# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 12 01:28:01 2022
#   Inital geometry file: a 94 line input string
#   Ligand name: O-[(R)-{[(3R)-4-amino-3-hydroxy-2,2-dimethyl-4-oxobutyl]oxy}(hydroxy)phosphoryl]-L-serine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(CO[P@](O)(=O)OC[C@H](N)C(O)=O)[C@@H](O)C(N)=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
 GVL  GVL  O-[(R)-{[(3R)-4-amino-3-hydroxy-2,2-dimethyl-4-oxobutyl]oxy}(hydroxy)phosphoryl]-L-serine  L-peptide  37  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_GVL
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
 GVL  O     O  O      0  -0.609  -14.2165  -22.3611  -22.4263
 GVL  C     C  C      0   0.412  -13.9152  -23.5471  -22.1844
 GVL  CA    C  CH1    0  -0.250  -14.2870  -24.5752  -23.2865
 GVL  N     N  NH2    0  -0.811  -14.0742  -25.9468  -22.8519
 GVL  CB    C  CH2    0  -0.139  -15.7166  -24.3829  -23.7572
 GVL  O25   O  O2     0  -0.612  -16.6014  -24.5362  -22.6556
 GVL  P24   P  P      0   1.398  -18.1787  -24.1798  -22.8446
 GVL  O23   O  OP    -1  -0.773  -18.7053  -24.6998  -24.1397
 GVL  O26   O  O      0  -0.793  -18.8137  -24.5612  -21.5260
 GVL  O27   O  O2     0  -0.625  -18.1700  -22.5479  -22.9840
 GVL  C28   C  CH2    0  -0.161  -17.8898  -21.7171  -21.8690
 GVL  C29   C  CT     0  -0.142  -19.0727  -20.8017  -21.5274
 GVL  C30   C  CH3    0  -0.661  -18.6575  -19.9798  -20.3063
 GVL  C31   C  CH3    0  -0.644  -19.3274  -19.8683  -22.7126
 GVL  C32   C  CH1    0  -0.024  -20.3205  -21.6792  -21.2126
 GVL  O33   O  OH1    0  -0.723  -20.0495  -22.6559  -20.2488
 GVL  C34   C  C      0   0.473  -21.5038  -20.8381  -20.7373
 GVL  O35   O  O      0  -0.490  -22.1377  -20.1213  -21.5016
 GVL  N36   N  NH2    0  -0.791  -21.7881  -20.9423  -19.4325
 GVL  OXT   O  OC    -1  -0.596  -13.3172  -23.9777  -21.1803
 GVL  HA    H  HCH1   0   0.203  -13.6598  -24.3124  -24.1561
 GVL  HN1   H  HNH2   0   0.329  -13.8672  -26.5322  -23.6504
 GVL  HN2   H  HNH2   0   0.332  -13.2636  -25.9706  -22.2489
 GVL  HBC1  H  HCH2   0   0.196  -15.8141  -23.3913  -24.2067
 GVL  HBC2  H  HCH2   0   0.202  -15.9521  -25.1186  -24.5343
 GVL  H281  H  HCH2   0   0.219  -17.5933  -22.2974  -20.9901
 GVL  H282  H  HCH2   0   0.223  -17.0318  -21.0872  -22.1249
 GVL  H301  H  HCH3   0   0.230  -18.5331  -20.6044  -19.4210
 GVL  H302  H  HCH3   0   0.230  -17.7078  -19.4737  -20.4913
 GVL  H303  H  HCH3   0   0.233  -19.3924  -19.2073  -20.0754
 GVL  H311  H  HCH3   0   0.232  -20.0630  -19.1020  -22.4774
 GVL  H312  H  HCH3   0   0.217  -18.4016  -19.3587  -22.9889
 GVL  H313  H  HCH3   0   0.224  -19.6823  -20.4098  -23.5902
 GVL  H32   H  HCH1   0   0.229  -20.6495  -22.1357  -22.1579
 GVL  H33   H  HOH1   0   0.465  -19.5830  -23.4137  -20.6910
 GVL  H361  H  HNH2   0   0.404  -21.3040  -21.6069  -18.8542
 GVL  H362  H  HNH2   0   0.392  -22.5776  -20.4525  -19.0453

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
 GVL  O    C     deloc   1.231  0.020  1.231
 GVL  C    CA    single  1.525  0.021  1.525
 GVL  CA   N     single  1.458  0.019  1.458
 GVL  CA   CB    single  1.530  0.020  1.530
 GVL  CB   O25   single  1.421  0.020  1.421
 GVL  O25  P24   single  1.628  0.020  1.628
 GVL  P24  O23   deloc   1.492  0.020  1.492
 GVL  P24  O26   deloc   1.512  0.020  1.512
 GVL  P24  O27   single  1.638  0.020  1.638
 GVL  O27  C28   single  1.418  0.020  1.418
 GVL  C28  C29   single  1.534  0.020  1.534
 GVL  C29  C30   single  1.529  0.020  1.529
 GVL  C29  C31   single  1.530  0.020  1.530
 GVL  C29  C32   single  1.558  0.020  1.558
 GVL  C32  O33   single  1.399  0.020  1.399
 GVL  C32  C34   single  1.528  0.020  1.528
 GVL  C34  O35   double  1.225  0.020  1.225
 GVL  C34  N36   single  1.339  0.020  1.339
 GVL  C    OXT   deloc   1.245  0.020  1.245
 GVL  CA   HA    single  0.970  0.020  0.970
 GVL  N    HN1   single  0.890  0.020  1.040
 GVL  N    HN2   single  0.890  0.020  1.040
 GVL  CB   HBC1  single  0.970  0.020  1.090
 GVL  CB   HBC2  single  0.970  0.020  1.090
 GVL  C28  H281  single  0.970  0.020  1.090
 GVL  C28  H282  single  0.970  0.020  1.090
 GVL  C30  H301  single  0.970  0.020  1.090
 GVL  C30  H302  single  0.970  0.020  1.090
 GVL  C30  H303  single  0.970  0.020  1.090
 GVL  C31  H311  single  0.970  0.020  1.090
 GVL  C31  H312  single  0.970  0.020  1.090
 GVL  C31  H313  single  0.970  0.020  1.090
 GVL  C32  H32   single  0.970  0.020  1.090
 GVL  O33  H33   single  0.850  0.020  0.980
 GVL  N36  H361  single  0.860  0.020  1.020
 GVL  N36  H362  single  0.860  0.020  1.020

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
 GVL  OXT   C    CA    117.28  3.000
 GVL  OXT   C    O     126.95  3.000
 GVL  CA    C    O     120.80  1.700
 GVL  HA    CA   CB    109.00  3.000
 GVL  HA    CA   N     110.00  3.000
 GVL  CB    CA   N     110.50  1.700
 GVL  HA    CA   C     109.00  3.000
 GVL  CB    CA   C     110.10  1.900
 GVL  N     CA   C     111.00  2.800
 GVL  HN2   N    HN1   107.06  3.000
 GVL  HN2   N    CA    108.53  3.000
 GVL  HN1   N    CA    109.86  3.000
 GVL  HBC2  CB   HBC1  107.36  3.000
 GVL  HBC2  CB   O25   110.09  3.000
 GVL  HBC1  CB   O25   111.17  3.000
 GVL  HBC2  CB   CA    109.71  3.000
 GVL  HBC1  CB   CA    109.06  3.000
 GVL  O25   CB   CA    109.42  3.000
 GVL  P24   O25  CB    119.31  3.000
 GVL  O27   P24  O26   109.13  3.000
 GVL  O27   P24  O23   105.98  3.000
 GVL  O26   P24  O23   121.39  3.000
 GVL  O27   P24  O25   102.88  3.000
 GVL  O26   P24  O25   104.50  3.000
 GVL  O23   P24  O25   111.50  3.000
 GVL  C28   O27  P24   121.17  3.000
 GVL  H282  C28  H281  106.29  3.000
 GVL  H282  C28  C29   108.24  3.000
 GVL  H281  C28  C29   110.27  3.000
 GVL  H282  C28  O27   107.94  3.000
 GVL  H281  C28  O27   111.99  3.000
 GVL  C29   C28  O27   111.85  3.000
 GVL  C32   C29  C31   111.52  3.000
 GVL  C32   C29  C30   111.03  3.000
 GVL  C31   C29  C30   109.62  3.000
 GVL  C32   C29  C28   109.06  3.000
 GVL  C31   C29  C28   108.66  3.000
 GVL  C30   C29  C28   106.80  3.000
 GVL  H303  C30  H302  107.07  3.000
 GVL  H303  C30  H301  108.09  3.000
 GVL  H302  C30  H301  107.69  3.000
 GVL  H303  C30  C29   111.51  3.000
 GVL  H302  C30  C29   110.48  3.000
 GVL  H301  C30  C29   111.80  3.000
 GVL  H313  C31  H312  107.69  3.000
 GVL  H313  C31  H311  107.68  3.000
 GVL  H312  C31  H311  107.41  3.000
 GVL  H313  C31  C29   111.99  3.000
 GVL  H312  C31  C29   109.84  3.000
 GVL  H311  C31  C29   112.02  3.000
 GVL  H32   C32  C34   105.32  3.000
 GVL  H32   C32  O33   111.12  3.000
 GVL  C34   C32  O33   108.67  3.000
 GVL  H32   C32  C29   107.44  3.000
 GVL  C34   C32  C29   111.91  3.000
 GVL  O33   C32  C29   112.17  3.000
 GVL  H33   O33  C32   108.47  3.000
 GVL  N36   C34  O35   122.93  3.000
 GVL  N36   C34  C32   115.13  3.000
 GVL  O35   C34  C32   121.94  3.000
 GVL  H362  N36  H361  118.56  3.000
 GVL  H362  N36  C34   120.23  3.000
 GVL  H361  N36  C34   120.64  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
 GVL  CONST_01  H361  N36  C34  C32     0.00   0.0  0
 GVL  CONST_02  H362  N36  C34  C32   180.00   0.0  0
 GVL  Var_01    O23   P24  O25  CB     42.83  30.0  3
 GVL  Var_02    C29   C28  O27  P24  -118.49  30.0  3
 GVL  Var_03    C30   C29  C28  O27   179.14  30.0  3
 GVL  Var_04    HBC1  CB   O25  P24    51.20  30.0  1
 GVL  Var_05    H301  C30  C29  C28   -66.37  30.0  3
 GVL  Var_06    H311  C31  C29  C28  -171.97  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
 GVL  chir_01  CA   C    N    CB   negativ
 GVL  chir_03  C32  C29  O33  C34  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
 GVL  plan-1  C32   0.020
 GVL  plan-1  C34   0.020
 GVL  plan-1  O35   0.020
 GVL  plan-1  N36   0.020
 GVL  plan-1  H361  0.020
 GVL  plan-1  H362  0.020
 GVL  plan-2  O     0.020
 GVL  plan-2  C     0.020
 GVL  plan-2  CA    0.020
 GVL  plan-2  OXT   0.020

