# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 12:15:44 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: 6-phenyl-N-(pyridin-4-yl)pyrrolo[2,1-f][1,2,4]triazin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N(c1ccncc1)c2ncnn3cc(cc23)c4ccccc4
#
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
 3D9  3D9  6-phenyl-N-(pyridin-4-yl)pyrrolo[2,1-f][1,2,4]triazin-4-amine  ligand  35  22  .  2022-07-22  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_3D9
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
 3D9  C4   C  CR6   0   0.099   3.6290  -0.3259   0.0297
 3D9  C5   C  CR16  0  -0.341   3.7487  -1.7135   0.1341
 3D9  C6   C  CR16  0  -0.232   4.9944  -2.3215   0.1712
 3D9  C7   C  CR5   0   0.069   2.3112   0.3133  -0.0076
 3D9  C8   C  CR15  0  -0.531   1.0595  -0.3338   0.0088
 3D9  C9   C  CR56  0   0.373   0.0922   0.6501  -0.0366
 3D9  C10  C  CR6   0   0.513  -1.3297   0.7126  -0.0469
 3D9  C12  C  CR16  0   0.074  -1.1735   2.9769  -0.1422
 3D9  C3   C  CR16  0  -0.342   4.8012   0.4321  -0.0361
 3D9  C1   C  CR16  0  -0.274   6.1512  -1.5564   0.1065
 3D9  C2   C  CR16  0  -0.231   6.0466  -0.1752   0.0020
 3D9  N11  N  N     0  -0.493  -1.9438   1.8679  -0.1010
 3D9  N13  N  N     0  -0.268   0.1175   3.0595  -0.1347
 3D9  N14  N  N     0  -0.367   0.7388   1.8689  -0.0808
 3D9  C15  C  CR15  0  -0.065   2.0698   1.6825  -0.0635
 3D9  N16  N  NH1   0  -0.776  -2.0050  -0.4589   0.0034
 3D9  C17  C  CR6   0   0.464  -3.3659  -0.7168   0.0000
 3D9  C18  C  CR16  0  -0.367  -4.3753   0.2422  -0.0846
 3D9  C19  C  CR16  0  -0.070  -5.6915  -0.1934  -0.0794
 3D9  N20  N  N     0  -0.417  -6.0720  -1.4619   0.0023
 3D9  C21  C  CR16  0  -0.060  -5.1009  -2.3674   0.0832
 3D9  C22  C  CR16  0  -0.435  -3.7562  -2.0565   0.0859
 3D9  H1   H  HCR6  0   0.252   2.8640  -2.3346   0.1886
 3D9  H2   H  HCR6  0   0.258   5.0598  -3.3989   0.2511
 3D9  H3   H  HCR5  0   0.268   0.8848  -1.3977   0.0464
 3D9  H4   H  HCR6  0   0.282  -1.6967   3.9235  -0.1866
 3D9  H5   H  HCR6  0   0.250   4.7485   1.5102  -0.1188
 3D9  H6   H  HCR6  0   0.257   7.1234  -2.0307   0.1371
 3D9  H7   H  HCR6  0   0.259   6.9385   0.4356  -0.0512
 3D9  H8   H  HCR5  0   0.300   2.7408   2.5247  -0.0892
 3D9  H9   H  HNH1  0   0.433  -1.4285  -1.2850   0.0597
 3D9  H10  H  HCR6  0   0.299  -4.1570   1.2941  -0.1524
 3D9  H11  H  HCR6  0   0.266  -6.4829   0.5450  -0.1467
 3D9  H12  H  HCR6  0   0.268  -5.4058  -3.4057   0.1510
 3D9  H13  H  HCR6  0   0.286  -3.0210  -2.8486   0.1538

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
 3D9  C6   C5   aromatic  1.387  0.020  1.387
 3D9  C6   C1   aromatic  1.388  0.020  1.388
 3D9  C21  C22  aromatic  1.380  0.020  1.380
 3D9  C21  N20  aromatic  1.330  0.020  1.330
 3D9  C5   C4   aromatic  1.397  0.020  1.397
 3D9  C22  C17  aromatic  1.398  0.020  1.398
 3D9  C1   C2   aromatic  1.389  0.020  1.389
 3D9  N20  C19  aromatic  1.327  0.020  1.327
 3D9  C4   C7   single    1.465  0.020  1.465
 3D9  C4   C3   aromatic  1.397  0.020  1.397
 3D9  C2   C3   aromatic  1.386  0.020  1.386
 3D9  C17  N16  single    1.385  0.020  1.385
 3D9  C17  C18  aromatic  1.395  0.020  1.395
 3D9  C8   C7   aromatic  1.409  0.020  1.409
 3D9  C8   C9   aromatic  1.381  0.020  1.381
 3D9  N16  C10  single    1.353  0.020  1.353
 3D9  C7   C15  aromatic  1.391  0.020  1.391
 3D9  C19  C18  aromatic  1.386  0.020  1.386
 3D9  C9   C10  aromatic  1.423  0.020  1.423
 3D9  C9   N14  aromatic  1.380  0.020  1.380
 3D9  C10  N11  aromatic  1.309  0.020  1.309
 3D9  C15  N14  aromatic  1.344  0.020  1.344
 3D9  N14  N13  aromatic  1.344  0.020  1.344
 3D9  N11  C12  aromatic  1.351  0.020  1.351
 3D9  N13  C12  aromatic  1.294  0.020  1.294
 3D9  C5   H1   single    0.930  0.020  1.080
 3D9  C6   H2   single    0.930  0.020  1.080
 3D9  C8   H3   single    0.930  0.020  1.080
 3D9  C12  H4   single    0.930  0.020  1.080
 3D9  C3   H5   single    0.930  0.020  1.080
 3D9  C1   H6   single    0.930  0.020  1.080
 3D9  C2   H7   single    0.930  0.020  1.080
 3D9  C15  H8   single    0.930  0.020  1.080
 3D9  N16  H9   single    0.860  0.020  1.020
 3D9  C18  H10  single    0.930  0.020  1.080
 3D9  C19  H11  single    0.930  0.020  1.080
 3D9  C21  H12  single    0.930  0.020  1.080
 3D9  C22  H13  single    0.930  0.020  1.080

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
 3D9  C3   C4   C7   121.11  3.000
 3D9  C3   C4   C5   118.07  3.000
 3D9  C7   C4   C5   120.82  3.000
 3D9  H1   C5   C6   118.77  3.000
 3D9  H1   C5   C4   120.26  3.000
 3D9  C6   C5   C4   120.97  3.000
 3D9  H2   C6   C1   120.11  3.000
 3D9  H2   C6   C5   119.52  3.000
 3D9  C1   C6   C5   120.37  3.000
 3D9  C15  C7   C8   107.35  3.000
 3D9  C15  C7   C4   125.90  3.000
 3D9  C8   C7   C4   126.75  3.000
 3D9  H3   C8   C9   126.20  3.000
 3D9  H3   C8   C7   126.66  3.000
 3D9  C9   C8   C7   107.14  3.000
 3D9  N14  C9   C10  115.40  3.000
 3D9  N14  C9   C8   107.59  3.000
 3D9  C10  C9   C8   137.01  3.000
 3D9  N16  C10  N11  122.09  3.000
 3D9  N11  C10  C9   120.50  3.000
 3D9  N16  C10  C9   117.41  3.000
 3D9  H4   C12  N13  115.26  3.000
 3D9  H4   C12  N11  116.33  3.000
 3D9  N13  C12  N11  128.41  3.000
 3D9  H5   C3   C2   118.83  3.000
 3D9  H5   C3   C4   120.19  3.000
 3D9  C2   C3   C4   120.98  3.000
 3D9  H6   C1   C2   120.37  3.000
 3D9  H6   C1   C6   120.37  3.000
 3D9  C2   C1   C6   119.26  3.000
 3D9  H7   C2   C1   120.19  3.000
 3D9  H7   C2   C3   119.46  3.000
 3D9  C1   C2   C3   120.36  3.000
 3D9  C12  N11  C10  117.26  3.000
 3D9  N14  N13  C12  113.89  3.000
 3D9  C15  N14  N13  125.53  3.000
 3D9  N13  N14  C9   124.53  3.000
 3D9  C15  N14  C9   109.94  3.000
 3D9  H8   C15  N14  120.54  3.000
 3D9  H8   C15  C7   131.47  3.000
 3D9  N14  C15  C7   107.99  3.000
 3D9  H9   N16  C17  114.15  3.000
 3D9  H9   N16  C10  115.20  3.000
 3D9  C17  N16  C10  130.65  3.000
 3D9  C22  C17  C18  117.42  3.000
 3D9  C18  C17  N16  125.67  3.000
 3D9  C22  C17  N16  116.91  3.000
 3D9  H10  C18  C19  119.99  3.000
 3D9  H10  C18  C17  121.93  3.000
 3D9  C19  C18  C17  118.08  3.000
 3D9  H11  C19  N20  116.45  3.000
 3D9  H11  C19  C18  118.60  3.000
 3D9  N20  C19  C18  124.95  3.000
 3D9  C21  N20  C19  116.44  3.000
 3D9  H12  C21  C22  119.31  3.000
 3D9  H12  C21  N20  116.77  3.000
 3D9  C22  C21  N20  123.92  3.000
 3D9  H13  C22  C21  119.79  3.000
 3D9  H13  C22  C17  121.02  3.000
 3D9  C21  C22  C17  119.19  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
 3D9  CONST_01  C1   C6   C5   C4      0.00   0.0  0
 3D9  CONST_02  C9   C8   C7   C4    180.00   0.0  0
 3D9  CONST_03  N14  C15  C7   C4    180.00   0.0  0
 3D9  CONST_04  C1   C2   C3   C4      0.00   0.0  0
 3D9  CONST_05  C2   C1   C6   C5      0.00   0.0  0
 3D9  CONST_06  C8   C7   C4   C5      0.00   0.0  0
 3D9  CONST_07  C15  C7   C4   C5    180.00   0.0  0
 3D9  CONST_08  C2   C3   C4   C5      0.00   0.0  0
 3D9  CONST_09  C7   C4   C5   C6    180.00   0.0  0
 3D9  CONST_10  C3   C4   C5   C6      0.00   0.0  0
 3D9  CONST_11  C3   C2   C1   C6      0.00   0.0  0
 3D9  CONST_12  C2   C3   C4   C7    180.00   0.0  0
 3D9  CONST_13  C10  C9   C8   C7    180.00   0.0  0
 3D9  CONST_14  N14  C9   C8   C7      0.00   0.0  0
 3D9  CONST_15  C9   N14  C15  C7      0.00   0.0  0
 3D9  CONST_16  N13  N14  C15  C7    180.00   0.0  0
 3D9  CONST_17  C3   C4   C7   C8    180.00   0.0  0
 3D9  CONST_18  N14  C15  C7   C8      0.00   0.0  0
 3D9  CONST_19  N11  C10  C9   C8    180.00   0.0  0
 3D9  CONST_20  C15  N14  C9   C8      0.00   0.0  0
 3D9  CONST_21  N13  N14  C9   C8    180.00   0.0  0
 3D9  CONST_22  C15  C7   C8   C9      0.00   0.0  0
 3D9  CONST_23  C12  N11  C10  C9      0.00   0.0  0
 3D9  CONST_24  C12  N13  N14  C9      0.00   0.0  0
 3D9  CONST_25  C15  N14  C9   C10   180.00   0.0  0
 3D9  CONST_26  N13  N14  C9   C10     0.00   0.0  0
 3D9  CONST_27  N13  C12  N11  C10     0.00   0.0  0
 3D9  CONST_28  C15  N14  N13  C12   180.00   0.0  0
 3D9  CONST_29  C15  C7   C4   C3      0.00   0.0  0
 3D9  CONST_30  N14  C9   C10  N11     0.00   0.0  0
 3D9  CONST_31  N14  N13  C12  N11     0.00   0.0  0
 3D9  CONST_32  N20  C21  C22  C17     0.00   0.0  0
 3D9  CONST_33  N20  C19  C18  C17     0.00   0.0  0
 3D9  CONST_34  C21  C22  C17  C18     0.00   0.0  0
 3D9  CONST_35  C21  N20  C19  C18     0.00   0.0  0
 3D9  CONST_36  C22  C21  N20  C19     0.00   0.0  0
 3D9  CONST_37  C22  C17  C18  C19     0.00   0.0  0
 3D9  CONST_38  N16  C10  C9   C8      0.00   0.0  0
 3D9  CONST_39  N16  C10  N11  C12   180.00   0.0  0
 3D9  CONST_40  N16  C10  C9   N14   180.00   0.0  0
 3D9  CONST_41  C21  C22  C17  N16   180.00   0.0  0
 3D9  CONST_42  C19  C18  C17  N16   180.00   0.0  0
 3D9  CONST_43  H2   C6   C5   C4    180.00   0.0  0
 3D9  CONST_44  H3   C8   C7   C4      0.00   0.0  0
 3D9  CONST_45  H8   C15  C7   C4      0.00   0.0  0
 3D9  CONST_46  H7   C2   C3   C4    180.00   0.0  0
 3D9  CONST_47  H6   C1   C6   C5    180.00   0.0  0
 3D9  CONST_48  H5   C3   C4   C5    180.00   0.0  0
 3D9  CONST_49  H1   C5   C4   C7      0.00   0.0  0
 3D9  CONST_50  H4   C12  N11  C10   180.00   0.0  0
 3D9  CONST_51  H12  C21  C22  C17   180.00   0.0  0
 3D9  CONST_52  H11  C19  C18  C17   180.00   0.0  0
 3D9  CONST_53  H13  C22  C17  C18   180.00   0.0  0
 3D9  CONST_54  H10  C18  C19  N20   180.00   0.0  0
 3D9  Var_01    C17  N16  C10  C9   -179.56  30.0  1
 3D9  Var_02    C22  C17  N16  C10  -178.91  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
 3D9  plan-1  C4   0.020
 3D9  plan-1  C5   0.020
 3D9  plan-1  C6   0.020
 3D9  plan-1  C7   0.020
 3D9  plan-1  C3   0.020
 3D9  plan-1  C1   0.020
 3D9  plan-1  C2   0.020
 3D9  plan-1  H1   0.020
 3D9  plan-1  H2   0.020
 3D9  plan-1  H5   0.020
 3D9  plan-1  H6   0.020
 3D9  plan-1  H7   0.020
 3D9  plan-2  N16  0.020
 3D9  plan-2  C17  0.020
 3D9  plan-2  C18  0.020
 3D9  plan-2  C19  0.020
 3D9  plan-2  N20  0.020
 3D9  plan-2  C21  0.020
 3D9  plan-2  C22  0.020
 3D9  plan-2  H10  0.020
 3D9  plan-2  H11  0.020
 3D9  plan-2  H12  0.020
 3D9  plan-2  H13  0.020
 3D9  plan-3  C4   0.020
 3D9  plan-3  C7   0.020
 3D9  plan-3  C8   0.020
 3D9  plan-3  C9   0.020
 3D9  plan-3  C10  0.020
 3D9  plan-3  C12  0.020
 3D9  plan-3  N11  0.020
 3D9  plan-3  N13  0.020
 3D9  plan-3  N14  0.020
 3D9  plan-3  C15  0.020
 3D9  plan-3  N16  0.020
 3D9  plan-3  H3   0.020
 3D9  plan-3  H4   0.020
 3D9  plan-3  H8   0.020

