# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 06:41:50 2020
#   Inital geometry file: a 46 line input string
#   Ligand name: [(1R)-1-aminopropyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H](N)[P](O)(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
 3V2  3V2  '[(1R)-1-aminopropyl]phosphonic acid'  ligand  16  8  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3V2
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
 3V2  N   N  NH2    0  -0.808  -0.5829   2.1198   0.2685
 3V2  CA  C  CH1    0  -0.323  -0.6879   0.6720   0.4754
 3V2  CB  C  CH2    0  -0.431  -1.9246   0.0834  -0.2150
 3V2  CG  C  CH3    0  -0.673  -2.3555  -1.2900   0.2805
 3V2  P1  P  P      0   1.166   0.9253  -0.0949  -0.1002
 3V2  O2  O  OP    -1  -0.892   0.7702  -1.6174   0.0372
 3V2  O3  O  O      0  -0.913   1.0389   0.3807  -1.5607
 3V2  O1  O  OP    -1  -0.912   2.0094   0.4803   0.8201
 3V2  H1  H  HNH2   0   0.312  -0.2724   2.2656  -0.6858
 3V2  H2  H  HNH2   0   0.312  -1.5056   2.5382   0.3222
 3V2  H4  H  HCH1   0   0.161  -0.7948   0.4957   1.5562
 3V2  H5  H  HCH2   0   0.185  -2.7636   0.7791  -0.0792
 3V2  H6  H  HCH2   0   0.189  -1.7388   0.0513  -1.2942
 3V2  H7  H  HCH3   0   0.230  -1.5544  -2.0115   0.1383
 3V2  H8  H  HCH3   0   0.196  -2.5966  -1.2623   1.3463
 3V2  H9  H  HCH3   0   0.202  -3.2452  -1.6424  -0.2451

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
 3V2  N   CA  single  1.466  0.020  1.466
 3V2  O3  P1  deloc   1.540  0.020  1.540
 3V2  P1  CA  single  1.877  0.020  1.877
 3V2  P1  O2  deloc   1.537  0.020  1.537
 3V2  CA  CB  single  1.534  0.020  1.534
 3V2  CB  CG  single  1.522  0.020  1.522
 3V2  P1  O1  deloc   1.534  0.020  1.534
 3V2  N   H1  single  0.890  0.020  1.040
 3V2  N   H2  single  0.890  0.020  1.040
 3V2  CA  H4  single  0.970  0.020  1.090
 3V2  CB  H5  single  0.970  0.020  1.090
 3V2  CB  H6  single  0.970  0.020  1.090
 3V2  CG  H7  single  0.970  0.020  1.090
 3V2  CG  H8  single  0.970  0.020  1.090
 3V2  CG  H9  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
 3V2  H2  N   H1  105.60  3.000
 3V2  H2  N   CA  109.55  3.000
 3V2  H1  N   CA  107.26  3.000
 3V2  H4  CA  P1  108.63  3.000
 3V2  H4  CA  CB  107.60  3.000
 3V2  P1  CA  CB  113.47  3.000
 3V2  H4  CA  N   107.69  3.000
 3V2  CB  CA  N   111.91  3.000
 3V2  P1  CA  N   107.37  3.000
 3V2  H6  CB  H5  105.66  3.000
 3V2  H6  CB  CG  110.01  3.000
 3V2  H5  CB  CG  108.36  3.000
 3V2  H6  CB  CA  108.54  3.000
 3V2  H5  CB  CA  108.49  3.000
 3V2  CG  CB  CA  115.33  3.000
 3V2  H9  CG  H8  107.33  3.000
 3V2  H9  CG  H7  108.86  3.000
 3V2  H8  CG  H7  107.87  3.000
 3V2  H9  CG  CB  111.41  3.000
 3V2  H8  CG  CB  110.91  3.000
 3V2  H7  CG  CB  110.33  3.000
 3V2  O1  P1  O3  113.64  3.000
 3V2  O1  P1  O2  112.91  3.000
 3V2  O3  P1  O2  113.47  3.000
 3V2  O1  P1  CA  105.68  3.000
 3V2  O2  P1  CA  106.90  3.000
 3V2  O3  P1  CA  103.19  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
 3V2  Var_01  H7  CG  CB  CA  -59.58  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
 3V2  chir_01  CA  N  P1  CB  positiv

