# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 12:15:51 2022
#   Inital geometry file: a 104 line input string
#   Ligand name: N-{(1S)-3-[(4-aminobutyl)amino]-1-methylpropyl}benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](CCNCCCCN)NC(=O)c1ccccc1
#
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
 SP8  SP8  N-{(1S)-3-[(4-aminobutyl)amino]-1-methylpropyl}benzamide  ligand  44  19  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_SP8
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
 SP8  CAE   C  CR16  0  -0.268  -4.3304  -1.1928  -1.0138
 SP8  CAD   C  CR16  0  -0.240  -5.0123  -2.3509  -0.6746
 SP8  CAC   C  CR16  0  -0.254  -4.8068  -2.9437   0.5640
 SP8  CAR   C  CR16  0  -0.236  -3.9142  -2.3702   1.4588
 SP8  CAS   C  CR16  0  -0.299  -3.2300  -1.2131   1.1171
 SP8  CAF   C  CR6   0  -0.041  -3.4292  -0.6089  -0.1245
 SP8  CAG   C  C     0   0.558  -2.7360   0.6469  -0.5704
 SP8  OAA   O  O     0  -0.493  -2.9996   1.1491  -1.6568
 SP8  NAH   N  NH1   0  -0.659  -1.8245   1.1670   0.2636
 SP8  CAI   C  CH1   0  -0.091  -1.0979   2.4028   0.0186
 SP8  CAB   C  CH3   0  -0.647  -1.8134   3.5894   0.6548
 SP8  CAJ   C  CH2   0  -0.463   0.3279   2.2564   0.5419
 SP8  CAK   C  CH2   0  -0.242   1.1631   1.2589  -0.2454
 SP8  NAL   N  NH1   0  -0.602   2.4620   1.0682   0.3688
 SP8  CAM   C  CH2   0  -0.248   3.3285   0.1898  -0.3938
 SP8  CAN   C  CH2   0  -0.444   4.6627  -0.0161   0.3057
 SP8  CAO   C  CH2   0  -0.430   5.6133  -0.9007  -0.4887
 SP8  CAP   C  CH2   0  -0.270   6.9344  -1.1334   0.2280
 SP8  NAQ   N  NH2   0  -0.801   7.8193  -1.9729  -0.5674
 SP8  HAE   H  HCR6  0   0.259  -4.4982  -0.7377  -1.9801
 SP8  HAD   H  HCR6  0   0.262  -5.7073  -2.7903  -1.3779
 SP8  HAC   H  HCR6  0   0.265  -5.3382  -3.8477   0.8311
 SP8  HAR   H  HCR6  0   0.266  -3.7479  -2.8211   2.4281
 SP8  HAS   H  HCR6  0   0.250  -2.5470  -0.8027   1.8496
 SP8  HNAH  H  HNH1  0   0.403  -1.6800   0.7481   1.1673
 SP8  HAI   H  HCH1  0   0.246  -1.0658   2.5521  -1.0622
 SP8  HAB   H  HCH3  0   0.231  -1.2984   4.5201   0.4143
 SP8  HABA  H  HCH3  0   0.236  -2.8382   3.6694   0.2921
 SP8  HABB  H  HCH3  0   0.222  -1.8437   3.4924   1.7416
 SP8  HAJ   H  HCH2  0   0.237   0.8090   3.2381   0.5093
 SP8  HAJA  H  HCH2  0   0.226   0.3007   1.9624   1.5969
 SP8  HAK   H  HCH2  0   0.216   0.6534   0.2909  -0.2746
 SP8  HAKA  H  HCH2  0   0.187   1.2334   1.5984  -1.2923
 SP8  HNAL  H  HNH1  0   0.335   2.9177   1.9702   0.4571
 SP8  HAM   H  HCH2  0   0.213   2.8248  -0.7762  -0.5036
 SP8  HAMA  H  HCH2  0   0.184   3.5042   0.5584  -1.4182
 SP8  HAN   H  HCH2  0   0.213   5.1353   0.9573   0.4800
 SP8  HANA  H  HCH2  0   0.215   4.4827  -0.4524   1.2929
 SP8  HAO   H  HCH2  0   0.212   5.1342  -1.8670  -0.6843
 SP8  HAOA  H  HCH2  0   0.214   5.8121  -0.4513  -1.4665
 SP8  HAP   H  HCH2  0   0.211   7.4280  -0.1703   0.3878
 SP8  HAPA  H  HCH2  0   0.186   6.7271  -1.5401   1.2289
 SP8  HNAQ  H  HNH2  0   0.345   8.6930  -2.1040  -0.0740
 SP8  HNAA  H  HNH2  0   0.336   7.4136  -2.8975  -0.6476

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
 SP8  CAE  CAD   aromatic  1.386  0.020  1.386
 SP8  CAE  CAF   aromatic  1.394  0.020  1.394
 SP8  CAD  CAC   aromatic  1.388  0.020  1.388
 SP8  CAC  CAR   aromatic  1.388  0.020  1.388
 SP8  CAR  CAS   aromatic  1.387  0.020  1.387
 SP8  CAS  CAF   aromatic  1.395  0.020  1.395
 SP8  CAF  CAG   single    1.502  0.020  1.502
 SP8  CAG  OAA   double    1.226  0.020  1.226
 SP8  CAG  NAH   single    1.341  0.020  1.341
 SP8  NAH  CAI   single    1.454  0.020  1.454
 SP8  CAI  CAB   single    1.525  0.020  1.525
 SP8  CAI  CAJ   single    1.526  0.020  1.526
 SP8  CAJ  CAK   single    1.521  0.020  1.521
 SP8  CAK  NAL   single    1.449  0.020  1.449
 SP8  NAL  CAM   single    1.450  0.020  1.450
 SP8  CAM  CAN   single    1.520  0.020  1.520
 SP8  CAN  CAO   single    1.522  0.020  1.522
 SP8  CAO  CAP   single    1.521  0.020  1.521
 SP8  CAP  NAQ   single    1.456  0.020  1.456
 SP8  CAE  HAE   single    0.930  0.020  1.080
 SP8  CAD  HAD   single    0.930  0.020  1.080
 SP8  CAC  HAC   single    0.930  0.020  1.080
 SP8  CAR  HAR   single    0.930  0.020  1.080
 SP8  CAS  HAS   single    0.930  0.020  1.080
 SP8  NAH  HNAH  single    0.860  0.020  1.020
 SP8  CAI  HAI   single    0.970  0.020  1.090
 SP8  CAB  HAB   single    0.970  0.020  1.090
 SP8  CAB  HABA  single    0.970  0.020  1.090
 SP8  CAB  HABB  single    0.970  0.020  1.090
 SP8  CAJ  HAJ   single    0.970  0.020  1.090
 SP8  CAJ  HAJA  single    0.970  0.020  1.090
 SP8  CAK  HAK   single    0.970  0.020  1.090
 SP8  CAK  HAKA  single    0.970  0.020  1.090
 SP8  NAL  HNAL  single    0.890  0.020  1.040
 SP8  CAM  HAM   single    0.970  0.020  1.090
 SP8  CAM  HAMA  single    0.970  0.020  1.090
 SP8  CAN  HAN   single    0.970  0.020  1.090
 SP8  CAN  HANA  single    0.970  0.020  1.090
 SP8  CAO  HAO   single    0.970  0.020  1.090
 SP8  CAO  HAOA  single    0.970  0.020  1.090
 SP8  CAP  HAP   single    0.970  0.020  1.090
 SP8  CAP  HAPA  single    0.970  0.020  1.090
 SP8  NAQ  HNAQ  single    0.890  0.020  1.040
 SP8  NAQ  HNAA  single    0.890  0.020  1.040

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
 SP8  HAE   CAE  CAF   119.61  3.000
 SP8  HAE   CAE  CAD   119.60  3.000
 SP8  CAF   CAE  CAD   120.79  3.000
 SP8  HAD   CAD  CAC   120.11  3.000
 SP8  HAD   CAD  CAE   119.75  3.000
 SP8  CAC   CAD  CAE   120.14  3.000
 SP8  HAC   CAC  CAR   120.12  3.000
 SP8  HAC   CAC  CAD   120.28  3.000
 SP8  CAR   CAC  CAD   119.60  3.000
 SP8  HAR   CAR  CAS   119.51  3.000
 SP8  HAR   CAR  CAC   120.29  3.000
 SP8  CAS   CAR  CAC   120.21  3.000
 SP8  HAS   CAS  CAF   121.89  3.000
 SP8  HAS   CAS  CAR   117.44  3.000
 SP8  CAF   CAS  CAR   120.67  3.000
 SP8  CAG   CAF  CAS   124.08  3.000
 SP8  CAG   CAF  CAE   117.33  3.000
 SP8  CAS   CAF  CAE   118.59  3.000
 SP8  NAH   CAG  OAA   122.60  3.000
 SP8  NAH   CAG  CAF   116.97  3.000
 SP8  OAA   CAG  CAF   120.43  3.000
 SP8  HNAH  NAH  CAI   115.67  3.000
 SP8  HNAH  NAH  CAG   119.65  3.000
 SP8  CAI   NAH  CAG   124.38  3.000
 SP8  HAI   CAI  CAJ   108.98  3.000
 SP8  HAI   CAI  CAB   108.69  3.000
 SP8  CAJ   CAI  CAB   111.72  3.000
 SP8  HAI   CAI  NAH   107.32  3.000
 SP8  CAJ   CAI  NAH   109.12  3.000
 SP8  CAB   CAI  NAH   110.89  3.000
 SP8  HABB  CAB  HABA  108.16  3.000
 SP8  HABB  CAB  HAB   107.97  3.000
 SP8  HABA  CAB  HAB   107.94  3.000
 SP8  HABB  CAB  CAI   111.06  3.000
 SP8  HABA  CAB  CAI   111.06  3.000
 SP8  HAB   CAB  CAI   110.52  3.000
 SP8  HAJA  CAJ  HAJ   106.28  3.000
 SP8  HAJA  CAJ  CAK   109.65  3.000
 SP8  HAJ   CAJ  CAK   109.37  3.000
 SP8  HAJA  CAJ  CAI   109.44  3.000
 SP8  HAJ   CAJ  CAI   108.34  3.000
 SP8  CAK   CAJ  CAI   113.49  3.000
 SP8  HAKA  CAK  HAK   106.06  3.000
 SP8  HAKA  CAK  NAL   112.69  3.000
 SP8  HAK   CAK  NAL   108.20  3.000
 SP8  HAKA  CAK  CAJ   108.94  3.000
 SP8  HAK   CAK  CAJ   109.76  3.000
 SP8  NAL   CAK  CAJ   111.05  3.000
 SP8  HNAL  NAL  CAM   108.41  3.000
 SP8  HNAL  NAL  CAK   108.81  3.000
 SP8  CAM   NAL  CAK   113.09  3.000
 SP8  HAMA  CAM  HAM   105.97  3.000
 SP8  HAMA  CAM  CAN   109.44  3.000
 SP8  HAM   CAM  CAN   109.29  3.000
 SP8  HAMA  CAM  NAL   112.40  3.000
 SP8  HAM   CAM  NAL   108.19  3.000
 SP8  CAN   CAM  NAL   111.36  3.000
 SP8  HANA  CAN  HAN   106.36  3.000
 SP8  HANA  CAN  CAO   109.99  3.000
 SP8  HAN   CAN  CAO   109.25  3.000
 SP8  HANA  CAN  CAM   108.95  3.000
 SP8  HAN   CAN  CAM   109.35  3.000
 SP8  CAO   CAN  CAM   112.74  3.000
 SP8  HAOA  CAO  HAO   106.39  3.000
 SP8  HAOA  CAO  CAP   109.03  3.000
 SP8  HAO   CAO  CAP   109.20  3.000
 SP8  HAOA  CAO  CAN   109.94  3.000
 SP8  HAO   CAO  CAN   109.42  3.000
 SP8  CAP   CAO  CAN   112.67  3.000
 SP8  HAPA  CAP  HAP   106.12  3.000
 SP8  HAPA  CAP  NAQ   113.47  3.000
 SP8  HAP   CAP  NAQ   108.25  3.000
 SP8  HAPA  CAP  CAO   108.76  3.000
 SP8  HAP   CAP  CAO   109.04  3.000
 SP8  NAQ   CAP  CAO   111.02  3.000
 SP8  HNAA  NAQ  HNAQ  105.44  3.000
 SP8  HNAA  NAQ  CAP   109.03  3.000
 SP8  HNAQ  NAQ  CAP   109.45  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
 SP8  CONST_01  CAR   CAC  CAD  CAE     0.00   0.0  0
 SP8  CONST_02  CAR   CAS  CAF  CAE     0.00   0.0  0
 SP8  CONST_03  CAS   CAF  CAE  CAD     0.00   0.0  0
 SP8  CONST_04  CAS   CAR  CAC  CAD     0.00   0.0  0
 SP8  CONST_05  CAF   CAE  CAD  CAC     0.00   0.0  0
 SP8  CONST_06  CAF   CAS  CAR  CAC     0.00   0.0  0
 SP8  CONST_07  CAG   CAF  CAE  CAD   180.00   0.0  0
 SP8  CONST_08  CAG   CAF  CAS  CAR   180.00   0.0  0
 SP8  CONST_09  HAC   CAC  CAD  CAE   180.00   0.0  0
 SP8  CONST_10  HAS   CAS  CAF  CAE   180.00   0.0  0
 SP8  CONST_11  HAR   CAR  CAC  CAD   180.00   0.0  0
 SP8  CONST_12  HAE   CAE  CAD  CAC   180.00   0.0  0
 SP8  CONST_13  HAD   CAD  CAC  CAR   180.00   0.0  0
 SP8  CONST_14  CAI   NAH  CAG  CAF   180.00   0.0  0
 SP8  CONST_15  HNAH  NAH  CAG  CAF     0.00   0.0  0
 SP8  CONST_16  CAI   NAH  CAG  OAA     0.00   0.0  0
 SP8  Var_01    OAA   CAG  CAF  CAE     2.46  30.0  2
 SP8  Var_02    NAL   CAK  CAJ  CAI  -174.66  30.0  3
 SP8  Var_03    CAM   NAL  CAK  CAJ  -176.27  30.0  3
 SP8  Var_04    CAN   CAM  NAL  CAK  -178.28  30.0  3
 SP8  Var_05    CAO   CAN  CAM  NAL  -178.28  30.0  3
 SP8  Var_06    CAP   CAO  CAN  CAM  -178.59  30.0  3
 SP8  Var_07    NAQ   CAP  CAO  CAN  -179.50  30.0  3
 SP8  Var_08    HNAQ  NAQ  CAP  CAO   179.39  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
 SP8  chir_01  CAI  NAH  CAB  CAJ  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
 SP8  plan-1  CAE   0.020
 SP8  plan-1  CAD   0.020
 SP8  plan-1  CAC   0.020
 SP8  plan-1  CAR   0.020
 SP8  plan-1  CAS   0.020
 SP8  plan-1  CAF   0.020
 SP8  plan-1  CAG   0.020
 SP8  plan-1  HAE   0.020
 SP8  plan-1  HAD   0.020
 SP8  plan-1  HAC   0.020
 SP8  plan-1  HAR   0.020
 SP8  plan-1  HAS   0.020
 SP8  plan-2  CAF   0.020
 SP8  plan-2  CAG   0.020
 SP8  plan-2  OAA   0.020
 SP8  plan-2  NAH   0.020
 SP8  plan-2  CAI   0.020
 SP8  plan-2  HNAH  0.020

