# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  1 15:59:35 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: N-acetyl-5-oxo-5-(phosphonooxy)-L-norvaline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H](CCC(=O)O[P](O)(O)=O)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
 X2W  X2W  N-acetyl-5-oxo-5-(phosphonooxy)-L-norvaline  L-peptide  29  17  .  2022-09-22  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_X2W
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
 X2W  CA    C  CH1   0  -0.194   2.4036   0.4373  -0.3004
 X2W  CB    C  CH2   0  -0.470   1.0199   0.9332   0.1285
 X2W  CG    C  CH2   0  -0.580  -0.0804   0.0168  -0.3823
 X2W  C3    C  C     0   0.615  -1.4455   0.4727   0.0322
 X2W  C     C  C     0   0.550   3.4736   1.4460   0.0989
 X2W  O     O  O     0  -0.428   4.2735   1.2790   0.9807
 X2W  OXT   O  OH1   0  -0.590   3.3959   2.5439  -0.6385
 X2W  C1    C  C     0   0.534   3.6649  -1.6433  -0.1746
 X2W  O1    O  O     0  -0.498   4.3267  -1.3582  -1.1616
 X2W  P     P  P     0   1.457  -3.9879  -0.1720  -0.0699
 X2W  O2P   O  OH1   0  -0.722  -4.4303  -1.6151  -0.5653
 X2W  O1P   O  O     0  -0.682  -4.5719   1.0009  -0.7332
 X2W  O3P   O  OH1   0  -0.728  -4.1744  -0.1062   1.5045
 X2W  N1    N  NH1   0  -0.629   2.6771  -0.8463   0.2806
 X2W  C2    C  CH3   0  -0.779   3.8870  -2.9107   0.6080
 X2W  O2    O  O     0  -0.403  -1.7177   1.4865   0.6057
 X2W  OE2   O  O2    0  -0.585  -2.3914  -0.4267  -0.3373
 X2W  HA    H  HCH1  0   0.295   2.4225   0.3465  -1.3902
 X2W  HB1C  H  HCH2  0   0.264   0.9810   1.0035   1.2187
 X2W  HB2C  H  HCH2  0   0.279   0.8682   1.9404  -0.2585
 X2W  H1    H  HNH1  0   0.407   2.2530  -1.0624   1.1692
 X2W  HG1C  H  HCH2  0   0.302  -0.0734  -0.0286  -1.4748
 X2W  HG2C  H  HCH2  0   0.296   0.0562  -1.0131  -0.0432
 X2W  HXT   H  HOH1  0   0.486   4.0527   3.1942  -0.3467
 X2W  H21C  H  HCH3  0   0.270   4.8830  -2.8896   1.0513
 X2W  H22C  H  HCH3  0   0.251   3.1601  -3.0623   1.4033
 X2W  H23C  H  HCH3  0   0.268   3.8489  -3.7657  -0.0660
 X2W  H3P   H  HOH1  0   0.503  -3.9046  -0.8873   2.0069
 X2W  H2P   H  HOH1  0   0.510  -5.3858  -1.7207  -0.6755

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
 X2W  CA   CB    single  1.530  0.020  1.530
 X2W  CA   C     single  1.525  0.021  1.525
 X2W  CA   N1    single  1.435  0.020  1.435
 X2W  CB   CG    single  1.520  0.020  1.520
 X2W  C    O     double  1.231  0.020  1.231
 X2W  C    OXT   single  1.325  0.020  1.325
 X2W  C1   O1    double  1.222  0.020  1.222
 X2W  C1   N1    single  1.348  0.020  1.348
 X2W  C1   C2    single  1.506  0.020  1.506
 X2W  P    O3P   single  1.587  0.020  1.587
 X2W  P    O2P   single  1.589  0.020  1.589
 X2W  P    O1P   double  1.469  0.020  1.469
 X2W  P    OE2   single  1.639  0.020  1.639
 X2W  C3   O2    double  1.196  0.020  1.196
 X2W  C3   CG    single  1.498  0.020  1.498
 X2W  C3   OE2   single  1.357  0.020  1.357
 X2W  CA   HA    single  0.970  0.020  0.970
 X2W  CB   HB1C  single  0.970  0.020  1.090
 X2W  CB   HB2C  single  0.970  0.020  1.090
 X2W  N1   H1    single  0.860  0.020  1.020
 X2W  CG   HG1C  single  0.970  0.020  1.090
 X2W  CG   HG2C  single  0.970  0.020  1.090
 X2W  OXT  HXT   single  0.850  0.020  0.980
 X2W  C2   H21C  single  0.970  0.020  1.090
 X2W  C2   H22C  single  0.970  0.020  1.090
 X2W  C2   H23C  single  0.970  0.020  1.090
 X2W  O3P  H3P   single  0.850  0.020  0.980
 X2W  O2P  H2P   single  0.850  0.020  0.980

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
 X2W  HA    CA   N1    109.02  3.000
 X2W  HA    CA   C     109.00  3.000
 X2W  N1    CA   C     110.62  3.000
 X2W  HA    CA   CB    109.00  3.000
 X2W  N1    CA   CB    110.39  3.000
 X2W  C     CA   CB    110.10  1.900
 X2W  HB2C  CB   HB1C  106.85  3.000
 X2W  HB2C  CB   CG    109.70  3.000
 X2W  HB1C  CB   CG    110.37  3.000
 X2W  HB2C  CB   CA    109.01  3.000
 X2W  HB1C  CB   CA    109.41  3.000
 X2W  CG    CB   CA    111.39  3.000
 X2W  HG2C  CG   HG1C  105.67  3.000
 X2W  HG2C  CG   C3    108.36  3.000
 X2W  HG1C  CG   C3    107.16  3.000
 X2W  HG2C  CG   CB    111.92  3.000
 X2W  HG1C  CG   CB    110.86  3.000
 X2W  C3    CG   CB    112.53  3.000
 X2W  OE2   C3   O2    122.27  3.000
 X2W  OE2   C3   CG    111.00  3.000
 X2W  O2    C3   CG    126.74  3.000
 X2W  OXT   C    O     124.22  3.000
 X2W  OXT   C    CA    111.19  3.000
 X2W  O     C    CA    120.80  1.700
 X2W  HXT   OXT  C     110.41  3.000
 X2W  C2    C1   N1    115.47  3.000
 X2W  C2    C1   O1    122.43  3.000
 X2W  N1    C1   O1    122.10  3.000
 X2W  OE2   P    O3P   106.43  3.000
 X2W  OE2   P    O1P   115.97  3.000
 X2W  O3P   P    O1P   111.61  3.000
 X2W  OE2   P    O2P    94.55  3.000
 X2W  O1P   P    O2P   118.29  3.000
 X2W  O3P   P    O2P   108.32  3.000
 X2W  H2P   O2P  P     114.18  3.000
 X2W  H3P   O3P  P     116.69  3.000
 X2W  H1    N1   C1    118.62  3.000
 X2W  H1    N1   CA    117.93  3.000
 X2W  C1    N1   CA    122.11  3.000
 X2W  H23C  C2   H22C  108.64  3.000
 X2W  H23C  C2   H21C  107.38  3.000
 X2W  H22C  C2   H21C  108.41  3.000
 X2W  H23C  C2   C1    109.50  3.000
 X2W  H22C  C2   C1    113.48  3.000
 X2W  H21C  C2   C1    109.25  3.000
 X2W  P     OE2  C3    122.13  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
 X2W  CONST_01  O1    C1   N1   CA    0.00   0.0  0
 X2W  CONST_02  C2    C1   N1   CA  180.00   0.0  0
 X2W  CONST_03  H1    N1   C1   O1  180.00   0.0  0
 X2W  CONST_04  HXT   OXT  C    CA  180.00   0.0  0
 X2W  Var_01    C3    CG   CB   CA  179.54  30.0  3
 X2W  Var_02    O2    C3   CG   CB    5.81  30.0  1
 X2W  Var_03    O3P   P    OE2  C3  -63.20  30.0  2
 X2W  Var_04    H21C  C2   C1   O1   64.14  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
 X2W  chir_01  CA  CB  C  N1  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
 X2W  plan-1  CA   0.020
 X2W  plan-1  C1   0.020
 X2W  plan-1  O1   0.020
 X2W  plan-1  N1   0.020
 X2W  plan-1  C2   0.020
 X2W  plan-1  H1   0.020
 X2W  plan-2  CA   0.020
 X2W  plan-2  C    0.020
 X2W  plan-2  O    0.020
 X2W  plan-2  OXT  0.020
 X2W  plan-2  HXT  0.020
 X2W  plan-3  CG   0.020
 X2W  plan-3  C3   0.020
 X2W  plan-3  O2   0.020
 X2W  plan-3  OE2  0.020

