# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 12:10:04 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: (R)-[(3R,4S,5S,7R)-4,8-dihydroxy-3,5,7-trimethyl-2-oxooctyl]phosphinic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](CO)C[C@H](C)[C@H](O)[C@@H](C)C(=O)C[P@@H](O)=O
#
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
 YML  YML  '(R)-[(3R,4S,5S,7R)-4,8-dihydroxy-3,5,7-trimethyl-2-oxooctyl]phosphinic acid'  ligand  39  17  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YML
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
 YML  C8    C  CH1    0  -0.269   4.5047   0.1143  -0.2072
 YML  C4    C  CH1    0  -0.416  -0.5690  -0.5237  -0.4838
 YML  C3    C  C      0   0.456  -1.8637   0.2609  -0.6148
 YML  C7    C  CH2    0  -0.424   3.1576   0.6627  -0.6882
 YML  C6    C  CH1    0  -0.273   1.9962  -0.3395  -0.6024
 YML  C2    C  CH2    0  -0.844  -3.1522  -0.5033  -0.6069
 YML  C5    C  CH1    0   0.073   0.6570   0.3983  -0.4431
 YML  C9    C  CH2    0  -0.127   4.5496   0.1464   1.3136
 YML  P1    P  P      0   0.972  -4.1366  -0.1529   0.9281
 YML  O1P   O  OP    -1  -0.808  -5.4016  -0.9751   0.8625
 YML  O2P   O  O      0  -0.795  -3.2309  -0.2370   2.1326
 YML  OC3   O  O      0  -0.421  -1.8743   1.4643  -0.7749
 YML  OC5   O  OH1    0  -0.667   0.6457   1.1881   0.7307
 YML  CAB   C  CH3    0  -0.679   2.0095  -1.2555  -1.8238
 YML  CAA   C  CH3    0  -0.658   5.6616   0.9014  -0.8141
 YML  OC9   O  OH1    0  -0.675   5.7040  -0.5225   1.7737
 YML  H8    H  HCH1   0   0.219   4.5963  -0.9323  -0.5249
 YML  H4    H  HCH1   0   0.274  -0.5347  -1.1047  -1.4152
 YML  H71   H  HCH2   0   0.229   2.9264   1.5644  -0.1134
 YML  H72   H  HCH2   0   0.225   3.2503   0.9901  -1.7292
 YML  H6    H  HCH1   0   0.220   2.1395  -0.9735   0.2836
 YML  H21   H  HCH2   0   0.284  -3.7636  -0.1829  -1.4543
 YML  H22   H  HCH2   0   0.265  -3.0107  -1.5822  -0.6837
 YML  H5    H  HCH1   0   0.225   0.5745   1.1075  -1.2737
 YML  H91   H  HCH2   0   0.184   4.5374   1.1967   1.6404
 YML  H92   H  HCH2   0   0.194   3.6401  -0.3166   1.7203
 YML  HP1   H  H      0  -0.043  -4.4568   1.2197   0.6887
 YML  HOC5  H  HOH1   0   0.438   0.8435   0.6191   1.4814
 YML  HAB1  H  HCH3   0   0.237   3.0118  -1.6490  -1.9990
 YML  HAB2  H  HCH3   0   0.232   1.3457  -2.1140  -1.7154
 YML  HAB3  H  HCH3   0   0.223   1.7115  -0.7129  -2.7246
 YML  HAA1  H  HCH3   0   0.229   6.6285   0.5492  -0.4553
 YML  HAA2  H  HCH3   0   0.226   5.6596   0.8164  -1.9020
 YML  HAA3  H  HCH3   0   0.212   5.5800   1.9630  -0.5672
 YML  HOC9  H  HOH1   0   0.452   5.7337  -0.4427   2.7309
 YML  CAC   C  CH3    0  -0.680  -0.5866  -1.5274   0.6715
 YML  HAC1  H  HCH3   0   0.233  -0.6556  -1.0333   1.6387
 YML  HAC2  H  HCH3   0   0.244  -1.4328  -2.2065   0.6063
 YML  HAC3  H  HCH3   0   0.239   0.3158  -2.1384   0.6552

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
 YML  C8   C7    single  1.532  0.020  1.532
 YML  C8   C9    single  1.522  0.020  1.522
 YML  C8   CAA   single  1.525  0.020  1.525
 YML  C8   H8    single  0.939  0.020  1.096
 YML  C4   C3    single  1.520  0.020  1.520
 YML  C4   C5    single  1.535  0.020  1.535
 YML  C4   CAC   single  1.530  0.020  1.530
 YML  C4   H4    single  0.939  0.020  1.096
 YML  C3   C2    single  1.498  0.020  1.498
 YML  C3   OC3   double  1.214  0.020  1.214
 YML  C7   C6    single  1.536  0.020  1.536
 YML  C7   H71   single  0.939  0.020  1.096
 YML  C7   H72   single  0.939  0.020  1.096
 YML  C6   C5    single  1.537  0.020  1.537
 YML  C6   CAB   single  1.527  0.020  1.527
 YML  C6   H6    single  0.939  0.020  1.096
 YML  C2   P1    single  1.857  0.020  1.857
 YML  C2   H21   single  0.939  0.020  1.096
 YML  C2   H22   single  0.939  0.020  1.096
 YML  C5   OC5   single  1.415  0.020  1.415
 YML  C5   H5    single  0.939  0.020  1.096
 YML  C9   OC9   single  1.411  0.020  1.411
 YML  C9   H91   single  0.939  0.020  1.096
 YML  C9   H92   single  0.939  0.020  1.096
 YML  P1   O1P   deloc   1.510  0.020  1.510
 YML  P1   O2P   deloc   1.509  0.020  1.509
 YML  P1   HP1   single  1.209  0.020  1.412
 YML  CAC  HAC1  single  0.970  0.020  1.090
 YML  CAC  HAC2  single  0.970  0.020  1.090
 YML  CAC  HAC3  single  0.970  0.020  1.090
 YML  OC5  HOC5  single  0.850  0.020  0.980
 YML  CAB  HAB1  single  0.970  0.020  1.090
 YML  CAB  HAB2  single  0.970  0.020  1.090
 YML  CAB  HAB3  single  0.970  0.020  1.090
 YML  CAA  HAA1  single  0.970  0.020  1.090
 YML  CAA  HAA2  single  0.970  0.020  1.090
 YML  CAA  HAA3  single  0.970  0.020  1.090
 YML  OC9  HOC9  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
 YML  H8    C8   CAA   108.28  3.000
 YML  H8    C8   C9    107.87  3.000
 YML  CAA   C8   C9    111.37  3.000
 YML  H8    C8   C7    108.89  3.000
 YML  CAA   C8   C7    110.94  3.000
 YML  C9    C8   C7    109.40  3.000
 YML  H4    C4   CAC   107.08  3.000
 YML  H4    C4   C5    108.38  3.000
 YML  CAC   C4   C5    112.53  3.000
 YML  H4    C4   C3    103.09  3.000
 YML  CAC   C4   C3    113.20  3.000
 YML  C5    C4   C3    111.89  3.000
 YML  OC3   C3   C2    119.92  3.000
 YML  OC3   C3   C4    122.05  3.000
 YML  C2    C3   C4    117.97  3.000
 YML  H72   C7   H71   105.72  3.000
 YML  H72   C7   C6    108.19  3.000
 YML  H71   C7   C6    110.40  3.000
 YML  H72   C7   C8    109.33  3.000
 YML  H71   C7   C8    108.42  3.000
 YML  C6    C7   C8    114.44  3.000
 YML  H6    C6   CAB   107.32  3.000
 YML  H6    C6   C5    107.87  3.000
 YML  CAB   C6   C5    112.23  3.000
 YML  H6    C6   C7    108.84  3.000
 YML  CAB   C6   C7    109.88  3.000
 YML  C5    C6   C7    110.56  3.000
 YML  H22   C2   H21   107.93  3.000
 YML  H22   C2   P1    108.27  3.000
 YML  H21   C2   P1    106.80  3.000
 YML  H22   C2   C3    113.12  3.000
 YML  H21   C2   C3    109.12  3.000
 YML  P1    C2   C3    111.35  3.000
 YML  H5    C5   OC5   105.49  3.000
 YML  H5    C5   C6    107.33  3.000
 YML  OC5   C5   C6    111.15  3.000
 YML  H5    C5   C4    107.98  3.000
 YML  OC5   C5   C4    110.54  3.000
 YML  C6    C5   C4    113.89  3.000
 YML  H92   C9   H91   106.45  3.000
 YML  H92   C9   OC9   110.90  3.000
 YML  H91   C9   OC9   111.40  3.000
 YML  H92   C9   C8    109.67  3.000
 YML  H91   C9   C8    108.46  3.000
 YML  OC9   C9   C8    109.87  3.000
 YML  HP1   P1   O2P   108.75  3.000
 YML  HP1   P1   O1P   109.14  3.000
 YML  O2P   P1   O1P   120.46  3.000
 YML  HP1   P1   C2     99.29  3.000
 YML  O2P   P1   C2    109.33  3.000
 YML  O1P   P1   C2    107.78  3.000
 YML  HOC5  OC5  C5    108.39  3.000
 YML  HAB3  CAB  HAB2  107.86  3.000
 YML  HAB3  CAB  HAB1  107.30  3.000
 YML  HAB2  CAB  HAB1  106.93  3.000
 YML  HAB3  CAB  C6    111.04  3.000
 YML  HAB2  CAB  C6    112.80  3.000
 YML  HAB1  CAB  C6    110.66  3.000
 YML  HAA3  CAA  HAA2  107.50  3.000
 YML  HAA3  CAA  HAA1  107.80  3.000
 YML  HAA2  CAA  HAA1  107.74  3.000
 YML  HAA3  CAA  C8    110.78  3.000
 YML  HAA2  CAA  C8    110.80  3.000
 YML  HAA1  CAA  C8    112.04  3.000
 YML  HOC9  OC9  C9    108.10  3.000
 YML  HAC3  CAC  HAC2  107.05  3.000
 YML  HAC3  CAC  HAC1  108.69  3.000
 YML  HAC2  CAC  HAC1  106.71  3.000
 YML  HAC3  CAC  C4    110.29  3.000
 YML  HAC2  CAC  C4    111.93  3.000
 YML  HAC1  CAC  C4    111.96  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
 YML  Var_01  P1   C2  C3  C4   111.92  30.0  3
 YML  Var_02  O1P  P1  C2  C3  -179.17  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
 YML  chir_01  C8  C7   C9  CAA  positiv
 YML  chir_02  C4  C3   C5  CAC  negativ
 YML  chir_03  C6  C7   C5  CAB  negativ
 YML  chir_04  C5  OC5  C6  C4   negativ

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
 YML  plan-1  C4   0.020
 YML  plan-1  C3   0.020
 YML  plan-1  C2   0.020
 YML  plan-1  OC3  0.020

