# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 15:17:18 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: 5H-pyrimido[5,4-b]indole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [nH]1c2ccccc2c3ncncc13
#
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
 Z0W  Z0W  '5H-pyrimido[5,4-b]indole '  ligand  20  13  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Z0W
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
 Z0W  C2   C  CR16  0   0.006  -2.8376   1.0780  -0.0010
 Z0W  N3   N  N     0  -0.400  -3.2916  -0.1759   0.0044
 Z0W  C4   C  CR16  0  -0.063  -2.4118  -1.1670   0.0026
 Z0W  C5   C  CR56  0   0.247  -1.0578  -0.8755  -0.0058
 Z0W  N1   N  N     0  -0.405  -1.5742   1.4666  -0.0080
 Z0W  C6   C  CR56  0   0.184  -0.6821   0.4827  -0.0106
 Z0W  C7   C  CR56  0   0.009   0.7527   0.5133  -0.0174
 Z0W  C8   C  CR16  0  -0.320   1.6976   1.5397  -0.0251
 Z0W  C12  C  CR56  0   0.352   1.1672  -0.8344  -0.0167
 Z0W  C11  C  CR16  0  -0.307   2.5181  -1.1772  -0.0239
 Z0W  C10  C  CR16  0  -0.258   3.4350  -0.1436  -0.0317
 Z0W  C9   C  CR16  0  -0.272   3.0361   1.2028  -0.0321
 Z0W  N2   N  NR15  0  -0.775   0.0645  -1.6498  -0.0100
 Z0W  H2   H  HCR6  0   0.253  -3.5884   1.8594   0.0006
 Z0W  HN2  H  HNR5  0   0.418   0.0835  -2.6563  -0.0068
 Z0W  H4   H  HCR6  0   0.284  -2.7883  -2.1843   0.0078
 Z0W  H8   H  HCR6  0   0.257   1.3838   2.5758  -0.0253
 Z0W  H9   H  HCR6  0   0.259   3.7891   1.9790  -0.0381
 Z0W  H11  H  HCR6  0   0.269   2.8372  -2.2112  -0.0248
 Z0W  H10  H  HCR6  0   0.263   4.4914  -0.3786  -0.0377

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
 Z0W  C2   N3   aromatic  1.334  0.020  1.334
 Z0W  C2   N1   aromatic  1.322  0.020  1.322
 Z0W  N3   C4   aromatic  1.325  0.020  1.325
 Z0W  C4   C5   aromatic  1.385  0.020  1.385
 Z0W  C5   C6   aromatic  1.409  0.020  1.409
 Z0W  C5   N2   aromatic  1.364  0.020  1.364
 Z0W  N1   C6   aromatic  1.328  0.020  1.328
 Z0W  C6   C7   aromatic  1.435  0.020  1.435
 Z0W  C7   C8   aromatic  1.395  0.020  1.395
 Z0W  C7   C12  aromatic  1.410  0.020  1.410
 Z0W  C8   C9   aromatic  1.380  0.020  1.380
 Z0W  C12  C11  aromatic  1.394  0.020  1.394
 Z0W  C12  N2   aromatic  1.371  0.020  1.371
 Z0W  C11  C10  aromatic  1.382  0.020  1.382
 Z0W  C10  C9   aromatic  1.404  0.020  1.404
 Z0W  C2   H2   single    0.930  0.020  1.080
 Z0W  C4   H4   single    0.930  0.020  1.080
 Z0W  C8   H8   single    0.930  0.020  1.080
 Z0W  C9   H9   single    0.930  0.020  1.080
 Z0W  C11  H11  single    0.930  0.020  1.080
 Z0W  C10  H10  single    0.930  0.020  1.080
 Z0W  N2   HN2  single    0.860  0.020  1.020

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
 Z0W  H2   C2   N1   116.76  3.000
 Z0W  H2   C2   N3   116.24  3.000
 Z0W  N1   C2   N3   127.01  3.000
 Z0W  C4   N3   C2   118.50  3.000
 Z0W  H4   C4   C5   122.46  3.000
 Z0W  H4   C4   N3   118.10  3.000
 Z0W  C5   C4   N3   119.44  3.000
 Z0W  N2   C5   C6   109.14  3.000
 Z0W  N2   C5   C4   133.25  3.000
 Z0W  C6   C5   C4   117.61  3.000
 Z0W  C6   N1   C2   115.09  3.000
 Z0W  C7   C6   N1   130.97  3.000
 Z0W  C7   C6   C5   106.69  3.000
 Z0W  N1   C6   C5   122.34  3.000
 Z0W  C12  C7   C8   120.27  3.000
 Z0W  C12  C7   C6   105.87  3.000
 Z0W  C8   C7   C6   133.86  3.000
 Z0W  H8   C8   C9   120.98  3.000
 Z0W  H8   C8   C7   120.52  3.000
 Z0W  C9   C8   C7   118.50  3.000
 Z0W  N2   C12  C11  129.28  3.000
 Z0W  N2   C12  C7   109.38  3.000
 Z0W  C11  C12  C7   121.33  3.000
 Z0W  H11  C11  C10  121.28  3.000
 Z0W  H11  C11  C12  121.39  3.000
 Z0W  C10  C11  C12  117.34  3.000
 Z0W  H10  C10  C9   119.04  3.000
 Z0W  H10  C10  C11  119.03  3.000
 Z0W  C9   C10  C11  121.93  3.000
 Z0W  H9   C9   C10  119.37  3.000
 Z0W  H9   C9   C8   120.00  3.000
 Z0W  C10  C9   C8   120.63  3.000
 Z0W  HN2  N2   C12  125.40  3.000
 Z0W  HN2  N2   C5   125.68  3.000
 Z0W  C12  N2   C5   108.92  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
 Z0W  CONST_01  C5   C4   N3   C2     0.00  0.0  0
 Z0W  CONST_02  C5   C6   N1   C2     0.00  0.0  0
 Z0W  CONST_03  C7   C6   N1   C2   180.00  0.0  0
 Z0W  CONST_04  C6   N1   C2   N3     0.00  0.0  0
 Z0W  CONST_05  C6   C5   C4   N3     0.00  0.0  0
 Z0W  CONST_06  N2   C5   C4   N3   180.00  0.0  0
 Z0W  CONST_07  N1   C2   N3   C4     0.00  0.0  0
 Z0W  CONST_08  N1   C6   C5   C4     0.00  0.0  0
 Z0W  CONST_09  C7   C6   C5   C4   180.00  0.0  0
 Z0W  CONST_10  C12  N2   C5   C4   180.00  0.0  0
 Z0W  CONST_11  C8   C7   C6   C5   180.00  0.0  0
 Z0W  CONST_12  C12  C7   C6   C5     0.00  0.0  0
 Z0W  CONST_13  C7   C12  N2   C5     0.00  0.0  0
 Z0W  CONST_14  C11  C12  N2   C5   180.00  0.0  0
 Z0W  CONST_15  N2   C5   C6   N1   180.00  0.0  0
 Z0W  CONST_16  C8   C7   C6   N1     0.00  0.0  0
 Z0W  CONST_17  C12  C7   C6   N1   180.00  0.0  0
 Z0W  CONST_18  C12  N2   C5   C6     0.00  0.0  0
 Z0W  CONST_19  C9   C8   C7   C6   180.00  0.0  0
 Z0W  CONST_20  C11  C12  C7   C6   180.00  0.0  0
 Z0W  CONST_21  N2   C12  C7   C6     0.00  0.0  0
 Z0W  CONST_22  N2   C5   C6   C7     0.00  0.0  0
 Z0W  CONST_23  C10  C9   C8   C7     0.00  0.0  0
 Z0W  CONST_24  C10  C11  C12  C7     0.00  0.0  0
 Z0W  CONST_25  C11  C12  C7   C8     0.00  0.0  0
 Z0W  CONST_26  N2   C12  C7   C8   180.00  0.0  0
 Z0W  CONST_27  C11  C10  C9   C8     0.00  0.0  0
 Z0W  CONST_28  C9   C8   C7   C12    0.00  0.0  0
 Z0W  CONST_29  C9   C10  C11  C12    0.00  0.0  0
 Z0W  CONST_30  N2   C12  C11  C10  180.00  0.0  0
 Z0W  CONST_31  H4   C4   N3   C2   180.00  0.0  0
 Z0W  CONST_32  H2   C2   N3   C4   180.00  0.0  0
 Z0W  CONST_33  HN2  N2   C5   C4     0.00  0.0  0
 Z0W  CONST_34  H8   C8   C7   C6     0.00  0.0  0
 Z0W  CONST_35  H9   C9   C8   C7   180.00  0.0  0
 Z0W  CONST_36  H11  C11  C12  C7   180.00  0.0  0
 Z0W  CONST_37  H10  C10  C9   C8   180.00  0.0  0

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
 Z0W  plan-1  C2   0.020
 Z0W  plan-1  N3   0.020
 Z0W  plan-1  C4   0.020
 Z0W  plan-1  C5   0.020
 Z0W  plan-1  N1   0.020
 Z0W  plan-1  C6   0.020
 Z0W  plan-1  C7   0.020
 Z0W  plan-1  C8   0.020
 Z0W  plan-1  C12  0.020
 Z0W  plan-1  C11  0.020
 Z0W  plan-1  C10  0.020
 Z0W  plan-1  C9   0.020
 Z0W  plan-1  N2   0.020
 Z0W  plan-1  H2   0.020
 Z0W  plan-1  HN2  0.020
 Z0W  plan-1  H4   0.020
 Z0W  plan-1  H8   0.020
 Z0W  plan-1  H9   0.020
 Z0W  plan-1  H11  0.020
 Z0W  plan-1  H10  0.020

