# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 01:06:03 2021
#   Inital geometry file: a 124 line input string
#   Ligand name: ~{N}-[5-[6-[(dimethylamino)methyl]-2,3-dihydro-1,4-benzoxazin-4-yl]-2-methoxy-pyridin-3-yl]methanesulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ncc(cc1N[S](C)(=O)=O)N2CCOc3ccc(CN(C)C)cc23
#
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
 QDE  QDE  ~{N}-[5-[6-[(dimethylamino)methyl]-2,3-dihydro-1,4-benzoxazin-4-yl]-2-methoxy-pyridin-3-yl]methanesulfonamide  ligand  51  27  .  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_QDE
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
 QDE  N1   N  NC1   0  -0.842  -10.2663  -30.1110  21.2099
 QDE  N3   N  NT    0  -0.397   -5.9345  -34.5193  23.4321
 QDE  C4   C  CR16  0  -0.166   -9.2807  -29.8001  23.4010
 QDE  C5   C  CR6   0   0.170  -10.3898  -29.9532  22.6031
 QDE  C6   C  CH3   0  -0.788   -8.1133  -31.3338  20.1321
 QDE  C7   C  CH2   0  -0.321   -7.9297  -28.2090  25.9847
 QDE  C8   C  CH2   0  -0.217   -6.8540  -28.2572  27.0434
 QDE  C10  C  CR16  0  -0.351   -5.0072  -31.1514  26.0181
 QDE  C13  C  CH2   0  -0.335   -6.7983  -34.1429  24.5351
 QDE  C15  C  CH3   0  -0.522   -6.0815  -35.9242  23.1184
 QDE  C17  C  CR6   0   0.303   -7.3035  -30.5196  25.5944
 QDE  O2   O  OS    0  -0.640   -9.8367  -32.5739  21.6766
 QDE  S    S  S     0   1.325   -9.8031  -31.5988  20.5995
 QDE  O1   O  OS    0  -0.662  -10.5827  -31.8220  19.3922
 QDE  C1   C  CR6   0   0.518  -11.6508  -29.9593  23.2334
 QDE  O    O  O2    0  -0.466  -12.7112  -30.1071  22.4459
 QDE  C    C  CH3   0  -0.416  -14.0014  -30.0891  23.0440
 QDE  C3   C  CR6   0   0.153   -9.4283  -29.7014  24.7863
 QDE  C2   C  CR16  0  -0.081  -10.7118  -29.7104  25.2937
 QDE  N    N  N     0  -0.458  -11.7970  -29.8156  24.5286
 QDE  N2   N  NT    0  -0.606   -8.3188  -29.5669  25.6465
 QDE  C9   C  CR6   0   0.288   -6.0208  -30.2046  26.0665
 QDE  O3   O  O2    0  -0.481   -5.7278  -28.9788  26.5746
 QDE  C16  C  CR16  0  -0.399   -7.5226  -31.8099  25.1039
 QDE  C12  C  CR6   0   0.102   -6.5119  -32.7588  25.0534
 QDE  C11  C  CR16  0  -0.312   -5.2405  -32.4163  25.5030
 QDE  C14  C  CH3   0  -0.521   -6.1711  -33.7002  22.2630
 QDE  H1   H  HNC1  0   0.423  -10.9835  -29.6751  20.6407
 QDE  H3   H  HCR6  0   0.288   -8.2938  -29.7688  22.9560
 QDE  H4   H  HCH3  0   0.284   -7.5355  -31.0436  21.0062
 QDE  H5   H  HCH3  0   0.303   -7.7268  -32.2670  19.7260
 QDE  H6   H  HCH3  0   0.305   -8.0736  -30.5500  19.3799
 QDE  H7   H  HCH2  0   0.242   -7.5675  -27.6583  25.1069
 QDE  H8   H  HCH2  0   0.266   -8.7958  -27.6725  26.3749
 QDE  H9   H  HCH2  0   0.257   -6.5112  -27.2520  27.2820
 QDE  H10  H  HCH2  0   0.236   -7.2427  -28.7164  27.9586
 QDE  H11  H  HCR6  0   0.258   -4.0244  -30.8792  26.3841
 QDE  H12  H  HCH2  0   0.206   -7.8655  -34.2141  24.2616
 QDE  H13  H  HCH2  0   0.244   -6.6414  -34.8669  25.3407
 QDE  H14  H  HCH3  0   0.232   -5.8473  -36.5313  23.9944
 QDE  H15  H  HCH3  0   0.191   -7.0969  -36.1917  22.7859
 QDE  H16  H  HCH3  0   0.233   -5.3892  -36.2028  22.3226
 QDE  H17  H  HCH3  0   0.251  -14.7051  -30.2537  22.2328
 QDE  H18  H  HCH3  0   0.234  -14.1126  -30.8795  23.7864
 QDE  H19  H  HCH3  0   0.234  -14.2107  -29.1290  23.5165
 QDE  H20  H  HCR6  0   0.275  -10.8722  -29.6291  26.3633
 QDE  H21  H  HCR6  0   0.261   -8.5065  -32.0825  24.7416
 QDE  H22  H  HCR6  0   0.239   -4.4350  -33.1381  25.4614
 QDE  H23  H  HCH3  0   0.234   -5.9701  -32.6517  22.4846
 QDE  H24  H  HCH3  0   0.232   -5.5026  -34.0030  21.4557
 QDE  H25  H  HCH3  0   0.192   -7.2049  -33.7734  21.8896

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
 QDE  O1   S    double    1.454  0.020  1.454
 QDE  S    C6   single    1.773  0.020  1.773
 QDE  S    N1   single    1.674  0.020  1.674
 QDE  S    O2   double    1.453  0.020  1.453
 QDE  N1   C5   single    1.408  0.020  1.408
 QDE  C14  N3   single    1.447  0.020  1.447
 QDE  O    C    single    1.422  0.020  1.422
 QDE  O    C1   single    1.329  0.020  1.329
 QDE  C5   C1   aromatic  1.410  0.020  1.410
 QDE  C5   C4   aromatic  1.375  0.020  1.375
 QDE  C15  N3   single    1.447  0.020  1.447
 QDE  C1   N    aromatic  1.311  0.020  1.311
 QDE  N3   C13  single    1.451  0.020  1.451
 QDE  C4   C3   aromatic  1.397  0.020  1.397
 QDE  C13  C12  single    1.505  0.020  1.505
 QDE  N    C2   aromatic  1.332  0.020  1.332
 QDE  C3   C2   aromatic  1.380  0.020  1.380
 QDE  C3   N2   single    1.410  0.020  1.410
 QDE  C12  C16  aromatic  1.387  0.020  1.387
 QDE  C12  C11  aromatic  1.391  0.020  1.391
 QDE  C16  C17  aromatic  1.398  0.020  1.398
 QDE  C11  C10  aromatic  1.385  0.020  1.385
 QDE  C17  N2   single    1.393  0.020  1.393
 QDE  C17  C9   aromatic  1.403  0.020  1.403
 QDE  N2   C7   single    1.452  0.020  1.452
 QDE  C10  C9   aromatic  1.388  0.020  1.388
 QDE  C9   O3   single    1.359  0.020  1.359
 QDE  C7   C8   single    1.510  0.020  1.510
 QDE  O3   C8   single    1.417  0.020  1.417
 QDE  N1   H1   single    0.890  0.020  1.040
 QDE  C4   H3   single    0.930  0.020  1.080
 QDE  C6   H4   single    0.970  0.020  1.090
 QDE  C6   H5   single    0.970  0.020  1.090
 QDE  C6   H6   single    0.970  0.020  1.090
 QDE  C7   H7   single    0.970  0.020  1.090
 QDE  C7   H8   single    0.970  0.020  1.090
 QDE  C8   H9   single    0.970  0.020  1.090
 QDE  C8   H10  single    0.970  0.020  1.090
 QDE  C10  H11  single    0.930  0.020  1.080
 QDE  C13  H12  single    0.970  0.020  1.090
 QDE  C13  H13  single    0.970  0.020  1.090
 QDE  C15  H14  single    0.970  0.020  1.090
 QDE  C15  H15  single    0.970  0.020  1.090
 QDE  C15  H16  single    0.970  0.020  1.090
 QDE  C    H17  single    0.970  0.020  1.090
 QDE  C    H18  single    0.970  0.020  1.090
 QDE  C    H19  single    0.970  0.020  1.090
 QDE  C2   H20  single    0.930  0.020  1.080
 QDE  C16  H21  single    0.930  0.020  1.080
 QDE  C11  H22  single    0.930  0.020  1.080
 QDE  C14  H23  single    0.970  0.020  1.090
 QDE  C14  H24  single    0.970  0.020  1.090
 QDE  C14  H25  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
 QDE  H1   N1   S    111.91  3.000
 QDE  H1   N1   C5   116.45  3.000
 QDE  S    N1   C5   119.01  3.000
 QDE  C14  N3   C15  110.97  3.000
 QDE  C15  N3   C13  110.87  3.000
 QDE  C14  N3   C13  111.72  3.000
 QDE  H3   C4   C3   120.12  3.000
 QDE  H3   C4   C5   119.99  3.000
 QDE  C3   C4   C5   119.88  3.000
 QDE  C1   C5   C4   117.56  3.000
 QDE  C4   C5   N1   121.07  3.000
 QDE  C1   C5   N1   121.37  3.000
 QDE  H6   C6   H5   110.31  3.000
 QDE  H6   C6   H4   110.15  3.000
 QDE  H5   C6   H4   109.88  3.000
 QDE  H6   C6   S    108.97  3.000
 QDE  H5   C6   S    107.97  3.000
 QDE  H4   C6   S    109.54  3.000
 QDE  H8   C7   H7   107.53  3.000
 QDE  H8   C7   N2   109.29  3.000
 QDE  H7   C7   N2   111.79  3.000
 QDE  H8   C7   C8   109.30  3.000
 QDE  H7   C7   C8   109.97  3.000
 QDE  N2   C7   C8   108.92  3.000
 QDE  H10  C8   H9   108.40  3.000
 QDE  H10  C8   O3   110.18  3.000
 QDE  H9   C8   O3   107.00  3.000
 QDE  H10  C8   C7   110.26  3.000
 QDE  H9   C8   C7   110.40  3.000
 QDE  O3   C8   C7   110.51  3.000
 QDE  H11  C10  C11  120.51  3.000
 QDE  H11  C10  C9   118.64  3.000
 QDE  C11  C10  C9   120.85  3.000
 QDE  H13  C13  H12  106.16  3.000
 QDE  H13  C13  C12  109.12  3.000
 QDE  H12  C13  C12  109.18  3.000
 QDE  H13  C13  N3   107.62  3.000
 QDE  H12  C13  N3   111.74  3.000
 QDE  C12  C13  N3   112.77  3.000
 QDE  H16  C15  H15  107.63  3.000
 QDE  H16  C15  H14  107.89  3.000
 QDE  H15  C15  H14  107.76  3.000
 QDE  H16  C15  N3   109.98  3.000
 QDE  H15  C15  N3   113.26  3.000
 QDE  H14  C15  N3   110.14  3.000
 QDE  C16  C17  C9   117.95  3.000
 QDE  C9   C17  N2   120.02  3.000
 QDE  C16  C17  N2   122.02  3.000
 QDE  O1   S    O2   119.99  3.000
 QDE  O2   S    C6   108.53  3.000
 QDE  O1   S    C6   108.36  3.000
 QDE  O2   S    N1   108.64  3.000
 QDE  C6   S    N1   103.12  3.000
 QDE  O1   S    N1   106.91  3.000
 QDE  N    C1   O    120.56  3.000
 QDE  N    C1   C5   122.74  3.000
 QDE  O    C1   C5   116.69  3.000
 QDE  C    O    C1   118.24  3.000
 QDE  H19  C    H18  108.89  3.000
 QDE  H19  C    H17  109.42  3.000
 QDE  H18  C    H17  109.43  3.000
 QDE  H19  C    O    111.56  3.000
 QDE  H18  C    O    111.71  3.000
 QDE  H17  C    O    105.77  3.000
 QDE  N2   C3   C2   120.53  3.000
 QDE  N2   C3   C4   121.91  3.000
 QDE  C2   C3   C4   117.55  3.000
 QDE  H20  C2   N    116.87  3.000
 QDE  H20  C2   C3   119.97  3.000
 QDE  N    C2   C3   123.16  3.000
 QDE  C2   N    C1   119.02  3.000
 QDE  C3   N2   C17  119.03  3.000
 QDE  C17  N2   C7   116.92  3.000
 QDE  C3   N2   C7   116.22  3.000
 QDE  O3   C9   C17  121.70  3.000
 QDE  O3   C9   C10  118.10  3.000
 QDE  C17  C9   C10  120.20  3.000
 QDE  C9   O3   C8   114.30  3.000
 QDE  H21  C16  C12  118.51  3.000
 QDE  H21  C16  C17  119.48  3.000
 QDE  C12  C16  C17  122.01  3.000
 QDE  C11  C12  C16  119.05  3.000
 QDE  C11  C12  C13  120.76  3.000
 QDE  C16  C12  C13  120.19  3.000
 QDE  H22  C11  C12  120.23  3.000
 QDE  H22  C11  C10  119.85  3.000
 QDE  C12  C11  C10  119.92  3.000
 QDE  H25  C14  H24  107.80  3.000
 QDE  H25  C14  H23  107.80  3.000
 QDE  H24  C14  H23  107.72  3.000
 QDE  H25  C14  N3   112.94  3.000
 QDE  H24  C14  N3   109.91  3.000
 QDE  H23  C14  N3   110.49  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
 QDE  CONST_01  N    C1   C5   C4      0.00   0.0  0
 QDE  CONST_02  N    C2   C3   C4      0.00   0.0  0
 QDE  CONST_03  C2   N    C1   C5      0.00   0.0  0
 QDE  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 QDE  CONST_05  C16  C12  C11  C10     0.00   0.0  0
 QDE  CONST_06  C16  C17  C9   C10     0.00   0.0  0
 QDE  CONST_07  C11  C12  C16  C17     0.00   0.0  0
 QDE  CONST_08  C11  C10  C9   C17     0.00   0.0  0
 QDE  CONST_09  C3   C4   C5   C1      0.00   0.0  0
 QDE  CONST_10  C3   C2   N    C1      0.00   0.0  0
 QDE  CONST_11  C12  C16  C17  C9      0.00   0.0  0
 QDE  CONST_12  C12  C11  C10  C9      0.00   0.0  0
 QDE  CONST_13  N2   C3   C4   C5    180.00   0.0  0
 QDE  CONST_14  N2   C3   C2   N     180.00   0.0  0
 QDE  CONST_15  N    C1   C5   N1    180.00   0.0  0
 QDE  CONST_16  C3   C4   C5   N1    180.00   0.0  0
 QDE  CONST_17  O    C1   C5   C4    180.00   0.0  0
 QDE  CONST_18  C13  C12  C11  C10   180.00   0.0  0
 QDE  CONST_19  C17  C16  C12  C13   180.00   0.0  0
 QDE  CONST_20  C2   N    C1   O     180.00   0.0  0
 QDE  CONST_21  H20  C2   C3   C4    180.00   0.0  0
 QDE  CONST_22  H11  C10  C9   C17   180.00   0.0  0
 QDE  CONST_23  H3   C4   C5   C1    180.00   0.0  0
 QDE  CONST_24  H21  C16  C17  N2      0.00   0.0  0
 QDE  CONST_25  H22  C11  C10  C9    180.00   0.0  0
 QDE  Var_01    C17  N2   C3   C4    -55.64  30.0  2
 QDE  Var_02    C16  C17  N2   C7   -171.02  30.0  1
 QDE  Var_03    C3   N2   C7   C8    172.69  30.0  1
 QDE  Var_04    C17  C9   O3   C8     22.30  30.0  1
 QDE  Var_05    O3   C8   C7   N2     59.20  30.0  1
 QDE  Var_06    C16  C12  C13  N3    123.88  30.0  2
 QDE  Var_07    N    C1   O    C       0.72  30.0  2
 QDE  Var_08    O1   S    N1   C5    141.05  30.0  1
 QDE  Var_09    C12  C13  N3   C15   170.10  30.0  3
 QDE  Var_10    H17  C    O    C1   -178.38  30.0  3
 QDE  Var_11    H4   C6   S    N1     59.97  30.0  3
 QDE  Var_12    H23  C14  N3   C13    60.86  30.0  3
 QDE  Var_13    H14  C15  N3   C13   -58.30  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
 QDE  plan-1  N1   0.020
 QDE  plan-1  C4   0.020
 QDE  plan-1  C5   0.020
 QDE  plan-1  C1   0.020
 QDE  plan-1  O    0.020
 QDE  plan-1  C3   0.020
 QDE  plan-1  C2   0.020
 QDE  plan-1  N    0.020
 QDE  plan-1  N2   0.020
 QDE  plan-1  H3   0.020
 QDE  plan-1  H20  0.020
 QDE  plan-2  C10  0.020
 QDE  plan-2  C13  0.020
 QDE  plan-2  C17  0.020
 QDE  plan-2  N2   0.020
 QDE  plan-2  C9   0.020
 QDE  plan-2  O3   0.020
 QDE  plan-2  C16  0.020
 QDE  plan-2  C12  0.020
 QDE  plan-2  C11  0.020
 QDE  plan-2  H11  0.020
 QDE  plan-2  H21  0.020
 QDE  plan-2  H22  0.020
 QDE  plan-3  N1   0.020
 QDE  plan-3  C5   0.020
 QDE  plan-3  S    0.020
 QDE  plan-3  H1   0.020

