# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 10:44:50 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: ~{N}-[3-[2-(dimethylamino)ethyl]-2-oxidanylidene-1,3-benzoxazol-5-yl]-1-methyl-6-oxidanylidene-pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)CCN1C(=O)Oc2ccc(NC(=O)C3=CN(C)C(=O)C=C3)cc12
#
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
 D9B  D9B  ~{N}-[3-[2-(dimethylamino)ethyl]-2-oxidanylidene-1,3-benzoxazol-5-yl]-1-methyl-6-oxidanylidene-pyridine-3-carboxamide  ligand  46  26  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D9B
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
 D9B  C01   C  CH3   0  -0.530  -2.3536  -3.7994  -0.3745
 D9B  C03   C  CH3   0  -0.520  -4.0273  -4.2623   1.2546
 D9B  C04   C  CH2   0  -0.274  -3.6270  -1.9956   0.5787
 D9B  C05   C  CH2   0  -0.336  -3.7715  -1.0728  -0.6284
 D9B  C07   C  CR5   0   0.670  -4.7065   1.1501  -0.0163
 D9B  C10   C  CR56  0   0.285  -2.8467   2.2874   0.3254
 D9B  C11   C  CR56  0   0.384  -2.4738   1.0047  -0.0320
 D9B  C12   C  CR16  0  -0.390  -1.1540   0.6129  -0.1228
 D9B  C13   C  CR6   0   0.390  -0.1932   1.5897   0.1666
 D9B  C15   C  C     0   0.553   1.8462   0.1975  -0.1296
 D9B  C17   C  CR6   0  -0.212   3.3231   0.2669  -0.0136
 D9B  C18   C  CR16  0   0.091   4.0332  -0.8075  -0.4729
 D9B  C21   C  CR6   0   0.568   6.1609   0.1500   0.1177
 D9B  C23   C  CR16  0  -0.445   5.4218   1.2786   0.6140
 D9B  C24   C  CR16  0  -0.141   4.0695   1.3341   0.5511
 D9B  C25   C  CR16  0  -0.383  -0.5833   2.8880   0.5207
 D9B  C26   C  CR16  0  -0.314  -1.9201   3.2597   0.6057
 D9B  N02   N  NT    0  -0.410  -3.6287  -3.3853   0.1735
 D9B  N06   N  NR5   0  -0.591  -3.6528   0.3190  -0.2541
 D9B  N19   N  NR6   0  -0.506   5.3727  -0.8722  -0.4192
 D9B  O08   O  O     0  -0.455  -5.8845   0.9194  -0.0858
 D9B  O09   O  O     0  -0.469  -4.2096   2.3679   0.3319
 D9B  O16   O  O     0  -0.469   1.2851  -0.8403  -0.4469
 D9B  O22   O  O     0  -0.494   7.3786   0.0345   0.1393
 D9B  H012  H  HCH3  0   0.197  -1.5324  -3.7321   0.3561
 D9B  H011  H  HCH3  0   0.240  -2.4150  -4.8342  -0.7130
 D9B  H013  H  HCH3  0   0.234  -2.0777  -3.1974  -1.2406
 D9B  H033  H  HCH3  0   0.195  -3.3220  -4.2633   2.1000
 D9B  H032  H  HCH3  0   0.236  -5.0069  -3.9703   1.6345
 D9B  H031  H  HCH3  0   0.234  -4.1031  -5.2874   0.8888
 D9B  H042  H  HCH2  0   0.208  -2.7240  -1.7295   1.1536
 D9B  H041  H  HCH2  0   0.250  -4.4773  -1.8216   1.2419
 D9B  H051  H  HCH2  0   0.268  -3.0158  -1.2752  -1.3881
 D9B  H052  H  HCH2  0   0.282  -4.7424  -1.2212  -1.0974
 D9B  H121  H  HCR6  0   0.298  -0.8804  -0.3901  -0.4040
 D9B  H181  H  HCR6  0   0.315   3.5349  -1.6618  -0.9078
 D9B  H202  H  HCH3  0   0.267   6.7554  -1.7661  -1.7247
 D9B  H201  H  HCH3  0   0.267   6.6236  -2.5358  -0.1359
 D9B  H203  H  HCH3  0   0.262   5.3342  -2.7426  -1.3294
 D9B  H231  H  HCR6  0   0.283   5.9905   2.0878   1.0503
 D9B  H241  H  HCR6  0   0.271   3.5821   2.2094   0.9617
 D9B  H251  H  HCR6  0   0.280   0.1763   3.6286   0.7383
 D9B  H261  H  HCR6  0   0.286  -2.2030   4.2660   0.8813
 D9B  H141  H  HNH1  0   0.428   1.7402   2.1695   0.3273
 D9B  N14   N  NH1   0  -0.781   1.1843   1.3530   0.1316
 D9B  C20   C  CH3   0  -0.521   6.0663  -2.0471  -0.9318

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
 D9B  C24  C23   double    1.355  0.020  1.355
 D9B  C24  C17   single    1.419  0.020  1.419
 D9B  O16  C15   double    1.222  0.020  1.222
 D9B  C23  C21   single    1.437  0.020  1.437
 D9B  C15  C17   single    1.483  0.020  1.483
 D9B  C15  N14   single    1.357  0.020  1.357
 D9B  C17  C18   double    1.367  0.020  1.367
 D9B  N14  C13   single    1.398  0.020  1.398
 D9B  C13  C12   aromatic  1.400  0.020  1.400
 D9B  C13  C25   aromatic  1.401  0.020  1.401
 D9B  C12  C11   aromatic  1.380  0.020  1.380
 D9B  C05  N06   single    1.446  0.020  1.446
 D9B  C05  C04   single    1.526  0.020  1.526
 D9B  C21  O22   double    1.223  0.020  1.223
 D9B  C21  N19   single    1.398  0.020  1.398
 D9B  C11  N06   single    1.382  0.020  1.382
 D9B  C11  C10   aromatic  1.383  0.020  1.383
 D9B  C25  C26   aromatic  1.390  0.020  1.390
 D9B  N06  C07   single    1.363  0.020  1.363
 D9B  C10  C26   aromatic  1.372  0.020  1.372
 D9B  C10  O09   single    1.365  0.020  1.365
 D9B  C18  N19   single    1.342  0.020  1.342
 D9B  C07  O08   double    1.202  0.020  1.202
 D9B  C07  O09   single    1.361  0.020  1.361
 D9B  N19  C20   single    1.458  0.020  1.458
 D9B  C01  N02   single    1.448  0.020  1.448
 D9B  N02  C04   single    1.448  0.020  1.448
 D9B  N02  C03   single    1.448  0.020  1.448
 D9B  C01  H012  single    0.970  0.020  1.090
 D9B  C01  H011  single    0.970  0.020  1.090
 D9B  C01  H013  single    0.970  0.020  1.090
 D9B  C03  H033  single    0.970  0.020  1.090
 D9B  C03  H032  single    0.970  0.020  1.090
 D9B  C03  H031  single    0.970  0.020  1.090
 D9B  C04  H042  single    0.970  0.020  1.090
 D9B  C04  H041  single    0.970  0.020  1.090
 D9B  C05  H051  single    0.970  0.020  1.090
 D9B  C05  H052  single    0.970  0.020  1.090
 D9B  C12  H121  single    0.930  0.020  1.080
 D9B  C18  H181  single    0.930  0.020  1.080
 D9B  C20  H202  single    0.970  0.020  1.090
 D9B  C20  H201  single    0.970  0.020  1.090
 D9B  C20  H203  single    0.970  0.020  1.090
 D9B  C23  H231  single    0.930  0.020  1.080
 D9B  C24  H241  single    0.930  0.020  1.080
 D9B  C25  H251  single    0.930  0.020  1.080
 D9B  C26  H261  single    0.930  0.020  1.080
 D9B  N14  H141  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
 D9B  H013  C01  H011  106.95  3.000
 D9B  H013  C01  H012  107.74  3.000
 D9B  H011  C01  H012  107.81  3.000
 D9B  H013  C01  N02   111.44  3.000
 D9B  H011  C01  N02   109.83  3.000
 D9B  H012  C01  N02   112.83  3.000
 D9B  H031  C03  H032  107.82  3.000
 D9B  H031  C03  H033  107.53  3.000
 D9B  H032  C03  H033  107.94  3.000
 D9B  H031  C03  N02   109.75  3.000
 D9B  H032  C03  N02   110.19  3.000
 D9B  H033  C03  N02   113.42  3.000
 D9B  H041  C04  H042  106.40  3.000
 D9B  H041  C04  N02   108.78  3.000
 D9B  H042  C04  N02   112.24  3.000
 D9B  H041  C04  C05   108.07  3.000
 D9B  H042  C04  C05   110.11  3.000
 D9B  N02   C04  C05   111.04  3.000
 D9B  H052  C05  H051  107.02  3.000
 D9B  H052  C05  N06   108.42  3.000
 D9B  H051  C05  N06   107.58  3.000
 D9B  H052  C05  C04   110.04  3.000
 D9B  H051  C05  C04   111.91  3.000
 D9B  N06   C05  C04   111.68  3.000
 D9B  O09   C07  O08   122.97  3.000
 D9B  O09   C07  N06   107.94  3.000
 D9B  O08   C07  N06   129.08  3.000
 D9B  O09   C10  C26   129.15  3.000
 D9B  O09   C10  C11   108.98  3.000
 D9B  C26   C10  C11   121.87  3.000
 D9B  N06   C11  C12   131.66  3.000
 D9B  N06   C11  C10   105.77  3.000
 D9B  C12   C11  C10   122.57  3.000
 D9B  H121  C12  C13   121.95  3.000
 D9B  H121  C12  C11   121.64  3.000
 D9B  C13   C12  C11   116.40  3.000
 D9B  N14   C13  C25   115.95  3.000
 D9B  C25   C13  C12   120.50  3.000
 D9B  N14   C13  C12   123.55  3.000
 D9B  O16   C15  N14   123.32  3.000
 D9B  N14   C15  C17   115.52  3.000
 D9B  O16   C15  C17   121.16  3.000
 D9B  C24   C17  C18   116.83  3.000
 D9B  C18   C17  C15   117.01  3.000
 D9B  C24   C17  C15   126.15  3.000
 D9B  H181  C18  N19   116.00  3.000
 D9B  H181  C18  C17   121.13  3.000
 D9B  N19   C18  C17   122.87  3.000
 D9B  O22   C21  N19   119.93  3.000
 D9B  N19   C21  C23   114.64  3.000
 D9B  O22   C21  C23   125.43  3.000
 D9B  H231  C23  C24   120.87  3.000
 D9B  H231  C23  C21   117.17  3.000
 D9B  C24   C23  C21   121.96  3.000
 D9B  H241  C24  C23   117.70  3.000
 D9B  H241  C24  C17   121.46  3.000
 D9B  C23   C24  C17   120.83  3.000
 D9B  H251  C25  C26   118.64  3.000
 D9B  H251  C25  C13   119.29  3.000
 D9B  C26   C25  C13   122.07  3.000
 D9B  H261  C26  C25   121.07  3.000
 D9B  H261  C26  C10   122.35  3.000
 D9B  C25   C26  C10   116.58  3.000
 D9B  C04   N02  C03   111.89  3.000
 D9B  C03   N02  C01   110.59  3.000
 D9B  C04   N02  C01   112.29  3.000
 D9B  C11   N06  C07   109.21  3.000
 D9B  C07   N06  C05   124.65  3.000
 D9B  C11   N06  C05   126.10  3.000
 D9B  C21   N19  C20   117.14  3.000
 D9B  C20   N19  C18   119.98  3.000
 D9B  C21   N19  C18   122.88  3.000
 D9B  C10   O09  C07   108.09  3.000
 D9B  H141  N14  C15   117.29  3.000
 D9B  H141  N14  C13   113.69  3.000
 D9B  C15   N14  C13   129.02  3.000
 D9B  H203  C20  H201  109.02  3.000
 D9B  H203  C20  H202  109.02  3.000
 D9B  H201  C20  H202  108.97  3.000
 D9B  H203  C20  N19   108.93  3.000
 D9B  H201  C20  N19   110.40  3.000
 D9B  H202  C20  N19   110.46  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
 D9B  CONST_01  C13   C12  C11  C10     0.00   0.0  0
 D9B  CONST_02  C13   C25  C26  C10     0.00   0.0  0
 D9B  CONST_03  C25   C13  C12  C11     0.00   0.0  0
 D9B  CONST_04  C25   C26  C10  C11     0.00   0.0  0
 D9B  CONST_05  C26   C25  C13  C12     0.00   0.0  0
 D9B  CONST_06  C26   C10  C11  C12     0.00   0.0  0
 D9B  CONST_07  C23   C21  N19  C18     0.00   0.0  0
 D9B  CONST_08  N14   C13  C12  C11   180.00   0.0  0
 D9B  CONST_09  N14   C13  C25  C26   180.00   0.0  0
 D9B  CONST_10  O22   C21  N19  C18   180.00   0.0  0
 D9B  CONST_11  C23   C21  N19  C20   180.00   0.0  0
 D9B  CONST_12  H121  C12  C11  C10   180.00   0.0  0
 D9B  CONST_13  H251  C25  C26  C10   180.00   0.0  0
 D9B  CONST_14  H261  C26  C10  C11   180.00   0.0  0
 D9B  CONST_15  C17   C15  N14  C13   180.00   0.0  0
 D9B  CONST_16  C15   N14  C13  C12     0.00   0.0  0
 D9B  CONST_17  C25   C13  N14  C15   180.00   0.0  0
 D9B  CONST_18  O22   C21  N19  C20     0.00   0.0  0
 D9B  CONST_19  H141  N14  C13  C12   180.00   0.0  0
 D9B  CONST_20  O16   C15  N14  C13     0.00   0.0  0
 D9B  Var_01    C11   N06  C05  C04    80.38  30.0  3
 D9B  Var_02    O16   C15  C17  C18     9.83  30.0  2
 D9B  Var_03    H202  C20  N19  C18   120.84  30.0  3
 D9B  Var_04    N06   C05  C04  N02  -174.90  30.0  2
 D9B  Var_05    C05   C04  N02  C01    78.02  30.0  3
 D9B  Var_06    H033  C03  N02  C01    61.23  30.0  3
 D9B  Var_07    H012  C01  N02  C03   -63.16  30.0  3

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
 D9B  plan-1  C15   0.020
 D9B  plan-1  C17   0.020
 D9B  plan-1  C18   0.020
 D9B  plan-1  C21   0.020
 D9B  plan-1  C23   0.020
 D9B  plan-1  C24   0.020
 D9B  plan-1  N19   0.020
 D9B  plan-1  O22   0.020
 D9B  plan-1  H181  0.020
 D9B  plan-1  H231  0.020
 D9B  plan-1  H241  0.020
 D9B  plan-1  C20   0.020
 D9B  plan-2  C05   0.020
 D9B  plan-2  C07   0.020
 D9B  plan-2  C10   0.020
 D9B  plan-2  C11   0.020
 D9B  plan-2  C12   0.020
 D9B  plan-2  C13   0.020
 D9B  plan-2  C25   0.020
 D9B  plan-2  C26   0.020
 D9B  plan-2  N06   0.020
 D9B  plan-2  O08   0.020
 D9B  plan-2  O09   0.020
 D9B  plan-2  H121  0.020
 D9B  plan-2  H251  0.020
 D9B  plan-2  H261  0.020
 D9B  plan-2  N14   0.020
 D9B  plan-3  C13   0.020
 D9B  plan-3  C15   0.020
 D9B  plan-3  C17   0.020
 D9B  plan-3  O16   0.020
 D9B  plan-3  H141  0.020
 D9B  plan-3  N14   0.020

