# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:33:01 2022
#   Inital geometry file: a 140 line input string
#   Ligand name: (1R)-9-[(1,3-dimethylazetidin-3-yl)(methyl)amino]-1-methyl-8-phenyl-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]1N2C(=NNC1=O)COc3cc(c4ccccc4)c(cc23)N(C)C5(C)CN(C)C5
#
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
 3L0  3L0  (1R)-9-[(1,3-dimethylazetidin-3-yl)(methyl)amino]-1-methyl-8-phenyl-3,5-dihydro[1,2,4]triazino[3,4-c][1,4]benzoxazin-2(1H)-one  ligand  57  30  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_3L0
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
 3L0  C1   C  CH3   0  -0.522   3.0885   3.6103  -2.0838
 3L0  N2   N  N     0  -0.406   2.3156   3.4998  -0.8772
 3L0  C3   C  C     0  -0.255   2.9510   2.9315   0.3072
 3L0  C4   C  C     0   0.041   1.6137   2.2320   0.6551
 3L0  C5   C  CH3   0  -0.668   0.8024   3.0647   1.6450
 3L0  C6   C  C     0  -0.258   1.2521   2.5010  -0.8216
 3L0  N7   N  NT    0  -0.515   1.7838   0.8362   0.9980
 3L0  C8   C  CH3   0  -0.548   2.4085   0.6143   2.2862
 3L0  C9   C  CR6   0   0.301   0.8438  -0.1065   0.5695
 3L0  C10  C  CR16  0  -0.421  -0.4956   0.2309   0.3686
 3L0  C11  C  CR6   0   0.375  -1.4306  -0.6991  -0.0704
 3L0  N12  N  NT    0  -0.598  -2.7466  -0.3572  -0.3939
 3L0  C13  C  CH1   0  -0.249  -3.2160   1.0179  -0.3266
 3L0  C15  C  CH3   0  -0.660  -3.6075   1.4409   1.0900
 3L0  C16  C  C     0   0.545  -4.4050   1.1989  -1.2512
 3L0  O17  O  O     0  -0.466  -4.7187   2.2966  -1.6760
 3L0  N18  N  NH1   0  -0.509  -5.1112   0.0830  -1.5052
 3L0  N19  N  N     0  -0.298  -4.8203  -1.1836  -1.0822
 3L0  C20  C  C     0   0.440  -3.6647  -1.3537  -0.5728
 3L0  C21  C  CH2   0  -0.267  -3.2260  -2.7181  -0.1462
 3L0  O22  O  O2    0  -0.476  -1.9260  -2.9625  -0.6517
 3L0  C23  C  CR6   0   0.315  -1.0285  -2.0246  -0.2452
 3L0  C24  C  CR16  0  -0.415   0.2935  -2.3725  -0.0511
 3L0  C25  C  CR6   0   0.026   1.2513  -1.4282   0.3088
 3L0  C26  C  CR6   0   0.034   2.6717  -1.8410   0.3519
 3L0  C27  C  CR16  0  -0.256   3.6281  -1.1653  -0.4081
 3L0  C28  C  CR16  0  -0.248   4.9508  -1.5791  -0.4077
 3L0  C29  C  CR16  0  -0.267   5.3443  -2.6713   0.3578
 3L0  C30  C  CR16  0  -0.244   4.4017  -3.3498   1.1166
 3L0  C31  C  CR16  0  -0.291   3.0748  -2.9377   1.1117
 3L0  H1   H  HCH3  0   0.189   3.5476   2.6590  -2.3958
 3L0  H2   H  HCH3  0   0.232   2.4576   3.9610  -2.9023
 3L0  H3   H  HCH3  0   0.233   3.8887   4.3397  -1.9489
 3L0  H5   H  H     0   0.212   3.7294   2.1884   0.0839
 3L0  H6   H  H     0   0.226   3.3530   3.6618   1.0157
 3L0  H7   H  HCH3  0   0.239   1.2664   3.0675   2.6320
 3L0  H8   H  HCH3  0   0.238   0.7465   4.0989   1.3042
 3L0  H9   H  HCH3  0   0.228  -0.2205   2.7057   1.7661
 3L0  H10  H  H     0   0.227   0.2483   2.8778  -1.0416
 3L0  H11  H  H     0   0.217   1.4421   1.6231  -1.4545
 3L0  H12  H  HCH3  0   0.221   1.7316   0.7928   3.1299
 3L0  H13  H  HCH3  0   0.256   2.7817  -0.4041   2.3693
 3L0  H14  H  HCH3  0   0.240   3.2653   1.2811   2.3938
 3L0  H15  H  HCR6  0   0.259  -0.8128   1.2423   0.5685
 3L0  H16  H  HCH1  0   0.298  -2.4275   1.6678  -0.7113
 3L0  H17  H  HCH3  0   0.256  -2.7770   1.3131   1.7831
 3L0  H18  H  HCH3  0   0.259  -3.8980   2.4902   1.1044
 3L0  H19  H  HCH3  0   0.250  -4.4442   0.8456   1.4568
 3L0  H20  H  HNH1  0   0.419  -5.9619   0.1556  -2.0440
 3L0  H21  H  HCH2  0   0.259  -3.2285  -2.7883   0.9484
 3L0  H22  H  HCH2  0   0.282  -3.8945  -3.4743  -0.5497
 3L0  H23  H  HCR6  0   0.265   0.5944  -3.3944  -0.2500
 3L0  H24  H  HCR6  0   0.240   3.3306  -0.3123  -1.0037
 3L0  H25  H  HCR6  0   0.254   5.6768  -1.0523  -1.0137
 3L0  H26  H  HCR6  0   0.254   6.3793  -2.9875   0.3635
 3L0  H27  H  HCR6  0   0.255   4.6967  -4.2007   1.7173
 3L0  H28  H  HCR6  0   0.251   2.3501  -3.4645   1.7208

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
 3L0  N18  N19  single    1.367  0.020  1.367
 3L0  N18  C16  single    1.345  0.020  1.345
 3L0  N19  C20  double    1.274  0.020  1.274
 3L0  O17  C16  double    1.218  0.020  1.218
 3L0  C16  C13  single    1.517  0.020  1.517
 3L0  C20  C21  single    1.495  0.020  1.495
 3L0  C20  N12  single    1.367  0.020  1.367
 3L0  C21  O22  single    1.416  0.020  1.416
 3L0  N12  C13  single    1.455  0.020  1.455
 3L0  N12  C11  single    1.398  0.020  1.398
 3L0  C13  C15  single    1.529  0.020  1.529
 3L0  O22  C23  single    1.360  0.020  1.360
 3L0  C11  C23  aromatic  1.396  0.020  1.396
 3L0  C11  C10  aromatic  1.390  0.020  1.390
 3L0  C23  C24  aromatic  1.381  0.020  1.381
 3L0  C10  C9   aromatic  1.396  0.020  1.396
 3L0  C24  C25  aromatic  1.392  0.020  1.392
 3L0  C5   C4   single    1.527  0.020  1.527
 3L0  C9   C25  aromatic  1.407  0.020  1.407
 3L0  C9   N7   single    1.399  0.020  1.399
 3L0  C6   C4   single    1.544  0.020  1.544
 3L0  C6   N2   single    1.460  0.020  1.460
 3L0  C25  C26  single    1.480  0.020  1.480
 3L0  C4   N7   single    1.447  0.020  1.447
 3L0  C4   C3   single    1.549  0.020  1.549
 3L0  N7   C8   single    1.449  0.020  1.449
 3L0  N2   C3   single    1.459  0.020  1.459
 3L0  N2   C1   single    1.437  0.020  1.437
 3L0  C27  C26  aromatic  1.396  0.020  1.396
 3L0  C27  C28  aromatic  1.386  0.020  1.386
 3L0  C26  C31  aromatic  1.394  0.020  1.394
 3L0  C28  C29  aromatic  1.391  0.020  1.391
 3L0  C31  C30  aromatic  1.389  0.020  1.389
 3L0  C29  C30  aromatic  1.387  0.020  1.387
 3L0  C1   H1   single    0.970  0.020  1.090
 3L0  C1   H2   single    0.970  0.020  1.090
 3L0  C1   H3   single    0.970  0.020  1.090
 3L0  C3   H5   single    0.970  0.020  1.090
 3L0  C3   H6   single    0.970  0.020  1.090
 3L0  C5   H7   single    0.970  0.020  1.090
 3L0  C5   H8   single    0.970  0.020  1.090
 3L0  C5   H9   single    0.970  0.020  1.090
 3L0  C6   H10  single    0.970  0.020  1.090
 3L0  C6   H11  single    0.970  0.020  1.090
 3L0  C8   H12  single    0.970  0.020  1.090
 3L0  C8   H13  single    0.970  0.020  1.090
 3L0  C8   H14  single    0.970  0.020  1.090
 3L0  C10  H15  single    0.930  0.020  1.080
 3L0  C13  H16  single    0.970  0.020  1.090
 3L0  C15  H17  single    0.970  0.020  1.090
 3L0  C15  H18  single    0.970  0.020  1.090
 3L0  C15  H19  single    0.970  0.020  1.090
 3L0  N18  H20  single    0.860  0.020  1.020
 3L0  C21  H21  single    0.970  0.020  1.090
 3L0  C21  H22  single    0.970  0.020  1.090
 3L0  C24  H23  single    0.930  0.020  1.080
 3L0  C27  H24  single    0.930  0.020  1.080
 3L0  C28  H25  single    0.930  0.020  1.080
 3L0  C29  H26  single    0.930  0.020  1.080
 3L0  C30  H27  single    0.930  0.020  1.080
 3L0  C31  H28  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
 3L0  H3   C1   H2   107.57  3.000
 3L0  H3   C1   H1   107.86  3.000
 3L0  H2   C1   H1   107.82  3.000
 3L0  H3   C1   N2   110.00  3.000
 3L0  H2   C1   N2   110.09  3.000
 3L0  H1   C1   N2   113.31  3.000
 3L0  C6   N2   C3    91.14  3.000
 3L0  C3   N2   C1   118.50  3.000
 3L0  C6   N2   C1   118.44  3.000
 3L0  H6   C3   H5   108.82  3.000
 3L0  H6   C3   C4   118.25  3.000
 3L0  H5   C3   C4   110.60  3.000
 3L0  H6   C3   N2   115.19  3.000
 3L0  H5   C3   N2   114.00  3.000
 3L0  C4   C3   N2    88.98  3.000
 3L0  N7   C4   C6   114.97  3.000
 3L0  N7   C4   C5   115.77  3.000
 3L0  C6   C4   C5   113.62  3.000
 3L0  N7   C4   C3   112.78  3.000
 3L0  C6   C4   C3    84.76  3.000
 3L0  C5   C4   C3   110.98  3.000
 3L0  H9   C5   H8   107.38  3.000
 3L0  H9   C5   H7   107.41  3.000
 3L0  H8   C5   H7   107.60  3.000
 3L0  H9   C5   C4   113.00  3.000
 3L0  H8   C5   C4   109.99  3.000
 3L0  H7   C5   C4   111.23  3.000
 3L0  H11  C6   H10  108.54  3.000
 3L0  H11  C6   C4   111.79  3.000
 3L0  H10  C6   C4   117.84  3.000
 3L0  H11  C6   N2   113.49  3.000
 3L0  H10  C6   N2   115.14  3.000
 3L0  C4   C6   N2    89.14  3.000
 3L0  C9   N7   C8   117.32  3.000
 3L0  C8   N7   C4   114.14  3.000
 3L0  C9   N7   C4   119.90  3.000
 3L0  H14  C8   H13  107.17  3.000
 3L0  H14  C8   H12  108.03  3.000
 3L0  H13  C8   H12  107.79  3.000
 3L0  H14  C8   N7   109.43  3.000
 3L0  H13  C8   N7   111.05  3.000
 3L0  H12  C8   N7   113.15  3.000
 3L0  C25  C9   C10  118.57  3.000
 3L0  C25  C9   N7   119.68  3.000
 3L0  C10  C9   N7   121.74  3.000
 3L0  H15  C10  C11  119.21  3.000
 3L0  H15  C10  C9   118.83  3.000
 3L0  C11  C10  C9   121.95  3.000
 3L0  C23  C11  N12  118.32  3.000
 3L0  C23  C11  C10  118.76  3.000
 3L0  N12  C11  C10  122.88  3.000
 3L0  C20  N12  C13  118.59  3.000
 3L0  C13  N12  C11  121.63  3.000
 3L0  C20  N12  C11  118.98  3.000
 3L0  H16  C13  C16  106.28  3.000
 3L0  H16  C13  C15  110.28  3.000
 3L0  C16  C13  C15  109.33  3.000
 3L0  H16  C13  N12  108.26  3.000
 3L0  C15  C13  N12  112.76  3.000
 3L0  C16  C13  N12  109.72  3.000
 3L0  H19  C15  H18  108.48  3.000
 3L0  H19  C15  H17  107.88  3.000
 3L0  H18  C15  H17  107.95  3.000
 3L0  H19  C15  C13  110.92  3.000
 3L0  H18  C15  C13  110.30  3.000
 3L0  H17  C15  C13  111.21  3.000
 3L0  N18  C16  O17  123.14  3.000
 3L0  O17  C16  C13  121.46  3.000
 3L0  N18  C16  C13  115.32  3.000
 3L0  H20  N18  N19  114.28  3.000
 3L0  H20  N18  C16  118.92  3.000
 3L0  N19  N18  C16  126.78  3.000
 3L0  C20  N19  N18  116.14  3.000
 3L0  C21  C20  N19  120.12  3.000
 3L0  C21  C20  N12  115.52  3.000
 3L0  N19  C20  N12  124.34  3.000
 3L0  H22  C21  H21  108.94  3.000
 3L0  H22  C21  O22  108.18  3.000
 3L0  H21  C21  O22  110.32  3.000
 3L0  H22  C21  C20  110.39  3.000
 3L0  H21  C21  C20  110.03  3.000
 3L0  O22  C21  C20  108.96  3.000
 3L0  C23  O22  C21  112.33  3.000
 3L0  C24  C23  O22  120.00  3.000
 3L0  C24  C23  C11  119.83  3.000
 3L0  O22  C23  C11  120.13  3.000
 3L0  H23  C24  C25  119.74  3.000
 3L0  H23  C24  C23  118.53  3.000
 3L0  C25  C24  C23  121.60  3.000
 3L0  C26  C25  C24  118.60  3.000
 3L0  C26  C25  C9   122.31  3.000
 3L0  C24  C25  C9   119.05  3.000
 3L0  C31  C26  C27  118.66  3.000
 3L0  C31  C26  C25  120.86  3.000
 3L0  C27  C26  C25  120.45  3.000
 3L0  H24  C27  C28  119.86  3.000
 3L0  H24  C27  C26  119.53  3.000
 3L0  C28  C27  C26  120.61  3.000
 3L0  H25  C28  C29  120.04  3.000
 3L0  H25  C28  C27  119.65  3.000
 3L0  C29  C28  C27  120.31  3.000
 3L0  H26  C29  C30  120.26  3.000
 3L0  H26  C29  C28  120.20  3.000
 3L0  C30  C29  C28  119.54  3.000
 3L0  H27  C30  C31  119.70  3.000
 3L0  H27  C30  C29  120.18  3.000
 3L0  C31  C30  C29  120.12  3.000
 3L0  H28  C31  C30  119.51  3.000
 3L0  H28  C31  C26  119.72  3.000
 3L0  C30  C31  C26  120.76  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
 3L0  CONST_01  C23  C11  C10  C9      0.00   0.0  0
 3L0  CONST_02  C23  C24  C25  C9      0.00   0.0  0
 3L0  CONST_05  C24  C23  C11  C10     0.00   0.0  0
 3L0  CONST_06  C24  C25  C9   C10     0.00   0.0  0
 3L0  CONST_07  C26  C25  C9   C10   180.00   0.0  0
 3L0  CONST_08  C25  C24  C23  C11     0.00   0.0  0
 3L0  CONST_09  C25  C9   C10  C11     0.00   0.0  0
 3L0  CONST_10  C26  C25  C24  C23   180.00   0.0  0
 3L0  CONST_13  C28  C27  C26  C25   180.00   0.0  0
 3L0  CONST_14  C30  C31  C26  C25   180.00   0.0  0
 3L0  CONST_15  C29  C28  C27  C26     0.00   0.0  0
 3L0  CONST_16  C29  C30  C31  C26     0.00   0.0  0
 3L0  CONST_17  C30  C31  C26  C27     0.00   0.0  0
 3L0  CONST_18  C30  C29  C28  C27     0.00   0.0  0
 3L0  CONST_19  C31  C26  C27  C28     0.00   0.0  0
 3L0  CONST_20  C31  C30  C29  C28     0.00   0.0  0
 3L0  CONST_21  N19  C20  N12  C11   180.00   0.0  0
 3L0  CONST_22  C21  C20  N12  C11     0.00   0.0  0
 3L0  CONST_23  N18  N19  C20  N12     0.00   0.0  0
 3L0  CONST_24  N19  N18  C16  C13     0.00   0.0  0
 3L0  CONST_27  C21  C20  N19  N18   180.00   0.0  0
 3L0  CONST_28  C11  C10  C9   N7    180.00   0.0  0
 3L0  CONST_29  C24  C25  C9   N7    180.00   0.0  0
 3L0  CONST_30  C26  C25  C9   N7      0.00   0.0  0
 3L0  CONST_33  N19  N18  C16  O17   180.00   0.0  0
 3L0  CONST_34  H23  C24  C25  C9    180.00   0.0  0
 3L0  CONST_35  H15  C10  C11  N12     0.00   0.0  0
 3L0  CONST_36  H24  C27  C26  C25     0.00   0.0  0
 3L0  CONST_37  H28  C31  C26  C25     0.00   0.0  0
 3L0  CONST_38  H25  C28  C27  C26   180.00   0.0  0
 3L0  CONST_39  H27  C30  C31  C26   180.00   0.0  0
 3L0  CONST_40  H26  C29  C28  C27   180.00   0.0  0
 3L0  CONST_41  H20  N18  C16  C13   180.00   0.0  0
 3L0  Var_01    C4   C6   N2   C3     18.90  30.0  1
 3L0  Var_02    C20  N12  C11  C10  -167.80  30.0  1
 3L0  Var_03    O22  C21  C20  N12   -46.81  30.0  1
 3L0  Var_04    C24  C23  O22  C21   148.40  30.0  1
 3L0  Var_05    H1   C1   N2   C3     53.80  30.0  3
 3L0  Var_06    H12  C8   N7   C4     75.64  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
 3L0  chir_01  C4   C6   N7   C3   negativ
 3L0  chir_02  C13  N12  C15  C16  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
 3L0  plan-1  C25  0.020
 3L0  plan-1  C26  0.020
 3L0  plan-1  C27  0.020
 3L0  plan-1  C28  0.020
 3L0  plan-1  C29  0.020
 3L0  plan-1  C30  0.020
 3L0  plan-1  C31  0.020
 3L0  plan-1  H24  0.020
 3L0  plan-1  H25  0.020
 3L0  plan-1  H26  0.020
 3L0  plan-1  H27  0.020
 3L0  plan-1  H28  0.020
 3L0  plan-2  N7   0.020
 3L0  plan-2  C9   0.020
 3L0  plan-2  C10  0.020
 3L0  plan-2  C11  0.020
 3L0  plan-2  N12  0.020
 3L0  plan-2  O22  0.020
 3L0  plan-2  C23  0.020
 3L0  plan-2  C24  0.020
 3L0  plan-2  C25  0.020
 3L0  plan-2  C26  0.020
 3L0  plan-2  H15  0.020
 3L0  plan-2  H23  0.020
 3L0  plan-3  C4   0.020
 3L0  plan-3  N7   0.020
 3L0  plan-3  C8   0.020
 3L0  plan-3  C9   0.020
 3L0  plan-4  C11  0.020
 3L0  plan-4  N12  0.020
 3L0  plan-4  C13  0.020
 3L0  plan-4  C16  0.020
 3L0  plan-4  O17  0.020
 3L0  plan-4  N18  0.020
 3L0  plan-4  N19  0.020
 3L0  plan-4  C20  0.020
 3L0  plan-4  C21  0.020
 3L0  plan-4  H20  0.020

