# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 16:03:03 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: 2-methoxy-6,7-dimethyl-9-(4-methylpyridin-3-yl)imidazo[1,5-a]pyrido[3,2-e]pyrazine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2nc(C)c3n(c2n1)c(nc3C)c4cnccc4C
#
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
 546  546  2-methoxy-6,7-dimethyl-9-(4-methylpyridin-3-yl)imidazo[1,5-a]pyrido[3,2-e]pyrazine  ligand  41  24  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_546
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
 546  C1    C  CH3   0  -0.716   1.5150   2.2647   1.9509
 546  N1    N  N     0  -0.408   3.2391   1.0132  -1.7863
 546  O1    O  O2    0  -0.460   2.0839  -3.0394   0.5220
 546  C2    C  CR6   0   0.199   2.1113   1.8270   0.6513
 546  N2    N  N     0  -0.426  -0.8735   2.5290  -0.4409
 546  C3    C  CR16  0  -0.346   3.4864   1.8190   0.4482
 546  N3    N  N     0  -0.587  -0.9586   0.3593  -0.1549
 546  C4    C  CR16  0  -0.041   3.9979   1.4105  -0.7718
 546  N4    N  N     0  -0.483   0.5792  -1.3600   0.1807
 546  C5    C  CR16  0  -0.043   1.9283   1.0180  -1.5984
 546  N5    N  N     0  -0.435  -3.0870  -1.4041   0.1201
 546  C6    C  CR6   0  -0.061   1.3150   1.4086  -0.4149
 546  C7    C  CR5   0   0.373  -0.1535   1.4357  -0.3271
 546  C8    C  CR5   0   0.084  -2.1785   2.1807  -0.3534
 546  C9    C  CR56  0   0.314  -2.2726   0.8138  -0.1766
 546  C10   C  CR66  0   0.517  -0.6807  -0.9793   0.0768
 546  C11   C  CR66  0   0.101  -1.7813  -1.8273   0.1957
 546  C12   C  CR16  0  -0.168  -1.4859  -3.1810   0.4180
 546  C13   C  CR16  0  -0.366  -0.1856  -3.5999   0.5195
 546  C14   C  CR6   0   0.528   0.8261  -2.6303   0.3999
 546  C15   C  CH3   0  -0.403   3.1111  -2.0617   0.4332
 546  C16   C  CR6   0   0.161  -3.3284  -0.1465  -0.0436
 546  C17   C  CH3   0  -0.745  -4.7525   0.3031  -0.0919
 546  C18   C  CH3   0  -0.743  -3.2477   3.2104  -0.4780
 546  H1    H  HCH3  0   0.255   1.0013   3.2205   1.8405
 546  H1A   H  HCH3  0   0.244   0.7786   1.5475   2.3149
 546  H1B   H  HCH3  0   0.243   2.2784   2.3835   2.7169
 546  H3    H  HCR6  0   0.240   4.1613   2.1276   1.2355
 546  H4    H  HCR6  0   0.247   5.0695   1.4035  -0.9349
 546  H5    H  HCR6  0   0.241   1.3193   0.6908  -2.4348
 546  H12   H  HCR6  0   0.260  -2.3024  -3.8839   0.5117
 546  H13   H  HCR6  0   0.258   0.0638  -4.6358   0.6974
 546  H15   H  HCH3  0   0.234   3.1247  -1.5793  -0.5442
 546  H15A  H  HCH3  0   0.228   3.0010  -1.2903   1.1959
 546  H15B  H  HCH3  0   0.232   4.0445  -2.5964   0.5870
 546  H17   H  HCH3  0   0.261  -5.4109  -0.5603  -0.0457
 546  H17A  H  HCH3  0   0.241  -4.9850   0.9553   0.7516
 546  H17B  H  HCH3  0   0.244  -4.9691   0.8604  -1.0040
 546  H18   H  HCH3  0   0.240  -3.5314   3.3678  -1.5207
 546  H18A  H  HCH3  0   0.235  -4.1487   2.9434   0.0692
 546  H18B  H  HCH3  0   0.251  -2.8895   4.1638  -0.0931

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
 546  C1   C2    single    1.495  0.020  1.495
 546  C1   H1    single    0.970  0.020  1.090
 546  C1   H1A   single    0.970  0.020  1.090
 546  C1   H1B   single    0.970  0.020  1.090
 546  C4   N1    aromatic  1.328  0.020  1.328
 546  N1   C5    aromatic  1.324  0.020  1.324
 546  C15  O1    single    1.421  0.020  1.421
 546  O1   C14   single    1.328  0.020  1.328
 546  C2   C3    aromatic  1.390  0.020  1.390
 546  C2   C6    aromatic  1.395  0.020  1.395
 546  C7   N2    aromatic  1.314  0.020  1.314
 546  N2   C8    aromatic  1.353  0.020  1.353
 546  C3   C4    aromatic  1.384  0.020  1.384
 546  C3   H3    single    0.930  0.020  1.080
 546  C10  N3    aromatic  1.387  0.020  1.387
 546  N3   C7    aromatic  1.355  0.020  1.355
 546  N3   C9    aromatic  1.391  0.020  1.391
 546  C4   H4    single    0.930  0.020  1.080
 546  C14  N4    aromatic  1.312  0.020  1.312
 546  N4   C10   aromatic  1.320  0.020  1.320
 546  C5   C6    aromatic  1.389  0.020  1.389
 546  C5   H5    single    0.930  0.020  1.080
 546  C11  N5    aromatic  1.375  0.020  1.375
 546  N5   C16   aromatic  1.291  0.020  1.291
 546  C6   C7    single    1.471  0.020  1.471
 546  C9   C8    aromatic  1.382  0.020  1.382
 546  C8   C18   single    1.490  0.020  1.490
 546  C9   C16   aromatic  1.433  0.020  1.433
 546  C10  C11   aromatic  1.394  0.020  1.394
 546  C12  C11   aromatic  1.403  0.020  1.403
 546  C13  C12   aromatic  1.370  0.020  1.370
 546  C12  H12   single    0.930  0.020  1.080
 546  C14  C13   aromatic  1.406  0.020  1.406
 546  C13  H13   single    0.930  0.020  1.080
 546  C15  H15   single    0.970  0.020  1.090
 546  C15  H15A  single    0.970  0.020  1.090
 546  C15  H15B  single    0.970  0.020  1.090
 546  C16  C17   single    1.494  0.020  1.494
 546  C17  H17   single    0.970  0.020  1.090
 546  C17  H17A  single    0.970  0.020  1.090
 546  C17  H17B  single    0.970  0.020  1.090
 546  C18  H18   single    0.970  0.020  1.090
 546  C18  H18A  single    0.970  0.020  1.090
 546  C18  H18B  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
 546  H1B   C1   H1A   108.10  3.000
 546  H1B   C1   H1    107.83  3.000
 546  H1A   C1   H1    106.99  3.000
 546  H1B   C1   C2    111.35  3.000
 546  H1A   C1   C2    111.52  3.000
 546  H1    C1   C2    110.87  3.000
 546  C5    N1   C4    117.15  3.000
 546  C15   O1   C14   117.83  3.000
 546  C6    C2   C3    116.83  3.000
 546  C6    C2   C1    121.63  3.000
 546  C3    C2   C1    121.54  3.000
 546  C8    N2   C7    107.98  3.000
 546  H3    C3   C4    119.67  3.000
 546  H3    C3   C2    120.60  3.000
 546  C4    C3   C2    119.73  3.000
 546  C10   N3   C9    120.50  3.000
 546  C9    N3   C7    107.45  3.000
 546  C10   N3   C7    131.98  3.000
 546  H4    C4   C3    119.98  3.000
 546  H4    C4   N1    116.62  3.000
 546  C3    C4   N1    123.40  3.000
 546  C14   N4   C10   118.15  3.000
 546  H5    C5   C6    119.59  3.000
 546  H5    C5   N1    116.43  3.000
 546  C6    C5   N1    123.98  3.000
 546  C16   N5   C11   118.97  3.000
 546  C7    C6   C5    119.78  3.000
 546  C7    C6   C2    121.24  3.000
 546  C5    C6   C2    118.92  3.000
 546  C6    C7   N3    125.87  3.000
 546  C6    C7   N2    123.85  3.000
 546  N3    C7   N2    110.26  3.000
 546  C18   C8   C9    130.22  3.000
 546  C18   C8   N2    120.59  3.000
 546  C9    C8   N2    109.18  3.000
 546  C16   C9   C8    136.46  3.000
 546  C16   C9   N3    118.40  3.000
 546  C8    C9   N3    105.13  3.000
 546  C11   C10  N4    124.83  3.000
 546  C11   C10  N3    116.30  3.000
 546  N4    C10  N3    118.86  3.000
 546  C12   C11  C10   115.72  3.000
 546  C12   C11  N5    120.37  3.000
 546  C10   C11  N5    123.90  3.000
 546  H12   C12  C13   120.76  3.000
 546  H12   C12  C11   118.80  3.000
 546  C13   C12  C11   120.43  3.000
 546  H13   C13  C14   120.60  3.000
 546  H13   C13  C12   121.64  3.000
 546  C14   C13  C12   117.76  3.000
 546  C13   C14  N4    123.10  3.000
 546  C13   C14  O1    117.45  3.000
 546  N4    C14  O1    119.45  3.000
 546  H15B  C15  H15A  109.63  3.000
 546  H15B  C15  H15   109.51  3.000
 546  H15A  C15  H15   108.39  3.000
 546  H15B  C15  O1    105.87  3.000
 546  H15A  C15  O1    111.72  3.000
 546  H15   C15  O1    111.69  3.000
 546  C17   C16  C9    119.83  3.000
 546  C17   C16  N5    118.39  3.000
 546  C9    C16  N5    121.78  3.000
 546  H17B  C17  H17A  107.38  3.000
 546  H17B  C17  H17   108.74  3.000
 546  H17A  C17  H17   108.23  3.000
 546  H17B  C17  C16   111.72  3.000
 546  H17A  C17  C16   110.97  3.000
 546  H17   C17  C16   109.69  3.000
 546  H18B  C18  H18A  108.05  3.000
 546  H18B  C18  H18   107.26  3.000
 546  H18A  C18  H18   107.50  3.000
 546  H18B  C18  C8    109.84  3.000
 546  H18A  C18  C8    112.52  3.000
 546  H18   C18  C8    111.47  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
 546  CONST_01  C2   C3   C4   N1     0.00   0.0  0
 546  CONST_02  C2   C6   C5   N1     0.00   0.0  0
 546  CONST_03  C7   C6   C5   N1   180.00   0.0  0
 546  CONST_06  C10  N3   C7   N2   180.00   0.0  0
 546  CONST_07  C9   N3   C7   N2     0.00   0.0  0
 546  CONST_09  N3   C9   C8   N2     0.00   0.0  0
 546  CONST_10  C16  C9   C8   N2   180.00   0.0  0
 546  CONST_11  C5   C6   C2   C3     0.00   0.0  0
 546  CONST_12  C7   C6   C2   C3   180.00   0.0  0
 546  CONST_13  C5   N1   C4   C3     0.00   0.0  0
 546  CONST_14  C14  N4   C10  N3   180.00   0.0  0
 546  CONST_15  N5   C11  C10  N3     0.00   0.0  0
 546  CONST_16  C12  C11  C10  N3   180.00   0.0  0
 546  CONST_17  C8   N2   C7   N3     0.00   0.0  0
 546  CONST_19  N5   C16  C9   N3     0.00   0.0  0
 546  CONST_20  C6   C5   N1   C4     0.00   0.0  0
 546  CONST_21  C6   C2   C3   C4     0.00   0.0  0
 546  CONST_22  C12  C13  C14  N4     0.00   0.0  0
 546  CONST_23  C7   N3   C10  N4     0.00   0.0  0
 546  CONST_24  C9   N3   C10  N4   180.00   0.0  0
 546  CONST_25  N5   C11  C10  N4   180.00   0.0  0
 546  CONST_26  C12  C11  C10  N4     0.00   0.0  0
 546  CONST_27  C13  C12  C11  N5   180.00   0.0  0
 546  CONST_28  C8   C9   C16  N5   180.00   0.0  0
 546  CONST_29  C8   N2   C7   C6   180.00   0.0  0
 546  CONST_30  C10  N3   C7   C6     0.00   0.0  0
 546  CONST_31  C9   N3   C7   C6   180.00   0.0  0
 546  CONST_32  C9   C8   N2   C7     0.00   0.0  0
 546  CONST_33  C11  C10  N3   C7   180.00   0.0  0
 546  CONST_34  C8   C9   N3   C7     0.00   0.0  0
 546  CONST_35  C16  C9   N3   C7   180.00   0.0  0
 546  CONST_36  C10  N3   C9   C8   180.00   0.0  0
 546  CONST_37  C11  C10  N3   C9     0.00   0.0  0
 546  CONST_38  C11  N5   C16  C9     0.00   0.0  0
 546  CONST_39  C16  C9   N3   C10    0.00   0.0  0
 546  CONST_40  C13  C14  N4   C10    0.00   0.0  0
 546  CONST_41  C16  N5   C11  C10    0.00   0.0  0
 546  CONST_42  C13  C12  C11  C10    0.00   0.0  0
 546  CONST_43  C14  N4   C10  C11    0.00   0.0  0
 546  CONST_44  C14  C13  C12  C11    0.00   0.0  0
 546  CONST_45  C16  N5   C11  C12  180.00   0.0  0
 546  CONST_46  C4   C3   C2   C1   180.00   0.0  0
 546  CONST_47  C5   C6   C2   C1   180.00   0.0  0
 546  CONST_48  C7   C6   C2   C1     0.00   0.0  0
 546  CONST_49  C10  N4   C14  O1   180.00   0.0  0
 546  CONST_50  C12  C13  C14  O1   180.00   0.0  0
 546  CONST_51  C18  C8   C9   N3   180.00   0.0  0
 546  CONST_52  C17  C16  C9   N3   180.00   0.0  0
 546  CONST_53  C18  C8   N2   C7   180.00   0.0  0
 546  CONST_54  C17  C16  C9   C8     0.00   0.0  0
 546  CONST_55  C17  C16  N5   C11  180.00   0.0  0
 546  CONST_56  C18  C8   C9   C16    0.00   0.0  0
 546  CONST_57  H3   C3   C4   N1   180.00   0.0  0
 546  CONST_58  H4   C4   C3   C2   180.00   0.0  0
 546  CONST_59  H5   C5   C6   C2   180.00   0.0  0
 546  CONST_60  H13  C13  C14  N4   180.00   0.0  0
 546  CONST_61  H12  C12  C11  N5     0.00   0.0  0
 546  Var_01    H18  C18  C8   N2    87.52  30.0  2
 546  Var_02    H1   C1   C2   C3   109.80  30.0  2
 546  Var_03    H17  C17  C16  N5    -4.03  30.0  2
 546  Var_04    H15  C15  O1   C14  -62.50  30.0  3

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
 546  plan-1  C1   0.020
 546  plan-1  N1   0.020
 546  plan-1  C2   0.020
 546  plan-1  C3   0.020
 546  plan-1  C4   0.020
 546  plan-1  C5   0.020
 546  plan-1  C6   0.020
 546  plan-1  C7   0.020
 546  plan-1  H3   0.020
 546  plan-1  H4   0.020
 546  plan-1  H5   0.020
 546  plan-2  O1   0.020
 546  plan-2  N2   0.020
 546  plan-2  N3   0.020
 546  plan-2  N4   0.020
 546  plan-2  N5   0.020
 546  plan-2  C6   0.020
 546  plan-2  C7   0.020
 546  plan-2  C8   0.020
 546  plan-2  C9   0.020
 546  plan-2  C10  0.020
 546  plan-2  C11  0.020
 546  plan-2  C12  0.020
 546  plan-2  C13  0.020
 546  plan-2  C14  0.020
 546  plan-2  C16  0.020
 546  plan-2  C17  0.020
 546  plan-2  C18  0.020
 546  plan-2  H12  0.020
 546  plan-2  H13  0.020

