# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 18:26:54 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: (1R)-9-[(3S,4S)-1,3-dimethylpiperidin-4-yl]-8-(2-fluorophenyl)-1-methyl-3,5-dihydro[1,2,4]triazino[3,4-c][1,4]benzoxazin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1CN(C)CC[C@@H]1c2cc3N4[C@H](C)C(=O)NN=C4COc3cc2c5ccccc5F
#
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
 3KZ  3KZ  (1R)-9-[(3S,4S)-1,3-dimethylpiperidin-4-yl]-8-(2-fluorophenyl)-1-methyl-3,5-dihydro[1,2,4]triazino[3,4-c][1,4]benzoxazin-2(1H)-one  ligand  58  31  .  2022-07-22  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_3KZ
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
 3KZ  C26  C  CR16  0  -0.261   4.3725   2.3158   1.4546
 3KZ  C27  C  CR16  0  -0.245   5.0436   2.6630   0.2891
 3KZ  C25  C  CR16  0  -0.258   3.0535   1.8923   1.3923
 3KZ  C28  C  CR16  0  -0.406   4.3971   2.5851  -0.9357
 3KZ  C3   C  CR16  0  -0.379  -0.0042   2.3474  -0.1652
 3KZ  C4   C  CR16  0  -0.435  -0.7897  -0.2531   0.2824
 3KZ  C24  C  CR6   0  -0.201   2.3783   1.8040   0.1758
 3KZ  C2   C  CR6   0   0.033   0.9587   1.3790   0.1067
 3KZ  C1   C  CR6   0   0.168   0.5691   0.0502   0.3124
 3KZ  C5   C  CR6   0   0.375  -1.7586   0.7128   0.0402
 3KZ  C6   C  CR6   0   0.314  -1.3453   2.0260  -0.2039
 3KZ  C29  C  CR6   0   0.529   3.0827   2.1594  -0.9644
 3KZ  C9   C  C     0   0.440  -4.0036   1.3824  -0.3968
 3KZ  C14  C  C     0   0.544  -5.0567  -0.7775   0.9256
 3KZ  C8   C  CH2   0  -0.264  -3.3912   2.5124  -1.1603
 3KZ  C22  C  CH2   0  -0.435   1.1480  -2.2461   1.3016
 3KZ  C21  C  CH2   0  -0.277   2.2910  -3.2407   1.4372
 3KZ  C19  C  CH2   0  -0.268   3.2504  -2.5388  -0.6367
 3KZ  C12  C  CH1   0  -0.342   1.5975  -1.0434   0.4751
 3KZ  C13  C  CH1   0  -0.247  -3.6355  -0.8800   0.4051
 3KZ  C18  C  CH1   0  -0.230   2.1418  -1.5204  -0.8891
 3KZ  C17  C  CH3   0  -0.656  -3.5961  -1.8403  -0.7842
 3KZ  C23  C  CH3   0  -0.666   1.0720  -2.0761  -1.8228
 3KZ  N16  N  NH1   0  -0.509  -5.7413   0.3095   0.5291
 3KZ  N10  N  NT    0  -0.600  -3.1298   0.4443   0.0755
 3KZ  N11  N  N     0  -0.299  -5.2654   1.3453  -0.2241
 3KZ  N20  N  NT    0  -0.405   2.7763  -3.6671   0.1397
 3KZ  O15  O  O     0  -0.466  -5.5455  -1.6586   1.6099
 3KZ  O7   O  O2    0  -0.474  -2.2608   2.9958  -0.4567
 3KZ  F30  F  F     0  -0.307   2.4621   2.0746  -2.1531
 3KZ  H1   H  HCR6  0   0.262   4.8735   2.3810   2.4110
 3KZ  H2   H  HCR6  0   0.268   6.0722   2.9958   0.3294
 3KZ  H3   H  HCR6  0   0.266   2.5280   1.6258   2.3011
 3KZ  H4   H  HCR6  0   0.279   4.9033   2.8469  -1.8557
 3KZ  H5   H  HCR6  0   0.265   0.2897   3.3766  -0.3334
 3KZ  H6   H  HCR6  0   0.259  -1.0927  -1.2774   0.4444
 3KZ  H7   H  HCH2  0   0.261  -3.0995   2.1752  -2.1620
 3KZ  H8   H  HCH2  0   0.283  -4.1010   3.3297  -1.2569
 3KZ  H9   H  HCH2  0   0.222   0.2948  -2.7547   0.8452
 3KZ  H10  H  HCH2  0   0.242   0.8297  -1.9222   2.2952
 3KZ  H11  H  HCH2  0   0.184   3.1000  -2.7855   2.0392
 3KZ  H12  H  HCH2  0   0.235   1.9488  -4.1192   1.9903
 3KZ  H13  H  HCH2  0   0.231   3.6314  -2.9071  -1.5938
 3KZ  H14  H  HCH2  0   0.193   4.0963  -2.0327  -0.1337
 3KZ  H15  H  HCH1  0   0.243   2.4538  -0.6183   1.0101
 3KZ  H16  H  HCH1  0   0.302  -3.0400  -1.2777   1.2288
 3KZ  H17  H  HCH1  0   0.239   2.6050  -0.6627  -1.3860
 3KZ  H18  H  HCH3  0   0.252  -2.5843  -1.9382  -1.1758
 3KZ  H19  H  HCH3  0   0.258  -3.9334  -2.8303  -0.4815
 3KZ  H20  H  HCH3  0   0.248  -4.2356  -1.4884  -1.5944
 3KZ  H21  H  HCH3  0   0.222   0.6162  -2.9860  -1.4315
 3KZ  H22  H  HCH3  0   0.231   0.2774  -1.3506  -2.0002
 3KZ  H23  H  HCH3  0   0.231   1.5125  -2.3235  -2.7901
 3KZ  H24  H  HCH3  0   0.188   4.6944  -4.3412   0.7917
 3KZ  H25  H  HCH3  0   0.230   3.3979  -5.5452   0.8106
 3KZ  H26  H  HCH3  0   0.231   4.0974  -5.0334  -0.7248
 3KZ  H27  H  HNH1  0   0.419  -6.7198   0.3834   0.7651
 3KZ  C31  C  CH3   0  -0.517   3.7912  -4.6868   0.2633

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
 3KZ  C28  C27  aromatic  1.387  0.020  1.387
 3KZ  C28  C29  aromatic  1.382  0.020  1.382
 3KZ  C27  C26  aromatic  1.389  0.020  1.389
 3KZ  F30  C29  single    1.344  0.020  1.344
 3KZ  C29  C24  aromatic  1.387  0.020  1.387
 3KZ  C19  C18  single    1.526  0.020  1.526
 3KZ  C19  N20  single    1.449  0.020  1.449
 3KZ  C26  C25  aromatic  1.387  0.020  1.387
 3KZ  C31  N20  single    1.444  0.020  1.444
 3KZ  C18  C23  single    1.525  0.020  1.525
 3KZ  C18  C12  single    1.544  0.020  1.544
 3KZ  C24  C25  aromatic  1.394  0.020  1.394
 3KZ  C24  C2   single    1.483  0.020  1.483
 3KZ  N20  C21  single    1.449  0.020  1.449
 3KZ  C12  C1   single    1.510  0.020  1.510
 3KZ  C12  C22  single    1.527  0.020  1.527
 3KZ  C2   C1   aromatic  1.400  0.020  1.400
 3KZ  C2   C3   aromatic  1.392  0.020  1.392
 3KZ  C21  C22  single    1.521  0.020  1.521
 3KZ  C1   C4   aromatic  1.393  0.020  1.393
 3KZ  C3   C6   aromatic  1.380  0.020  1.380
 3KZ  C4   C5   aromatic  1.389  0.020  1.389
 3KZ  C17  C13  single    1.529  0.020  1.529
 3KZ  C6   C5   aromatic  1.398  0.020  1.398
 3KZ  C6   O7   single    1.357  0.020  1.357
 3KZ  C5   N10  single    1.398  0.020  1.398
 3KZ  O7   C8   single    1.417  0.020  1.417
 3KZ  C13  N10  single    1.455  0.020  1.455
 3KZ  C13  C14  single    1.517  0.020  1.517
 3KZ  N10  C9   single    1.366  0.020  1.366
 3KZ  C8   C9   single    1.495  0.020  1.495
 3KZ  C9   N11  double    1.274  0.020  1.274
 3KZ  C14  O15  double    1.218  0.020  1.218
 3KZ  C14  N16  single    1.344  0.020  1.344
 3KZ  N11  N16  single    1.366  0.020  1.366
 3KZ  C26  H1   single    0.930  0.020  1.080
 3KZ  C27  H2   single    0.930  0.020  1.080
 3KZ  C25  H3   single    0.930  0.020  1.080
 3KZ  C28  H4   single    0.930  0.020  1.080
 3KZ  C3   H5   single    0.930  0.020  1.080
 3KZ  C4   H6   single    0.930  0.020  1.080
 3KZ  C8   H7   single    0.970  0.020  1.090
 3KZ  C8   H8   single    0.970  0.020  1.090
 3KZ  C22  H9   single    0.970  0.020  1.090
 3KZ  C22  H10  single    0.970  0.020  1.090
 3KZ  C21  H11  single    0.970  0.020  1.090
 3KZ  C21  H12  single    0.970  0.020  1.090
 3KZ  C19  H13  single    0.970  0.020  1.090
 3KZ  C19  H14  single    0.970  0.020  1.090
 3KZ  C12  H15  single    0.970  0.020  1.090
 3KZ  C13  H16  single    0.970  0.020  1.090
 3KZ  C18  H17  single    0.970  0.020  1.090
 3KZ  C17  H18  single    0.970  0.020  1.090
 3KZ  C17  H19  single    0.970  0.020  1.090
 3KZ  C17  H20  single    0.970  0.020  1.090
 3KZ  C23  H21  single    0.970  0.020  1.090
 3KZ  C23  H22  single    0.970  0.020  1.090
 3KZ  C23  H23  single    0.970  0.020  1.090
 3KZ  C31  H24  single    0.970  0.020  1.090
 3KZ  C31  H25  single    0.970  0.020  1.090
 3KZ  C31  H26  single    0.970  0.020  1.090
 3KZ  N16  H27  single    0.860  0.020  1.020

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
 3KZ  H1   C26  C25  119.91  3.000
 3KZ  H1   C26  C27  120.20  3.000
 3KZ  C25  C26  C27  119.89  3.000
 3KZ  H2   C27  C28  119.56  3.000
 3KZ  H2   C27  C26  120.34  3.000
 3KZ  C28  C27  C26  120.11  3.000
 3KZ  H3   C25  C24  118.79  3.000
 3KZ  H3   C25  C26  119.93  3.000
 3KZ  C24  C25  C26  121.28  3.000
 3KZ  H4   C28  C29  120.11  3.000
 3KZ  H4   C28  C27  121.27  3.000
 3KZ  C29  C28  C27  118.61  3.000
 3KZ  H5   C3   C6   118.73  3.000
 3KZ  H5   C3   C2   120.22  3.000
 3KZ  C6   C3   C2   121.04  3.000
 3KZ  H6   C4   C5   119.32  3.000
 3KZ  H6   C4   C1   118.49  3.000
 3KZ  C5   C4   C1   122.19  3.000
 3KZ  C29  C24  C2   121.42  3.000
 3KZ  C2   C24  C25  121.48  3.000
 3KZ  C29  C24  C25  117.08  3.000
 3KZ  C1   C2   C24  122.10  3.000
 3KZ  C1   C2   C3   119.76  3.000
 3KZ  C24  C2   C3   118.14  3.000
 3KZ  C12  C1   C2   120.91  3.000
 3KZ  C2   C1   C4   118.37  3.000
 3KZ  C12  C1   C4   120.60  3.000
 3KZ  N10  C5   C6   118.35  3.000
 3KZ  N10  C5   C4   123.10  3.000
 3KZ  C6   C5   C4   118.51  3.000
 3KZ  O7   C6   C5   120.28  3.000
 3KZ  O7   C6   C3   119.63  3.000
 3KZ  C5   C6   C3   120.08  3.000
 3KZ  F30  C29  C24  118.47  3.000
 3KZ  C24  C29  C28  123.03  3.000
 3KZ  F30  C29  C28  118.50  3.000
 3KZ  N11  C9   N10  124.51  3.000
 3KZ  N11  C9   C8   119.80  3.000
 3KZ  N10  C9   C8   115.69  3.000
 3KZ  O15  C14  N16  123.11  3.000
 3KZ  N16  C14  C13  115.50  3.000
 3KZ  O15  C14  C13  121.32  3.000
 3KZ  H8   C8   H7   108.90  3.000
 3KZ  H8   C8   O7   107.98  3.000
 3KZ  H7   C8   O7   110.27  3.000
 3KZ  H8   C8   C9   110.26  3.000
 3KZ  H7   C8   C9   110.07  3.000
 3KZ  O7   C8   C9   109.34  3.000
 3KZ  H10  C22  H9   106.87  3.000
 3KZ  H10  C22  C12  110.15  3.000
 3KZ  H9   C22  C12  111.73  3.000
 3KZ  H10  C22  C21  109.37  3.000
 3KZ  H9   C22  C21  108.63  3.000
 3KZ  C12  C22  C21  110.00  3.000
 3KZ  H12  C21  H11  106.52  3.000
 3KZ  H12  C21  N20  108.75  3.000
 3KZ  H11  C21  N20  111.30  3.000
 3KZ  H12  C21  C22  109.59  3.000
 3KZ  H11  C21  C22  109.20  3.000
 3KZ  N20  C21  C22  111.35  3.000
 3KZ  H14  C19  H13  106.59  3.000
 3KZ  H14  C19  N20  111.26  3.000
 3KZ  H13  C19  N20  108.69  3.000
 3KZ  H14  C19  C18  108.98  3.000
 3KZ  H13  C19  C18  109.45  3.000
 3KZ  N20  C19  C18  111.74  3.000
 3KZ  H15  C12  C18  106.01  3.000
 3KZ  H15  C12  C22  105.75  3.000
 3KZ  C18  C12  C22  109.79  3.000
 3KZ  H15  C12  C1   107.70  3.000
 3KZ  C22  C12  C1   115.36  3.000
 3KZ  C18  C12  C1   111.62  3.000
 3KZ  H16  C13  N10  108.23  3.000
 3KZ  H16  C13  C17  110.13  3.000
 3KZ  N10  C13  C17  112.73  3.000
 3KZ  H16  C13  C14  106.07  3.000
 3KZ  N10  C13  C14  109.98  3.000
 3KZ  C17  C13  C14  109.48  3.000
 3KZ  H17  C18  C23  107.73  3.000
 3KZ  H17  C18  C12  107.96  3.000
 3KZ  C23  C18  C12  113.97  3.000
 3KZ  H17  C18  C19  106.89  3.000
 3KZ  C12  C18  C19  108.42  3.000
 3KZ  C23  C18  C19  111.57  3.000
 3KZ  H20  C17  H19  108.55  3.000
 3KZ  H20  C17  H18  107.85  3.000
 3KZ  H19  C17  H18  107.82  3.000
 3KZ  H20  C17  C13  111.11  3.000
 3KZ  H19  C17  C13  110.29  3.000
 3KZ  H18  C17  C13  111.10  3.000
 3KZ  H23  C23  H22  107.50  3.000
 3KZ  H23  C23  H21  107.31  3.000
 3KZ  H22  C23  H21  108.00  3.000
 3KZ  H23  C23  C18  110.01  3.000
 3KZ  H22  C23  C18  111.61  3.000
 3KZ  H21  C23  C18  112.19  3.000
 3KZ  H27  N16  N11  114.27  3.000
 3KZ  H27  N16  C14  118.94  3.000
 3KZ  N11  N16  C14  126.74  3.000
 3KZ  C13  N10  C9   118.74  3.000
 3KZ  C9   N10  C5   119.13  3.000
 3KZ  C13  N10  C5   121.43  3.000
 3KZ  N16  N11  C9   116.22  3.000
 3KZ  C31  N20  C19  111.45  3.000
 3KZ  C31  N20  C21  111.49  3.000
 3KZ  C19  N20  C21  111.11  3.000
 3KZ  C8   O7   C6   112.76  3.000
 3KZ  H26  C31  H25  107.78  3.000
 3KZ  H26  C31  H24  107.69  3.000
 3KZ  H25  C31  H24  107.56  3.000
 3KZ  H26  C31  N20  110.13  3.000
 3KZ  H25  C31  N20  110.19  3.000
 3KZ  H24  C31  N20  113.31  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
 3KZ  CONST_01  C29  C28  C27  C26    0.00   0.0  0
 3KZ  CONST_02  C29  C24  C25  C26    0.00   0.0  0
 3KZ  CONST_03  C2   C24  C25  C26  180.00   0.0  0
 3KZ  CONST_04  C24  C29  C28  C27    0.00   0.0  0
 3KZ  CONST_05  C24  C25  C26  C27    0.00   0.0  0
 3KZ  CONST_06  C28  C27  C26  C25    0.00   0.0  0
 3KZ  CONST_07  C28  C29  C24  C25    0.00   0.0  0
 3KZ  CONST_10  C2   C24  C29  C28  180.00   0.0  0
 3KZ  CONST_12  C4   C1   C2   C3     0.00   0.0  0
 3KZ  CONST_13  C4   C5   C6   C3     0.00   0.0  0
 3KZ  CONST_14  C24  C2   C1   C4   180.00   0.0  0
 3KZ  CONST_15  C6   C3   C2   C24  180.00   0.0  0
 3KZ  CONST_16  C5   C4   C1   C2     0.00   0.0  0
 3KZ  CONST_17  C5   C6   C3   C2     0.00   0.0  0
 3KZ  CONST_19  C6   C3   C2   C1     0.00   0.0  0
 3KZ  CONST_20  C6   C5   C4   C1     0.00   0.0  0
 3KZ  CONST_21  C12  C1   C2   C3   180.00   0.0  0
 3KZ  CONST_22  C12  C1   C2   C24    0.00   0.0  0
 3KZ  CONST_23  C12  C1   C4   C5   180.00   0.0  0
 3KZ  CONST_24  C8   C9   N10  C5     0.00   0.0  0
 3KZ  CONST_25  N11  C9   N10  C5   180.00   0.0  0
 3KZ  CONST_27  N16  N11  C9   C8   180.00   0.0  0
 3KZ  CONST_29  N11  N16  C14  C13    0.00   0.0  0
 3KZ  CONST_30  N10  C9   N11  N16    0.00   0.0  0
 3KZ  CONST_31  F30  C29  C28  C27  180.00   0.0  0
 3KZ  CONST_32  F30  C29  C24  C25  180.00   0.0  0
 3KZ  CONST_33  F30  C29  C24  C2     0.00   0.0  0
 3KZ  CONST_34  O15  C14  N16  N11  180.00   0.0  0
 3KZ  CONST_35  H4   C28  C27  C26  180.00   0.0  0
 3KZ  CONST_36  H3   C25  C26  C27  180.00   0.0  0
 3KZ  CONST_37  H2   C27  C26  C25  180.00   0.0  0
 3KZ  CONST_38  H1   C26  C27  C28  180.00   0.0  0
 3KZ  CONST_39  H5   C3   C2   C24    0.00   0.0  0
 3KZ  CONST_40  H6   C4   C1   C2   180.00   0.0  0
 3KZ  CONST_41  H27  N16  C14  C13  180.00   0.0  0
 3KZ  Var_01    C13  N10  C5   C4     1.50  30.0  1
 3KZ  Var_02    C9   C8   O7   C6    55.96  30.0  1
 3KZ  Var_03    C19  N20  C21  C22   59.42  30.0  1
 3KZ  Var_04    C18  C19  N20  C21  -60.65  30.0  1
 3KZ  Var_05    N20  C21  C22  C12  -57.05  30.0  1
 3KZ  Var_06    O7   C8   C9   N10  -45.94  30.0  1
 3KZ  Var_07    H24  C31  N20  C21  -62.70  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
 3KZ  chir_01  C12  C18  C1   C22  negativ
 3KZ  chir_02  C13  C17  N10  C14  negativ
 3KZ  chir_03  C18  C12  C23  C19  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
 3KZ  plan-1  C26  0.020
 3KZ  plan-1  C27  0.020
 3KZ  plan-1  C25  0.020
 3KZ  plan-1  C28  0.020
 3KZ  plan-1  C24  0.020
 3KZ  plan-1  C2   0.020
 3KZ  plan-1  C29  0.020
 3KZ  plan-1  F30  0.020
 3KZ  plan-1  H1   0.020
 3KZ  plan-1  H2   0.020
 3KZ  plan-1  H3   0.020
 3KZ  plan-1  H4   0.020
 3KZ  plan-2  C3   0.020
 3KZ  plan-2  C4   0.020
 3KZ  plan-2  C24  0.020
 3KZ  plan-2  C2   0.020
 3KZ  plan-2  C1   0.020
 3KZ  plan-2  C5   0.020
 3KZ  plan-2  C6   0.020
 3KZ  plan-2  C12  0.020
 3KZ  plan-2  N10  0.020
 3KZ  plan-2  O7   0.020
 3KZ  plan-2  H5   0.020
 3KZ  plan-2  H6   0.020
 3KZ  plan-3  C5   0.020
 3KZ  plan-3  C9   0.020
 3KZ  plan-3  C14  0.020
 3KZ  plan-3  C8   0.020
 3KZ  plan-3  C13  0.020
 3KZ  plan-3  N16  0.020
 3KZ  plan-3  N10  0.020
 3KZ  plan-3  N11  0.020
 3KZ  plan-3  O15  0.020
 3KZ  plan-3  H27  0.020

