# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 20:46:37 2020
#   Inital geometry file: a 170 line input string
#   Ligand name: ~{N}-[2-[(2~{S})-2-[(dipropylamino)methyl]piperidin-1-yl]ethyl]-6-oxidanylidene-5~{H}-pyrido[2,3-b][1,4]benzodiazepine-11-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCN(CCC)C[C@@H]1CCCCN1CCNC(=O)N2c3ccccc3C(=O)Nc4cccnc24
#
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
 82F  82F  ~{N}-[2-[(2~{S})-2-[(dipropylamino)methyl]piperidin-1-yl]ethyl]-6-oxidanylidene-5~{H}-pyrido[2,3-b][1,4]benzodiazepine-11-carboxamide  ligand  73  35  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_82F
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
 82F  C4   C  CR16  0  -0.075  -2.7633  -0.5511  -3.6798
 82F  C5   C  CR6   0   0.316  -2.9703  -0.2402  -1.4340
 82F  C6   C  CR6   0   0.319  -4.1715   0.8364   0.3274
 82F  N1   N  N     0  -0.383  -2.7422   0.2620  -2.6329
 82F  C7   C  CR16  0  -0.250  -4.7896   2.0803   0.2857
 82F  C8   C  CR16  0  -0.262  -6.0131   2.2656   0.9058
 82F  N2   N  NT    0  -0.670  -2.9337   0.6292  -0.3254
 82F  C9   C  CR16  0  -0.240  -6.6302   1.2075   1.5638
 82F  C10  C  CR16  0  -0.291  -6.0141  -0.0295   1.6085
 82F  C11  C  CR6   0  -0.091  -4.7822  -0.2295   0.9843
 82F  C12  C  C     0   0.736  -1.7960   1.2856   0.1264
 82F  N3   N  NH1   0  -0.690  -0.6541   1.0220  -0.5327
 82F  C13  C  CH2   0  -0.243   0.6121   1.5644  -0.0845
 82F  C14  C  CH2   0  -0.343   1.7133   1.1257  -1.0440
 82F  C15  C  CH2   0  -0.286   3.1938   2.9829  -0.9229
 82F  N4   N  NT    0  -0.433   3.0193   1.5720  -0.5955
 82F  N    N  NH1   0  -0.741  -3.4561  -2.0927   0.0720
 82F  C    C  C     0   0.508  -4.1606  -1.5761   1.1180
 82F  O    O  O     0  -0.449  -4.3182  -2.2340   2.1312
 82F  C1   C  CR6   0   0.300  -3.2676  -1.5835  -1.2105
 82F  C16  C  CH2   0  -0.433   4.4747   3.5601  -0.3525
 82F  C17  C  CH2   0  -0.441   5.6676   2.7818  -0.8792
 82F  C18  C  CH2   0  -0.415   5.4654   1.3061  -0.5791
 82F  C19  C  CH1   0  -0.047   4.1357   0.7650  -1.1050
 82F  C2   C  CR16  0  -0.194  -3.3026  -2.4282  -2.3148
 82F  C20  C  CH2   0  -0.327   4.0676  -0.7390  -0.7948
 82F  C21  C  CH2   0  -0.274   3.2092  -0.9039   1.4619
 82F  C22  C  CH2   0  -0.435   3.5946  -0.7918   2.9306
 82F  C23  C  CH3   0  -0.667   2.3785  -0.5217   3.8070
 82F  C24  C  CH2   0  -0.268   4.8946  -2.4571   0.6634
 82F  C25  C  CH2   0  -0.425   6.3891  -2.5016   0.3731
 82F  C26  C  CH3   0  -0.668   6.9493  -3.9145   0.4619
 82F  C3   C  CR16  0  -0.317  -3.0415  -1.9058  -3.5678
 82F  N5   N  NT    0  -0.406   4.3421  -1.1151   0.5786
 82F  O1   O  O     0  -0.517  -1.8550   2.0387   1.0848
 82F  H1   H  HCR6  0   0.276  -2.5501  -0.1073  -4.6443
 82F  H2   H  HCR6  0   0.268  -4.3092   2.8977  -0.2342
 82F  H3   H  HCR6  0   0.271  -6.4888   3.2368   0.8734
 82F  H4   H  HCR6  0   0.268  -7.5891   1.3502   2.0432
 82F  H5   H  HCR6  0   0.272  -6.4905  -0.8501   2.1273
 82F  H6   H  HNH1  0   0.408  -0.6379   0.3578  -1.2883
 82F  H7   H  HCH2  0   0.240   0.5427   2.6518  -0.0292
 82F  H8   H  HCH2  0   0.231   0.8535   1.2054   0.9201
 82F  H9   H  HCH2  0   0.248   1.6895   0.0369  -1.0869
 82F  H10  H  HCH2  0   0.222   1.4848   1.4800  -2.0630
 82F  H11  H  HCH2  0   0.184   3.1894   3.1299  -2.0186
 82F  H12  H  HCH2  0   0.237   2.3413   3.5435  -0.5352
 82F  H14  H  HNH1  0   0.416  -3.1714  -3.0545   0.2076
 82F  H15  H  HCH2  0   0.229   4.5405   4.6186  -0.6142
 82F  H16  H  HCH2  0   0.214   4.4446   3.4991   0.7395
 82F  H17  H  HCH2  0   0.207   5.7597   2.9376  -1.9597
 82F  H18  H  HCH2  0   0.228   6.5981   3.1372  -0.4304
 82F  H19  H  HCH2  0   0.218   6.2745   0.7106  -1.0109
 82F  H20  H  HCH2  0   0.226   5.4995   1.1392   0.4995
 82F  H21  H  HCH1  0   0.187   4.1556   0.8348  -2.2103
 82F  H22  H  HCR6  0   0.297  -3.5218  -3.4806  -2.1876
 82F  H23  H  HCH2  0   0.216   3.1279  -1.1867  -1.1565
 82F  H24  H  HCH2  0   0.242   4.8423  -1.1796  -1.4257
 82F  H25  H  HCH2  0   0.175   2.4381  -1.6870   1.3392
 82F  H26  H  HCH2  0   0.246   2.7476   0.0403   1.1782
 82F  H27  H  HCH2  0   0.215   4.0902  -1.7024   3.2774
 82F  H28  H  HCH2  0   0.214   4.3232   0.0162   3.0367
 82F  H29  H  HCH3  0   0.216   1.8862   0.4122   3.5276
 82F  H30  H  HCH3  0   0.217   1.6411  -1.3212   3.7159
 82F  H31  H  HCH3  0   0.230   2.6541  -0.4453   4.8591
 82F  H32  H  HCH2  0   0.188   4.3642  -3.1578  -0.0051
 82F  H33  H  HCH2  0   0.223   4.7350  -2.8390   1.6742
 82F  H34  H  HCH2  0   0.214   6.5963  -2.0918  -0.6199
 82F  H35  H  HCH2  0   0.214   6.8978  -1.8470   1.0851
 82F  H36  H  HCH3  0   0.216   6.7867  -4.3441   1.4524
 82F  H37  H  HCH3  0   0.217   6.4752  -4.5769  -0.2650
 82F  H38  H  HCH3  0   0.229   8.0222  -3.9307   0.2686
 82F  H39  H  HCR6  0   0.285  -3.0584  -2.5371  -4.4448

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
 82F  C17  C18  single    1.519  0.020  1.519
 82F  C17  C16  single    1.519  0.020  1.519
 82F  C20  C19  single    1.537  0.020  1.537
 82F  C20  N5   single    1.450  0.020  1.450
 82F  C18  C19  single    1.529  0.020  1.529
 82F  C16  C15  single    1.516  0.020  1.516
 82F  C24  N5   single    1.454  0.020  1.454
 82F  C24  C25  single    1.523  0.020  1.523
 82F  C19  N4   single    1.469  0.020  1.469
 82F  N5   C21  single    1.452  0.020  1.452
 82F  C15  N4   single    1.459  0.020  1.459
 82F  C26  C25  single    1.522  0.020  1.522
 82F  C21  C22  single    1.523  0.020  1.523
 82F  N4   C14  single    1.451  0.020  1.451
 82F  C22  C23  single    1.523  0.020  1.523
 82F  C14  C13  single    1.525  0.020  1.525
 82F  C13  N3   single    1.449  0.020  1.449
 82F  O1   C12  double    1.220  0.020  1.220
 82F  O    C    double    1.218  0.020  1.218
 82F  N3   C12  single    1.345  0.020  1.345
 82F  C12  N2   single    1.389  0.020  1.389
 82F  N    C    single    1.363  0.020  1.363
 82F  N    C1   single    1.393  0.020  1.393
 82F  C    C11  single    1.489  0.020  1.489
 82F  C1   C2   aromatic  1.391  0.020  1.391
 82F  C1   C5   aromatic  1.394  0.020  1.394
 82F  N2   C5   single    1.409  0.020  1.409
 82F  N2   C6   single    1.415  0.020  1.415
 82F  C2   C3   aromatic  1.382  0.020  1.382
 82F  C5   N1   aromatic  1.320  0.020  1.320
 82F  C11  C6   aromatic  1.393  0.020  1.393
 82F  C11  C10  aromatic  1.395  0.020  1.395
 82F  C6   C7   aromatic  1.390  0.020  1.390
 82F  C3   C4   aromatic  1.387  0.020  1.387
 82F  N1   C4   aromatic  1.326  0.020  1.326
 82F  C10  C9   aromatic  1.383  0.020  1.383
 82F  C7   C8   aromatic  1.384  0.020  1.384
 82F  C9   C8   aromatic  1.390  0.020  1.390
 82F  C4   H1   single    0.930  0.020  1.080
 82F  C7   H2   single    0.930  0.020  1.080
 82F  C8   H3   single    0.930  0.020  1.080
 82F  C9   H4   single    0.930  0.020  1.080
 82F  C10  H5   single    0.930  0.020  1.080
 82F  N3   H6   single    0.860  0.020  1.020
 82F  C13  H7   single    0.970  0.020  1.090
 82F  C13  H8   single    0.970  0.020  1.090
 82F  C14  H9   single    0.970  0.020  1.090
 82F  C14  H10  single    0.970  0.020  1.090
 82F  C15  H11  single    0.970  0.020  1.090
 82F  C15  H12  single    0.970  0.020  1.090
 82F  N    H14  single    0.860  0.020  1.020
 82F  C16  H15  single    0.970  0.020  1.090
 82F  C16  H16  single    0.970  0.020  1.090
 82F  C17  H17  single    0.970  0.020  1.090
 82F  C17  H18  single    0.970  0.020  1.090
 82F  C18  H19  single    0.970  0.020  1.090
 82F  C18  H20  single    0.970  0.020  1.090
 82F  C19  H21  single    0.970  0.020  1.090
 82F  C2   H22  single    0.930  0.020  1.080
 82F  C20  H23  single    0.970  0.020  1.090
 82F  C20  H24  single    0.970  0.020  1.090
 82F  C21  H25  single    0.970  0.020  1.090
 82F  C21  H26  single    0.970  0.020  1.090
 82F  C22  H27  single    0.970  0.020  1.090
 82F  C22  H28  single    0.970  0.020  1.090
 82F  C23  H29  single    0.970  0.020  1.090
 82F  C23  H30  single    0.970  0.020  1.090
 82F  C23  H31  single    0.970  0.020  1.090
 82F  C24  H32  single    0.970  0.020  1.090
 82F  C24  H33  single    0.970  0.020  1.090
 82F  C25  H34  single    0.970  0.020  1.090
 82F  C25  H35  single    0.970  0.020  1.090
 82F  C26  H36  single    0.970  0.020  1.090
 82F  C26  H37  single    0.970  0.020  1.090
 82F  C26  H38  single    0.970  0.020  1.090
 82F  C3   H39  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
 82F  H1   C4   C3   120.76  3.000
 82F  H1   C4   N1   116.67  3.000
 82F  C3   C4   N1   122.57  3.000
 82F  C1   C5   N2   118.29  3.000
 82F  N2   C5   N1   118.38  3.000
 82F  C1   C5   N1   123.32  3.000
 82F  C11  C6   N2   119.28  3.000
 82F  C11  C6   C7   120.27  3.000
 82F  N2   C6   C7   120.43  3.000
 82F  C5   N1   C4   118.77  3.000
 82F  H2   C7   C8   120.46  3.000
 82F  H2   C7   C6   119.56  3.000
 82F  C8   C7   C6   119.97  3.000
 82F  H3   C8   C9   120.14  3.000
 82F  H3   C8   C7   119.70  3.000
 82F  C9   C8   C7   120.16  3.000
 82F  C12  N2   C6   119.83  3.000
 82F  C6   N2   C5   115.51  3.000
 82F  C12  N2   C5   124.65  3.000
 82F  H4   C9   C10  119.92  3.000
 82F  H4   C9   C8   120.19  3.000
 82F  C10  C9   C8   119.89  3.000
 82F  H5   C10  C11  119.65  3.000
 82F  H5   C10  C9   119.87  3.000
 82F  C11  C10  C9   120.47  3.000
 82F  C    C11  C10  117.25  3.000
 82F  C10  C11  C6   119.23  3.000
 82F  C    C11  C6   123.46  3.000
 82F  O1   C12  N3   123.17  3.000
 82F  N3   C12  N2   116.33  3.000
 82F  O1   C12  N2   120.50  3.000
 82F  H6   N3   C13  117.74  3.000
 82F  H6   N3   C12  120.75  3.000
 82F  C13  N3   C12  121.15  3.000
 82F  H8   C13  H7   107.14  3.000
 82F  H8   C13  C14  108.91  3.000
 82F  H7   C13  C14  111.38  3.000
 82F  H8   C13  N3   110.74  3.000
 82F  H7   C13  N3   109.47  3.000
 82F  C14  C13  N3   109.20  3.000
 82F  H10  C14  H9   106.27  3.000
 82F  H10  C14  N4   111.91  3.000
 82F  H9   C14  N4   109.82  3.000
 82F  H10  C14  C13  109.83  3.000
 82F  H9   C14  C13  107.24  3.000
 82F  N4   C14  C13  111.53  3.000
 82F  H12  C15  H11  106.30  3.000
 82F  H12  C15  C16  109.31  3.000
 82F  H11  C15  C16  109.00  3.000
 82F  H12  C15  N4   108.88  3.000
 82F  H11  C15  N4   110.52  3.000
 82F  C16  C15  N4   112.63  3.000
 82F  C19  N4   C15  111.27  3.000
 82F  C15  N4   C14  109.62  3.000
 82F  C19  N4   C14  114.07  3.000
 82F  H14  N    C1   115.64  3.000
 82F  H14  N    C    113.75  3.000
 82F  C1   N    C    129.65  3.000
 82F  O    C    N    120.03  3.000
 82F  N    C    C11  119.31  3.000
 82F  O    C    C11  120.60  3.000
 82F  C2   C1   N    120.38  3.000
 82F  C2   C1   C5   117.60  3.000
 82F  N    C1   C5   121.93  3.000
 82F  H16  C16  H15  107.14  3.000
 82F  H16  C16  C17  109.83  3.000
 82F  H15  C16  C17  111.48  3.000
 82F  H16  C16  C15  109.33  3.000
 82F  H15  C16  C15  109.25  3.000
 82F  C17  C16  C15  109.76  3.000
 82F  H18  C17  H17  106.70  3.000
 82F  H18  C17  C18  110.38  3.000
 82F  H17  C17  C18  110.13  3.000
 82F  H18  C17  C16  111.09  3.000
 82F  H17  C17  C16  109.59  3.000
 82F  C18  C17  C16  108.95  3.000
 82F  H20  C18  H19  106.48  3.000
 82F  H20  C18  C19  108.23  3.000
 82F  H19  C18  C19  108.36  3.000
 82F  H20  C18  C17  109.84  3.000
 82F  H19  C18  C17  110.63  3.000
 82F  C19  C18  C17  113.05  3.000
 82F  H21  C19  C20  105.30  3.000
 82F  H21  C19  C18  107.77  3.000
 82F  C20  C19  C18  108.38  3.000
 82F  H21  C19  N4   108.98  3.000
 82F  C18  C19  N4   110.32  3.000
 82F  C20  C19  N4   115.72  3.000
 82F  H22  C2   C3   120.80  3.000
 82F  H22  C2   C1   120.15  3.000
 82F  C3   C2   C1   119.04  3.000
 82F  H24  C20  H23  104.56  3.000
 82F  H24  C20  N5   107.95  3.000
 82F  H23  C20  N5   111.53  3.000
 82F  H24  C20  C19  104.28  3.000
 82F  H23  C20  C19  111.66  3.000
 82F  N5   C20  C19  115.88  3.000
 82F  H26  C21  H25  106.84  3.000
 82F  H26  C21  N5   107.37  3.000
 82F  H25  C21  N5   111.94  3.000
 82F  H26  C21  C22  107.15  3.000
 82F  H25  C21  C22  109.61  3.000
 82F  N5   C21  C22  113.58  3.000
 82F  H28  C22  H27  106.43  3.000
 82F  H28  C22  C23  110.20  3.000
 82F  H27  C22  C23  109.09  3.000
 82F  H28  C22  C21  108.47  3.000
 82F  H27  C22  C21  111.06  3.000
 82F  C23  C22  C21  111.47  3.000
 82F  H31  C23  H30  107.62  3.000
 82F  H31  C23  H29  107.51  3.000
 82F  H30  C23  H29  107.49  3.000
 82F  H31  C23  C22  111.46  3.000
 82F  H30  C23  C22  111.19  3.000
 82F  H29  C23  C22  111.37  3.000
 82F  H33  C24  H32  105.56  3.000
 82F  H33  C24  N5   108.73  3.000
 82F  H32  C24  N5   111.58  3.000
 82F  H33  C24  C25  108.04  3.000
 82F  H32  C24  C25  109.72  3.000
 82F  N5   C24  C25  112.88  3.000
 82F  H35  C25  H34  106.19  3.000
 82F  H35  C25  C26  110.28  3.000
 82F  H34  C25  C26  109.32  3.000
 82F  H35  C25  C24  108.37  3.000
 82F  H34  C25  C24  110.36  3.000
 82F  C26  C25  C24  112.15  3.000
 82F  H38  C26  H37  107.47  3.000
 82F  H38  C26  H36  107.55  3.000
 82F  H37  C26  H36  107.49  3.000
 82F  H38  C26  C25  111.44  3.000
 82F  H37  C26  C25  111.37  3.000
 82F  H36  C26  C25  111.31  3.000
 82F  H39  C3   C2   120.78  3.000
 82F  H39  C3   C4   120.54  3.000
 82F  C2   C3   C4   118.68  3.000
 82F  C24  N5   C21  113.29  3.000
 82F  C21  N5   C20  113.00  3.000
 82F  C24  N5   C20  111.51  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
 82F  CONST_01  C1   C2   C3   C4      0.00   0.0  0
 82F  CONST_02  C3   C4   N1   C5      0.00   0.0  0
 82F  CONST_03  C9   C8   C7   C6      0.00   0.0  0
 82F  CONST_04  C2   C3   C4   N1      0.00   0.0  0
 82F  CONST_05  C10  C9   C8   C7      0.00   0.0  0
 82F  CONST_06  C11  C10  C9   C8      0.00   0.0  0
 82F  CONST_07  H22  C2   C3   C4    180.00   0.0  0
 82F  CONST_08  H1   C4   N1   C5    180.00   0.0  0
 82F  CONST_09  H3   C8   C7   C6    180.00   0.0  0
 82F  CONST_10  H39  C3   C4   N1    180.00   0.0  0
 82F  CONST_11  H4   C9   C8   C7    180.00   0.0  0
 82F  CONST_12  H5   C10  C9   C8    180.00   0.0  0
 82F  CONST_13  H2   C7   C8   C9    180.00   0.0  0
 82F  CONST_14  C13  N3   C12  N2    180.00   0.0  0
 82F  CONST_15  H6   N3   C12  N2      0.00   0.0  0
 82F  CONST_16  O1   C12  N3   C13     0.00   0.0  0
 82F  Var_01    C18  C17  C16  C15   -54.45  30.0  1
 82F  Var_02    C17  C16  C15  N4     58.50  30.0  1
 82F  Var_03    C19  C18  C17  C16    54.15  30.0  1
 82F  Var_04    C19  N4   C15  C16   -59.08  30.0  1
 82F  Var_05    N4   C14  C13  N3   -176.39  30.0  2
 82F  Var_06    C24  N5   C20  C19  -151.86  30.0  3
 82F  Var_07    C14  C13  N3   C12  -178.56  30.0  1
 82F  Var_08    C25  C24  N5   C20    81.30  30.0  1
 82F  Var_09    C22  C21  N5   C20  -158.71  30.0  3
 82F  Var_10    N5   C21  C22  C23   177.97  30.0  1
 82F  Var_11    N5   C24  C25  C26  -179.82  30.0  1
 82F  Var_12    H29  C23  C22  C21   -60.16  30.0  3
 82F  Var_13    H36  C26  C25  C24   -58.99  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 82F  chir_01  C19  C20  C18  N4  positiv

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
 82F  plan-1  C5   0.020
 82F  plan-1  C6   0.020
 82F  plan-1  N2   0.020
 82F  plan-1  C12  0.020
 82F  plan-1  N3   0.020
 82F  plan-1  C13  0.020
 82F  plan-1  O1   0.020
 82F  plan-1  H6   0.020
 82F  plan-2  C4   0.020
 82F  plan-2  C5   0.020
 82F  plan-2  C6   0.020
 82F  plan-2  N1   0.020
 82F  plan-2  C7   0.020
 82F  plan-2  C8   0.020
 82F  plan-2  N2   0.020
 82F  plan-2  C9   0.020
 82F  plan-2  C10  0.020
 82F  plan-2  C11  0.020
 82F  plan-2  N    0.020
 82F  plan-2  C    0.020
 82F  plan-2  O    0.020
 82F  plan-2  C1   0.020
 82F  plan-2  C2   0.020
 82F  plan-2  C3   0.020
 82F  plan-2  H1   0.020
 82F  plan-2  H2   0.020
 82F  plan-2  H3   0.020
 82F  plan-2  H4   0.020
 82F  plan-2  H5   0.020
 82F  plan-2  H14  0.020
 82F  plan-2  H22  0.020
 82F  plan-2  H39  0.020

