# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 09:05:29 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: (2~{E},4~{E},6~{E},8~{E})-3,7-dimethyl-9-(2,6,6-trimethylcyclohexen-1-yl)nona-2,4,6,8-tetraen-1-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=C/CN)\C=C\C=C(C)\C=C\C1=C(C)CCCC1(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
 RNE  RNE  (2~{E},4~{E},6~{E},8~{E})-3,7-dimethyl-9-(2,6,6-trimethylcyclohexen-1-yl)nona-2,4,6,8-tetraen-1-amine  ligand  52  21  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_RNE
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
 RNE  NAA   N  NH2   0  -0.797   8.3603   1.5765  -0.1742
 RNE  CAB   C  CH2   0  -0.342   7.7054   0.3616  -0.6551
 RNE  CAC   C  C1    0  -0.284   6.2203   0.5308  -0.6330
 RNE  CAD   C  C     0   0.131   5.2899  -0.2695  -0.0836
 RNE  CAG   C  C1    0  -0.287   3.8909   0.1116  -0.2220
 RNE  CAF   C  C1    0  -0.260   2.8344  -0.5668   0.2680
 RNE  CAE   C  C1    0  -0.304   1.4764  -0.1239   0.0792
 RNE  CAH   C  C     0   0.116   0.3465  -0.7136   0.5376
 RNE  CAI   C  C1    0  -0.254  -0.9271  -0.0864   0.2233
 RNE  CAJ   C  C1    0  -0.317  -2.1355  -0.5339   0.6002
 RNE  CAK   C  C     0   0.123  -3.4115   0.1126   0.2639
 RNE  CAL   C  C     0   0.019  -3.6168   1.4309   0.4462
 RNE  CAM   C  CH2   0  -0.480  -4.8784   2.1258   0.0111
 RNE  CAN   C  CH2   0  -0.449  -5.7545   1.2912  -0.9046
 RNE  CAO   C  CH2   0  -0.412  -5.8428  -0.1236  -0.3647
 RNE  CAP   C  CT    0  -0.145  -4.4764  -0.8159  -0.3237
 RNE  CAQ   C  CH3   0  -0.660  -4.6279  -2.0854   0.5252
 RNE  CAR   C  CH3   0  -0.635  -4.0496  -1.2309  -1.7381
 RNE  CAS   C  CH3   0  -0.733  -2.6448   2.3578   1.1192
 RNE  CAT   C  CH3   0  -0.762   0.3329  -1.9709   1.3534
 RNE  CAU   C  CH3   0  -0.761   5.5966  -1.5359   0.6608
 RNE  HAA2  H  HNH2  0   0.349   9.3633   1.4444  -0.2169
 RNE  HAA1  H  HNH2  0   0.341   8.1646   2.3343  -0.8178
 RNE  HAB2  H  HCH2  0   0.213   8.0023   0.0911  -1.6798
 RNE  HAB1  H  HCH2  0   0.233   8.0193  -0.4681  -0.0215
 RNE  HAC1  H  H     0   0.239   5.8653   1.4194  -1.1520
 RNE  HAG1  H  H     0   0.237   3.7003   1.0277  -0.7760
 RNE  HAF1  H  H     0   0.250   3.0046  -1.4811   0.8247
 RNE  HAE1  H  H     0   0.236   1.3603   0.7891  -0.5001
 RNE  HAI1  H  H     0   0.234  -0.8734   0.8153  -0.3806
 RNE  HAJ1  H  H     0   0.247  -2.1918  -1.4631   1.1595
 RNE  HAM2  H  HCH2  0   0.232  -5.4399   2.4241   0.9057
 RNE  HAM1  H  HCH2  0   0.238  -4.6039   3.0671  -0.4772
 RNE  HAN1  H  HCH2  0   0.231  -6.7480   1.7372  -0.9868
 RNE  HAN2  H  HCH2  0   0.220  -5.3364   1.2832  -1.9151
 RNE  HAO1  H  HCH2  0   0.218  -6.2569  -0.0892   0.6497
 RNE  HAO2  H  HCH2  0   0.224  -6.5317  -0.7300  -0.9604
 RNE  HAQ3  H  HCH3  0   0.227  -4.8127  -1.8470   1.5747
 RNE  HAQ1  H  HCH3  0   0.231  -5.4774  -2.6674   0.1621
 RNE  HAQ2  H  HCH3  0   0.226  -3.7508  -2.7309   0.4722
 RNE  HAR1  H  HCH3  0   0.227  -3.0610  -1.6935  -1.7292
 RNE  HAR2  H  HCH3  0   0.220  -4.7520  -1.9561  -2.1558
 RNE  HAR3  H  HCH3  0   0.227  -4.0073  -0.3773  -2.4159
 RNE  HAS3  H  HCH3  0   0.237  -2.0986   2.9646   0.3923
 RNE  HAS1  H  HCH3  0   0.234  -3.1861   3.0603   1.7586
 RNE  HAS2  H  HCH3  0   0.242  -1.9091   1.8414   1.7320
 RNE  HAT2  H  HCH3  0   0.246  -0.1207  -1.7945   2.3311
 RNE  HAT3  H  HCH3  0   0.243  -0.2625  -2.7465   0.8670
 RNE  HAT1  H  HCH3  0   0.255   1.3258  -2.3798   1.5218
 RNE  HAU3  H  HCH3  0   0.243   5.2533  -1.4735   1.6955
 RNE  HAU1  H  HCH3  0   0.243   5.0845  -2.3878   0.2096
 RNE  HAU2  H  HCH3  0   0.253   6.6583  -1.7671   0.6803

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
 RNE  NAA  CAB   single  1.462  0.020  1.462
 RNE  CAB  CAC   single  1.495  0.020  1.495
 RNE  CAC  CAD   double  1.345  0.020  1.345
 RNE  CAU  CAD   single  1.501  0.020  1.501
 RNE  CAD  CAG   single  1.457  0.020  1.457
 RNE  CAG  CAF   double  1.348  0.020  1.348
 RNE  CAF  CAE   single  1.441  0.020  1.441
 RNE  CAE  CAH   double  1.354  0.020  1.354
 RNE  CAT  CAH   single  1.499  0.020  1.499
 RNE  CAH  CAI   single  1.454  0.020  1.454
 RNE  CAI  CAJ   double  1.343  0.020  1.343
 RNE  CAQ  CAP   single  1.535  0.020  1.535
 RNE  CAJ  CAK   single  1.469  0.020  1.469
 RNE  CAK  CAP   single  1.530  0.020  1.530
 RNE  CAK  CAL   double  1.347  0.020  1.347
 RNE  CAP  CAR   single  1.535  0.020  1.535
 RNE  CAP  CAO   single  1.532  0.020  1.532
 RNE  CAS  CAL   single  1.502  0.020  1.502
 RNE  CAL  CAM   single  1.505  0.020  1.505
 RNE  CAO  CAN   single  1.517  0.020  1.517
 RNE  CAM  CAN   single  1.517  0.020  1.517
 RNE  NAA  HAA2  single  0.890  0.020  1.040
 RNE  NAA  HAA1  single  0.890  0.020  1.040
 RNE  CAB  HAB2  single  0.970  0.020  1.090
 RNE  CAB  HAB1  single  0.970  0.020  1.090
 RNE  CAC  HAC1  single  0.930  0.020  1.080
 RNE  CAG  HAG1  single  0.930  0.020  1.080
 RNE  CAF  HAF1  single  0.930  0.020  1.080
 RNE  CAE  HAE1  single  0.930  0.020  1.080
 RNE  CAI  HAI1  single  0.930  0.020  1.080
 RNE  CAJ  HAJ1  single  0.930  0.020  1.080
 RNE  CAM  HAM2  single  0.970  0.020  1.090
 RNE  CAM  HAM1  single  0.970  0.020  1.090
 RNE  CAN  HAN1  single  0.970  0.020  1.090
 RNE  CAN  HAN2  single  0.970  0.020  1.090
 RNE  CAO  HAO1  single  0.970  0.020  1.090
 RNE  CAO  HAO2  single  0.970  0.020  1.090
 RNE  CAQ  HAQ3  single  0.970  0.020  1.090
 RNE  CAQ  HAQ1  single  0.970  0.020  1.090
 RNE  CAQ  HAQ2  single  0.970  0.020  1.090
 RNE  CAR  HAR1  single  0.970  0.020  1.090
 RNE  CAR  HAR2  single  0.970  0.020  1.090
 RNE  CAR  HAR3  single  0.970  0.020  1.090
 RNE  CAS  HAS3  single  0.970  0.020  1.090
 RNE  CAS  HAS1  single  0.970  0.020  1.090
 RNE  CAS  HAS2  single  0.970  0.020  1.090
 RNE  CAT  HAT2  single  0.970  0.020  1.090
 RNE  CAT  HAT3  single  0.970  0.020  1.090
 RNE  CAT  HAT1  single  0.970  0.020  1.090
 RNE  CAU  HAU3  single  0.970  0.020  1.090
 RNE  CAU  HAU1  single  0.970  0.020  1.090
 RNE  CAU  HAU2  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
 RNE  HAA1  NAA  HAA2  105.19  3.000
 RNE  HAA1  NAA  CAB   109.03  3.000
 RNE  HAA2  NAA  CAB   108.75  3.000
 RNE  HAB1  CAB  HAB2  106.05  3.000
 RNE  HAB1  CAB  CAC   111.32  3.000
 RNE  HAB2  CAB  CAC   108.03  3.000
 RNE  HAB1  CAB  NAA   108.20  3.000
 RNE  HAB2  CAB  NAA   112.95  3.000
 RNE  CAC   CAB  NAA   110.26  3.000
 RNE  HAC1  CAC  CAD   117.07  3.000
 RNE  HAC1  CAC  CAB   114.16  3.000
 RNE  CAD   CAC  CAB   128.77  3.000
 RNE  CAU   CAD  CAG   117.66  3.000
 RNE  CAG   CAD  CAC   118.04  3.000
 RNE  CAU   CAD  CAC   124.30  3.000
 RNE  HAG1  CAG  CAF   118.15  3.000
 RNE  HAG1  CAG  CAD   115.92  3.000
 RNE  CAF   CAG  CAD   125.92  3.000
 RNE  HAF1  CAF  CAE   118.33  3.000
 RNE  HAF1  CAF  CAG   119.22  3.000
 RNE  CAE   CAF  CAG   122.45  3.000
 RNE  HAE1  CAE  CAH   117.17  3.000
 RNE  HAE1  CAE  CAF   115.37  3.000
 RNE  CAH   CAE  CAF   127.45  3.000
 RNE  CAT   CAH  CAI   118.13  3.000
 RNE  CAI   CAH  CAE   118.02  3.000
 RNE  CAT   CAH  CAE   123.85  3.000
 RNE  HAI1  CAI  CAJ   118.49  3.000
 RNE  HAI1  CAI  CAH   115.78  3.000
 RNE  CAJ   CAI  CAH   125.73  3.000
 RNE  HAJ1  CAJ  CAK   116.70  3.000
 RNE  HAJ1  CAJ  CAI   118.45  3.000
 RNE  CAK   CAJ  CAI   124.80  3.000
 RNE  CAP   CAK  CAL   122.68  3.000
 RNE  CAL   CAK  CAJ   122.15  3.000
 RNE  CAP   CAK  CAJ   115.16  3.000
 RNE  CAS   CAL  CAM   112.77  3.000
 RNE  CAM   CAL  CAK   122.74  3.000
 RNE  CAS   CAL  CAK   124.48  3.000
 RNE  HAM1  CAM  HAM2  104.95  3.000
 RNE  HAM1  CAM  CAN   110.38  3.000
 RNE  HAM2  CAM  CAN   110.25  3.000
 RNE  HAM1  CAM  CAL   108.40  3.000
 RNE  HAM2  CAM  CAL   108.59  3.000
 RNE  CAN   CAM  CAL   113.87  3.000
 RNE  HAN2  CAN  HAN1  106.33  3.000
 RNE  HAN2  CAN  CAO   110.14  3.000
 RNE  HAN1  CAN  CAO   110.77  3.000
 RNE  HAN2  CAN  CAM   109.94  3.000
 RNE  HAN1  CAN  CAM   110.25  3.000
 RNE  CAO   CAN  CAM   109.38  3.000
 RNE  HAO2  CAO  HAO1  106.46  3.000
 RNE  HAO2  CAO  CAP   109.00  3.000
 RNE  HAO1  CAO  CAP   109.05  3.000
 RNE  HAO2  CAO  CAN   111.09  3.000
 RNE  HAO1  CAO  CAN   108.79  3.000
 RNE  CAP   CAO  CAN   112.27  3.000
 RNE  CAR   CAP  CAQ   108.28  3.000
 RNE  CAR   CAP  CAO   110.22  3.000
 RNE  CAQ   CAP  CAO   107.49  3.000
 RNE  CAO   CAP  CAK   110.90  3.000
 RNE  CAR   CAP  CAK   108.93  3.000
 RNE  CAQ   CAP  CAK   110.99  3.000
 RNE  HAQ2  CAQ  HAQ1  107.11  3.000
 RNE  HAQ2  CAQ  HAQ3  108.19  3.000
 RNE  HAQ1  CAQ  HAQ3  107.71  3.000
 RNE  HAQ2  CAQ  CAP   112.55  3.000
 RNE  HAQ1  CAQ  CAP   109.50  3.000
 RNE  HAQ3  CAQ  CAP   111.58  3.000
 RNE  HAR3  CAR  HAR2  107.86  3.000
 RNE  HAR3  CAR  HAR1  107.56  3.000
 RNE  HAR2  CAR  HAR1  107.70  3.000
 RNE  HAR3  CAR  CAP   111.83  3.000
 RNE  HAR2  CAR  CAP   110.68  3.000
 RNE  HAR1  CAR  CAP   111.04  3.000
 RNE  HAS2  CAS  HAS1  108.08  3.000
 RNE  HAS2  CAS  HAS3  107.46  3.000
 RNE  HAS1  CAS  HAS3  106.24  3.000
 RNE  HAS2  CAS  CAL   113.39  3.000
 RNE  HAS1  CAS  CAL   109.77  3.000
 RNE  HAS3  CAS  CAL   111.59  3.000
 RNE  HAT1  CAT  HAT3  107.45  3.000
 RNE  HAT1  CAT  HAT2  107.54  3.000
 RNE  HAT3  CAT  HAT2  106.68  3.000
 RNE  HAT1  CAT  CAH   113.05  3.000
 RNE  HAT3  CAT  CAH   111.00  3.000
 RNE  HAT2  CAT  CAH   110.83  3.000
 RNE  HAU2  CAU  HAU1  107.44  3.000
 RNE  HAU2  CAU  HAU3  107.60  3.000
 RNE  HAU1  CAU  HAU3  106.78  3.000
 RNE  HAU2  CAU  CAD   112.84  3.000
 RNE  HAU1  CAU  CAD   110.96  3.000
 RNE  HAU3  CAU  CAD   110.95  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
 RNE  Var_01  CAN   CAO  CAP  CAK    45.59  30.0  1
 RNE  Var_02  CAN   CAM  CAL  CAK   -12.52  30.0  1
 RNE  Var_03  CAO   CAP  CAK  CAL   -12.65  30.0  1
 RNE  Var_04  CAO   CAN  CAM  CAL    44.14  30.0  1
 RNE  Var_05  CAP   CAK  CAL  CAM    -3.88  30.0  1
 RNE  Var_06  CAP   CAO  CAN  CAM   -62.12  30.0  1
 RNE  Var_07  HAQ3  CAQ  CAP  CAK    53.58  30.0  3
 RNE  Var_08  HAR1  CAR  CAP  CAK    56.07  30.0  3
 RNE  Var_09  HAS3  CAS  CAL  CAK   102.73  30.0  3
 RNE  Var_10  CAK   CAJ  CAI  CAH  -179.62   0.0  2
 RNE  Var_11  CAU   CAD  CAC  CAB     0.84   0.0  2
 RNE  Var_12  CAE   CAF  CAG  CAD  -179.61   0.0  2
 RNE  Var_13  CAT   CAH  CAE  CAF     0.28   0.0  2
 RNE  Var_14  CAD   CAC  CAB  NAA  -128.32  30.0  3
 RNE  Var_15  CAF   CAG  CAD  CAC  -179.72  30.0  2
 RNE  Var_16  CAH   CAE  CAF  CAG  -179.14  30.0  2
 RNE  Var_17  CAJ   CAI  CAH  CAE  -179.80  30.0  2
 RNE  Var_18  HAA2  NAA  CAB  CAC  -178.83  30.0  3
 RNE  Var_19  HAU3  CAU  CAD  CAC   118.59  30.0  3
 RNE  Var_20  HAT2  CAT  CAH  CAE   119.40  30.0  3

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
 RNE  plan-1  CAB   0.020
 RNE  plan-1  CAC   0.020
 RNE  plan-1  CAD   0.020
 RNE  plan-1  CAG   0.020
 RNE  plan-1  CAU   0.020
 RNE  plan-1  HAC1  0.020
 RNE  plan-2  CAD   0.020
 RNE  plan-2  CAG   0.020
 RNE  plan-2  CAF   0.020
 RNE  plan-2  CAE   0.020
 RNE  plan-2  HAG1  0.020
 RNE  plan-2  HAF1  0.020
 RNE  plan-3  CAF   0.020
 RNE  plan-3  CAE   0.020
 RNE  plan-3  CAH   0.020
 RNE  plan-3  CAI   0.020
 RNE  plan-3  CAT   0.020
 RNE  plan-3  HAE1  0.020
 RNE  plan-4  CAH   0.020
 RNE  plan-4  CAI   0.020
 RNE  plan-4  CAJ   0.020
 RNE  plan-4  CAK   0.020
 RNE  plan-4  HAI1  0.020
 RNE  plan-4  HAJ1  0.020

