# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Sep 19 15:59:24 2022
#   Inital geometry file: a 99 line input string
#   Ligand name: [(3~{S})-3,7-dimethyloct-6-enyl] phosphono hydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](CCO[P](O)(=O)O[P](O)(O)=O)CCC=C(C)C
#
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
 83B  83B  "[(3S)-3,7-dimethyloct-6-enyl] phosphono hydrogen phosphate"  ligand  41  19  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_83B
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
 83B  C1    C  CH3   0  -0.703    0.8340   3.2054  14.4335
 83B  C2    C  C     0   0.081   -0.6140   3.3722  14.0719
 83B  C3    C  C1    0  -0.250   -1.2813   2.4060  13.4361
 83B  C4    C  CH2   0  -0.504   -2.7236   2.3936  13.0322
 83B  C5    C  CH2   0  -0.414   -3.5451   1.4936  13.9611
 83B  C6    C  CH1   0  -0.239   -4.9831   1.2132  13.5134
 83B  C7    C  CH2   0  -0.459   -5.7706   2.5145  13.3354
 83B  C8    C  CH2   0  -0.184   -7.2632   2.2676  13.2672
 83B  C10   C  CH3   0  -0.719   -1.2049   4.6859  14.4902
 83B  C11   C  CH3   0  -0.665   -5.0311   0.3332  12.2656
 83B  O9    O  O2    0  -0.576   -8.0108   3.4991  13.2512
 83B  O13   O  O2    0  -0.703   -9.0544   3.2896  10.9443
 83B  O15   O  OH1   0  -0.733  -10.8017   2.3414  12.5270
 83B  O16   O  O     0  -0.667   -7.1857   4.9742  11.2364
 83B  O17   O  O     0  -0.671  -11.5469   3.5662  10.3355
 83B  O18   O  OH1   0  -0.728   -9.4544   5.2628  12.5202
 83B  O19   O  OH1   0  -0.716  -10.3490   1.2285  10.4235
 83B  P12   P  P     0   1.480   -8.3043   4.3298  11.9408
 83B  P14   P  P     0   1.453  -10.5670   2.6921  10.9963
 83B  H012  H  HCH3  0   0.228    0.9824   3.3122  15.5112
 83B  H011  H  HCH3  0   0.234    1.2249   2.2332  14.1339
 83B  H013  H  HCH3  0   0.229    1.4471   3.9770  13.9602
 83B  H031  H  H     0   0.218   -0.7378   1.4918  13.2070
 83B  H041  H  HCH2  0   0.235   -3.1406   3.4020  13.0265
 83B  H042  H  HCH2  0   0.231   -2.7988   2.0270  12.0037
 83B  H052  H  HCH2  0   0.223   -3.0266   0.5365  14.0795
 83B  H051  H  HCH2  0   0.224   -3.5669   1.9518  14.9545
 83B  H061  H  HCH1  0   0.226   -5.4520   0.6531  14.3320
 83B  H071  H  HCH2  0   0.239   -5.5686   3.1792  14.1811
 83B  H072  H  HCH2  0   0.234   -5.4355   3.0339  12.4334
 83B  H081  H  HCH2  0   0.252   -7.6021   1.7467  14.1627
 83B  H082  H  HCH2  0   0.238   -7.5385   1.6522  12.4082
 83B  H101  H  HCH3  0   0.232   -0.6581   5.5166  14.0365
 83B  H103  H  HCH3  0   0.238   -2.2553   4.7961  14.2284
 83B  H102  H  HCH3  0   0.233   -1.1169   4.8152  15.5720
 83B  H111  H  HCH3  0   0.231   -6.0449   0.0040  12.0345
 83B  H112  H  HCH3  0   0.220   -4.6535   0.8606  11.3876
 83B  H113  H  HCH3  0   0.229   -4.4255  -0.5644  12.4000
 83B  H1    H  HOH1  0   0.508  -11.4609   2.8947  12.9683
 83B  H2    H  HOH1  0   0.506   -9.5812   6.0887  12.0312
 83B  H3    H  HOH1  0   0.507  -10.3076   1.1707   9.4582

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
 83B  O17  P14   double  1.470  0.020  1.470
 83B  O19  P14   single  1.587  0.020  1.587
 83B  O16  P12   double  1.471  0.020  1.471
 83B  P14  O13   single  1.627  0.020  1.627
 83B  P14  O15   single  1.588  0.020  1.588
 83B  C11  C6    single  1.528  0.020  1.528
 83B  O13  P12   single  1.624  0.020  1.624
 83B  P12  O18   single  1.590  0.020  1.590
 83B  P12  O9    single  1.579  0.020  1.579
 83B  C4   C3    single  1.498  0.020  1.498
 83B  C4   C5    single  1.532  0.020  1.532
 83B  C6   C5    single  1.532  0.020  1.532
 83B  C6   C7    single  1.531  0.020  1.531
 83B  C3   C2    double  1.335  0.020  1.335
 83B  O9   C8    single  1.441  0.020  1.441
 83B  C7   C8    single  1.514  0.020  1.514
 83B  C2   C10   single  1.500  0.020  1.500
 83B  C2   C1    single  1.502  0.020  1.502
 83B  C1   H012  single  0.970  0.020  1.090
 83B  C1   H011  single  0.970  0.020  1.090
 83B  C1   H013  single  0.970  0.020  1.090
 83B  C3   H031  single  0.930  0.020  1.080
 83B  C4   H041  single  0.970  0.020  1.090
 83B  C4   H042  single  0.970  0.020  1.090
 83B  C5   H052  single  0.970  0.020  1.090
 83B  C5   H051  single  0.970  0.020  1.090
 83B  C6   H061  single  0.970  0.020  1.090
 83B  C7   H071  single  0.970  0.020  1.090
 83B  C7   H072  single  0.970  0.020  1.090
 83B  C8   H081  single  0.970  0.020  1.090
 83B  C8   H082  single  0.970  0.020  1.090
 83B  C10  H101  single  0.970  0.020  1.090
 83B  C10  H103  single  0.970  0.020  1.090
 83B  C10  H102  single  0.970  0.020  1.090
 83B  C11  H111  single  0.970  0.020  1.090
 83B  C11  H112  single  0.970  0.020  1.090
 83B  C11  H113  single  0.970  0.020  1.090
 83B  O15  H1    single  0.850  0.020  0.980
 83B  O18  H2    single  0.850  0.020  0.980
 83B  O19  H3    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
 83B  H013  C1   H011  108.03  3.000
 83B  H013  C1   H012  106.37  3.000
 83B  H011  C1   H012  108.03  3.000
 83B  H013  C1   C2    110.98  3.000
 83B  H011  C1   C2    112.25  3.000
 83B  H012  C1   C2    110.94  3.000
 83B  C10   C2   C3    124.72  3.000
 83B  C10   C2   C1    114.20  3.000
 83B  C3    C2   C1    121.07  3.000
 83B  H031  C3   C4    114.66  3.000
 83B  H031  C3   C2    117.30  3.000
 83B  C4    C3   C2    128.00  3.000
 83B  H042  C4   H041  106.17  3.000
 83B  H042  C4   C5    109.64  3.000
 83B  H041  C4   C5    109.94  3.000
 83B  H042  C4   C3    108.80  3.000
 83B  H041  C4   C3    111.20  3.000
 83B  C5    C4   C3    110.95  3.000
 83B  H051  C5   H052  106.10  3.000
 83B  H051  C5   C6    108.85  3.000
 83B  H052  C5   C6    108.43  3.000
 83B  H051  C5   C4    108.36  3.000
 83B  H052  C5   C4    108.98  3.000
 83B  C6    C5   C4    115.70  3.000
 83B  H061  C6   C11   107.58  3.000
 83B  H061  C6   C7    107.50  3.000
 83B  C11   C6   C7    112.23  3.000
 83B  H061  C6   C5    106.06  3.000
 83B  C7    C6   C5    111.17  3.000
 83B  C11   C6   C5    111.94  3.000
 83B  H072  C7   H071  107.00  3.000
 83B  H072  C7   C8    110.02  3.000
 83B  H071  C7   C8    108.40  3.000
 83B  H072  C7   C6    110.00  3.000
 83B  H071  C7   C6    109.34  3.000
 83B  C8    C7   C6    111.93  3.000
 83B  H082  C8   H081  107.37  3.000
 83B  H082  C8   O9    110.01  3.000
 83B  H081  C8   O9    104.85  3.000
 83B  H082  C8   C7    112.07  3.000
 83B  H081  C8   C7    110.33  3.000
 83B  O9    C8   C7    111.87  3.000
 83B  H102  C10  H103  107.69  3.000
 83B  H102  C10  H101  106.30  3.000
 83B  H103  C10  H101  107.82  3.000
 83B  H102  C10  C2    110.36  3.000
 83B  H103  C10  C2    113.70  3.000
 83B  H101  C10  C2    110.65  3.000
 83B  H113  C11  H112  107.73  3.000
 83B  H113  C11  H111  107.08  3.000
 83B  H112  C11  H111  107.27  3.000
 83B  H113  C11  C6    110.84  3.000
 83B  H112  C11  C6    111.58  3.000
 83B  H111  C11  C6    112.10  3.000
 83B  P12   O9   C8    123.73  3.000
 83B  P14   O13  P12   130.16  3.000
 83B  H1    O15  P14   114.47  3.000
 83B  H2    O18  P12   114.28  3.000
 83B  H3    O19  P14   114.89  3.000
 83B  O18   P12  O16   117.87  3.000
 83B  O18   P12  O13   105.38  3.000
 83B  O16   P12  O13   109.76  3.000
 83B  O18   P12  O9     98.09  3.000
 83B  O13   P12  O9    104.96  3.000
 83B  O16   P12  O9    119.12  3.000
 83B  O19   P14  O17   118.54  3.000
 83B  O19   P14  O15    99.47  3.000
 83B  O17   P14  O15   117.79  3.000
 83B  O15   P14  O13   104.43  3.000
 83B  O19   P14  O13   101.50  3.000
 83B  O17   P14  O13   112.77  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
 83B  Var_01  C4    C3   C2   C1    178.44   0.0  2
 83B  Var_02  C10   C2   C3   C4     -1.33   0.0  2
 83B  Var_03  C5    C4   C3   C2   -104.49  30.0  1
 83B  Var_04  C6    C5   C4   C3   -170.16  30.0  3
 83B  Var_05  O9    C8   C7   C6    173.49  30.0  3
 83B  Var_06  P12   O9   C8   C7     84.64  30.0  2
 83B  Var_07  O16   P12  O9   C8    -66.90  30.0  2
 83B  Var_08  O13   P12  O9   C8     56.43  30.0  2
 83B  Var_09  O18   P12  O9   C8    164.80  30.0  2
 83B  Var_10  P14   O13  P12  O9     73.20  30.0  1
 83B  Var_11  P12   O13  P14  O15   -42.86  30.0  3
 83B  Var_12  P14   O13  P12  O16  -157.65  30.0  1
 83B  Var_13  P12   O13  P14  O17    86.20  30.0  3
 83B  Var_14  P14   O13  P12  O18   -29.77  30.0  1
 83B  Var_15  P12   O13  P14  O19  -145.91  30.0  3
 83B  Var_16  H031  C3   C2   C1      0.95   0.0  2
 83B  Var_17  H031  C3   C2   C10  -178.82   0.0  2
 83B  Var_18  H101  C10  C2   C1     58.77  30.0  3
 83B  Var_19  H103  C10  C2   C1   -179.73  30.0  3
 83B  Var_20  H102  C10  C2   C1    -58.61  30.0  3
 83B  Var_21  H041  C4   C3   C2     18.21  30.0  1
 83B  Var_22  H042  C4   C3   C2    134.80  30.0  1
 83B  Var_23  H052  C5   C4   C3    -47.71  30.0  3
 83B  Var_24  H051  C5   C4   C3     67.32  30.0  3
 83B  Var_25  H101  C10  C2   C3   -121.45  30.0  3
 83B  Var_26  H103  C10  C2   C3      0.05  30.0  3
 83B  Var_27  H102  C10  C2   C3    121.18  30.0  3
 83B  Var_28  H012  C1   C2   C3   -121.96  30.0  3
 83B  Var_29  H011  C1   C2   C3     -0.99  30.0  3
 83B  Var_30  H013  C1   C2   C3    120.01  30.0  3
 83B  Var_31  H031  C3   C4   C5     73.06  30.0  3
 83B  Var_32  H041  C4   C5   C6     66.41  30.0  1
 83B  Var_33  H042  C4   C5   C6    -49.95  30.0  1
 83B  Var_34  H081  C8   C7   C6     57.18  30.0  3
 83B  Var_35  H082  C8   C7   C6    -62.41  30.0  3
 83B  Var_36  H012  C1   C2   C10    57.83  30.0  3
 83B  Var_37  H011  C1   C2   C10   178.80  30.0  3
 83B  Var_38  H013  C1   C2   C10   -60.20  30.0  3
 83B  Var_39  H071  C7   C8   O9     52.81  30.0  2
 83B  Var_40  H072  C7   C8   O9    -63.89  30.0  2
 83B  Var_41  H081  C8   O9   P12  -155.78  30.0  3
 83B  Var_42  H082  C8   O9   P12   -40.61  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
 83B  chir_01  C6   C11  C5   C7  negativ
 83B  chir_02  P12  O13  O18  O9  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
 83B  plan-1  C1    0.020
 83B  plan-1  C2    0.020
 83B  plan-1  C3    0.020
 83B  plan-1  C4    0.020
 83B  plan-1  C10   0.020
 83B  plan-1  H031  0.020

