# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 12:15:09 2022
#   Inital geometry file: a 84 line input string
#   Ligand name: N-{(1S)-3-[(4-aminobutyl)amino]-1-methylpropyl}acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](CCNCCCCN)NC(C)=O
#
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
 SP7  SP7  N-{(1S)-3-[(4-aminobutyl)amino]-1-methylpropyl}acetamide  ligand  37  14  .  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_SP7
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
 SP7  CAC   C  CH3   0  -0.777  -4.2732   2.3431  -0.7292
 SP7  CAD   C  C     0   0.522  -3.9980   1.1373   0.1360
 SP7  OAA   O  O     0  -0.514  -4.4552   1.0435   1.2691
 SP7  NAE   N  NH1   0  -0.620  -3.2077   0.2030  -0.4158
 SP7  CAF   C  CH1   0  -0.084  -2.8279  -1.0396   0.2336
 SP7  CAB   C  CH3   0  -0.647  -3.8358  -2.1457  -0.0600
 SP7  CAG   C  CH2   0  -0.463  -1.4170  -1.4307  -0.1942
 SP7  CAH   C  CH2   0  -0.242  -0.3559  -0.4317   0.2417
 SP7  NAI   N  NH1   0  -0.602   0.9628  -0.8483  -0.1917
 SP7  CAJ   C  CH2   0  -0.246   2.0118   0.0613   0.2283
 SP7  CAK   C  CH2   0  -0.445   3.3777  -0.4078  -0.2472
 SP7  CAL   C  CH2   0  -0.427   4.5047   0.5100   0.2069
 SP7  CAM   C  CH2   0  -0.271   5.8686   0.0503  -0.2844
 SP7  NAN   N  NH2   0  -0.801   6.9206   0.9460   0.1763
 SP7  HAC   H  HCH3  0   0.266  -3.8044   3.2204  -0.2824
 SP7  HACA  H  HCH3  0   0.246  -3.9060   2.2442  -1.7490
 SP7  HACB  H  HCH3  0   0.262  -5.3457   2.5304  -0.7630
 SP7  HNAE  H  HNH1  0   0.394  -2.9148   0.3312  -1.3717
 SP7  HAF   H  HCH1  0   0.240  -2.8242  -0.8509   1.3098
 SP7  HAB   H  HCH3  0   0.228  -3.5555  -3.0654   0.4552
 SP7  HABA  H  HCH3  0   0.235  -4.8338  -1.8627   0.2750
 SP7  HABB  H  HCH3  0   0.221  -3.8821  -2.3590  -1.1293
 SP7  HAG   H  HCH2  0   0.235  -1.1918  -2.4096   0.2400
 SP7  HAGA  H  HCH2  0   0.225  -1.3787  -1.5604  -1.2814
 SP7  HAH   H  HCH2  0   0.216  -0.5659   0.5476  -0.1985
 SP7  HAHA  H  HCH2  0   0.186  -0.4219  -0.2942   1.3342
 SP7  HNAI  H  HNH1  0   0.334   1.1587  -1.7649   0.1955
 SP7  HAJ   H  HCH2  0   0.212   1.7997   1.0478  -0.1973
 SP7  HAJA  H  HCH2  0   0.183   2.0341   0.2001   1.3221
 SP7  HAK   H  HCH2  0   0.213   3.5618  -1.4217   0.1260
 SP7  HAKA  H  HCH2  0   0.215   3.3716  -0.4777  -1.3392
 SP7  HAL   H  HCH2  0   0.213   4.3232   1.5301  -0.1457
 SP7  HALA  H  HCH2  0   0.211   4.5135   0.5586   1.3017
 SP7  HAM   H  HCH2  0   0.187   6.0203  -0.9965   0.0179
 SP7  HAMA  H  HCH2  0   0.211   5.8741   0.0546  -1.3781
 SP7  HNAN  H  HNH2  0   0.336   7.0218   0.8512   1.1797
 SP7  HNAA  H  HNH2  0   0.345   7.8075   0.6523  -0.2129

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
 SP7  CAC  CAD   single  1.509  0.020  1.509
 SP7  CAD  OAA   double  1.225  0.020  1.225
 SP7  CAD  NAE   single  1.342  0.020  1.342
 SP7  NAE  CAF   single  1.453  0.020  1.453
 SP7  CAF  CAB   single  1.525  0.020  1.525
 SP7  CAF  CAG   single  1.525  0.020  1.525
 SP7  CAG  CAH   single  1.521  0.020  1.521
 SP7  CAH  NAI   single  1.449  0.020  1.449
 SP7  NAI  CAJ   single  1.451  0.020  1.451
 SP7  CAJ  CAK   single  1.520  0.020  1.520
 SP7  CAK  CAL   single  1.523  0.020  1.523
 SP7  CAL  CAM   single  1.521  0.020  1.521
 SP7  CAM  NAN   single  1.457  0.020  1.457
 SP7  CAC  HAC   single  0.970  0.020  1.090
 SP7  CAC  HACA  single  0.970  0.020  1.090
 SP7  CAC  HACB  single  0.970  0.020  1.090
 SP7  NAE  HNAE  single  0.860  0.020  1.020
 SP7  CAF  HAF   single  0.970  0.020  1.090
 SP7  CAB  HAB   single  0.970  0.020  1.090
 SP7  CAB  HABA  single  0.970  0.020  1.090
 SP7  CAB  HABB  single  0.970  0.020  1.090
 SP7  CAG  HAG   single  0.970  0.020  1.090
 SP7  CAG  HAGA  single  0.970  0.020  1.090
 SP7  CAH  HAH   single  0.970  0.020  1.090
 SP7  CAH  HAHA  single  0.970  0.020  1.090
 SP7  NAI  HNAI  single  0.890  0.020  1.040
 SP7  CAJ  HAJ   single  0.970  0.020  1.090
 SP7  CAJ  HAJA  single  0.970  0.020  1.090
 SP7  CAK  HAK   single  0.970  0.020  1.090
 SP7  CAK  HAKA  single  0.970  0.020  1.090
 SP7  CAL  HAL   single  0.970  0.020  1.090
 SP7  CAL  HALA  single  0.970  0.020  1.090
 SP7  CAM  HAM   single  0.970  0.020  1.090
 SP7  CAM  HAMA  single  0.970  0.020  1.090
 SP7  NAN  HNAN  single  0.890  0.020  1.040
 SP7  NAN  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
 SP7  HACB  CAC  HACA  108.59  3.000
 SP7  HACB  CAC  HAC   107.32  3.000
 SP7  HACA  CAC  HAC   108.18  3.000
 SP7  HACB  CAC  CAD   109.55  3.000
 SP7  HACA  CAC  CAD   113.76  3.000
 SP7  HAC   CAC  CAD   109.24  3.000
 SP7  NAE   CAD  OAA   123.13  3.000
 SP7  NAE   CAD  CAC   115.33  3.000
 SP7  OAA   CAD  CAC   121.54  3.000
 SP7  HNAE  NAE  CAF   117.18  3.000
 SP7  HNAE  NAE  CAD   118.19  3.000
 SP7  CAF   NAE  CAD   124.44  3.000
 SP7  HAF   CAF  CAG   108.51  3.000
 SP7  HAF   CAF  CAB   108.49  3.000
 SP7  CAG   CAF  CAB   111.80  3.000
 SP7  HAF   CAF  NAE   107.06  3.000
 SP7  CAG   CAF  NAE   109.62  3.000
 SP7  CAB   CAF  NAE   111.19  3.000
 SP7  HABB  CAB  HABA  108.24  3.000
 SP7  HABB  CAB  HAB   107.99  3.000
 SP7  HABA  CAB  HAB   108.00  3.000
 SP7  HABB  CAB  CAF   111.00  3.000
 SP7  HABA  CAB  CAF   110.96  3.000
 SP7  HAB   CAB  CAF   110.53  3.000
 SP7  HAGA  CAG  HAG   106.30  3.000
 SP7  HAGA  CAG  CAH   109.74  3.000
 SP7  HAG   CAG  CAH   109.28  3.000
 SP7  HAGA  CAG  CAF   109.94  3.000
 SP7  HAG   CAG  CAF   107.96  3.000
 SP7  CAH   CAG  CAF   113.36  3.000
 SP7  HAHA  CAH  HAH   105.99  3.000
 SP7  HAHA  CAH  NAI   112.73  3.000
 SP7  HAH   CAH  NAI   108.16  3.000
 SP7  HAHA  CAH  CAG   108.90  3.000
 SP7  HAH   CAH  CAG   109.80  3.000
 SP7  NAI   CAH  CAG   111.11  3.000
 SP7  HNAI  NAI  CAJ   108.46  3.000
 SP7  HNAI  NAI  CAH   108.75  3.000
 SP7  CAJ   NAI  CAH   113.02  3.000
 SP7  HAJA  CAJ  HAJ   106.03  3.000
 SP7  HAJA  CAJ  CAK   109.32  3.000
 SP7  HAJ   CAJ  CAK   109.29  3.000
 SP7  HAJA  CAJ  NAI   112.38  3.000
 SP7  HAJ   CAJ  NAI   108.20  3.000
 SP7  CAK   CAJ  NAI   111.44  3.000
 SP7  HAKA  CAK  HAK   106.36  3.000
 SP7  HAKA  CAK  CAL   109.89  3.000
 SP7  HAK   CAK  CAL   109.37  3.000
 SP7  HAKA  CAK  CAJ   109.07  3.000
 SP7  HAK   CAK  CAJ   109.26  3.000
 SP7  CAL   CAK  CAJ   112.69  3.000
 SP7  HALA  CAL  HAL   106.37  3.000
 SP7  HALA  CAL  CAM   109.21  3.000
 SP7  HAL   CAL  CAM   109.05  3.000
 SP7  HALA  CAL  CAK   109.30  3.000
 SP7  HAL   CAL  CAK   110.05  3.000
 SP7  CAM   CAL  CAK   112.66  3.000
 SP7  HAMA  CAM  HAM   106.13  3.000
 SP7  HAMA  CAM  NAN   108.08  3.000
 SP7  HAM   CAM  NAN   113.50  3.000
 SP7  HAMA  CAM  CAL   109.05  3.000
 SP7  HAM   CAM  CAL   108.81  3.000
 SP7  NAN   CAM  CAL   111.08  3.000
 SP7  HNAA  NAN  HNAN  105.44  3.000
 SP7  HNAA  NAN  CAM   109.44  3.000
 SP7  HNAN  NAN  CAM   109.14  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
 SP7  CONST_01  CAF   NAE  CAD  CAC   180.00   0.0  0
 SP7  CONST_02  CAF   NAE  CAD  OAA     0.00   0.0  0
 SP7  CONST_03  HNAE  NAE  CAD  CAC     0.00   0.0  0
 SP7  Var_01    NAI   CAH  CAG  CAF  -179.87  30.0  3
 SP7  Var_02    CAJ   NAI  CAH  CAG  -178.72  30.0  3
 SP7  Var_03    CAK   CAJ  NAI  CAH  -179.88  30.0  3
 SP7  Var_04    CAL   CAK  CAJ  NAI  -178.63  30.0  3
 SP7  Var_05    CAM   CAL  CAK  CAJ  -179.24  30.0  3
 SP7  Var_06    NAN   CAM  CAL  CAK  -179.62  30.0  3
 SP7  Var_07    HAC   CAC  CAD  OAA    65.85  30.0  3
 SP7  Var_08    HNAN  NAN  CAM  CAL    68.71  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
 SP7  chir_01  CAF  NAE  CAB  CAG  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
 SP7  plan-1  CAC   0.020
 SP7  plan-1  CAD   0.020
 SP7  plan-1  OAA   0.020
 SP7  plan-1  NAE   0.020
 SP7  plan-1  CAF   0.020
 SP7  plan-1  HNAE  0.020

