# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 08:05:56 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: [(4S)-2,2-dimethyl-1,3-dioxolan-4-yl]methyl hydrogen (S)-hex-5-en-1-ylphosphonate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(C)OC[C@@H](CO[P@](O)(=O)CCCCC=C)O1
#
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
 RIL  RIL  '[(4S)-2,2-dimethyl-1,3-dioxolan-4-yl]methyl hydrogen (S)-hex-5-en-1-ylphosphonate'  ligand  40  18  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_RIL
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
 RIL  C1    C  C2     0  -0.542  -2.8441  -0.9793  -2.9128
 RIL  C2    C  C1     0  -0.151  -2.0722  -0.0604  -2.3433
 RIL  C5    C  CH2    0  -0.485  -0.7077  -0.3046  -1.7836
 RIL  C7    C  CH2    0  -0.418  -0.6317  -0.0268  -0.2818
 RIL  C10   C  CH2    0  -0.425   0.7765  -0.2029   0.2717
 RIL  C13   C  CH2    0  -0.750   0.8809   0.1463   1.7509
 RIL  P16   P  P      0   1.288   2.5492  -0.0762   2.4676
 RIL  O20   O  O      0  -0.806   3.0358  -1.4748   2.2037
 RIL  O21   O  O2     0  -0.629   3.4904   0.8732   1.4836
 RIL  C23   C  CH2    0  -0.157   3.3582   2.2725   1.5261
 RIL  C24   C  CH1    0  -0.041   3.8466   2.8603   0.2190
 RIL  C27   C  CH2    0  -0.233   3.7492   4.3928   0.1993
 RIL  O28   O  O2     0  -0.500   3.0530   2.4573  -0.8819
 RIL  C30   C  CT     0   0.477   2.3927   3.5847  -1.4227
 RIL  O31   O  O2     0  -0.500   3.2030   4.6823  -1.0674
 RIL  C34   C  CH3    0  -0.683   2.3596   3.4615  -2.9325
 RIL  C38   C  CH3    0  -0.680   0.9895   3.7282  -0.8394
 RIL  O1    O  OP    -1  -0.811   2.5686   0.4914   3.8627
 RIL  H11   H  H      0   0.233  -3.8299  -0.7398  -3.2900
 RIL  H12   H  H      0   0.229  -2.5176  -2.0070  -3.0250
 RIL  H2    H  H      0   0.236  -2.4475   0.9563  -2.2505
 RIL  H51   H  HCH2   0   0.229  -0.3951  -1.3330  -1.9860
 RIL  H52   H  HCH2   0   0.223   0.0127   0.3462  -2.2936
 RIL  H71   H  HCH2   0   0.221  -1.3269  -0.6888   0.2440
 RIL  H72   H  HCH2   0   0.211  -0.9769   0.9947  -0.0854
 RIL  H101  H  HCH2   0   0.213   1.1047  -1.2349   0.1165
 RIL  H102  H  HCH2   0   0.228   1.4633   0.4284  -0.2971
 RIL  H131  H  HCH2   0   0.232   0.5440   1.1749   1.9133
 RIL  H132  H  HCH2   0   0.241   0.1999  -0.4819   2.3352
 RIL  H231  H  HCH2   0   0.202   2.3205   2.5883   1.6914
 RIL  H232  H  HCH2   0   0.217   3.9516   2.7004   2.3444
 RIL  H24   H  HCH1   0   0.239   4.8755   2.5295   0.0376
 RIL  H271  H  HCH2   0   0.220   3.1112   4.7655   1.0120
 RIL  H272  H  HCH2   0   0.254   4.7205   4.8791   0.2885
 RIL  H341  H  HCH3   0   0.236   1.9068   4.3456  -3.3809
 RIL  H342  H  HCH3   0   0.241   3.3654   3.3416  -3.3361
 RIL  H343  H  HCH3   0   0.234   1.7637   2.5984  -3.2301
 RIL  H381  H  HCH3   0   0.234   0.4100   2.8192  -1.0047
 RIL  H382  H  HCH3   0   0.237   1.0049   3.9167   0.2355
 RIL  H383  H  HCH3   0   0.235   0.4611   4.5559  -1.3137

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
 RIL  C1   C2    double  1.328  0.020  1.328
 RIL  C1   H11   single  0.930  0.020  1.080
 RIL  C1   H12   single  0.930  0.020  1.080
 RIL  C2   C5    single  1.495  0.020  1.495
 RIL  C2   H2    single  0.930  0.020  1.080
 RIL  C5   C7    single  1.529  0.020  1.529
 RIL  C5   H51   single  0.970  0.020  1.090
 RIL  C5   H52   single  0.970  0.020  1.090
 RIL  C7   C10   single  1.523  0.020  1.523
 RIL  C7   H71   single  0.970  0.020  1.090
 RIL  C7   H72   single  0.970  0.020  1.090
 RIL  C10  C13   single  1.523  0.020  1.523
 RIL  C10  H101  single  0.970  0.020  1.090
 RIL  C10  H102  single  0.970  0.020  1.090
 RIL  C13  P16   single  1.829  0.020  1.829
 RIL  C13  H131  single  0.970  0.020  1.090
 RIL  C13  H132  single  0.970  0.020  1.090
 RIL  P16  O20   deloc   1.504  0.020  1.504
 RIL  P16  O21   single  1.660  0.020  1.660
 RIL  P16  O1    deloc   1.506  0.020  1.506
 RIL  O21  C23   single  1.406  0.020  1.406
 RIL  C23  C24   single  1.514  0.020  1.514
 RIL  C23  H231  single  0.970  0.020  1.090
 RIL  C23  H232  single  0.970  0.020  1.090
 RIL  C24  C27   single  1.536  0.020  1.536
 RIL  C24  O28   single  1.416  0.020  1.416
 RIL  C24  H24   single  0.970  0.020  1.090
 RIL  C27  O31   single  1.410  0.020  1.410
 RIL  C27  H271  single  0.970  0.020  1.090
 RIL  C27  H272  single  0.970  0.020  1.090
 RIL  O28  C30   single  1.414  0.020  1.414
 RIL  C30  O31   single  1.410  0.020  1.410
 RIL  C30  C34   single  1.515  0.020  1.515
 RIL  C30  C38   single  1.526  0.020  1.526
 RIL  C34  H341  single  0.970  0.020  1.090
 RIL  C34  H342  single  0.970  0.020  1.090
 RIL  C34  H343  single  0.970  0.020  1.090
 RIL  C38  H381  single  0.970  0.020  1.090
 RIL  C38  H382  single  0.970  0.020  1.090
 RIL  C38  H383  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
 RIL  H12   C1   H11   116.62  3.000
 RIL  H12   C1   C2    121.68  3.000
 RIL  H11   C1   C2    121.71  3.000
 RIL  H2    C2   C5    115.83  3.000
 RIL  H2    C2   C1    118.86  3.000
 RIL  C5    C2   C1    125.30  3.000
 RIL  H52   C5   H51   106.51  3.000
 RIL  H52   C5   C7    108.44  3.000
 RIL  H51   C5   C7    109.78  3.000
 RIL  H52   C5   C2    109.18  3.000
 RIL  H51   C5   C2    110.19  3.000
 RIL  C7    C5   C2    112.54  3.000
 RIL  H72   C7   H71   106.12  3.000
 RIL  H72   C7   C10   109.50  3.000
 RIL  H71   C7   C10   110.04  3.000
 RIL  H72   C7   C5    109.25  3.000
 RIL  H71   C7   C5    109.29  3.000
 RIL  C10   C7   C5    112.44  3.000
 RIL  H102  C10  H101  106.43  3.000
 RIL  H102  C10  C13   109.26  3.000
 RIL  H101  C10  C13   109.47  3.000
 RIL  H102  C10  C7    108.97  3.000
 RIL  H101  C10  C7    109.56  3.000
 RIL  C13   C10  C7    112.93  3.000
 RIL  H132  C13  H131  105.57  3.000
 RIL  H132  C13  P16   106.75  3.000
 RIL  H131  C13  P16   109.69  3.000
 RIL  H132  C13  C10   110.12  3.000
 RIL  H131  C13  C10   109.78  3.000
 RIL  P16   C13  C10   114.52  3.000
 RIL  O1    P16  O21   109.04  3.000
 RIL  O1    P16  O20   120.58  3.000
 RIL  O21   P16  O20   104.15  3.000
 RIL  O1    P16  C13   109.20  3.000
 RIL  O21   P16  C13   102.43  3.000
 RIL  O20   P16  C13   109.84  3.000
 RIL  C23   O21  P16   119.86  3.000
 RIL  H232  C23  H231  106.67  3.000
 RIL  H232  C23  C24   108.53  3.000
 RIL  H231  C23  C24   108.87  3.000
 RIL  H232  C23  O21   111.08  3.000
 RIL  H231  C23  O21   112.32  3.000
 RIL  C24   C23  O21   109.26  3.000
 RIL  H24   C24  O28   108.17  3.000
 RIL  H24   C24  C27   111.02  3.000
 RIL  O28   C24  C27   103.80  3.000
 RIL  H24   C24  C23   109.18  3.000
 RIL  O28   C24  C23   112.33  3.000
 RIL  C27   C24  C23   112.21  3.000
 RIL  H272  C27  H271  107.80  3.000
 RIL  H272  C27  O31   109.10  3.000
 RIL  H271  C27  O31   111.72  3.000
 RIL  H272  C27  C24   112.81  3.000
 RIL  H271  C27  C24   111.47  3.000
 RIL  O31   C27  C24   103.95  3.000
 RIL  C30   O28  C24   109.40  3.000
 RIL  C38   C30  C34   111.62  3.000
 RIL  C38   C30  O31   111.03  3.000
 RIL  C34   C30  O31   109.09  3.000
 RIL  C38   C30  O28   110.98  3.000
 RIL  C34   C30  O28   109.06  3.000
 RIL  O31   C30  O28   104.83  3.000
 RIL  C30   O31  C27   106.82  3.000
 RIL  H343  C34  H342  108.42  3.000
 RIL  H343  C34  H341  107.63  3.000
 RIL  H342  C34  H341  108.66  3.000
 RIL  H343  C34  C30   110.39  3.000
 RIL  H342  C34  C30   110.96  3.000
 RIL  H341  C34  C30   110.68  3.000
 RIL  H383  C38  H382  107.70  3.000
 RIL  H383  C38  H381  108.01  3.000
 RIL  H382  C38  H381  107.50  3.000
 RIL  H383  C38  C30   110.52  3.000
 RIL  H382  C38  C30   112.32  3.000
 RIL  H381  C38  C30   110.62  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
 RIL  Var_01  O28   C30  O31  C27   -34.51  30.0  1
 RIL  Var_02  H271  C27  O31  C30   -90.63  30.0  1
 RIL  Var_03  H341  C34  C30  O28  -176.73  30.0  3
 RIL  Var_04  H381  C38  C30  O28   -56.33  30.0  3
 RIL  Var_05  C24   C23  O21  P16  -156.79  30.0  3
 RIL  Var_06  C7    C5   C2   C1   -118.02  30.0  3
 RIL  Var_07  C10   C7   C5   C2   -176.88  30.0  3
 RIL  Var_08  C13   C10  C7   C5    176.79  30.0  3
 RIL  Var_09  P16   C13  C10  C7    179.05  30.0  3
 RIL  Var_10  O20   P16  C13  C10   -54.07  30.0  3
 RIL  Var_11  H11   C1   C2   C5    179.34   0.0  2

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
 RIL  chir_02  C24  C23  C27  O28  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 RIL  plan-1  C1   0.020
 RIL  plan-1  C2   0.020
 RIL  plan-1  C5   0.020
 RIL  plan-1  H11  0.020
 RIL  plan-1  H12  0.020
 RIL  plan-1  H2   0.020

