# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 27 06:30:49 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: [(4R)-2,2-dimethyl-1,3-dioxolan-4-yl]methyl hydrogen (R)-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
 SIL  SIL  '[(4R)-2,2-dimethyl-1,3-dioxolan-4-yl]methyl hydrogen (R)-hex-5-en-1-ylphosphonate'  ligand  41  18  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SIL
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
 SIL  C1    C  C2    0  -0.540  -3.5331  -5.9664   1.4655
 SIL  C2    C  C1    0  -0.154  -2.6670  -5.0713   1.9265
 SIL  C5    C  CH2   0  -0.484  -1.5887  -4.4239   1.1176
 SIL  C7    C  CH2   0  -0.411  -0.1915  -4.7970   1.6132
 SIL  C10   C  CH2   0  -0.437   0.9073  -4.1013   0.8207
 SIL  C13   C  CH2   0  -0.774   2.2965  -4.4550   1.3499
 SIL  P16   P  P     0   1.400   3.6125  -3.8449   0.2842
 SIL  O20   O  O     0  -0.708   3.6998  -4.4674  -1.0585
 SIL  O21   O  O2    0  -0.595   3.3800  -2.2613   0.1012
 SIL  C23   C  CH2   0  -0.196   3.3592  -1.3466   1.1920
 SIL  C24   C  CH1   0  -0.023   2.6591  -0.0848   0.7454
 SIL  C27   C  CH2   0  -0.233   2.6037   0.9672   1.8578
 SIL  O28   O  O2    0  -0.509   3.3558   0.5615  -0.2995
 SIL  C30   C  CT    0   0.473   3.6802   1.8873   0.0914
 SIL  O31   O  O2    0  -0.497   2.8189   2.1750   1.1681
 SIL  C34   C  CH3   0  -0.672   5.1425   1.9683   0.5154
 SIL  C38   C  CH3   0  -0.681   3.3760   2.8351  -1.0514
 SIL  O1    O  OH1   0  -0.750   4.9033  -4.0083   1.2287
 SIL  H11   H  H     0   0.234  -4.2850  -6.4120   2.1040
 SIL  H12   H  H     0   0.230  -3.5213  -6.2887   0.4304
 SIL  H2    H  H     0   0.238  -2.7154  -4.7832   2.9738
 SIL  H51   H  HCH2  0   0.231  -1.6939  -4.7016   0.0651
 SIL  H52   H  HCH2  0   0.232  -1.6997  -3.3353   1.1693
 SIL  H71   H  HCH2  0   0.227  -0.0610  -5.8811   1.5453
 SIL  H72   H  HCH2  0   0.224  -0.0965  -4.5402   2.6729
 SIL  H101  H  HCH2  0   0.238   0.8253  -4.3823  -0.2330
 SIL  H102  H  HCH2  0   0.235   0.7559  -3.0190   0.8645
 SIL  H131  H  HCH2  0   0.284   2.4285  -4.0827   2.3687
 SIL  H132  H  HCH2  0   0.294   2.4185  -5.5407   1.4014
 SIL  H231  H  HCH2  0   0.240   2.8171  -1.7571   2.0516
 SIL  H232  H  HCH2  0   0.244   4.3805  -1.1267   1.5153
 SIL  H24   H  HCH1  0   0.244   1.6501  -0.3395   0.3995
 SIL  H271  H  HCH2  0   0.261   1.6352   1.0044   2.3550
 SIL  H272  H  HCH2  0   0.223   3.3719   0.7895   2.6217
 SIL  H341  H  HCH3  0   0.236   5.7942   1.6839  -0.3109
 SIL  H342  H  HCH3  0   0.233   5.3970   2.9872   0.8081
 SIL  H343  H  HCH3  0   0.235   5.3657   1.3090   1.3563
 SIL  H381  H  HCH3  0   0.237   3.9901   2.5900  -1.9179
 SIL  H382  H  HCH3  0   0.241   2.3269   2.7744  -1.3418
 SIL  H383  H  HCH3  0   0.236   3.6006   3.8630  -0.7664
 SIL  HO1   H  HOH1  0   0.493   5.7476  -3.9013   0.7689

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
 SIL  C1   C2    double  1.328  0.020  1.328
 SIL  C1   H11   single  0.930  0.020  1.080
 SIL  C1   H12   single  0.930  0.020  1.080
 SIL  C2   C5    single  1.495  0.020  1.495
 SIL  C2   H2    single  0.930  0.020  1.080
 SIL  C5   C7    single  1.529  0.020  1.529
 SIL  C5   H51   single  0.970  0.020  1.090
 SIL  C5   H52   single  0.970  0.020  1.090
 SIL  C7   C10   single  1.523  0.020  1.523
 SIL  C7   H71   single  0.970  0.020  1.090
 SIL  C7   H72   single  0.970  0.020  1.090
 SIL  C10  C13   single  1.528  0.020  1.528
 SIL  C10  H101  single  0.970  0.020  1.090
 SIL  C10  H102  single  0.970  0.020  1.090
 SIL  C13  P16   single  1.800  0.020  1.800
 SIL  C13  H131  single  0.970  0.020  1.090
 SIL  C13  H132  single  0.970  0.020  1.090
 SIL  P16  O20   double  1.483  0.020  1.483
 SIL  P16  O21   single  1.611  0.020  1.611
 SIL  P16  O1    single  1.608  0.020  1.608
 SIL  O21  C23   single  1.424  0.020  1.424
 SIL  C23  C24   single  1.510  0.020  1.510
 SIL  C23  H231  single  0.970  0.020  1.090
 SIL  C23  H232  single  0.970  0.020  1.090
 SIL  C24  C27   single  1.532  0.020  1.532
 SIL  C24  O28   single  1.412  0.020  1.412
 SIL  C24  H24   single  0.970  0.020  1.090
 SIL  C27  O31   single  1.407  0.020  1.407
 SIL  C27  H271  single  0.970  0.020  1.090
 SIL  C27  H272  single  0.970  0.020  1.090
 SIL  O28  C30   single  1.420  0.020  1.420
 SIL  C30  O31   single  1.409  0.020  1.409
 SIL  C30  C34   single  1.525  0.020  1.525
 SIL  C30  C38   single  1.516  0.020  1.516
 SIL  C34  H341  single  0.970  0.020  1.090
 SIL  C34  H342  single  0.970  0.020  1.090
 SIL  C34  H343  single  0.970  0.020  1.090
 SIL  C38  H381  single  0.970  0.020  1.090
 SIL  C38  H382  single  0.970  0.020  1.090
 SIL  C38  H383  single  0.970  0.020  1.090
 SIL  O1   HO1   single  0.850  0.020  0.980

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
 SIL  H12   C1   H11   116.64  3.000
 SIL  H12   C1   C2    121.64  3.000
 SIL  H11   C1   C2    121.72  3.000
 SIL  H2    C2   C5    116.00  3.000
 SIL  H2    C2   C1    118.94  3.000
 SIL  C5    C2   C1    125.05  3.000
 SIL  H52   C5   H51   106.74  3.000
 SIL  H52   C5   C7    108.65  3.000
 SIL  H51   C5   C7    109.75  3.000
 SIL  H52   C5   C2    109.37  3.000
 SIL  H51   C5   C2    109.96  3.000
 SIL  C7    C5   C2    112.21  3.000
 SIL  H72   C7   H71   106.39  3.000
 SIL  H72   C7   C10   109.51  3.000
 SIL  H71   C7   C10   109.53  3.000
 SIL  H72   C7   C5    109.63  3.000
 SIL  H71   C7   C5    109.32  3.000
 SIL  C10   C7   C5    112.29  3.000
 SIL  H102  C10  H101  106.41  3.000
 SIL  H102  C10  C13   109.93  3.000
 SIL  H101  C10  C13   110.03  3.000
 SIL  H102  C10  C7    109.35  3.000
 SIL  H101  C10  C7    109.26  3.000
 SIL  C13   C10  C7    111.72  3.000
 SIL  H132  C13  H131  106.31  3.000
 SIL  H132  C13  P16   106.42  3.000
 SIL  H131  C13  P16   110.38  3.000
 SIL  H132  C13  C10   110.33  3.000
 SIL  H131  C13  C10   110.73  3.000
 SIL  P16   C13  C10   112.41  3.000
 SIL  O1    P16  O21   106.41  3.000
 SIL  O1    P16  O20   116.24  3.000
 SIL  O21   P16  O20   108.56  3.000
 SIL  O1    P16  C13   101.82  3.000
 SIL  O21   P16  C13   107.15  3.000
 SIL  O20   P16  C13   115.91  3.000
 SIL  C23   O21  P16   123.14  3.000
 SIL  H232  C23  H231  107.77  3.000
 SIL  H232  C23  C24   110.62  3.000
 SIL  H231  C23  C24   108.40  3.000
 SIL  H232  C23  O21   110.00  3.000
 SIL  H231  C23  O21   111.56  3.000
 SIL  C24   C23  O21   108.48  3.000
 SIL  H24   C24  O28   109.07  3.000
 SIL  H24   C24  C27   110.80  3.000
 SIL  O28   C24  C27   103.93  3.000
 SIL  H24   C24  C23   109.01  3.000
 SIL  O28   C24  C23   111.86  3.000
 SIL  C27   C24  C23   112.07  3.000
 SIL  H272  C27  H271  108.06  3.000
 SIL  H272  C27  O31   111.89  3.000
 SIL  H271  C27  O31   109.29  3.000
 SIL  H272  C27  C24   111.64  3.000
 SIL  H271  C27  C24   112.77  3.000
 SIL  O31   C27  C24   103.18  3.000
 SIL  C30   O28  C24   109.65  3.000
 SIL  C38   C30  C34   111.65  3.000
 SIL  C38   C30  O31   109.02  3.000
 SIL  C34   C30  O31   111.28  3.000
 SIL  C38   C30  O28   109.30  3.000
 SIL  C34   C30  O28   110.20  3.000
 SIL  O31   C30  O28   105.16  3.000
 SIL  C30   O31  C27   107.02  3.000
 SIL  H343  C34  H342  108.06  3.000
 SIL  H343  C34  H341  107.71  3.000
 SIL  H342  C34  H341  107.92  3.000
 SIL  H343  C34  C30   112.23  3.000
 SIL  H342  C34  C30   110.38  3.000
 SIL  H341  C34  C30   110.40  3.000
 SIL  H383  C38  H382  108.68  3.000
 SIL  H383  C38  H381  107.68  3.000
 SIL  H382  C38  H381  108.54  3.000
 SIL  H383  C38  C30   110.56  3.000
 SIL  H382  C38  C30   111.05  3.000
 SIL  H381  C38  C30   110.23  3.000
 SIL  HO1   O1   P16   114.22  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
 SIL  Var_01  O28   C30  O31  C27    32.54  30.0  1
 SIL  Var_02  H271  C27  O31  C30  -152.82  30.0  1
 SIL  Var_03  H341  C34  C30  O28    60.28  30.0  3
 SIL  Var_04  H381  C38  C30  O28   -62.10  30.0  3
 SIL  Var_05  C24   C23  O21  P16  -160.44  30.0  3
 SIL  Var_06  C7    C5   C2   C1   -115.55  30.0  3
 SIL  Var_07  C10   C7   C5   C2   -178.05  30.0  3
 SIL  Var_08  C13   C10  C7   C5    178.52  30.0  3
 SIL  Var_09  P16   C13  C10  C7    171.47  30.0  3
 SIL  Var_10  O20   P16  C13  C10   -66.65  30.0  3
 SIL  Var_11  H11   C1   C2   C5    179.11   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
 SIL  chir_02  C24  C23  C27  O28  negativ
 SIL  chir_03  P16  O20  O21  O1   both

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
 SIL  plan-1  C1   0.020
 SIL  plan-1  C2   0.020
 SIL  plan-1  C5   0.020
 SIL  plan-1  H11  0.020
 SIL  plan-1  H12  0.020
 SIL  plan-1  H2   0.020

