# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 07:23:38 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: 2-[(~{E},6~{R},10~{S})-6,10-bis(oxidanyl)undec-1-enyl]-4,6-bis(oxidanyl)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](O)CCC[C@H](O)CCC/C=C/c1cc(O)cc(O)c1C(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
 C3L  C3L  '2-[(~{E},6~{R},10~{S})-6,10-bis(oxidanyl)undec-1-enyl]-4,6-bis(oxidanyl)benzoic acid'  ligand  49  24  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C3L
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
 C3L  CAA  C  CH3    0  -0.680   9.8689   0.9514   0.4545
 C3L  CAF  C  C1     0  -0.196  -1.3909  -0.1289  -0.9616
 C3L  CAG  C  C1     0  -0.310  -2.4298   0.4591  -0.3660
 C3L  CAH  C  CR16   0  -0.490  -6.2224  -1.3575   0.3151
 C3L  CAI  C  CR16   0  -0.501  -3.8419  -1.5539   0.0182
 C3L  CAJ  C  CH2    0  -0.483  -0.0687   0.5243  -1.1979
 C3L  CAM  C  CH2    0  -0.445   7.4046   0.6396   0.0328
 C3L  CAN  C  CH2    0  -0.444   2.4321   0.4166  -0.7994
 C3L  CAO  C  CH2    0  -0.444   4.9166   0.4593  -0.3853
 C3L  CAR  C  CR6    0   0.382  -5.0769  -2.1441   0.2305
 C3L  CAS  C  CR6    0   0.365  -6.1124   0.0192   0.1763
 C3L  CAT  C  CR6    0   0.124  -3.7385  -0.1640  -0.1168
 C3L  CAU  C  CR6    0  -0.194  -4.8784   0.6391  -0.0348
 C3L  CAV  C  CH1    0   0.033   8.6403   0.1016   0.7478
 C3L  CAW  C  CH1    0   0.041   3.6025  -0.2586  -0.0903
 C3L  OAB  O  O      0  -0.604  -4.3779   2.8067   0.7535
 C3L  OAE  O  OH1    0  -0.670   3.6744  -1.6404  -0.3934
 C3L  OAP  O  OC    -1  -0.593  -5.2275   2.5921  -1.2981
 C3L  OAV  O  OH1    0  -0.669   8.8744  -1.2645   0.4516
 C3L  H1   H  HCH3   0   0.224   9.7115   1.9844   0.7677
 C3L  H2   H  HCH3   0   0.232  10.7458   0.5724   0.9809
 C3L  H3   H  HCH3   0   0.217  10.0936   0.9614  -0.6153
 C3L  H4   H  H      0   0.238  -1.4791  -1.1549  -1.3117
 C3L  H5   H  H      0   0.240  -2.3246   1.4923  -0.0504
 C3L  H6   H  HCR6   0   0.267  -7.1850  -1.8237   0.4968
 C3L  H7   H  HCR6   0   0.254  -2.9511  -2.1709  -0.0209
 C3L  H8   H  HCH2   0   0.230   0.1453   0.5186  -2.2730
 C3L  H9   H  HCH2   0   0.230  -0.1088   1.5737  -0.8928
 C3L  H10  H  HCH2   0   0.218   0.9006  -0.1394   0.6088
 C3L  H11  H  HCH2   0   0.220   1.0657  -1.2485  -0.7363
 C3L  H12  H  HCH2   0   0.216   6.2476  -1.1756   0.0532
 C3L  H13  H  HCH2   0   0.211   7.5871   0.6407  -1.0496
 C3L  H14  H  HCH2   0   0.214   2.5963   0.3818  -1.8839
 C3L  H15  H  HCH2   0   0.221   2.4317   1.4779  -0.5310
 C3L  H16  H  HCH2   0   0.218   4.8015   1.5118  -0.1068
 C3L  H17  H  HCH2   0   0.212   5.0924   0.4532  -1.4688
 C3L  H18  H  HCH1   0   0.212   8.4507   0.1278   1.8264
 C3L  H19  H  HCH1   0   0.210   3.4228  -0.2150   0.9908
 C3L  H20  H  HOH1   0   0.472  -4.3787  -3.9201   0.2918
 C3L  H21  H  HOH1   0   0.471  -7.9896   0.2952   0.4050
 C3L  H22  H  HOH1   0   0.438   3.8459  -1.7276  -1.3376
 C3L  H24  H  HOH1   0   0.438   9.0063  -1.3426  -0.4995
 C3L  H25  H  HCH2   0   0.218   7.2756   1.6895   0.3154
 C3L  H26  H  HCH2   0   0.207   5.9430  -0.1173   1.4154
 C3L  OAC  O  OH1    0  -0.641  -5.2308  -3.4786   0.3769
 C3L  CAQ  C  C      0   0.347  -4.8239   2.1521  -0.2076
 C3L  CAL  C  CH2    0  -0.408   6.1239  -0.1283   0.3344
 C3L  CAK  C  CH2    0  -0.416   1.0735  -0.1881  -0.4710
 C3L  OAD  O  OH1    0  -0.631  -7.1967   0.8218   0.2567

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
 C3L  OAB  CAQ  deloc     1.245  0.020  1.245
 C3L  OAD  CAS  single    1.351  0.020  1.351
 C3L  CAQ  OAP  deloc     1.243  0.020  1.243
 C3L  CAQ  CAU  single    1.524  0.020  1.524
 C3L  CAS  CAU  aromatic  1.397  0.020  1.397
 C3L  CAS  CAH  aromatic  1.388  0.020  1.388
 C3L  CAU  CAT  aromatic  1.397  0.020  1.397
 C3L  CAH  CAR  aromatic  1.392  0.020  1.392
 C3L  CAT  CAG  single    1.471  0.020  1.471
 C3L  CAT  CAI  aromatic  1.400  0.020  1.400
 C3L  OAV  CAV  single    1.417  0.020  1.417
 C3L  CAR  CAI  aromatic  1.385  0.020  1.385
 C3L  CAR  OAC  single    1.351  0.020  1.351
 C3L  CAG  CAF  double    1.334  0.020  1.334
 C3L  CAA  CAV  single    1.522  0.020  1.522
 C3L  CAV  CAM  single    1.526  0.020  1.526
 C3L  CAF  CAJ  single    1.494  0.020  1.494
 C3L  CAM  CAL  single    1.523  0.020  1.523
 C3L  CAJ  CAK  single    1.530  0.020  1.530
 C3L  CAO  CAL  single    1.523  0.020  1.523
 C3L  CAO  CAW  single    1.526  0.020  1.526
 C3L  CAW  CAN  single    1.526  0.020  1.526
 C3L  CAW  OAE  single    1.416  0.020  1.416
 C3L  CAK  CAN  single    1.523  0.020  1.523
 C3L  CAA  H1   single    0.970  0.020  1.090
 C3L  CAA  H2   single    0.970  0.020  1.090
 C3L  CAA  H3   single    0.970  0.020  1.090
 C3L  CAF  H4   single    0.930  0.020  1.080
 C3L  CAG  H5   single    0.930  0.020  1.080
 C3L  CAH  H6   single    0.930  0.020  1.080
 C3L  CAI  H7   single    0.930  0.020  1.080
 C3L  CAJ  H8   single    0.970  0.020  1.090
 C3L  CAJ  H9   single    0.970  0.020  1.090
 C3L  CAK  H10  single    0.970  0.020  1.090
 C3L  CAK  H11  single    0.970  0.020  1.090
 C3L  CAL  H12  single    0.970  0.020  1.090
 C3L  CAM  H13  single    0.970  0.020  1.090
 C3L  CAN  H14  single    0.970  0.020  1.090
 C3L  CAN  H15  single    0.970  0.020  1.090
 C3L  CAO  H16  single    0.970  0.020  1.090
 C3L  CAO  H17  single    0.970  0.020  1.090
 C3L  CAV  H18  single    0.970  0.020  1.090
 C3L  CAW  H19  single    0.970  0.020  1.090
 C3L  OAC  H20  single    0.850  0.020  0.980
 C3L  OAD  H21  single    0.850  0.020  0.980
 C3L  OAE  H22  single    0.850  0.020  0.980
 C3L  OAV  H24  single    0.850  0.020  0.980
 C3L  CAM  H25  single    0.970  0.020  1.090
 C3L  CAL  H26  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
 C3L  H3   CAA  H2   108.07  3.000
 C3L  H3   CAA  H1   107.57  3.000
 C3L  H2   CAA  H1   107.85  3.000
 C3L  H3   CAA  CAV  111.07  3.000
 C3L  H2   CAA  CAV  111.21  3.000
 C3L  H1   CAA  CAV  110.91  3.000
 C3L  H4   CAF  CAJ  115.68  3.000
 C3L  H4   CAF  CAG  119.76  3.000
 C3L  CAJ  CAF  CAG  124.56  3.000
 C3L  H5   CAG  CAT  116.12  3.000
 C3L  H5   CAG  CAF  118.29  3.000
 C3L  CAT  CAG  CAF  125.58  3.000
 C3L  H6   CAH  CAS  120.88  3.000
 C3L  H6   CAH  CAR  119.83  3.000
 C3L  CAS  CAH  CAR  119.29  3.000
 C3L  H7   CAI  CAT  120.05  3.000
 C3L  H7   CAI  CAR  119.70  3.000
 C3L  CAT  CAI  CAR  120.23  3.000
 C3L  H9   CAJ  H8   106.60  3.000
 C3L  H9   CAJ  CAK  109.98  3.000
 C3L  H8   CAJ  CAK  108.53  3.000
 C3L  H9   CAJ  CAF  110.06  3.000
 C3L  H8   CAJ  CAF  109.01  3.000
 C3L  CAK  CAJ  CAF  112.47  3.000
 C3L  H25  CAM  H13  105.85  3.000
 C3L  H25  CAM  CAV  108.21  3.000
 C3L  H13  CAM  CAV  109.13  3.000
 C3L  H25  CAM  CAL  109.47  3.000
 C3L  H13  CAM  CAL  109.60  3.000
 C3L  CAV  CAM  CAL  114.23  3.000
 C3L  H15  CAN  H14  105.85  3.000
 C3L  H15  CAN  CAW  108.38  3.000
 C3L  H14  CAN  CAW  109.29  3.000
 C3L  H15  CAN  CAK  109.38  3.000
 C3L  H14  CAN  CAK  109.51  3.000
 C3L  CAW  CAN  CAK  114.10  3.000
 C3L  H17  CAO  H16  105.86  3.000
 C3L  H17  CAO  CAW  109.03  3.000
 C3L  H16  CAO  CAW  108.21  3.000
 C3L  H17  CAO  CAL  109.71  3.000
 C3L  H16  CAO  CAL  109.51  3.000
 C3L  CAW  CAO  CAL  114.18  3.000
 C3L  OAC  CAR  CAI  122.61  3.000
 C3L  OAC  CAR  CAH  117.24  3.000
 C3L  CAI  CAR  CAH  120.14  3.000
 C3L  OAD  CAS  CAU  117.01  3.000
 C3L  CAU  CAS  CAH  121.68  3.000
 C3L  OAD  CAS  CAH  121.30  3.000
 C3L  CAU  CAT  CAI  120.32  3.000
 C3L  CAI  CAT  CAG  120.17  3.000
 C3L  CAU  CAT  CAG  119.50  3.000
 C3L  CAT  CAU  CAS  118.33  3.000
 C3L  CAT  CAU  CAQ  122.35  3.000
 C3L  CAS  CAU  CAQ  119.30  3.000
 C3L  H18  CAV  OAV  104.92  3.000
 C3L  H18  CAV  CAM  108.23  3.000
 C3L  OAV  CAV  CAM  112.07  3.000
 C3L  H18  CAV  CAA  108.43  3.000
 C3L  CAM  CAV  CAA  111.50  3.000
 C3L  OAV  CAV  CAA  111.38  3.000
 C3L  H19  CAW  OAE  104.95  3.000
 C3L  H19  CAW  CAO  108.24  3.000
 C3L  OAE  CAW  CAO  111.94  3.000
 C3L  H19  CAW  CAN  108.35  3.000
 C3L  OAE  CAW  CAN  111.79  3.000
 C3L  CAO  CAW  CAN  111.25  3.000
 C3L  H22  OAE  CAW  107.88  3.000
 C3L  H24  OAV  CAV  107.89  3.000
 C3L  H20  OAC  CAR  110.01  3.000
 C3L  OAP  CAQ  OAB  127.38  3.000
 C3L  OAP  CAQ  CAU  116.06  3.000
 C3L  OAB  CAQ  CAU  116.56  3.000
 C3L  H26  CAL  H12  106.40  3.000
 C3L  H26  CAL  CAO  109.35  3.000
 C3L  H12  CAL  CAO  109.77  3.000
 C3L  H26  CAL  CAM  109.20  3.000
 C3L  H12  CAL  CAM  109.72  3.000
 C3L  CAO  CAL  CAM  112.23  3.000
 C3L  H11  CAK  H10  106.35  3.000
 C3L  H11  CAK  CAN  109.83  3.000
 C3L  H10  CAK  CAN  109.62  3.000
 C3L  H11  CAK  CAJ  109.34  3.000
 C3L  H10  CAK  CAJ  109.27  3.000
 C3L  CAN  CAK  CAJ  112.25  3.000
 C3L  H21  OAD  CAS  110.17  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
 C3L  CONST_01  CAT  CAU  CAS  CAH     0.00   0.0  0
 C3L  CONST_02  CAT  CAI  CAR  CAH     0.00   0.0  0
 C3L  CONST_03  CAS  CAU  CAT  CAI     0.00   0.0  0
 C3L  CONST_04  CAS  CAH  CAR  CAI     0.00   0.0  0
 C3L  CONST_05  CAU  CAS  CAH  CAR     0.00   0.0  0
 C3L  CONST_06  CAU  CAT  CAI  CAR     0.00   0.0  0
 C3L  CONST_07  CAS  CAU  CAT  CAG   180.00   0.0  0
 C3L  CONST_08  CAR  CAI  CAT  CAG   180.00   0.0  0
 C3L  CONST_09  CAQ  CAU  CAS  CAH   180.00   0.0  0
 C3L  CONST_10  CAQ  CAU  CAT  CAI   180.00   0.0  0
 C3L  CONST_11  OAD  CAS  CAH  CAR   180.00   0.0  0
 C3L  CONST_12  OAC  CAR  CAH  CAS   180.00   0.0  0
 C3L  CONST_13  OAD  CAS  CAU  CAT   180.00   0.0  0
 C3L  CONST_14  OAC  CAR  CAI  CAT   180.00   0.0  0
 C3L  CONST_15  H7   CAI  CAR  CAH   180.00   0.0  0
 C3L  CONST_16  H6   CAH  CAR  CAI   180.00   0.0  0
 C3L  Var_01    CAU  CAT  CAG  CAF  -152.62  30.0  3
 C3L  Var_02    OAB  CAQ  CAU  CAS   105.93  30.0  3
 C3L  Var_03    CAT  CAG  CAF  CAJ  -179.71   0.0  2
 C3L  Var_04    CAN  CAK  CAJ  CAF   175.64  30.0  3
 C3L  Var_05    CAK  CAJ  CAF  CAG   118.04  30.0  3
 C3L  Var_06    CAW  CAN  CAK  CAJ   179.71  30.0  3
 C3L  Var_07    CAW  CAO  CAL  CAM  -178.74  30.0  1
 C3L  Var_08    CAV  CAM  CAL  CAO   179.13  30.0  1

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
 C3L  chir_01  CAV  OAV  CAA  CAM  negativ
 C3L  chir_02  CAW  OAE  CAO  CAN  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
 C3L  plan-1  CAG  0.020
 C3L  plan-1  CAH  0.020
 C3L  plan-1  CAI  0.020
 C3L  plan-1  CAR  0.020
 C3L  plan-1  CAS  0.020
 C3L  plan-1  CAT  0.020
 C3L  plan-1  CAU  0.020
 C3L  plan-1  H6   0.020
 C3L  plan-1  H7   0.020
 C3L  plan-1  OAC  0.020
 C3L  plan-1  CAQ  0.020
 C3L  plan-1  OAD  0.020
 C3L  plan-2  CAU  0.020
 C3L  plan-2  OAB  0.020
 C3L  plan-2  OAP  0.020
 C3L  plan-2  CAQ  0.020
 C3L  plan-3  CAF  0.020
 C3L  plan-3  CAG  0.020
 C3L  plan-3  CAJ  0.020
 C3L  plan-3  CAT  0.020
 C3L  plan-3  H4   0.020
 C3L  plan-3  H5   0.020

