# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 05:08:13 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: butyl hydrogen (R)-methylphosphonate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCO[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
 CVX  CVX  'butyl hydrogen (R)-methylphosphonate'  ligand  21  9  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CVX
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
 CVX  C5    C  CH3    0  -0.660   4.6625  -0.3633   0.0191
 CVX  C4    C  CH2    0  -0.430   3.3703   0.4416   0.0072
 CVX  C3    C  CH2    0  -0.451   2.1320  -0.4464   0.0464
 CVX  C2    C  CH2    0  -0.125   0.8474   0.3593   0.0218
 CVX  O3    O  O2     0  -0.636  -0.2594  -0.5177   0.1210
 CVX  P     P  P      0   1.247  -1.7542   0.0582  -0.3080
 CVX  C1    C  CH3    0  -0.949  -2.7404  -1.3279   0.3390
 CVX  O2    O  O      0  -0.812  -1.8490   0.1007  -1.8120
 CVX  OX0   O  OP    -1  -0.818  -2.0365   1.3163   0.4730
 CVX  H51C  H  HCH3   0   0.227   5.5397   0.2841  -0.0020
 CVX  H52C  H  HCH3   0   0.217   4.7304  -0.9833   0.9152
 CVX  H53C  H  HCH3   0   0.217   4.7205  -1.0271  -0.8456
 CVX  H41C  H  HCH2   0   0.215   3.3558   1.1243   0.8621
 CVX  H42C  H  HCH2   0   0.215   3.3398   1.0728  -0.8863
 CVX  H31C  H  HCH2   0   0.215   2.1475  -1.1334  -0.8057
 CVX  H32C  H  HCH2   0   0.216   2.1569  -1.0648   0.9499
 CVX  H21C  H  HCH2   0   0.195   0.8440   1.0761   0.8517
 CVX  H22C  H  HCH2   0   0.191   0.8086   0.9470  -0.9049
 CVX  H11C  H  HCH3   0   0.240  -2.6478  -1.4202   1.4211
 CVX  H12C  H  HCH3   0   0.244  -3.7929  -1.1580   0.1081
 CVX  H13C  H  HCH3   0   0.242  -2.4520  -2.2771  -0.1130

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
 CVX  C5  C4    single  1.522  0.020  1.522
 CVX  C4  C3    single  1.524  0.020  1.524
 CVX  C3  C2    single  1.517  0.020  1.517
 CVX  C2  O3    single  1.416  0.020  1.416
 CVX  O3  P     single  1.658  0.020  1.658
 CVX  P   C1    single  1.820  0.020  1.820
 CVX  P   O2    deloc   1.508  0.020  1.508
 CVX  P   OX0   deloc   1.508  0.020  1.508
 CVX  C5  H51C  single  0.970  0.020  1.090
 CVX  C5  H52C  single  0.970  0.020  1.090
 CVX  C5  H53C  single  0.970  0.020  1.090
 CVX  C4  H41C  single  0.970  0.020  1.090
 CVX  C4  H42C  single  0.970  0.020  1.090
 CVX  C3  H31C  single  0.970  0.020  1.090
 CVX  C3  H32C  single  0.970  0.020  1.090
 CVX  C2  H21C  single  0.970  0.020  1.090
 CVX  C2  H22C  single  0.970  0.020  1.090
 CVX  C1  H11C  single  0.970  0.020  1.090
 CVX  C1  H12C  single  0.970  0.020  1.090
 CVX  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
 CVX  H53C  C5  H52C  107.55  3.000
 CVX  H53C  C5  H51C  107.64  3.000
 CVX  H52C  C5  H51C  107.64  3.000
 CVX  H53C  C5  C4    111.12  3.000
 CVX  H52C  C5  C4    111.07  3.000
 CVX  H51C  C5  C4    111.64  3.000
 CVX  H42C  C4  H41C  106.12  3.000
 CVX  H42C  C4  C3    109.53  3.000
 CVX  H41C  C4  C3    109.43  3.000
 CVX  H42C  C4  C5    109.57  3.000
 CVX  H41C  C4  C5    109.57  3.000
 CVX  C3    C4  C5    112.42  3.000
 CVX  H32C  C3  H31C  106.71  3.000
 CVX  H32C  C3  C2    109.43  3.000
 CVX  H31C  C3  C2    109.43  3.000
 CVX  H32C  C3  C4    109.38  3.000
 CVX  H31C  C3  C4    109.52  3.000
 CVX  C2    C3  C4    112.22  3.000
 CVX  H22C  C2  H21C  106.78  3.000
 CVX  H22C  C2  O3    111.29  3.000
 CVX  H21C  C2  O3    110.45  3.000
 CVX  H22C  C2  C3    109.15  3.000
 CVX  H21C  C2  C3    109.73  3.000
 CVX  O3    C2  C3    109.39  3.000
 CVX  P     O3  C2    118.13  3.000
 CVX  OX0   P   O2    118.79  3.000
 CVX  OX0   P   C1    110.49  3.000
 CVX  O2    P   C1    110.01  3.000
 CVX  OX0   P   O3    108.94  3.000
 CVX  O2    P   O3    108.94  3.000
 CVX  C1    P   O3     97.58  3.000
 CVX  H13C  C1  H12C  107.64  3.000
 CVX  H13C  C1  H11C  108.39  3.000
 CVX  H12C  C1  H11C  107.77  3.000
 CVX  H13C  C1  P     111.87  3.000
 CVX  H12C  C1  P     109.21  3.000
 CVX  H11C  C1  P     111.80  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
 CVX  Var_01  C2    C3  C4  C5  -179.48  30.0  3
 CVX  Var_02  O3    C2  C3  C4  -177.38  30.0  3
 CVX  Var_03  C1    P   O3  C2  -169.02  30.0  3
 CVX  Var_04  H51C  C5  C4  C3  -179.59  30.0  3
 CVX  Var_05  H11C  C1  P   O3    63.42  30.0  3

