# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 22:09:09 2022
#   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-L-GLUTAMYL 5-PHOSPHATE"  L-peptide  26  17  .  2022-09-22  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_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  -0.196   2.4289   0.4321  -0.3020
 X2W  CB    C  CH2    0  -0.451   1.0373   0.8807   0.1422
 X2W  CG    C  CH2    0  -0.568  -0.0581  -0.0581  -0.3359
 X2W  C3    C  C      0   0.567  -1.4598   0.3474   0.0791
 X2W  C     C  C      0   0.412   3.4968   1.5069   0.0374
 X2W  O     O  O      0  -0.596   4.3861   1.2057   0.8503
 X2W  OXT   O  OC    -1  -0.617   3.3468   2.5966  -0.5513
 X2W  C1    C  C      0   0.520   3.6872  -1.6653  -0.1996
 X2W  O1    O  O      0  -0.523   4.2715  -1.4630  -1.2588
 X2W  P     P  P      0   1.225  -4.1184  -0.3703  -0.0301
 X2W  O2P   O  OP    -1  -0.875  -4.5461  -1.6285  -0.7596
 X2W  O1P   O  O      0  -0.875  -4.4954   0.9355  -0.6954
 X2W  O3P   O  OP    -1  -0.875  -4.2153  -0.4217   1.4792
 X2W  N1    N  NH1    0  -0.609   2.7299  -0.8571   0.2743
 X2W  C2    C  CH3    0  -0.781   3.9955  -2.8732   0.6522
 X2W  O2    O  O      0  -0.494  -1.6836   1.3503   0.7263
 X2W  OE2   O  O2     0  -0.619  -2.3527  -0.5025  -0.3409
 X2W  HA    H  HCH1   0   0.233   2.4175   0.3158  -1.3898
 X2W  HB1C  H  HCH2   0   0.223   1.0127   0.9671   1.2335
 X2W  HB2C  H  HCH2   0   0.239   0.8666   1.8830  -0.2495
 X2W  H1    H  HNH1   0   0.387   2.3909  -1.0337   1.2067
 X2W  HG1C  H  HCH2   0   0.253  -0.0324  -0.1301  -1.4286
 X2W  HG2C  H  HCH2   0   0.254   0.1179  -1.0770   0.0217
 X2W  H21C  H  HCH3   0   0.262   4.9944  -2.7668   1.0779
 X2W  H22C  H  HCH3   0   0.244   3.2925  -3.0186   1.4704
 X2W  H23C  H  HCH3   0   0.258   3.9999  -3.7698   0.0336

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  1.444  0.020  1.444
 X2W  CB  CG    single  1.520  0.020  1.520
 X2W  C   O     deloc   1.231  0.020  1.231
 X2W  C   OXT   deloc   1.248  0.020  1.248
 X2W  C1  O1    double  1.226  0.020  1.226
 X2W  C1  N1    single  1.340  0.020  1.340
 X2W  C1  C2    single  1.510  0.020  1.510
 X2W  P   O3P   deloc   1.513  0.020  1.513
 X2W  P   O2P   deloc   1.516  0.020  1.516
 X2W  P   O1P   deloc   1.513  0.020  1.513
 X2W  P   OE2   single  1.798  0.020  1.798
 X2W  C3  O2    double  1.214  0.020  1.214
 X2W  C3  CG    single  1.517  0.020  1.517
 X2W  C3  OE2   single  1.302  0.020  1.302
 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  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

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    107.71  3.000
 X2W  HA    CA   C     109.00  3.000
 X2W  N1    CA   C     112.80  3.000
 X2W  HA    CA   CB    109.00  3.000
 X2W  N1    CA   CB    109.63  3.000
 X2W  C     CA   CB    110.10  1.900
 X2W  HB2C  CB   HB1C  106.39  3.000
 X2W  HB2C  CB   CG    110.01  3.000
 X2W  HB1C  CB   CG    110.25  3.000
 X2W  HB2C  CB   CA    107.95  3.000
 X2W  HB1C  CB   CA    109.47  3.000
 X2W  CG    CB   CA    112.56  3.000
 X2W  HG2C  CG   HG1C  105.13  3.000
 X2W  HG2C  CG   C3    107.95  3.000
 X2W  HG1C  CG   C3    108.19  3.000
 X2W  HG2C  CG   CB    110.89  3.000
 X2W  HG1C  CG   CB    109.73  3.000
 X2W  C3    CG   CB    114.50  3.000
 X2W  OE2   C3   O2    125.76  3.000
 X2W  OE2   C3   CG    111.77  3.000
 X2W  O2    C3   CG    122.47  3.000
 X2W  OXT   C    O     127.36  3.000
 X2W  OXT   C    CA    114.76  3.000
 X2W  O     C    CA    120.80  1.700
 X2W  C2    C1   N1    115.40  3.000
 X2W  C2    C1   O1    121.46  3.000
 X2W  N1    C1   O1    123.13  3.000
 X2W  OE2   P    O3P   103.47  3.000
 X2W  OE2   P    O1P   103.43  3.000
 X2W  O3P   P    O1P   116.86  3.000
 X2W  OE2   P    O2P    97.64  3.000
 X2W  O1P   P    O2P   115.74  3.000
 X2W  O3P   P    O2P   115.70  3.000
 X2W  H1    N1   C1    117.52  3.000
 X2W  H1    N1   CA    117.11  3.000
 X2W  C1    N1   CA    123.13  3.000
 X2W  H23C  C2   H22C  108.63  3.000
 X2W  H23C  C2   H21C  107.35  3.000
 X2W  H22C  C2   H21C  108.12  3.000
 X2W  H23C  C2   C1    109.81  3.000
 X2W  H22C  C2   C1    113.52  3.000
 X2W  H21C  C2   C1    109.22  3.000
 X2W  P     OE2  C3    124.73  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  H1    N1   C1   C2      0.00   0.0  0
 X2W  Var_01    C3    CG   CB   CA   -179.91  30.0  3
 X2W  Var_02    O2    C3   CG   CB      0.87  30.0  2
 X2W  Var_03    OE2   C3   CG   CB   -179.05  30.0  2
 X2W  Var_04    P     OE2  C3   CG    179.28  30.0  3
 X2W  Var_05    O3P   P    OE2  C3    -60.94  30.0  2
 X2W  Var_06    O2P   P    OE2  C3   -179.76  30.0  2
 X2W  Var_07    O1P   P    OE2  C3     61.39  30.0  2
 X2W  Var_08    O2    C3   OE2  P      -0.64  30.0  2
 X2W  Var_09    HG1C  CG   CB   CA    -58.04  30.0  3
 X2W  Var_10    HG2C  CG   CB   CA     57.65  30.0  3
 X2W  Var_11    HB1C  CB   CG   C3     57.55  30.0  1
 X2W  Var_12    HB2C  CB   CG   C3    -59.48  30.0  1
 X2W  Var_13    H21C  C2   C1   O1     69.12  30.0  3
 X2W  Var_14    H22C  C2   C1   O1   -170.15  30.0  3
 X2W  Var_15    H23C  C2   C1   O1    -48.34  30.0  3
 X2W  Var_16    H21C  C2   C1   N1   -111.76  30.0  3
 X2W  Var_17    H22C  C2   C1   N1      8.97  30.0  3
 X2W  Var_18    H23C  C2   C1   N1    130.78  30.0  3
 X2W  Var_19    HG1C  CG   C3   O2   -121.83  30.0  3
 X2W  Var_20    HG2C  CG   C3   O2    124.89  30.0  3
 X2W  Var_21    HG1C  CG   C3   OE2    58.25  30.0  3
 X2W  Var_22    HG2C  CG   C3   OE2   -55.03  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-3  CG   0.020
 X2W  plan-3  C3   0.020
 X2W  plan-3  O2   0.020
 X2W  plan-3  OE2  0.020

