# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 03:27:02 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: (6S)-6-[(2H-1,3-benzodioxol-4-yl)methyl]-5,6,7,8-tetrahydroimidazo[1,5-a]pyridin-3-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncc2CC[C@H](Cn12)Cc3cccc4OCOc34
#
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
 7WD  7WD  (6S)-6-[(2H-1,3-benzodioxol-4-yl)methyl]-5,6,7,8-tetrahydroimidazo[1,5-a]pyridin-3-amine  ligand  37  20  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_7WD
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
 7WD  C1   C  CR56  0   0.306   3.4435  -0.6527  -0.4580
 7WD  C2   C  CR56  0   0.261   2.5089   0.2254   0.0647
 7WD  C3   C  CR6   0   0.026   1.6691  -0.1067   1.1047
 7WD  C11  C  CH1   0  -0.269  -0.5814   1.0008   0.7195
 7WD  C12  C  CH2   0  -0.444  -1.5981   1.9691   1.3185
 7WD  C13  C  CH2   0  -0.508  -2.7251   2.2435   0.3263
 7WD  C14  C  CR5   0   0.306  -3.2710   0.9675  -0.2169
 7WD  C16  C  CH2   0  -0.258  -1.2345  -0.3549   0.4663
 7WD  C17  C  CR15  0  -0.285  -4.4247   0.6169  -0.8457
 7WD  C19  C  CR5   0   0.577  -3.2697  -1.1715  -0.7411
 7WD  C4   C  CR16  0  -0.324   1.8246  -1.4091   1.6058
 7WD  C5   C  CR16  0  -0.261   2.7550  -2.2939   1.0844
 7WD  C6   C  CR16  0  -0.360   3.5952  -1.9293   0.0263
 7WD  O7   O  O     0  -0.487   4.1037  -0.0498  -1.4792
 7WD  C8   C  CH2   0   0.068   3.7266   1.3190  -1.4323
 7WD  O9   O  O     0  -0.486   2.5640   1.3981  -0.6208
 7WD  C10  C  CH2   0  -0.506   0.6375   0.8443   1.6351
 7WD  N15  N  NR5   0  -0.508  -2.5245  -0.1949  -0.1715
 7WD  N18  N  N     0  -0.498  -4.4208  -0.7214  -1.1675
 7WD  N20  N  NH2   0  -0.855  -2.7860  -2.4558  -0.8925
 7WD  H1   H  HCH1  0   0.251  -0.2492   1.4104  -0.2418
 7WD  H2   H  HCH2  0   0.230  -1.9981   1.5507   2.2487
 7WD  H3   H  HCH2  0   0.249  -1.1065   2.9080   1.5813
 7WD  H4   H  HCH2  0   0.257  -3.5216   2.8251   0.7930
 7WD  H5   H  HCH2  0   0.244  -2.3287   2.8577  -0.4884
 7WD  H6   H  HCH2  0   0.263  -0.6010  -0.9779  -0.1683
 7WD  H7   H  HCH2  0   0.243  -1.3603  -0.8821   1.4193
 7WD  H8   H  HCR5  0   0.239  -5.2626   1.2544  -1.0866
 7WD  H9   H  HCR6  0   0.251   1.1984  -1.7243   2.4319
 7WD  H10  H  HCR6  0   0.257   2.8404  -3.2866   1.5054
 7WD  H11  H  HCR6  0   0.271   4.3220  -2.6158  -0.3861
 7WD  H12  H  HCH2  0   0.230   4.5334   1.9118  -0.9858
 7WD  H13  H  HCH2  0   0.251   0.3034   0.5001   2.6179
 7WD  H14  H  HCH2  0   0.259   1.0805   1.8320   1.7882
 7WD  H15  H  HNH2  0   0.384  -2.3859  -2.8532  -0.0538
 7WD  H16  H  HNH2  0   0.381  -3.4988  -3.0752  -1.2485
 7WD  H17  H  HCH2  0   0.246   3.5018   1.6758  -2.4368

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
 7WD  N20  C19  single    1.381  0.020  1.381
 7WD  N18  C19  aromatic  1.307  0.020  1.307
 7WD  N18  C17  aromatic  1.376  0.020  1.376
 7WD  C19  N15  aromatic  1.354  0.020  1.354
 7WD  C17  C14  aromatic  1.360  0.020  1.360
 7WD  N15  C14  aromatic  1.382  0.020  1.382
 7WD  N15  C16  single    1.448  0.020  1.448
 7WD  C14  C13  single    1.490  0.020  1.490
 7WD  C16  C11  single    1.526  0.020  1.526
 7WD  C13  C12  single    1.526  0.020  1.526
 7WD  C11  C12  single    1.526  0.020  1.526
 7WD  C11  C10  single    1.533  0.020  1.533
 7WD  C4   C5   aromatic  1.386  0.020  1.386
 7WD  C4   C3   aromatic  1.404  0.020  1.404
 7WD  C5   C6   aromatic  1.400  0.020  1.400
 7WD  C3   C10  single    1.500  0.020  1.500
 7WD  C3   C2   aromatic  1.377  0.020  1.377
 7WD  C6   C1   aromatic  1.374  0.020  1.374
 7WD  C2   C1   aromatic  1.385  0.020  1.385
 7WD  C2   O9   single    1.359  0.020  1.359
 7WD  C1   O7   single    1.357  0.020  1.357
 7WD  O9   C8   single    1.420  0.020  1.420
 7WD  O7   C8   single    1.421  0.020  1.421
 7WD  C11  H1   single    0.970  0.020  1.090
 7WD  C12  H2   single    0.970  0.020  1.090
 7WD  C12  H3   single    0.970  0.020  1.090
 7WD  C13  H4   single    0.970  0.020  1.090
 7WD  C13  H5   single    0.970  0.020  1.090
 7WD  C16  H6   single    0.970  0.020  1.090
 7WD  C16  H7   single    0.970  0.020  1.090
 7WD  C17  H8   single    0.930  0.020  1.080
 7WD  C4   H9   single    0.930  0.020  1.080
 7WD  C5   H10  single    0.930  0.020  1.080
 7WD  C6   H11  single    0.930  0.020  1.080
 7WD  C8   H12  single    0.970  0.020  1.090
 7WD  C10  H13  single    0.970  0.020  1.090
 7WD  C10  H14  single    0.970  0.020  1.090
 7WD  N20  H15  single    0.890  0.020  1.040
 7WD  N20  H16  single    0.890  0.020  1.040
 7WD  C8   H17  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
 7WD  O7   C1   C6   128.63  3.000
 7WD  O7   C1   C2   109.30  3.000
 7WD  C6   C1   C2   122.05  3.000
 7WD  O9   C2   C3   127.84  3.000
 7WD  O9   C2   C1   109.23  3.000
 7WD  C3   C2   C1   122.93  3.000
 7WD  C10  C3   C4   122.55  3.000
 7WD  C10  C3   C2   122.24  3.000
 7WD  C4   C3   C2   115.19  3.000
 7WD  H1   C11  C10  108.72  3.000
 7WD  H1   C11  C16  108.43  3.000
 7WD  C10  C11  C16  110.42  3.000
 7WD  H1   C11  C12  107.99  3.000
 7WD  C10  C11  C12  111.10  3.000
 7WD  C16  C11  C12  110.10  3.000
 7WD  H3   C12  H2   106.76  3.000
 7WD  H3   C12  C13  109.53  3.000
 7WD  H2   C12  C13  110.55  3.000
 7WD  H3   C12  C11  109.88  3.000
 7WD  H2   C12  C11  109.52  3.000
 7WD  C13  C12  C11  110.53  3.000
 7WD  H5   C13  H4   106.47  3.000
 7WD  H5   C13  C14  109.98  3.000
 7WD  H4   C13  C14  110.18  3.000
 7WD  H5   C13  C12  108.50  3.000
 7WD  H4   C13  C12  110.90  3.000
 7WD  C14  C13  C12  110.70  3.000
 7WD  N15  C14  C17  104.86  3.000
 7WD  N15  C14  C13  120.68  3.000
 7WD  C17  C14  C13  134.43  3.000
 7WD  H7   C16  H6   107.30  3.000
 7WD  H7   C16  N15  109.50  3.000
 7WD  H6   C16  N15  108.90  3.000
 7WD  H7   C16  C11  109.39  3.000
 7WD  H6   C16  C11  110.80  3.000
 7WD  N15  C16  C11  110.87  3.000
 7WD  H8   C17  N18  121.60  3.000
 7WD  H8   C17  C14  127.52  3.000
 7WD  N18  C17  C14  110.88  3.000
 7WD  N20  C19  N18  126.37  3.000
 7WD  N18  C19  N15  111.92  3.000
 7WD  N20  C19  N15  121.62  3.000
 7WD  H9   C4   C5   119.28  3.000
 7WD  H9   C4   C3   118.56  3.000
 7WD  C5   C4   C3   122.16  3.000
 7WD  H10  C5   C6   119.07  3.000
 7WD  H10  C5   C4   119.51  3.000
 7WD  C6   C5   C4   121.41  3.000
 7WD  H11  C6   C5   121.76  3.000
 7WD  H11  C6   C1   121.98  3.000
 7WD  C5   C6   C1   116.25  3.000
 7WD  C8   O7   C1   105.90  3.000
 7WD  H17  C8   H12  110.50  3.000
 7WD  H17  C8   O9   109.86  3.000
 7WD  H12  C8   O9   109.86  3.000
 7WD  H17  C8   O7   109.87  3.000
 7WD  H12  C8   O7   109.82  3.000
 7WD  O9   C8   O7   106.85  3.000
 7WD  C8   O9   C2   105.86  3.000
 7WD  H14  C10  H13  106.40  3.000
 7WD  H14  C10  C11  108.28  3.000
 7WD  H13  C10  C11  109.02  3.000
 7WD  H14  C10  C3   110.10  3.000
 7WD  H13  C10  C3   109.17  3.000
 7WD  C11  C10  C3   113.61  3.000
 7WD  C19  N15  C16  126.57  3.000
 7WD  C16  N15  C14  126.06  3.000
 7WD  C19  N15  C14  107.19  3.000
 7WD  C19  N18  C17  105.13  3.000
 7WD  H16  N20  H15  109.33  3.000
 7WD  H16  N20  C19  111.23  3.000
 7WD  H15  N20  C19  114.42  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
 7WD  CONST_01  C4   C5   C6   C1     0.00   0.0  0
 7WD  CONST_02  C4   C3   C2   C1     0.00   0.0  0
 7WD  CONST_03  C5   C4   C3   C2     0.00   0.0  0
 7WD  CONST_04  C5   C6   C1   C2     0.00   0.0  0
 7WD  CONST_05  C6   C5   C4   C3     0.00   0.0  0
 7WD  CONST_06  C6   C1   C2   C3     0.00   0.0  0
 7WD  CONST_07  C19  N18  C17  C14    0.00   0.0  0
 7WD  CONST_08  N18  C19  N15  C14    0.00   0.0  0
 7WD  CONST_09  N15  C19  N18  C17    0.00   0.0  0
 7WD  CONST_10  C19  N15  C14  C17    0.00   0.0  0
 7WD  CONST_11  N18  C17  C14  N15    0.00   0.0  0
 7WD  CONST_12  C10  C3   C2   C1   180.00   0.0  0
 7WD  CONST_13  N20  C19  N15  C14  180.00   0.0  0
 7WD  CONST_14  N20  C19  N15  C16    0.00   0.0  0
 7WD  CONST_15  N20  C19  N18  C17  180.00   0.0  0
 7WD  CONST_16  C10  C3   C4   C5   180.00   0.0  0
 7WD  CONST_17  C10  C3   C2   O9     0.00   0.0  0
 7WD  CONST_18  H10  C5   C6   C1   180.00   0.0  0
 7WD  CONST_19  H9   C4   C3   C2   180.00   0.0  0
 7WD  CONST_20  H11  C6   C1   C2   180.00   0.0  0
 7WD  CONST_21  H8   C17  C14  C13    0.00   0.0  0
 7WD  CONST_23  H16  N20  C19  N15  180.00   0.0  0
 7WD  Var_01    O9   C8   O7   C1   -16.42  30.0  1
 7WD  Var_02    O7   C8   O9   C2    16.44  30.0  1
 7WD  Var_03    C19  N15  C16  C11  167.94  30.0  1
 7WD  Var_04    C14  C13  C12  C11   49.74  30.0  1
 7WD  Var_05    C17  C14  C13  C12  161.41  30.0  1
 7WD  Var_06    C11  C10  C3   C2    74.71  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
 7WD  chir_01  C11  C16  C12  C10  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
 7WD  plan-1  C1   0.020
 7WD  plan-1  C2   0.020
 7WD  plan-1  C3   0.020
 7WD  plan-1  C4   0.020
 7WD  plan-1  C5   0.020
 7WD  plan-1  C6   0.020
 7WD  plan-1  O7   0.020
 7WD  plan-1  O9   0.020
 7WD  plan-1  C10  0.020
 7WD  plan-1  H9   0.020
 7WD  plan-1  H10  0.020
 7WD  plan-1  H11  0.020
 7WD  plan-2  C19  0.020
 7WD  plan-2  N20  0.020
 7WD  plan-2  H15  0.020
 7WD  plan-2  H16  0.020
 7WD  plan-3  C13  0.020
 7WD  plan-3  C14  0.020
 7WD  plan-3  C16  0.020
 7WD  plan-3  C17  0.020
 7WD  plan-3  C19  0.020
 7WD  plan-3  N15  0.020
 7WD  plan-3  N18  0.020
 7WD  plan-3  N20  0.020
 7WD  plan-3  H8   0.020

