# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 20:35:10 2022
#   Inital geometry file: a 69 line input string
#   Ligand name: O-[(R)-hydroxy(1-methylethoxy)phosphoryl]-L-serine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)O[P@@](O)(=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
 MIS  MIS  O-[(R)-hydroxy(1-methylethoxy)phosphoryl]-L-serine  L-peptide  26  14  .  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_MIS
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
 MIS  N    N  NH2    0  -0.808   8.6488  40.6692  32.7552
 MIS  CA   C  CH1    0  -0.258   7.3532  41.0141  32.1919
 MIS  CB   C  CH2    0  -0.116   6.3102  40.0035  32.6397
 MIS  OG   O  O2     0  -0.633   6.7051  38.7053  32.2192
 MIS  P    P  P      0   1.343   6.1573  37.3759  33.0232
 MIS  O1P  O  OP    -1  -0.787   4.8351  36.9508  32.4644
 MIS  O2P  O  O      0  -0.805   6.3339  37.5816  34.4989
 MIS  O3P  O  O2     0  -0.620   7.2588  36.3122  32.4460
 MIS  C1   C  CH1    0   0.041   8.6085  36.3514  32.9064
 MIS  C2   C  CH3    0  -0.664   9.5159  36.1181  31.7115
 MIS  C3   C  CH3    0  -0.662   8.8157  35.3075  33.9905
 MIS  C    C  C      0   0.408   6.9295  42.4520  32.5930
 MIS  O    O  O      0  -0.605   5.7244  42.7320  32.4379
 MIS  OXT  O  OC    -1  -0.598   7.8264  43.2150  33.0005
 MIS  H    H  HNH2   0   0.331   9.2431  41.4856  32.7059
 MIS  H2   H  HNH2   0   0.331   9.0870  39.9469  32.2004
 MIS  HA   H  HCH1   0   0.197   7.3663  41.0075  31.0871
 MIS  HB2  H  HCH2   0   0.185   6.2186  40.0461  33.7302
 MIS  HB3  H  HCH2   0   0.191   5.3380  40.2577  32.2111
 MIS  H1   H  HCH1   0   0.200   8.8398  37.3378  33.3254
 MIS  H21  H  HCH3   0   0.220  10.5621  36.1451  32.0179
 MIS  H22  H  HCH3   0   0.219   9.3251  35.1430  31.2592
 MIS  H23  H  HCH3   0   0.229   9.3697  36.8855  30.9506
 MIS  H31  H  HCH3   0   0.217   9.8472  35.3222  34.3452
 MIS  H32  H  HCH3   0   0.230   8.1645  35.5000  34.8421
 MIS  H33  H  HCH3   0   0.216   8.6057  34.3047  33.6129

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
 MIS  N    CA   single  1.458  0.019  1.458
 MIS  N    H    single  0.860  0.020  0.860
 MIS  N    H2   single  0.890  0.020  1.040
 MIS  CA   CB   single  1.530  0.020  1.530
 MIS  CA   C    single  1.525  0.021  1.525
 MIS  CA   HA   single  0.970  0.020  0.970
 MIS  CB   OG   single  1.421  0.020  1.421
 MIS  CB   HB2  single  0.970  0.020  1.090
 MIS  CB   HB3  single  0.970  0.020  1.090
 MIS  OG   P    single  1.647  0.020  1.647
 MIS  P    O1P  deloc   1.497  0.020  1.497
 MIS  P    O2P  deloc   1.500  0.020  1.500
 MIS  P    O3P  single  1.636  0.020  1.636
 MIS  O3P  C1   single  1.427  0.020  1.427
 MIS  C1   C2   single  1.518  0.020  1.518
 MIS  C1   C3   single  1.519  0.020  1.519
 MIS  C1   H1   single  0.970  0.020  1.090
 MIS  C2   H21  single  0.970  0.020  1.090
 MIS  C2   H22  single  0.970  0.020  1.090
 MIS  C2   H23  single  0.970  0.020  1.090
 MIS  C3   H31  single  0.970  0.020  1.090
 MIS  C3   H32  single  0.970  0.020  1.090
 MIS  C3   H33  single  0.970  0.020  1.090
 MIS  C    O    deloc   1.231  0.020  1.231
 MIS  C    OXT  deloc   1.246  0.020  1.246

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
 MIS  H2   N    H    107.18  3.000
 MIS  H2   N    CA   110.07  3.000
 MIS  H    N    CA   114.00  3.000
 MIS  HA   CA   C    109.00  3.000
 MIS  HA   CA   CB   109.00  3.000
 MIS  C    CA   CB   110.10  1.900
 MIS  HA   CA   N    110.00  3.000
 MIS  C    CA   N    111.00  2.800
 MIS  CB   CA   N    110.50  1.700
 MIS  HB3  CB   HB2  107.89  3.000
 MIS  HB3  CB   OG   110.11  3.000
 MIS  HB2  CB   OG   110.70  3.000
 MIS  HB3  CB   CA   109.90  3.000
 MIS  HB2  CB   CA   108.96  3.000
 MIS  OG   CB   CA   109.25  3.000
 MIS  P    OG   CB   120.04  3.000
 MIS  O3P  P    O2P  110.90  3.000
 MIS  O3P  P    O1P  106.16  3.000
 MIS  O2P  P    O1P  120.67  3.000
 MIS  O3P  P    OG    97.39  3.000
 MIS  O2P  P    OG   109.28  3.000
 MIS  O1P  P    OG   109.92  3.000
 MIS  C1   O3P  P    120.34  3.000
 MIS  H1   C1   C3   108.47  3.000
 MIS  H1   C1   C2   108.23  3.000
 MIS  C3   C1   C2   112.00  3.000
 MIS  H1   C1   O3P  110.34  3.000
 MIS  C3   C1   O3P  109.90  3.000
 MIS  C2   C1   O3P  107.89  3.000
 MIS  H23  C2   H22  108.42  3.000
 MIS  H23  C2   H21  107.90  3.000
 MIS  H22  C2   H21  107.83  3.000
 MIS  H23  C2   C1   111.16  3.000
 MIS  H22  C2   C1   111.03  3.000
 MIS  H21  C2   C1   110.39  3.000
 MIS  H33  C3   H32  108.52  3.000
 MIS  H33  C3   H31  107.85  3.000
 MIS  H32  C3   H31  107.98  3.000
 MIS  H33  C3   C1   110.98  3.000
 MIS  H32  C3   C1   110.80  3.000
 MIS  H31  C3   C1   110.60  3.000
 MIS  OXT  C    O    126.79  3.000
 MIS  OXT  C    CA   117.09  3.000
 MIS  O    C    CA   120.80  1.700

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
 MIS  Var_01  O1P  P   OG   CB     86.76  30.0  3
 MIS  Var_02  C2   C1  O3P  P    -139.50  30.0  3
 MIS  Var_03  HB2  CB  OG   P      35.49  30.0  1
 MIS  Var_04  H21  C2  C1   O3P   179.71  30.0  3
 MIS  Var_05  H31  C3  C1   O3P   179.54  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
 MIS  chir_01  CA  N  CB  C  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
 MIS  plan-1  CA   0.020
 MIS  plan-1  C    0.020
 MIS  plan-1  O    0.020
 MIS  plan-1  OXT  0.020

