# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 04:00:59 2022
#   Inital geometry file: a 81 line input string
#   Ligand name: 4-(phosphonomethyl)-L-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccc(C[P](O)(O)=O)cc1)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
 PM3  PM3  4-(phosphonomethyl)-L-phenylalanine  L-peptide  28  17  .  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_PM3
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
 PM3  N     N  NH2    0  -0.797  13.5871  18.9794  13.6083
 PM3  CA    C  CH1    0  -0.189  12.4897  18.4332  14.3848
 PM3  CB    C  CH2    0  -0.520  11.4826  19.4904  14.9021
 PM3  CG    C  CR6    0   0.102  12.1335  20.5578  15.7330
 PM3  CD1   C  CR16   0  -0.311  12.5566  21.7643  15.1784
 PM3  CE1   C  CR16   0  -0.311  13.2116  22.7218  15.9432
 PM3  CD2   C  CR16   0  -0.296  12.3885  20.3553  17.0894
 PM3  CE2   C  CR16   0  -0.299  13.0422  21.3111  17.8511
 PM3  CZ    C  CR6    0   0.161  13.4689  22.5230  17.3001
 PM3  CH4   C  CH2    0  -0.808  14.2242  23.5142  18.1102
 PM3  P     P  P      0   1.171  16.0907  23.1788  18.1349
 PM3  O1    O  OP    -1  -0.894  16.2190  21.7532  18.6856
 PM3  O2    O  O      0  -0.895  16.5375  23.3319  16.6760
 PM3  O3    O  OP    -1  -0.900  16.6326  24.2629  19.0761
 PM3  C     C  C      0   0.397  11.6968  17.3870  13.5666
 PM3  OXT   O  OC    -1  -0.612  11.0748  16.5315  14.2267
 PM3  O     O  O      0  -0.602  11.7044  17.5176  12.3258
 PM3  H     H  HNH2   0   0.334  13.9532  19.8091  14.0603
 PM3  H2    H  HNH2   0   0.322  13.2267  19.2714  12.7081
 PM3  HA    H  HCH1   0   0.201  12.9083  17.9331  15.2653
 PM3  HB2   H  HCH2   0   0.227  10.7164  18.9787  15.4901
 PM3  HB3   H  HCH2   0   0.224  10.9765  19.9424  14.0429
 PM3  HD1   H  HCR6   0   0.231  12.3640  21.9615  14.1292
 PM3  HE1   H  HCR6   0   0.222  13.5182  23.6513  15.4769
 PM3  HD2   H  HCR6   0   0.227  12.0695  19.4295  17.5572
 PM3  HE2   H  HCR6   0   0.220  13.2174  21.1203  18.9033
 PM3  HH42  H  HCH2   0   0.197  13.8670  23.5017  19.1443
 PM3  HH43  H  HCH2   0   0.198  14.0564  24.5248  17.7259

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
 PM3  N    CA    single    1.458  0.019  1.458
 PM3  N    H     single    0.860  0.020  0.860
 PM3  N    H2    single    0.890  0.020  1.040
 PM3  CA   CB    single    1.530  0.020  1.530
 PM3  CA   C     single    1.525  0.021  1.525
 PM3  CA   HA    single    0.970  0.020  0.970
 PM3  CB   CG    single    1.501  0.020  1.501
 PM3  CB   HB2   single    0.970  0.020  1.090
 PM3  CB   HB3   single    0.970  0.020  1.090
 PM3  CG   CD1   aromatic  1.394  0.020  1.394
 PM3  CG   CD2   aromatic  1.395  0.020  1.395
 PM3  CD1  CE1   aromatic  1.389  0.020  1.389
 PM3  CD1  HD1   single    0.930  0.020  1.080
 PM3  CE1  CZ    aromatic  1.395  0.020  1.395
 PM3  CE1  HE1   single    0.930  0.020  1.080
 PM3  CD2  CE2   aromatic  1.386  0.020  1.386
 PM3  CD2  HD2   single    0.930  0.020  1.080
 PM3  CE2  CZ    aromatic  1.398  0.020  1.398
 PM3  CE2  HE2   single    0.930  0.020  1.080
 PM3  CZ   CH4   single    1.486  0.020  1.486
 PM3  CH4  P     single    1.897  0.020  1.897
 PM3  CH4  HH42  single    0.970  0.020  1.090
 PM3  CH4  HH43  single    0.970  0.020  1.090
 PM3  P    O1    deloc     1.534  0.020  1.534
 PM3  P    O2    deloc     1.533  0.020  1.533
 PM3  P    O3    deloc     1.535  0.020  1.535
 PM3  C    OXT   deloc     1.247  0.020  1.247
 PM3  C    O     deloc     1.231  0.020  1.231

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
 PM3  H2    N    H     106.80  3.000
 PM3  H2    N    CA    108.36  3.000
 PM3  H     N    CA    114.00  3.000
 PM3  HA    CA   C     109.00  3.000
 PM3  HA    CA   CB    109.00  3.000
 PM3  C     CA   CB    110.10  1.900
 PM3  HA    CA   N     110.00  3.000
 PM3  C     CA   N     111.00  2.800
 PM3  CB    CA   N     110.50  1.700
 PM3  HB3   CB   HB2   106.94  3.000
 PM3  HB3   CB   CG    109.96  3.000
 PM3  HB2   CB   CG    109.82  3.000
 PM3  HB3   CB   CA    108.67  3.000
 PM3  HB2   CB   CA    108.42  3.000
 PM3  CG    CB   CA    112.85  3.000
 PM3  CD2   CG   CD1   117.20  3.000
 PM3  CD2   CG   CB    120.95  3.000
 PM3  CD1   CG   CB    121.80  3.000
 PM3  HD1   CD1  CE1   119.39  3.000
 PM3  HD1   CD1  CG    119.23  3.000
 PM3  CE1   CD1  CG    121.37  3.000
 PM3  HE1   CE1  CZ    119.23  3.000
 PM3  HE1   CE1  CD1   119.17  3.000
 PM3  CZ    CE1  CD1   121.60  3.000
 PM3  HD2   CD2  CE2   119.34  3.000
 PM3  HD2   CD2  CG    119.29  3.000
 PM3  CE2   CD2  CG    121.37  3.000
 PM3  HE2   CE2  CZ    119.08  3.000
 PM3  HE2   CE2  CD2   119.24  3.000
 PM3  CZ    CE2  CD2   121.68  3.000
 PM3  CH4   CZ   CE2   121.22  3.000
 PM3  CH4   CZ   CE1   121.92  3.000
 PM3  CE2   CZ   CE1   116.78  3.000
 PM3  HH43  CH4  HH42  107.00  3.000
 PM3  HH43  CH4  P     108.59  3.000
 PM3  HH42  CH4  P     107.88  3.000
 PM3  HH43  CH4  CZ    110.28  3.000
 PM3  HH42  CH4  CZ    109.98  3.000
 PM3  P     CH4  CZ    112.91  3.000
 PM3  O3    P    O2    114.21  3.000
 PM3  O3    P    O1    114.01  3.000
 PM3  O2    P    O1    114.21  3.000
 PM3  O3    P    CH4   103.33  3.000
 PM3  O2    P    CH4   104.88  3.000
 PM3  O1    P    CH4   104.56  3.000
 PM3  O     C    OXT   126.97  3.000
 PM3  O     C    CA    120.80  1.700
 PM3  OXT   C    CA    116.09  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
 PM3  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 PM3  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 PM3  CONST_03  CE2  CD2  CG   CD1    0.00   0.0  0
 PM3  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 PM3  CONST_05  CD2  CG   CD1  CE1    0.00   0.0  0
 PM3  CONST_06  CD2  CE2  CZ   CE1    0.00   0.0  0
 PM3  CONST_07  CE1  CD1  CG   CB   180.00   0.0  0
 PM3  CONST_08  CE2  CD2  CG   CB   180.00   0.0  0
 PM3  CONST_09  CH4  CZ   CE1  CD1  180.00   0.0  0
 PM3  CONST_10  CH4  CZ   CE2  CD2  180.00   0.0  0
 PM3  CONST_11  HE1  CE1  CD1  CG   180.00   0.0  0
 PM3  CONST_12  HE2  CE2  CD2  CG   180.00   0.0  0
 PM3  CONST_13  HD2  CD2  CG   CD1  180.00   0.0  0
 PM3  CONST_14  HD1  CD1  CG   CD2  180.00   0.0  0
 PM3  Var_01    CD1  CG   CB   CA    94.10  30.0  2
 PM3  Var_02    P    CH4  CZ   CE1  -90.99  30.0  2
 PM3  Var_03    O1   P    CH4  CZ   -57.47  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
 PM3  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
 PM3  plan-1  CB   0.020
 PM3  plan-1  CG   0.020
 PM3  plan-1  CD1  0.020
 PM3  plan-1  CE1  0.020
 PM3  plan-1  CD2  0.020
 PM3  plan-1  CE2  0.020
 PM3  plan-1  CZ   0.020
 PM3  plan-1  CH4  0.020
 PM3  plan-1  HD1  0.020
 PM3  plan-1  HE1  0.020
 PM3  plan-1  HD2  0.020
 PM3  plan-1  HE2  0.020
 PM3  plan-2  CA   0.020
 PM3  plan-2  C    0.020
 PM3  plan-2  OXT  0.020
 PM3  plan-2  O    0.020

