# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 24 03:51:46 2021
#   Inital geometry file: a 149 line input string
#   Ligand name: 4-[6-methoxy-5-(methylsulfamoyl)pyridin-3-yl]-~{N}-(1-methylpiperidin-4-yl)-2,3-dihydro-1,4-benzoxazine-6-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN[S](=O)(=O)c1cc(cnc1OC)N2CCOc3ccc(cc23)C(=O)NC4CCN(C)CC4
#
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
 QD2  QD2  4-[6-methoxy-5-(methylsulfamoyl)pyridin-3-yl]-~{N}-(1-methylpiperidin-4-yl)-2,3-dihydro-1,4-benzoxazine-6-carboxamide  ligand  62  33  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_QD2
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
 QD2  N1   N  N     0  -0.458  -10.6916  -30.1518  23.8682
 QD2  N3   N  NH1   0  -0.657   -4.2278  -34.3994  24.3581
 QD2  C4   C  CR16  0  -0.047   -9.6985  -29.8367  24.6883
 QD2  C5   C  CR6   0   0.583  -10.4376  -30.3742  22.5953
 QD2  C6   C  CH3   0  -0.420  -12.7321  -30.8575  22.3292
 QD2  C7   C  CH2   0  -0.324   -7.1471  -27.9227  25.3713
 QD2  C8   C  CH2   0  -0.216   -6.2055  -27.7182  26.5331
 QD2  C10  C  CR16  0  -0.352   -3.9938  -30.5115  26.0899
 QD2  C13  C  CR16  0  -0.372   -6.3279  -31.5383  25.0347
 QD2  C17  C  CH2   0  -0.449   -2.8234  -36.3676  24.0350
 QD2  C20  C  CH2   0  -0.283   -4.4426  -37.2070  21.8056
 QD2  C21  C  CH2   0  -0.430   -4.5627  -35.7908  22.3459
 QD2  O4   O  O     0  -0.494   -6.4492  -34.3463  24.7607
 QD2  C16  C  CH1   0  -0.067   -4.1991  -35.7481  23.8280
 QD2  N4   N  NT    0  -0.409   -3.1081  -37.7349  22.0140
 QD2  C19  C  CH3   0  -0.517   -2.9522  -39.0389  21.4119
 QD2  C18  C  CH2   0  -0.280   -2.7672  -37.7594  23.4229
 QD2  C12  C  CR6   0  -0.042   -5.2159  -32.3624  25.1732
 QD2  C11  C  CR16  0  -0.315   -4.0394  -31.8406  25.7016
 QD2  C14  C  CR6   0   0.314   -6.2848  -30.1889  25.3720
 QD2  C9   C  CR6   0   0.319   -5.0938  -29.6836  25.9257
 QD2  O3   O  O2    0  -0.473   -4.9774  -28.3935  26.3081
 QD2  N2   N  NT    0  -0.606   -7.3801  -29.3474  25.2017
 QD2  C3   C  CR6   0   0.145   -8.3834  -29.7063  24.2786
 QD2  C2   C  CR16  0  -0.097   -8.1115  -29.9097  22.9291
 QD2  O2   O  O2    0  -0.450  -11.4185  -30.7374  21.7902
 QD2  C1   C  CR6   0  -0.376   -9.1360  -30.2536  22.0704
 QD2  S    S  S     0   1.380   -8.7215  -30.4977  20.3599
 QD2  O    O  OS    0  -0.662   -7.4747  -29.7903  20.1035
 QD2  O1   O  OS    0  -0.637   -9.8779  -30.1753  19.5424
 QD2  N    N  NC1   0  -0.718   -8.3364  -32.0983  20.3287
 QD2  C    C  CH3   0  -0.521   -9.4087  -33.0832  20.3529
 QD2  H1   H  HNH1  0   0.399   -3.4055  -33.8360  24.2085
 QD2  H2   H  HCR6  0   0.289   -9.9577  -29.6742  25.7290
 QD2  H3   H  HCH3  0   0.254  -13.3604  -31.1569  21.4954
 QD2  H4   H  HCH3  0   0.238  -12.7781  -31.6154  23.1108
 QD2  H5   H  HCH3  0   0.239  -13.0874  -29.9092  22.7315
 QD2  H6   H  HCH2  0   0.248   -6.7332  -27.4678  24.4628
 QD2  H7   H  HCH2  0   0.271   -8.0948  -27.4278  25.5875
 QD2  H8   H  HCH2  0   0.262   -5.9678  -26.6627  26.6487
 QD2  H9   H  HCH2  0   0.243   -6.6645  -28.0741  27.4610
 QD2  H10  H  HCR6  0   0.270   -3.0915  -30.1000  26.5243
 QD2  H11  H  HCR6  0   0.270   -7.2415  -31.9603  24.6382
 QD2  H13  H  HCH2  0   0.245   -2.5900  -36.4280  25.1001
 QD2  H14  H  HCH2  0   0.187   -5.2094  -37.8455  22.2822
 QD2  H15  H  HCH2  0   0.238   -4.6581  -37.2100  20.7344
 QD2  H16  H  HCH2  0   0.220   -3.8912  -35.1292  21.7903
 QD2  H17  H  HCH2  0   0.239   -5.5808  -35.4267  22.1947
 QD2  H18  H  HCH1  0   0.238   -4.9324  -36.3375  24.3853
 QD2  H20  H  HCH3  0   0.231   -1.9226  -39.3825  21.5248
 QD2  H21  H  HCH3  0   0.190   -3.6090  -39.8051  21.8537
 QD2  H22  H  HCH3  0   0.232   -3.1731  -38.9881  20.3446
 QD2  H23  H  HCH2  0   0.188   -3.4375  -38.4323  23.9882
 QD2  H24  H  HCH2  0   0.239   -1.7575  -38.1621  23.5339
 QD2  H25  H  HCR6  0   0.255   -3.1653  -32.4598  25.8557
 QD2  H26  H  HCR6  0   0.306   -7.0984  -29.8039  22.5608
 QD2  H27  H  HNC1  0   0.419   -7.6299  -32.2740  19.6217
 QD2  H28  H  HCH3  0   0.268   -8.9456  -34.0649  20.3014
 QD2  H29  H  HCH3  0   0.253   -9.9537  -33.0286  21.2931
 QD2  H30  H  HCH3  0   0.242  -10.1135  -32.9836  19.5267
 QD2  C15  C  C     0   0.535   -5.3590  -33.7874  24.7515
 QD2  H12  H  HCH2  0   0.225   -2.0595  -35.7374  23.5669

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
 QD2  O1   S    double    1.452  0.020  1.452
 QD2  O    S    double    1.456  0.020  1.456
 QD2  S    N    single    1.647  0.020  1.647
 QD2  S    C1   single    1.777  0.020  1.777
 QD2  N    C    single    1.456  0.020  1.456
 QD2  C20  C21  single    1.521  0.020  1.521
 QD2  C20  N4   single    1.450  0.020  1.450
 QD2  C19  N4   single    1.445  0.020  1.445
 QD2  O2   C6   single    1.425  0.020  1.425
 QD2  O2   C5   single    1.320  0.020  1.320
 QD2  C21  C16  single    1.527  0.020  1.527
 QD2  C1   C5   aromatic  1.409  0.020  1.409
 QD2  C1   C2   aromatic  1.380  0.020  1.380
 QD2  N4   C18  single    1.450  0.020  1.450
 QD2  C5   N1   aromatic  1.317  0.020  1.317
 QD2  C2   C3   aromatic  1.392  0.020  1.392
 QD2  C16  N3   single    1.449  0.020  1.449
 QD2  C16  C17  single    1.523  0.020  1.523
 QD2  O4   C15  double    1.225  0.020  1.225
 QD2  C18  C17  single    1.521  0.020  1.521
 QD2  N3   C15  single    1.345  0.020  1.345
 QD2  N1   C4   aromatic  1.326  0.020  1.326
 QD2  C15  C12  single    1.493  0.020  1.493
 QD2  C3   C4   aromatic  1.384  0.020  1.384
 QD2  C3   N2   single    1.410  0.020  1.410
 QD2  C13  C12  aromatic  1.391  0.020  1.391
 QD2  C13  C14  aromatic  1.392  0.020  1.392
 QD2  C12  C11  aromatic  1.391  0.020  1.391
 QD2  N2   C14  single    1.392  0.020  1.392
 QD2  N2   C7   single    1.454  0.020  1.454
 QD2  C14  C9   aromatic  1.407  0.020  1.407
 QD2  C11  C10  aromatic  1.385  0.020  1.385
 QD2  C7   C8   single    1.509  0.020  1.509
 QD2  C9   C10  aromatic  1.387  0.020  1.387
 QD2  C9   O3   single    1.351  0.020  1.351
 QD2  O3   C8   single    1.420  0.020  1.420
 QD2  N3   H1   single    0.860  0.020  1.020
 QD2  C4   H2   single    0.930  0.020  1.080
 QD2  C6   H3   single    0.970  0.020  1.090
 QD2  C6   H4   single    0.970  0.020  1.090
 QD2  C6   H5   single    0.970  0.020  1.090
 QD2  C7   H6   single    0.970  0.020  1.090
 QD2  C7   H7   single    0.970  0.020  1.090
 QD2  C8   H8   single    0.970  0.020  1.090
 QD2  C8   H9   single    0.970  0.020  1.090
 QD2  C10  H10  single    0.930  0.020  1.080
 QD2  C13  H11  single    0.930  0.020  1.080
 QD2  C17  H12  single    0.970  0.020  1.090
 QD2  C17  H13  single    0.970  0.020  1.090
 QD2  C20  H14  single    0.970  0.020  1.090
 QD2  C20  H15  single    0.970  0.020  1.090
 QD2  C21  H16  single    0.970  0.020  1.090
 QD2  C21  H17  single    0.970  0.020  1.090
 QD2  C16  H18  single    0.970  0.020  1.090
 QD2  C19  H20  single    0.970  0.020  1.090
 QD2  C19  H21  single    0.970  0.020  1.090
 QD2  C19  H22  single    0.970  0.020  1.090
 QD2  C18  H23  single    0.970  0.020  1.090
 QD2  C18  H24  single    0.970  0.020  1.090
 QD2  C11  H25  single    0.930  0.020  1.080
 QD2  C2   H26  single    0.930  0.020  1.080
 QD2  N    H27  single    0.890  0.020  1.040
 QD2  C    H28  single    0.970  0.020  1.090
 QD2  C    H29  single    0.970  0.020  1.090
 QD2  C    H30  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
 QD2  C5   N1   C4   119.57  3.000
 QD2  H1   N3   C16  116.72  3.000
 QD2  H1   N3   C15  118.37  3.000
 QD2  C16  N3   C15  123.17  3.000
 QD2  H2   C4   C3   119.80  3.000
 QD2  H2   C4   N1   116.75  3.000
 QD2  C3   C4   N1   123.45  3.000
 QD2  C1   C5   O2   118.88  3.000
 QD2  C1   C5   N1   121.60  3.000
 QD2  O2   C5   N1   119.52  3.000
 QD2  H5   C6   H4   109.07  3.000
 QD2  H5   C6   H3   109.55  3.000
 QD2  H4   C6   H3   109.54  3.000
 QD2  H5   C6   O2   111.53  3.000
 QD2  H4   C6   O2   111.64  3.000
 QD2  H3   C6   O2   105.44  3.000
 QD2  H7   C7   H6   107.69  3.000
 QD2  H7   C7   N2   109.19  3.000
 QD2  H6   C7   N2   111.73  3.000
 QD2  H7   C7   C8   109.14  3.000
 QD2  H6   C7   C8   110.23  3.000
 QD2  N2   C7   C8   108.82  3.000
 QD2  H9   C8   H8   108.48  3.000
 QD2  H9   C8   O3   110.03  3.000
 QD2  H8   C8   O3   106.81  3.000
 QD2  H9   C8   C7   110.29  3.000
 QD2  H8   C8   C7   110.46  3.000
 QD2  O3   C8   C7   110.68  3.000
 QD2  H10  C10  C9   118.80  3.000
 QD2  H10  C10  C11  120.30  3.000
 QD2  C9   C10  C11  120.90  3.000
 QD2  H11  C13  C14  119.56  3.000
 QD2  H11  C13  C12  118.72  3.000
 QD2  C14  C13  C12  121.71  3.000
 QD2  H13  C17  H12  107.43  3.000
 QD2  H13  C17  C18  109.50  3.000
 QD2  H12  C17  C18  109.19  3.000
 QD2  H13  C17  C16  110.37  3.000
 QD2  H12  C17  C16  109.75  3.000
 QD2  C18  C17  C16  110.54  3.000
 QD2  H15  C20  H14  106.51  3.000
 QD2  H15  C20  N4   108.74  3.000
 QD2  H14  C20  N4   111.47  3.000
 QD2  H15  C20  C21  109.60  3.000
 QD2  H14  C20  C21  109.26  3.000
 QD2  N4   C20  C21  111.14  3.000
 QD2  H17  C21  H16  107.48  3.000
 QD2  H17  C21  C16  110.32  3.000
 QD2  H16  C21  C16  109.26  3.000
 QD2  H17  C21  C20  109.58  3.000
 QD2  H16  C21  C20  109.52  3.000
 QD2  C16  C21  C20  110.62  3.000
 QD2  H18  C16  C21  108.66  3.000
 QD2  H18  C16  C17  108.50  3.000
 QD2  C21  C16  C17  109.62  3.000
 QD2  H18  C16  N3   107.57  3.000
 QD2  C17  C16  N3   110.29  3.000
 QD2  C21  C16  N3   112.11  3.000
 QD2  C18  N4   C19  111.37  3.000
 QD2  C18  N4   C20  111.23  3.000
 QD2  C19  N4   C20  111.59  3.000
 QD2  H22  C19  H21  107.69  3.000
 QD2  H22  C19  H20  107.87  3.000
 QD2  H21  C19  H20  107.58  3.000
 QD2  H22  C19  N4   110.11  3.000
 QD2  H21  C19  N4   113.35  3.000
 QD2  H20  C19  N4   110.05  3.000
 QD2  H24  C18  H23  106.50  3.000
 QD2  H24  C18  N4   108.79  3.000
 QD2  H23  C18  N4   111.39  3.000
 QD2  H24  C18  C17  109.30  3.000
 QD2  H23  C18  C17  109.20  3.000
 QD2  N4   C18  C17  111.52  3.000
 QD2  C11  C12  C15  123.11  3.000
 QD2  C11  C12  C13  119.45  3.000
 QD2  C15  C12  C13  117.44  3.000
 QD2  H25  C11  C12  121.50  3.000
 QD2  H25  C11  C10  118.84  3.000
 QD2  C12  C11  C10  119.61  3.000
 QD2  N2   C14  C9   119.81  3.000
 QD2  C9   C14  C13  118.02  3.000
 QD2  N2   C14  C13  122.16  3.000
 QD2  O3   C9   C14  121.82  3.000
 QD2  O3   C9   C10  117.93  3.000
 QD2  C14  C9   C10  120.24  3.000
 QD2  C9   O3   C8   115.14  3.000
 QD2  C3   N2   C14  119.10  3.000
 QD2  C14  N2   C7   116.89  3.000
 QD2  C3   N2   C7   116.11  3.000
 QD2  C2   C3   N2   122.22  3.000
 QD2  N2   C3   C4   120.44  3.000
 QD2  C2   C3   C4   117.33  3.000
 QD2  H26  C2   C1   120.47  3.000
 QD2  H26  C2   C3   119.88  3.000
 QD2  C1   C2   C3   119.65  3.000
 QD2  C6   O2   C5   118.52  3.000
 QD2  S    C1   C2   117.39  3.000
 QD2  C2   C1   C5   118.38  3.000
 QD2  S    C1   C5   124.23  3.000
 QD2  N    S    O1   113.04  3.000
 QD2  N    S    O    105.58  3.000
 QD2  O1   S    O    118.34  3.000
 QD2  N    S    C1   101.91  3.000
 QD2  O    S    C1   107.61  3.000
 QD2  O1   S    C1   109.00  3.000
 QD2  H27  N    C    114.03  3.000
 QD2  H27  N    S    110.14  3.000
 QD2  C    N    S    119.01  3.000
 QD2  H30  C    H29  109.04  3.000
 QD2  H30  C    H28  108.79  3.000
 QD2  H29  C    H28  107.45  3.000
 QD2  H30  C    N    113.67  3.000
 QD2  H29  C    N    110.44  3.000
 QD2  H28  C    N    107.24  3.000
 QD2  C12  C15  O4   121.23  3.000
 QD2  C12  C15  N3   115.87  3.000
 QD2  O4   C15  N3   122.89  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
 QD2  CONST_01  C2   C1   C5   N1      0.00   0.0  0
 QD2  CONST_02  C2   C3   C4   N1      0.00   0.0  0
 QD2  CONST_03  C1   C5   N1   C4      0.00   0.0  0
 QD2  CONST_04  C1   C2   C3   C4      0.00   0.0  0
 QD2  CONST_05  C3   C2   C1   C5      0.00   0.0  0
 QD2  CONST_06  C3   C4   N1   C5      0.00   0.0  0
 QD2  CONST_07  C13  C12  C11  C10     0.00   0.0  0
 QD2  CONST_08  C13  C14  C9   C10     0.00   0.0  0
 QD2  CONST_09  C9   C14  C13  C12     0.00   0.0  0
 QD2  CONST_10  C9   C10  C11  C12     0.00   0.0  0
 QD2  CONST_11  C14  C13  C12  C11     0.00   0.0  0
 QD2  CONST_12  C14  C9   C10  C11     0.00   0.0  0
 QD2  CONST_13  N2   C3   C4   N1    180.00   0.0  0
 QD2  CONST_14  C1   C2   C3   N2    180.00   0.0  0
 QD2  CONST_15  S    C1   C5   N1    180.00   0.0  0
 QD2  CONST_16  O2   C5   N1   C4    180.00   0.0  0
 QD2  CONST_17  C15  C12  C11  C10   180.00   0.0  0
 QD2  CONST_18  C14  C13  C12  C15   180.00   0.0  0
 QD2  CONST_19  S    C1   C2   C3    180.00   0.0  0
 QD2  CONST_20  O2   C5   C1   C2    180.00   0.0  0
 QD2  CONST_21  H26  C2   C3   C4    180.00   0.0  0
 QD2  CONST_22  H2   C4   N1   C5    180.00   0.0  0
 QD2  CONST_23  H25  C11  C12  C13   180.00   0.0  0
 QD2  CONST_24  H10  C10  C11  C12   180.00   0.0  0
 QD2  CONST_25  H11  C13  C12  C11   180.00   0.0  0
 QD2  CONST_26  C12  C15  N3   C16   180.00   0.0  0
 QD2  CONST_27  C16  N3   C15  O4      0.00   0.0  0
 QD2  CONST_28  H1   N3   C15  C12     0.00   0.0  0
 QD2  Var_01    C14  N2   C3   C4    122.83  30.0  2
 QD2  Var_02    C13  C14  N2   C7   -169.74  30.0  1
 QD2  Var_03    C3   N2   C7   C8    171.43  30.0  1
 QD2  Var_04    C14  C9   O3   C8     19.96  30.0  1
 QD2  Var_05    C20  N4   C18  C17   -59.35  30.0  1
 QD2  Var_06    C18  N4   C20  C21    59.47  30.0  1
 QD2  Var_07    N4   C20  C21  C16   -56.99  30.0  1
 QD2  Var_08    N4   C18  C17  C16    56.56  30.0  1
 QD2  Var_09    N2   C7   C8   O3     58.69  30.0  1
 QD2  Var_10    H8   C8   O3   C9   -169.69  30.0  1
 QD2  Var_11    C13  C12  C15  N3    153.04  30.0  2
 QD2  Var_12    O1   S    C1   C5     28.02  30.0  2
 QD2  Var_13    C1   C5   O2   C6    179.98  30.0  2
 QD2  Var_14    H20  C19  N4   C20   176.19  30.0  3
 QD2  Var_15    C    N    S    C1     76.83  30.0  3
 QD2  Var_16    H3   C6   O2   C5    179.72  30.0  3
 QD2  Var_17    H28  C    N    S     178.63  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
 QD2  chir_01  C16  C21  N3  C17  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
 QD2  plan-1  N1   0.020
 QD2  plan-1  C4   0.020
 QD2  plan-1  C5   0.020
 QD2  plan-1  N2   0.020
 QD2  plan-1  C3   0.020
 QD2  plan-1  C2   0.020
 QD2  plan-1  O2   0.020
 QD2  plan-1  C1   0.020
 QD2  plan-1  S    0.020
 QD2  plan-1  H2   0.020
 QD2  plan-1  H26  0.020
 QD2  plan-2  C10  0.020
 QD2  plan-2  C13  0.020
 QD2  plan-2  C12  0.020
 QD2  plan-2  C11  0.020
 QD2  plan-2  C14  0.020
 QD2  plan-2  C9   0.020
 QD2  plan-2  O3   0.020
 QD2  plan-2  N2   0.020
 QD2  plan-2  H10  0.020
 QD2  plan-2  H11  0.020
 QD2  plan-2  H25  0.020
 QD2  plan-2  C15  0.020
 QD2  plan-3  N3   0.020
 QD2  plan-3  O4   0.020
 QD2  plan-3  C16  0.020
 QD2  plan-3  C12  0.020
 QD2  plan-3  H1   0.020
 QD2  plan-3  C15  0.020

