# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 01:22:51 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: [(2S,3R)-2-formyl-1-{[4-(methylamino)butyl]carbamoyl}pyrrolidin-3-yl]sulfamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNCCCCNC(=O)N1CC[C@@H](N[S](O)(=O)=O)[C@H]1C=O
#
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
 3S2  3S2  '[(2S,3R)-2-formyl-1-{[4-(methylamino)butyl]carbamoyl}pyrrolidin-3-yl]sulfamic acid'  ligand  43  21  .  2022-07-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_3S2
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
 3S2  C4    C  CH2   0  -0.444   -5.9154   0.3068   0.0853
 3S2  C5    C  CH2   0  -0.470   -4.5583  -0.3704  -0.0497
 3S2  C6    C  CH2   0  -0.250   -7.0623  -0.6912   0.0809
 3S2  C7    C  CH2   0  -0.229   -3.4217   0.6390  -0.0424
 3S2  C8    C  C1    0   0.199    1.7624   1.7057  -0.4399
 3S2  C10   C  CR15  0  -0.140    1.4277   0.4312   0.3085
 3S2  N12   N  NH1   0  -0.593   -8.3445  -0.0274   0.2098
 3S2  C1    C  CH3   0  -0.517   -9.4534  -0.9589   0.2195
 3S2  C2    C  CH2   0  -0.500    1.7465  -1.4437  -1.1921
 3S2  C3    C  CH2   0  -0.294    0.2726  -1.3803  -0.8288
 3S2  C9    C  CR15  0  -0.112    2.4153  -0.7080  -0.0363
 3S2  C11   C  C     0   0.761   -0.9812   0.5836   0.1305
 3S2  N13   N  NH1   0  -0.701   -2.1445  -0.0301  -0.1751
 3S2  N14   N  NC1   0  -0.776    3.7368  -0.2296  -0.4127
 3S2  N15   N  NR5   0  -0.537    0.1635  -0.1041  -0.1406
 3S2  O16   O  OS    0  -0.640    4.2325   0.6715   1.8578
 3S2  O17   O  O     0  -0.364    2.3189   2.6532   0.0463
 3S2  O18   O  O     0  -0.549   -0.9285   1.7027   0.6383
 3S2  O19   O  OS    0  -0.718    5.2728  -1.4494   1.1220
 3S2  O20   O  OS    0  -0.640    5.9975   0.6795   0.0815
 3S2  S21   S  S     0   1.581    4.8653   0.0492   0.7176
 3S2  H4    H  HCH2  0   0.220   -5.9419   0.8858   1.0151
 3S2  H4A   H  HCH2  0   0.222   -6.0576   1.0215  -0.7307
 3S2  H5    H  HCH2  0   0.230   -4.4144  -1.0833   0.7677
 3S2  H5A   H  HCH2  0   0.227   -4.5306  -0.9493  -0.9794
 3S2  H6    H  HCH2  0   0.213   -7.0569  -1.2434  -0.8652
 3S2  H6A   H  HCH2  0   0.184   -6.8946  -1.4422   0.8715
 3S2  H7    H  HCH2  0   0.223   -3.5689   1.3650  -0.8497
 3S2  H7A   H  HCH2  0   0.234   -3.4371   1.1985   0.8939
 3S2  H8    H  H     0   0.191    1.4547   1.6958  -1.5033
 3S2  H10   H  HCR5  0   0.285    1.4344   0.6382   1.3802
 3S2  HN12  H  HNH1  0   0.340   -8.3523   0.4987   1.0754
 3S2  H1    H  HCH3  0   0.220   -9.5203  -1.4648  -0.7459
 3S2  H1A   H  HCH3  0   0.191   -9.3792  -1.7374   0.9918
 3S2  H1B   H  HCH3  0   0.230  -10.3900  -0.4228   0.3736
 3S2  H2    H  HCH2  0   0.285    2.1099  -2.4644  -1.2984
 3S2  H2A   H  HCH2  0   0.264    1.9283  -0.9182  -2.1328
 3S2  H3    H  HCH2  0   0.265   -0.3574  -1.4094  -1.7191
 3S2  H3A   H  HCH2  0   0.253   -0.0130  -2.2153  -0.1816
 3S2  H9    H  HCR5  0   0.307    2.4700  -1.3818   0.8231
 3S2  HN13  H  HNH1  0   0.407   -2.1406  -0.9166  -0.6530
 3S2  HN14  H  HNC1  0   0.440    4.1088  -0.5656  -1.2940
 3S2  HO19  H  H     0   0.503    5.8202  -1.4709   1.9253

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
 3S2  C5   C4    single  1.523  0.020  1.523
 3S2  C4   C6    single  1.520  0.020  1.520
 3S2  C4   H4    single  0.970  0.020  1.090
 3S2  C4   H4A   single  0.970  0.020  1.090
 3S2  C7   C5    single  1.520  0.020  1.520
 3S2  C5   H5    single  0.970  0.020  1.090
 3S2  C5   H5A   single  0.970  0.020  1.090
 3S2  C6   N12   single  1.450  0.020  1.450
 3S2  C6   H6    single  0.970  0.020  1.090
 3S2  C6   H6A   single  0.970  0.020  1.090
 3S2  C7   N13   single  1.448  0.020  1.448
 3S2  C7   H7    single  0.970  0.020  1.090
 3S2  C7   H7A   single  0.970  0.020  1.090
 3S2  O17  C8    double  1.202  0.020  1.202
 3S2  C8   C10   single  1.515  0.020  1.515
 3S2  C8   H8    single  0.930  0.020  1.080
 3S2  N15  C10   single  1.444  0.020  1.444
 3S2  C9   C10   single  1.547  0.020  1.547
 3S2  C10  H10   single  0.970  0.020  1.090
 3S2  N12  C1    single  1.448  0.020  1.448
 3S2  N12  HN12  single  0.890  0.020  1.040
 3S2  C1   H1    single  0.970  0.020  1.090
 3S2  C1   H1A   single  0.970  0.020  1.090
 3S2  C1   H1B   single  0.970  0.020  1.090
 3S2  C2   C3    single  1.519  0.020  1.519
 3S2  C2   C9    single  1.525  0.020  1.525
 3S2  C2   H2    single  0.970  0.020  1.090
 3S2  C2   H2A   single  0.970  0.020  1.090
 3S2  C3   N15   single  1.454  0.020  1.454
 3S2  C3   H3    single  0.970  0.020  1.090
 3S2  C3   H3A   single  0.970  0.020  1.090
 3S2  N14  C9    single  1.455  0.020  1.455
 3S2  C9   H9    single  0.970  0.020  1.090
 3S2  N13  C11   single  1.350  0.020  1.350
 3S2  C11  N15   single  1.363  0.020  1.363
 3S2  C11  O18   double  1.230  0.020  1.230
 3S2  N13  HN13  single  0.860  0.020  1.020
 3S2  S21  N14   single  1.621  0.020  1.621
 3S2  N14  HN14  single  0.890  0.020  1.040
 3S2  O16  S21   double  1.445  0.020  1.445
 3S2  S21  O19   single  1.605  0.020  1.605
 3S2  O19  HO19  single  0.850  0.020  0.980
 3S2  S21  O20   double  1.443  0.020  1.443

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
 3S2  H4A   C4   H4   106.54  3.000
 3S2  H4A   C4   C6   109.19  3.000
 3S2  H4    C4   C6   109.33  3.000
 3S2  H4A   C4   C5   109.89  3.000
 3S2  H4    C4   C5   109.38  3.000
 3S2  C6    C4   C5   112.34  3.000
 3S2  H5A   C5   H5   106.64  3.000
 3S2  H5A   C5   C7   109.64  3.000
 3S2  H5    C5   C7   109.31  3.000
 3S2  H5A   C5   C4   109.44  3.000
 3S2  H5    C5   C4   109.92  3.000
 3S2  C7    C5   C4   111.75  3.000
 3S2  H6A   C6   H6   105.97  3.000
 3S2  H6A   C6   N12  112.49  3.000
 3S2  H6    C6   N12  108.18  3.000
 3S2  H6A   C6   C4   109.28  3.000
 3S2  H6    C6   C4   109.24  3.000
 3S2  N12   C6   C4   111.49  3.000
 3S2  H7A   C7   H7   106.89  3.000
 3S2  H7A   C7   N13  109.15  3.000
 3S2  H7    C7   N13  110.93  3.000
 3S2  H7A   C7   C5   109.52  3.000
 3S2  H7    C7   C5   109.64  3.000
 3S2  N13   C7   C5   110.63  3.000
 3S2  H8    C8   O17  121.63  3.000
 3S2  H8    C8   C10  113.92  3.000
 3S2  O17   C8   C10  124.45  3.000
 3S2  H10   C10  N15  112.39  3.000
 3S2  H10   C10  C9   110.77  3.000
 3S2  N15   C10  C9   102.51  3.000
 3S2  H10   C10  C8   108.91  3.000
 3S2  C9    C10  C8   111.61  3.000
 3S2  N15   C10  C8   110.57  3.000
 3S2  HN12  N12  C1   108.81  3.000
 3S2  HN12  N12  C6   108.70  3.000
 3S2  C1    N12  C6   112.54  3.000
 3S2  H1B   C1   H1A  107.88  3.000
 3S2  H1B   C1   H1   107.46  3.000
 3S2  H1A   C1   H1   107.29  3.000
 3S2  H1B   C1   N12  110.02  3.000
 3S2  H1A   C1   N12  114.12  3.000
 3S2  H1    C1   N12  109.81  3.000
 3S2  H2A   C2   H2   108.14  3.000
 3S2  H2A   C2   C9   110.34  3.000
 3S2  H2    C2   C9   112.33  3.000
 3S2  H2A   C2   C3   110.31  3.000
 3S2  H2    C2   C3   112.72  3.000
 3S2  C9    C2   C3   102.95  3.000
 3S2  H3A   C3   H3   108.15  3.000
 3S2  H3A   C3   N15  111.73  3.000
 3S2  H3    C3   N15  111.49  3.000
 3S2  H3A   C3   C2   111.27  3.000
 3S2  H3    C3   C2   111.34  3.000
 3S2  N15   C3   C2   102.86  3.000
 3S2  H9    C9   N14  111.13  3.000
 3S2  H9    C9   C2   108.69  3.000
 3S2  N14   C9   C2   111.16  3.000
 3S2  H9    C9   C10  108.09  3.000
 3S2  N14   C9   C10  113.29  3.000
 3S2  C2    C9   C10  104.14  3.000
 3S2  O18   C11  N15  120.35  3.000
 3S2  O18   C11  N13  122.94  3.000
 3S2  N15   C11  N13  116.70  3.000
 3S2  HN13  N13  C11  120.27  3.000
 3S2  HN13  N13  C7   116.98  3.000
 3S2  C11   N13  C7   121.95  3.000
 3S2  HN14  N14  S21  114.05  3.000
 3S2  HN14  N14  C9   116.69  3.000
 3S2  S21   N14  C9   120.55  3.000
 3S2  C11   N15  C3   126.88  3.000
 3S2  C11   N15  C10  119.10  3.000
 3S2  C3    N15  C10  114.00  3.000
 3S2  HO19  O19  S21  111.83  3.000
 3S2  O20   S21  O19  108.64  3.000
 3S2  O20   S21  O16  120.21  3.000
 3S2  O19   S21  O16  108.33  3.000
 3S2  O20   S21  N14  108.29  3.000
 3S2  O19   S21  N14  101.06  3.000
 3S2  O16   S21  N14  108.63  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
 3S2  CONST_01  O18   C11  N15  C10     0.00   0.0  0
 3S2  CONST_02  O18   C11  N15  C3    180.00   0.0  0
 3S2  CONST_03  N13   C11  N15  C10   180.00   0.0  0
 3S2  CONST_04  N13   C11  N15  C3      0.00   0.0  0
 3S2  CONST_05  N15   C11  N13  C7    180.00   0.0  0
 3S2  CONST_06  HN13  N13  C11  N15     0.00   0.0  0
 3S2  CONST_07  O18   C11  N13  C7      0.00   0.0  0
 3S2  Var_01    C2    C3   N15  C10   -17.42  30.0  1
 3S2  Var_02    N15   C3   C2   C9     32.72  30.0  1
 3S2  Var_03    O16   S21  N14  C9    -40.27  30.0  1
 3S2  Var_04    N13   C7   C5   C4   -179.86  30.0  1
 3S2  Var_05    C1    N12  C6   C4   -179.51  30.0  3
 3S2  Var_06    N12   C6   C4   C5   -179.98  30.0  3
 3S2  Var_07    C11   N13  C7   C5   -163.30  30.0  3
 3S2  Var_08    C7    C5   C4   C6   -179.94  30.0  1
 3S2  Var_09    H1    C1   N12  C6    -65.06  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
 3S2  chir_01  C10  C8   N15  C9  negativ
 3S2  chir_02  C9   N14  C10  C2  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
 3S2  plan-1  C7    0.020
 3S2  plan-1  C10   0.020
 3S2  plan-1  C3    0.020
 3S2  plan-1  C11   0.020
 3S2  plan-1  N13   0.020
 3S2  plan-1  N15   0.020
 3S2  plan-1  O18   0.020
 3S2  plan-1  HN13  0.020
 3S2  plan-2  C8    0.020
 3S2  plan-2  C10   0.020
 3S2  plan-2  O17   0.020
 3S2  plan-2  H8    0.020

