# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 04:57:00 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: N-[(2E)-3,7-dimethylocta-2,6-dien-1-yl]-N'-[(1R,3S,5R,7R)-tricyclo[3.3.1.1~3,7~]dec-2-yl]ethane-1,2-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)=CCCC(/C)=C/CNCCNC1C2CC3CC(C2)CC1C3
#
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
 3RX  3RX  N-[(2E)-3,7-dimethylocta-2,6-dien-1-yl]-N'-[(1R,3S,5R,7R)-tricyclo[3.3.1.1~3,7~]dec-2-yl]ethane-1,2-diamine  ligand  62  24  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3RX
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
 3RX  CAA   C  CH3   0  -0.721  -6.8111   2.8017   0.7651
 3RX  CAB   C  CH3   0  -0.704  -9.2098   2.0384   0.6256
 3RX  CAC   C  CH3   0  -0.733  -4.1769  -2.0553  -1.8760
 3RX  CAD   C  C1    0  -0.253  -7.4378   0.6797  -0.4300
 3RX  CAE   C  C1    0  -0.302  -3.2706  -1.5204   0.4091
 3RX  CAF   C  CH2   0  -0.493  -6.0715   0.2358  -0.8491
 3RX  CAG   C  CH2   0  -0.324  -1.8675  -2.0066   0.2264
 3RX  CAH   C  CH2   0  -0.274   0.4566  -1.3555   0.3716
 3RX  CAI   C  CH2   0  -0.282   1.4172  -0.1851   0.5049
 3RX  CAJ   C  CH2   0  -0.481  -5.6292  -1.0129  -0.0699
 3RX  CAK   C  C     0  -0.420   7.0064   0.3381  -0.8580
 3RX  CAL   C  C     0  -0.422   5.1255   1.9814  -0.7229
 3RX  CAM   C  C     0  -0.410   4.7108  -0.3286  -1.5858
 3RX  CAN   C  CH2   0  -0.420   6.0909   1.0258   1.3627
 3RX  CAO   C  CH2   0  -0.412   5.6793  -1.2834   0.5061
 3RX  NAP   N  NH1   0  -0.600  -0.9227  -0.9101   0.3716
 3RX  NAQ   N  NH1   0  -0.610   2.7754  -0.6652   0.6575
 3RX  CAR   C  C     0   0.078  -7.7765   1.7668   0.2680
 3RX  CAS   C  C     0   0.126  -4.2752  -1.5368  -0.4712
 3RX  CAT   C  CR16  0  -0.243   6.4157   1.4999  -0.0554
 3RX  CAU   C  CR16  0  -0.246   5.9990  -0.8135  -0.9155
 3RX  CAV   C  CR16  0  -0.254   4.1160   0.8324  -0.7854
 3RX  CAW   C  CH1   0  -0.282   5.0803  -0.1222   1.3048
 3RX  CAX   C  CH1   0  -0.008   3.7879   0.3766   0.6453
 3RX  HAA   H  HCH3  0   0.235  -6.8499   2.8642   1.8558
 3RX  HAAA  H  HCH3  0   0.239  -5.7785   2.6103   0.4810
 3RX  HAAB  H  HCH3  0   0.234  -7.0825   3.7920   0.3908
 3RX  HAB   H  HCH3  0   0.230  -9.5468   2.9868   0.1990
 3RX  HABA  H  HCH3  0   0.235  -9.8785   1.2533   0.2730
 3RX  HABB  H  HCH3  0   0.230  -9.3316   2.1262   1.7086
 3RX  HAC   H  HCH3  0   0.244  -3.2036  -2.4785  -2.1136
 3RX  HACA  H  HCH3  0   0.235  -4.9298  -2.8274  -2.0533
 3RX  HACB  H  HCH3  0   0.241  -4.3719  -1.2609  -2.6002
 3RX  HAD   H  H     0   0.220  -8.2390   0.0005  -0.7153
 3RX  HAE   H  H     0   0.223  -3.4749  -1.1078   1.3946
 3RX  HAF   H  HCH2  0   0.234  -6.0901   0.0078  -1.9187
 3RX  HAFA  H  HCH2  0   0.236  -5.3268   1.0228  -0.7167
 3RX  HAG   H  HCH2  0   0.227  -1.6491  -2.7324   1.0177
 3RX  HAGA  H  HCH2  0   0.208  -1.7454  -2.5509  -0.7199
 3RX  HAH   H  HCH2  0   0.189   0.7270  -1.9352  -0.5247
 3RX  HAHA  H  HCH2  0   0.213   0.5909  -2.0295   1.2253
 3RX  HAI   H  HCH2  0   0.220   1.3558   0.4320  -0.3962
 3RX  HAIA  H  HCH2  0   0.189   1.0929   0.4553   1.3403
 3RX  HAJ   H  HCH2  0   0.235  -5.6314  -0.7774   0.9970
 3RX  HAJA  H  HCH2  0   0.228  -6.3788  -1.7993  -0.2166
 3RX  HAKA  H  H     0   0.218   7.9415   0.0024  -0.3975
 3RX  HAL   H  H     0   0.220   4.7079   2.8239  -0.1610
 3RX  HALA  H  H     0   0.221   5.3347   2.3506  -1.7322
 3RX  HAM   H  H     0   0.214   4.9185  -0.0009  -2.6099
 3RX  HAMA  H  H     0   0.224   3.9876  -1.1449  -1.6535
 3RX  HAN   H  HCH2  0   0.222   7.0022   0.6915   1.8699
 3RX  HANA  H  HCH2  0   0.221   5.6882   1.8553   1.9537
 3RX  HAO   H  HCH2  0   0.223   4.9880  -2.1301   0.4793
 3RX  HAOA  H  HCH2  0   0.216   6.5897  -1.6352   1.0026
 3RX  HNAP  H  HNH1  0   0.337  -1.0653  -0.2603  -0.3931
 3RX  HNAQ  H  HNH1  0   0.337   2.8349  -1.1675   1.5363
 3RX  HAT   H  HCR6  0   0.220   7.1369   2.3217  -0.0119
 3RX  HAU   H  HCR6  0   0.217   6.4235  -1.6427  -1.4902
 3RX  HAV   H  HCR6  0   0.222   3.2035   1.1853  -1.2769
 3RX  HAW   H  HCH1  0   0.222   4.8511  -0.4526   2.3251
 3RX  HAX   H  HCH1  0   0.192   3.4453   1.2610   1.2141
 3RX  HAK   H  H     0   0.218   7.2564   0.6705  -1.8708

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
 3RX  CAR  CAA   single  1.500  0.020  1.500
 3RX  CAA  HAA   single  0.970  0.020  1.090
 3RX  CAA  HAAA  single  0.970  0.020  1.090
 3RX  CAA  HAAB  single  0.970  0.020  1.090
 3RX  CAB  CAR   single  1.502  0.020  1.502
 3RX  CAB  HAB   single  0.970  0.020  1.090
 3RX  CAB  HABA  single  0.970  0.020  1.090
 3RX  CAB  HABB  single  0.970  0.020  1.090
 3RX  CAS  CAC   single  1.501  0.020  1.501
 3RX  CAC  HAC   single  0.970  0.020  1.090
 3RX  CAC  HACA  single  0.970  0.020  1.090
 3RX  CAC  HACB  single  0.970  0.020  1.090
 3RX  CAR  CAD   double  1.336  0.020  1.336
 3RX  CAF  CAD   single  1.497  0.020  1.497
 3RX  CAD  HAD   single  0.930  0.020  1.080
 3RX  CAE  CAG   single  1.496  0.020  1.496
 3RX  CAE  CAS   double  1.336  0.020  1.336
 3RX  CAE  HAE   single  0.930  0.020  1.080
 3RX  CAF  CAJ   single  1.537  0.020  1.537
 3RX  CAF  HAF   single  0.970  0.020  1.090
 3RX  CAF  HAFA  single  0.970  0.020  1.090
 3RX  CAG  NAP   single  1.455  0.020  1.455
 3RX  CAG  HAG   single  0.970  0.020  1.090
 3RX  CAG  HAGA  single  0.970  0.020  1.090
 3RX  CAH  CAI   single  1.520  0.020  1.520
 3RX  CAH  NAP   single  1.450  0.020  1.450
 3RX  CAH  HAH   single  0.970  0.020  1.090
 3RX  CAH  HAHA  single  0.970  0.020  1.090
 3RX  NAQ  CAI   single  1.449  0.020  1.449
 3RX  CAI  HAI   single  0.970  0.020  1.090
 3RX  CAI  HAIA  single  0.970  0.020  1.090
 3RX  CAS  CAJ   single  1.506  0.020  1.506
 3RX  CAJ  HAJ   single  0.970  0.020  1.090
 3RX  CAJ  HAJA  single  0.970  0.020  1.090
 3RX  CAU  CAK   single  1.531  0.020  1.531
 3RX  CAK  CAT   single  1.531  0.020  1.531
 3RX  CAK  HAK   single  0.970  0.020  1.090
 3RX  CAK  HAKA  single  0.970  0.020  1.090
 3RX  CAV  CAL   single  1.531  0.020  1.531
 3RX  CAT  CAL   single  1.530  0.020  1.530
 3RX  CAL  HAL   single  0.970  0.020  1.090
 3RX  CAL  HALA  single  0.970  0.020  1.090
 3RX  CAU  CAM   single  1.531  0.020  1.531
 3RX  CAM  CAV   single  1.531  0.020  1.531
 3RX  CAM  HAM   single  0.970  0.020  1.090
 3RX  CAM  HAMA  single  0.970  0.020  1.090
 3RX  CAW  CAN   single  1.531  0.020  1.531
 3RX  CAN  CAT   single  1.530  0.020  1.530
 3RX  CAN  HAN   single  0.970  0.020  1.090
 3RX  CAN  HANA  single  0.970  0.020  1.090
 3RX  CAO  CAU   single  1.531  0.020  1.531
 3RX  CAO  CAW   single  1.531  0.020  1.531
 3RX  CAO  HAO   single  0.970  0.020  1.090
 3RX  CAO  HAOA  single  0.970  0.020  1.090
 3RX  NAP  HNAP  single  0.890  0.020  1.040
 3RX  NAQ  CAX   single  1.453  0.020  1.453
 3RX  NAQ  HNAQ  single  0.890  0.020  1.040
 3RX  CAT  HAT   single  0.970  0.020  1.090
 3RX  CAU  HAU   single  0.970  0.020  1.090
 3RX  CAX  CAV   single  1.537  0.020  1.537
 3RX  CAV  HAV   single  0.970  0.020  1.090
 3RX  CAW  CAX   single  1.534  0.020  1.534
 3RX  CAW  HAW   single  0.970  0.020  1.090
 3RX  CAX  HAX   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
 3RX  HAAB  CAA  HAAA  107.80  3.000
 3RX  HAAB  CAA  HAA   106.32  3.000
 3RX  HAAA  CAA  HAA   107.71  3.000
 3RX  HAAB  CAA  CAR   110.60  3.000
 3RX  HAAA  CAA  CAR   113.77  3.000
 3RX  HAA   CAA  CAR   110.32  3.000
 3RX  HABB  CAB  HABA  108.06  3.000
 3RX  HABB  CAB  HAB   106.41  3.000
 3RX  HABA  CAB  HAB   108.03  3.000
 3RX  HABB  CAB  CAR   110.90  3.000
 3RX  HABA  CAB  CAR   112.22  3.000
 3RX  HAB   CAB  CAR   110.99  3.000
 3RX  HACB  CAC  HACA  106.45  3.000
 3RX  HACB  CAC  HAC   107.33  3.000
 3RX  HACA  CAC  HAC   107.82  3.000
 3RX  HACB  CAC  CAS   110.96  3.000
 3RX  HACA  CAC  CAS   110.54  3.000
 3RX  HAC   CAC  CAS   113.43  3.000
 3RX  HAD   CAD  CAR   117.28  3.000
 3RX  HAD   CAD  CAF   114.43  3.000
 3RX  CAR   CAD  CAF   128.27  3.000
 3RX  HAE   CAE  CAS   117.42  3.000
 3RX  HAE   CAE  CAG   114.21  3.000
 3RX  CAS   CAE  CAG   128.37  3.000
 3RX  HAFA  CAF  HAF   106.29  3.000
 3RX  HAFA  CAF  CAJ   109.15  3.000
 3RX  HAF   CAF  CAJ   109.34  3.000
 3RX  HAFA  CAF  CAD   112.03  3.000
 3RX  HAF   CAF  CAD   108.67  3.000
 3RX  CAJ   CAF  CAD   111.21  3.000
 3RX  HAGA  CAG  HAG   105.77  3.000
 3RX  HAGA  CAG  NAP   112.79  3.000
 3RX  HAG   CAG  NAP   107.32  3.000
 3RX  HAGA  CAG  CAE   111.74  3.000
 3RX  HAG   CAG  CAE   108.30  3.000
 3RX  NAP   CAG  CAE   110.60  3.000
 3RX  HAHA  CAH  HAH   106.27  3.000
 3RX  HAHA  CAH  NAP   107.79  3.000
 3RX  HAH   CAH  NAP   113.30  3.000
 3RX  HAHA  CAH  CAI   109.14  3.000
 3RX  HAH   CAH  CAI   108.76  3.000
 3RX  NAP   CAH  CAI   111.39  3.000
 3RX  HAIA  CAI  HAI   106.28  3.000
 3RX  HAIA  CAI  NAQ   112.88  3.000
 3RX  HAI   CAI  NAQ   109.05  3.000
 3RX  HAIA  CAI  CAH   109.16  3.000
 3RX  HAI   CAI  CAH   109.06  3.000
 3RX  NAQ   CAI  CAH   110.28  3.000
 3RX  HAJA  CAJ  HAJ   106.49  3.000
 3RX  HAJA  CAJ  CAS   109.24  3.000
 3RX  HAJ   CAJ  CAS   109.69  3.000
 3RX  HAJA  CAJ  CAF   108.55  3.000
 3RX  HAJ   CAJ  CAF   108.62  3.000
 3RX  CAS   CAJ  CAF   113.97  3.000
 3RX  HAKA  CAK  HAK   106.68  3.000
 3RX  HAKA  CAK  CAU   110.31  3.000
 3RX  HAK   CAK  CAU   110.11  3.000
 3RX  HAKA  CAK  CAT   109.98  3.000
 3RX  HAK   CAK  CAT   110.04  3.000
 3RX  CAU   CAK  CAT   109.68  3.000
 3RX  HALA  CAL  HAL   106.64  3.000
 3RX  HALA  CAL  CAV   109.96  3.000
 3RX  HAL   CAL  CAV   110.29  3.000
 3RX  HALA  CAL  CAT   110.31  3.000
 3RX  HAL   CAL  CAT   109.86  3.000
 3RX  CAV   CAL  CAT   109.74  3.000
 3RX  HAMA  CAM  HAM   106.93  3.000
 3RX  HAMA  CAM  CAV   109.99  3.000
 3RX  HAM   CAM  CAV   109.62  3.000
 3RX  HAMA  CAM  CAU   110.33  3.000
 3RX  HAM   CAM  CAU   110.16  3.000
 3RX  CAV   CAM  CAU   109.77  3.000
 3RX  HANA  CAN  HAN   106.70  3.000
 3RX  HANA  CAN  CAW   110.22  3.000
 3RX  HAN   CAN  CAW   109.76  3.000
 3RX  HANA  CAN  CAT   110.08  3.000
 3RX  HAN   CAN  CAT   110.31  3.000
 3RX  CAW   CAN  CAT   109.72  3.000
 3RX  HAOA  CAO  HAO   106.74  3.000
 3RX  HAOA  CAO  CAW   109.41  3.000
 3RX  HAO   CAO  CAW   110.65  3.000
 3RX  HAOA  CAO  CAU   110.24  3.000
 3RX  HAO   CAO  CAU   110.30  3.000
 3RX  CAW   CAO  CAU   109.47  3.000
 3RX  HNAP  NAP  CAH   109.32  3.000
 3RX  HNAP  NAP  CAG   108.45  3.000
 3RX  CAH   NAP  CAG   112.73  3.000
 3RX  HNAQ  NAQ  CAX   108.76  3.000
 3RX  HNAQ  NAQ  CAI   108.09  3.000
 3RX  CAX   NAQ  CAI   114.51  3.000
 3RX  CAD   CAR  CAB   120.90  3.000
 3RX  CAD   CAR  CAA   124.86  3.000
 3RX  CAB   CAR  CAA   114.24  3.000
 3RX  CAJ   CAS  CAE   119.75  3.000
 3RX  CAJ   CAS  CAC   115.37  3.000
 3RX  CAE   CAS  CAC   124.88  3.000
 3RX  HAT   CAT  CAN   109.62  3.000
 3RX  HAT   CAT  CAL   109.68  3.000
 3RX  CAN   CAT  CAL   108.83  3.000
 3RX  HAT   CAT  CAK   109.67  3.000
 3RX  CAN   CAT  CAK   109.43  3.000
 3RX  CAL   CAT  CAK   109.60  3.000
 3RX  HAU   CAU  CAO   109.64  3.000
 3RX  HAU   CAU  CAM   109.66  3.000
 3RX  CAO   CAU  CAM   109.15  3.000
 3RX  HAU   CAU  CAK   109.53  3.000
 3RX  CAO   CAU  CAK   109.47  3.000
 3RX  CAM   CAU  CAK   109.38  3.000
 3RX  HAV   CAV  CAX   109.60  3.000
 3RX  HAV   CAV  CAM   109.49  3.000
 3RX  CAX   CAV  CAM   110.17  3.000
 3RX  HAV   CAV  CAL   109.03  3.000
 3RX  CAX   CAV  CAL   108.99  3.000
 3RX  CAM   CAV  CAL   109.54  3.000
 3RX  HAW   CAW  CAX   108.78  3.000
 3RX  HAW   CAW  CAO   109.79  3.000
 3RX  CAX   CAW  CAO   110.59  3.000
 3RX  HAW   CAW  CAN   109.19  3.000
 3RX  CAX   CAW  CAN   109.19  3.000
 3RX  CAO   CAW  CAN   109.28  3.000
 3RX  HAX   CAX  CAW   107.45  3.000
 3RX  HAX   CAX  CAV   107.92  3.000
 3RX  CAW   CAX  CAV   108.47  3.000
 3RX  HAX   CAX  NAQ   110.68  3.000
 3RX  CAW   CAX  NAQ   110.50  3.000
 3RX  CAV   CAX  NAQ   111.67  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
 3RX  Var_01  CAX  NAQ  CAI  CAH  173.55  30.0  2
 3RX  Var_02  CAF  CAD  CAR  CAA    1.06   0.0  2
 3RX  Var_03  CAG  CAE  CAS  CAC   -0.73   0.0  2
 3RX  Var_04  CAF  CAJ  CAS  CAC  -64.99  30.0  3
 3RX  Var_05  CAS  CAJ  CAF  CAD  178.37  30.0  3
 3RX  Var_06  CAH  NAP  CAG  CAE  172.69  30.0  3
 3RX  Var_07  CAI  CAH  NAP  CAG  179.19  30.0  1
 3RX  Var_08  CAR  CAD  CAF  CAJ  109.58  30.0  3
 3RX  Var_09  CAS  CAE  CAG  NAP  118.05  30.0  2
 3RX  Var_10  NAQ  CAI  CAH  NAP  173.42  30.0  3
 3RX  Var_11  HAB  CAB  CAR  CAA   60.61  30.0  3
 3RX  Var_12  HAA  CAA  CAR  CAB   60.25  30.0  3
 3RX  Var_13  HAC  CAC  CAS  CAE    3.07  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
 3RX  chir_01  CAT  CAK  CAL  CAN  negativ
 3RX  chir_02  CAU  CAO  CAM  CAK  negativ
 3RX  chir_03  CAV  CAL  CAM  CAX  negativ
 3RX  chir_04  CAW  CAN  CAO  CAX  positiv
 3RX  chir_05  CAX  NAQ  CAW  CAV  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
 3RX  plan-1  CAA  0.020
 3RX  plan-1  CAB  0.020
 3RX  plan-1  CAD  0.020
 3RX  plan-1  CAF  0.020
 3RX  plan-1  CAR  0.020
 3RX  plan-1  HAD  0.020
 3RX  plan-2  CAC  0.020
 3RX  plan-2  CAE  0.020
 3RX  plan-2  CAG  0.020
 3RX  plan-2  CAJ  0.020
 3RX  plan-2  CAS  0.020
 3RX  plan-2  HAE  0.020

