# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 12:10:14 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  31  12  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.747   0.4162  -0.0910  -0.0385
 HEE  C2    C  CH2   0  -0.431  -0.3550   0.0031   1.2775
 HEE  C3    C  CH2   0  -0.407   0.5734  -0.0766   2.4833
 HEE  C4    C  CH2   0  -0.408  -0.1687   0.0323   3.8086
 HEE  C5    C  CH2   0  -0.419   0.7556  -0.0264   5.0191
 HEE  C6    C  CH3   0  -0.662   0.0061   0.0969   6.3385
 HEE  P     P  P     0   1.389  -0.6509   0.0989  -1.4745
 HEE  O1P   O  O     0  -0.724  -1.4702   1.3352  -1.5282
 HEE  O2P   O  O2    0  -0.596   0.3899  -0.0912  -2.6827
 HEE  O3P   O  OH1   0  -0.755  -1.6371  -1.1766  -1.5166
 HEE  C1'   C  CH2   0  -0.170  -0.0085   0.1719  -4.0393
 HEE  C2'   C  CH3   0  -0.684   1.1515  -0.1544  -4.9479
 HEE  H11   H  HCH2  0   0.283   1.1721   0.6973  -0.0897
 HEE  H12   H  HCH2  0   0.282   0.9495  -1.0435  -0.1056
 HEE  H21   H  HCH2  0   0.232  -1.0952  -0.7996   1.3349
 HEE  H22   H  HCH2  0   0.233  -0.9126   0.9430   1.3104
 HEE  H31   H  HCH2  0   0.215   1.3199   0.7220   2.4166
 HEE  H32   H  HCH2  0   0.215   1.1309  -1.0192   2.4517
 HEE  H41   H  HCH2  0   0.210  -0.9096  -0.7717   3.8796
 HEE  H42   H  HCH2  0   0.209  -0.7357   0.9698   3.8313
 HEE  H51   H  HCH2  0   0.211   1.4993   0.7726   4.9433
 HEE  H52   H  HCH2  0   0.211   1.3166  -0.9660   5.0006
 HEE  H61   H  HCH3  0   0.226   0.6837   0.0542   7.1919
 HEE  H62   H  HCH3  0   0.216  -0.5364   1.0427   6.3944
 HEE  H63   H  HCH3  0   0.216  -0.7233  -0.7071   6.4547
 HEE  HOP3  H  HOH1  0   0.488  -1.2005  -2.0378  -1.4846
 HEE  H1'1  H  HCH2  0   0.229  -0.8786  -0.4366  -4.2987
 HEE  H1'2  H  HCH2  0   0.233  -0.2914   1.2217  -4.1403
 HEE  H2'1  H  HCH3  0   0.237   0.8725   0.0608  -5.9792
 HEE  H2'2  H  HCH3  0   0.235   2.0269   0.4479  -4.7046
 HEE  H2'3  H  HCH3  0   0.235   1.4244  -1.2078  -4.8864

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  1.528  0.020  1.528
 HEE  C1   P     single  1.799  0.020  1.799
 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   double  1.484  0.020  1.484
 HEE  P    O2P   single  1.606  0.020  1.606
 HEE  P    O3P   single  1.613  0.020  1.613
 HEE  O2P  C1'   single  1.438  0.020  1.438
 HEE  O3P  HOP3  single  0.850  0.020  0.980
 HEE  C1'  C2'   single  1.509  0.020  1.509
 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   106.74  3.000
 HEE  H12   C1   P     109.40  3.000
 HEE  H11   C1   P     107.25  3.000
 HEE  H12   C1   C2    110.64  3.000
 HEE  H11   C1   C2    110.17  3.000
 HEE  P     C1   C2    112.42  3.000
 HEE  H22   C2   H21   106.52  3.000
 HEE  H22   C2   C3    109.38  3.000
 HEE  H21   C2   C3    109.42  3.000
 HEE  H22   C2   C1    109.64  3.000
 HEE  H21   C2   C1    109.98  3.000
 HEE  C3    C2   C1    111.76  3.000
 HEE  H32   C3   H31   106.18  3.000
 HEE  H32   C3   C4    109.55  3.000
 HEE  H31   C3   C4    109.45  3.000
 HEE  H32   C3   C2    109.41  3.000
 HEE  H31   C3   C2    109.21  3.000
 HEE  C4    C3   C2    112.83  3.000
 HEE  H42   C4   H41   106.06  3.000
 HEE  H42   C4   C5    109.28  3.000
 HEE  H41   C4   C5    109.29  3.000
 HEE  H42   C4   C3    109.35  3.000
 HEE  H41   C4   C3    109.48  3.000
 HEE  C5    C4   C3    113.13  3.000
 HEE  H52   C5   H51   106.10  3.000
 HEE  H52   C5   C6    109.67  3.000
 HEE  H51   C5   C6    109.60  3.000
 HEE  H52   C5   C4    109.29  3.000
 HEE  H51   C5   C4    109.21  3.000
 HEE  C6    C5   C4    112.74  3.000
 HEE  H63   C6   H62   107.48  3.000
 HEE  H63   C6   H61   107.64  3.000
 HEE  H62   C6   H61   107.62  3.000
 HEE  H63   C6   C5    111.19  3.000
 HEE  H62   C6   C5    111.05  3.000
 HEE  H61   C6   C5    111.66  3.000
 HEE  O3P   P    O2P   106.44  3.000
 HEE  O3P   P    O1P   108.68  3.000
 HEE  O2P   P    O1P   115.41  3.000
 HEE  O3P   P    C1    107.46  3.000
 HEE  O2P   P    C1    101.75  3.000
 HEE  O1P   P    C1    116.38  3.000
 HEE  C1'   O2P  P     120.56  3.000
 HEE  HOP3  O3P  P     115.33  3.000
 HEE  H1'2  C1'  H1'1  107.88  3.000
 HEE  H1'2  C1'  C2'   110.57  3.000
 HEE  H1'1  C1'  C2'   110.40  3.000
 HEE  H1'2  C1'  O2P   109.56  3.000
 HEE  H1'1  C1'  O2P   110.03  3.000
 HEE  C2'   C1'  O2P   108.39  3.000
 HEE  H2'3  C2'  H2'2  108.68  3.000
 HEE  H2'3  C2'  H2'1  107.96  3.000
 HEE  H2'2  C2'  H2'1  107.92  3.000
 HEE  H2'3  C2'  C1'   111.56  3.000
 HEE  H2'2  C2'  C1'   111.31  3.000
 HEE  H2'1  C2'  C1'   109.28  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    179.29  30.0  3
 HEE  Var_02  O1P   P    C1   C2     55.57  30.0  3
 HEE  Var_03  C5    C4   C3   C2   -179.17  30.0  3
 HEE  Var_04  P     C1   C2   C3   -176.61  30.0  1
 HEE  Var_05  C6    C5   C4   C3    179.44  30.0  3
 HEE  Var_06  C2'   C1'  O2P  P    -177.38  30.0  3
 HEE  Var_07  H61   C6   C5   C4   -179.92  30.0  3
 HEE  Var_08  H2'1  C2'  C1'  O2P  -178.76  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
 HEE  chir_01  P  O1P  O2P  O3P  both

