# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 16:01:22 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: 3-[(6-benzoyl-5-methylpyrrolo[2,1-f][1,2,4]triazin-4-yl)amino]-N-cyclopropyl-4-methylbenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(cc1Nc2ncnn3cc(c(C)c23)C(=O)c4ccccc4)C(=O)NC5CC5
#
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
 NK0  NK0  3-[(6-benzoyl-5-methylpyrrolo[2,1-f][1,2,4]triazin-4-yl)amino]-N-cyclopropyl-4-methylbenzamide  ligand  55  32  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_NK0
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
 NK0  C1    C  CR16  0  -0.242  -7.4016  -0.9988   0.9410
 NK0  N1    N  N     0  -0.366  -1.9363  -1.2720   0.4836
 NK0  O1    O  O     0  -0.402  -4.6007   1.4501  -1.9315
 NK0  C2    C  CR16  0  -0.249  -8.3597  -1.1956  -0.0435
 NK0  N2    N  N     0  -0.480   0.6470  -1.1462   1.1928
 NK0  O2    O  O     0  -0.483   5.0486  -1.8799   0.0764
 NK0  C3    C  CR16  0  -0.245  -8.0937  -0.8216  -1.3559
 NK0  N3    N  N     0  -0.277  -1.3896  -2.3711   1.0448
 NK0  C4    C  CR16  0  -0.276  -6.8752  -0.2479  -1.6798
 NK0  N4    N  NH1   0  -0.782   0.8601   1.0097   0.4052
 NK0  C5    C  CR6   0  -0.032  -5.8975  -0.0715  -0.7004
 NK0  N5    N  NH1   0  -0.660   6.7106  -0.3708  -0.0844
 NK0  C6    C  CR16  0  -0.284  -6.1706  -0.4474   0.6139
 NK0  C7    C  C     0   0.334  -4.6111   0.5774  -1.0814
 NK0  C8    C  CR5   0  -0.147  -3.3800   0.1114  -0.4382
 NK0  C9    C  CR15  0  -0.022  -3.2028  -1.1703   0.0790
 NK0  C10   C  CR56  0   0.339  -1.2648  -0.0807   0.2535
 NK0  C11   C  CR5   0  -0.037  -2.1519   0.8109  -0.3270
 NK0  C12   C  CH3   0  -0.825  -1.8717   2.2349  -0.6850
 NK0  C13   C  CR6   0   0.482   0.1141  -0.0850   0.6323
 NK0  C14   C  CR16  0   0.068  -0.1459  -2.2209   1.3667
 NK0  C15   C  CR6   0   0.307   2.2327   1.1669   0.6785
 NK0  C16   C  CR16  0  -0.283   3.1505   0.1836   0.3380
 NK0  C17   C  CR6   0  -0.051   4.5079   0.3779   0.5633
 NK0  C18   C  CR16  0  -0.291   4.9352   1.5666   1.1482
 NK0  C19   C  CR16  0  -0.294   4.0128   2.5428   1.4859
 NK0  C20   C  CR6   0   0.068   2.6514   2.3686   1.2616
 NK0  C21   C  CH3   0  -0.752   1.6658   3.4328   1.6380
 NK0  C22   C  C     0   0.538   5.4385  -0.7248   0.1699
 NK0  C23   C  CH1   0  -0.078   7.7004  -1.3280  -0.4562
 NK0  C24   C  CH2   0  -0.518   8.7537  -0.8962  -1.4218
 NK0  C25   C  CH2   0  -0.482   7.7029  -1.8747  -1.8494
 NK0  H1    H  HCR6  0   0.265  -7.6118  -1.2735   1.9661
 NK0  H2    H  HCR6  0   0.266  -9.3141  -1.6376   0.2115
 NK0  H3    H  HCR6  0   0.264  -8.8381  -0.9752  -2.1259
 NK0  H4    H  HCR6  0   0.264  -6.6741   0.0462  -2.7018
 NK0  HN4   H  HNH1  0   0.435   0.3988   1.8049  -0.0066
 NK0  HN5   H  HNH1  0   0.409   6.9826   0.5975  -0.0421
 NK0  H6    H  HCR6  0   0.272  -5.4357  -0.2874   1.3922
 NK0  H9    H  HCR5  0   0.312  -3.8780  -2.0067   0.1487
 NK0  H12   H  HCH3  0   0.243  -1.4532   2.7837   0.1615
 NK0  H12A  H  HCH3  0   0.261  -1.1751   2.3150  -1.5225
 NK0  H12B  H  HCH3  0   0.285  -2.7764   2.7569  -0.9788
 NK0  H14   H  HCR6  0   0.279   0.3134  -3.0846   1.8311
 NK0  H16   H  HCR6  0   0.270   2.8127  -0.7337  -0.1204
 NK0  H18   H  HCR6  0   0.260   5.9799   1.7422   1.3705
 NK0  H19   H  HCR6  0   0.262   4.3564   3.4593   1.9486
 NK0  H21   H  HCH3  0   0.258   0.8749   3.0377   2.2774
 NK0  H21A  H  HCH3  0   0.266   2.1560   4.2441   2.1721
 NK0  H21B  H  HCH3  0   0.253   1.1832   3.8702   0.7604
 NK0  H23   H  HCH1  0   0.269   8.0043  -2.0015   0.3389
 NK0  H24   H  HCH2  0   0.259   8.6942   0.1109  -1.8163
 NK0  H24A  H  HCH2  0   0.261   9.7619  -1.2506  -1.2547
 NK0  H25   H  HCH2  0   0.255   7.9796  -2.9119  -1.9858
 NK0  H25A  H  HCH2  0   0.256   6.9336  -1.5198  -2.5227

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
 NK0  C1   C2    aromatic  1.388  0.020  1.388
 NK0  C1   C6    aromatic  1.388  0.020  1.388
 NK0  N1   N3    aromatic  1.350  0.020  1.350
 NK0  N1   C9    aromatic  1.333  0.020  1.333
 NK0  N1   C10   aromatic  1.387  0.020  1.387
 NK0  O1   C7    double    1.218  0.020  1.218
 NK0  C2   C3    aromatic  1.390  0.020  1.390
 NK0  N2   C13   aromatic  1.313  0.020  1.313
 NK0  N2   C14   aromatic  1.347  0.020  1.347
 NK0  O2   C22   double    1.223  0.020  1.223
 NK0  C3   C4    aromatic  1.385  0.020  1.385
 NK0  N3   C14   aromatic  1.293  0.020  1.293
 NK0  C4   C5    aromatic  1.395  0.020  1.395
 NK0  N4   C13   single    1.344  0.020  1.344
 NK0  N4   C15   single    1.408  0.020  1.408
 NK0  C5   C6    aromatic  1.394  0.020  1.394
 NK0  C5   C7    single    1.490  0.020  1.490
 NK0  N5   C22   single    1.345  0.020  1.345
 NK0  N5   C23   single    1.426  0.020  1.426
 NK0  C7   C8    single    1.465  0.020  1.465
 NK0  C8   C9    aromatic  1.393  0.020  1.393
 NK0  C8   C11   aromatic  1.418  0.020  1.418
 NK0  C10  C11   aromatic  1.385  0.020  1.385
 NK0  C10  C13   aromatic  1.430  0.020  1.430
 NK0  C11  C12   single    1.495  0.020  1.495
 NK0  C15  C16   aromatic  1.388  0.020  1.388
 NK0  C15  C20   aromatic  1.400  0.020  1.400
 NK0  C16  C17   aromatic  1.390  0.020  1.390
 NK0  C17  C18   aromatic  1.392  0.020  1.392
 NK0  C17  C22   single    1.496  0.020  1.496
 NK0  C18  C19   aromatic  1.385  0.020  1.385
 NK0  C19  C20   aromatic  1.391  0.020  1.391
 NK0  C20  C21   single    1.499  0.020  1.499
 NK0  C23  C24   single    1.493  0.020  1.493
 NK0  C23  C25   single    1.497  0.020  1.497
 NK0  C24  C25   single    1.498  0.020  1.498
 NK0  C1   H1    single    0.930  0.020  1.080
 NK0  C2   H2    single    0.930  0.020  1.080
 NK0  C3   H3    single    0.930  0.020  1.080
 NK0  C4   H4    single    0.930  0.020  1.080
 NK0  N4   HN4   single    0.860  0.020  1.020
 NK0  N5   HN5   single    0.860  0.020  1.020
 NK0  C6   H6    single    0.930  0.020  1.080
 NK0  C9   H9    single    0.930  0.020  1.080
 NK0  C12  H12   single    0.970  0.020  1.090
 NK0  C12  H12A  single    0.970  0.020  1.090
 NK0  C12  H12B  single    0.970  0.020  1.090
 NK0  C14  H14   single    0.930  0.020  1.080
 NK0  C16  H16   single    0.930  0.020  1.080
 NK0  C18  H18   single    0.930  0.020  1.080
 NK0  C19  H19   single    0.930  0.020  1.080
 NK0  C21  H21   single    0.970  0.020  1.090
 NK0  C21  H21A  single    0.970  0.020  1.090
 NK0  C21  H21B  single    0.970  0.020  1.090
 NK0  C23  H23   single    0.970  0.020  1.090
 NK0  C24  H24   single    0.970  0.020  1.090
 NK0  C24  H24A  single    0.970  0.020  1.090
 NK0  C25  H25   single    0.970  0.020  1.090
 NK0  C25  H25A  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
 NK0  H1    C1   C6    119.77  3.000
 NK0  H1    C1   C2    120.13  3.000
 NK0  C6    C1   C2    120.10  3.000
 NK0  C10   N1   C9    110.12  3.000
 NK0  C10   N1   N3    124.92  3.000
 NK0  C9    N1   N3    124.96  3.000
 NK0  H2    C2   C3    120.07  3.000
 NK0  H2    C2   C1    119.97  3.000
 NK0  C3    C2   C1    119.96  3.000
 NK0  C14   N2   C13   117.46  3.000
 NK0  H3    C3   C4    119.84  3.000
 NK0  H3    C3   C2    120.13  3.000
 NK0  C4    C3   C2    120.03  3.000
 NK0  C14   N3   N1    113.47  3.000
 NK0  H4    C4   C5    119.88  3.000
 NK0  H4    C4   C3    119.79  3.000
 NK0  C5    C4   C3    120.31  3.000
 NK0  HN4   N4   C15   115.95  3.000
 NK0  HN4   N4   C13   117.25  3.000
 NK0  C15   N4   C13   126.81  3.000
 NK0  C7    C5   C6    121.85  3.000
 NK0  C7    C5   C4    118.72  3.000
 NK0  C6    C5   C4    119.37  3.000
 NK0  HN5   N5   C23   117.97  3.000
 NK0  HN5   N5   C22   120.05  3.000
 NK0  C23   N5   C22   121.95  3.000
 NK0  H6    C6   C5    120.33  3.000
 NK0  H6    C6   C1    119.44  3.000
 NK0  C5    C6   C1    120.21  3.000
 NK0  C8    C7   C5    118.33  3.000
 NK0  C8    C7   O1    121.80  3.000
 NK0  C5    C7   O1    119.85  3.000
 NK0  C11   C8   C9    108.33  3.000
 NK0  C11   C8   C7    127.26  3.000
 NK0  C9    C8   C7    124.22  3.000
 NK0  H9    C9   C8    131.18  3.000
 NK0  H9    C9   N1    121.10  3.000
 NK0  C8    C9   N1    107.68  3.000
 NK0  C13   C10  C11   136.93  3.000
 NK0  C13   C10  N1    114.86  3.000
 NK0  C11   C10  N1    108.20  3.000
 NK0  C12   C11  C10   126.40  3.000
 NK0  C12   C11  C8    127.85  3.000
 NK0  C10   C11  C8    105.67  3.000
 NK0  H12B  C12  H12A  106.79  3.000
 NK0  H12B  C12  H12   106.71  3.000
 NK0  H12A  C12  H12   108.23  3.000
 NK0  H12B  C12  C11   111.53  3.000
 NK0  H12A  C12  C11   111.91  3.000
 NK0  H12   C12  C11   111.40  3.000
 NK0  C10   C13  N4    119.21  3.000
 NK0  C10   C13  N2    120.45  3.000
 NK0  N4    C13  N2    120.34  3.000
 NK0  H14   C14  N3    114.96  3.000
 NK0  H14   C14  N2    116.24  3.000
 NK0  N3    C14  N2    128.80  3.000
 NK0  C20   C15  C16   120.85  3.000
 NK0  C20   C15  N4    117.92  3.000
 NK0  C16   C15  N4    121.19  3.000
 NK0  H16   C16  C17   119.56  3.000
 NK0  H16   C16  C15   119.96  3.000
 NK0  C17   C16  C15   120.48  3.000
 NK0  C22   C17  C18   123.31  3.000
 NK0  C22   C17  C16   117.52  3.000
 NK0  C18   C17  C16   119.17  3.000
 NK0  H18   C18  C19   118.58  3.000
 NK0  H18   C18  C17   121.41  3.000
 NK0  C19   C18  C17   120.00  3.000
 NK0  H19   C19  C20   119.05  3.000
 NK0  H19   C19  C18   119.31  3.000
 NK0  C20   C19  C18   121.63  3.000
 NK0  C21   C20  C19   120.96  3.000
 NK0  C21   C20  C15   121.17  3.000
 NK0  C19   C20  C15   117.87  3.000
 NK0  H21B  C21  H21A  107.14  3.000
 NK0  H21B  C21  H21   107.18  3.000
 NK0  H21A  C21  H21   108.00  3.000
 NK0  H21B  C21  C20   111.90  3.000
 NK0  H21A  C21  C20   110.89  3.000
 NK0  H21   C21  C20   111.52  3.000
 NK0  C17   C22  N5    116.38  3.000
 NK0  C17   C22  O2    121.21  3.000
 NK0  N5    C22  O2    122.40  3.000
 NK0  H23   C23  C25   117.05  3.000
 NK0  H23   C23  C24   117.11  3.000
 NK0  C25   C23  C24    60.15  3.000
 NK0  H23   C23  N5    114.83  3.000
 NK0  C25   C23  N5    119.27  3.000
 NK0  C24   C23  N5    117.66  3.000
 NK0  H24A  C24  H24   114.34  3.000
 NK0  H24A  C24  C25   118.94  3.000
 NK0  H24   C24  C25   117.69  3.000
 NK0  H24A  C24  C23   117.58  3.000
 NK0  H24   C24  C23   117.76  3.000
 NK0  C25   C24  C23    60.05  3.000
 NK0  H25A  C25  H25   114.69  3.000
 NK0  H25A  C25  C24   117.51  3.000
 NK0  H25   C25  C24   118.86  3.000
 NK0  H25A  C25  C23   117.27  3.000
 NK0  H25   C25  C23   117.90  3.000
 NK0  C24   C25  C23    59.79  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
 NK0  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 NK0  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 NK0  CONST_03  N2   C14  N3   N1      0.00   0.0  0
 NK0  CONST_04  C11  C8   C9   N1      0.00   0.0  0
 NK0  CONST_05  C8   C11  C10  N1      0.00   0.0  0
 NK0  CONST_06  N2   C13  C10  N1      0.00   0.0  0
 NK0  CONST_07  C5   C6   C1   C2      0.00   0.0  0
 NK0  CONST_08  C5   C4   C3   C2      0.00   0.0  0
 NK0  CONST_09  C11  C10  C13  N2    180.00   0.0  0
 NK0  CONST_10  C6   C1   C2   C3      0.00   0.0  0
 NK0  CONST_11  C6   C5   C4   C3      0.00   0.0  0
 NK0  CONST_12  C8   C9   N1   N3    180.00   0.0  0
 NK0  CONST_13  C11  C10  N1   N3    180.00   0.0  0
 NK0  CONST_14  C13  C10  N1   N3      0.00   0.0  0
 NK0  CONST_15  C13  N2   C14  N3      0.00   0.0  0
 NK0  CONST_16  C10  N1   C9   C8      0.00   0.0  0
 NK0  CONST_17  C13  C10  C11  C8    180.00   0.0  0
 NK0  CONST_18  C14  N3   N1   C9    180.00   0.0  0
 NK0  CONST_19  C11  C10  N1   C9      0.00   0.0  0
 NK0  CONST_20  C13  C10  N1   C9    180.00   0.0  0
 NK0  CONST_21  C10  C11  C8   C9      0.00   0.0  0
 NK0  CONST_22  C14  N3   N1   C10     0.00   0.0  0
 NK0  CONST_23  C14  N2   C13  C10     0.00   0.0  0
 NK0  CONST_24  C18  C17  C16  C15     0.00   0.0  0
 NK0  CONST_25  C18  C19  C20  C15     0.00   0.0  0
 NK0  CONST_26  C19  C20  C15  C16     0.00   0.0  0
 NK0  CONST_27  C19  C18  C17  C16     0.00   0.0  0
 NK0  CONST_28  C20  C15  C16  C17     0.00   0.0  0
 NK0  CONST_29  C20  C19  C18  C17     0.00   0.0  0
 NK0  CONST_30  C7   C5   C6   C1    180.00   0.0  0
 NK0  CONST_31  C7   C8   C9   N1    180.00   0.0  0
 NK0  CONST_32  C12  C11  C10  N1    180.00   0.0  0
 NK0  CONST_33  N4   C13  C10  N1    180.00   0.0  0
 NK0  CONST_34  C7   C5   C4   C3    180.00   0.0  0
 NK0  CONST_35  C14  N2   C13  N4    180.00   0.0  0
 NK0  CONST_36  C11  C10  C13  N4      0.00   0.0  0
 NK0  CONST_37  C17  C16  C15  N4    180.00   0.0  0
 NK0  CONST_38  C19  C20  C15  N4    180.00   0.0  0
 NK0  CONST_39  C10  C11  C8   C7    180.00   0.0  0
 NK0  CONST_40  C12  C11  C8   C9    180.00   0.0  0
 NK0  CONST_41  C13  C10  C11  C12     0.00   0.0  0
 NK0  CONST_42  C22  C17  C16  C15   180.00   0.0  0
 NK0  CONST_43  C21  C20  C15  C16   180.00   0.0  0
 NK0  CONST_44  C21  C20  C19  C18   180.00   0.0  0
 NK0  CONST_45  C22  C17  C18  C19   180.00   0.0  0
 NK0  CONST_46  H3   C3   C2   C1    180.00   0.0  0
 NK0  CONST_47  H14  C14  N3   N1    180.00   0.0  0
 NK0  CONST_48  H6   C6   C1   C2    180.00   0.0  0
 NK0  CONST_49  H4   C4   C3   C2    180.00   0.0  0
 NK0  CONST_50  H1   C1   C2   C3    180.00   0.0  0
 NK0  CONST_51  H9   C9   N1   N3      0.00   0.0  0
 NK0  CONST_52  H2   C2   C3   C4    180.00   0.0  0
 NK0  CONST_53  H19  C19  C20  C15   180.00   0.0  0
 NK0  CONST_54  H18  C18  C17  C16   180.00   0.0  0
 NK0  CONST_55  H16  C16  C17  C18   180.00   0.0  0
 NK0  CONST_56  C23  N5   C22  C17   180.00   0.0  0
 NK0  CONST_57  C23  N5   C22  O2      0.00   0.0  0
 NK0  CONST_58  HN5  N5   C22  C17     0.00   0.0  0
 NK0  Var_01    C15  N4   C13  N2      1.71  30.0  1
 NK0  Var_02    C8   C7   C5   C4   -144.55  30.0  2
 NK0  Var_03    C9   C8   C7   C5     26.30  30.0  2
 NK0  Var_04    C25  C24  C23  N5   -109.62  30.0  1
 NK0  Var_05    C16  C15  N4   C13    45.63  30.0  2
 NK0  Var_06    H25  C25  C24  C23  -107.30  30.0  1
 NK0  Var_07    C16  C17  C22  O2    -23.52  30.0  2
 NK0  Var_08    C24  C23  N5   C22   145.64  30.0  3
 NK0  Var_09    H12  C12  C11  C8    124.53  30.0  2
 NK0  Var_10    H21  C21  C20  C15    53.51  30.0  2

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
 NK0  chir_01  C23  N5  C24  C25  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
 NK0  plan-1  C1   0.020
 NK0  plan-1  C2   0.020
 NK0  plan-1  C3   0.020
 NK0  plan-1  C4   0.020
 NK0  plan-1  C5   0.020
 NK0  plan-1  C6   0.020
 NK0  plan-1  C7   0.020
 NK0  plan-1  H1   0.020
 NK0  plan-1  H2   0.020
 NK0  plan-1  H3   0.020
 NK0  plan-1  H4   0.020
 NK0  plan-1  H6   0.020
 NK0  plan-2  N4   0.020
 NK0  plan-2  C15  0.020
 NK0  plan-2  C16  0.020
 NK0  plan-2  C17  0.020
 NK0  plan-2  C18  0.020
 NK0  plan-2  C19  0.020
 NK0  plan-2  C20  0.020
 NK0  plan-2  C21  0.020
 NK0  plan-2  C22  0.020
 NK0  plan-2  H16  0.020
 NK0  plan-2  H18  0.020
 NK0  plan-2  H19  0.020
 NK0  plan-3  N1   0.020
 NK0  plan-3  N2   0.020
 NK0  plan-3  N3   0.020
 NK0  plan-3  N4   0.020
 NK0  plan-3  C7   0.020
 NK0  plan-3  C8   0.020
 NK0  plan-3  C9   0.020
 NK0  plan-3  C10  0.020
 NK0  plan-3  C11  0.020
 NK0  plan-3  C12  0.020
 NK0  plan-3  C13  0.020
 NK0  plan-3  C14  0.020
 NK0  plan-3  H9   0.020
 NK0  plan-3  H14  0.020
 NK0  plan-4  O1   0.020
 NK0  plan-4  C5   0.020
 NK0  plan-4  C7   0.020
 NK0  plan-4  C8   0.020
 NK0  plan-5  O2   0.020
 NK0  plan-5  N5   0.020
 NK0  plan-5  C17  0.020
 NK0  plan-5  C22  0.020
 NK0  plan-5  C23  0.020
 NK0  plan-5  HN5  0.020

