# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 06:36:59 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: N-{cis-3-[methyl(7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino]cyclobutyl}propane-1-sulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC[S](=O)(=O)N[C@@H]1C[C@@H](C1)N(C)c2ncnc3[nH]ccc23
#
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
 D7D  D7D  N-{cis-3-[methyl(7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino]cyclobutyl}propane-1-sulfonamide  ligand  43  22  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_D7D
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
 D7D  C1   C  CR56  0   0.468  -5.0304   0.2270  -0.3940
 D7D  C2   C  CR56  0  -0.073  -3.9115  -0.6104  -0.2418
 D7D  N3   N  NC1   0  -0.733   2.4309   1.1069  -0.4589
 D7D  C4   C  C     0  -0.049  -0.4817   0.1490   1.0712
 D7D  C5   C  C     0  -0.496   0.9070  -0.4950   0.9046
 D7D  C6   C  C     0  -0.092   1.4449   0.9122   0.5833
 D7D  C8   C  CH2   0  -0.606   4.3415  -0.7997   0.1782
 D7D  C9   C  CH2   0  -0.435   5.8120  -1.0764   0.4642
 D7D  C10  C  CH3   0  -0.662   6.0409  -2.5590   0.7249
 D7D  C11  C  CH3   0  -0.555  -1.5275  -2.0649   0.5972
 D7D  C12  C  CR15  0  -0.439  -4.2732  -1.8781  -0.8051
 D7D  C13  C  CR15  0  -0.017  -5.5567  -1.7565  -1.2456
 D7D  O1   O  OS    0  -0.674   4.7410   1.2981  -1.3643
 D7D  O    O  OS    0  -0.677   4.3125   1.6777   1.0821
 D7D  C7   C  C     0  -0.440   0.0147   1.3378   0.2294
 D7D  C3   C  CR6   0   0.493  -2.7841   0.0087   0.3546
 D7D  N    N  N     0  -0.489  -2.8639   1.3000   0.6946
 D7D  N4   N  NR15  0  -0.657  -6.0099  -0.4882  -0.9919
 D7D  N1   N  N     0  -0.455  -5.1151   1.5125  -0.0408
 D7D  C    C  CR16  0   0.033  -3.9948   1.9640   0.4824
 D7D  H8   H  HNC1  0   0.410   2.1745   0.7191  -1.3615
 D7D  H    H  H     0   0.250  -0.6307   0.4639   2.1090
 D7D  H4   H  H     0   0.261   1.3287  -1.0335   1.7529
 D7D  H5   H  H     0   0.252   0.9490  -1.1282   0.0160
 D7D  H1   H  H     0   0.281   1.7867   1.4212   1.4839
 D7D  H10  H  HCH2  0   0.293   3.9955  -1.3444  -0.7024
 D7D  H9   H  HCH2  0   0.290   3.7145  -1.0871   1.0248
 D7D  H11  H  HCH2  0   0.246   6.4190  -0.7531  -0.3828
 D7D  H12  H  HCH2  0   0.246   6.1333  -0.4952   1.3302
 D7D  H15  H  HCH3  0   0.228   5.7553  -3.1619  -0.1380
 D7D  H14  H  HCH3  0   0.241   7.0920  -2.7535   0.9352
 D7D  H13  H  HCH3  0   0.228   5.4594  -2.9052   1.5803
 D7D  H18  H  HCH3  0   0.275  -0.7220  -2.3803   1.2551
 D7D  H17  H  HCH3  0   0.257  -2.4412  -2.5119   0.9839
 D7D  H16  H  HCH3  0   0.243  -1.3285  -2.4747  -0.3955
 D7D  H19  H  HCR5  0   0.258  -3.6749  -2.7689  -0.8897
 D7D  H20  H  HCR5  0   0.285  -6.1925  -2.4817  -1.7258
 D7D  H7   H  H     0   0.242  -0.1935   1.1747  -0.8309
 D7D  H6   H  H     0   0.257  -0.3036   2.3374   0.5121
 D7D  H2   H  HNR5  0   0.411  -6.9225  -0.1344  -1.2290
 D7D  H3   H  HCR6  0   0.241  -3.9892   3.0067   0.7850
 D7D  N2   N  NT    0  -0.493  -1.6170  -0.6195   0.6004
 D7D  S    S  S     0   1.351   4.0376   0.9355  -0.1416

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
 D7D  O    S    double    1.457  0.020  1.457
 D7D  C9   C8   single    1.523  0.020  1.523
 D7D  C9   C10  single    1.523  0.020  1.523
 D7D  C8   S    single    1.790  0.020  1.790
 D7D  S    N3   single    1.647  0.020  1.647
 D7D  S    O1   double    1.456  0.020  1.456
 D7D  N3   C6   single    1.448  0.020  1.448
 D7D  C6   C7   single    1.534  0.020  1.534
 D7D  C6   C5   single    1.540  0.020  1.540
 D7D  C7   C4   single    1.539  0.020  1.539
 D7D  C5   C4   single    1.540  0.020  1.540
 D7D  C11  N2   single    1.448  0.020  1.448
 D7D  C4   N2   single    1.450  0.020  1.450
 D7D  N2   C3   single    1.348  0.020  1.348
 D7D  C3   N    aromatic  1.338  0.020  1.338
 D7D  C3   C2   aromatic  1.418  0.020  1.418
 D7D  C12  C2   aromatic  1.434  0.020  1.434
 D7D  C12  C13  aromatic  1.362  0.020  1.362
 D7D  N    C    aromatic  1.329  0.020  1.329
 D7D  C2   C1   aromatic  1.406  0.020  1.406
 D7D  C13  N4   aromatic  1.371  0.020  1.371
 D7D  C    N1   aromatic  1.316  0.020  1.316
 D7D  C1   N4   aromatic  1.352  0.020  1.352
 D7D  C1   N1   aromatic  1.336  0.020  1.336
 D7D  N3   H8   single    0.890  0.020  1.040
 D7D  C4   H    single    0.970  0.020  1.090
 D7D  C5   H4   single    0.970  0.020  1.090
 D7D  C5   H5   single    0.970  0.020  1.090
 D7D  C6   H1   single    0.970  0.020  1.090
 D7D  C8   H10  single    0.970  0.020  1.090
 D7D  C8   H9   single    0.970  0.020  1.090
 D7D  C9   H11  single    0.970  0.020  1.090
 D7D  C9   H12  single    0.970  0.020  1.090
 D7D  C10  H15  single    0.970  0.020  1.090
 D7D  C10  H14  single    0.970  0.020  1.090
 D7D  C10  H13  single    0.970  0.020  1.090
 D7D  C11  H18  single    0.970  0.020  1.090
 D7D  C11  H17  single    0.970  0.020  1.090
 D7D  C11  H16  single    0.970  0.020  1.090
 D7D  C12  H19  single    0.930  0.020  1.080
 D7D  C13  H20  single    0.930  0.020  1.080
 D7D  C7   H7   single    0.970  0.020  1.090
 D7D  C7   H6   single    0.970  0.020  1.090
 D7D  N4   H2   single    0.860  0.020  1.020
 D7D  C    H3   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
 D7D  N1   C1   N4   125.45  3.000
 D7D  N1   C1   C2   126.52  3.000
 D7D  N4   C1   C2   108.02  3.000
 D7D  C3   C2   C12  138.77  3.000
 D7D  C12  C2   C1   106.46  3.000
 D7D  C3   C2   C1   114.73  3.000
 D7D  H8   N3   S    112.20  3.000
 D7D  H8   N3   C6   114.62  3.000
 D7D  S    N3   C6   120.78  3.000
 D7D  H    C4   N2   110.72  3.000
 D7D  H    C4   C7   109.89  3.000
 D7D  N2   C4   C7   118.98  3.000
 D7D  H    C4   C5   110.22  3.000
 D7D  N2   C4   C5   116.71  3.000
 D7D  C7   C4   C5    88.45  3.000
 D7D  H5   C5   H4   109.39  3.000
 D7D  H5   C5   C6   110.28  3.000
 D7D  H4   C5   C6   118.60  3.000
 D7D  H5   C5   C4   111.42  3.000
 D7D  H4   C5   C4   118.13  3.000
 D7D  C6   C5   C4    87.45  3.000
 D7D  H1   C6   C7   110.71  3.000
 D7D  H1   C6   C5   111.34  3.000
 D7D  C7   C6   C5    88.62  3.000
 D7D  H1   C6   N3   108.58  3.000
 D7D  C5   C6   N3   120.72  3.000
 D7D  C7   C6   N3   115.57  3.000
 D7D  H9   C8   H10  108.18  3.000
 D7D  H9   C8   S    107.22  3.000
 D7D  H10  C8   S    106.60  3.000
 D7D  H9   C8   C9   111.16  3.000
 D7D  H10  C8   C9   111.52  3.000
 D7D  S    C8   C9   111.92  3.000
 D7D  H12  C9   H11  107.12  3.000
 D7D  H12  C9   C10  109.78  3.000
 D7D  H11  C9   C10  109.74  3.000
 D7D  H12  C9   C8   109.66  3.000
 D7D  H11  C9   C8   109.72  3.000
 D7D  C10  C9   C8   110.74  3.000
 D7D  H13  C10  H14  107.84  3.000
 D7D  H13  C10  H15  107.78  3.000
 D7D  H14  C10  H15  107.86  3.000
 D7D  H13  C10  C9   111.29  3.000
 D7D  H14  C10  C9   110.60  3.000
 D7D  H15  C10  C9   111.31  3.000
 D7D  H16  C11  H17  108.78  3.000
 D7D  H16  C11  H18  107.83  3.000
 D7D  H17  C11  H18  106.73  3.000
 D7D  H16  C11  N2   112.81  3.000
 D7D  H17  C11  N2   110.93  3.000
 D7D  H18  C11  N2   109.52  3.000
 D7D  H19  C12  C13  124.90  3.000
 D7D  H19  C12  C2   128.49  3.000
 D7D  C13  C12  C2   106.61  3.000
 D7D  H20  C13  N4   120.69  3.000
 D7D  H20  C13  C12  129.79  3.000
 D7D  N4   C13  C12  109.52  3.000
 D7D  H6   C7   H7   109.51  3.000
 D7D  H6   C7   C6   117.94  3.000
 D7D  H7   C7   C6   111.11  3.000
 D7D  H6   C7   C4   118.28  3.000
 D7D  H7   C7   C4   110.73  3.000
 D7D  C6   C7   C4    87.72  3.000
 D7D  N    C3   N2   117.07  3.000
 D7D  N    C3   C2   118.75  3.000
 D7D  N2   C3   C2   124.17  3.000
 D7D  C    N    C3   119.52  3.000
 D7D  H2   N4   C13  125.53  3.000
 D7D  H2   N4   C1   125.08  3.000
 D7D  C13  N4   C1   109.38  3.000
 D7D  C    N1   C1   112.41  3.000
 D7D  H3   C    N1   116.40  3.000
 D7D  H3   C    N    115.54  3.000
 D7D  N1   C    N    128.06  3.000
 D7D  C3   N2   C11  121.21  3.000
 D7D  C3   N2   C4   119.36  3.000
 D7D  C11  N2   C4   118.78  3.000
 D7D  O    S    O1   119.15  3.000
 D7D  O1   S    C8   108.01  3.000
 D7D  O    S    C8   108.16  3.000
 D7D  O1   S    N3   106.47  3.000
 D7D  C8   S    N3   107.51  3.000
 D7D  O    S    N3   107.03  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
 D7D  CONST_01  N    C3   C2   C1      0.00   0.0  0
 D7D  CONST_02  C13  C12  C2   C1      0.00   0.0  0
 D7D  CONST_03  C12  C13  N4   C1      0.00   0.0  0
 D7D  CONST_04  N    C    N1   C1      0.00   0.0  0
 D7D  CONST_05  C    N    C3   C2      0.00   0.0  0
 D7D  CONST_06  N4   C13  C12  C2      0.00   0.0  0
 D7D  CONST_07  C13  N4   C1   C2      0.00   0.0  0
 D7D  CONST_08  C    N1   C1   C2      0.00   0.0  0
 D7D  CONST_09  N    C3   C2   C12   180.00   0.0  0
 D7D  CONST_10  N4   C1   C2   C12     0.00   0.0  0
 D7D  CONST_11  N1   C1   C2   C12   180.00   0.0  0
 D7D  CONST_12  C3   C2   C12  C13   180.00   0.0  0
 D7D  CONST_13  N1   C1   N4   C13   180.00   0.0  0
 D7D  CONST_14  N1   C    N    C3      0.00   0.0  0
 D7D  CONST_15  N4   C1   C2   C3    180.00   0.0  0
 D7D  CONST_16  N1   C1   C2   C3      0.00   0.0  0
 D7D  CONST_17  C    N1   C1   N4    180.00   0.0  0
 D7D  CONST_18  N2   C3   C2   C1    180.00   0.0  0
 D7D  CONST_19  N2   C3   C2   C12     0.00   0.0  0
 D7D  CONST_20  C    N    C3   N2    180.00   0.0  0
 D7D  CONST_21  C4   N2   C3   C2    180.00   0.0  0
 D7D  CONST_22  N    C3   N2   C4      0.00   0.0  0
 D7D  CONST_23  H19  C12  C2   C1    180.00   0.0  0
 D7D  CONST_24  H20  C13  N4   C1    180.00   0.0  0
 D7D  CONST_25  H3   C    N1   C1    180.00   0.0  0
 D7D  CONST_26  H2   N4   C1   C2    180.00   0.0  0
 D7D  Var_01    O    S    N3   C6    -47.28  30.0  2
 D7D  Var_02    H18  C11  N2   C4     18.34  30.0  3
 D7D  Var_03    C9   C8   S    N3    179.11  30.0  1
 D7D  Var_04    S    C8   C9   C10  -179.71  30.0  3
 D7D  Var_05    H15  C10  C9   C8     60.46  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
 D7D  chir_01  C4  C7  C5  N2  positiv
 D7D  chir_02  C6  N3  C7  C5  negativ

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
 D7D  plan-1  C1   0.020
 D7D  plan-1  C2   0.020
 D7D  plan-1  C12  0.020
 D7D  plan-1  C13  0.020
 D7D  plan-1  C3   0.020
 D7D  plan-1  N    0.020
 D7D  plan-1  N4   0.020
 D7D  plan-1  N1   0.020
 D7D  plan-1  C    0.020
 D7D  plan-1  H19  0.020
 D7D  plan-1  H20  0.020
 D7D  plan-1  H2   0.020
 D7D  plan-1  H3   0.020
 D7D  plan-1  N2   0.020
 D7D  plan-2  C4   0.020
 D7D  plan-2  C11  0.020
 D7D  plan-2  C3   0.020
 D7D  plan-2  N2   0.020

