# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 15:00:23 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: 2-methylpropyl hydrogen (R)-methylphosphonate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)CO[P](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
 VR  VR  '2-methylpropyl hydrogen (R)-methylphosphonate'  ligand  21  9  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VR
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
 VR  C4    C  CH3    0  -0.662   3.5493  -0.8556  -0.1323
 VR  C3    C  CH1    0  -0.275   2.4086   0.0170   0.3811
 VR  C5    C  CH3    0  -0.651   2.6292   1.4773   0.0027
 VR  C2    C  CH2    0  -0.110   1.0878  -0.5134  -0.1556
 VR  O2    O  O2     0  -0.631   0.0134   0.2398   0.3700
 VR  P1    P  P      0   1.248  -1.5305  -0.2732   0.0497
 VR  C1    C  CH3    0  -0.947  -2.4095   1.1477   0.7709
 VR  O1    O  O      0  -0.815  -1.8092  -1.5178   0.8536
 VR  O3    O  OP    -1  -0.818  -1.7346  -0.3125  -1.4436
 VR  H41C  H  HCH3   0   0.231   4.5081  -0.5218   0.2662
 VR  H42C  H  HCH3   0   0.226   3.4185  -1.9010   0.1537
 VR  H43C  H  HCH3   0   0.215   3.6146  -0.8150  -1.2225
 VR  H3    H  HCH1   0   0.217   2.3838  -0.0628   1.4741
 VR  H51C  H  HCH3   0   0.229   1.8330   2.1206   0.3769
 VR  H52C  H  HCH3   0   0.223   3.5725   1.8470   0.4081
 VR  H53C  H  HCH3   0   0.210   2.6701   1.5922  -1.0837
 VR  H21C  H  HCH2   0   0.187   1.0978  -0.4612  -1.2528
 VR  H22C  H  HCH2   0   0.199   0.9885  -1.5735   0.1120
 VR  H11C  H  HCH3   0   0.240  -2.1380   2.0822   0.2799
 VR  H12C  H  HCH3   0   0.243  -3.4838   1.0059   0.6442
 VR  H13C  H  HCH3   0   0.240  -2.2118   1.2497   1.8380

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
 VR  C4  C3    single  1.525  0.020  1.525
 VR  C3  C5    single  1.525  0.020  1.525
 VR  C3  C2    single  1.521  0.020  1.521
 VR  C2  O2    single  1.413  0.020  1.413
 VR  O2  P1    single  1.658  0.020  1.658
 VR  P1  C1    single  1.820  0.020  1.820
 VR  P1  O1    deloc   1.508  0.020  1.508
 VR  P1  O3    deloc   1.508  0.020  1.508
 VR  C4  H41C  single  0.970  0.020  1.090
 VR  C4  H42C  single  0.970  0.020  1.090
 VR  C4  H43C  single  0.970  0.020  1.090
 VR  C3  H3    single  0.970  0.020  1.090
 VR  C5  H51C  single  0.970  0.020  1.090
 VR  C5  H52C  single  0.970  0.020  1.090
 VR  C5  H53C  single  0.970  0.020  1.090
 VR  C2  H21C  single  0.970  0.020  1.090
 VR  C2  H22C  single  0.970  0.020  1.090
 VR  C1  H11C  single  0.970  0.020  1.090
 VR  C1  H12C  single  0.970  0.020  1.090
 VR  C1  H13C  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
 VR  H43C  C4  H42C  107.70  3.000
 VR  H43C  C4  H41C  107.49  3.000
 VR  H42C  C4  H41C  107.62  3.000
 VR  H43C  C4  C3    111.05  3.000
 VR  H42C  C4  C3    111.72  3.000
 VR  H41C  C4  C3    111.06  3.000
 VR  H3    C3  C2    107.87  3.000
 VR  H3    C3  C5    108.69  3.000
 VR  C2    C3  C5    111.84  3.000
 VR  H3    C3  C4    108.11  3.000
 VR  C2    C3  C4    109.34  3.000
 VR  C5    C3  C4    110.87  3.000
 VR  H53C  C5  H52C  107.53  3.000
 VR  H53C  C5  H51C  107.85  3.000
 VR  H52C  C5  H51C  107.70  3.000
 VR  H53C  C5  C3    110.66  3.000
 VR  H52C  C5  C3    110.93  3.000
 VR  H51C  C5  C3    111.99  3.000
 VR  H22C  C2  H21C  106.86  3.000
 VR  H22C  C2  O2    110.81  3.000
 VR  H21C  C2  O2    110.67  3.000
 VR  H22C  C2  C3    109.22  3.000
 VR  H21C  C2  C3    109.15  3.000
 VR  O2    C2  C3    110.06  3.000
 VR  P1    O2  C2    118.10  3.000
 VR  O3    P1  O1    118.79  3.000
 VR  O3    P1  C1    110.34  3.000
 VR  O1    P1  C1    110.12  3.000
 VR  O3    P1  O2    108.99  3.000
 VR  O1    P1  O2    108.93  3.000
 VR  C1    P1  O2     97.56  3.000
 VR  H13C  C1  H12C  107.73  3.000
 VR  H13C  C1  H11C  108.40  3.000
 VR  H12C  C1  H11C  107.72  3.000
 VR  H13C  C1  P1    111.93  3.000
 VR  H12C  C1  P1    109.15  3.000
 VR  H11C  C1  P1    111.75  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
 VR  Var_01  O2    C2  C3  C4   176.79  30.0  3
 VR  Var_02  C1    P1  O2  C2  -173.37  30.0  3
 VR  Var_03  H51C  C5  C3  C4  -178.95  30.0  3
 VR  Var_04  H41C  C4  C3  C5    58.34  30.0  3
 VR  Var_05  H11C  C1  P1  O2    60.11  30.0  3

