# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 13:25:23 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: ethyl hydrogen (S)-hexylphosphonate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCC[P@@](O)(=O)OCC
#
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
 HEE  HEE  'ethyl hydrogen (S)-hexylphosphonate'  ligand  30  12  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_HEE
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
 HEE  C1    C  CH2    0  -0.716   0.4128  -0.0959  -0.0590
 HEE  C2    C  CH2    0  -0.423  -0.3399   0.0315   1.2635
 HEE  C3    C  CH2    0  -0.403   0.5642  -0.1038   2.4824
 HEE  C4    C  CH2    0  -0.406  -0.1895   0.0215   3.8002
 HEE  C5    C  CH2    0  -0.418   0.7111  -0.0816   5.0253
 HEE  C6    C  CH3    0  -0.662  -0.0561   0.0497   6.3338
 HEE  P     P  P      0   1.275  -0.7054   0.1303  -1.4834
 HEE  O1P   O  O      0  -0.818  -1.2197   1.5482  -1.5183
 HEE  O2P   O  O2     0  -0.631   0.4166  -0.0661  -2.6905
 HEE  O3P   O  OP    -1  -0.818  -1.7015  -1.0005  -1.5496
 HEE  C1'   C  CH2    0  -0.147  -0.0286   0.0539  -4.0310
 HEE  C2'   C  CH3    0  -0.684   1.1467  -0.1264  -4.9669
 HEE  H11   H  HCH2   0   0.231   1.2129   0.6497  -0.1005
 HEE  H12   H  HCH2   0   0.231   0.8943  -1.0768  -0.1158
 HEE  H21   H  HCH2   0   0.213  -1.1264  -0.7280   1.3084
 HEE  H22   H  HCH2   0   0.212  -0.8495   0.9995   1.2985
 HEE  H31   H  HCH2   0   0.206   1.3486   0.6600   2.4377
 HEE  H32   H  HCH2   0   0.206   1.0806  -1.0700   2.4481
 HEE  H41   H  HCH2   0   0.206  -0.9623  -0.7537   3.8524
 HEE  H42   H  HCH2   0   0.205  -0.7217   0.9795   3.8235
 HEE  H51   H  HCH2   0   0.210   1.4811   0.6943   4.9728
 HEE  H52   H  HCH2   0   0.209   1.2434  -1.0379   5.0050
 HEE  H61   H  HCH3   0   0.225   0.6057  -0.0179   7.1981
 HEE  H62   H  HCH3   0   0.215  -0.5753   1.0086   6.3893
 HEE  H63   H  HCH3   0   0.215  -0.8080  -0.7358   6.4315
 HEE  H1'1  H  HCH2   0   0.197  -0.7969  -0.6958  -4.2514
 HEE  H1'2  H  HCH2   0   0.197  -0.4843   1.0362  -4.1992
 HEE  H2'1  H  HCH3   0   0.225   0.8130  -0.0375  -6.0013
 HEE  H2'2  H  HCH3   0   0.224   1.9105   0.6330  -4.7955
 HEE  H2'3  H  HCH3   0   0.224   1.6057  -1.1086  -4.8481

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
 HEE  C1   C2    single  1.527  0.020  1.527
 HEE  C1   P     single  1.825  0.020  1.825
 HEE  C1   H11   single  0.970  0.020  1.090
 HEE  C1   H12   single  0.970  0.020  1.090
 HEE  C2   C3    single  1.524  0.020  1.524
 HEE  C2   H21   single  0.970  0.020  1.090
 HEE  C2   H22   single  0.970  0.020  1.090
 HEE  C3   C4    single  1.523  0.020  1.523
 HEE  C3   H31   single  0.970  0.020  1.090
 HEE  C3   H32   single  0.970  0.020  1.090
 HEE  C4   C5    single  1.524  0.020  1.524
 HEE  C4   H41   single  0.970  0.020  1.090
 HEE  C4   H42   single  0.970  0.020  1.090
 HEE  C5   C6    single  1.522  0.020  1.522
 HEE  C5   H51   single  0.970  0.020  1.090
 HEE  C5   H52   single  0.970  0.020  1.090
 HEE  C6   H61   single  0.970  0.020  1.090
 HEE  C6   H62   single  0.970  0.020  1.090
 HEE  C6   H63   single  0.970  0.020  1.090
 HEE  P    O1P   deloc   1.509  0.020  1.509
 HEE  P    O2P   single  1.660  0.020  1.660
 HEE  P    O3P   deloc   1.508  0.020  1.508
 HEE  O2P  C1'   single  1.418  0.020  1.418
 HEE  C1'  C2'   single  1.513  0.020  1.513
 HEE  C1'  H1'1  single  0.970  0.020  1.090
 HEE  C1'  H1'2  single  0.970  0.020  1.090
 HEE  C2'  H2'1  single  0.970  0.020  1.090
 HEE  C2'  H2'2  single  0.970  0.020  1.090
 HEE  C2'  H2'3  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
 HEE  H12   C1   H11   106.68  3.000
 HEE  H12   C1   P     109.89  3.000
 HEE  H11   C1   P     109.50  3.000
 HEE  H12   C1   C2    109.67  3.000
 HEE  H11   C1   C2    109.66  3.000
 HEE  P     C1   C2    111.32  3.000
 HEE  H22   C2   H21   106.13  3.000
 HEE  H22   C2   C3    109.23  3.000
 HEE  H21   C2   C3    109.39  3.000
 HEE  H22   C2   C1    109.33  3.000
 HEE  H21   C2   C1    109.38  3.000
 HEE  C3    C2   C1    113.14  3.000
 HEE  H32   C3   H31   106.02  3.000
 HEE  H32   C3   C4    109.43  3.000
 HEE  H31   C3   C4    109.39  3.000
 HEE  H32   C3   C2    109.44  3.000
 HEE  H31   C3   C2    109.29  3.000
 HEE  C4    C3   C2    113.03  3.000
 HEE  H42   C4   H41   105.95  3.000
 HEE  H42   C4   C5    109.20  3.000
 HEE  H41   C4   C5    109.31  3.000
 HEE  H42   C4   C3    109.29  3.000
 HEE  H41   C4   C3    109.39  3.000
 HEE  C5    C4   C3    113.42  3.000
 HEE  H52   C5   H51   106.04  3.000
 HEE  H52   C5   C6    109.65  3.000
 HEE  H51   C5   C6    109.56  3.000
 HEE  H52   C5   C4    109.36  3.000
 HEE  H51   C5   C4    109.22  3.000
 HEE  C6    C5   C4    112.79  3.000
 HEE  H63   C6   H62   107.45  3.000
 HEE  H63   C6   H61   107.60  3.000
 HEE  H62   C6   H61   107.62  3.000
 HEE  H63   C6   C5    111.22  3.000
 HEE  H62   C6   C5    111.04  3.000
 HEE  H61   C6   C5    111.71  3.000
 HEE  O3P   P    O2P   109.01  3.000
 HEE  O3P   P    O1P   118.58  3.000
 HEE  O2P   P    O1P   108.96  3.000
 HEE  O3P   P    C1    110.24  3.000
 HEE  O2P   P    C1     97.98  3.000
 HEE  O1P   P    C1    110.08  3.000
 HEE  C1'   O2P  P     117.74  3.000
 HEE  H1'2  C1'  H1'1  106.91  3.000
 HEE  H1'2  C1'  C2'   109.56  3.000
 HEE  H1'1  C1'  C2'   109.79  3.000
 HEE  H1'2  C1'  O2P   110.59  3.000
 HEE  H1'1  C1'  O2P   110.64  3.000
 HEE  C2'   C1'  O2P   109.32  3.000
 HEE  H2'3  C2'  H2'2  108.37  3.000
 HEE  H2'3  C2'  H2'1  107.79  3.000
 HEE  H2'2  C2'  H2'1  107.85  3.000
 HEE  H2'3  C2'  C1'   111.52  3.000
 HEE  H2'2  C2'  C1'   111.33  3.000
 HEE  H2'1  C2'  C1'   109.84  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
 HEE  Var_01  C4    C3   C2   C1   -179.91  30.0  3
 HEE  Var_02  O1P   P    C1   C2     66.33  30.0  3
 HEE  Var_03  C5    C4   C3   C2   -178.72  30.0  3
 HEE  Var_04  P     C1   C2   C3   -178.06  30.0  1
 HEE  Var_05  C6    C5   C4   C3    179.83  30.0  3
 HEE  Var_06  C2'   C1'  O2P  P     178.70  30.0  3
 HEE  Var_07  H61   C6   C5   C4   -179.51  30.0  3
 HEE  Var_08  H2'1  C2'  C1'  O2P   179.90  30.0  3

