# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 28 23:21:09 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: [(3S)-2-[(benzyloxy)carbonyl]-3-(methylcarbamoyl)-1,2,3,4-tetrahydroisoquinolin-7-yl]sulfamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)[C@@H]1Cc2ccc(N[S](O)(=O)=O)cc2CN1C(=O)OCc3ccccc3
#
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
 SK2  SK2  '[(3S)-2-[(benzyloxy)carbonyl]-3-(methylcarbamoyl)-1,2,3,4-tetrahydroisoquinolin-7-yl]sulfamic acid'  ligand  50  29  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_SK2
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
 SK2  O6    O  OS    0  -0.708  -10.5733  47.1159  46.2973
 SK2  S1    S  S     0   1.562   -9.3050  47.6574  47.1066
 SK2  O4    O  OS    0  -0.637   -8.4348  46.5123  47.1676
 SK2  O5    O  OS    0  -0.641   -8.8684  48.9095  46.5369
 SK2  N3    N  NC1   0  -0.831   -9.8271  47.9935  48.6289
 SK2  C15   C  CR6   0   0.278  -10.3689  46.9441  49.4230
 SK2  C16   C  CR16  0  -0.251   -9.5106  46.0669  50.0737
 SK2  C14   C  CR16  0  -0.318  -11.7422  46.8234  49.5801
 SK2  C13   C  CR6   0   0.042  -12.2669  45.8252  50.3900
 SK2  C12   C  CH2   0  -0.310  -13.7575  45.6638  50.4948
 SK2  N2    N  NT    0  -0.535  -14.1784  45.0584  51.7601
 SK2  C4    C  CH1   0  -0.251  -13.1849  44.5710  52.6973
 SK2  C5    C  C     0   0.567  -12.6413  45.6468  53.6408
 SK2  O1    O  O     0  -0.499  -11.7166  45.3814  54.3973
 SK2  N1    N  NH1   0  -0.623  -13.2297  46.8429  53.5985
 SK2  C6    C  CH3   0  -0.513  -12.8230  47.9328  54.4537
 SK2  C3    C  CH2   0  -0.491  -12.0336  43.9172  51.9381
 SK2  C2    C  CR6   0   0.095  -11.4126  44.9372  51.0375
 SK2  C1    C  CR16  0  -0.323  -10.0389  45.0695  50.8764
 SK2  C7    C  C     0   0.782  -15.4857  44.7721  51.9942
 SK2  O3    O  O     0  -0.513  -15.9049  44.2216  52.9919
 SK2  O2    O  O2    0  -0.472  -16.2623  45.1845  50.9957
 SK2  C8    C  CH2   0  -0.237  -17.6681  44.9210  51.1121
 SK2  C11   C  CR6   0   0.076  -18.3143  45.4313  49.8612
 SK2  C19   C  CR16  0  -0.297  -18.9840  46.6499  49.8575
 SK2  C9    C  CR16  0  -0.241  -19.5758  47.1264  48.6944
 SK2  C18   C  CR16  0  -0.282  -18.2370  44.6955  48.6810
 SK2  C10   C  CR16  0  -0.243  -18.8225  45.1703  47.5168
 SK2  C17   C  CR16  0  -0.261  -19.4950  46.3872  47.5225
 SK2  HO6   H  H     0   0.504  -11.1901  47.8285  46.0608
 SK2  HN3   H  HNC1  0   0.431  -10.3265  48.8764  48.6774
 SK2  H16   H  HCR6  0   0.268   -8.4399  46.1793  49.9732
 SK2  H14   H  HCR6  0   0.265  -12.4056  47.5157  49.0740
 SK2  H121  H  HCH2  0   0.282  -14.0925  45.0397  49.6608
 SK2  H122  H  HCH2  0   0.269  -14.2326  46.6377  50.3646
 SK2  H4    H  HCH1  0   0.313  -13.6597  43.8207  53.3305
 SK2  HN1   H  HNH1  0   0.411  -13.9954  46.9941  52.9647
 SK2  H61   H  HCH3  0   0.240  -11.7661  48.1658  54.3251
 SK2  H62   H  HCH3  0   0.251  -13.4034  48.8113  54.1878
 SK2  H63   H  HCH3  0   0.240  -12.9989  47.7084  55.5064
 SK2  H31   H  HCH2  0   0.277  -12.4304  43.0753  51.3635
 SK2  H32   H  HCH2  0   0.274  -11.3069  43.5081  52.6378
 SK2  H1    H  HCR6  0   0.259   -9.3726  44.3943  51.3991
 SK2  H81   H  HCH2  0   0.252  -18.0726  45.4242  51.9922
 SK2  H82   H  HCH2  0   0.251  -17.8331  43.8479  51.2264
 SK2  H19   H  HCR6  0   0.256  -19.0498  47.2278  50.7718
 SK2  H9    H  HCR6  0   0.259  -20.1006  48.0729  48.7053
 SK2  H18   H  HCR6  0   0.255  -17.7201  43.7431  48.6735
 SK2  H10   H  HCR6  0   0.259  -18.7573  44.5901  46.6056
 SK2  H17   H  HCR6  0   0.259  -19.9577  46.7550  46.6158

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
 SK2  O6   S1    single    1.599  0.020  1.599
 SK2  O6   HO6   single    0.850  0.020  0.980
 SK2  S1   O4    double    1.440  0.020  1.440
 SK2  S1   O5    double    1.443  0.020  1.443
 SK2  S1   N3    single    1.644  0.020  1.644
 SK2  N3   C15   single    1.423  0.020  1.423
 SK2  N3   HN3   single    0.890  0.020  1.040
 SK2  C15  C16   aromatic  1.389  0.020  1.389
 SK2  C15  C14   aromatic  1.388  0.020  1.388
 SK2  C16  C1    aromatic  1.385  0.020  1.385
 SK2  C16  H16   single    0.930  0.020  1.080
 SK2  C14  C13   aromatic  1.388  0.020  1.388
 SK2  C14  H14   single    0.930  0.020  1.080
 SK2  C13  C12   single    1.503  0.020  1.503
 SK2  C13  C2    aromatic  1.392  0.020  1.392
 SK2  C12  N2    single    1.465  0.020  1.465
 SK2  C12  H121  single    0.970  0.020  1.090
 SK2  C12  H122  single    0.970  0.020  1.090
 SK2  N2   C4    single    1.450  0.020  1.450
 SK2  N2   C7    single    1.359  0.020  1.359
 SK2  C4   C5    single    1.531  0.020  1.531
 SK2  C4   C3    single    1.526  0.020  1.526
 SK2  C4   H4    single    0.970  0.020  1.090
 SK2  C5   O1    double    1.224  0.020  1.224
 SK2  C5   N1    single    1.334  0.020  1.334
 SK2  N1   C6    single    1.444  0.020  1.444
 SK2  N1   HN1   single    0.860  0.020  1.020
 SK2  C6   H61   single    0.970  0.020  1.090
 SK2  C6   H62   single    0.970  0.020  1.090
 SK2  C6   H63   single    0.970  0.020  1.090
 SK2  C3   C2    single    1.496  0.020  1.496
 SK2  C3   H31   single    0.970  0.020  1.090
 SK2  C3   H32   single    0.970  0.020  1.090
 SK2  C2   C1    aromatic  1.389  0.020  1.389
 SK2  C1   H1    single    0.930  0.020  1.080
 SK2  C7   O3    double    1.214  0.020  1.214
 SK2  C7   O2    single    1.330  0.020  1.330
 SK2  O2   C8    single    1.435  0.020  1.435
 SK2  C8   C11   single    1.498  0.020  1.498
 SK2  C8   H81   single    0.970  0.020  1.090
 SK2  C8   H82   single    0.970  0.020  1.090
 SK2  C11  C19   aromatic  1.391  0.020  1.391
 SK2  C11  C18   aromatic  1.393  0.020  1.393
 SK2  C19  C9    aromatic  1.389  0.020  1.389
 SK2  C19  H19   single    0.930  0.020  1.080
 SK2  C9   C17   aromatic  1.388  0.020  1.388
 SK2  C9   H9    single    0.930  0.020  1.080
 SK2  C18  C10   aromatic  1.387  0.020  1.387
 SK2  C18  H18   single    0.930  0.020  1.080
 SK2  C10  C17   aromatic  1.390  0.020  1.390
 SK2  C10  H10   single    0.930  0.020  1.080
 SK2  C17  H17   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
 SK2  HO6   O6   S1    112.23  3.000
 SK2  N3    S1   O5    106.52  3.000
 SK2  N3    S1   O4    108.38  3.000
 SK2  O5    S1   O4    121.60  3.000
 SK2  N3    S1   O6    106.62  3.000
 SK2  O5    S1   O6    109.51  3.000
 SK2  O4    S1   O6    103.39  3.000
 SK2  HN3   N3   C15   115.29  3.000
 SK2  HN3   N3   S1    112.22  3.000
 SK2  C15   N3   S1    119.13  3.000
 SK2  C14   C15  C16   120.24  3.000
 SK2  C14   C15  N3    120.27  3.000
 SK2  C16   C15  N3    119.46  3.000
 SK2  H16   C16  C1    120.43  3.000
 SK2  H16   C16  C15   120.17  3.000
 SK2  C1    C16  C15   119.38  3.000
 SK2  H14   C14  C13   120.01  3.000
 SK2  H14   C14  C15   119.82  3.000
 SK2  C13   C14  C15   120.17  3.000
 SK2  C2    C13  C12   120.51  3.000
 SK2  C2    C13  C14   119.87  3.000
 SK2  C12   C13  C14   119.52  3.000
 SK2  H122  C12  H121  106.55  3.000
 SK2  H122  C12  N2    110.29  3.000
 SK2  H121  C12  N2    109.55  3.000
 SK2  H122  C12  C13   109.13  3.000
 SK2  H121  C12  C13   108.17  3.000
 SK2  N2    C12  C13   112.94  3.000
 SK2  C7    N2   C4    118.49  3.000
 SK2  C7    N2   C12   120.83  3.000
 SK2  C4    N2   C12   120.03  3.000
 SK2  H4    C4   C3    108.82  3.000
 SK2  H4    C4   C5    106.28  3.000
 SK2  C3    C4   C5    109.86  3.000
 SK2  H4    C4   N2    107.95  3.000
 SK2  C3    C4   N2    109.83  3.000
 SK2  C5    C4   N2    113.92  3.000
 SK2  N1    C5   O1    123.19  3.000
 SK2  N1    C5   C4    117.01  3.000
 SK2  O1    C5   C4    119.80  3.000
 SK2  HN1   N1   C6    118.32  3.000
 SK2  HN1   N1   C5    119.39  3.000
 SK2  C6    N1   C5    122.28  3.000
 SK2  H63   C6   H62   108.46  3.000
 SK2  H63   C6   H61   108.32  3.000
 SK2  H62   C6   H61   108.44  3.000
 SK2  H63   C6   N1    111.77  3.000
 SK2  H62   C6   N1    108.37  3.000
 SK2  H61   C6   N1    111.39  3.000
 SK2  H32   C3   H31   106.89  3.000
 SK2  H32   C3   C2    111.48  3.000
 SK2  H31   C3   C2    111.05  3.000
 SK2  H32   C3   C4    110.17  3.000
 SK2  H31   C3   C4    108.50  3.000
 SK2  C2    C3   C4    108.70  3.000
 SK2  C1    C2   C3    123.04  3.000
 SK2  C1    C2   C13   119.47  3.000
 SK2  C3    C2   C13   117.41  3.000
 SK2  H1    C1   C2    119.53  3.000
 SK2  H1    C1   C16   119.60  3.000
 SK2  C2    C1   C16   120.86  3.000
 SK2  O2    C7   O3    123.76  3.000
 SK2  O2    C7   N2    111.53  3.000
 SK2  O3    C7   N2    124.70  3.000
 SK2  C8    O2   C7    117.00  3.000
 SK2  H82   C8   H81   108.23  3.000
 SK2  H82   C8   C11   110.93  3.000
 SK2  H81   C8   C11   110.88  3.000
 SK2  H82   C8   O2    109.70  3.000
 SK2  H81   C8   O2    110.10  3.000
 SK2  C11   C8   O2    107.00  3.000
 SK2  C18   C11  C19   119.17  3.000
 SK2  C18   C11  C8    120.25  3.000
 SK2  C19   C11  C8    120.58  3.000
 SK2  H19   C19  C9    119.84  3.000
 SK2  H19   C19  C11   119.63  3.000
 SK2  C9    C19  C11   120.53  3.000
 SK2  H9    C9   C17   120.16  3.000
 SK2  H9    C9   C19   119.87  3.000
 SK2  C17   C9   C19   119.96  3.000
 SK2  H18   C18  C10   119.77  3.000
 SK2  H18   C18  C11   119.77  3.000
 SK2  C10   C18  C11   120.46  3.000
 SK2  H10   C10  C17   120.12  3.000
 SK2  H10   C10  C18   119.85  3.000
 SK2  C17   C10  C18   120.03  3.000
 SK2  H17   C17  C10   120.06  3.000
 SK2  H17   C17  C9    120.09  3.000
 SK2  C10   C17  C9    119.85  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
 SK2  CONST_01  C2   C1   C16  C15     0.00   0.0  0
 SK2  CONST_02  C2   C13  C14  C15     0.00   0.0  0
 SK2  CONST_03  C13  C14  C15  C16     0.00   0.0  0
 SK2  CONST_04  C13  C2   C1   C16     0.00   0.0  0
 SK2  CONST_05  C1   C16  C15  C14     0.00   0.0  0
 SK2  CONST_06  C1   C2   C13  C14     0.00   0.0  0
 SK2  CONST_07  C17  C9   C19  C11     0.00   0.0  0
 SK2  CONST_08  C17  C10  C18  C11     0.00   0.0  0
 SK2  CONST_09  C10  C18  C11  C19     0.00   0.0  0
 SK2  CONST_10  C10  C17  C9   C19     0.00   0.0  0
 SK2  CONST_11  C18  C11  C19  C9      0.00   0.0  0
 SK2  CONST_12  C18  C10  C17  C9      0.00   0.0  0
 SK2  CONST_13  C1   C16  C15  N3    180.00   0.0  0
 SK2  CONST_14  C13  C14  C15  N3    180.00   0.0  0
 SK2  CONST_15  C9   C19  C11  C8    180.00   0.0  0
 SK2  CONST_16  C10  C18  C11  C8    180.00   0.0  0
 SK2  CONST_17  H1   C1   C16  C15   180.00   0.0  0
 SK2  CONST_18  H14  C14  C15  C16   180.00   0.0  0
 SK2  CONST_19  H16  C16  C15  C14   180.00   0.0  0
 SK2  CONST_20  H9   C9   C19  C11   180.00   0.0  0
 SK2  CONST_21  H10  C10  C18  C11   180.00   0.0  0
 SK2  CONST_22  H18  C18  C11  C19   180.00   0.0  0
 SK2  CONST_23  H17  C17  C9   C19   180.00   0.0  0
 SK2  CONST_24  H19  C19  C11  C18   180.00   0.0  0
 SK2  CONST_28  C6   N1   C5   C4    180.00   0.0  0
 SK2  CONST_29  HN1  N1   C5   C4      0.00   0.0  0
 SK2  CONST_30  C6   N1   C5   O1      0.00   0.0  0
 SK2  Var_01    N2   C12  C13  C14  -153.60  30.0  1
 SK2  Var_02    C4   N2   C12  C13    -5.76  30.0  1
 SK2  Var_03    C4   C3   C2   C13   -39.12  30.0  1
 SK2  Var_04    O3   C7   N2   C12   176.83  30.0  2
 SK2  Var_05    C19  C11  C8   O2   -101.34  30.0  2
 SK2  Var_06    C15  N3   S1   O6     60.79  30.0  3
 SK2  Var_07    C11  C8   O2   C7   -178.12  30.0  3
 SK2  Var_08    H61  C6   N1   C5     57.15  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
 SK2  chir_01  C4  N2  C5  C3  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
 SK2  plan-1  C8   0.020
 SK2  plan-1  C11  0.020
 SK2  plan-1  C19  0.020
 SK2  plan-1  C9   0.020
 SK2  plan-1  C18  0.020
 SK2  plan-1  C10  0.020
 SK2  plan-1  C17  0.020
 SK2  plan-1  H19  0.020
 SK2  plan-1  H9   0.020
 SK2  plan-1  H18  0.020
 SK2  plan-1  H10  0.020
 SK2  plan-1  H17  0.020
 SK2  plan-2  N3   0.020
 SK2  plan-2  C15  0.020
 SK2  plan-2  C16  0.020
 SK2  plan-2  C14  0.020
 SK2  plan-2  C13  0.020
 SK2  plan-2  C12  0.020
 SK2  plan-2  C3   0.020
 SK2  plan-2  C2   0.020
 SK2  plan-2  C1   0.020
 SK2  plan-2  H16  0.020
 SK2  plan-2  H14  0.020
 SK2  plan-2  H1   0.020
 SK2  plan-3  C4   0.020
 SK2  plan-3  C5   0.020
 SK2  plan-3  O1   0.020
 SK2  plan-3  N1   0.020
 SK2  plan-3  C6   0.020
 SK2  plan-3  HN1  0.020
 SK2  plan-4  S1   0.020
 SK2  plan-4  N3   0.020
 SK2  plan-4  C15  0.020
 SK2  plan-4  HN3  0.020
 SK2  plan-5  N2   0.020
 SK2  plan-5  C7   0.020
 SK2  plan-5  O3   0.020
 SK2  plan-5  O2   0.020

