# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 01:09:51 2022
#   Inital geometry file: a 121 line input string
#   Ligand name: (2R)-N-[3-(heptylamino)-3-oxopropyl]-2,4-dihydroxy-3,3-dimethylbutanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)CO
#
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
 RNH  RNH  (2R)-N-[3-(heptylamino)-3-oxopropyl]-2,4-dihydroxy-3,3-dimethylbutanamide  ligand  54  22  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_RNH
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
 RNH  CAA   C  CH2   0  -0.407   8.4368   0.1039   0.0047
 RNH  CAB   C  CH3   0  -0.669  -4.5028   2.0536   0.3911
 RNH  CAC   C  CH3   0  -0.646  -6.6899   1.4072   1.3880
 RNH  OAD   O  O     0  -0.503   1.0059  -1.5600  -1.5025
 RNH  OAE   O  O     0  -0.502  -4.1571  -1.7046  -0.8954
 RNH  OAG   O  OH1   0  -0.664  -6.0006  -1.3637   1.0109
 RNH  CAJ   C  CH2   0  -0.412   7.0396   0.5249   0.4424
 RNH  CAK   C  CH2   0  -0.416   5.9346  -0.2155  -0.2998
 RNH  CAL   C  CH2   0  -0.475   4.5384   0.1915   0.1521
 RNH  CAM   C  CH2   0  -0.232   3.4560  -0.5631  -0.6021
 RNH  CAN   C  CH2   0  -0.233  -1.4974  -0.9516  -0.4599
 RNH  CAO   C  CH2   0  -0.639  -0.2585  -0.2628   0.0826
 RNH  CAP   C  CH2   0  -0.130  -6.1869   0.8274  -1.0081
 RNH  NAQ   N  NH1   0  -0.647   2.1398  -0.1919  -0.1228
 RNH  NAR   N  NH1   0  -0.639  -2.6595  -0.5057   0.2847
 RNH  OAS   O  OH1   0  -0.672  -6.7784   2.0440  -1.4072
 RNH  CAT   C  C     0   0.569   1.0114  -0.7380  -0.5960
 RNH  CAU   C  C     0   0.520  -3.8975  -0.9150   0.0068
 RNH  CAV   C  CH1   0  -0.033  -5.0206  -0.3675   0.8911
 RNH  CAW   C  CT    0  -0.143  -5.6008   0.9870   0.3961
 RNH  CAY   C  CH2   0  -0.421   9.5482   0.8391   0.7434
 RNH  CAZ   C  CH3   0  -0.661  10.9390   0.4060   0.3007
 RNH  HAA   H  HCH2  0   0.207   8.5528  -0.9752   0.1560
 RNH  HAAA  H  HCH2  0   0.207   8.5452   0.2711  -1.0728
 RNH  HAB   H  HCH3  0   0.226  -3.9842   2.0908   1.3526
 RNH  HABA  H  HCH3  0   0.230  -3.7585   1.8830  -0.3881
 RNH  HABB  H  HCH3  0   0.245  -4.9302   3.0409   0.2215
 RNH  HAC   H  HCH3  0   0.235  -7.1107   2.3751   1.1178
 RNH  HACA  H  HCH3  0   0.230  -7.5061   0.6858   1.4275
 RNH  HACB  H  HCH3  0   0.223  -6.2763   1.5003   2.3950
 RNH  HOAG  H  HOH1  0   0.443  -6.0048  -1.8641   0.1843
 RNH  HAJ   H  HCH2  0   0.209   6.9308   0.3558   1.5193
 RNH  HAJA  H  HCH2  0   0.210   6.9212   1.6035   0.2912
 RNH  HAK   H  HCH2  0   0.215   6.0366  -0.0370  -1.3755
 RNH  HAKA  H  HCH2  0   0.215   6.0606  -1.2940  -0.1563
 RNH  HAL   H  HCH2  0   0.228   4.4346   0.0031   1.2256
 RNH  HALA  H  HCH2  0   0.230   4.4050   1.2683   0.0076
 RNH  HAM   H  HCH2  0   0.230   3.5369  -0.3541  -1.6725
 RNH  HAMA  H  HCH2  0   0.228   3.6039  -1.6403  -0.4789
 RNH  HAN   H  HCH2  0   0.248  -1.6276  -0.7233  -1.5189
 RNH  HANA  H  HCH2  0   0.246  -1.3977  -2.0355  -0.3730
 RNH  HAO   H  HCH2  0   0.284  -0.3431   0.8214  -0.0396
 RNH  HAOA  H  HCH2  0   0.280  -0.1693  -0.4431   1.1583
 RNH  HAP   H  HCH2  0   0.198  -6.9284   0.0183  -1.0075
 RNH  HAPA  H  HCH2  0   0.202  -5.3907   0.5380  -1.7067
 RNH  HNAQ  H  HNH1  0   0.402   2.0792   0.4652   0.6386
 RNH  HNAR  H  HNH1  0   0.407  -2.5200   0.0999   1.0776
 RNH  HOAS  H  HOH1  0   0.454  -7.1389   1.9200  -2.2894
 RNH  HAV   H  HCH1  0   0.249  -4.6194  -0.1855   1.8957
 RNH  HAY   H  HCH2  0   0.211   9.4330   1.9167   0.5898
 RNH  HAYA  H  HCH2  0   0.211   9.4380   0.6738   1.8198
 RNH  HAZ   H  HCH3  0   0.216  11.0919  -0.6608   0.4738
 RNH  HAZA  H  HCH3  0   0.216  11.0878   0.5899  -0.7649
 RNH  HAZB  H  HCH3  0   0.225  11.7189   0.9438   0.8409

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
 RNH  CAA  CAJ   single  1.523  0.020  1.523
 RNH  CAA  CAY   single  1.524  0.020  1.524
 RNH  CAB  CAW   single  1.531  0.020  1.531
 RNH  CAC  CAW   single  1.532  0.020  1.532
 RNH  OAD  CAT   double  1.224  0.020  1.224
 RNH  OAE  CAU   double  1.227  0.020  1.227
 RNH  OAG  CAV   single  1.402  0.020  1.402
 RNH  CAJ  CAK   single  1.523  0.020  1.523
 RNH  CAK  CAL   single  1.523  0.020  1.523
 RNH  CAL  CAM   single  1.520  0.020  1.520
 RNH  CAM  NAQ   single  1.449  0.020  1.449
 RNH  CAN  CAO   single  1.518  0.020  1.518
 RNH  CAN  NAR   single  1.451  0.020  1.451
 RNH  CAO  CAT   single  1.516  0.020  1.516
 RNH  CAP  OAS   single  1.410  0.020  1.410
 RNH  CAP  CAW   single  1.530  0.020  1.530
 RNH  NAQ  CAT   single  1.340  0.020  1.340
 RNH  NAR  CAU   single  1.333  0.020  1.333
 RNH  CAU  CAV   single  1.531  0.020  1.531
 RNH  CAV  CAW   single  1.554  0.020  1.554
 RNH  CAY  CAZ   single  1.522  0.020  1.522
 RNH  CAA  HAA   single  0.970  0.020  1.090
 RNH  CAA  HAAA  single  0.970  0.020  1.090
 RNH  CAB  HAB   single  0.970  0.020  1.090
 RNH  CAB  HABA  single  0.970  0.020  1.090
 RNH  CAB  HABB  single  0.970  0.020  1.090
 RNH  CAC  HAC   single  0.970  0.020  1.090
 RNH  CAC  HACA  single  0.970  0.020  1.090
 RNH  CAC  HACB  single  0.970  0.020  1.090
 RNH  OAG  HOAG  single  0.850  0.020  0.980
 RNH  CAJ  HAJ   single  0.970  0.020  1.090
 RNH  CAJ  HAJA  single  0.970  0.020  1.090
 RNH  CAK  HAK   single  0.970  0.020  1.090
 RNH  CAK  HAKA  single  0.970  0.020  1.090
 RNH  CAL  HAL   single  0.970  0.020  1.090
 RNH  CAL  HALA  single  0.970  0.020  1.090
 RNH  CAM  HAM   single  0.970  0.020  1.090
 RNH  CAM  HAMA  single  0.970  0.020  1.090
 RNH  CAN  HAN   single  0.970  0.020  1.090
 RNH  CAN  HANA  single  0.970  0.020  1.090
 RNH  CAO  HAO   single  0.970  0.020  1.090
 RNH  CAO  HAOA  single  0.970  0.020  1.090
 RNH  CAP  HAP   single  0.970  0.020  1.090
 RNH  CAP  HAPA  single  0.970  0.020  1.090
 RNH  NAQ  HNAQ  single  0.860  0.020  1.020
 RNH  NAR  HNAR  single  0.860  0.020  1.020
 RNH  OAS  HOAS  single  0.850  0.020  0.980
 RNH  CAV  HAV   single  0.970  0.020  1.090
 RNH  CAY  HAY   single  0.970  0.020  1.090
 RNH  CAY  HAYA  single  0.970  0.020  1.090
 RNH  CAZ  HAZ   single  0.970  0.020  1.090
 RNH  CAZ  HAZA  single  0.970  0.020  1.090
 RNH  CAZ  HAZB  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
 RNH  HAAA  CAA  HAA   105.99  3.000
 RNH  HAAA  CAA  CAY   109.33  3.000
 RNH  HAA   CAA  CAY   109.33  3.000
 RNH  HAAA  CAA  CAJ   109.33  3.000
 RNH  HAA   CAA  CAJ   109.24  3.000
 RNH  CAY   CAA  CAJ   113.35  3.000
 RNH  HABB  CAB  HABA  107.35  3.000
 RNH  HABB  CAB  HAB   106.99  3.000
 RNH  HABA  CAB  HAB   108.05  3.000
 RNH  HABB  CAB  CAW   110.53  3.000
 RNH  HABA  CAB  CAW   112.50  3.000
 RNH  HAB   CAB  CAW   111.17  3.000
 RNH  HACB  CAC  HACA  107.84  3.000
 RNH  HACB  CAC  HAC   107.40  3.000
 RNH  HACA  CAC  HAC   107.93  3.000
 RNH  HACB  CAC  CAW   110.55  3.000
 RNH  HACA  CAC  CAW   111.98  3.000
 RNH  HAC   CAC  CAW   110.96  3.000
 RNH  HOAG  OAG  CAV   107.33  3.000
 RNH  HAJA  CAJ  HAJ   106.07  3.000
 RNH  HAJA  CAJ  CAK   109.45  3.000
 RNH  HAJ   CAJ  CAK   109.38  3.000
 RNH  HAJA  CAJ  CAA   109.37  3.000
 RNH  HAJ   CAJ  CAA   109.32  3.000
 RNH  CAK   CAJ  CAA   113.02  3.000
 RNH  HAKA  CAK  HAK   106.17  3.000
 RNH  HAKA  CAK  CAL   109.25  3.000
 RNH  HAK   CAK  CAL   109.47  3.000
 RNH  HAKA  CAK  CAJ   109.36  3.000
 RNH  HAK   CAK  CAJ   109.38  3.000
 RNH  CAL   CAK  CAJ   112.99  3.000
 RNH  HALA  CAL  HAL   106.69  3.000
 RNH  HALA  CAL  CAM   109.64  3.000
 RNH  HAL   CAL  CAM   109.49  3.000
 RNH  HALA  CAL  CAK   109.60  3.000
 RNH  HAL   CAL  CAK   109.39  3.000
 RNH  CAM   CAL  CAK   111.90  3.000
 RNH  HAMA  CAM  HAM   106.75  3.000
 RNH  HAMA  CAM  NAQ   109.74  3.000
 RNH  HAM   CAM  NAQ   110.00  3.000
 RNH  HAMA  CAM  CAL   109.67  3.000
 RNH  HAM   CAM  CAL   109.77  3.000
 RNH  NAQ   CAM  CAL   110.83  3.000
 RNH  HANA  CAN  HAN   107.21  3.000
 RNH  HANA  CAN  NAR   109.72  3.000
 RNH  HAN   CAN  NAR   109.77  3.000
 RNH  HANA  CAN  CAO   110.34  3.000
 RNH  HAN   CAN  CAO   110.45  3.000
 RNH  NAR   CAN  CAO   109.33  3.000
 RNH  HAOA  CAO  HAO   106.22  3.000
 RNH  HAOA  CAO  CAT   108.66  3.000
 RNH  HAO   CAO  CAT   108.98  3.000
 RNH  HAOA  CAO  CAN   110.06  3.000
 RNH  HAO   CAO  CAN   110.28  3.000
 RNH  CAT   CAO  CAN   112.42  3.000
 RNH  HAPA  CAP  HAP   107.21  3.000
 RNH  HAPA  CAP  CAW   109.49  3.000
 RNH  HAP   CAP  CAW   109.59  3.000
 RNH  HAPA  CAP  OAS   110.57  3.000
 RNH  HAP   CAP  OAS   110.65  3.000
 RNH  CAW   CAP  OAS   109.29  3.000
 RNH  HNAQ  NAQ  CAT   118.82  3.000
 RNH  HNAQ  NAQ  CAM   118.14  3.000
 RNH  CAT   NAQ  CAM   122.93  3.000
 RNH  HNAR  NAR  CAU   118.50  3.000
 RNH  HNAR  NAR  CAN   118.55  3.000
 RNH  CAU   NAR  CAN   122.86  3.000
 RNH  HOAS  OAS  CAP   107.80  3.000
 RNH  NAQ   CAT  CAO   114.80  3.000
 RNH  NAQ   CAT  OAD   122.63  3.000
 RNH  CAO   CAT  OAD   122.57  3.000
 RNH  CAV   CAU  NAR   116.82  3.000
 RNH  CAV   CAU  OAE   119.99  3.000
 RNH  NAR   CAU  OAE   123.19  3.000
 RNH  HAV   CAV  CAW   106.47  3.000
 RNH  HAV   CAV  CAU   108.67  3.000
 RNH  CAW   CAV  CAU   113.67  3.000
 RNH  HAV   CAV  OAG   107.17  3.000
 RNH  CAW   CAV  OAG   112.66  3.000
 RNH  CAU   CAV  OAG   107.94  3.000
 RNH  CAV   CAW  CAP   110.14  3.000
 RNH  CAV   CAW  CAC   107.35  3.000
 RNH  CAP   CAW  CAC   110.52  3.000
 RNH  CAV   CAW  CAB   109.91  3.000
 RNH  CAP   CAW  CAB   110.15  3.000
 RNH  CAC   CAW  CAB   108.72  3.000
 RNH  HAYA  CAY  HAY   106.03  3.000
 RNH  HAYA  CAY  CAZ   109.57  3.000
 RNH  HAY   CAY  CAZ   109.60  3.000
 RNH  HAYA  CAY  CAA   109.30  3.000
 RNH  HAY   CAY  CAA   109.29  3.000
 RNH  CAZ   CAY  CAA   112.83  3.000
 RNH  HAZB  CAZ  HAZA  107.64  3.000
 RNH  HAZB  CAZ  HAZ   107.65  3.000
 RNH  HAZA  CAZ  HAZ   107.48  3.000
 RNH  HAZB  CAZ  CAY   111.66  3.000
 RNH  HAZA  CAZ  CAY   111.13  3.000
 RNH  HAZ   CAZ  CAY   111.09  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
 RNH  CONST_01  CAM   NAQ  CAT  OAD     0.00   0.0  0
 RNH  CONST_02  CAN   NAR  CAU  OAE     0.00   0.0  0
 RNH  CONST_03  CAO   CAT  NAQ  CAM   180.00   0.0  0
 RNH  CONST_04  CAV   CAU  NAR  CAN   180.00   0.0  0
 RNH  CONST_05  HNAQ  NAQ  CAT  OAD   180.00   0.0  0
 RNH  CONST_06  HNAR  NAR  CAU  OAE   180.00   0.0  0
 RNH  Var_01    CAL   CAK  CAJ  CAA   179.18  30.0  3
 RNH  Var_02    OAS   CAP  CAW  CAB   -62.07  30.0  3
 RNH  Var_03    CAN   CAO  CAT  OAD     1.84  30.0  2
 RNH  Var_04    CAZ   CAY  CAA  CAJ   179.80  30.0  3
 RNH  Var_05    CAM   CAL  CAK  CAJ  -179.91  30.0  3
 RNH  Var_06    CAY   CAA  CAJ  CAK  -179.95  30.0  1
 RNH  Var_07    NAQ   CAM  CAL  CAK   178.05  30.0  3
 RNH  Var_08    CAT   NAQ  CAM  CAL  -178.19  30.0  3
 RNH  Var_09    CAU   NAR  CAN  CAO   178.13  30.0  3
 RNH  Var_10    CAT   CAO  CAN  NAR   176.77  30.0  3
 RNH  Var_11    HAZ   CAZ  CAY  CAA   -59.83  30.0  3
 RNH  Var_12    HAC   CAC  CAW  CAB    58.84  30.0  3
 RNH  Var_13    HAB   CAB  CAW  CAC    66.12  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
 RNH  chir_01  CAV  OAG  CAU  CAW  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
 RNH  plan-1  OAD   0.020
 RNH  plan-1  CAM   0.020
 RNH  plan-1  CAO   0.020
 RNH  plan-1  NAQ   0.020
 RNH  plan-1  CAT   0.020
 RNH  plan-1  HNAQ  0.020
 RNH  plan-2  OAE   0.020
 RNH  plan-2  CAN   0.020
 RNH  plan-2  NAR   0.020
 RNH  plan-2  CAU   0.020
 RNH  plan-2  CAV   0.020
 RNH  plan-2  HNAR  0.020

