# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 16:37:59 2022
#   Inital geometry file: a 113 line input string
#   Ligand name: 5-(3,6-dihydro-2~{H}-pyran-4-yl)-2-methoxy-~{N}-(2-methylpyridin-4-yl)pyridine-3-sulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ncc(cc1[S](=O)(=O)Nc2ccnc(C)c2)C3=CCOCC3
#
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
 7VT  7VT  "5-[3,6-dihydro-2H-pyran-4-yl]-2-methoxy-N-[2-methylpyridin-4-yl]pyridine-3-sulfonamide"
  ligand  44  25  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7VT
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
 7VT  N1   N  NC1   0  -0.830  -10.2767  -32.4358  20.5077
 7VT  C4   C  CR16  0  -0.159   -8.6766  -30.0804  22.9452
 7VT  C5   C  CR6   0  -0.371   -9.7987  -30.3847  22.2047
 7VT  C6   C  CR6   0   0.438   -9.9598  -33.3806  21.4877
 7VT  C7   C  CR16  0  -0.390  -10.9567  -34.2430  21.9442
 7VT  C8   C  CR16  0  -0.071  -10.6247  -35.1693  22.9115
 7VT  C13  C  C1    0  -0.345   -6.5015  -30.1009  24.9858
 7VT  C15  C  CH2   0  -0.186   -6.5212  -28.3293  27.0637
 7VT  O2   O  OS    0  -0.626  -10.5005  -30.1080  19.6613
 7VT  S    S  S     0   1.380   -9.6422  -30.8951  20.5214
 7VT  O1   O  OS    0  -0.627   -8.2245  -30.9790  20.2262
 7VT  C11  C  CR16  0  -0.383   -8.6872  -33.5092  22.0292
 7VT  C9   C  CR6   0   0.242   -8.4644  -34.4625  23.0203
 7VT  N2   N  N     0  -0.432   -9.4157  -35.2831  23.4538
 7VT  C1   C  CR6   0   0.593  -11.0599  -30.2993  22.8180
 7VT  O    O  O2    0  -0.459  -12.1173  -30.6378  22.1018
 7VT  C    C  CH3   0  -0.419  -13.4019  -30.6040  22.7195
 7VT  C3   C  CR6   0  -0.001   -8.8074  -29.6894  24.2789
 7VT  C2   C  CR16  0  -0.076  -10.1064  -29.6089  24.7674
 7VT  N    N  N     0  -0.449  -11.1931  -29.9098  24.0649
 7VT  C12  C  C     0   0.083   -7.6275  -29.3951  25.1104
 7VT  C16  C  CH2   0  -0.521   -7.6995  -28.2690  26.1060
 7VT  O3   O  O2    0  -0.476   -5.3096  -28.5168  26.3678
 7VT  C14  C  CH2   0  -0.192   -5.2550  -29.7715  25.7416
 7VT  H1   H  HNC1  0   0.432  -11.2388  -32.4509  20.1862
 7VT  H3   H  HCR6  0   0.283  -11.9671  -34.1875  21.5597
 7VT  H4   H  HCR6  0   0.264  -11.3840  -35.8516  23.2776
 7VT  H8   H  H     0   0.259   -6.4467  -30.9587  24.3227
 7VT  H9   H  HCH2  0   0.240   -6.4312  -27.3975  27.6228
 7VT  H10  H  HCH2  0   0.207   -6.6795  -29.1382  27.7902
 7VT  H11  H  HCR6  0   0.288   -7.8601  -32.8981  21.6981
 7VT  H12  H  HCH3  0   0.256  -14.1003  -30.9392  21.9586
 7VT  H13  H  HCH3  0   0.240  -13.4475  -31.2731  23.5784
 7VT  H14  H  HCH3  0   0.241  -13.6635  -29.5952  23.0373
 7VT  H15  H  HCR6  0   0.276  -10.2894  -29.3031  25.7910
 7VT  H16  H  HCH2  0   0.256   -7.7285  -27.3105  25.5781
 7VT  H17  H  HCH2  0   0.251   -8.6213  -28.3204  26.6909
 7VT  H18  H  HCH2  0   0.217   -5.0469  -30.5713  26.4699
 7VT  H19  H  HCH2  0   0.245   -4.4047  -29.7515  25.0543
 7VT  C10  C  CH3   0  -0.732   -7.1038  -34.5806  23.6389
 7VT  H2   H  HCR6  0   0.296   -7.6962  -30.1343  22.4904
 7VT  H5   H  HCH3  0   0.250   -7.0620  -35.4249  24.3233
 7VT  H6   H  HCH3  0   0.251   -6.3337  -34.7120  22.8780
 7VT  H7   H  HCH3  0   0.256   -6.8515  -33.6757  24.1952

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
 7VT  O2   S    double    1.448  0.020  1.448
 7VT  O1   S    double    1.451  0.020  1.451
 7VT  S    N1   single    1.666  0.020  1.666
 7VT  S    C5   single    1.766  0.020  1.766
 7VT  N1   C6   single    1.398  0.020  1.398
 7VT  C6   C7   aromatic  1.395  0.020  1.395
 7VT  C6   C11  aromatic  1.389  0.020  1.389
 7VT  C7   C8   aromatic  1.380  0.020  1.380
 7VT  O    C    single    1.426  0.020  1.426
 7VT  O    C1   single    1.321  0.020  1.321
 7VT  C11  C9   aromatic  1.393  0.020  1.393
 7VT  C5   C1   aromatic  1.405  0.020  1.405
 7VT  C5   C4   aromatic  1.378  0.020  1.378
 7VT  C8   N2   aromatic  1.330  0.020  1.330
 7VT  C1   N    aromatic  1.313  0.020  1.313
 7VT  C9   N2   aromatic  1.329  0.020  1.329
 7VT  C9   C10  single    1.499  0.020  1.499
 7VT  C4   C3   aromatic  1.396  0.020  1.396
 7VT  N    C2   aromatic  1.328  0.020  1.328
 7VT  C3   C2   aromatic  1.390  0.020  1.390
 7VT  C3   C12  single    1.473  0.020  1.473
 7VT  C12  C13  double    1.335  0.020  1.335
 7VT  C12  C16  single    1.505  0.020  1.505
 7VT  C13  C14  single    1.494  0.020  1.494
 7VT  C16  C15  single    1.520  0.020  1.520
 7VT  C14  O3   single    1.403  0.020  1.403
 7VT  O3   C15  single    1.410  0.020  1.410
 7VT  N1   H1   single    0.890  0.020  1.040
 7VT  C4   H2   single    0.930  0.020  1.080
 7VT  C7   H3   single    0.930  0.020  1.080
 7VT  C8   H4   single    0.930  0.020  1.080
 7VT  C10  H5   single    0.970  0.020  1.090
 7VT  C10  H6   single    0.970  0.020  1.090
 7VT  C10  H7   single    0.970  0.020  1.090
 7VT  C13  H8   single    0.930  0.020  1.080
 7VT  C15  H9   single    0.970  0.020  1.090
 7VT  C15  H10  single    0.970  0.020  1.090
 7VT  C11  H11  single    0.930  0.020  1.080
 7VT  C    H12  single    0.970  0.020  1.090
 7VT  C    H13  single    0.970  0.020  1.090
 7VT  C    H14  single    0.970  0.020  1.090
 7VT  C2   H15  single    0.930  0.020  1.080
 7VT  C16  H16  single    0.970  0.020  1.090
 7VT  C16  H17  single    0.970  0.020  1.090
 7VT  C14  H18  single    0.970  0.020  1.090
 7VT  C14  H19  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
 7VT  H1   N1   S    112.18  3.000
 7VT  H1   N1   C6   115.29  3.000
 7VT  S    N1   C6   122.20  3.000
 7VT  H2   C4   C3   120.03  3.000
 7VT  H2   C4   C5   120.04  3.000
 7VT  C3   C4   C5   119.92  3.000
 7VT  C1   C5   S    120.88  3.000
 7VT  C1   C5   C4   118.87  3.000
 7VT  S    C5   C4   120.25  3.000
 7VT  C11  C6   C7   118.03  3.000
 7VT  C11  C6   N1   122.93  3.000
 7VT  C7   C6   N1   119.03  3.000
 7VT  H3   C7   C8   120.53  3.000
 7VT  H3   C7   C6   121.27  3.000
 7VT  C8   C7   C6   118.20  3.000
 7VT  H4   C8   N2   116.42  3.000
 7VT  H4   C8   C7   119.38  3.000
 7VT  N2   C8   C7   124.20  3.000
 7VT  H8   C13  C14  116.16  3.000
 7VT  H8   C13  C12  121.16  3.000
 7VT  C14  C13  C12  122.68  3.000
 7VT  H10  C15  H9   107.58  3.000
 7VT  H10  C15  O3   110.62  3.000
 7VT  H9   C15  O3   107.21  3.000
 7VT  H10  C15  C16  109.53  3.000
 7VT  H9   C15  C16  110.69  3.000
 7VT  O3   C15  C16  111.14  3.000
 7VT  O1   S    O2   119.34  3.000
 7VT  O1   S    C5   107.30  3.000
 7VT  O2   S    C5   110.89  3.000
 7VT  C5   S    N1   103.97  3.000
 7VT  O1   S    N1   108.48  3.000
 7VT  O2   S    N1   105.79  3.000
 7VT  H11  C11  C9   118.86  3.000
 7VT  H11  C11  C6   121.98  3.000
 7VT  C9   C11  C6   119.16  3.000
 7VT  N2   C9   C11  122.69  3.000
 7VT  N2   C9   C10  117.80  3.000
 7VT  C11  C9   C10  119.52  3.000
 7VT  C9   N2   C8   117.70  3.000
 7VT  N    C1   O    120.63  3.000
 7VT  N    C1   C5   121.57  3.000
 7VT  O    C1   C5   117.79  3.000
 7VT  C    O    C1   118.69  3.000
 7VT  H14  C    H13  109.19  3.000
 7VT  H14  C    H12  109.62  3.000
 7VT  H13  C    H12  109.63  3.000
 7VT  H14  C    O    111.38  3.000
 7VT  H13  C    O    111.38  3.000
 7VT  H12  C    O    105.58  3.000
 7VT  C12  C3   C2   122.58  3.000
 7VT  C12  C3   C4   121.34  3.000
 7VT  C2   C3   C4   116.07  3.000
 7VT  H15  C2   N    115.16  3.000
 7VT  H15  C2   C3   120.39  3.000
 7VT  N    C2   C3   124.43  3.000
 7VT  C2   N    C1   119.10  3.000
 7VT  C16  C12  C3   118.98  3.000
 7VT  C16  C12  C13  119.86  3.000
 7VT  C3   C12  C13  121.16  3.000
 7VT  H17  C16  H16  106.08  3.000
 7VT  H17  C16  C12  111.06  3.000
 7VT  H16  C16  C12  109.72  3.000
 7VT  H17  C16  C15  108.35  3.000
 7VT  H16  C16  C15  111.05  3.000
 7VT  C12  C16  C15  110.50  3.000
 7VT  C14  O3   C15  111.88  3.000
 7VT  H19  C14  H18  106.37  3.000
 7VT  H19  C14  O3   107.12  3.000
 7VT  H18  C14  O3   111.19  3.000
 7VT  H19  C14  C13  109.56  3.000
 7VT  H18  C14  C13  109.38  3.000
 7VT  O3   C14  C13  112.97  3.000
 7VT  H7   C10  H6   106.98  3.000
 7VT  H7   C10  H5   108.29  3.000
 7VT  H6   C10  H5   108.57  3.000
 7VT  H7   C10  C9   110.77  3.000
 7VT  H6   C10  C9   111.25  3.000
 7VT  H5   C10  C9   110.83  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
 7VT  CONST_01  N    C1   C5   C4      0.00   0.0  0
 7VT  CONST_02  N    C2   C3   C4      0.00   0.0  0
 7VT  CONST_03  C2   N    C1   C5      0.00   0.0  0
 7VT  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 7VT  CONST_05  N2   C8   C7   C6      0.00   0.0  0
 7VT  CONST_06  N2   C9   C11  C6      0.00   0.0  0
 7VT  CONST_07  C9   C11  C6   C7      0.00   0.0  0
 7VT  CONST_08  C9   N2   C8   C7      0.00   0.0  0
 7VT  CONST_09  C11  C6   C7   C8      0.00   0.0  0
 7VT  CONST_10  C11  C9   N2   C8      0.00   0.0  0
 7VT  CONST_11  C3   C4   C5   C1      0.00   0.0  0
 7VT  CONST_12  C3   C2   N    C1      0.00   0.0  0
 7VT  CONST_13  C12  C3   C4   C5    180.00   0.0  0
 7VT  CONST_14  C12  C3   C2   N     180.00   0.0  0
 7VT  CONST_15  C8   C7   C6   N1    180.00   0.0  0
 7VT  CONST_16  C9   C11  C6   N1    180.00   0.0  0
 7VT  CONST_17  O    C1   C5   C4    180.00   0.0  0
 7VT  CONST_18  C10  C9   C11  C6    180.00   0.0  0
 7VT  CONST_19  C10  C9   N2   C8    180.00   0.0  0
 7VT  CONST_20  N    C1   C5   S     180.00   0.0  0
 7VT  CONST_21  C3   C4   C5   S     180.00   0.0  0
 7VT  CONST_22  C2   N    C1   O     180.00   0.0  0
 7VT  CONST_23  H15  C2   C3   C4    180.00   0.0  0
 7VT  CONST_24  H4   C8   C7   C6    180.00   0.0  0
 7VT  CONST_25  H11  C11  C6   C7    180.00   0.0  0
 7VT  CONST_26  H3   C7   C6   C11   180.00   0.0  0
 7VT  CONST_27  H4   C8   N2   C9    180.00   0.0  0
 7VT  CONST_28  H3   C7   C8   N2    180.00   0.0  0
 7VT  CONST_29  H11  C11  C9   N2    180.00   0.0  0
 7VT  CONST_30  H2   C4   C5   C1    180.00   0.0  0
 7VT  CONST_31  H15  C2   N    C1    180.00   0.0  0
 7VT  CONST_32  H2   C4   C3   C2    180.00   0.0  0
 7VT  CONST_33  H2   C4   C3   C12     0.00   0.0  0
 7VT  CONST_34  H15  C2   C3   C12     0.00   0.0  0
 7VT  CONST_37  H1   N1   C6   C7      0.00   0.0  0
 7VT  CONST_38  H1   N1   C6   C11   180.00   0.0  0
 7VT  Var_01    C13  C12  C3   C4    -36.77  30.0  2
 7VT  Var_02    C16  C12  C3   C4    142.68  30.0  2
 7VT  Var_03    C2   C3   C12  C13   142.63  30.0  3
 7VT  Var_04    C15  C16  C12  C13   -13.29  30.0  1
 7VT  Var_05    C15  O3   C14  C13    46.94  30.0  1
 7VT  Var_06    C3   C12  C16  C15   167.25  30.0  1
 7VT  Var_07    C14  C13  C12  C3    175.58  30.0  1
 7VT  Var_08    C16  C12  C3   C2    -37.92  30.0  2
 7VT  Var_09    O3   C14  C13  C12   -12.03  30.0  1
 7VT  Var_10    O3   C15  C16  C12    47.21  30.0  1
 7VT  Var_11    C14  C13  C12  C16    -3.86  30.0  1
 7VT  Var_12    C14  O3   C15  C16   -66.15  30.0  1
 7VT  Var_13    H16  C16  C12  C13   109.49  30.0  1
 7VT  Var_14    H17  C16  C12  C13  -133.56  30.0  1
 7VT  Var_15    H18  C14  O3   C15   -76.50  30.0  1
 7VT  Var_16    H19  C14  O3   C15   167.67  30.0  1
 7VT  Var_17    H8   C13  C12  C3     -4.66  30.0  1
 7VT  Var_18    H16  C16  C12  C3    -69.97  30.0  1
 7VT  Var_19    H17  C16  C12  C3     46.98  30.0  1
 7VT  Var_20    H18  C14  C13  C12   112.39  30.0  1
 7VT  Var_21    H19  C14  C13  C12  -131.37  30.0  1
 7VT  Var_22    H9   C15  C16  C12   166.22  30.0  1
 7VT  Var_23    H10  C15  C16  C12   -75.33  30.0  1
 7VT  Var_24    H8   C13  C12  C16   175.89  30.0  1
 7VT  Var_25    H8   C13  C14  O3    168.20  30.0  1
 7VT  Var_26    H16  C16  C15  O3    -74.79  30.0  1
 7VT  Var_27    H17  C16  C15  O3    169.08  30.0  1
 7VT  Var_28    H9   C15  O3   C14   172.77  30.0  1
 7VT  Var_29    H10  C15  O3   C14    55.75  30.0  1
 7VT  Var_30    C1   C5   S    N1    -60.84  30.0  2
 7VT  Var_31    C4   C5   S    N1    118.26  30.0  2
 7VT  Var_32    O2   S    C5   C4   -128.47  30.0  3
 7VT  Var_33    O1   S    C5   C4      3.46  30.0  3
 7VT  Var_34    C6   N1   S    C5    -44.91  30.0  3
 7VT  Var_35    C    O    C1   C5    177.80  30.0  2
 7VT  Var_36    C1   C5   S    O2     52.43  30.0  2
 7VT  Var_37    C1   C5   S    O1   -175.64  30.0  2
 7VT  Var_38    N    C1   O    C      -1.56  30.0  2
 7VT  Var_39    H5   C10  C9   C11  -174.66  30.0  2
 7VT  Var_40    H6   C10  C9   C11   -53.75  30.0  2
 7VT  Var_41    H7   C10  C9   C11    65.11  30.0  2
 7VT  Var_42    H5   C10  C9   N2      5.54  30.0  2
 7VT  Var_43    H6   C10  C9   N2    126.44  30.0  2
 7VT  Var_44    H7   C10  C9   N2   -114.70  30.0  2
 7VT  Var_45    O2   S    N1   C6   -161.80  30.0  2
 7VT  Var_46    O1   S    N1   C6     69.05  30.0  2
 7VT  Var_47    H1   N1   S    C5     98.40  30.0  3
 7VT  Var_48    H12  C    O    C1   -178.67  30.0  3
 7VT  Var_49    H13  C    O    C1    -59.75  30.0  3
 7VT  Var_50    H14  C    O    C1     62.41  30.0  3
 7VT  Var_51    H1   N1   S    O2    -18.49  30.0  3
 7VT  Var_52    H1   N1   S    O1   -147.64  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
 7VT  plan-1  C4   0.020
 7VT  plan-1  C5   0.020
 7VT  plan-1  S    0.020
 7VT  plan-1  C1   0.020
 7VT  plan-1  O    0.020
 7VT  plan-1  C3   0.020
 7VT  plan-1  C2   0.020
 7VT  plan-1  N    0.020
 7VT  plan-1  C12  0.020
 7VT  plan-1  H15  0.020
 7VT  plan-1  H2   0.020
 7VT  plan-2  N1   0.020
 7VT  plan-2  C6   0.020
 7VT  plan-2  C7   0.020
 7VT  plan-2  C8   0.020
 7VT  plan-2  C11  0.020
 7VT  plan-2  C9   0.020
 7VT  plan-2  N2   0.020
 7VT  plan-2  H3   0.020
 7VT  plan-2  H4   0.020
 7VT  plan-2  H11  0.020
 7VT  plan-2  C10  0.020
 7VT  plan-3  N1   0.020
 7VT  plan-3  C6   0.020
 7VT  plan-3  S    0.020
 7VT  plan-3  H1   0.020

