# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 20:20:56 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: 3-[4-(4-methylpiperazin-1-yl)phenyl]-9H-pyrrolo[2,3-b:5,4-c']dipyridine-6-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCN(CC1)c2ccc(cc2)c3cnc4[nH]c5cnc(cc5c4c3)C#N
#
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
 3DX  3DX  3-[4-(4-methylpiperazin-1-yl)phenyl]-9H-pyrrolo[2,3-b:5,4-c']dipyridine-6-carbonitrile  ligand  48  28  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3DX
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
 3DX  N6   N  NS    0  -0.248  -7.0151  -3.9870  -0.3891
 3DX  C22  C  CSP   0   0.049  -6.6020  -2.9147  -0.3095
 3DX  C9   C  CR6   0   0.173  -6.0814  -1.5825  -0.2096
 3DX  N3   N  N     0  -0.411  -6.9986  -0.6053  -0.1674
 3DX  C10  C  CR16  0  -0.097  -6.5974   0.6435  -0.0770
 3DX  C7   C  CR56  0   0.287  -5.2381   0.9542  -0.0258
 3DX  N2   N  NR15  0  -0.756  -4.6095   2.1576   0.0657
 3DX  C2   C  CR56  0   0.472  -3.2563   1.9521   0.0837
 3DX  C8   C  CR16  0  -0.386  -4.7095  -1.3862  -0.1648
 3DX  C6   C  CR56  0   0.141  -4.2737  -0.0739  -0.0694
 3DX  C1   C  CR56  0   0.026  -2.9944   0.5706   0.0031
 3DX  C5   C  CR16  0  -0.291  -1.6712   0.1584  -0.0040
 3DX  C4   C  CR6   0  -0.006  -0.6810   1.1325   0.0776
 3DX  C3   C  CR16  0  -0.108  -1.0862   2.4772   0.1656
 3DX  N1   N  N     0  -0.420  -2.3411   2.8991   0.1658
 3DX  C11  C  CR6   0   0.054   0.7487   0.7830   0.0801
 3DX  C16  C  CR16  0  -0.300   1.2159  -0.3568   0.7289
 3DX  C15  C  CR16  0  -0.349   2.5599  -0.6937   0.7377
 3DX  C14  C  CR6   0   0.369   3.5116   0.0959   0.0768
 3DX  C13  C  CR16  0  -0.322   3.0375   1.2459  -0.5772
 3DX  C12  C  CR16  0  -0.298   1.6969   1.5757  -0.5713
 3DX  N4   N  NT    0  -0.518   4.8557  -0.2439   0.0266
 3DX  C20  C  CH2   0  -0.313   5.2853  -1.4906   0.6277
 3DX  C19  C  CH2   0  -0.278   6.6542  -1.8891   0.1064
 3DX  N5   N  NT    0  -0.413   7.6269  -0.8408   0.3230
 3DX  C21  C  CH3   0  -0.519   8.9491  -1.2419  -0.0982
 3DX  C18  C  CH2   0  -0.283   7.1939   0.3721  -0.3371
 3DX  C17  C  CH2   0  -0.307   5.8435   0.8127   0.1891
 3DX  H1   H  HCR6  0   0.292  -7.3568   1.4159  -0.0445
 3DX  H2   H  HNR5  0   0.423  -5.0579   3.0595   0.1127
 3DX  H3   H  HCR6  0   0.291  -4.0238  -2.2218  -0.2027
 3DX  H4   H  HCR6  0   0.268  -1.4151  -0.8908  -0.0886
 3DX  H5   H  HCR6  0   0.266  -0.3321   3.2510   0.2571
 3DX  H6   H  HCR6  0   0.252   0.5253  -0.9894   1.2738
 3DX  H7   H  HCR6  0   0.269   2.8555  -1.5763   1.2868
 3DX  H8   H  HCR6  0   0.263   3.7152   1.8803  -1.1322
 3DX  H9   H  HCR6  0   0.251   1.3840   2.4580  -1.1166
 3DX  H10  H  HCH2  0   0.216   5.3122  -1.4231   1.7255
 3DX  H11  H  HCH2  0   0.253   4.5874  -2.2856   0.3643
 3DX  H12  H  HCH2  0   0.242   6.9746  -2.7927   0.6303
 3DX  H13  H  HCH2  0   0.194   6.5677  -2.1488  -0.9632
 3DX  H15  H  HCH3  0   0.193   9.0113  -1.4793  -1.1717
 3DX  H16  H  HCH3  0   0.234   9.6650  -0.4448   0.1084
 3DX  H17  H  HCH3  0   0.234   9.2652  -2.1268   0.4564
 3DX  H18  H  HCH2  0   0.241   7.9204   1.1659  -0.1477
 3DX  H19  H  HCH2  0   0.194   7.1302   0.2432  -1.4316
 3DX  H20  H  HCH2  0   0.256   5.5383   1.7048  -0.3523
 3DX  H21  H  HCH2  0   0.220   5.9372   1.0905   1.2486

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
 3DX  N6   C22  triple    1.152  0.020  1.152
 3DX  C22  C9   single    1.434  0.020  1.434
 3DX  C9   C8   aromatic  1.387  0.020  1.387
 3DX  C9   N3   aromatic  1.341  0.020  1.341
 3DX  C8   C6   aromatic  1.386  0.020  1.386
 3DX  N3   C10  aromatic  1.315  0.020  1.315
 3DX  C15  C16  aromatic  1.386  0.020  1.386
 3DX  C15  C14  aromatic  1.402  0.020  1.402
 3DX  C20  C19  single    1.518  0.020  1.518
 3DX  C20  N4   single    1.449  0.020  1.449
 3DX  C16  C11  aromatic  1.392  0.020  1.392
 3DX  C6   C7   aromatic  1.410  0.020  1.410
 3DX  C6   C1   aromatic  1.434  0.020  1.434
 3DX  C10  C7   aromatic  1.395  0.020  1.395
 3DX  C5   C1   aromatic  1.386  0.020  1.386
 3DX  C5   C4   aromatic  1.391  0.020  1.391
 3DX  C19  N5   single    1.446  0.020  1.446
 3DX  C7   N2   aromatic  1.361  0.020  1.361
 3DX  C1   C2   aromatic  1.408  0.020  1.408
 3DX  N4   C14  single    1.387  0.020  1.387
 3DX  N4   C17  single    1.456  0.020  1.456
 3DX  C14  C13  aromatic  1.405  0.020  1.405
 3DX  N5   C21  single    1.444  0.020  1.444
 3DX  N5   C18  single    1.447  0.020  1.447
 3DX  C11  C4   single    1.472  0.020  1.472
 3DX  C11  C12  aromatic  1.397  0.020  1.397
 3DX  C4   C3   aromatic  1.407  0.020  1.407
 3DX  C17  C18  single    1.515  0.020  1.515
 3DX  N2   C2   aromatic  1.369  0.020  1.369
 3DX  C2   N1   aromatic  1.320  0.020  1.320
 3DX  C3   N1   aromatic  1.324  0.020  1.324
 3DX  C13  C12  aromatic  1.381  0.020  1.381
 3DX  C10  H1   single    0.930  0.020  1.080
 3DX  N2   H2   single    0.860  0.020  1.020
 3DX  C8   H3   single    0.930  0.020  1.080
 3DX  C5   H4   single    0.930  0.020  1.080
 3DX  C3   H5   single    0.930  0.020  1.080
 3DX  C16  H6   single    0.930  0.020  1.080
 3DX  C15  H7   single    0.930  0.020  1.080
 3DX  C13  H8   single    0.930  0.020  1.080
 3DX  C12  H9   single    0.930  0.020  1.080
 3DX  C20  H10  single    0.970  0.020  1.090
 3DX  C20  H11  single    0.970  0.020  1.090
 3DX  C19  H12  single    0.970  0.020  1.090
 3DX  C19  H13  single    0.970  0.020  1.090
 3DX  C21  H15  single    0.970  0.020  1.090
 3DX  C21  H16  single    0.970  0.020  1.090
 3DX  C21  H17  single    0.970  0.020  1.090
 3DX  C18  H18  single    0.970  0.020  1.090
 3DX  C18  H19  single    0.970  0.020  1.090
 3DX  C17  H20  single    0.970  0.020  1.090
 3DX  C17  H21  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
 3DX  C9   C22  N6   180.00  3.000
 3DX  C8   C9   N3   124.93  3.000
 3DX  N3   C9   C22  115.53  3.000
 3DX  C8   C9   C22  119.54  3.000
 3DX  C10  N3   C9   119.06  3.000
 3DX  H1   C10  C7   121.52  3.000
 3DX  H1   C10  N3   117.73  3.000
 3DX  C7   C10  N3   120.75  3.000
 3DX  C6   C7   N2   109.32  3.000
 3DX  N2   C7   C10  130.50  3.000
 3DX  C6   C7   C10  120.18  3.000
 3DX  H2   N2   C2   124.98  3.000
 3DX  H2   N2   C7   126.06  3.000
 3DX  C2   N2   C7   108.96  3.000
 3DX  N1   C2   C1   125.35  3.000
 3DX  N1   C2   N2   125.36  3.000
 3DX  C1   C2   N2   109.29  3.000
 3DX  H3   C8   C6   122.31  3.000
 3DX  H3   C8   C9   121.12  3.000
 3DX  C6   C8   C9   116.57  3.000
 3DX  C1   C6   C8   135.18  3.000
 3DX  C1   C6   C7   106.31  3.000
 3DX  C8   C6   C7   118.51  3.000
 3DX  C5   C1   C6   135.87  3.000
 3DX  C5   C1   C2   118.00  3.000
 3DX  C6   C1   C2   106.13  3.000
 3DX  H4   C5   C4   120.95  3.000
 3DX  H4   C5   C1   120.94  3.000
 3DX  C4   C5   C1   118.10  3.000
 3DX  C11  C4   C3   120.43  3.000
 3DX  C3   C4   C5   117.88  3.000
 3DX  C11  C4   C5   121.68  3.000
 3DX  H5   C3   N1   115.58  3.000
 3DX  H5   C3   C4   119.14  3.000
 3DX  N1   C3   C4   125.28  3.000
 3DX  C3   N1   C2   115.39  3.000
 3DX  C12  C11  C16  117.01  3.000
 3DX  C12  C11  C4   121.59  3.000
 3DX  C16  C11  C4   121.41  3.000
 3DX  H6   C16  C15  118.23  3.000
 3DX  H6   C16  C11  119.90  3.000
 3DX  C15  C16  C11  121.84  3.000
 3DX  H7   C15  C14  120.92  3.000
 3DX  H7   C15  C16  117.85  3.000
 3DX  C14  C15  C16  121.22  3.000
 3DX  N4   C14  C13  120.70  3.000
 3DX  C13  C14  C15  116.82  3.000
 3DX  N4   C14  C15  122.46  3.000
 3DX  H8   C13  C12  118.07  3.000
 3DX  H8   C13  C14  120.49  3.000
 3DX  C12  C13  C14  121.41  3.000
 3DX  H9   C12  C13  118.22  3.000
 3DX  H9   C12  C11  120.06  3.000
 3DX  C13  C12  C11  121.70  3.000
 3DX  C17  N4   C20  112.14  3.000
 3DX  C17  N4   C14  118.40  3.000
 3DX  C20  N4   C14  118.88  3.000
 3DX  H11  C20  H10  107.54  3.000
 3DX  H11  C20  C19  107.63  3.000
 3DX  H10  C20  C19  109.68  3.000
 3DX  H11  C20  N4   109.71  3.000
 3DX  H10  C20  N4   111.61  3.000
 3DX  C19  C20  N4   110.53  3.000
 3DX  H13  C19  H12  107.04  3.000
 3DX  H13  C19  N5   111.60  3.000
 3DX  H12  C19  N5   109.29  3.000
 3DX  H13  C19  C20  108.90  3.000
 3DX  H12  C19  C20  108.48  3.000
 3DX  N5   C19  C20  111.39  3.000
 3DX  C18  N5   C21  111.94  3.000
 3DX  C18  N5   C19  109.75  3.000
 3DX  C21  N5   C19  111.75  3.000
 3DX  H17  C21  H16  107.83  3.000
 3DX  H17  C21  H15  107.72  3.000
 3DX  H16  C21  H15  107.76  3.000
 3DX  H17  C21  N5   110.01  3.000
 3DX  H16  C21  N5   110.02  3.000
 3DX  H15  C21  N5   113.32  3.000
 3DX  H19  C18  H18  107.16  3.000
 3DX  H19  C18  C17  109.08  3.000
 3DX  H18  C18  C17  108.74  3.000
 3DX  H19  C18  N5   111.81  3.000
 3DX  H18  C18  N5   109.32  3.000
 3DX  C17  C18  N5   110.61  3.000
 3DX  H21  C17  H20  107.24  3.000
 3DX  H21  C17  C18  109.41  3.000
 3DX  H20  C17  C18  108.42  3.000
 3DX  H21  C17  N4   110.42  3.000
 3DX  H20  C17  N4   110.46  3.000
 3DX  C18  C17  N4   110.80  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
 3DX  CONST_01  C7   C6   C8   C9      0.00   0.0  0
 3DX  CONST_02  C1   C6   C8   C9    180.00   0.0  0
 3DX  CONST_03  C7   C10  N3   C9      0.00   0.0  0
 3DX  CONST_04  C6   C8   C9   N3      0.00   0.0  0
 3DX  CONST_05  C6   C7   C10  N3      0.00   0.0  0
 3DX  CONST_06  N2   C7   C10  N3    180.00   0.0  0
 3DX  CONST_07  C8   C9   N3   C10     0.00   0.0  0
 3DX  CONST_08  C8   C6   C7   C10     0.00   0.0  0
 3DX  CONST_09  C1   C6   C7   C10   180.00   0.0  0
 3DX  CONST_10  C2   N2   C7   C10   180.00   0.0  0
 3DX  CONST_11  C5   C1   C6   C7    180.00   0.0  0
 3DX  CONST_12  C2   C1   C6   C7      0.00   0.0  0
 3DX  CONST_13  C1   C2   N2   C7      0.00   0.0  0
 3DX  CONST_14  N1   C2   N2   C7    180.00   0.0  0
 3DX  CONST_15  C8   C6   C7   N2    180.00   0.0  0
 3DX  CONST_16  C1   C6   C7   N2      0.00   0.0  0
 3DX  CONST_17  C6   C1   C2   N2      0.00   0.0  0
 3DX  CONST_18  C5   C1   C2   N2    180.00   0.0  0
 3DX  CONST_19  C3   N1   C2   N2    180.00   0.0  0
 3DX  CONST_20  C8   C6   C1   C2    180.00   0.0  0
 3DX  CONST_21  C4   C5   C1   C2      0.00   0.0  0
 3DX  CONST_22  C6   C7   N2   C2      0.00   0.0  0
 3DX  CONST_23  C4   C3   N1   C2      0.00   0.0  0
 3DX  CONST_24  C5   C1   C6   C8      0.00   0.0  0
 3DX  CONST_25  C4   C5   C1   C6    180.00   0.0  0
 3DX  CONST_26  N1   C2   C1   C6    180.00   0.0  0
 3DX  CONST_27  C11  C4   C5   C1    180.00   0.0  0
 3DX  CONST_28  C3   C4   C5   C1      0.00   0.0  0
 3DX  CONST_29  C3   N1   C2   C1      0.00   0.0  0
 3DX  CONST_30  N1   C2   C1   C5      0.00   0.0  0
 3DX  CONST_33  N1   C3   C4   C5      0.00   0.0  0
 3DX  CONST_34  C15  C16  C11  C4    180.00   0.0  0
 3DX  CONST_35  C13  C12  C11  C4    180.00   0.0  0
 3DX  CONST_38  C11  C4   C3   N1    180.00   0.0  0
 3DX  CONST_39  C14  C15  C16  C11     0.00   0.0  0
 3DX  CONST_40  C14  C13  C12  C11     0.00   0.0  0
 3DX  CONST_41  C13  C14  C15  C16     0.00   0.0  0
 3DX  CONST_42  C13  C12  C11  C16     0.00   0.0  0
 3DX  CONST_43  C12  C11  C16  C15     0.00   0.0  0
 3DX  CONST_44  C12  C13  C14  C15     0.00   0.0  0
 3DX  CONST_45  N4   C14  C15  C16   180.00   0.0  0
 3DX  CONST_46  N4   C14  C13  C12   180.00   0.0  0
 3DX  CONST_47  C6   C8   C9   C22   180.00   0.0  0
 3DX  CONST_48  C10  N3   C9   C22   180.00   0.0  0
 3DX  CONST_49  H1   C10  N3   C9    180.00   0.0  0
 3DX  CONST_50  H3   C8   C9   N3    180.00   0.0  0
 3DX  CONST_51  H2   N2   C7   C10     0.00   0.0  0
 3DX  CONST_52  H4   C5   C1   C2    180.00   0.0  0
 3DX  CONST_53  H5   C3   N1   C2    180.00   0.0  0
 3DX  CONST_54  H6   C16  C11  C4      0.00   0.0  0
 3DX  CONST_55  H9   C12  C11  C4      0.00   0.0  0
 3DX  CONST_56  H7   C15  C16  C11   180.00   0.0  0
 3DX  CONST_57  H8   C13  C12  C11   180.00   0.0  0
 3DX  Var_01    C20  N4   C14  C15     2.81  30.0  3
 3DX  Var_02    C19  C20  N4   C14   162.25  30.0  1
 3DX  Var_03    C18  C17  N4   C14  -161.24  30.0  1
 3DX  Var_04    N5   C19  C20  N4     55.82  30.0  1
 3DX  Var_05    N5   C18  C17  N4    -56.77  30.0  1
 3DX  Var_06    C18  N5   C19  C20   -58.61  30.0  1
 3DX  Var_07    C17  C18  N5   C19    58.85  30.0  1
 3DX  Var_08    H15  C21  N5   C19    61.19  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
 3DX  plan-1  C4   0.020
 3DX  plan-1  C11  0.020
 3DX  plan-1  C16  0.020
 3DX  plan-1  C15  0.020
 3DX  plan-1  C14  0.020
 3DX  plan-1  C13  0.020
 3DX  plan-1  C12  0.020
 3DX  plan-1  N4   0.020
 3DX  plan-1  H6   0.020
 3DX  plan-1  H7   0.020
 3DX  plan-1  H8   0.020
 3DX  plan-1  H9   0.020
 3DX  plan-2  N6   0.020
 3DX  plan-2  C22  0.020
 3DX  plan-2  C9   0.020
 3DX  plan-2  N3   0.020
 3DX  plan-2  C10  0.020
 3DX  plan-2  C7   0.020
 3DX  plan-2  N2   0.020
 3DX  plan-2  C2   0.020
 3DX  plan-2  C8   0.020
 3DX  plan-2  C6   0.020
 3DX  plan-2  C1   0.020
 3DX  plan-2  C5   0.020
 3DX  plan-2  C4   0.020
 3DX  plan-2  C3   0.020
 3DX  plan-2  N1   0.020
 3DX  plan-2  C11  0.020
 3DX  plan-2  H1   0.020
 3DX  plan-2  H2   0.020
 3DX  plan-2  H3   0.020
 3DX  plan-2  H4   0.020
 3DX  plan-2  H5   0.020

