# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 06:48:18 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  42  21  .  2022-07-22  2022-07-26
;
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  -0.442   -5.9431   0.2429  -0.0196
 3S2  C5    C  CH2    0  -0.478   -4.5552  -0.3826  -0.0556
 3S2  C6    C  CH2    0  -0.250   -7.0510  -0.7972  -0.0530
 3S2  C7    C  CH2    0  -0.223   -3.4636   0.6724   0.0134
 3S2  C8    C  C1     0   0.182    1.5936   1.8708  -0.7626
 3S2  C10   C  CH1    0  -0.137    1.3772   0.8356   0.3177
 3S2  N12   N  NH1    0  -0.593   -8.3609  -0.1767  -0.0250
 3S2  C1    C  CH3    0  -0.517   -9.4362  -1.1465  -0.0491
 3S2  C2    C  CH2    0  -0.472    1.8129  -1.3585  -0.6090
 3S2  C3    C  CH2    0  -0.298    0.3420  -1.2955  -0.2329
 3S2  C9    C  CH1    0  -0.133    2.4452  -0.2904   0.2823
 3S2  C11   C  C      0   0.758   -1.0282   0.7924   0.0838
 3S2  N13   N  NH1    0  -0.698   -2.1544   0.0537  -0.0321
 3S2  N14   N  NC1    0  -0.766    3.7529   0.1968  -0.0905
 3S2  N15   N  NT     0  -0.535    0.1493   0.1119   0.0914
 3S2  O16   O  OS     0  -0.756    4.9763  -0.5050   1.9695
 3S2  O17   O  O      0  -0.373    2.1599   2.9186  -0.5901
 3S2  O18   O  O      0  -0.549   -1.0442   2.0208   0.1632
 3S2  O19   O  OS    -1  -0.750    4.9757  -2.0673   0.0820
 3S2  O20   O  OS     0  -0.754    6.2223   0.0405  -0.0960
 3S2  S21   S  S      0   1.504    5.0873  -0.6632   0.5131
 3S2  H4    H  HCH2   0   0.219   -6.0435   0.8511   0.8863
 3S2  H4A   H  HCH2   0   0.222   -6.0647   0.9251  -0.8662
 3S2  H5    H  HCH2   0   0.229   -4.4422  -1.0781   0.7829
 3S2  H5A   H  HCH2   0   0.231   -4.4400  -0.9728  -0.9703
 3S2  H6    H  HCH2   0   0.213   -6.9706  -1.3835  -0.9748
 3S2  H6A   H  HCH2   0   0.184   -6.9048  -1.5123   0.7743
 3S2  H7    H  HCH2   0   0.228   -3.5724   1.3667  -0.8234
 3S2  H7A   H  HCH2   0   0.223   -3.5823   1.2601   0.9293
 3S2  H8    H  H      0   0.190    1.2193   1.5718  -1.7608
 3S2  H10   H  HCH1   0   0.280    1.3970   1.3385   1.2883
 3S2  HN12  H  HNH1   0   0.339   -8.4388   0.3766   0.8198
 3S2  H1    H  HCH3   0   0.220   -9.4301  -1.6827  -1.0003
 3S2  H1A   H  HCH3   0   0.191   -9.3814  -1.8984   0.7506
 3S2  H1B   H  HCH3   0   0.230  -10.3975  -0.6390   0.0338
 3S2  H2    H  HCH2   0   0.266    2.2457  -2.3427  -0.4458
 3S2  H2A   H  HCH2   0   0.244    1.9480  -1.0979  -1.6627
 3S2  H3    H  HCH2   0   0.259   -0.3049  -1.6038  -1.0558
 3S2  H3A   H  HCH2   0   0.245    0.1247  -1.9382   0.6263
 3S2  H9    H  HCH1   0   0.284    2.5100  -0.6737   1.3029
 3S2  HN13  H  HNH1   0   0.406   -2.1120  -0.9412   0.1166
 3S2  HN14  H  HNC1   0   0.379    3.8522   0.3064  -1.0955

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  1.449  0.020  1.449
 3S2  C7   H7    single  0.970  0.020  1.090
 3S2  C7   H7A   single  0.970  0.020  1.090
 3S2  O17  C8    double  1.203  0.020  1.203
 3S2  C8   C10   single  1.512  0.020  1.512
 3S2  C8   H8    single  0.930  0.020  1.080
 3S2  N15  C10   single  1.443  0.020  1.443
 3S2  C9   C10   single  1.552  0.020  1.552
 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  1.528  0.020  1.528
 3S2  C2   H2    single  0.970  0.020  1.090
 3S2  C2   H2A   single  0.970  0.020  1.090
 3S2  C3   N15   single  1.457  0.020  1.457
 3S2  C3   H3    single  0.970  0.020  1.090
 3S2  C3   H3A   single  0.970  0.020  1.090
 3S2  N14  C9    single  1.444  0.020  1.444
 3S2  C9   H9    single  0.970  0.020  1.090
 3S2  N13  C11   single  1.352  0.020  1.352
 3S2  C11  N15   single  1.360  0.020  1.360
 3S2  C11  O18   double  1.231  0.020  1.231
 3S2  N13  HN13  single  0.860  0.020  1.020
 3S2  S21  N14   single  1.698  0.020  1.698
 3S2  N14  HN14  single  0.890  0.020  1.040
 3S2  O16  S21   deloc   1.469  0.020  1.469
 3S2  S21  O19   deloc   1.473  0.020  1.473
 3S2  S21  O20   deloc   1.468  0.020  1.468

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   106.46  3.000
 3S2  H4A   C4   C6   109.19  3.000
 3S2  H4    C4   C6   109.34  3.000
 3S2  H4A   C4   C5   109.83  3.000
 3S2  H4    C4   C5   109.33  3.000
 3S2  C6    C4   C5   112.50  3.000
 3S2  H5A   C5   H5   106.65  3.000
 3S2  H5A   C5   C7   109.67  3.000
 3S2  H5    C5   C7   109.39  3.000
 3S2  H5A   C5   C4   109.70  3.000
 3S2  H5    C5   C4   109.68  3.000
 3S2  C7    C5   C4   111.62  3.000
 3S2  H6A   C6   H6   105.93  3.000
 3S2  H6A   C6   N12  112.50  3.000
 3S2  H6    C6   N12  108.16  3.000
 3S2  H6A   C6   C4   109.30  3.000
 3S2  H6    C6   C4   109.34  3.000
 3S2  N12   C6   C4   111.42  3.000
 3S2  H7A   C7   H7   106.79  3.000
 3S2  H7A   C7   N13  110.70  3.000
 3S2  H7    C7   N13  109.71  3.000
 3S2  H7A   C7   C5   109.44  3.000
 3S2  H7    C7   C5   109.56  3.000
 3S2  N13   C7   C5   110.56  3.000
 3S2  H8    C8   O17  121.56  3.000
 3S2  H8    C8   C10  114.26  3.000
 3S2  O17   C8   C10  124.13  3.000
 3S2  H10   C10  N15  112.66  3.000
 3S2  H10   C10  C9   109.96  3.000
 3S2  N15   C10  C9   102.59  3.000
 3S2  H10   C10  C8   108.47  3.000
 3S2  C9    C10  C8   112.45  3.000
 3S2  N15   C10  C8   110.68  3.000
 3S2  HN12  N12  C1   108.82  3.000
 3S2  HN12  N12  C6   108.63  3.000
 3S2  C1    N12  C6   112.58  3.000
 3S2  H1B   C1   H1A  107.89  3.000
 3S2  H1B   C1   H1   107.44  3.000
 3S2  H1A   C1   H1   107.31  3.000
 3S2  H1B   C1   N12  109.99  3.000
 3S2  H1A   C1   N12  114.14  3.000
 3S2  H1    C1   N12  109.82  3.000
 3S2  H2A   C2   H2   108.12  3.000
 3S2  H2A   C2   C9   110.14  3.000
 3S2  H2    C2   C9   112.35  3.000
 3S2  H2A   C2   C3   110.38  3.000
 3S2  H2    C2   C3   112.68  3.000
 3S2  C9    C2   C3   103.13  3.000
 3S2  H3A   C3   H3   107.96  3.000
 3S2  H3A   C3   N15  111.47  3.000
 3S2  H3    C3   N15  111.24  3.000
 3S2  H3A   C3   C2   111.23  3.000
 3S2  H3    C3   C2   112.06  3.000
 3S2  N15   C3   C2   102.89  3.000
 3S2  H9    C9   N14  107.81  3.000
 3S2  H9    C9   C2   108.92  3.000
 3S2  N14   C9   C2   117.38  3.000
 3S2  H9    C9   C10  105.91  3.000
 3S2  N14   C9   C10  112.59  3.000
 3S2  C2    C9   C10  103.63  3.000
 3S2  O18   C11  N15  120.67  3.000
 3S2  O18   C11  N13  122.69  3.000
 3S2  N15   C11  N13  116.64  3.000
 3S2  HN13  N13  C11  119.48  3.000
 3S2  HN13  N13  C7   117.10  3.000
 3S2  C11   N13  C7   121.11  3.000
 3S2  HN14  N14  S21  109.23  3.000
 3S2  HN14  N14  C9   112.34  3.000
 3S2  S21   N14  C9   116.67  3.000
 3S2  C11   N15  C3   126.62  3.000
 3S2  C11   N15  C10  119.12  3.000
 3S2  C3    N15  C10  114.00  3.000
 3S2  O20   S21  O19  113.22  3.000
 3S2  O20   S21  O16  114.72  3.000
 3S2  O19   S21  O16  112.77  3.000
 3S2  O20   S21  N14  102.55  3.000
 3S2  O19   S21  N14  108.61  3.000
 3S2  O16   S21  N14  103.79  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   -16.28  30.0  1
 3S2  Var_02    N15   C3   C2   C9     32.47  30.0  1
 3S2  Var_03    O16   S21  N14  C9    -62.94  30.0  3
 3S2  Var_04    N13   C7   C5   C4   -179.59  30.0  2
 3S2  Var_05    C1    N12  C6   C4   -179.71  30.0  3
 3S2  Var_06    N12   C6   C4   C5   -179.70  30.0  3
 3S2  Var_07    C11   N13  C7   C5   -176.61  30.0  3
 3S2  Var_08    C7    C5   C4   C6   -178.59  30.0  1
 3S2  Var_09    H1    C1   N12  C6    -65.35  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

