# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 23 19:33:35 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: [(1R)-1-amino-2-methylpropyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[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
 PVA  PVA  '[(1R)-1-amino-2-methylpropyl]phosphonic acid'  ligand  21  9  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PVA
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
 PVA  C1    C  CH1   0  -0.365  -0.5962   0.6826   0.4427
 PVA  C2    C  CH1   0  -0.248   0.0323   0.2470   1.7823
 PVA  C3    C  CH3   0  -0.662  -0.0933  -1.2448   2.0764
 PVA  CM    C  CH3   0  -0.669   1.4706   0.7221   1.9680
 PVA  N     N  NH2   0  -0.798  -2.0483   0.5833   0.3863
 PVA  P     P  P     0   1.370  -0.0327  -0.1991  -1.0524
 PVA  O1P   O  O     0  -0.720  -0.5414  -1.5847  -1.2043
 PVA  O2P   O  OH1   0  -0.748  -0.4773   0.8392  -2.1990
 PVA  O3P   O  OH1   0  -0.744   1.5783  -0.2247  -1.0866
 PVA  H1    H  HCH1  0   0.283  -0.3373   1.7364   0.2924
 PVA  H2    H  HCH1  0   0.240  -0.5709   0.7784   2.5279
 PVA  H31   H  HCH3  0   0.235   0.2130  -1.4474   3.1030
 PVA  H32   H  HCH3  0   0.224  -1.1179  -1.6041   1.9701
 PVA  H33   H  HCH3  0   0.223   0.5413  -1.8438   1.4222
 PVA  HM1   H  HCH3  0   0.223   2.1792   0.1462   1.3742
 PVA  HM2   H  HCH3  0   0.229   1.5838   1.7752   1.7027
 PVA  HM3   H  HCH3  0   0.235   1.7657   0.6150   3.0127
 PVA  HN1   H  HNH2  0   0.351  -2.3485  -0.3585   0.6055
 PVA  HN2   H  HNH2  0   0.362  -2.4510   1.1844   1.0947
 PVA  HOP2  H  HOH1  0   0.491  -0.4385   0.4729  -3.0932
 PVA  HOP3  H  HOH1  0   0.488   2.0090   0.6397  -1.0983

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
 PVA  C1   C2    single  1.543  0.020  1.543
 PVA  C1   N     single  1.457  0.020  1.457
 PVA  C1   P     single  1.825  0.020  1.825
 PVA  C1   H1    single  0.970  0.020  1.090
 PVA  C2   C3    single  1.526  0.020  1.526
 PVA  C2   CM    single  1.526  0.020  1.526
 PVA  C2   H2    single  0.970  0.020  1.090
 PVA  C3   H31   single  0.970  0.020  1.090
 PVA  C3   H32   single  0.970  0.020  1.090
 PVA  C3   H33   single  0.970  0.020  1.090
 PVA  CM   HM1   single  0.970  0.020  1.090
 PVA  CM   HM2   single  0.970  0.020  1.090
 PVA  CM   HM3   single  0.970  0.020  1.090
 PVA  N    HN1   single  0.890  0.020  1.040
 PVA  N    HN2   single  0.890  0.020  1.040
 PVA  P    O1P   double  1.484  0.020  1.484
 PVA  P    O2P   single  1.610  0.020  1.610
 PVA  P    O3P   single  1.611  0.020  1.611
 PVA  O2P  HOP2  single  0.850  0.020  0.980
 PVA  O3P  HOP3  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
 PVA  H1    C1   P    106.23  3.000
 PVA  H1    C1   N    107.21  3.000
 PVA  P     C1   N    104.08  3.000
 PVA  H1    C1   C2   107.13  3.000
 PVA  P     C1   C2   116.69  3.000
 PVA  N     C1   C2   114.87  3.000
 PVA  H2    C2   CM   106.55  3.000
 PVA  H2    C2   C3   107.31  3.000
 PVA  CM    C2   C3   111.01  3.000
 PVA  H2    C2   C1   103.27  3.000
 PVA  CM    C2   C1   113.69  3.000
 PVA  C3    C2   C1   114.21  3.000
 PVA  H33   C3   H32  107.89  3.000
 PVA  H33   C3   H31  107.41  3.000
 PVA  H32   C3   H31  107.12  3.000
 PVA  H33   C3   C2   111.93  3.000
 PVA  H32   C3   C2   112.37  3.000
 PVA  H31   C3   C2   109.88  3.000
 PVA  HM3   CM   HM2  107.42  3.000
 PVA  HM3   CM   HM1  107.11  3.000
 PVA  HM2   CM   HM1  108.06  3.000
 PVA  HM3   CM   C2   109.94  3.000
 PVA  HM2   CM   C2   111.62  3.000
 PVA  HM1   CM   C2   112.47  3.000
 PVA  HN2   N    HN1  106.43  3.000
 PVA  HN2   N    C1   109.20  3.000
 PVA  HN1   N    C1   110.52  3.000
 PVA  O3P   P    O2P  105.74  3.000
 PVA  O3P   P    O1P  109.01  3.000
 PVA  O2P   P    O1P  115.77  3.000
 PVA  O3P   P    C1   109.50  3.000
 PVA  O2P   P    C1   100.76  3.000
 PVA  O1P   P    C1   115.42  3.000
 PVA  HOP2  O2P  P    113.78  3.000
 PVA  HOP3  O3P  P    115.59  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
 PVA  Var_01  H31  C3  C2  C1  -170.21  30.0  3
 PVA  Var_02  HM1  CM  C2  C1   -75.44  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
 PVA  chir_01  C1  C2  N  P  positiv

