# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 09:46:00 2022
#   Inital geometry file: a 79 line input string
#   Ligand name: O-[(R)-methyl(2-methylpropoxy)phosphoryl]-L-serine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)CO[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
 RVX  RVX  O-[(R)-methyl(2-methylpropoxy)phosphoryl]-L-serine  L-peptide  32  15  .  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_RVX
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
 RVX  N     N  NH2    0  -0.815   7.6584   5.1302  -37.0653
 RVX  CA    C  CH1    0  -0.240   8.2474   3.8901  -36.5728
 RVX  C     C  C      0   0.428   9.7686   4.0983  -36.3708
 RVX  O     O  O      0  -0.605  10.0848   5.1269  -35.7409
 RVX  CB    C  CH2    0  -0.142   7.9069   2.7950  -37.5660
 RVX  OG    O  O2     0  -0.601   8.1444   1.5066  -36.9936
 RVX  P1    P  P      0   1.375   9.1003   0.3871  -37.6305
 RVX  O1    O  O      0  -0.719   9.6143   0.6927  -38.9908
 RVX  C1    C  CH3    0  -0.941  10.3167  -0.0089  -36.3751
 RVX  O2    O  O2     0  -0.598   8.1783  -0.9331  -37.5513
 RVX  C2    C  CH2    0  -0.140   6.9881  -1.0474  -38.3353
 RVX  C3    C  CH1    0  -0.275   5.8734  -1.6670  -37.5090
 RVX  C5    C  CH3    0  -0.661   4.6617  -1.8923  -38.4077
 RVX  C4    C  CH3    0  -0.650   5.5060  -0.8051  -36.3064
 RVX  OXT   O  OC    -1  -0.583  10.5408   3.2353  -36.8312
 RVX  HN1   H  HNH2   0   0.336   6.6628   5.1354  -36.8831
 RVX  HN2   H  HNH2   0   0.338   8.0514   5.8947  -36.5322
 RVX  HA    H  HCH1   0   0.204   7.8344   3.5932  -35.5932
 RVX  HB1C  H  HCH2   0   0.218   6.8420   2.8355  -37.8131
 RVX  HB2C  H  HCH2   0   0.217   8.4661   2.9270  -38.4931
 RVX  H11C  H  HCH3   0   0.270  10.8937  -0.8806  -36.6805
 RVX  H12C  H  HCH3   0   0.283  10.9870   0.8383  -36.2547
 RVX  H13C  H  HCH3   0   0.270   9.8430  -0.2208  -35.4177
 RVX  H21C  H  HCH2   0   0.216   6.6588  -0.0708  -38.7096
 RVX  H22C  H  HCH2   0   0.235   7.2087  -1.6711  -39.2058
 RVX  H3    H  HCH1   0   0.228   6.2185  -2.6431  -37.1502
 RVX  H51C  H  HCH3   0   0.234   3.8536  -2.3715  -37.8545
 RVX  H52C  H  HCH3   0   0.219   4.2796  -0.9454  -38.7962
 RVX  H53C  H  HCH3   0   0.229   4.9038  -2.5292  -39.2600
 RVX  H41C  H  HCH3   0   0.226   4.6820  -1.2535  -35.7495
 RVX  H42C  H  HCH3   0   0.230   6.3394  -0.6832  -35.6149
 RVX  H43C  H  HCH3   0   0.213   5.1865   0.1898  -36.6255

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
 RVX  N   CA    single  1.458  0.019  1.458
 RVX  CA  C     single  1.525  0.021  1.525
 RVX  CA  CB    single  1.530  0.020  1.530
 RVX  C   O     deloc   1.231  0.020  1.231
 RVX  C   OXT   deloc   1.246  0.020  1.246
 RVX  CB  OG    single  1.430  0.020  1.430
 RVX  OG  P1    single  1.604  0.020  1.604
 RVX  P1  O1    double  1.486  0.020  1.486
 RVX  P1  C1    single  1.792  0.020  1.792
 RVX  P1  O2    single  1.612  0.020  1.612
 RVX  O2  C2    single  1.430  0.020  1.430
 RVX  C2  C3    single  1.520  0.020  1.520
 RVX  C3  C5    single  1.525  0.020  1.525
 RVX  C3  C4    single  1.525  0.020  1.525
 RVX  N   HN1   single  0.890  0.020  1.040
 RVX  N   HN2   single  0.890  0.020  1.040
 RVX  CA  HA    single  0.970  0.020  0.970
 RVX  CB  HB1C  single  0.970  0.020  1.090
 RVX  CB  HB2C  single  0.970  0.020  1.090
 RVX  C1  H11C  single  0.970  0.020  1.090
 RVX  C1  H12C  single  0.970  0.020  1.090
 RVX  C1  H13C  single  0.970  0.020  1.090
 RVX  C2  H21C  single  0.970  0.020  1.090
 RVX  C2  H22C  single  0.970  0.020  1.090
 RVX  C3  H3    single  0.970  0.020  1.090
 RVX  C5  H51C  single  0.970  0.020  1.090
 RVX  C5  H52C  single  0.970  0.020  1.090
 RVX  C5  H53C  single  0.970  0.020  1.090
 RVX  C4  H41C  single  0.970  0.020  1.090
 RVX  C4  H42C  single  0.970  0.020  1.090
 RVX  C4  H43C  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
 RVX  HN2   N   HN1   106.46  3.000
 RVX  HN2   N   CA    107.92  3.000
 RVX  HN1   N   CA    109.93  3.000
 RVX  HA    CA  CB    109.00  3.000
 RVX  HA    CA  C     109.00  3.000
 RVX  CB    CA  C     110.10  1.900
 RVX  HA    CA  N     110.00  3.000
 RVX  CB    CA  N     110.50  1.700
 RVX  C     CA  N     111.00  2.800
 RVX  OXT   C   O     126.92  3.000
 RVX  OXT   C   CA    117.87  3.000
 RVX  O     C   CA    120.80  1.700
 RVX  HB2C  CB  HB1C  107.61  3.000
 RVX  HB2C  CB  OG    111.36  3.000
 RVX  HB1C  CB  OG    106.58  3.000
 RVX  HB2C  CB  CA    110.74  3.000
 RVX  HB1C  CB  CA    109.86  3.000
 RVX  OG    CB  CA    110.56  3.000
 RVX  P1    OG  CB    124.68  3.000
 RVX  O2    P1  C1     99.95  3.000
 RVX  O2    P1  O1    114.28  3.000
 RVX  C1    P1  O1    116.87  3.000
 RVX  O2    P1  OG    102.19  3.000
 RVX  C1    P1  OG    106.29  3.000
 RVX  O1    P1  OG    115.22  3.000
 RVX  H13C  C1  H12C  108.82  3.000
 RVX  H13C  C1  H11C  108.74  3.000
 RVX  H12C  C1  H11C  109.16  3.000
 RVX  H13C  C1  P1    111.32  3.000
 RVX  H12C  C1  P1    108.90  3.000
 RVX  H11C  C1  P1    109.87  3.000
 RVX  C2    O2  P1    120.97  3.000
 RVX  H22C  C2  H21C  107.27  3.000
 RVX  H22C  C2  C3    110.38  3.000
 RVX  H21C  C2  C3    109.18  3.000
 RVX  H22C  C2  O2    108.32  3.000
 RVX  H21C  C2  O2    111.47  3.000
 RVX  C3    C2  O2    110.18  3.000
 RVX  H3    C3  C4    108.74  3.000
 RVX  H3    C3  C5    108.15  3.000
 RVX  C4    C3  C5    110.91  3.000
 RVX  H3    C3  C2    108.08  3.000
 RVX  C4    C3  C2    112.03  3.000
 RVX  C5    C3  C2    108.82  3.000
 RVX  H53C  C5  H52C  107.80  3.000
 RVX  H53C  C5  H51C  107.72  3.000
 RVX  H52C  C5  H51C  107.58  3.000
 RVX  H53C  C5  C3    111.72  3.000
 RVX  H52C  C5  C3    111.06  3.000
 RVX  H51C  C5  C3    110.78  3.000
 RVX  H43C  C4  H42C  107.89  3.000
 RVX  H43C  C4  H41C  107.61  3.000
 RVX  H42C  C4  H41C  107.44  3.000
 RVX  H43C  C4  C3    110.79  3.000
 RVX  H42C  C4  C3    112.30  3.000
 RVX  H41C  C4  C3    110.63  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
 RVX  Var_01  O1    P1  OG  CB    -7.92  30.0  3
 RVX  Var_02  C3    C2  O2  P1  -138.48  30.0  3
 RVX  Var_03  C5    C3  C2  O2  -174.86  30.0  3
 RVX  Var_04  H11C  C1  P1  OG   170.53  30.0  3
 RVX  Var_05  HB1C  CB  OG  P1   116.68  30.0  1
 RVX  Var_06  H51C  C5  C3  C2   177.88  30.0  3
 RVX  Var_07  H41C  C4  C3  C2   178.07  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
 RVX  chir_01  CA  N   C   CB  positiv
 RVX  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
 RVX  plan-1  CA   0.020
 RVX  plan-1  C    0.020
 RVX  plan-1  O    0.020
 RVX  plan-1  OXT  0.020

