# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 07:20:33 2022
#   Inital geometry file: a 166 line input string
#   Ligand name: [(2~{R})-2-butanoyloxy-3-[oxidanyl-[(2~{R},3~{R},5~{S},6~{R})-2,4,6-tris(oxidanyl)-3,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] butanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC(=O)OC[C@H](CO[P](O)(=O)O[C@@H]1[C@H](O)[C@H](O[P](O)(O)=O)[C@@H](O)[C@H](O[P](O)(O)=O)[C@H]1O)OC(=O)CCC
#
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
 I35  I35  '[(2~{R})-2-butanoyloxy-3-[oxidanyl-[(2~{R},3~{R},5~{S},6~{R})-2,4,6-tris(oxidanyl)-3,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] butanoate'  ligand  67  39  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_I35
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
 I35  C1   C  CH1    0   0.040   2.9921  15.2247   -4.1791
 I35  C2   C  CH1    0  -0.079   3.4922  13.9706   -3.4705
 I35  C3   C  CH1    0   0.092   3.4317  14.1609   -1.9447
 I35  C4   C  CH1    0   0.053   2.0205  14.5453   -1.5200
 I35  C5   C  CH1    0  -0.049   1.5207  15.7788   -2.2662
 I35  C6   C  CH1    0   0.072   1.5695  15.6037   -3.7836
 I35  O1   O  O2     0  -0.636   3.0448  15.0511   -5.5861
 I35  O2   O  OH1    0  -0.731   2.7834  12.8363   -3.8835
 I35  O3   O  O2     0  -0.668   3.7980  13.0200   -1.2148
 I35  O4   O  OH1    0  -0.688   1.9995  14.7905   -0.1289
 I35  O5   O  O2     0  -0.675   0.2063  16.0334   -1.8303
 I35  O6   O  OH1    0  -0.738   1.1812  16.7614   -4.4685
 I35  P1   P  P      0   1.353   4.1764  15.7573   -6.5295
 I35  O11  O  OP    -1  -0.789   4.5812  17.0962   -5.9978
 I35  O12  O  O      0  -0.782   3.6854  15.5963   -7.9350
 I35  O13  O  O2     0  -0.621   5.5068  14.8092   -6.2711
 I35  P3   P  P      0   1.261   5.0485  11.9608   -1.6684
 I35  O31  O  OP    -1  -0.862   5.1539  11.0749   -0.4416
 I35  O32  O  OP    -1  -0.876   6.2598  12.8269   -1.9807
 I35  O33  O  O      0  -0.879   4.4792  11.2265   -2.9115
 I35  P5   P  P      0   1.251  -0.2154  17.6489   -1.4737
 I35  O51  O  OP    -1  -0.857  -1.7112  17.5478   -1.2539
 I35  O52  O  O      0  -0.874   0.1962  18.4005   -2.7621
 I35  O53  O  OP    -1  -0.869   0.6248  18.0167   -0.2599
 I35  C7   C  CH2    0  -0.212   5.5200  13.4034   -6.3493
 I35  C8   C  CH1    0  -0.045   5.3412  12.8319   -7.7589
 I35  C9   C  CH2    0  -0.215   6.2770  11.6502   -7.9722
 I35  C10  C  C      0   0.601   6.4752   9.8871   -9.5403
 I35  C11  C  CH2    0  -0.571   6.0068   9.4211  -10.8919
 I35  C12  C  CH2    0  -0.423   6.4633   8.0161  -11.2498
 I35  C13  C  CH3    0  -0.662   5.9623   7.6023  -12.6258
 I35  C15  C  CH2    0  -0.529   1.8943  11.4743   -7.9952
 I35  C16  C  CH2    0  -0.440   1.0450  12.6008   -7.3955
 I35  C17  C  CH3    0  -0.661  -0.4105  12.4889   -7.8214
 I35  O14  O  O2     0  -0.453   3.9805  12.5285   -8.0881
 I35  O15  O  O2     0  -0.463   5.9524  11.0721   -9.2331
 I35  O16  O  O      0  -0.443   7.2297   9.2883   -8.8173
 I35  O17  O  O      0  -0.453   3.7895  10.7807   -6.6935
 I35  H1   H  HCH1   0   0.197   3.6465  16.0543   -3.8785
 I35  H2   H  HCH1   0   0.204   4.5562  13.8764   -3.7285
 I35  H3   H  HCH1   0   0.160   4.1010  15.0050   -1.7010
 I35  H4   H  HCH1   0   0.167   1.3538  13.7034   -1.7691
 I35  H5   H  HCH1   0   0.180   2.1928  16.6118   -1.9987
 I35  H6   H  HCH1   0   0.158   0.8983  14.7666   -4.0437
 I35  H7   H  HOH1   0   0.440   3.3719  12.0760   -3.5648
 I35  H8   H  HOH1   0   0.430   1.2523  15.3799    0.0335
 I35  H9   H  HOH1   0   0.441   0.7861  17.4251   -3.8190
 I35  H15  H  HCH2   0   0.242   4.7935  12.9562   -5.6681
 I35  H16  H  HCH2   0   0.236   6.5051  13.1003   -5.9821
 I35  H17  H  HCH1   0   0.271   5.6009  13.6067   -8.4813
 I35  H18  H  HCH2   0   0.254   6.2008  10.9154   -7.1728
 I35  H19  H  HCH2   0   0.259   7.3023  12.0304   -7.9849
 I35  H20  H  HCH2   0   0.273   6.3655  10.1393  -11.6370
 I35  H21  H  HCH2   0   0.269   4.9152   9.4906  -10.9247
 I35  H22  H  HCH2   0   0.226   7.5535   7.9625  -11.2243
 I35  H23  H  HCH2   0   0.227   6.1013   7.3091  -10.5001
 I35  H24  H  HCH3   0   0.231   6.2865   6.5919  -12.8745
 I35  H25  H  HCH3   0   0.220   4.8722   7.6221  -12.6730
 I35  H26  H  HCH3   0   0.220   6.3377   8.2714  -13.4019
 I35  H27  H  HCH2   0   0.255   1.8668  11.5385   -9.0858
 I35  H28  H  HCH2   0   0.251   1.4779  10.5071   -7.7104
 I35  H29  H  HCH2   0   0.228   1.1186  12.5687   -6.3060
 I35  H30  H  HCH2   0   0.230   1.4467  13.5672   -7.7033
 I35  H31  H  HCH3   0   0.233  -1.0081  13.2909   -7.3876
 I35  H32  H  HCH3   0   0.220  -0.5100  12.5508   -8.9064
 I35  H33  H  HCH3   0   0.221  -0.8465  11.5407   -7.5030
 I35  C14  C  C      0   0.576   3.3195  11.5292   -7.5154

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
 I35  C12  C11  single  1.520  0.020  1.520
 I35  C12  C13  single  1.522  0.020  1.522
 I35  O15  C10  single  1.331  0.020  1.331
 I35  O15  C9   single  1.425  0.020  1.425
 I35  C10  O16  double  1.204  0.020  1.204
 I35  C10  C11  single  1.504  0.020  1.504
 I35  O14  C14  single  1.328  0.020  1.328
 I35  O14  C8   single  1.432  0.020  1.432
 I35  C14  O17  double  1.207  0.020  1.207
 I35  C14  C15  single  1.505  0.020  1.505
 I35  C15  C16  single  1.533  0.020  1.533
 I35  C8   C9   single  1.522  0.020  1.522
 I35  C8   C7   single  1.532  0.020  1.532
 I35  O12  P1   deloc   1.497  0.020  1.497
 I35  C16  C17  single  1.521  0.020  1.521
 I35  O13  C7   single  1.408  0.020  1.408
 I35  O13  P1   single  1.654  0.020  1.654
 I35  P1   O11  deloc   1.496  0.020  1.496
 I35  P1   O1   single  1.634  0.020  1.634
 I35  O1   C1   single  1.419  0.020  1.419
 I35  C1   C2   single  1.525  0.020  1.525
 I35  C1   C6   single  1.524  0.020  1.524
 I35  O2   C2   single  1.400  0.020  1.400
 I35  C2   C3   single  1.539  0.020  1.539
 I35  O6   C6   single  1.400  0.020  1.400
 I35  C6   C5   single  1.528  0.020  1.528
 I35  C3   O3   single  1.403  0.020  1.403
 I35  C3   C4   single  1.523  0.020  1.523
 I35  O3   P3   single  1.700  0.020  1.700
 I35  O33  P3   deloc   1.552  0.020  1.552
 I35  C5   C4   single  1.526  0.020  1.526
 I35  C5   O5   single  1.408  0.020  1.408
 I35  O31  P3   deloc   1.517  0.020  1.517
 I35  C4   O4   single  1.413  0.020  1.413
 I35  O52  P5   deloc   1.547  0.020  1.547
 I35  P3   O32  deloc   1.521  0.020  1.521
 I35  O5   P5   single  1.707  0.020  1.707
 I35  P5   O51  deloc   1.515  0.020  1.515
 I35  P5   O53  deloc   1.521  0.020  1.521
 I35  C1   H1   single  0.970  0.020  1.090
 I35  C2   H2   single  0.970  0.020  1.090
 I35  C3   H3   single  0.970  0.020  1.090
 I35  C4   H4   single  0.970  0.020  1.090
 I35  C5   H5   single  0.970  0.020  1.090
 I35  C6   H6   single  0.970  0.020  1.090
 I35  O2   H7   single  0.850  0.020  0.980
 I35  O4   H8   single  0.850  0.020  0.980
 I35  O6   H9   single  0.850  0.020  0.980
 I35  C7   H15  single  0.970  0.020  1.090
 I35  C7   H16  single  0.970  0.020  1.090
 I35  C8   H17  single  0.970  0.020  1.090
 I35  C9   H18  single  0.970  0.020  1.090
 I35  C9   H19  single  0.970  0.020  1.090
 I35  C11  H20  single  0.970  0.020  1.090
 I35  C11  H21  single  0.970  0.020  1.090
 I35  C12  H22  single  0.970  0.020  1.090
 I35  C12  H23  single  0.970  0.020  1.090
 I35  C13  H24  single  0.970  0.020  1.090
 I35  C13  H25  single  0.970  0.020  1.090
 I35  C13  H26  single  0.970  0.020  1.090
 I35  C15  H27  single  0.970  0.020  1.090
 I35  C15  H28  single  0.970  0.020  1.090
 I35  C16  H29  single  0.970  0.020  1.090
 I35  C16  H30  single  0.970  0.020  1.090
 I35  C17  H31  single  0.970  0.020  1.090
 I35  C17  H32  single  0.970  0.020  1.090
 I35  C17  H33  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
 I35  H1   C1   O1   109.97  3.000
 I35  H1   C1   C6   107.28  3.000
 I35  O1   C1   C6   108.81  3.000
 I35  H1   C1   C2   107.38  3.000
 I35  C6   C1   C2   112.96  3.000
 I35  O1   C1   C2   110.37  3.000
 I35  H2   C2   O2   110.58  3.000
 I35  H2   C2   C3   106.35  3.000
 I35  O2   C2   C3   111.89  3.000
 I35  H2   C2   C1   106.20  3.000
 I35  C3   C2   C1   110.26  3.000
 I35  O2   C2   C1   111.30  3.000
 I35  H3   C3   O3   110.40  3.000
 I35  H3   C3   C4   107.88  3.000
 I35  O3   C3   C4   107.58  3.000
 I35  H3   C3   C2   106.83  3.000
 I35  C4   C3   C2   110.13  3.000
 I35  O3   C3   C2   113.89  3.000
 I35  H4   C4   O4   110.25  3.000
 I35  H4   C4   C5   107.99  3.000
 I35  O4   C4   C5   109.66  3.000
 I35  H4   C4   C3   107.73  3.000
 I35  O4   C4   C3   109.40  3.000
 I35  C5   C4   C3   111.78  3.000
 I35  H5   C5   O5   110.92  3.000
 I35  H5   C5   C6   107.93  3.000
 I35  O5   C5   C6   110.97  3.000
 I35  H5   C5   C4   106.99  3.000
 I35  O5   C5   C4   107.49  3.000
 I35  C6   C5   C4   112.49  3.000
 I35  H6   C6   O6   110.07  3.000
 I35  H6   C6   C5   107.54  3.000
 I35  O6   C6   C5   112.47  3.000
 I35  H6   C6   C1   108.52  3.000
 I35  C5   C6   C1   108.41  3.000
 I35  O6   C6   C1   109.73  3.000
 I35  P1   O1   C1   123.06  3.000
 I35  H7   O2   C2   102.78  3.000
 I35  P3   O3   C3   124.04  3.000
 I35  H8   O4   C4   106.44  3.000
 I35  P5   O5   C5   117.80  3.000
 I35  H9   O6   C6   109.72  3.000
 I35  O13  P1   O12  110.41  3.000
 I35  O13  P1   O11  103.88  3.000
 I35  O12  P1   O11  121.23  3.000
 I35  O11  P1   O1   111.65  3.000
 I35  O13  P1   O1   102.66  3.000
 I35  O12  P1   O1   105.57  3.000
 I35  C7   O13  P1   124.84  3.000
 I35  O33  P3   O32  113.39  3.000
 I35  O32  P3   O31  116.30  3.000
 I35  O33  P3   O31  113.39  3.000
 I35  O32  P3   O3   106.60  3.000
 I35  O31  P3   O3   101.49  3.000
 I35  O33  P3   O3   103.80  3.000
 I35  O53  P5   O52  113.58  3.000
 I35  O53  P5   O51  116.46  3.000
 I35  O52  P5   O51  114.57  3.000
 I35  O53  P5   O5   105.01  3.000
 I35  O51  P5   O5   102.18  3.000
 I35  O52  P5   O5   102.71  3.000
 I35  H16  C7   H15  106.04  3.000
 I35  H16  C7   C8   108.10  3.000
 I35  H15  C7   C8   110.11  3.000
 I35  H16  C7   O13  105.45  3.000
 I35  H15  C7   O13  111.59  3.000
 I35  C8   C7   O13  114.99  3.000
 I35  H17  C8   O14  102.97  3.000
 I35  H17  C8   C9   108.20  3.000
 I35  O14  C8   C9   112.79  3.000
 I35  H17  C8   C7   108.47  3.000
 I35  C9   C8   C7   110.29  3.000
 I35  O14  C8   C7   113.67  3.000
 I35  H19  C9   H18  107.99  3.000
 I35  H19  C9   O15  110.15  3.000
 I35  H18  C9   O15  111.11  3.000
 I35  H19  C9   C8   107.94  3.000
 I35  H18  C9   C8   112.21  3.000
 I35  O15  C9   C8   107.39  3.000
 I35  O16  C10  O15  123.37  3.000
 I35  O16  C10  C11  125.48  3.000
 I35  O15  C10  C11  111.15  3.000
 I35  H21  C11  H20  105.34  3.000
 I35  H21  C11  C12  110.56  3.000
 I35  H20  C11  C12  110.33  3.000
 I35  H21  C11  C10  108.53  3.000
 I35  H20  C11  C10  107.82  3.000
 I35  C12  C11  C10  113.85  3.000
 I35  H23  C12  H22  106.44  3.000
 I35  H23  C12  C13  109.61  3.000
 I35  H22  C12  C13  109.66  3.000
 I35  H23  C12  C11  109.71  3.000
 I35  H22  C12  C11  109.87  3.000
 I35  C13  C12  C11  111.43  3.000
 I35  H26  C13  H25  107.56  3.000
 I35  H26  C13  H24  107.69  3.000
 I35  H25  C13  H24  107.70  3.000
 I35  H26  C13  C12  111.29  3.000
 I35  H25  C13  C12  111.28  3.000
 I35  H24  C13  C12  111.13  3.000
 I35  H28  C15  H27  107.64  3.000
 I35  H28  C15  C16  109.75  3.000
 I35  H27  C15  C16  109.47  3.000
 I35  H28  C15  C14  108.10  3.000
 I35  H27  C15  C14  109.87  3.000
 I35  C16  C15  C14  111.91  3.000
 I35  H30  C16  H29  106.41  3.000
 I35  H30  C16  C17  109.79  3.000
 I35  H29  C16  C17  109.98  3.000
 I35  H30  C16  C15  109.67  3.000
 I35  H29  C16  C15  109.34  3.000
 I35  C17  C16  C15  111.51  3.000
 I35  H33  C17  H32  107.64  3.000
 I35  H33  C17  H31  107.70  3.000
 I35  H32  C17  H31  107.70  3.000
 I35  H33  C17  C16  111.38  3.000
 I35  H32  C17  C16  111.19  3.000
 I35  H31  C17  C16  111.04  3.000
 I35  C14  O14  C8   122.22  3.000
 I35  C10  O15  C9   118.43  3.000
 I35  O17  C14  O14  124.50  3.000
 I35  O17  C14  C15  124.28  3.000
 I35  O14  C14  C15  111.19  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
 I35  Var_01  O12  P1   O1   C1   -166.62  30.0  2
 I35  Var_02  O33  P3   O3   C3    -71.06  30.0  3
 I35  Var_03  O52  P5   O5   C5     52.87  30.0  3
 I35  Var_04  C8   C7   O13  P1     69.12  30.0  3
 I35  Var_05  O17  C14  O14  C8     -1.06  30.0  3
 I35  Var_06  O16  C10  O15  C9     -1.45  30.0  3
 I35  Var_07  C13  C12  C11  C10  -179.89  30.0  2
 I35  Var_08  O15  C10  C11  C12  -174.63  30.0  2
 I35  Var_09  C17  C16  C15  C14  -176.66  30.0  3
 I35  Var_10  O14  C14  C15  C16   -73.66  30.0  1
 I35  Var_11  H18  C9   O15  C10   -45.46  30.0  3
 I35  Var_12  H24  C13  C12  C11  -179.60  30.0  3
 I35  Var_13  H31  C17  C16  C15   179.76  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
 I35  chir_01  C1  O1   C2  C6  positiv
 I35  chir_02  C2  O2   C1  C3  negativ
 I35  chir_03  C3  O3   C4  C2  positiv
 I35  chir_04  C4  O4   C3  C5  positiv
 I35  chir_05  C5  O5   C6  C4  positiv
 I35  chir_06  C6  O6   C5  C1  positiv
 I35  chir_08  C8  O14  C9  C7  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
 I35  plan-1  C10  0.020
 I35  plan-1  C11  0.020
 I35  plan-1  O15  0.020
 I35  plan-1  O16  0.020
 I35  plan-2  C15  0.020
 I35  plan-2  O14  0.020
 I35  plan-2  O17  0.020
 I35  plan-2  C14  0.020

