# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 23:01:28 2022
#   Inital geometry file: a 99 line input string
#   Ligand name: O-{(2S)-2-[methyl(methylsulfamoyl)amino]pentanoyl}-L-serine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC[C@H](N(C)[S](=O)(=O)NC)C(=O)OC[C@H](N)C(O)=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
 BG1  BG1  O-{(2S)-2-[methyl(methylsulfamoyl)amino]pentanoyl}-L-serine  L-peptide  40  20  .  2012-08-28  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_BG1
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
 BG1  N     N  NH2    0  -0.783  32.2856   6.8173  -0.7617
 BG1  CA    C  CH1    0  -0.247  31.0714   6.7181   0.0275
 BG1  CB    C  CH2    0  -0.185  30.1843   7.9306  -0.2245
 BG1  OG    O  O2     0  -0.449  30.9146   9.1328   0.0429
 BG1  C     C  C      0   0.386  30.2162   5.4352  -0.1822
 BG1  O     O  O      0  -0.590  30.6287   4.6062  -1.0125
 BG1  C1    C  CH3    0  -0.661  35.8306   9.8105  -1.8905
 BG1  C3    C  CH2    0  -0.473  33.8284  10.4132  -0.4915
 BG1  C4    C  CH1    0  -0.151  32.3766  10.9109  -0.4499
 BG1  C5    C  C      0   0.592  31.4375   9.8234  -0.9518
 BG1  C7    C  CH3    0  -0.523  31.6275  14.5230   1.1854
 BG1  N1    N  N      0  -0.605  32.0372  11.4227   0.8797
 BG1  O1    O  O      0  -0.447  31.2216   9.6376  -2.1226
 BG1  S     S  S      0   1.507  30.5419  12.0970   1.0617
 BG1  OXT   O  OC    -1  -0.609  29.1810   5.3635   0.5108
 BG1  HN1   H  HNH2   0   0.342  32.9428   6.1192  -0.4373
 BG1  HN2A  H  HNH2   0   0.329  32.0757   6.5495  -1.7164
 BG1  HA    H  HCH1   0   0.230  31.3655   6.7447   1.0834
 BG1  HB1   H  HCH2   0   0.230  29.8025   7.9371  -1.2473
 BG1  HB2   H  HCH2   0   0.245  29.3382   7.9326   0.4583
 BG1  H11   H  HCH3   0   0.230  36.1905   9.5876  -2.8951
 BG1  H12   H  HCH3   0   0.219  36.4104  10.6529  -1.5096
 BG1  H13   H  HCH3   0   0.219  36.0509   8.9461  -1.2618
 BG1  H21   H  HCH2   0   0.220  34.1461  10.9798  -2.5467
 BG1  H22   H  HCH2   0   0.228  33.8015   9.2771  -2.3305
 BG1  H31   H  HCH2   0   0.242  33.9443   9.5191   0.1262
 BG1  H32   H  HCH2   0   0.253  34.4537  11.1931  -0.0483
 BG1  H4    H  HCH1   0   0.290  32.3056  11.7378  -1.1578
 BG1  H61   H  HCH3   0   0.243  32.2431   9.8107   2.2684
 BG1  H62   H  HCH3   0   0.264  33.6827  10.8116   2.0101
 BG1  H63   H  HCH3   0   0.258  32.3533  11.4446   2.9443
 BG1  H71   H  HCH3   0   0.240  31.0301  14.9878   0.3996
 BG1  H72   H  HCH3   0   0.262  31.9019  15.2838   1.9119
 BG1  H73   H  HCH3   0   0.253  32.5453  14.1318   0.7503
 BG1  HN2   H  HNC1   0   0.413  30.1430  13.7804   2.4536
 BG1  C6    C  CH3    0  -0.527  32.5993  10.8246   2.0850
 BG1  C2    C  CH2    0  -0.423  34.3400  10.1210  -1.8983
 BG1  N2    N  NC1    0  -0.712  30.9278  13.4622   1.8956
 BG1  O2    O  OS     0  -0.656  30.0608  12.3751  -0.2849
 BG1  O3    O  OS     0  -0.655  29.6866  11.3320   1.9523

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
 BG1  N   CA    single  1.458  0.019  1.458
 BG1  C2  C1    single  1.523  0.020  1.523
 BG1  C2  C3    single  1.525  0.020  1.525
 BG1  O1  C5    double  1.205  0.020  1.205
 BG1  O2  S     double  1.457  0.020  1.457
 BG1  C5  C4    single  1.522  0.020  1.522
 BG1  C5  OG    single  1.319  0.020  1.319
 BG1  C3  C4    single  1.535  0.020  1.535
 BG1  C4  N1    single  1.465  0.020  1.465
 BG1  O   C     deloc   1.231  0.020  1.231
 BG1  CA  C     single  1.525  0.021  1.525
 BG1  CA  CB    single  1.530  0.020  1.530
 BG1  C   OXT   deloc   1.248  0.020  1.248
 BG1  OG  CB    single  1.432  0.020  1.432
 BG1  S   N1    single  1.650  0.020  1.650
 BG1  S   O3    double  1.453  0.020  1.453
 BG1  S   N2    single  1.646  0.020  1.646
 BG1  N1  C6    single  1.458  0.020  1.458
 BG1  N2  C7    single  1.456  0.020  1.456
 BG1  N   HN1   single  0.890  0.020  1.040
 BG1  N   HN2A  single  0.890  0.020  1.040
 BG1  CA  HA    single  0.970  0.020  0.970
 BG1  CB  HB1   single  0.970  0.020  1.090
 BG1  CB  HB2   single  0.970  0.020  1.090
 BG1  C1  H11   single  0.970  0.020  1.090
 BG1  C1  H12   single  0.970  0.020  1.090
 BG1  C1  H13   single  0.970  0.020  1.090
 BG1  C2  H21   single  0.970  0.020  1.090
 BG1  C2  H22   single  0.970  0.020  1.090
 BG1  C3  H31   single  0.970  0.020  1.090
 BG1  C3  H32   single  0.970  0.020  1.090
 BG1  C4  H4    single  0.970  0.020  1.090
 BG1  C6  H61   single  0.970  0.020  1.090
 BG1  C6  H62   single  0.970  0.020  1.090
 BG1  C6  H63   single  0.970  0.020  1.090
 BG1  C7  H71   single  0.970  0.020  1.090
 BG1  C7  H72   single  0.970  0.020  1.090
 BG1  C7  H73   single  0.970  0.020  1.090
 BG1  N2  HN2   single  0.890  0.020  1.040

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
 BG1  HN2A  N   HN1  104.72  3.000
 BG1  HN2A  N   CA   108.72  3.000
 BG1  HN1   N   CA   108.77  3.000
 BG1  HA    CA  C    109.00  3.000
 BG1  HA    CA  CB   109.00  3.000
 BG1  C     CA  CB   110.10  1.900
 BG1  HA    CA  N    110.00  3.000
 BG1  CB    CA  N    110.50  1.700
 BG1  C     CA  N    111.00  2.800
 BG1  HB2   CB  HB1  108.44  3.000
 BG1  HB2   CB  OG   106.15  3.000
 BG1  HB1   CB  OG   110.39  3.000
 BG1  HB2   CB  CA   110.53  3.000
 BG1  HB1   CB  CA   111.30  3.000
 BG1  OG    CB  CA   109.90  3.000
 BG1  C5    OG  CB   120.06  3.000
 BG1  OXT   C   O    127.41  3.000
 BG1  OXT   C   CA   115.37  3.000
 BG1  O     C   CA   120.80  1.700
 BG1  H13   C1  H12  107.64  3.000
 BG1  H13   C1  H11  107.59  3.000
 BG1  H12   C1  H11  107.71  3.000
 BG1  H13   C1  C2   111.23  3.000
 BG1  H12   C1  C2   111.38  3.000
 BG1  H11   C1  C2   111.11  3.000
 BG1  H32   C3  H31  107.08  3.000
 BG1  H32   C3  C4   107.37  3.000
 BG1  H31   C3  C4   110.50  3.000
 BG1  H32   C3  C2   108.58  3.000
 BG1  H31   C3  C2   109.20  3.000
 BG1  C4    C3  C2   113.85  3.000
 BG1  H4    C4  N1   108.01  3.000
 BG1  H4    C4  C5   106.71  3.000
 BG1  N1    C4  C5   113.96  3.000
 BG1  H4    C4  C3   106.84  3.000
 BG1  N1    C4  C3   110.92  3.000
 BG1  C5    C4  C3   110.05  3.000
 BG1  O1    C5  C4   122.76  3.000
 BG1  C4    C5  OG   111.71  3.000
 BG1  O1    C5  OG   125.52  3.000
 BG1  H73   C7  H72  107.81  3.000
 BG1  H73   C7  H71  109.08  3.000
 BG1  H72   C7  H71  108.75  3.000
 BG1  H73   C7  N2   109.78  3.000
 BG1  H72   C7  N2   107.77  3.000
 BG1  H71   C7  N2   113.49  3.000
 BG1  S     N1  C6   115.19  3.000
 BG1  C6    N1  C4   121.18  3.000
 BG1  S     N1  C4   116.93  3.000
 BG1  O3    S   O2   118.22  3.000
 BG1  O3    S   N2   105.33  3.000
 BG1  O2    S   N2   112.80  3.000
 BG1  N2    S   N1   100.51  3.000
 BG1  O3    S   N1   112.70  3.000
 BG1  O2    S   N1   105.98  3.000
 BG1  H63   C6  H62  106.68  3.000
 BG1  H63   C6  H61  108.86  3.000
 BG1  H62   C6  H61  109.05  3.000
 BG1  H63   C6  N1   109.39  3.000
 BG1  H62   C6  N1   109.42  3.000
 BG1  H61   C6  N1   113.23  3.000
 BG1  H22   C2  H21  106.57  3.000
 BG1  H22   C2  C3   110.38  3.000
 BG1  H21   C2  C3   109.69  3.000
 BG1  H22   C2  C1   109.13  3.000
 BG1  H21   C2  C1   109.68  3.000
 BG1  C3    C2  C1   111.27  3.000
 BG1  HN2   N2  S    110.95  3.000
 BG1  HN2   N2  C7   114.32  3.000
 BG1  S     N2  C7   118.04  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
 BG1  Var_01  O1   C5  OG  CB   10.15  30.0  1
 BG1  Var_02  C4   C3  C2  C1  172.50  30.0  3
 BG1  Var_03  O2   S   N1  C4  -16.79  30.0  1
 BG1  Var_04  H11  C1  C2  C3  179.16  30.0  3
 BG1  Var_05  H61  C6  N1  C4  -67.50  30.0  3
 BG1  Var_06  HB1  CB  OG  C5  -23.22  30.0  3
 BG1  Var_07  H71  C7  N2  S    66.15  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
 BG1  chir_01  CA  N   C   CB  positiv
 BG1  chir_02  C4  N1  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
 BG1  plan-1  CA   0.020
 BG1  plan-1  C    0.020
 BG1  plan-1  O    0.020
 BG1  plan-1  OXT  0.020
 BG1  plan-2  OG   0.020
 BG1  plan-2  C4   0.020
 BG1  plan-2  C5   0.020
 BG1  plan-2  O1   0.020

