# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 27 00:05:27 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: [(2S,3R)-1-{[(4S)-1-(2-aminoethyl)azepan-4-yl]carbamoyl}-2-formylpyrrolidin-3-yl]sulfamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCN1CCC[C@@H](CC1)NC(=O)N2CC[C@@H](N[S](O)(=O)=O)[C@H]2C=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
 S1Y  S1Y  '[(2S,3R)-1-{[(4S)-1-(2-aminoethyl)azepan-4-yl]carbamoyl}-2-formylpyrrolidin-3-yl]sulfamic acid'  ligand  52  25  .  2022-11-17  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_S1Y
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
 S1Y  S1    S  S     0   1.583  -5.2625  -0.3258  -1.1740
 S1Y  O2    O  OS    0  -0.641  -5.2158  -0.7143  -2.5636
 S1Y  O3    O  OS    0  -0.716  -6.0943   1.0403  -1.0427
 S1Y  O4    O  OS    0  -0.644  -5.7613  -1.2516  -0.1824
 S1Y  N5    N  NC1   0  -0.759  -3.7803   0.1624  -0.7466
 S1Y  C6    C  CH1   0  -0.166  -3.4926   0.6093   0.6175
 S1Y  C7    C  CH2   0  -0.480  -2.9526   2.0352   0.6394
 S1Y  C8    C  CH2   0  -0.309  -1.4834   1.8757   0.2526
 S1Y  N9    N  NT    0  -0.540  -1.1719   0.5236   0.6977
 S1Y  C10   C  CH1   0  -0.117  -2.3208  -0.1889   1.2087
 S1Y  C11   C  C1    0   0.191  -2.3416  -1.6308   0.7563
 S1Y  O12   O  O     0  -0.378  -2.8832  -2.5046   1.3816
 S1Y  C13   C  C     0   0.760   0.0695   0.0128   0.9283
 S1Y  O14   O  O     0  -0.547   0.1947  -1.0786   1.4851
 S1Y  N15   N  NH1   0  -0.694   1.1163   0.7674   0.5270
 S1Y  C16   C  CH1   0  -0.064   2.4849   0.2732   0.5730
 S1Y  C17   C  CH2   0  -0.424   2.7988  -0.6062  -0.6443
 S1Y  C18   C  CH2   0  -0.421   3.9325  -1.6081  -0.4383
 S1Y  C19   C  CH2   0  -0.311   5.1139  -1.0864   0.3714
 S1Y  N20   N  NT    0  -0.417   5.4980   0.2774   0.0357
 S1Y  C21   C  CH2   0  -0.277   6.9330   0.4458  -0.1007
 S1Y  C22   C  CH2   0  -0.289   7.4427  -0.1242  -1.4175
 S1Y  N23   N  NH2   0  -0.803   8.8875   0.0326  -1.5046
 S1Y  C24   C  CH2   0  -0.283   4.8796   1.2318   0.9364
 S1Y  C25   C  CH2   0  -0.434   3.4044   1.4930   0.6583
 S1Y  HO3   H  H     0   0.503  -7.0528   0.8786  -1.0408
 S1Y  HN5   H  HNC1  0   0.437  -3.2678   0.6099  -1.4988
 S1Y  H6    H  HCH1  0   0.314  -4.3809   0.4971   1.2361
 S1Y  H7    H  HCH2  0   0.281  -3.4999   2.7053  -0.0219
 S1Y  H7A   H  HCH2  0   0.277  -3.0338   2.4227   1.6552
 S1Y  H8    H  HCH2  0   0.255  -1.3297   1.9837  -0.8257
 S1Y  H8A   H  HCH2  0   0.267  -0.8594   2.6198   0.7511
 S1Y  H10   H  HCH1  0   0.284  -2.3828  -0.1589   2.3027
 S1Y  H11   H  H     0   0.198  -1.8732  -1.8180  -0.2246
 S1Y  HN15  H  HNH1  0   0.403   0.9469   1.5558  -0.0786
 S1Y  H16   H  HCH1  0   0.237   2.5735  -0.3188   1.4873
 S1Y  H17   H  HCH2  0   0.234   1.9017  -1.1610  -0.9271
 S1Y  H17A  H  HCH2  0   0.215   3.0295   0.0492  -1.4887
 S1Y  H18   H  HCH2  0   0.217   3.5488  -2.4979   0.0686
 S1Y  H18A  H  HCH2  0   0.222   4.2826  -1.9396  -1.4192
 S1Y  H19   H  HCH2  0   0.208   4.8854  -1.1590   1.4461
 S1Y  H19A  H  HCH2  0   0.238   5.9599  -1.7598   0.2167
 S1Y  H21   H  HCH2  0   0.226   7.1663   1.5127  -0.0875
 S1Y  H21A  H  HCH2  0   0.188   7.4910  -0.0041   0.7391
 S1Y  H22   H  HCH2  0   0.196   7.1107  -1.1661  -1.5315
 S1Y  H22A  H  HCH2  0   0.216   6.9785   0.4341  -2.2335
 S1Y  HN23  H  HNH2  0   0.339   9.3322  -0.6065  -0.8571
 S1Y  HN2A  H  HNH2  0   0.348   9.2021  -0.2516  -2.4231
 S1Y  H24   H  HCH2  0   0.190   5.0033   0.9253   1.9890
 S1Y  H24A  H  HCH2  0   0.235   5.3942   2.1899   0.8381
 S1Y  H25   H  HCH2  0   0.218   3.3212   2.0504  -0.2816
 S1Y  H25A  H  HCH2  0   0.236   3.0372   2.1543   1.4477

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
 S1Y  O2   S1    double  1.444  0.020  1.444
 S1Y  S1   O4    double  1.445  0.020  1.445
 S1Y  S1   N5    single  1.618  0.020  1.618
 S1Y  S1   O3    single  1.605  0.020  1.605
 S1Y  O3   HO3   single  0.850  0.020  0.980
 S1Y  N5   C6    single  1.464  0.020  1.464
 S1Y  N5   HN5   single  0.890  0.020  1.040
 S1Y  C7   C6    single  1.525  0.020  1.525
 S1Y  C6   C10   single  1.536  0.020  1.536
 S1Y  C6   H6    single  0.970  0.020  1.090
 S1Y  C7   C8    single  1.528  0.020  1.528
 S1Y  C7   H7    single  0.970  0.020  1.090
 S1Y  C7   H7A   single  0.970  0.020  1.090
 S1Y  C8   N9    single  1.457  0.020  1.457
 S1Y  C8   H8    single  0.970  0.020  1.090
 S1Y  C8   H8A   single  0.970  0.020  1.090
 S1Y  N9   C13   single  1.362  0.020  1.362
 S1Y  N9   C10   single  1.445  0.020  1.445
 S1Y  C11  C10   single  1.511  0.020  1.511
 S1Y  C10  H10   single  0.970  0.020  1.090
 S1Y  O12  C11   double  1.203  0.020  1.203
 S1Y  C11  H11   single  0.930  0.020  1.080
 S1Y  N15  C13   single  1.351  0.020  1.351
 S1Y  C13  O14   double  1.232  0.020  1.232
 S1Y  N15  C16   single  1.456  0.020  1.456
 S1Y  N15  HN15  single  0.860  0.020  1.020
 S1Y  C17  C16   single  1.534  0.020  1.534
 S1Y  C16  C25   single  1.530  0.020  1.530
 S1Y  C16  H16   single  0.970  0.020  1.090
 S1Y  C18  C17   single  1.527  0.020  1.527
 S1Y  C17  H17   single  0.970  0.020  1.090
 S1Y  C17  H17A  single  0.970  0.020  1.090
 S1Y  C18  C19   single  1.524  0.020  1.524
 S1Y  C18  H18   single  0.970  0.020  1.090
 S1Y  C18  H18A  single  0.970  0.020  1.090
 S1Y  C19  N20   single  1.456  0.020  1.456
 S1Y  C19  H19   single  0.970  0.020  1.090
 S1Y  C19  H19A  single  0.970  0.020  1.090
 S1Y  N20  C21   single  1.451  0.020  1.451
 S1Y  N20  C24   single  1.451  0.020  1.451
 S1Y  C22  C21   single  1.523  0.020  1.523
 S1Y  C21  H21   single  0.970  0.020  1.090
 S1Y  C21  H21A  single  0.970  0.020  1.090
 S1Y  C22  N23   single  1.456  0.020  1.456
 S1Y  C22  H22   single  0.970  0.020  1.090
 S1Y  C22  H22A  single  0.970  0.020  1.090
 S1Y  N23  HN23  single  0.890  0.020  1.040
 S1Y  N23  HN2A  single  0.890  0.020  1.040
 S1Y  C25  C24   single  1.524  0.020  1.524
 S1Y  C24  H24   single  0.970  0.020  1.090
 S1Y  C24  H24A  single  0.970  0.020  1.090
 S1Y  C25  H25   single  0.970  0.020  1.090
 S1Y  C25  H25A  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
 S1Y  N5    S1   O4    109.16  3.000
 S1Y  N5    S1   O3    101.32  3.000
 S1Y  O4    S1   O3    108.07  3.000
 S1Y  O3    S1   O2    108.94  3.000
 S1Y  N5    S1   O2    107.81  3.000
 S1Y  O4    S1   O2    119.95  3.000
 S1Y  HO3   O3   S1    111.70  3.000
 S1Y  HN5   N5   C6    117.19  3.000
 S1Y  HN5   N5   S1    113.59  3.000
 S1Y  C6    N5   S1    121.22  3.000
 S1Y  H6    C6   C10   110.50  3.000
 S1Y  H6    C6   C7    112.17  3.000
 S1Y  C10   C6   C7    102.13  3.000
 S1Y  H6    C6   N5    109.75  3.000
 S1Y  C10   C6   N5    110.48  3.000
 S1Y  C7    C6   N5    111.62  3.000
 S1Y  H7A   C7   H7    108.04  3.000
 S1Y  H7A   C7   C8    110.16  3.000
 S1Y  H7    C7   C8    113.20  3.000
 S1Y  H7A   C7   C6    108.62  3.000
 S1Y  H7    C7   C6    112.87  3.000
 S1Y  C8    C7   C6    103.85  3.000
 S1Y  H8A   C8   H8    107.60  3.000
 S1Y  H8A   C8   N9    111.77  3.000
 S1Y  H8    C8   N9    111.25  3.000
 S1Y  H8A   C8   C7    111.28  3.000
 S1Y  H8    C8   C7    111.97  3.000
 S1Y  N9    C8   C7    103.01  3.000
 S1Y  C13   N9   C10   118.68  3.000
 S1Y  C10   N9   C8    113.30  3.000
 S1Y  C13   N9   C8    126.48  3.000
 S1Y  H10   C10  C11   108.91  3.000
 S1Y  H10   C10  N9    112.60  3.000
 S1Y  C11   C10  N9    112.05  3.000
 S1Y  H10   C10  C6    109.07  3.000
 S1Y  C11   C10  C6    111.71  3.000
 S1Y  N9    C10  C6    102.37  3.000
 S1Y  H11   C11  O12   122.01  3.000
 S1Y  H11   C11  C10   114.98  3.000
 S1Y  O12   C11  C10   122.91  3.000
 S1Y  N15   C13  O14   123.39  3.000
 S1Y  O14   C13  N9    120.09  3.000
 S1Y  N15   C13  N9    116.51  3.000
 S1Y  HN15  N15  C16   116.25  3.000
 S1Y  HN15  N15  C13   118.99  3.000
 S1Y  C16   N15  C13   121.95  3.000
 S1Y  H16   C16  C25   109.66  3.000
 S1Y  H16   C16  C17   109.68  3.000
 S1Y  C25   C16  C17   112.23  3.000
 S1Y  H16   C16  N15   106.65  3.000
 S1Y  C25   C16  N15   107.22  3.000
 S1Y  C17   C16  N15   111.22  3.000
 S1Y  H17A  C17  H17   106.13  3.000
 S1Y  H17A  C17  C18   109.92  3.000
 S1Y  H17   C17  C18   108.15  3.000
 S1Y  H17A  C17  C16   108.20  3.000
 S1Y  H17   C17  C16   109.18  3.000
 S1Y  C18   C17  C16   114.90  3.000
 S1Y  H18A  C18  H18   106.35  3.000
 S1Y  H18A  C18  C19   109.41  3.000
 S1Y  H18   C18  C19   107.71  3.000
 S1Y  H18A  C18  C17   108.41  3.000
 S1Y  H18   C18  C17   109.63  3.000
 S1Y  C19   C18  C17   114.99  3.000
 S1Y  H19A  C19  H19   104.97  3.000
 S1Y  H19A  C19  N20   109.91  3.000
 S1Y  H19   C19  N20   109.98  3.000
 S1Y  H19A  C19  C18   108.30  3.000
 S1Y  H19   C19  C18   109.57  3.000
 S1Y  N20   C19  C18   113.73  3.000
 S1Y  C24   N20  C21   113.80  3.000
 S1Y  C24   N20  C19   111.14  3.000
 S1Y  C21   N20  C19   113.02  3.000
 S1Y  H21A  C21  H21   106.31  3.000
 S1Y  H21A  C21  C22   109.64  3.000
 S1Y  H21   C21  C22   107.73  3.000
 S1Y  H21A  C21  N20   112.39  3.000
 S1Y  H21   C21  N20   108.87  3.000
 S1Y  C22   C21  N20   111.64  3.000
 S1Y  H22A  C22  H22   106.17  3.000
 S1Y  H22A  C22  N23   108.78  3.000
 S1Y  H22   C22  N23   113.30  3.000
 S1Y  H22A  C22  C21   108.20  3.000
 S1Y  H22   C22  C21   110.08  3.000
 S1Y  N23   C22  C21   110.10  3.000
 S1Y  HN2A  N23  HN23  105.47  3.000
 S1Y  HN2A  N23  C22   109.43  3.000
 S1Y  HN23  N23  C22   109.24  3.000
 S1Y  H24A  C24  H24   106.07  3.000
 S1Y  H24A  C24  C25   106.82  3.000
 S1Y  H24   C24  C25   109.29  3.000
 S1Y  H24A  C24  N20   108.69  3.000
 S1Y  H24   C24  N20   111.21  3.000
 S1Y  C25   C24  N20   114.34  3.000
 S1Y  H25A  C25  H25   106.62  3.000
 S1Y  H25A  C25  C24   107.28  3.000
 S1Y  H25   C25  C24   108.50  3.000
 S1Y  H25A  C25  C16   108.70  3.000
 S1Y  H25   C25  C16   108.19  3.000
 S1Y  C24   C25  C16   117.09  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
 S1Y  CONST_01  O14   C13  N9   C8    180.00   0.0  0
 S1Y  CONST_02  O14   C13  N9   C10     0.00   0.0  0
 S1Y  CONST_03  N15   C13  N9   C8      0.00   0.0  0
 S1Y  CONST_04  C16   N15  C13  N9    180.00   0.0  0
 S1Y  CONST_05  N15   C13  N9   C10   180.00   0.0  0
 S1Y  CONST_06  C16   N15  C13  O14     0.00   0.0  0
 S1Y  CONST_07  HN15  N15  C13  N9      0.00   0.0  0
 S1Y  Var_01    N9    C8   C7   C6    -27.19  30.0  1
 S1Y  Var_02    C10   N9   C8   C7      4.87  30.0  1
 S1Y  Var_03    C6    N5   S1   O2   -179.29  30.0  3
 S1Y  Var_04    N23   C22  C21  N20  -178.60  30.0  2
 S1Y  Var_05    HN23  N23  C22  C21    71.39  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
 S1Y  chir_01  C6   N5   C7   C10  positiv
 S1Y  chir_02  C10  N9   C6   C11  negativ
 S1Y  chir_03  C16  N15  C17  C25  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
 S1Y  plan-1  C8    0.020
 S1Y  plan-1  N9    0.020
 S1Y  plan-1  C10   0.020
 S1Y  plan-1  C13   0.020
 S1Y  plan-1  O14   0.020
 S1Y  plan-1  N15   0.020
 S1Y  plan-1  C16   0.020
 S1Y  plan-1  HN15  0.020
 S1Y  plan-2  C10   0.020
 S1Y  plan-2  C11   0.020
 S1Y  plan-2  O12   0.020
 S1Y  plan-2  H11   0.020

