C  C21  C22  aromatic  1.365  0.020  1.365
 D7C  N20  C19  aromatic  1.372  0.020  1.372
 D7C  C22  C23  aromatic  1.418  0.020  1.418
 D7C  N18  C19  aromatic  1.321  0.020  1.321
 D7C  C19  N24  aromatic  1.332  0.020  1.332
 D7C  C23  N24  aromatic  1.314  0.020  1.314
 D7C  C23  C26  single    1.493  0.020  1.493
 D7C  C10  H1   single    0.930  0.020  1.080
 D7C  C11  H2   single    0.930  0.020  1.080
 D7C  C9   H3   single    0.930  0.020  1.080
 D7C  C12  H4   single    0.930  0.020  1.080
 D7C  C22  H5   single    0.930  0.020  1.080
 D7C  C1   H6   single    0.970  0.020  1.090
 D7C  C1   H7   single    0.970  0.020  1.090
 D7C  C2   H8   single    0.970  0.020  1.090
 D7C  C25  H9   single    0.970  0.020  1.090
 D7C  C25  H10  single    0.970  0.020  1.090
 D7C  C25  H11  single    0.970  0.020  1.090
 D7C  C26  H12  single    0.970  0.020  1.090
 D7C  C26  H13  single    0.970  0.020  1.090
 D7C  C26  H14  single    0.970  0.020  1.090
 D7C  C27  H15  single    0.970  0.020  1.090
 D7C  C27  H16  single    0.970  0.020  1.090
 D7C  C27  H17  single    0.970  0.020  1.090
 D7C  C15  H18  single    0.970  0.020  1.090
 D7C  C15  H19  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
 D7C  H1   C10  C9   119.31  3.000
 D7C  H1   C10  C11  119.16  3.000
 D7C  C9   C10  C11  121.53  3.000
 D7C  H2   C11  C12  119.25  3.000
 D7C  H2   C11  C10  119.33  3.000
 D7C  C12  C11  C10  121.42  3.000
 D7C  H3   C9   C8   120.82  3.000
 D7C  H3   C9   C10  121.07  3.000
 D7C  C8   C9   C10  118.10  3.000
 D7C  H4   C12  C7   121.87  3.000
 D7C  H4   C12  C11  121.49  3.000
 D7C  C7   C12  C11  116.65  3.000
 D7C  N6   C8   C7   110.91  3.000
 D7C  N6   C8   C9   129.61  3.000
 D7C  C7   C8   C9   119.48  3.000
 D7C  N4   C7   C8   103.91  3.000
 D7C  C8   C7   C12  122.83  3.000
 D7C  N4   C7   C12  133.25  3.000
 D7C  N17  C16  N18  115.74  3.000
 D7C  N18  C16  C15  122.78  3.000
 D7C  N17  C16  C15  121.48  3.000
 D7C  N20  C19  N24  122.32  3.000
 D7C  N24  C19  N18  129.09  3.000
 D7C  N20  C19  N18  108.58  3.000
 D7C  N3   C5   N4   109.21  3.000
 D7C  N3   C5   N6   135.30  3.000
 D7C  N4   C5   N6   115.50  3.000
 D7C  H5   C22  C23  120.03  3.000
 D7C  H5   C22  C21  119.52  3.000
 D7C  C23  C22  C21  120.45  3.000
 D7C  N20  C21  C25  118.69  3.000
 D7C  N20  C21  C22  115.16  3.000
 D7C  C25  C21  C22  126.15  3.000
 D7C  N24  C23  C26  118.27  3.000
 D7C  C26  C23  C22  119.19  3.000
 D7C  N24  C23  C22  122.54  3.000
 D7C  H7   C1   H6   108.83  3.000
 D7C  H7   C1   N4   111.92  3.000
 D7C  H6   C1   N4   110.79  3.000
 D7C  H7   C1   C2   111.68  3.000
 D7C  H6   C1   C2   112.36  3.000
 D7C  N4   C1   C2   101.15  3.000
 D7C  H8   C2   N3   109.04  3.000
 D7C  H8   C2   C27  110.50  3.000
 D7C  N3   C2   C27  111.22  3.000
 D7C  H8   C2   C1   110.51  3.000
 D7C  N3   C2   C1   103.14  3.000
 D7C  C27  C2   C1   112.18  3.000
 D7C  H11  C25  H10  108.88  3.000
 D7C  H11  C25  H9   107.40  3.000
 D7C  H10  C25  H9   108.90  3.000
 D7C  H11  C25  C21  110.69  3.000
 D7C  H10  C25  C21  110.20  3.000
 D7C  H9   C25  C21  110.70  3.000
 D7C  H14  C26  H13  108.98  3.000
 D7C  H14  C26  H12  106.88  3.000
 D7C  H13  C26  H12  108.68  3.000
 D7C  H14  C26  C23  110.64  3.000
 D7C  H13  C26  C23  111.03  3.000
 D7C  H12  C26  C23  110.51  3.000
 D7C  H17  C27  H16  108.59  3.000
 D7C  H17  C27  H15  108.15  3.000
 D7C  H16  C27  H15  107.96  3.000
 D7C  H17  C27  C2   111.10  3.000
 D7C  H16  C27  C2   111.41  3.000
 D7C  H15  C27  C2   109.52  3.000
 D7C  H19  C15  H18  106.31  3.000
 D7C  H19  C15  C13  109.96  3.000
 D7C  H18  C15  C13  109.41  3.000
 D7C  H19  C15  C16  110.03  3.000
 D7C  H18  C15  C16  110.37  3.000
 D7C  C13  C15  C16  110.66  3.000
 D7C  C5   N6   C8   102.94  3.000
 D7C  C19  N18  C16  103.34  3.000
 D7C  N20  N17  C16  102.21  3.000
 D7C  C23  N24  C19  116.83  3.000
 D7C  C1   N4   C5   113.17  3.000
 D7C  C5   N4   C7   106.72  3.000
 D7C  C1   N4   C7   139.48  3.000
 D7C  N17  N20  C21  127.18  3.000
 D7C  C21  N20  C19  122.69  3.000
 D7C  N17  N20  C19  110.13  3.000
 D7C  C2   N3   C13  122.40  3.000
 D7C  C13  N3   C5   128.80  3.000
 D7C  C2   N3   C5   108.79  3.000
 D7C  O14  C13  N3   120.49  3.000
 D7C  O14  C13  C15  122.65  3.000
 D7C  N3   C13  C15  116.86  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
 D7C  CONST_01  C7   C12  C11  C10     0.00   0.0  0
 D7C  CONST_02  C7   C8   C9   C10     0.00   0.0  0
 D7C  CONST_03  N6   C8   C9   C10   180.00   0.0  0
 D7C  CONST_04  N4   C7   C12  C11   180.00   0.0  0
 D7C  CONST_05  C8   C7   C12  C11     0.00   0.0  0
 D7C  CONST_06  C8   C9   C10  C11     0.00   0.0  0
 D7C  CONST_07  C12  C11  C10  C9      0.00   0.0  0
 D7C  CONST_08  C12  C7   C8   C9      0.00   0.0  0
 D7C  CONST_09  N4   C7   C8   C9    180.00   0.0  0
 D7C  CONST_10  C5   N6   C8   C9    180.00   0.0  0
 D7C  CONST_11  C5   N4   C7   C12   180.00   0.0  0
 D7C  CONST_12  N6   C8   C7   C12   180.00   0.0  0
 D7C  CONST_13  C5   N4   C7   C8      0.00   0.0  0
 D7C  CONST_14  N4   C5   N6   C8      0.00   0.0  0
 D7C  CONST_15  N6   C5   N4   C7      0.00   0.0  0
 D7C  CONST_16  C5   N6   C8   C7      0.00   0.0  0
 D7C  CONST_17  C21  N20  N17  C16   180.00   0.0  0
 D7C  CONST_18  C19  N20  N17  C16     0.00   0.0  0
 D7C  CONST_19  N20  C19  N18  C16     0.00   0.0  0
 D7C  CONST_20  N24  C19  N18  C16   180.00   0.0  0
 D7C  CONST_21  C22  C21  N20  C19     0.00   0.0  0
 D7C  CONST_22  N17  C16  N18  C19     0.00   0.0  0
 D7C  CONST_23  C22  C23  N24  C19     0.00   0.0  0
 D7C  CONST_24  N17  N20  C21  C22   180.00   0.0  0
 D7C  CONST_25  N18  C19  N20  C21   180.00   0.0  0
 D7C  CONST_26  N24  C19  N20  C21     0.00   0.0  0
 D7C  CONST_27  N24  C23  C22  C21     0.00   0.0  0
 D7C  CONST_28  N20  C21  C22  C23     0.00   0.0  0
 D7C  CONST_29  N20  C19  N24  C23     0.00   0.0  0
 D7C  CONST_30  N18  C19  N24  C23   180.00   0.0  0
 D7C  CONST_31  N4   C7   C8   N6      0.00   0.0  0
 D7C  CONST_32  N20  N17  C16  N18     0.00   0.0  0
 D7C  CONST_33  N17  N20  C19  N18     0.00   0.0  0
 D7C  CONST_34  N24  C19  N20  N17   180.00   0.0  0
 D7C  CONST_35  C25  C21  N20  C19   180.00   0.0  0
 D7C  CONST_36  C15  C16  N18  C19   180.00   0.0  0
 D7C  CONST_37  C26  C23  N24  C19   180.00   0.0  0
 D7C  CONST_38  C26  C23  C22  C21   180.00   0.0  0
 D7C  CONST_39  C25  C21  C22  C23   180.00   0.0  0
 D7C  CONST_40  N17  N20  C21  C25     0.00   0.0  0
 D7C  CONST_41  N20  N17  C16  C15   180.00   0.0  0
 D7C  CONST_42  H4   C12  C11  C10   180.00   0.0  0
 D7C  CONST_43  H3   C9   C10  C11   180.00   0.0  0
 D7C  CONST_44  H2   C11  C10  C9    180.00   0.0  0
 D7C  CONST_45  H1   C10  C11  C12   180.00   0.0  0
 D7C  CONST_46  H5   C22  C23  N24   180.00   0.0  0
 D7C  CONST_47  O14  C13  N3   C5    180.00   0.0  0
 D7C  CONST_48  C15  C13  N3   C5      0.00   0.0  0
 D7C  CONST_49  O14  C13  N3   C2      0.00   0.0  0
 D7C  CONST_50  C15  C13  N3   C2    180.00   0.0  0
 D7C  Var_01    C2   C1   N4   C7   -174.04  30.0  1
 D7C  Var_02    N4   C5   N3   C2     -9.22  30.0  1
 D7C  Var_03    N3   C13  C15  C16  -176.31  30.0  2
 D7C  Var_04    N17  C16  C15  C13   -98.59  30.0  2
 D7C  Var_05    H9   C25  C21  C22  -120.52  30.0  2
 D7C  Var_06    H12  C26  C23  C22    62.89  30.0  2

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
 D7C  chir_01  C2  C1  C27  N3  positiv

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
 D7C  plan-1  C16  0.020
 D7C  plan-1  C19  0.020
 D7C  plan-1  C22  0.020
 D7C  plan-1  C21  0.020
 D7C  plan-1  C23  0.020
 D7C  plan-1  C25  0.020
 D7C  plan-1  C26  0.020
 D7C  plan-1  C15  0.020
 D7C  plan-1  N18  0.020
 D7C  plan-1  N17  0.020
 D7C  plan-1  N24  0.020
 D7C  plan-1  N20  0.020
 D7C  plan-1  H5   0.020
 D7C  plan-2  C10  0.020
 D7C  plan-2  C11  0.020
 D7C  plan-2  C9   0.020
 D7C  plan-2  C12  0.020
 D7C  plan-2  C8   0.020
 D7C  plan-2  C7   0.020
 D7C  plan-2  C5   0.020
 D7C  plan-2  C1   0.020
 D7C  plan-2  N6   0.020
 D7C  plan-2  N4   0.020
 D7C  plan-2  N3   0.020
 D7C  plan-2  H1   0.020
 D7C  plan-2  H2   0.020
 D7C  plan-2  H3   0.020
 D7C  plan-2  H4   0.020
 D7C  plan-3  C5   0.020
 D7C  plan-3  C2   0.020
 D7C  plan-3  C15  0.020
 D7C  plan-3  N3   0.020
 D7C  plan-3  O14  0.020
 D7C  plan-3  C13  0.020

