# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 12:15:48 2022
#   Inital geometry file: a 104 line input string
#   Ligand name: N-{(1R)-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
 SP9  SP9  N-{(1R)-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_SP9
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
 SP9  CAE   C  CR16  0  -0.272  -4.0037  -1.4228   1.0710
 SP9  CAD   C  CR16  0  -0.242  -4.6711  -2.5842   0.7141
 SP9  CAC   C  CR16  0  -0.253  -4.8518  -2.9004  -0.6268
 SP9  CAR   C  CR16  0  -0.241  -4.3608  -2.0505  -1.6082
 SP9  CAS   C  CR16  0  -0.295  -3.6796  -0.8952  -1.2517
 SP9  CAF   C  CR6   0  -0.031  -3.4880  -0.5764   0.0915
 SP9  CAG   C  C     0   0.531  -2.7816   0.6687   0.5306
 SP9  OAA   O  O     0  -0.495  -3.0667   1.2124   1.5909
 SP9  NAH   N  NH1   0  -0.641  -1.8238   1.1192  -0.2925
 SP9  CAI   C  CH1   0  -0.087  -1.0825   2.3537  -0.0877
 SP9  CAB   C  CH3   0  -0.645  -1.7839   3.5265  -0.7640
 SP9  CAJ   C  CH2   0  -0.465   0.3434   2.1770  -0.5993
 SP9  CAK   C  CH2   0  -0.247   1.1745   1.2067   0.2266
 SP9  NAL   N  NH1   0  -0.603   2.4897   1.0294  -0.3579
 SP9  CAM   C  CH2   0  -0.244   3.3496   0.1629   0.4252
 SP9  CAN   C  CH2   0  -0.448   4.6876  -0.0575  -0.2625
 SP9  CAO   C  CH2   0  -0.429   5.6319  -0.9328   0.5496
 SP9  CAP   C  CH2   0  -0.270   6.9584  -1.1699  -0.1561
 SP9  NAQ   N  NH2   0  -0.801   7.8361  -2.0098   0.6463
 SP9  HAE   H  HCR6  0   0.260  -3.8734  -1.1764   2.1164
 SP9  HAD   H  HCR6  0   0.262  -5.0530  -3.2428   1.4832
 SP9  HAC   H  HCR6  0   0.264  -5.3776  -3.8042  -0.9059
 SP9  HAR   H  HCR6  0   0.264  -4.5112  -2.2834  -2.6540
 SP9  HAS   H  HCR6  0   0.258  -3.3268  -0.2356  -2.0351
 SP9  HNAH  H  HNH1  0   0.401  -1.6166   0.6005  -1.1316
 SP9  HAI   H  HCH1  0   0.244  -1.0512   2.5387   0.9883
 SP9  HAB   H  HCH3  0   0.236  -2.8086   3.6284  -0.4063
 SP9  HABA  H  HCH3  0   0.230  -1.2597   4.4592  -0.5520
 SP9  HABB  H  HCH3  0   0.222  -1.8131   3.3937  -1.8470
 SP9  HAJ   H  HCH2  0   0.224   0.3089   1.8456  -1.6446
 SP9  HAJA  H  HCH2  0   0.240   0.8370   3.1513  -0.6074
 SP9  HAK   H  HCH2  0   0.218   1.2998   1.6147   1.2349
 SP9  HAKA  H  HCH2  0   0.193   0.6351   0.2543   0.3487
 SP9  HNAL  H  HNH1  0   0.334   2.3789   0.6261  -1.2818
 SP9  HAM   H  HCH2  0   0.211   3.5163   0.6346   1.3996
 SP9  HAMA  H  HCH2  0   0.183   2.8850  -0.8147   0.6372
 SP9  HAN   H  HCH2  0   0.213   4.5168  -0.5197  -1.2417
 SP9  HANA  H  HCH2  0   0.217   5.1547   0.9128  -0.4572
 SP9  HAO   H  HCH2  0   0.212   5.8196  -0.4611   1.5210
 SP9  HAOA  H  HCH2  0   0.214   5.1610  -1.8979   0.7609
 SP9  HAP   H  HCH2  0   0.211   6.7693  -1.6797  -1.1052
 SP9  HAPA  H  HCH2  0   0.187   7.4001  -0.1963  -0.4159
 SP9  HNAQ  H  HNH2  0   0.345   8.7004  -2.1696   0.1449
 SP9  HNAA  H  HNH2  0   0.336   8.0996  -1.5070   1.4851

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
 SP9  CAE  CAD   aromatic  1.386  0.020  1.386
 SP9  CAE  CAF   aromatic  1.393  0.020  1.393
 SP9  CAD  CAC   aromatic  1.389  0.020  1.389
 SP9  CAC  CAR   aromatic  1.388  0.020  1.388
 SP9  CAR  CAS   aromatic  1.388  0.020  1.388
 SP9  CAS  CAF   aromatic  1.394  0.020  1.394
 SP9  CAF  CAG   single    1.497  0.020  1.497
 SP9  CAG  OAA   double    1.225  0.020  1.225
 SP9  CAG  NAH   single    1.341  0.020  1.341
 SP9  NAH  CAI   single    1.455  0.020  1.455
 SP9  CAI  CAB   single    1.525  0.020  1.525
 SP9  CAI  CAJ   single    1.525  0.020  1.525
 SP9  CAJ  CAK   single    1.521  0.020  1.521
 SP9  CAK  NAL   single    1.450  0.020  1.450
 SP9  NAL  CAM   single    1.450  0.020  1.450
 SP9  CAM  CAN   single    1.520  0.020  1.520
 SP9  CAN  CAO   single    1.522  0.020  1.522
 SP9  CAO  CAP   single    1.521  0.020  1.521
 SP9  CAP  NAQ   single    1.456  0.020  1.456
 SP9  CAE  HAE   single    0.930  0.020  1.080
 SP9  CAD  HAD   single    0.930  0.020  1.080
 SP9  CAC  HAC   single    0.930  0.020  1.080
 SP9  CAR  HAR   single    0.930  0.020  1.080
 SP9  CAS  HAS   single    0.930  0.020  1.080
 SP9  NAH  HNAH  single    0.860  0.020  1.020
 SP9  CAI  HAI   single    0.970  0.020  1.090
 SP9  CAB  HAB   single    0.970  0.020  1.090
 SP9  CAB  HABA  single    0.970  0.020  1.090
 SP9  CAB  HABB  single    0.970  0.020  1.090
 SP9  CAJ  HAJ   single    0.970  0.020  1.090
 SP9  CAJ  HAJA  single    0.970  0.020  1.090
 SP9  CAK  HAK   single    0.970  0.020  1.090
 SP9  CAK  HAKA  single    0.970  0.020  1.090
 SP9  NAL  HNAL  single    0.890  0.020  1.040
 SP9  CAM  HAM   single    0.970  0.020  1.090
 SP9  CAM  HAMA  single    0.970  0.020  1.090
 SP9  CAN  HAN   single    0.970  0.020  1.090
 SP9  CAN  HANA  single    0.970  0.020  1.090
 SP9  CAO  HAO   single    0.970  0.020  1.090
 SP9  CAO  HAOA  single    0.970  0.020  1.090
 SP9  CAP  HAP   single    0.970  0.020  1.090
 SP9  CAP  HAPA  single    0.970  0.020  1.090
 SP9  NAQ  HNAQ  single    0.890  0.020  1.040
 SP9  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
 SP9  HAE   CAE  CAF   119.76  3.000
 SP9  HAE   CAE  CAD   119.84  3.000
 SP9  CAF   CAE  CAD   120.40  3.000
 SP9  HAD   CAD  CAC   120.10  3.000
 SP9  HAD   CAD  CAE   119.79  3.000
 SP9  CAC   CAD  CAE   120.12  3.000
 SP9  HAC   CAC  CAR   120.06  3.000
 SP9  HAC   CAC  CAD   120.14  3.000
 SP9  CAR   CAC  CAD   119.80  3.000
 SP9  HAR   CAR  CAS   119.72  3.000
 SP9  HAR   CAR  CAC   120.16  3.000
 SP9  CAS   CAR  CAC   120.12  3.000
 SP9  HAS   CAS  CAF   120.86  3.000
 SP9  HAS   CAS  CAR   118.75  3.000
 SP9  CAF   CAS  CAR   120.37  3.000
 SP9  CAG   CAF  CAS   122.53  3.000
 SP9  CAG   CAF  CAE   118.26  3.000
 SP9  CAS   CAF  CAE   119.18  3.000
 SP9  NAH   CAG  OAA   123.26  3.000
 SP9  NAH   CAG  CAF   115.87  3.000
 SP9  OAA   CAG  CAF   120.87  3.000
 SP9  HNAH  NAH  CAI   116.69  3.000
 SP9  HNAH  NAH  CAG   119.01  3.000
 SP9  CAI   NAH  CAG   124.25  3.000
 SP9  HAI   CAI  CAJ   108.87  3.000
 SP9  HAI   CAI  CAB   108.66  3.000
 SP9  CAJ   CAI  CAB   111.74  3.000
 SP9  HAI   CAI  NAH   107.28  3.000
 SP9  CAJ   CAI  NAH   109.32  3.000
 SP9  CAB   CAI  NAH   110.85  3.000
 SP9  HABB  CAB  HABA  108.05  3.000
 SP9  HABB  CAB  HAB   108.17  3.000
 SP9  HABA  CAB  HAB   107.94  3.000
 SP9  HABB  CAB  CAI   111.03  3.000
 SP9  HABA  CAB  CAI   110.51  3.000
 SP9  HAB   CAB  CAI   111.02  3.000
 SP9  HAJA  CAJ  HAJ   106.06  3.000
 SP9  HAJA  CAJ  CAK   109.03  3.000
 SP9  HAJ   CAJ  CAK   109.99  3.000
 SP9  HAJA  CAJ  CAI   108.76  3.000
 SP9  HAJ   CAJ  CAI   108.98  3.000
 SP9  CAK   CAJ  CAI   113.73  3.000
 SP9  HAKA  CAK  HAK   106.04  3.000
 SP9  HAKA  CAK  NAL   112.53  3.000
 SP9  HAK   CAK  NAL   108.23  3.000
 SP9  HAKA  CAK  CAJ   110.13  3.000
 SP9  HAK   CAK  CAJ   108.96  3.000
 SP9  NAL   CAK  CAJ   110.77  3.000
 SP9  HNAL  NAL  CAM   108.60  3.000
 SP9  HNAL  NAL  CAK   108.46  3.000
 SP9  CAM   NAL  CAK   113.15  3.000
 SP9  HAMA  CAM  HAM   105.95  3.000
 SP9  HAMA  CAM  CAN   109.22  3.000
 SP9  HAM   CAM  CAN   109.31  3.000
 SP9  HAMA  CAM  NAL   112.56  3.000
 SP9  HAM   CAM  NAL   108.26  3.000
 SP9  CAN   CAM  NAL   111.36  3.000
 SP9  HANA  CAN  HAN   106.34  3.000
 SP9  HANA  CAN  CAO   109.88  3.000
 SP9  HAN   CAN  CAO   109.32  3.000
 SP9  HANA  CAN  CAM   109.12  3.000
 SP9  HAN   CAN  CAM   109.14  3.000
 SP9  CAO   CAN  CAM   112.83  3.000
 SP9  HAOA  CAO  HAO   106.38  3.000
 SP9  HAOA  CAO  CAP   109.11  3.000
 SP9  HAO   CAO  CAP   109.20  3.000
 SP9  HAOA  CAO  CAN   110.07  3.000
 SP9  HAO   CAO  CAN   109.36  3.000
 SP9  CAP   CAO  CAN   112.52  3.000
 SP9  HAPA  CAP  HAP   106.08  3.000
 SP9  HAPA  CAP  NAQ   113.49  3.000
 SP9  HAP   CAP  NAQ   108.27  3.000
 SP9  HAPA  CAP  CAO   108.77  3.000
 SP9  HAP   CAP  CAO   108.93  3.000
 SP9  NAQ   CAP  CAO   111.10  3.000
 SP9  HNAA  NAQ  HNAQ  105.45  3.000
 SP9  HNAA  NAQ  CAP   109.08  3.000
 SP9  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
 SP9  CONST_01  CAR   CAC  CAD  CAE     0.00   0.0  0
 SP9  CONST_02  CAR   CAS  CAF  CAE     0.00   0.0  0
 SP9  CONST_03  CAS   CAF  CAE  CAD     0.00   0.0  0
 SP9  CONST_04  CAS   CAR  CAC  CAD     0.00   0.0  0
 SP9  CONST_05  CAF   CAE  CAD  CAC     0.00   0.0  0
 SP9  CONST_06  CAF   CAS  CAR  CAC     0.00   0.0  0
 SP9  CONST_07  CAG   CAF  CAE  CAD   180.00   0.0  0
 SP9  CONST_08  CAG   CAF  CAS  CAR   180.00   0.0  0
 SP9  CONST_09  HAC   CAC  CAD  CAE   180.00   0.0  0
 SP9  CONST_10  HAS   CAS  CAF  CAE   180.00   0.0  0
 SP9  CONST_11  HAR   CAR  CAC  CAD   180.00   0.0  0
 SP9  CONST_12  HAE   CAE  CAD  CAC   180.00   0.0  0
 SP9  CONST_13  HAD   CAD  CAC  CAR   180.00   0.0  0
 SP9  CONST_14  CAI   NAH  CAG  CAF   180.00   0.0  0
 SP9  CONST_15  HNAH  NAH  CAG  CAF     0.00   0.0  0
 SP9  CONST_16  CAI   NAH  CAG  OAA     0.00   0.0  0
 SP9  Var_01    OAA   CAG  CAF  CAE   -27.97  30.0  2
 SP9  Var_02    NAL   CAK  CAJ  CAI   176.78  30.0  3
 SP9  Var_03    CAM   NAL  CAK  CAJ   177.19  30.0  3
 SP9  Var_04    CAN   CAM  NAL  CAK   176.79  30.0  3
 SP9  Var_05    CAO   CAN  CAM  NAL   178.43  30.0  3
 SP9  Var_06    CAP   CAO  CAN  CAM   178.94  30.0  3
 SP9  Var_07    NAQ   CAP  CAO  CAN  -179.97  30.0  3
 SP9  Var_08    HNAQ  NAQ  CAP  CAO   178.65  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
 SP9  chir_01  CAI  NAH  CAB  CAJ  positiv

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
 SP9  plan-1  CAE   0.020
 SP9  plan-1  CAD   0.020
 SP9  plan-1  CAC   0.020
 SP9  plan-1  CAR   0.020
 SP9  plan-1  CAS   0.020
 SP9  plan-1  CAF   0.020
 SP9  plan-1  CAG   0.020
 SP9  plan-1  HAE   0.020
 SP9  plan-1  HAD   0.020
 SP9  plan-1  HAC   0.020
 SP9  plan-1  HAR   0.020
 SP9  plan-1  HAS   0.020
 SP9  plan-2  CAF   0.020
 SP9  plan-2  CAG   0.020
 SP9  plan-2  OAA   0.020
 SP9  plan-2  NAH   0.020
 SP9  plan-2  CAI   0.020
 SP9  plan-2  HNAH  0.020

