# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 25 22:24:25 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  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_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  -0.541  -3.0020  -0.6986  -2.7861
 RIL  C2    C  C1    0  -0.152  -2.1202   0.1270  -2.2341
 RIL  C5    C  CH2   0  -0.490  -0.7444  -0.2538  -1.7881
 RIL  C7    C  CH2   0  -0.422  -0.5496  -0.0506  -0.2854
 RIL  C10   C  CH2   0  -0.442   0.8861  -0.3008   0.1555
 RIL  C13   C  CH2   0  -0.775   1.0538  -0.0847   1.6593
 RIL  P16   P  P     0   1.401   2.7604  -0.2718   2.1991
 RIL  O20   O  O     0  -0.709   3.3830  -1.5946   1.9522
 RIL  O21   O  O2    0  -0.596   3.6289   0.8566   1.4444
 RIL  C23   C  CH2   0  -0.188   3.3238   2.2457   1.5236
 RIL  C24   C  CH1   0  -0.036   3.8413   2.9295   0.2794
 RIL  C27   C  CH2   0  -0.233   3.5459   4.4360   0.2997
 RIL  O28   O  O2    0  -0.502   3.1929   2.4689  -0.8883
 RIL  C30   C  CT    0   0.474   2.4758   3.5389  -1.4832
 RIL  O31   O  O2    0  -0.496   3.1089   4.7052  -1.0116
 RIL  C34   C  CH3   0  -0.682   2.6274   3.4564  -2.9894
 RIL  C38   C  CH3   0  -0.680   1.0097   3.4986  -1.0622
 RIL  O1    O  OH1   0  -0.751   2.6631   0.1931   3.7355
 RIL  H11   H  H     0   0.235  -3.9879  -0.3641  -3.0802
 RIL  H12   H  H     0   0.231  -2.7683  -1.7415  -2.9677
 RIL  H2    H  H     0   0.238  -2.4009   1.1647  -2.0683
 RIL  H51   H  HCH2  0   0.237  -0.5357  -1.2933  -2.0557
 RIL  H52   H  HCH2  0   0.228  -0.0107   0.3596  -2.3244
 RIL  H71   H  HCH2  0   0.234  -1.2296  -0.7113   0.2601
 RIL  H72   H  HCH2  0   0.221  -0.8350   0.9726  -0.0163
 RIL  H101  H  HCH2  0   0.240   1.1836  -1.3201  -0.1057
 RIL  H102  H  HCH2  0   0.239   1.5502   0.3703  -0.3949
 RIL  H131  H  HCH2  0   0.279   0.6779   0.9008   1.9468
 RIL  H132  H  HCH2  0   0.297   0.4593  -0.8122   2.2187
 RIL  H231  H  HCH2  0   0.228   2.2468   2.4175   1.6188
 RIL  H232  H  HCH2  0   0.254   3.8070   2.6810   2.4033
 RIL  H24   H  HCH1  0   0.253   4.9157   2.7393   0.1818
 RIL  H271  H  HCH2  0   0.225   2.7776   4.6857   1.0435
 RIL  H272  H  HCH2  0   0.261   4.4295   5.0362   0.5140
 RIL  H341  H  HCH3  0   0.238   2.1128   4.2868  -3.4725
 RIL  H342  H  HCH3  0   0.243   3.6783   3.4818  -3.2790
 RIL  H343  H  HCH3  0   0.237   2.1869   2.5318  -3.3622
 RIL  H381  H  HCH3  0   0.233   0.5543   2.5577  -1.3724
 RIL  H382  H  HCH3  0   0.237   0.8846   3.5874   0.0188
 RIL  H383  H  HCH3  0   0.241   0.4543   4.3107  -1.5322
 RIL  HO1   H  HOH1  0   0.493   3.4547   0.0069   4.2595

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  1.496  0.020  1.496
 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  1.529  0.020  1.529
 RIL  C10  H101  single  0.970  0.020  1.090
 RIL  C10  H102  single  0.970  0.020  1.090
 RIL  C13  P16   single  1.800  0.020  1.800
 RIL  C13  H131  single  0.970  0.020  1.090
 RIL  C13  H132  single  0.970  0.020  1.090
 RIL  P16  O20   double  1.483  0.020  1.483
 RIL  P16  O21   single  1.612  0.020  1.612
 RIL  P16  O1    single  1.608  0.020  1.608
 RIL  O21  C23   single  1.424  0.020  1.424
 RIL  C23  C24   single  1.511  0.020  1.511
 RIL  C23  H231  single  0.970  0.020  1.090
 RIL  C23  H232  single  0.970  0.020  1.090
 RIL  C24  C27   single  1.535  0.020  1.535
 RIL  C24  O28   single  1.413  0.020  1.413
 RIL  C24  H24   single  0.970  0.020  1.090
 RIL  C27  O31   single  1.408  0.020  1.408
 RIL  C27  H271  single  0.970  0.020  1.090
 RIL  C27  H272  single  0.970  0.020  1.090
 RIL  O28  C30   single  1.419  0.020  1.419
 RIL  C30  O31   single  1.408  0.020  1.408
 RIL  C30  C34   single  1.516  0.020  1.516
 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
 RIL  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
 RIL  H12   C1   H11   116.64  3.000
 RIL  H12   C1   C2    121.63  3.000
 RIL  H11   C1   C2    121.73  3.000
 RIL  H2    C2   C5    115.78  3.000
 RIL  H2    C2   C1    119.01  3.000
 RIL  C5    C2   C1    125.20  3.000
 RIL  H52   C5   H51   106.52  3.000
 RIL  H52   C5   C7    108.74  3.000
 RIL  H51   C5   C7    110.03  3.000
 RIL  H52   C5   C2    109.10  3.000
 RIL  H51   C5   C2    110.16  3.000
 RIL  C7    C5   C2    112.12  3.000
 RIL  H72   C7   H71   106.24  3.000
 RIL  H72   C7   C10   109.14  3.000
 RIL  H71   C7   C10   110.03  3.000
 RIL  H72   C7   C5    109.40  3.000
 RIL  H71   C7   C5    109.31  3.000
 RIL  C10   C7   C5    112.51  3.000
 RIL  H102  C10  H101  106.67  3.000
 RIL  H102  C10  C13   110.00  3.000
 RIL  H101  C10  C13   109.69  3.000
 RIL  H102  C10  C7    109.04  3.000
 RIL  H101  C10  C7    109.91  3.000
 RIL  C13   C10  C7    111.41  3.000
 RIL  H132  C13  H131  106.16  3.000
 RIL  H132  C13  P16   107.03  3.000
 RIL  H131  C13  P16   109.93  3.000
 RIL  H132  C13  C10   110.46  3.000
 RIL  H131  C13  C10   110.39  3.000
 RIL  P16   C13  C10   112.61  3.000
 RIL  O1    P16  O21   106.12  3.000
 RIL  O1    P16  O20   116.26  3.000
 RIL  O21   P16  O20   108.69  3.000
 RIL  O1    P16  C13   101.49  3.000
 RIL  O21   P16  C13   107.32  3.000
 RIL  O20   P16  C13   116.17  3.000
 RIL  C23   O21  P16   122.78  3.000
 RIL  H232  C23  H231  107.59  3.000
 RIL  H232  C23  C24   109.31  3.000
 RIL  H231  C23  C24   109.72  3.000
 RIL  H232  C23  O21   109.77  3.000
 RIL  H231  C23  O21   111.63  3.000
 RIL  C24   C23  O21   108.79  3.000
 RIL  H24   C24  O28   108.65  3.000
 RIL  H24   C24  C27   111.11  3.000
 RIL  O28   C24  C27   104.04  3.000
 RIL  H24   C24  C23   109.31  3.000
 RIL  O28   C24  C23   112.07  3.000
 RIL  C27   C24  C23   111.55  3.000
 RIL  H272  C27  H271  108.00  3.000
 RIL  H272  C27  O31   109.24  3.000
 RIL  H271  C27  O31   111.72  3.000
 RIL  H272  C27  C24   112.78  3.000
 RIL  H271  C27  C24   111.51  3.000
 RIL  O31   C27  C24   103.59  3.000
 RIL  C30   O28  C24   109.43  3.000
 RIL  C38   C30  C34   111.64  3.000
 RIL  C38   C30  O31   111.18  3.000
 RIL  C34   C30  O31   109.44  3.000
 RIL  C38   C30  O28   110.49  3.000
 RIL  C34   C30  O28   108.97  3.000
 RIL  O31   C30  O28   104.89  3.000
 RIL  C30   O31  C27   107.04  3.000
 RIL  H343  C34  H342  108.56  3.000
 RIL  H343  C34  H341  107.69  3.000
 RIL  H342  C34  H341  108.63  3.000
 RIL  H343  C34  C30   110.22  3.000
 RIL  H342  C34  C30   111.04  3.000
 RIL  H341  C34  C30   110.60  3.000
 RIL  H383  C38  H382  107.94  3.000
 RIL  H383  C38  H381  107.90  3.000
 RIL  H382  C38  H381  107.70  3.000
 RIL  H383  C38  C30   110.53  3.000
 RIL  H382  C38  C30   112.40  3.000
 RIL  H381  C38  C30   110.21  3.000
 RIL  HO1   O1   P16   114.35  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   -33.92  30.0  1
 RIL  Var_02  H271  C27  O31  C30   -89.49  30.0  1
 RIL  Var_03  H341  C34  C30  O28  -178.14  30.0  3
 RIL  Var_04  H381  C38  C30  O28   -59.86  30.0  3
 RIL  Var_05  C24   C23  O21  P16  -153.54  30.0  3
 RIL  Var_06  C7    C5   C2   C1   -118.28  30.0  3
 RIL  Var_07  C10   C7   C5   C2   -174.22  30.0  3
 RIL  Var_08  C13   C10  C7   C5    179.74  30.0  3
 RIL  Var_09  P16   C13  C10  C7   -176.42  30.0  3
 RIL  Var_10  O20   P16  C13  C10   -60.07  30.0  3
 RIL  Var_11  H11   C1   C2   C5    179.42   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
 RIL  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
 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

