# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 12:39:58 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: 7-[(3-aminophenyl)methyl]-7H-pyrrolo[3,2-f]quinazoline-1,3-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cccc(Cn2ccc3c2ccc4nc(N)nc(N)c34)c1
#
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
 PQD  PQD  7-[(3-aminophenyl)methyl]-7H-pyrrolo[3,2-f]quinazoline-1,3-diamine  ligand  39  23  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PQD
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
 PQD  CAK  C  CR16  0  -0.386  -3.8939   0.9220   0.8171
 PQD  CAO  C  CR6   0   0.322  -4.6447   1.6675  -0.1008
 PQD  NAA  N  NH2   0  -0.861  -5.3502   2.7788   0.3069
 PQD  CAE  C  CR16  0  -0.338  -4.6092   1.2889  -1.4473
 PQD  CAD  C  CR16  0  -0.236  -3.8469   0.2028  -1.8468
 PQD  CAF  C  CR16  0  -0.319  -3.1081  -0.5331  -0.9311
 PQD  CAP  C  CR6   0   0.114  -3.1366  -0.1667   0.4113
 PQD  CAL  C  CH2   0  -0.389  -2.3759  -0.9592   1.4469
 PQD  NAW  N  NR5   0  -0.509  -1.0595  -1.3548   1.0037
 PQD  CAU  C  CR56  0   0.343  -0.0132  -0.5040   0.7742
 PQD  CAH  C  CR16  0  -0.271   0.0346   0.8877   0.9390
 PQD  CAG  C  CR16  0  -0.361   1.1905   1.5398   0.6149
 PQD  C4   C  CR66  0   0.232   2.3311   0.8375   0.1346
 PQD  N3   N  N     0  -0.526   3.4264   1.5656  -0.1831
 PQD  C2   C  CR6   0   0.506   4.4687   0.8972  -0.6243
 PQD  NAB  N  NH2   0  -0.828   5.5906   1.5979  -0.9364
 PQD  N1   N  N     0  -0.503   4.5652  -0.4376  -0.7517
 PQD  C6   C  CR6   0   0.434   3.5136  -1.1652  -0.4345
 PQD  NAC  N  NH2   0  -0.829   3.6377  -2.5009  -0.5648
 PQD  C5   C  CR66  0  -0.117   2.2887  -0.5665   0.0023
 PQD  CAT  C  CR56  0   0.089   1.0776  -1.2534   0.3016
 PQD  CAI  C  CR15  0  -0.500   0.6256  -2.6056   0.2358
 PQD  CAJ  C  CR15  0  -0.017  -0.6735  -2.6135   0.6705
 PQD  HAK  H  HCR6  0   0.253  -3.9036   1.2070   1.8644
 PQD  HAN  H  HNH2  0   0.379  -5.6291   2.7895   1.2748
 PQD  HAA  H  HNH2  0   0.379  -6.1013   3.0661  -0.2998
 PQD  HAE  H  HCR6  0   0.255  -5.1808   1.8487  -2.1783
 PQD  HAD  H  HCR6  0   0.251  -3.8340  -0.0755  -2.8932
 PQD  HAF  H  HCR6  0   0.243  -2.5199  -1.3797  -1.2626
 PQD  H1   H  HCH2  0   0.276  -2.2887  -0.3859   2.3725
 PQD  H2   H  HCH2  0   0.289  -2.9191  -1.8710   1.7000
 PQD  HAH  H  HCR6  0   0.269  -0.8241   1.4387   1.3021
 PQD  HAG  H  HCR6  0   0.251   1.2620   2.6148   0.7141
 PQD  HAB  H  HNH2  0   0.384   5.4883   2.5871  -1.0869
 PQD  HAO  H  HNH2  0   0.385   6.2758   1.1401  -1.5126
 PQD  HAP  H  HNH2  0   0.408   3.0417  -3.1156  -0.0409
 PQD  HAC  H  HNH2  0   0.394   4.5656  -2.8528  -0.7366
 PQD  HAI  H  HCR5  0   0.244   1.1427  -3.4865  -0.1059
 PQD  HAJ  H  HCR5  0   0.291  -1.3587  -3.4416   0.7624

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
 PQD  NAC  C6   single    1.348  0.020  1.348
 PQD  CAJ  CAI  aromatic  1.370  0.020  1.370
 PQD  CAJ  NAW  aromatic  1.358  0.020  1.358
 PQD  CAI  CAT  aromatic  1.427  0.020  1.427
 PQD  C6   C5   aromatic  1.432  0.020  1.432
 PQD  C6   N1   aromatic  1.318  0.020  1.318
 PQD  NAW  CAL  single    1.444  0.020  1.444
 PQD  NAW  CAU  aromatic  1.368  0.020  1.368
 PQD  CAT  C5   aromatic  1.424  0.020  1.424
 PQD  CAT  CAU  aromatic  1.405  0.020  1.405
 PQD  CAF  CAD  aromatic  1.388  0.020  1.388
 PQD  CAF  CAP  aromatic  1.392  0.020  1.392
 PQD  CAL  CAP  single    1.510  0.020  1.510
 PQD  CAD  CAE  aromatic  1.386  0.020  1.386
 PQD  C5   C4   aromatic  1.411  0.020  1.411
 PQD  N1   C2   aromatic  1.344  0.020  1.344
 PQD  CAP  CAK  aromatic  1.387  0.020  1.387
 PQD  CAU  CAH  aromatic  1.402  0.020  1.402
 PQD  CAE  CAO  aromatic  1.399  0.020  1.399
 PQD  CAK  CAO  aromatic  1.401  0.020  1.401
 PQD  CAO  NAA  single    1.378  0.020  1.378
 PQD  C2   N3   aromatic  1.314  0.020  1.314
 PQD  C2   NAB  single    1.359  0.020  1.359
 PQD  C4   N3   aromatic  1.353  0.020  1.353
 PQD  C4   CAG  aromatic  1.423  0.020  1.423
 PQD  CAH  CAG  aromatic  1.366  0.020  1.366
 PQD  CAK  HAK  single    0.930  0.020  1.080
 PQD  NAA  HAN  single    0.890  0.020  1.040
 PQD  NAA  HAA  single    0.890  0.020  1.040
 PQD  CAE  HAE  single    0.930  0.020  1.080
 PQD  CAD  HAD  single    0.930  0.020  1.080
 PQD  CAF  HAF  single    0.930  0.020  1.080
 PQD  CAL  H1   single    0.970  0.020  1.090
 PQD  CAL  H2   single    0.970  0.020  1.090
 PQD  CAH  HAH  single    0.930  0.020  1.080
 PQD  CAG  HAG  single    0.930  0.020  1.080
 PQD  NAB  HAB  single    0.890  0.020  1.040
 PQD  NAB  HAO  single    0.890  0.020  1.040
 PQD  NAC  HAP  single    0.890  0.020  1.040
 PQD  NAC  HAC  single    0.890  0.020  1.040
 PQD  CAI  HAI  single    0.930  0.020  1.080
 PQD  CAJ  HAJ  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
 PQD  HAK  CAK  CAP  119.56  3.000
 PQD  HAK  CAK  CAO  119.19  3.000
 PQD  CAP  CAK  CAO  121.24  3.000
 PQD  CAE  CAO  NAA  121.06  3.000
 PQD  NAA  CAO  CAK  120.65  3.000
 PQD  CAE  CAO  CAK  118.23  3.000
 PQD  HAA  NAA  HAN  111.67  3.000
 PQD  HAA  NAA  CAO  115.70  3.000
 PQD  HAN  NAA  CAO  115.76  3.000
 PQD  HAE  CAE  CAD  120.03  3.000
 PQD  HAE  CAE  CAO  119.74  3.000
 PQD  CAD  CAE  CAO  120.23  3.000
 PQD  HAD  CAD  CAF  119.67  3.000
 PQD  HAD  CAD  CAE  119.11  3.000
 PQD  CAF  CAD  CAE  121.22  3.000
 PQD  HAF  CAF  CAP  120.81  3.000
 PQD  HAF  CAF  CAD  120.11  3.000
 PQD  CAP  CAF  CAD  119.07  3.000
 PQD  CAL  CAP  CAF  120.87  3.000
 PQD  CAL  CAP  CAK  119.11  3.000
 PQD  CAF  CAP  CAK  120.00  3.000
 PQD  H2   CAL  H1   106.37  3.000
 PQD  H2   CAL  NAW  107.22  3.000
 PQD  H1   CAL  NAW  109.34  3.000
 PQD  H2   CAL  CAP  110.30  3.000
 PQD  H1   CAL  CAP  110.24  3.000
 PQD  NAW  CAL  CAP  113.11  3.000
 PQD  CAJ  NAW  CAU  108.53  3.000
 PQD  CAU  NAW  CAL  125.33  3.000
 PQD  CAJ  NAW  CAL  126.04  3.000
 PQD  CAT  CAU  CAH  122.84  3.000
 PQD  CAH  CAU  NAW  128.58  3.000
 PQD  CAT  CAU  NAW  108.57  3.000
 PQD  HAH  CAH  CAG  120.50  3.000
 PQD  HAH  CAH  CAU  121.15  3.000
 PQD  CAG  CAH  CAU  118.34  3.000
 PQD  HAG  CAG  C4   117.93  3.000
 PQD  HAG  CAG  CAH  120.56  3.000
 PQD  C4   CAG  CAH  121.51  3.000
 PQD  C5   C4   N3   122.54  3.000
 PQD  N3   C4   CAG  117.55  3.000
 PQD  C5   C4   CAG  119.91  3.000
 PQD  C2   N3   C4   116.56  3.000
 PQD  N1   C2   NAB  115.52  3.000
 PQD  NAB  C2   N3   118.00  3.000
 PQD  N1   C2   N3   126.42  3.000
 PQD  HAO  NAB  HAB  115.56  3.000
 PQD  HAO  NAB  C2   117.35  3.000
 PQD  HAB  NAB  C2   117.22  3.000
 PQD  C6   N1   C2   117.91  3.000
 PQD  C5   C6   NAC  121.51  3.000
 PQD  C5   C6   N1   121.70  3.000
 PQD  NAC  C6   N1   116.78  3.000
 PQD  HAC  NAC  HAP  114.97  3.000
 PQD  HAC  NAC  C6   116.59  3.000
 PQD  HAP  NAC  C6   120.12  3.000
 PQD  CAT  C5   C6   126.16  3.000
 PQD  CAT  C5   C4   119.07  3.000
 PQD  C6   C5   C4   114.77  3.000
 PQD  CAI  CAT  C5   135.77  3.000
 PQD  C5   CAT  CAU  118.26  3.000
 PQD  CAI  CAT  CAU  105.96  3.000
 PQD  HAI  CAI  CAJ  123.45  3.000
 PQD  HAI  CAI  CAT  129.60  3.000
 PQD  CAJ  CAI  CAT  106.93  3.000
 PQD  HAJ  CAJ  CAI  129.33  3.000
 PQD  HAJ  CAJ  NAW  120.66  3.000
 PQD  CAI  CAJ  NAW  110.00  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
 PQD  CONST_01  CAD  CAF  CAP  CAK     0.00   0.0  0
 PQD  CONST_02  CAD  CAE  CAO  CAK     0.00   0.0  0
 PQD  CONST_03  CAF  CAD  CAE  CAO     0.00   0.0  0
 PQD  CONST_04  CAF  CAP  CAK  CAO     0.00   0.0  0
 PQD  CONST_05  CAP  CAF  CAD  CAE     0.00   0.0  0
 PQD  CONST_06  CAP  CAK  CAO  CAE     0.00   0.0  0
 PQD  CONST_07  CAT  CAI  CAJ  NAW     0.00   0.0  0
 PQD  CONST_08  CAI  CAT  CAU  NAW     0.00   0.0  0
 PQD  CONST_09  C5   CAT  CAU  NAW   180.00   0.0  0
 PQD  CONST_10  CAG  CAH  CAU  NAW   180.00   0.0  0
 PQD  CONST_11  CAI  CAJ  NAW  CAU     0.00   0.0  0
 PQD  CONST_12  CAJ  CAI  CAT  CAU     0.00   0.0  0
 PQD  CONST_13  C6   C5   CAT  CAU   180.00   0.0  0
 PQD  CONST_14  C4   C5   CAT  CAU     0.00   0.0  0
 PQD  CONST_15  C4   CAG  CAH  CAU     0.00   0.0  0
 PQD  CONST_16  CAJ  NAW  CAU  CAH   180.00   0.0  0
 PQD  CONST_17  CAI  CAT  CAU  CAH   180.00   0.0  0
 PQD  CONST_18  C5   CAT  CAU  CAH     0.00   0.0  0
 PQD  CONST_19  C5   C4   CAG  CAH     0.00   0.0  0
 PQD  CONST_20  N3   C4   CAG  CAH   180.00   0.0  0
 PQD  CONST_21  C6   C5   C4   CAG   180.00   0.0  0
 PQD  CONST_22  CAT  C5   C4   CAG     0.00   0.0  0
 PQD  CONST_23  C2   N3   C4   CAG   180.00   0.0  0
 PQD  CONST_24  CAT  CAU  CAH  CAG     0.00   0.0  0
 PQD  CONST_25  N1   C6   C5   C4      0.00   0.0  0
 PQD  CONST_26  CAI  CAT  C5   C4    180.00   0.0  0
 PQD  CONST_27  N1   C2   N3   C4      0.00   0.0  0
 PQD  CONST_28  C6   N1   C2   N3      0.00   0.0  0
 PQD  CONST_29  C6   C5   C4   N3      0.00   0.0  0
 PQD  CONST_30  CAT  C5   C4   N3    180.00   0.0  0
 PQD  CONST_31  C5   C6   N1   C2      0.00   0.0  0
 PQD  CONST_32  C5   C4   N3   C2      0.00   0.0  0
 PQD  CONST_33  CAT  C5   C6   N1    180.00   0.0  0
 PQD  CONST_34  CAI  CAT  C5   C6      0.00   0.0  0
 PQD  CONST_35  CAJ  CAI  CAT  C5    180.00   0.0  0
 PQD  CONST_36  CAJ  NAW  CAU  CAT     0.00   0.0  0
 PQD  CONST_37  CAL  CAP  CAK  CAO   180.00   0.0  0
 PQD  CONST_38  CAD  CAE  CAO  NAA   180.00   0.0  0
 PQD  CONST_39  CAP  CAK  CAO  NAA   180.00   0.0  0
 PQD  CONST_40  CAL  CAP  CAF  CAD   180.00   0.0  0
 PQD  CONST_41  CAI  CAJ  NAW  CAL   180.00   0.0  0
 PQD  CONST_42  CAT  CAU  NAW  CAL   180.00   0.0  0
 PQD  CONST_43  CAH  CAU  NAW  CAL     0.00   0.0  0
 PQD  CONST_44  NAC  C6   C5   C4    180.00   0.0  0
 PQD  CONST_45  NAB  C2   N3   C4    180.00   0.0  0
 PQD  CONST_46  NAC  C6   N1   C2    180.00   0.0  0
 PQD  CONST_47  C6   N1   C2   NAB   180.00   0.0  0
 PQD  CONST_48  CAT  C5   C6   NAC     0.00   0.0  0
 PQD  CONST_49  HAF  CAF  CAP  CAK   180.00   0.0  0
 PQD  CONST_50  HAE  CAE  CAO  CAK   180.00   0.0  0
 PQD  CONST_51  HAD  CAD  CAE  CAO   180.00   0.0  0
 PQD  CONST_52  HAK  CAK  CAO  CAE   180.00   0.0  0
 PQD  CONST_53  HAI  CAI  CAJ  NAW   180.00   0.0  0
 PQD  CONST_54  HAH  CAH  CAU  NAW     0.00   0.0  0
 PQD  CONST_55  HAJ  CAJ  NAW  CAU   180.00   0.0  0
 PQD  CONST_56  HAG  CAG  CAH  CAU   180.00   0.0  0
 PQD  CONST_62  HAC  NAC  C6   N1      0.00   0.0  0
 PQD  Var_01    NAW  CAL  CAP  CAK  -139.56  30.0  3
 PQD  Var_02    CAJ  NAW  CAL  CAP  -108.05  30.0  2

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
 PQD  plan-1  CAK  0.020
 PQD  plan-1  CAO  0.020
 PQD  plan-1  NAA  0.020
 PQD  plan-1  CAE  0.020
 PQD  plan-1  CAD  0.020
 PQD  plan-1  CAF  0.020
 PQD  plan-1  CAP  0.020
 PQD  plan-1  CAL  0.020
 PQD  plan-1  HAK  0.020
 PQD  plan-1  HAE  0.020
 PQD  plan-1  HAD  0.020
 PQD  plan-1  HAF  0.020
 PQD  plan-2  CAL  0.020
 PQD  plan-2  NAW  0.020
 PQD  plan-2  CAU  0.020
 PQD  plan-2  CAH  0.020
 PQD  plan-2  CAG  0.020
 PQD  plan-2  C4   0.020
 PQD  plan-2  N3   0.020
 PQD  plan-2  C2   0.020
 PQD  plan-2  NAB  0.020
 PQD  plan-2  N1   0.020
 PQD  plan-2  C6   0.020
 PQD  plan-2  NAC  0.020
 PQD  plan-2  C5   0.020
 PQD  plan-2  CAT  0.020
 PQD  plan-2  CAI  0.020
 PQD  plan-2  CAJ  0.020
 PQD  plan-2  HAH  0.020
 PQD  plan-2  HAG  0.020
 PQD  plan-2  HAI  0.020
 PQD  plan-2  HAJ  0.020
 PQD  plan-3  CAO  0.020
 PQD  plan-3  NAA  0.020
 PQD  plan-3  HAN  0.020
 PQD  plan-3  HAA  0.020
 PQD  plan-4  C2   0.020
 PQD  plan-4  NAB  0.020
 PQD  plan-4  HAB  0.020
 PQD  plan-4  HAO  0.020
 PQD  plan-5  C6   0.020
 PQD  plan-5  NAC  0.020
 PQD  plan-5  HAP  0.020
 PQD  plan-5  HAC  0.020

