# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 00:05:26 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: (3R)-3-[(carboxymethyl)sulfanyl]nonanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCC[C@H](CC(O)=O)SCC(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
 B6X  B6X  '(3R)-3-[(carboxymethyl)sulfanyl]nonanoic acid'  ligand  36  16  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_B6X
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
 B6X  OAB  O  O     0  -0.430  -2.1963  -2.9405  -1.1244
 B6X  CAN  C  C     0   0.572  -1.8042  -2.7235  -0.0077
 B6X  OAD  O  OH1   0  -0.586  -1.8593  -3.6004   0.9836
 B6X  CAK  C  CH2   0  -0.691  -1.1797  -1.4299   0.4423
 B6X  SAM  S  S2    0   0.013  -1.2175  -0.2490  -0.9245
 B6X  CAP  C  CH1   0  -0.380  -0.6547   1.2718  -0.0805
 B6X  CAL  C  CH2   0  -0.547  -1.7482   1.8324   0.8188
 B6X  CAO  C  C     0   0.550  -3.0039   2.1754   0.0623
 B6X  OAE  O  O     0  -0.442  -3.0244   2.6115  -1.0616
 B6X  OAC  O  OH1   0  -0.590  -4.0987   1.9823   0.7872
 B6X  CAJ  C  CH2   0  -0.413   0.6619   1.1160   0.6720
 B6X  CAI  C  CH2   0  -0.410   1.8288   0.6470  -0.1856
 B6X  CAH  C  CH2   0  -0.412   3.1379   0.5909   0.5924
 B6X  CAG  C  CH2   0  -0.407   4.3274   0.1807  -0.2669
 B6X  CAF  C  CH2   0  -0.419   5.6334   0.1016   0.5146
 B6X  CAA  C  CH3   0  -0.662   6.8219  -0.2879  -0.3534
 B6X  H1   H  HOH1  0   0.487  -2.2596  -4.4283   0.6766
 B6X  H2   H  HCH2  0   0.308  -1.7243  -1.0548   1.3120
 B6X  H3   H  HCH2  0   0.308  -0.1560  -1.6329   0.7668
 B6X  H4   H  HCH1  0   0.291  -0.4985   1.9631  -0.9127
 B6X  H5   H  HCH2  0   0.268  -1.9687   1.1563   1.6467
 B6X  H6   H  HCH2  0   0.299  -1.3897   2.7609   1.2795
 B6X  H7   H  HOH1  0   0.479  -4.8809   2.2544   0.2835
 B6X  H8   H  HCH2  0   0.244   0.9061   2.0941   1.1000
 B6X  H9   H  HCH2  0   0.229   0.5321   0.4449   1.5268
 B6X  H10  H  HCH2  0   0.217   1.6113  -0.3400  -0.6049
 B6X  H11  H  HCH2  0   0.215   1.9372   1.3231  -1.0403
 B6X  H12  H  HCH2  0   0.209   3.3392   1.5697   1.0413
 B6X  H13  H  HCH2  0   0.210   3.0345  -0.1110   1.4271
 B6X  H14  H  HCH2  0   0.207   4.1230  -0.7900  -0.7323
 B6X  H15  H  HCH2  0   0.207   4.4402   0.8943  -1.0904
 B6X  H16  H  HCH2  0   0.210   5.8291   1.0682   0.9893
 B6X  H17  H  HCH2  0   0.210   5.5235  -0.6198   1.3301
 B6X  H18  H  HCH3  0   0.216   6.6714  -1.2664  -0.8134
 B6X  H19  H  HCH3  0   0.216   6.9752   0.4331  -1.1586
 B6X  H20  H  HCH3  0   0.226   7.7442  -0.3356   0.2270

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
 B6X  CAA  CAF  single  1.522  0.020  1.522
 B6X  CAF  CAG  single  1.524  0.020  1.524
 B6X  CAG  CAH  single  1.524  0.020  1.524
 B6X  CAH  CAI  single  1.524  0.020  1.524
 B6X  CAI  CAJ  single  1.522  0.020  1.522
 B6X  CAJ  CAP  single  1.524  0.020  1.524
 B6X  OAE  CAO  double  1.206  0.020  1.206
 B6X  OAC  CAO  single  1.327  0.020  1.327
 B6X  CAO  CAL  single  1.506  0.020  1.506
 B6X  CAP  SAM  single  1.828  0.020  1.828
 B6X  CAP  CAL  single  1.523  0.020  1.523
 B6X  SAM  CAK  single  1.807  0.020  1.807
 B6X  CAK  CAN  single  1.505  0.020  1.505
 B6X  OAB  CAN  double  1.203  0.020  1.203
 B6X  CAN  OAD  single  1.325  0.020  1.325
 B6X  OAD  H1   single  0.850  0.020  0.980
 B6X  CAK  H2   single  0.970  0.020  1.090
 B6X  CAK  H3   single  0.970  0.020  1.090
 B6X  CAP  H4   single  0.970  0.020  1.090
 B6X  CAL  H5   single  0.970  0.020  1.090
 B6X  CAL  H6   single  0.970  0.020  1.090
 B6X  OAC  H7   single  0.850  0.020  0.980
 B6X  CAJ  H8   single  0.970  0.020  1.090
 B6X  CAJ  H9   single  0.970  0.020  1.090
 B6X  CAI  H10  single  0.970  0.020  1.090
 B6X  CAI  H11  single  0.970  0.020  1.090
 B6X  CAH  H12  single  0.970  0.020  1.090
 B6X  CAH  H13  single  0.970  0.020  1.090
 B6X  CAG  H14  single  0.970  0.020  1.090
 B6X  CAG  H15  single  0.970  0.020  1.090
 B6X  CAF  H16  single  0.970  0.020  1.090
 B6X  CAF  H17  single  0.970  0.020  1.090
 B6X  CAA  H18  single  0.970  0.020  1.090
 B6X  CAA  H19  single  0.970  0.020  1.090
 B6X  CAA  H20  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
 B6X  CAK  CAN  OAD  111.25  3.000
 B6X  OAD  CAN  OAB  124.16  3.000
 B6X  CAK  CAN  OAB  124.58  3.000
 B6X  H1   OAD  CAN  110.21  3.000
 B6X  H3   CAK  H2   107.12  3.000
 B6X  H3   CAK  SAM  111.45  3.000
 B6X  H2   CAK  SAM  111.56  3.000
 B6X  H3   CAK  CAN  108.52  3.000
 B6X  H2   CAK  CAN  109.04  3.000
 B6X  SAM  CAK  CAN  109.08  3.000
 B6X  CAP  SAM  CAK  100.84  3.000
 B6X  H4   CAP  CAJ  108.49  3.000
 B6X  H4   CAP  CAL  108.63  3.000
 B6X  CAJ  CAP  CAL  111.49  3.000
 B6X  H4   CAP  SAM  102.63  3.000
 B6X  CAL  CAP  SAM  110.97  3.000
 B6X  CAJ  CAP  SAM  114.13  3.000
 B6X  H6   CAL  H5   105.77  3.000
 B6X  H6   CAL  CAO  106.90  3.000
 B6X  H5   CAL  CAO  110.72  3.000
 B6X  H6   CAL  CAP  108.97  3.000
 B6X  H5   CAL  CAP  111.41  3.000
 B6X  CAO  CAL  CAP  112.71  3.000
 B6X  OAC  CAO  OAE  123.21  3.000
 B6X  OAC  CAO  CAL  112.36  3.000
 B6X  OAE  CAO  CAL  124.40  3.000
 B6X  H7   OAC  CAO  109.94  3.000
 B6X  H9   CAJ  H8   105.59  3.000
 B6X  H9   CAJ  CAI  110.00  3.000
 B6X  H8   CAJ  CAI  108.93  3.000
 B6X  H9   CAJ  CAP  110.23  3.000
 B6X  H8   CAJ  CAP  107.11  3.000
 B6X  CAI  CAJ  CAP  114.55  3.000
 B6X  H11  CAI  H10  106.11  3.000
 B6X  H11  CAI  CAH  109.64  3.000
 B6X  H10  CAI  CAH  109.46  3.000
 B6X  H11  CAI  CAJ  108.99  3.000
 B6X  H10  CAI  CAJ  109.96  3.000
 B6X  CAH  CAI  CAJ  112.47  3.000
 B6X  H13  CAH  H12  106.11  3.000
 B6X  H13  CAH  CAG  109.32  3.000
 B6X  H12  CAH  CAG  109.16  3.000
 B6X  H13  CAH  CAI  109.36  3.000
 B6X  H12  CAH  CAI  109.53  3.000
 B6X  CAG  CAH  CAI  113.12  3.000
 B6X  H15  CAG  H14  106.08  3.000
 B6X  H15  CAG  CAF  109.33  3.000
 B6X  H14  CAG  CAF  109.37  3.000
 B6X  H15  CAG  CAH  109.20  3.000
 B6X  H14  CAG  CAH  109.42  3.000
 B6X  CAF  CAG  CAH  113.19  3.000
 B6X  H17  CAF  H16  106.08  3.000
 B6X  H17  CAF  CAA  109.55  3.000
 B6X  H16  CAF  CAA  109.49  3.000
 B6X  H17  CAF  CAG  109.29  3.000
 B6X  H16  CAF  CAG  109.26  3.000
 B6X  CAA  CAF  CAG  112.94  3.000
 B6X  H20  CAA  H19  107.61  3.000
 B6X  H20  CAA  H18  107.56  3.000
 B6X  H19  CAA  H18  107.49  3.000
 B6X  H20  CAA  CAF  111.59  3.000
 B6X  H19  CAA  CAF  111.18  3.000
 B6X  H18  CAA  CAF  111.22  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
 B6X  CONST_01  H1   OAD  CAN  OAB     0.00   0.0  0
 B6X  CONST_02  H7   OAC  CAO  CAL   180.00   0.0  0
 B6X  Var_01    SAM  CAK  CAN  OAB     3.56  30.0  1
 B6X  Var_02    CAH  CAI  CAJ  CAP   176.43  30.0  1
 B6X  Var_03    OAE  CAO  CAL  CAP   -35.03  30.0  1
 B6X  Var_04    CAG  CAH  CAI  CAJ  -177.53  30.0  1
 B6X  Var_05    CAF  CAG  CAH  CAI  -179.04  30.0  1
 B6X  Var_06    CAA  CAF  CAG  CAH  -179.12  30.0  1
 B6X  Var_07    H18  CAA  CAF  CAG   -60.03  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
 B6X  chir_01  CAP  CAJ  SAM  CAL  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
 B6X  plan-1  OAB  0.020
 B6X  plan-1  CAN  0.020
 B6X  plan-1  OAD  0.020
 B6X  plan-1  CAK  0.020
 B6X  plan-1  H1   0.020
 B6X  plan-2  CAL  0.020
 B6X  plan-2  CAO  0.020
 B6X  plan-2  OAE  0.020
 B6X  plan-2  OAC  0.020
 B6X  plan-2  H7   0.020

