# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 10:19:55 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: 2-aminoethyl (2R)-2,3-dihydroxypropyl hydrogen (S)-phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCO[P@@](O)(=O)OC[C@H](O)CO
#
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
 GPE  GPE  '2-aminoethyl (2R)-2,3-dihydroxypropyl hydrogen (S)-phosphate'  ligand  26  13  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_GPE
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
 GPE  P     P  P      0   1.337  -1.0566   0.5931   0.8968
 GPE  O11   O  O2     0  -0.614  -0.2237  -0.0367  -0.3712
 GPE  O12   O  O2     0  -0.619  -0.1417  -0.1945   2.0047
 GPE  O14   O  OP    -1  -0.804  -2.4583   0.0619   0.9138
 GPE  O13   O  O      0  -0.799  -0.8281   2.0718   0.9775
 GPE  C1    C  CH2    0  -0.159  -0.5696   0.4211  -1.6608
 GPE  C2    C  CH1    0  -0.044   0.2121  -0.3694  -2.6980
 GPE  C3    C  CH2    0  -0.163  -0.2087   0.0682  -4.0921
 GPE  O31   O  OH1    0  -0.669   0.4314  -0.7479  -5.0425
 GPE  O21   O  OH1    0  -0.658   1.6037  -0.2790  -2.5049
 GPE  C11   C  CH2    0  -0.151  -0.5905  -0.1918   3.3521
 GPE  C12   C  CH2    0  -0.314   0.5356  -0.6686   4.2407
 GPE  N     N  NH2    0  -0.800   1.6471   0.2685   4.2325
 GPE  H11   H  HCH2   0   0.210  -1.6416   0.2913  -1.8511
 GPE  H12   H  HCH2   0   0.207  -0.3506   1.4920  -1.7678
 GPE  H2    H  HCH1   0   0.230  -0.0349  -1.4301  -2.5801
 GPE  H31   H  HCH2   0   0.199  -1.3017  -0.0024  -4.1672
 GPE  H32   H  HCH2   0   0.194   0.0489   1.1289  -4.2282
 GPE  HO1   H  HOH1   0   0.455   0.1652  -0.4508  -5.9170
 GPE  HO2   H  HOH1   0   0.442   1.8683   0.6424  -2.6027
 GPE  H111  H  HCH2   0   0.211  -1.4544  -0.8535   3.4710
 GPE  H112  H  HCH2   0   0.201  -0.8946   0.8142   3.6648
 GPE  H121  H  HCH2   0   0.198   0.8098  -1.6921   3.9467
 GPE  H122  H  HCH2   0   0.223   0.1405  -0.7365   5.2574
 GPE  HN1   H  HNH2   0   0.348   2.3852  -0.0807   4.8297
 GPE  HN2   H  HNH2   0   0.339   2.0442   0.3061   3.3023

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
 GPE  P    O11   single  1.643  0.020  1.643
 GPE  P    O12   single  1.639  0.020  1.639
 GPE  P    O14   deloc   1.499  0.020  1.499
 GPE  P    O13   deloc   1.499  0.020  1.499
 GPE  O11  C1    single  1.411  0.020  1.411
 GPE  O12  C11   single  1.420  0.020  1.420
 GPE  C1   C2    single  1.520  0.020  1.520
 GPE  C1   H11   single  0.970  0.020  1.090
 GPE  C1   H12   single  0.970  0.020  1.090
 GPE  C2   C3    single  1.520  0.020  1.520
 GPE  C2   O21   single  1.408  0.020  1.408
 GPE  C2   H2    single  0.970  0.020  1.090
 GPE  C3   O31   single  1.407  0.020  1.407
 GPE  C3   H31   single  0.970  0.020  1.090
 GPE  C3   H32   single  0.970  0.020  1.090
 GPE  O31  HO1   single  0.850  0.020  0.980
 GPE  O21  HO2   single  0.850  0.020  0.980
 GPE  C11  C12   single  1.512  0.020  1.512
 GPE  C11  H111  single  0.970  0.020  1.090
 GPE  C11  H112  single  0.970  0.020  1.090
 GPE  C12  N     single  1.454  0.020  1.454
 GPE  C12  H121  single  0.970  0.020  1.090
 GPE  C12  H122  single  0.970  0.020  1.090
 GPE  N    HN1   single  0.890  0.020  1.040
 GPE  N    HN2   single  0.890  0.020  1.040

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
 GPE  O13   P    O14   119.45  3.000
 GPE  O13   P    O12   110.65  3.000
 GPE  O14   P    O12   110.13  3.000
 GPE  O13   P    O11   110.04  3.000
 GPE  O14   P    O11   110.31  3.000
 GPE  O12   P    O11    93.13  3.000
 GPE  C1    O11  P     117.17  3.000
 GPE  C11   O12  P     117.66  3.000
 GPE  H12   C1   H11   107.07  3.000
 GPE  H12   C1   C2    109.75  3.000
 GPE  H11   C1   C2    108.82  3.000
 GPE  H12   C1   O11   110.88  3.000
 GPE  H11   C1   O11   111.09  3.000
 GPE  C2    C1   O11   109.19  3.000
 GPE  H2    C2   O21   105.68  3.000
 GPE  H2    C2   C3    108.36  3.000
 GPE  O21   C2   C3    112.39  3.000
 GPE  H2    C2   C1    108.30  3.000
 GPE  O21   C2   C1    112.40  3.000
 GPE  C3    C2   C1    109.49  3.000
 GPE  H32   C3   H31   106.66  3.000
 GPE  H32   C3   O31   111.66  3.000
 GPE  H31   C3   O31   111.69  3.000
 GPE  H32   C3   C2    109.04  3.000
 GPE  H31   C3   C2    108.65  3.000
 GPE  O31   C3   C2    109.06  3.000
 GPE  HO1   O31  C3    108.02  3.000
 GPE  HO2   O21  C2    108.60  3.000
 GPE  H112  C11  H111  107.74  3.000
 GPE  H112  C11  C12   109.17  3.000
 GPE  H111  C11  C12   109.48  3.000
 GPE  H112  C11  O12   111.09  3.000
 GPE  H111  C11  O12   110.57  3.000
 GPE  C12   C11  O12   108.76  3.000
 GPE  H122  C12  H121  106.32  3.000
 GPE  H122  C12  N     108.76  3.000
 GPE  H121  C12  N     114.07  3.000
 GPE  H122  C12  C11   107.28  3.000
 GPE  H121  C12  C11   108.79  3.000
 GPE  N     C12  C11   111.28  3.000
 GPE  HN2   N    HN1   105.61  3.000
 GPE  HN2   N    C12   109.21  3.000
 GPE  HN1   N    C12   109.39  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
 GPE  Var_01  C2   C1   O11  P    -174.63  30.0  3
 GPE  Var_02  C12  C11  O12  P    -166.57  30.0  3
 GPE  Var_03  N    C12  C11  O12    65.74  30.0  3
 GPE  Var_04  HN1  N    C12  C11  -179.61  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
 GPE  chir_02  C2  C1  C3  O21  negativ

