# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 19:48:19 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: N-(3-{[6,7-dimethoxy-2-(pyrrolidin-1-yl)quinazolin-4-yl]amino}propyl)propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)NCCCNc1nc(nc2cc(OC)c(OC)cc12)N3CCCC3
#
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
 7BY  7BY  N-(3-{[6,7-dimethoxy-2-(pyrrolidin-1-yl)quinazolin-4-yl]amino}propyl)propanamide  ligand  57  28  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7BY
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
 7BY  C4   C  CR66  0   0.253   2.7764   0.1098   0.1756
 7BY  C5   C  CR66  0  -0.043   1.5348   0.7279  -0.0423
 7BY  C6   C  CR6   0   0.522   0.4260  -0.1715  -0.2067
 7BY  N1   N  N     0  -0.524   0.5929  -1.4760  -0.1718
 7BY  N3   N  N     0  -0.550   2.9318  -1.2326   0.2219
 7BY  CAY  C  CH2   0  -0.253   3.2314  -3.9720   0.1927
 7BY  CAZ  C  CH2   0  -0.480   2.9060  -5.4059  -0.2110
 7BY  CBA  C  CH2   0  -0.482   1.4489  -5.5645   0.2137
 7BY  CBB  C  CH2   0  -0.246   0.8368  -4.2052  -0.1128
 7BY  NAX  N  NT    0  -0.509   1.9559  -3.2924   0.0536
 7BY  C2   C  CR6   0   0.594   1.8385  -1.9504   0.0386
 7BY  CAO  C  CR16  0  -0.483   3.9147   0.9296   0.3583
 7BY  CAP  C  CR6   0   0.333   3.8170   2.2973   0.3185
 7BY  OAQ  O  O2    0  -0.457   4.8394   3.1458   0.4810
 7BY  CAR  C  CH3   0  -0.439   6.1200   2.6060   0.7467
 7BY  CAS  C  CR6   0   0.322   2.5520   2.9193   0.0918
 7BY  OAT  O  O2    0  -0.466   2.5753   4.2663   0.0699
 7BY  CAU  C  CH3   0  -0.441   1.3576   4.9425  -0.1577
 7BY  CAV  C  CR16  0  -0.468   1.4416   2.1368  -0.0768
 7BY  NAI  N  NH1   0  -0.681  -0.8193   0.2915  -0.3902
 7BY  CAH  C  CH2   0  -0.235  -1.9700  -0.5667  -0.5604
 7BY  CAG  C  CH2   0  -0.487  -3.2468   0.2574  -0.5302
 7BY  CAF  C  CH2   0  -0.279  -4.4788  -0.6342  -0.6407
 7BY  NAE  N  NH1   0  -0.635  -5.7162   0.1100  -0.6704
 7BY  CAC  C  C     0   0.553  -6.3359   0.5618   0.4341
 7BY  OAD  O  O     0  -0.505  -5.9440   0.3020   1.5642
 7BY  CAB  C  CH2   0  -0.572  -7.5456   1.4362   0.1760
 7BY  CAA  C  CH3   0  -0.658  -8.6021   1.3341   1.2638
 7BY  H2   H  HCH2  0   0.236   3.9933  -3.5166  -0.4409
 7BY  H3   H  HCH2  0   0.234   2.9992  -5.5200  -1.2935
 7BY  H4   H  HCH2  0   0.246   3.5737  -6.1291   0.2564
 7BY  H5   H  HCH2  0   0.246   0.9367  -6.3804  -0.2952
 7BY  H6   H  HCH2  0   0.234   1.3891  -5.7534   1.2880
 7BY  H7   H  HCH2  0   0.221   0.4521  -4.1769  -1.1377
 7BY  H8   H  HCH2  0   0.238   0.0092  -3.9475   0.5488
 7BY  H9   H  HCR6  0   0.275   4.8619   0.4365   0.5315
 7BY  H10  H  HCH3  0   0.264   6.7920   3.4516   0.8664
 7BY  H11  H  HCH3  0   0.232   6.1259   2.0152   1.6661
 7BY  H12  H  HCH3  0   0.232   6.4768   1.9820  -0.0766
 7BY  H13  H  HCH3  0   0.261   1.5871   6.0052  -0.1578
 7BY  H14  H  HCH3  0   0.227   0.9160   4.6762  -1.1222
 7BY  H15  H  HCH3  0   0.227   0.6247   4.7406   0.6291
 7BY  H16  H  HCR6  0   0.272   0.4837   2.6129  -0.2394
 7BY  H17  H  HNH1  0   0.408  -0.9575   1.2773  -0.5278
 7BY  H18  H  HCH2  0   0.228  -1.9034  -1.1239  -1.5015
 7BY  H19  H  HCH2  0   0.235  -1.9846  -1.3119   0.2383
 7BY  H20  H  HCH2  0   0.242  -3.2934   0.8276   0.4014
 7BY  H21  H  HCH2  0   0.237  -3.2455   0.9785  -1.3528
 7BY  H22  H  HCH2  0   0.250  -4.4301  -1.2290  -1.5538
 7BY  H23  H  HCH2  0   0.242  -4.5064  -1.3356   0.1944
 7BY  H24  H  HNH1  0   0.399  -6.0746   0.3845  -1.5702
 7BY  H25  H  HCH2  0   0.268  -7.1851   2.4676   0.1049
 7BY  H26  H  HCH2  0   0.249  -7.9760   1.2033  -0.8000
 7BY  H27  H  HCH3  0   0.234  -9.4356   1.9993   1.0407
 7BY  H28  H  HCH3  0   0.228  -8.9991   0.3216   1.3421
 7BY  H29  H  HCH3  0   0.229  -8.2031   1.6147   2.2372
 7BY  H1   H  HCH2  0   0.222   3.5954  -3.9204   1.2247

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
 7BY  CAA  CAB  single    1.520  0.020  1.520
 7BY  CAB  CAC  single    1.515  0.020  1.515
 7BY  CAC  NAE  single    1.345  0.020  1.345
 7BY  CAC  OAD  double    1.224  0.020  1.224
 7BY  NAE  CAF  single    1.444  0.020  1.444
 7BY  CAF  CAG  single    1.525  0.020  1.525
 7BY  CAG  CAH  single    1.520  0.020  1.520
 7BY  CAH  NAI  single    1.445  0.020  1.445
 7BY  NAI  C6   single    1.341  0.020  1.341
 7BY  CAY  CAZ  single    1.525  0.020  1.525
 7BY  CAY  NAX  single    1.452  0.020  1.452
 7BY  C6   N1   aromatic  1.316  0.020  1.316
 7BY  C6   C5   aromatic  1.437  0.020  1.437
 7BY  N1   C2   aromatic  1.349  0.020  1.349
 7BY  CAZ  CBA  single    1.526  0.020  1.526
 7BY  NAX  C2   single    1.347  0.020  1.347
 7BY  NAX  CBB  single    1.454  0.020  1.454
 7BY  C2   N3   aromatic  1.321  0.020  1.321
 7BY  C5   CAV  aromatic  1.412  0.020  1.412
 7BY  C5   C4   aromatic  1.404  0.020  1.404
 7BY  CAV  CAS  aromatic  1.369  0.020  1.369
 7BY  CAU  OAT  single    1.411  0.020  1.411
 7BY  CBA  CBB  single    1.526  0.020  1.526
 7BY  C4   N3   aromatic  1.352  0.020  1.352
 7BY  C4   CAO  aromatic  1.415  0.020  1.415
 7BY  CAS  OAT  single    1.347  0.020  1.347
 7BY  CAS  CAP  aromatic  1.428  0.020  1.428
 7BY  CAO  CAP  aromatic  1.372  0.020  1.372
 7BY  CAP  OAQ  single    1.339  0.020  1.339
 7BY  OAQ  CAR  single    1.415  0.020  1.415
 7BY  CAY  H1   single    0.970  0.020  1.090
 7BY  CAY  H2   single    0.970  0.020  1.090
 7BY  CAZ  H3   single    0.970  0.020  1.090
 7BY  CAZ  H4   single    0.970  0.020  1.090
 7BY  CBA  H5   single    0.970  0.020  1.090
 7BY  CBA  H6   single    0.970  0.020  1.090
 7BY  CBB  H7   single    0.970  0.020  1.090
 7BY  CBB  H8   single    0.970  0.020  1.090
 7BY  CAO  H9   single    0.930  0.020  1.080
 7BY  CAR  H10  single    0.970  0.020  1.090
 7BY  CAR  H11  single    0.970  0.020  1.090
 7BY  CAR  H12  single    0.970  0.020  1.090
 7BY  CAU  H13  single    0.970  0.020  1.090
 7BY  CAU  H14  single    0.970  0.020  1.090
 7BY  CAU  H15  single    0.970  0.020  1.090
 7BY  CAV  H16  single    0.930  0.020  1.080
 7BY  NAI  H17  single    0.860  0.020  1.020
 7BY  CAH  H18  single    0.970  0.020  1.090
 7BY  CAH  H19  single    0.970  0.020  1.090
 7BY  CAG  H20  single    0.970  0.020  1.090
 7BY  CAG  H21  single    0.970  0.020  1.090
 7BY  CAF  H22  single    0.970  0.020  1.090
 7BY  CAF  H23  single    0.970  0.020  1.090
 7BY  NAE  H24  single    0.860  0.020  1.020
 7BY  CAB  H25  single    0.970  0.020  1.090
 7BY  CAB  H26  single    0.970  0.020  1.090
 7BY  CAA  H27  single    0.970  0.020  1.090
 7BY  CAA  H28  single    0.970  0.020  1.090
 7BY  CAA  H29  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
 7BY  CAO  C4   N3   118.59  3.000
 7BY  CAO  C4   C5   118.45  3.000
 7BY  N3   C4   C5   122.96  3.000
 7BY  CAV  C5   C6   124.79  3.000
 7BY  CAV  C5   C4   120.09  3.000
 7BY  C6   C5   C4   115.12  3.000
 7BY  NAI  C6   N1   117.62  3.000
 7BY  N1   C6   C5   121.31  3.000
 7BY  NAI  C6   C5   121.07  3.000
 7BY  C2   N1   C6   118.02  3.000
 7BY  C2   N3   C4   116.09  3.000
 7BY  H2   CAY  H1   107.19  3.000
 7BY  H2   CAY  NAX  111.27  3.000
 7BY  H1   CAY  NAX  111.10  3.000
 7BY  H2   CAY  CAZ  112.83  3.000
 7BY  H1   CAY  CAZ  111.38  3.000
 7BY  NAX  CAY  CAZ  103.14  3.000
 7BY  H4   CAZ  H3   107.66  3.000
 7BY  H4   CAZ  CBA  113.38  3.000
 7BY  H3   CAZ  CBA  110.26  3.000
 7BY  H4   CAZ  CAY  112.33  3.000
 7BY  H3   CAZ  CAY  110.01  3.000
 7BY  CBA  CAZ  CAY  103.17  3.000
 7BY  H6   CBA  H5   107.70  3.000
 7BY  H6   CBA  CBB  110.03  3.000
 7BY  H5   CBA  CBB  112.25  3.000
 7BY  H6   CBA  CAZ  110.11  3.000
 7BY  H5   CBA  CAZ  113.37  3.000
 7BY  CBB  CBA  CAZ  103.35  3.000
 7BY  H8   CBB  H7   107.16  3.000
 7BY  H8   CBB  NAX  111.49  3.000
 7BY  H7   CBB  NAX  111.18  3.000
 7BY  H8   CBB  CBA  112.65  3.000
 7BY  H7   CBB  CBA  111.35  3.000
 7BY  NAX  CBB  CBA  103.06  3.000
 7BY  C2   NAX  CBB  123.86  3.000
 7BY  CBB  NAX  CAY  113.16  3.000
 7BY  C2   NAX  CAY  122.95  3.000
 7BY  NAX  C2   N3   117.89  3.000
 7BY  N3   C2   N1   126.49  3.000
 7BY  NAX  C2   N1   115.62  3.000
 7BY  H9   CAO  CAP  121.43  3.000
 7BY  H9   CAO  C4   117.45  3.000
 7BY  CAP  CAO  C4   121.12  3.000
 7BY  CAS  CAP  OAQ  114.82  3.000
 7BY  OAQ  CAP  CAO  125.04  3.000
 7BY  CAS  CAP  CAO  120.14  3.000
 7BY  CAR  OAQ  CAP  118.18  3.000
 7BY  H12  CAR  H11  108.86  3.000
 7BY  H12  CAR  H10  108.98  3.000
 7BY  H11  CAR  H10  108.94  3.000
 7BY  H12  CAR  OAQ  111.83  3.000
 7BY  H11  CAR  OAQ  111.67  3.000
 7BY  H10  CAR  OAQ  106.47  3.000
 7BY  CAV  CAS  OAT  125.70  3.000
 7BY  OAT  CAS  CAP  115.01  3.000
 7BY  CAV  CAS  CAP  119.29  3.000
 7BY  CAU  OAT  CAS  117.82  3.000
 7BY  H15  CAU  H14  108.59  3.000
 7BY  H15  CAU  H13  108.78  3.000
 7BY  H14  CAU  H13  108.85  3.000
 7BY  H15  CAU  OAT  111.94  3.000
 7BY  H14  CAU  OAT  111.96  3.000
 7BY  H13  CAU  OAT  106.63  3.000
 7BY  H16  CAV  CAS  119.02  3.000
 7BY  H16  CAV  C5   120.07  3.000
 7BY  CAS  CAV  C5   120.91  3.000
 7BY  H17  NAI  CAH  117.18  3.000
 7BY  H17  NAI  C6   119.01  3.000
 7BY  CAH  NAI  C6   123.39  3.000
 7BY  H19  CAH  H18  106.37  3.000
 7BY  H19  CAH  CAG  110.12  3.000
 7BY  H18  CAH  CAG  110.11  3.000
 7BY  H19  CAH  NAI  109.24  3.000
 7BY  H18  CAH  NAI  110.77  3.000
 7BY  CAG  CAH  NAI  110.15  3.000
 7BY  H21  CAG  H20  107.28  3.000
 7BY  H21  CAG  CAF  109.38  3.000
 7BY  H20  CAG  CAF  109.41  3.000
 7BY  H21  CAG  CAH  109.96  3.000
 7BY  H20  CAG  CAH  109.61  3.000
 7BY  CAF  CAG  CAH  111.12  3.000
 7BY  H23  CAF  H22  106.94  3.000
 7BY  H23  CAF  NAE  108.99  3.000
 7BY  H22  CAF  NAE  107.58  3.000
 7BY  H23  CAF  CAG  109.93  3.000
 7BY  H22  CAF  CAG  110.09  3.000
 7BY  NAE  CAF  CAG  113.10  3.000
 7BY  H24  NAE  CAC  118.59  3.000
 7BY  H24  NAE  CAF  117.64  3.000
 7BY  CAC  NAE  CAF  123.44  3.000
 7BY  CAB  CAC  OAD  122.39  3.000
 7BY  OAD  CAC  NAE  122.65  3.000
 7BY  CAB  CAC  NAE  114.96  3.000
 7BY  H26  CAB  H25  105.83  3.000
 7BY  H26  CAB  CAA  110.57  3.000
 7BY  H25  CAB  CAA  109.79  3.000
 7BY  H26  CAB  CAC  110.12  3.000
 7BY  H25  CAB  CAC  106.97  3.000
 7BY  CAA  CAB  CAC  113.23  3.000
 7BY  H29  CAA  H28  107.97  3.000
 7BY  H29  CAA  H27  107.82  3.000
 7BY  H28  CAA  H27  107.65  3.000
 7BY  H29  CAA  CAB  111.58  3.000
 7BY  H28  CAA  CAB  111.52  3.000
 7BY  H27  CAA  CAB  110.14  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
 7BY  CONST_01  N1   C6   C5   C4      0.00   0.0  0
 7BY  CONST_02  CAS  CAV  C5   C4      0.00   0.0  0
 7BY  CONST_03  N1   C2   N3   C4      0.00   0.0  0
 7BY  CONST_04  CAS  CAP  CAO  C4      0.00   0.0  0
 7BY  CONST_05  C2   N1   C6   C5      0.00   0.0  0
 7BY  CONST_06  CAP  CAS  CAV  C5      0.00   0.0  0
 7BY  CONST_07  C2   N3   C4   C5      0.00   0.0  0
 7BY  CONST_08  CAP  CAO  C4   C5      0.00   0.0  0
 7BY  CONST_09  N3   C2   N1   C6      0.00   0.0  0
 7BY  CONST_10  CAS  CAV  C5   C6    180.00   0.0  0
 7BY  CONST_11  N3   C4   C5   C6      0.00   0.0  0
 7BY  CONST_12  CAO  C4   C5   C6    180.00   0.0  0
 7BY  CONST_13  CAV  C5   C6   N1    180.00   0.0  0
 7BY  CONST_14  CAV  C5   C4   N3    180.00   0.0  0
 7BY  CONST_15  CAP  CAO  C4   N3    180.00   0.0  0
 7BY  CONST_16  CAO  C4   N3   C2    180.00   0.0  0
 7BY  CONST_17  CAV  C5   C4   CAO     0.00   0.0  0
 7BY  CONST_18  CAV  CAS  CAP  CAO     0.00   0.0  0
 7BY  CONST_19  NAX  C2   N3   C4    180.00   0.0  0
 7BY  CONST_20  NAX  C2   N1   C6    180.00   0.0  0
 7BY  CONST_21  NAI  C6   C5   C4    180.00   0.0  0
 7BY  CONST_22  OAQ  CAP  CAO  C4    180.00   0.0  0
 7BY  CONST_23  OAT  CAS  CAV  C5    180.00   0.0  0
 7BY  CONST_24  NAI  C6   N1   C2    180.00   0.0  0
 7BY  CONST_25  OAT  CAS  CAP  CAO   180.00   0.0  0
 7BY  CONST_26  CAV  CAS  CAP  OAQ   180.00   0.0  0
 7BY  CONST_27  NAI  C6   C5   CAV     0.00   0.0  0
 7BY  CONST_28  H16  CAV  C5   C4    180.00   0.0  0
 7BY  CONST_29  H9   CAO  C4   C5    180.00   0.0  0
 7BY  CONST_30  CAH  NAI  C6   C5    180.00   0.0  0
 7BY  CONST_31  CAH  NAI  C6   N1      0.00   0.0  0
 7BY  CONST_32  H17  NAI  C6   C5      0.00   0.0  0
 7BY  CONST_33  CAB  CAC  NAE  CAF   180.00   0.0  0
 7BY  CONST_34  OAD  CAC  NAE  CAF     0.00   0.0  0
 7BY  CONST_35  H24  NAE  CAC  OAD   180.00   0.0  0
 7BY  Var_01    CAY  NAX  C2   N1    176.49  30.0  1
 7BY  Var_02    CBB  CBA  CAZ  CAY    37.86  30.0  1
 7BY  Var_03    CBA  CBB  NAX  CAY    11.16  30.0  1
 7BY  Var_04    C2   NAX  CAY  CAZ  -165.62  30.0  1
 7BY  Var_05    NAX  CBB  CBA  CAZ   -30.02  30.0  1
 7BY  Var_06    NAX  CAY  CAZ  CBA   -30.70  30.0  1
 7BY  Var_07    CAS  CAP  OAQ  CAR   178.29  30.0  2
 7BY  Var_08    CAV  CAS  OAT  CAU    -0.60  30.0  1
 7BY  Var_09    CAG  CAH  NAI  C6    171.29  30.0  2
 7BY  Var_10    H10  CAR  OAQ  CAP  -178.70  30.0  3
 7BY  Var_11    H13  CAU  OAT  CAS  -178.91  30.0  3
 7BY  Var_12    CAF  CAG  CAH  NAI  -177.27  30.0  2
 7BY  Var_13    NAE  CAF  CAG  CAH  -177.66  30.0  2
 7BY  Var_14    CAC  NAE  CAF  CAG   -82.52  30.0  1
 7BY  Var_15    CAA  CAB  CAC  NAE   149.70  30.0  2
 7BY  Var_16    H27  CAA  CAB  CAC   178.61  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
 7BY  plan-1  C4   0.020
 7BY  plan-1  C5   0.020
 7BY  plan-1  C6   0.020
 7BY  plan-1  N1   0.020
 7BY  plan-1  N3   0.020
 7BY  plan-1  NAX  0.020
 7BY  plan-1  C2   0.020
 7BY  plan-1  CAO  0.020
 7BY  plan-1  CAP  0.020
 7BY  plan-1  OAQ  0.020
 7BY  plan-1  CAS  0.020
 7BY  plan-1  OAT  0.020
 7BY  plan-1  CAV  0.020
 7BY  plan-1  NAI  0.020
 7BY  plan-1  H9   0.020
 7BY  plan-1  H16  0.020
 7BY  plan-2  C6   0.020
 7BY  plan-2  NAI  0.020
 7BY  plan-2  CAH  0.020
 7BY  plan-2  H17  0.020
 7BY  plan-3  CAF  0.020
 7BY  plan-3  NAE  0.020
 7BY  plan-3  CAC  0.020
 7BY  plan-3  OAD  0.020
 7BY  plan-3  CAB  0.020
 7BY  plan-3  H24  0.020

