# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 15:15:33 2022
#   Inital geometry file: a 73 line input string
#   Ligand name: O-[(S)-methyl(1-methylethoxy)phosphoryl]-L-serine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)O[P@@](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
 SGB  SGB  O-[(S)-methyl(1-methylethoxy)phosphoryl]-L-serine  L-peptide  29  14  .  2016-04-26  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_SGB
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
 SGB  N     N  NH2    0  -0.797  25.4957  13.1167  14.5106
 SGB  CA    C  CH1    0  -0.239  26.5076  13.0548  13.4615
 SGB  C     C  C      0   0.412  27.5738  12.0111  13.8790
 SGB  O     O  O      0  -0.601  27.5249  10.8948  13.3314
 SGB  CB    C  CH2    0  -0.167  27.1305  14.4178  13.2182
 SGB  OG    O  O2     0  -0.592  28.0851  14.3135  12.1497
 SGB  O1    O  O      0  -0.712  30.2725  15.3932  13.1099
 SGB  P1    P  P      0   1.376  29.2645  15.3907  12.0188
 SGB  C1    C  CH3    0  -0.934  29.9133  15.0248  10.3885
 SGB  O2    O  O2     0  -0.608  28.4526  16.7713  11.8637
 SGB  C2    C  CH1    0   0.028  28.7990  17.9787  12.5736
 SGB  C4    C  CH3    0  -0.676  29.9873  18.6539  11.9172
 SGB  C3    C  CH3    0  -0.667  27.5633  18.8544  12.5706
 SGB  OXT   O  OC    -1  -0.607  28.3701  12.3857  14.7639
 SGB  HN1   H  HNH2   0   0.333  25.9291  13.4184  15.3755
 SGB  HN2   H  HNH2   0   0.342  24.7981  13.8163  14.2844
 SGB  HA    H  HCH1   0   0.210  26.0139  12.7223  12.5433
 SGB  HBC1  H  HCH2   0   0.211  27.6111  14.7630  14.1377
 SGB  HBC2  H  HCH2   0   0.225  26.3625  15.1456  12.9384
 SGB  H1C1  H  HCH3   0   0.276  29.1440  15.0979   9.6221
 SGB  H1C2  H  HCH3   0   0.278  30.3364  14.0212  10.3713
 SGB  H1C3  H  HCH3   0   0.278  30.7077  15.7338  10.1564
 SGB  H2    H  HCH1   0   0.229  29.0512  17.7226  13.6060
 SGB  H4C1  H  HCH3   0   0.229  29.7690  18.9075  10.8788
 SGB  H4C2  H  HCH3   0   0.237  30.8746  18.0204  11.9417
 SGB  H4C3  H  HCH3   0   0.236  30.2283  19.5765  12.4462
 SGB  H3C1  H  HCH3   0   0.239  26.7172  18.3489  13.0365
 SGB  H3C2  H  HCH3   0   0.228  27.2830  19.1389  11.5552
 SGB  H3C3  H  HCH3   0   0.232  27.7599  19.7673  13.1327

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
 SGB  N   CA    single  1.458  0.019  1.458
 SGB  CA  C     single  1.525  0.021  1.525
 SGB  C   O     deloc   1.231  0.020  1.231
 SGB  CA  CB    single  1.530  0.020  1.530
 SGB  CB  OG    single  1.437  0.020  1.437
 SGB  OG  P1    single  1.603  0.020  1.603
 SGB  O1  P1    double  1.485  0.020  1.485
 SGB  P1  C1    single  1.792  0.020  1.792
 SGB  P1  O2    single  1.609  0.020  1.609
 SGB  O2  C2    single  1.443  0.020  1.443
 SGB  C2  C4    single  1.516  0.020  1.516
 SGB  C2  C3    single  1.514  0.020  1.514
 SGB  C   OXT   deloc   1.248  0.020  1.248
 SGB  N   HN1   single  0.890  0.020  1.040
 SGB  N   HN2   single  0.890  0.020  1.040
 SGB  CA  HA    single  0.970  0.020  0.970
 SGB  CB  HBC1  single  0.970  0.020  1.090
 SGB  CB  HBC2  single  0.970  0.020  1.090
 SGB  C1  H1C1  single  0.970  0.020  1.090
 SGB  C1  H1C2  single  0.970  0.020  1.090
 SGB  C1  H1C3  single  0.970  0.020  1.090
 SGB  C2  H2    single  0.970  0.020  1.090
 SGB  C4  H4C1  single  0.970  0.020  1.090
 SGB  C4  H4C2  single  0.970  0.020  1.090
 SGB  C4  H4C3  single  0.970  0.020  1.090
 SGB  C3  H3C1  single  0.970  0.020  1.090
 SGB  C3  H3C2  single  0.970  0.020  1.090
 SGB  C3  H3C3  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
 SGB  HN2   N   HN1   106.22  3.000
 SGB  HN2   N   CA    110.25  3.000
 SGB  HN1   N   CA    109.25  3.000
 SGB  HA    CA  CB    109.00  3.000
 SGB  HA    CA  C     109.00  3.000
 SGB  CB    CA  C     110.10  1.900
 SGB  HA    CA  N     110.00  3.000
 SGB  CB    CA  N     110.50  1.700
 SGB  C     CA  N     111.00  2.800
 SGB  OXT   C   O     127.33  3.000
 SGB  OXT   C   CA    115.34  3.000
 SGB  O     C   CA    120.80  1.700
 SGB  HBC2  CB  HBC1  108.27  3.000
 SGB  HBC2  CB  OG    108.93  3.000
 SGB  HBC1  CB  OG    110.87  3.000
 SGB  HBC2  CB  CA    110.49  3.000
 SGB  HBC1  CB  CA    109.21  3.000
 SGB  OG    CB  CA    109.06  3.000
 SGB  P1    OG  CB    120.06  3.000
 SGB  O2    P1  C1    105.67  3.000
 SGB  O2    P1  O1    114.31  3.000
 SGB  C1    P1  O1    115.01  3.000
 SGB  O2    P1  OG    102.31  3.000
 SGB  C1    P1  OG    101.74  3.000
 SGB  O1    P1  OG    116.14  3.000
 SGB  H1C3  C1  H1C2  108.24  3.000
 SGB  H1C3  C1  H1C1  108.75  3.000
 SGB  H1C2  C1  H1C1  108.98  3.000
 SGB  H1C3  C1  P1    108.95  3.000
 SGB  H1C2  C1  P1    110.07  3.000
 SGB  H1C1  C1  P1    111.77  3.000
 SGB  C2    O2  P1    123.33  3.000
 SGB  H2    C2  C3    109.00  3.000
 SGB  H2    C2  C4    109.41  3.000
 SGB  C3    C2  C4    112.40  3.000
 SGB  H2    C2  O2    108.90  3.000
 SGB  C3    C2  O2    106.68  3.000
 SGB  C4    C2  O2    110.35  3.000
 SGB  H4C3  C4  H4C2  107.50  3.000
 SGB  H4C3  C4  H4C1  108.01  3.000
 SGB  H4C2  C4  H4C1  108.61  3.000
 SGB  H4C3  C4  C2    109.88  3.000
 SGB  H4C2  C4  C2    111.67  3.000
 SGB  H4C1  C4  C2    111.02  3.000
 SGB  H3C3  C3  H3C2  107.93  3.000
 SGB  H3C3  C3  H3C1  107.94  3.000
 SGB  H3C2  C3  H3C1  108.61  3.000
 SGB  H3C3  C3  C2    109.64  3.000
 SGB  H3C2  C3  C2    111.23  3.000
 SGB  H3C1  C3  C2    111.36  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
 SGB  Var_01  O1    P1  OG  CB   65.99  30.0  3
 SGB  Var_02  C4    C2  O2  P1   78.01  30.0  3
 SGB  Var_03  H1C1  C1  P1  OG   57.17  30.0  3
 SGB  Var_04  HBC1  CB  OG  P1  -37.04  30.0  1
 SGB  Var_05  H4C1  C4  C2  O2   59.32  30.0  3
 SGB  Var_06  H3C1  C3  C2  O2   58.31  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
 SGB  chir_01  CA  N   C   CB  positiv
 SGB  chir_02  P1  O1  C1  O2  both

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
 SGB  plan-1  CA   0.020
 SGB  plan-1  C    0.020
 SGB  plan-1  O    0.020
 SGB  plan-1  OXT  0.020

