# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 00:17:16 2020
#   Inital geometry file: a 149 line input string
#   Ligand name: 4-(2-cyclopropylethylidene)-6-{[(2R)-3,3-dimethylbutan-2-yl]amino}-9-(1H-pyrazol-4-yl)benzo[c][1,6]naphthyridin-1(4H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](Nc1nc2\C(=C\CC3CC3)C=NC(=O)c2c4cc(ccc14)c5c[nH]nc5)C(C)(C)C
#
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
 MP6  MP6  4-(2-cyclopropylethylidene)-6-{[(2R)-3,3-dimethylbutan-2-yl]amino}-9-(1H-pyrazol-4-yl)benzo[c][1,6]naphthyridin-1(4H)-one  ligand  61  32  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_MP6
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
 MP6  C     C  CR6   0   0.518  -0.3265  -1.2122   0.3206
 MP6  N     N  N     0  -0.528  -1.2802  -0.3141   0.4347
 MP6  O     O  O     0  -0.436   1.6030   3.4829   0.4556
 MP6  C1    C  CR66  0  -0.096   1.0624  -0.8304   0.1796
 MP6  C2    C  CR66  0   0.293   1.3854   0.5464   0.2093
 MP6  C3    C  CR16  0  -0.482   2.7392   0.9045   0.0643
 MP6  C4    C  CR6   0   0.174   3.7394  -0.0349  -0.1074
 MP6  C5    C  CR16  0  -0.340   3.3920  -1.3972  -0.1378
 MP6  C6    C  CR16  0  -0.287   2.0841  -1.7766   0.0005
 MP6  C7    C  CR66  0  -0.255   0.3089   1.4976   0.3643
 MP6  C8    C  CR66  0   0.293  -0.9777   0.9866   0.4491
 MP6  C9    C  CR6   0  -0.034  -2.1093   1.9094   0.5735
 MP6  C10   C  CR16  0  -0.072  -1.7844   3.3145   0.5756
 MP6  N11   N  N     0  -0.433  -0.6037   3.8001   0.5150
 MP6  C12   C  CR6   0   0.422   0.5069   2.9453   0.4442
 MP6  N13   N  NH1   0  -0.684  -0.6829  -2.5018   0.3196
 MP6  C14   C  CH1   0  -0.034  -2.0521  -2.9735   0.4631
 MP6  C15   C  CH3   0  -0.670  -2.4107  -3.0833   1.9424
 MP6  C16   C  CT    0  -0.118  -2.2612  -4.2685  -0.3571
 MP6  C17   C  CH3   0  -0.658  -1.4497  -5.4425   0.1974
 MP6  C18   C  CH3   0  -0.647  -3.7472  -4.6368  -0.3237
 MP6  C19   C  CH3   0  -0.632  -1.8660  -4.0118  -1.8143
 MP6  C20   C  C1    0  -0.175  -3.3782   1.4583   0.6770
 MP6  C21   C  CH2   0  -0.532  -4.6367   2.2397   0.7809
 MP6  C22   C  CH1   0  -0.237  -5.5308   1.9342  -0.4040
 MP6  C23   C  CH2   0  -0.492  -6.4979   2.9722  -0.8801
 MP6  C24   C  CH2   0  -0.480  -5.2909   2.6339  -1.7043
 MP6  C25   C  CR5   0  -0.104   5.1286   0.3821  -0.2597
 MP6  C26   C  CR15  0  -0.116   5.6562   1.6931  -0.2957
 MP6  N27   N  N     0  -0.257   6.9641   1.6881  -0.4473
 MP6  N28   N  NR15  0  -0.427   7.2959   0.4034  -0.5099
 MP6  C29   C  CR15  0  -0.001   6.2472  -0.4198  -0.4043
 MP6  H3    H  HCR6  0   0.265   2.9980   1.9491   0.0855
 MP6  H5    H  HCR6  0   0.254   4.1493  -2.1575  -0.2747
 MP6  H6    H  HCR6  0   0.246   1.8659  -2.8353  -0.0408
 MP6  H10   H  HCR6  0   0.272  -2.5977   4.0318   0.6308
 MP6  HN13  H  HNH1  0   0.402   0.0412  -3.1981   0.3625
 MP6  H14   H  HCH1  0   0.253  -2.6884  -2.2083   0.0150
 MP6  H15   H  HCH3  0   0.234  -3.4481  -3.3837   2.0850
 MP6  H15A  H  HCH3  0   0.226  -1.7741  -3.8022   2.4596
 MP6  H15B  H  HCH3  0   0.242  -2.2808  -2.1143   2.4237
 MP6  H17   H  HCH3  0   0.234  -1.7560  -5.7058   1.2107
 MP6  H17A  H  HCH3  0   0.237  -1.5951  -6.3253  -0.4279
 MP6  H17B  H  HCH3  0   0.220  -0.3741  -5.2499   0.2158
 MP6  H18   H  HCH3  0   0.226  -4.3711  -3.8057  -0.6610
 MP6  H18A  H  HCH3  0   0.232  -3.9398  -5.4799  -0.9897
 MP6  H18B  H  HCH3  0   0.230  -4.0827  -4.9254   0.6726
 MP6  H19   H  HCH3  0   0.223  -0.8069  -3.7764  -1.9269
 MP6  H19A  H  HCH3  0   0.228  -2.0723  -4.8945  -2.4222
 MP6  H19B  H  HCH3  0   0.225  -2.4362  -3.1796  -2.2334
 MP6  H20   H  H     0   0.294  -3.5058   0.3801   0.6632
 MP6  H21   H  HCH2  0   0.278  -5.1448   1.9334   1.7012
 MP6  H21A  H  HCH2  0   0.261  -4.4726   3.3148   0.8557
 MP6  H22   H  HCH1  0   0.264  -5.8585   0.9017  -0.4659
 MP6  H23   H  HCH2  0   0.255  -7.4689   2.6460  -1.2296
 MP6  H23A  H  HCH2  0   0.248  -6.5076   3.9254  -0.3657
 MP6  H24   H  HCH2  0   0.244  -4.4870   3.3599  -1.7464
 MP6  H24A  H  HCH2  0   0.253  -5.4328   2.0762  -2.6209
 MP6  H26   H  HCR5  0   0.260   5.1269   2.6310  -0.2167
 MP6  HN28  H  HNR5  0   0.426   8.2613   0.1385  -0.6249
 MP6  H29   H  HCR5  0   0.293   6.3668  -1.4904  -0.4367

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
 MP6  C    N     aromatic  1.315  0.020  1.315
 MP6  C    C1    aromatic  1.447  0.020  1.447
 MP6  C    N13   single    1.338  0.020  1.338
 MP6  N    C8    aromatic  1.336  0.020  1.336
 MP6  O    C12   double    1.221  0.020  1.221
 MP6  C1   C2    aromatic  1.414  0.020  1.414
 MP6  C1   C6    aromatic  1.404  0.020  1.404
 MP6  C2   C3    aromatic  1.408  0.020  1.408
 MP6  C2   C7    aromatic  1.445  0.020  1.445
 MP6  C3   C4    aromatic  1.383  0.020  1.383
 MP6  C4   C5    aromatic  1.406  0.020  1.406
 MP6  C4   C25   single    1.458  0.020  1.458
 MP6  C5   C6    aromatic  1.369  0.020  1.369
 MP6  C7   C8    aromatic  1.387  0.020  1.387
 MP6  C7   C12   single    1.463  0.020  1.463
 MP6  C8   C9    single    1.465  0.020  1.465
 MP6  C9   C10   single    1.442  0.020  1.442
 MP6  C9   C20   double    1.351  0.020  1.351
 MP6  C10  N11   double    1.278  0.020  1.278
 MP6  N11  C12   single    1.403  0.020  1.403
 MP6  N13  C14   single    1.455  0.020  1.455
 MP6  C14  C15   single    1.526  0.020  1.526
 MP6  C14  C16   single    1.547  0.020  1.547
 MP6  C16  C17   single    1.531  0.020  1.531
 MP6  C16  C18   single    1.531  0.020  1.531
 MP6  C16  C19   single    1.532  0.020  1.532
 MP6  C20  C21   single    1.485  0.020  1.485
 MP6  C21  C22   single    1.515  0.020  1.515
 MP6  C22  C23   single    1.496  0.020  1.496
 MP6  C22  C24   single    1.496  0.020  1.496
 MP6  C23  C24   single    1.500  0.020  1.500
 MP6  C25  C26   aromatic  1.414  0.020  1.414
 MP6  C25  C29   aromatic  1.384  0.020  1.384
 MP6  C26  N27   aromatic  1.317  0.020  1.317
 MP6  N27  N28   aromatic  1.328  0.020  1.328
 MP6  N28  C29   aromatic  1.337  0.020  1.337
 MP6  C3   H3    single    0.930  0.020  1.080
 MP6  C5   H5    single    0.930  0.020  1.080
 MP6  C6   H6    single    0.930  0.020  1.080
 MP6  C10  H10   single    0.930  0.020  1.080
 MP6  N13  HN13  single    0.860  0.020  1.020
 MP6  C14  H14   single    0.970  0.020  1.090
 MP6  C15  H15   single    0.970  0.020  1.090
 MP6  C15  H15A  single    0.970  0.020  1.090
 MP6  C15  H15B  single    0.970  0.020  1.090
 MP6  C17  H17   single    0.970  0.020  1.090
 MP6  C17  H17A  single    0.970  0.020  1.090
 MP6  C17  H17B  single    0.970  0.020  1.090
 MP6  C18  H18   single    0.970  0.020  1.090
 MP6  C18  H18A  single    0.970  0.020  1.090
 MP6  C18  H18B  single    0.970  0.020  1.090
 MP6  C19  H19   single    0.970  0.020  1.090
 MP6  C19  H19A  single    0.970  0.020  1.090
 MP6  C19  H19B  single    0.970  0.020  1.090
 MP6  C20  H20   single    0.930  0.020  1.080
 MP6  C21  H21   single    0.970  0.020  1.090
 MP6  C21  H21A  single    0.970  0.020  1.090
 MP6  C22  H22   single    0.970  0.020  1.090
 MP6  C23  H23   single    0.970  0.020  1.090
 MP6  C23  H23A  single    0.970  0.020  1.090
 MP6  C24  H24   single    0.970  0.020  1.090
 MP6  C24  H24A  single    0.970  0.020  1.090
 MP6  C26  H26   single    0.930  0.020  1.080
 MP6  N28  HN28  single    0.860  0.020  1.020
 MP6  C29  H29   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
 MP6  N13   C    C1    120.65  3.000
 MP6  N13   C    N     117.72  3.000
 MP6  C1    C    N     121.62  3.000
 MP6  C8    N    C     120.12  3.000
 MP6  C6    C1   C2    119.50  3.000
 MP6  C6    C1   C     122.20  3.000
 MP6  C2    C1   C     118.29  3.000
 MP6  C7    C2   C3    124.06  3.000
 MP6  C7    C2   C1    118.22  3.000
 MP6  C3    C2   C1    117.71  3.000
 MP6  H3    C3   C4    119.20  3.000
 MP6  H3    C3   C2    118.43  3.000
 MP6  C4    C3   C2    122.37  3.000
 MP6  C25   C4   C5    120.67  3.000
 MP6  C25   C4   C3    120.51  3.000
 MP6  C5    C4   C3    118.83  3.000
 MP6  H5    C5   C6    119.14  3.000
 MP6  H5    C5   C4    120.70  3.000
 MP6  C6    C5   C4    120.16  3.000
 MP6  H6    C6   C5    117.40  3.000
 MP6  H6    C6   C1    121.17  3.000
 MP6  C5    C6   C1    121.43  3.000
 MP6  C12   C7   C8    119.12  3.000
 MP6  C12   C7   C2    123.81  3.000
 MP6  C8    C7   C2    117.07  3.000
 MP6  C9    C8   C7    119.31  3.000
 MP6  C9    C8   N     116.06  3.000
 MP6  C7    C8   N     124.63  3.000
 MP6  C20   C9   C10   122.47  3.000
 MP6  C20   C9   C8    121.45  3.000
 MP6  C10   C9   C8    116.08  3.000
 MP6  H10   C10  N11   116.31  3.000
 MP6  H10   C10  C9    118.36  3.000
 MP6  N11   C10  C9    125.33  3.000
 MP6  C12   N11  C10   120.13  3.000
 MP6  N11   C12  C7    119.89  3.000
 MP6  N11   C12  O     116.22  3.000
 MP6  C7    C12  O     123.88  3.000
 MP6  HN13  N13  C14   116.68  3.000
 MP6  HN13  N13  C     118.40  3.000
 MP6  C14   N13  C     124.26  3.000
 MP6  H14   C14  C16   106.89  3.000
 MP6  H14   C14  C15   108.15  3.000
 MP6  C16   C14  C15   114.95  3.000
 MP6  H14   C14  N13   106.30  3.000
 MP6  C16   C14  N13   110.25  3.000
 MP6  C15   C14  N13   109.88  3.000
 MP6  H15B  C15  H15A  107.88  3.000
 MP6  H15B  C15  H15   107.51  3.000
 MP6  H15A  C15  H15   108.18  3.000
 MP6  H15B  C15  C14   109.64  3.000
 MP6  H15A  C15  C14   111.71  3.000
 MP6  H15   C15  C14   111.75  3.000
 MP6  C19   C16  C18   108.14  3.000
 MP6  C19   C16  C17   109.66  3.000
 MP6  C18   C16  C17   108.79  3.000
 MP6  C19   C16  C14   109.22  3.000
 MP6  C18   C16  C14   108.72  3.000
 MP6  C17   C16  C14   112.22  3.000
 MP6  H17B  C17  H17A  106.45  3.000
 MP6  H17B  C17  H17   107.65  3.000
 MP6  H17A  C17  H17   107.43  3.000
 MP6  H17B  C17  C16   113.12  3.000
 MP6  H17A  C17  C16   110.00  3.000
 MP6  H17   C17  C16   111.88  3.000
 MP6  H18B  C18  H18A  107.39  3.000
 MP6  H18B  C18  H18   107.92  3.000
 MP6  H18A  C18  H18   107.36  3.000
 MP6  H18B  C18  C16   112.47  3.000
 MP6  H18A  C18  C16   110.10  3.000
 MP6  H18   C18  C16   111.38  3.000
 MP6  H19B  C19  H19A  107.69  3.000
 MP6  H19B  C19  H19   107.63  3.000
 MP6  H19A  C19  H19   107.49  3.000
 MP6  H19B  C19  C16   110.98  3.000
 MP6  H19A  C19  C16   110.21  3.000
 MP6  H19   C19  C16   112.63  3.000
 MP6  H20   C20  C21   115.07  3.000
 MP6  H20   C20  C9    116.17  3.000
 MP6  C21   C20  C9    128.74  3.000
 MP6  H21A  C21  H21   106.74  3.000
 MP6  H21A  C21  C22   109.95  3.000
 MP6  H21   C21  C22   109.08  3.000
 MP6  H21A  C21  C20   113.34  3.000
 MP6  H21   C21  C20   107.76  3.000
 MP6  C22   C21  C20   109.83  3.000
 MP6  H22   C22  C24   116.35  3.000
 MP6  H22   C22  C23   116.53  3.000
 MP6  C24   C22  C23    60.18  3.000
 MP6  H22   C22  C21   114.49  3.000
 MP6  C24   C22  C21   119.39  3.000
 MP6  C23   C22  C21   119.36  3.000
 MP6  H23A  C23  H23   114.24  3.000
 MP6  H23A  C23  C24   117.81  3.000
 MP6  H23   C23  C24   118.46  3.000
 MP6  H23A  C23  C22   117.71  3.000
 MP6  H23   C23  C22   118.27  3.000
 MP6  C24   C23  C22    59.90  3.000
 MP6  H24A  C24  H24   114.17  3.000
 MP6  H24A  C24  C23   118.42  3.000
 MP6  H24   C24  C23   117.84  3.000
 MP6  H24A  C24  C22   118.30  3.000
 MP6  H24   C24  C22   117.77  3.000
 MP6  C23   C24  C22    59.93  3.000
 MP6  C29   C25  C26   103.48  3.000
 MP6  C29   C25  C4    127.96  3.000
 MP6  C26   C25  C4    128.56  3.000
 MP6  H26   C26  N27   119.90  3.000
 MP6  H26   C26  C25   128.37  3.000
 MP6  N27   C26  C25   111.73  3.000
 MP6  N28   N27  C26   104.90  3.000
 MP6  HN28  N28  C29   126.76  3.000
 MP6  HN28  N28  N27   119.93  3.000
 MP6  C29   N28  N27   113.31  3.000
 MP6  H29   C29  N28   121.47  3.000
 MP6  H29   C29  C25   131.95  3.000
 MP6  N28   C29  C25   106.58  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
 MP6  CONST_01  C7    C8   N    C       0.00   0.0  0
 MP6  CONST_02  C3    C2   C1   C     180.00   0.0  0
 MP6  CONST_03  C7    C2   C1   C       0.00   0.0  0
 MP6  CONST_04  C5    C6   C1   C     180.00   0.0  0
 MP6  CONST_05  C2    C1   C    N       0.00   0.0  0
 MP6  CONST_06  C6    C1   C    N     180.00   0.0  0
 MP6  CONST_07  C2    C7   C8   N       0.00   0.0  0
 MP6  CONST_08  C8    N    C    C1      0.00   0.0  0
 MP6  CONST_09  C4    C3   C2   C1      0.00   0.0  0
 MP6  CONST_10  C8    C7   C2   C1      0.00   0.0  0
 MP6  CONST_11  C4    C5   C6   C1      0.00   0.0  0
 MP6  CONST_12  C5    C6   C1   C2      0.00   0.0  0
 MP6  CONST_13  C5    C4   C3   C2      0.00   0.0  0
 MP6  CONST_14  C25   C4   C3   C2    180.00   0.0  0
 MP6  CONST_15  C6    C1   C2   C3      0.00   0.0  0
 MP6  CONST_16  C8    C7   C2   C3    180.00   0.0  0
 MP6  CONST_17  C6    C5   C4   C3      0.00   0.0  0
 MP6  CONST_18  C26   C25  C4   C3      0.00   0.0  0
 MP6  CONST_19  C29   C25  C4   C3    180.00   0.0  0
 MP6  CONST_20  C7    C2   C3   C4    180.00   0.0  0
 MP6  CONST_21  N27   C26  C25  C4    180.00   0.0  0
 MP6  CONST_22  N28   C29  C25  C4    180.00   0.0  0
 MP6  CONST_23  C26   C25  C4   C5    180.00   0.0  0
 MP6  CONST_24  C29   C25  C4   C5      0.00   0.0  0
 MP6  CONST_25  C7    C2   C1   C6    180.00   0.0  0
 MP6  CONST_26  C25   C4   C5   C6    180.00   0.0  0
 MP6  CONST_27  N28   N27  C26  C25     0.00   0.0  0
 MP6  CONST_28  N27   N28  C29  C25     0.00   0.0  0
 MP6  CONST_29  N28   C29  C25  C26     0.00   0.0  0
 MP6  CONST_30  C29   N28  N27  C26     0.00   0.0  0
 MP6  CONST_31  C29   C25  C26  N27     0.00   0.0  0
 MP6  CONST_32  N13   C    C1   C2    180.00   0.0  0
 MP6  CONST_33  N13   C    C1   C6      0.00   0.0  0
 MP6  CONST_34  N13   C    N    C8    180.00   0.0  0
 MP6  CONST_35  H6    C6   C1   C       0.00   0.0  0
 MP6  CONST_36  H3    C3   C2   C1    180.00   0.0  0
 MP6  CONST_37  H5    C5   C6   C1    180.00   0.0  0
 MP6  CONST_38  H26   C26  C25  C4      0.00   0.0  0
 MP6  CONST_39  H29   C29  C25  C4      0.00   0.0  0
 MP6  CONST_40  HN28  N28  C29  C25   180.00   0.0  0
 MP6  CONST_41  C14   N13  C    N       0.00   0.0  0
 MP6  CONST_42  C14   N13  C    C1    180.00   0.0  0
 MP6  CONST_43  HN13  N13  C    N     180.00   0.0  0
 MP6  Var_01    C24   C23  C22  C21   109.06  30.0  1
 MP6  Var_02    H24   C24  C23  C22  -107.64  30.0  1
 MP6  Var_03    C21   C20  C9   C8   -178.60  30.0  2
 MP6  Var_04    C22   C21  C20  C9    118.44  30.0  3
 MP6  Var_05    C23   C22  C21  C20  -152.03  30.0  3
 MP6  Var_06    H17   C17  C16  C14    62.75  30.0  3
 MP6  Var_07    H18   C18  C16  C14    54.44  30.0  3
 MP6  Var_08    H19   C19  C16  C14    63.87  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
 MP6  chir_01  C14  N13  C15  C16  positiv
 MP6  chir_02  C22  C21  C23  C24  both

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
 MP6  plan-1  C4    0.020
 MP6  plan-1  C25   0.020
 MP6  plan-1  C26   0.020
 MP6  plan-1  N27   0.020
 MP6  plan-1  N28   0.020
 MP6  plan-1  C29   0.020
 MP6  plan-1  H26   0.020
 MP6  plan-1  HN28  0.020
 MP6  plan-1  H29   0.020
 MP6  plan-2  C     0.020
 MP6  plan-2  N     0.020
 MP6  plan-2  O     0.020
 MP6  plan-2  C1    0.020
 MP6  plan-2  C2    0.020
 MP6  plan-2  C3    0.020
 MP6  plan-2  C4    0.020
 MP6  plan-2  C5    0.020
 MP6  plan-2  C6    0.020
 MP6  plan-2  C7    0.020
 MP6  plan-2  C8    0.020
 MP6  plan-2  C9    0.020
 MP6  plan-2  C10   0.020
 MP6  plan-2  N11   0.020
 MP6  plan-2  C12   0.020
 MP6  plan-2  N13   0.020
 MP6  plan-2  C20   0.020
 MP6  plan-2  C25   0.020
 MP6  plan-2  H3    0.020
 MP6  plan-2  H5    0.020
 MP6  plan-2  H6    0.020
 MP6  plan-2  H10   0.020
 MP6  plan-3  C     0.020
 MP6  plan-3  N13   0.020
 MP6  plan-3  C14   0.020
 MP6  plan-3  HN13  0.020

