# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 23:40:17 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: N-[3-({4-[(3-aminopropyl)amino]butyl}amino)propyl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)NCCCNCCCCNCCCN
#
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
 SP5  SP5  N-[3-({4-[(3-aminopropyl)amino]butyl}amino)propyl]acetamide  ligand  45  17  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_SP5
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
 SP5  CAB   C  CH3   0  -0.777    8.6645  -1.0599  -0.0141
 SP5  CAC   C  C     0   0.520    7.5806  -0.0105  -0.0180
 SP5  OAA   O  O     0  -0.514    7.8386   1.1871  -0.0511
 SP5  NAD   N  NH1   0  -0.633    6.3236  -0.4746   0.0180
 SP5  CAE   C  CH2   0  -0.236    5.1627   0.3908   0.0213
 SP5  CAF   C  CH2   0  -0.500    3.8850  -0.4320   0.0269
 SP5  CAG   C  CH2   0  -0.249    2.6479   0.4525   0.0279
 SP5  NAH   N  NH1   0  -0.601    1.4380  -0.3453   0.0341
 SP5  CAI   C  CH2   0  -0.248    0.2293   0.4569   0.0328
 SP5  CAJ   C  CH2   0  -0.445   -1.0158  -0.4162   0.0204
 SP5  CAK   C  CH2   0  -0.445   -2.3018   0.3997   0.0179
 SP5  CAL   C  CH2   0  -0.247   -3.5447  -0.4766   0.0067
 SP5  NAM   N  NH1   0  -0.600   -4.7577   0.3176  -0.0186
 SP5  CAN   C  CH2   0  -0.253   -5.9624  -0.4897  -0.0149
 SP5  CAO   C  CH2   0  -0.453   -7.2134   0.3741  -0.0282
 SP5  CAP   C  CH2   0  -0.274   -8.4880  -0.4559  -0.0338
 SP5  NAQ   N  NH2   0  -0.800   -9.6653   0.4010  -0.0600
 SP5  HAB   H  HCH3  0   0.264    9.3063  -0.9164   0.8550
 SP5  HABA  H  HCH3  0   0.247    8.2840  -2.0793   0.0049
 SP5  HABB  H  HCH3  0   0.264    9.2881  -0.9421  -0.9001
 SP5  HNAD  H  HNH1  0   0.401    6.1750  -1.4700   0.0490
 SP5  HAE   H  HCH2  0   0.231    5.1866   1.0448   0.8983
 SP5  HAEA  H  HCH2  0   0.231    5.1827   1.0409  -0.8581
 SP5  HAF   H  HCH2  0   0.233    3.8674  -1.0824  -0.8539
 SP5  HAFA  H  HCH2  0   0.236    3.8633  -1.0822   0.9061
 SP5  HAG   H  HCH2  0   0.218    2.6514   1.0777   0.9268
 SP5  HAGA  H  HCH2  0   0.190    2.6940   1.1461  -0.8280
 SP5  HNAH  H  HNH1  0   0.336    1.4347  -0.9355  -0.7908
 SP5  HAI   H  HCH2  0   0.213    0.2272   1.0752   0.9368
 SP5  HAIA  H  HCH2  0   0.185    0.1900   1.1586  -0.8170
 SP5  HAJ   H  HCH2  0   0.215   -0.9954  -1.0627  -0.8643
 SP5  HAJA  H  HCH2  0   0.218   -0.9958  -1.0801   0.8901
 SP5  HAK   H  HCH2  0   0.215   -2.3227   1.0488   0.9007
 SP5  HAKA  H  HCH2  0   0.217   -2.3223   1.0608  -0.8540
 SP5  HAL   H  HCH2  0   0.211   -3.5305  -1.1079  -0.8884
 SP5  HALA  H  HCH2  0   0.183   -3.5097  -1.1669   0.8663
 SP5  HNAM  H  HNH1  0   0.334   -4.7683   0.9196   0.7977
 SP5  HAN   H  HCH2  0   0.212   -5.9509  -1.1227  -0.9087
 SP5  HANA  H  HCH2  0   0.183   -6.0050  -1.1796   0.8449
 SP5  HAO   H  HCH2  0   0.216   -7.2204   1.0328   0.8464
 SP5  HAOA  H  HCH2  0   0.216   -7.1915   1.0218  -0.9109
 SP5  HAP   H  HCH2  0   0.188   -8.4458  -1.1666  -0.8722
 SP5  HAPA  H  HCH2  0   0.213   -8.5254  -1.0606   0.8767
 SP5  HNAQ  H  HNH2  0   0.337   -9.7022   0.8837  -0.9498
 SP5  HNAA  H  HNH2  0   0.345  -10.4993  -0.1715  -0.0294

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
 SP5  CAB  CAC   single  1.509  0.020  1.509
 SP5  CAC  OAA   double  1.226  0.020  1.226
 SP5  CAC  NAD   single  1.340  0.020  1.340
 SP5  NAD  CAE   single  1.448  0.020  1.448
 SP5  CAE  CAF   single  1.520  0.020  1.520
 SP5  CAF  CAG   single  1.521  0.020  1.521
 SP5  CAG  NAH   single  1.449  0.020  1.449
 SP5  NAH  CAI   single  1.451  0.020  1.451
 SP5  CAI  CAJ   single  1.521  0.020  1.521
 SP5  CAJ  CAK   single  1.523  0.020  1.523
 SP5  CAK  CAL   single  1.521  0.020  1.521
 SP5  CAL  NAM   single  1.450  0.020  1.450
 SP5  NAM  CAN   single  1.450  0.020  1.450
 SP5  CAN  CAO   single  1.520  0.020  1.520
 SP5  CAO  CAP   single  1.521  0.020  1.521
 SP5  CAP  NAQ   single  1.456  0.020  1.456
 SP5  CAB  HAB   single  0.970  0.020  1.090
 SP5  CAB  HABA  single  0.970  0.020  1.090
 SP5  CAB  HABB  single  0.970  0.020  1.090
 SP5  NAD  HNAD  single  0.860  0.020  1.020
 SP5  CAE  HAE   single  0.970  0.020  1.090
 SP5  CAE  HAEA  single  0.970  0.020  1.090
 SP5  CAF  HAF   single  0.970  0.020  1.090
 SP5  CAF  HAFA  single  0.970  0.020  1.090
 SP5  CAG  HAG   single  0.970  0.020  1.090
 SP5  CAG  HAGA  single  0.970  0.020  1.090
 SP5  NAH  HNAH  single  0.890  0.020  1.040
 SP5  CAI  HAI   single  0.970  0.020  1.090
 SP5  CAI  HAIA  single  0.970  0.020  1.090
 SP5  CAJ  HAJ   single  0.970  0.020  1.090
 SP5  CAJ  HAJA  single  0.970  0.020  1.090
 SP5  CAK  HAK   single  0.970  0.020  1.090
 SP5  CAK  HAKA  single  0.970  0.020  1.090
 SP5  CAL  HAL   single  0.970  0.020  1.090
 SP5  CAL  HALA  single  0.970  0.020  1.090
 SP5  NAM  HNAM  single  0.890  0.020  1.040
 SP5  CAN  HAN   single  0.970  0.020  1.090
 SP5  CAN  HANA  single  0.970  0.020  1.090
 SP5  CAO  HAO   single  0.970  0.020  1.090
 SP5  CAO  HAOA  single  0.970  0.020  1.090
 SP5  CAP  HAP   single  0.970  0.020  1.090
 SP5  CAP  HAPA  single  0.970  0.020  1.090
 SP5  NAQ  HNAQ  single  0.890  0.020  1.040
 SP5  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
 SP5  HABB  CAB  HABA  108.39  3.000
 SP5  HABB  CAB  HAB   107.28  3.000
 SP5  HABA  CAB  HAB   108.38  3.000
 SP5  HABB  CAB  CAC   109.50  3.000
 SP5  HABA  CAB  CAC   113.61  3.000
 SP5  HAB   CAB  CAC   109.48  3.000
 SP5  NAD   CAC  OAA   122.44  3.000
 SP5  NAD   CAC  CAB   115.65  3.000
 SP5  OAA   CAC  CAB   121.91  3.000
 SP5  HNAD  NAD  CAE   118.19  3.000
 SP5  HNAD  NAD  CAC   118.78  3.000
 SP5  CAE   NAD  CAC   123.02  3.000
 SP5  HAEA  CAE  HAE   106.78  3.000
 SP5  HAEA  CAE  CAF   109.88  3.000
 SP5  HAE   CAE  CAF   109.81  3.000
 SP5  HAEA  CAE  NAD   109.80  3.000
 SP5  HAE   CAE  NAD   109.97  3.000
 SP5  CAF   CAE  NAD   110.52  3.000
 SP5  HAFA  CAF  HAF   107.05  3.000
 SP5  HAFA  CAF  CAG   109.22  3.000
 SP5  HAF   CAF  CAG   109.44  3.000
 SP5  HAFA  CAF  CAE   109.97  3.000
 SP5  HAF   CAF  CAE   109.40  3.000
 SP5  CAG   CAF  CAE   111.65  3.000
 SP5  HAGA  CAG  HAG   106.14  3.000
 SP5  HAGA  CAG  NAH   112.61  3.000
 SP5  HAG   CAG  NAH   108.27  3.000
 SP5  HAGA  CAG  CAF   109.35  3.000
 SP5  HAG   CAG  CAF   109.27  3.000
 SP5  NAH   CAG  CAF   111.03  3.000
 SP5  HNAH  NAH  CAI   108.56  3.000
 SP5  HNAH  NAH  CAG   108.64  3.000
 SP5  CAI   NAH  CAG   113.03  3.000
 SP5  HAIA  CAI  HAI   106.07  3.000
 SP5  HAIA  CAI  CAJ   109.26  3.000
 SP5  HAI   CAI  CAJ   109.23  3.000
 SP5  HAIA  CAI  NAH   112.47  3.000
 SP5  HAI   CAI  NAH   108.24  3.000
 SP5  CAJ   CAI  NAH   111.39  3.000
 SP5  HAJA  CAJ  HAJ   106.46  3.000
 SP5  HAJA  CAJ  CAK   109.98  3.000
 SP5  HAJ   CAJ  CAK   109.29  3.000
 SP5  HAJA  CAJ  CAI   109.08  3.000
 SP5  HAJ   CAJ  CAI   109.27  3.000
 SP5  CAK   CAJ  CAI   112.57  3.000
 SP5  HAKA  CAK  HAK   106.47  3.000
 SP5  HAKA  CAK  CAL   109.09  3.000
 SP5  HAK   CAK  CAL   109.37  3.000
 SP5  HAKA  CAK  CAJ   109.92  3.000
 SP5  HAK   CAK  CAJ   109.39  3.000
 SP5  CAL   CAK  CAJ   112.42  3.000
 SP5  HALA  CAL  HAL   106.00  3.000
 SP5  HALA  CAL  NAM   112.51  3.000
 SP5  HAL   CAL  NAM   108.19  3.000
 SP5  HALA  CAL  CAK   109.21  3.000
 SP5  HAL   CAL  CAK   109.12  3.000
 SP5  NAM   CAL  CAK   111.60  3.000
 SP5  HNAM  NAM  CAN   108.65  3.000
 SP5  HNAM  NAM  CAL   108.64  3.000
 SP5  CAN   NAM  CAL   112.95  3.000
 SP5  HANA  CAN  HAN   105.97  3.000
 SP5  HANA  CAN  CAO   109.29  3.000
 SP5  HAN   CAN  CAO   109.26  3.000
 SP5  HANA  CAN  NAM   112.47  3.000
 SP5  HAN   CAN  NAM   108.11  3.000
 SP5  CAO   CAN  NAM   111.54  3.000
 SP5  HAOA  CAO  HAO   106.75  3.000
 SP5  HAOA  CAO  CAP   109.67  3.000
 SP5  HAO   CAO  CAP   109.02  3.000
 SP5  HAOA  CAO  CAN   109.06  3.000
 SP5  HAO   CAO  CAN   109.88  3.000
 SP5  CAP   CAO  CAN   112.30  3.000
 SP5  HAPA  CAP  HAP   106.18  3.000
 SP5  HAPA  CAP  NAQ   108.22  3.000
 SP5  HAP   CAP  NAQ   113.43  3.000
 SP5  HAPA  CAP  CAO   109.10  3.000
 SP5  HAP   CAP  CAO   108.86  3.000
 SP5  NAQ   CAP  CAO   110.88  3.000
 SP5  HNAA  NAQ  HNAQ  105.43  3.000
 SP5  HNAA  NAQ  CAP   109.44  3.000
 SP5  HNAQ  NAQ  CAP   109.00  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
 SP5  CONST_01  CAE   NAD  CAC  CAB   180.00   0.0  0
 SP5  CONST_02  CAE   NAD  CAC  OAA     0.00   0.0  0
 SP5  CONST_03  HNAD  NAD  CAC  CAB     0.00   0.0  0
 SP5  Var_01    CAF   CAE  NAD  CAC   178.43  30.0  3
 SP5  Var_02    CAG   CAF  CAE  NAD  -179.90  30.0  3
 SP5  Var_03    NAH   CAG  CAF  CAE  -179.97  30.0  3
 SP5  Var_04    CAI   NAH  CAG  CAF  -179.90  30.0  3
 SP5  Var_05    CAJ   CAI  NAH  CAG   179.23  30.0  3
 SP5  Var_06    CAK   CAJ  CAI  NAH  -179.96  30.0  3
 SP5  Var_07    CAL   CAK  CAJ  CAI  -179.95  30.0  3
 SP5  Var_08    NAM   CAL  CAK  CAJ  -179.02  30.0  3
 SP5  Var_09    CAN   NAM  CAL  CAK  -179.36  30.0  3
 SP5  Var_10    CAO   CAN  NAM  CAL   179.45  30.0  3
 SP5  Var_11    CAP   CAO  CAN  NAM   179.62  30.0  3
 SP5  Var_12    NAQ   CAP  CAO  CAN  -179.44  30.0  3
 SP5  Var_13    HAB   CAB  CAC  OAA    59.39  30.0  3
 SP5  Var_14    HNAQ  NAQ  CAP  CAO    67.20  30.0  3

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
 SP5  plan-1  CAB   0.020
 SP5  plan-1  CAC   0.020
 SP5  plan-1  OAA   0.020
 SP5  plan-1  NAD   0.020
 SP5  plan-1  CAE   0.020
 SP5  plan-1  HNAD  0.020

