# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 09:19:02 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: N-{4-[(3-aminopropyl)amino]butyl}acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)NCCCCNCCCN
#
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
 Q9C  Q9C  N-{4-[(3-aminopropyl)amino]butyl}acetamide  ligand  34  13  .  2021-08-20  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Q9C
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
 Q9C  N     N  NH2   0  -0.800   7.1387  -0.4509  -0.0099
 Q9C  C     C  C     0   0.504  -5.1826  -0.1212   0.0221
 Q9C  O     O  O     0  -0.508  -5.4013  -1.3251  -0.0248
 Q9C  N01   N  NH1   0  -0.600   2.2318  -0.3354  -0.0023
 Q9C  N02   N  NH1   0  -0.626  -3.9383   0.3820   0.0439
 Q9C  C01   C  CH2   0  -0.254   3.4417   0.4645  -0.0020
 Q9C  C02   C  CH2   0  -0.274   5.9671   0.4141  -0.0097
 Q9C  C03   C  CH2   0  -0.247   1.0247   0.4676   0.0039
 Q9C  C04   C  CH2   0  -0.228  -2.7466  -0.4405   0.0216
 Q9C  C05   C  CH2   0  -0.453   4.6870  -0.4075  -0.0158
 Q9C  C06   C  CH2   0  -0.445  -0.2237  -0.4011  -0.0005
 Q9C  C07   C  CH2   0  -0.478  -1.4999   0.4293   0.0180
 Q9C  C08   C  CH3   0  -0.783  -6.2842   0.9126   0.0561
 Q9C  HN    H  HNH2  0   0.345   7.9763   0.1166  -0.0405
 Q9C  HNA   H  HNH2  0   0.337   7.1820  -0.9480   0.8716
 Q9C  HN01  H  HNH1  0   0.334   2.2291  -0.9193  -0.8316
 Q9C  HN02  H  HNH1  0   0.400  -3.8228   1.3813   0.0962
 Q9C  H01   H  HCH2  0   0.184   3.4811   1.1693  -0.8495
 Q9C  H01A  H  HCH2  0   0.212   3.4419   1.0809   0.9034
 Q9C  H02   H  HCH2  0   0.188   5.9388   1.1111   0.8407
 Q9C  H02A  H  HCH2  0   0.213   5.9991   1.0332  -0.9107
 Q9C  H03   H  HCH2  0   0.213   1.0291   1.0842   0.9091
 Q9C  H03A  H  HCH2  0   0.185   0.9805   1.1715  -0.8440
 Q9C  H04   H  HCH2  0   0.228  -2.7304  -1.1044   0.8913
 Q9C  H04A  H  HCH2  0   0.229  -2.7519  -1.0808  -0.8652
 Q9C  H05   H  HCH2  0   0.217   4.6696  -1.0699   0.8560
 Q9C  H05A  H  HCH2  0   0.216   4.6806  -1.0513  -0.9016
 Q9C  H06   H  HCH2  0   0.220  -0.2188  -1.0421  -0.8890
 Q9C  H06A  H  HCH2  0   0.222  -0.1997  -1.0681   0.8665
 Q9C  H07   H  HCH2  0   0.231  -1.5202   1.0916  -0.8536
 Q9C  H07A  H  HCH2  0   0.231  -1.5034   1.0739   0.9032
 Q9C  H08   H  HCH3  0   0.263  -6.2062   1.5891  -0.7958
 Q9C  H08A  H  HCH3  0   0.258  -7.2579   0.4304   0.0304
 Q9C  H08B  H  HCH3  0   0.263  -6.2194   1.5193   0.9602

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
 Q9C  N    C02   single  1.456  0.020  1.456
 Q9C  N    HN    single  0.890  0.020  1.040
 Q9C  N    HNA   single  0.890  0.020  1.040
 Q9C  O    C     double  1.225  0.020  1.225
 Q9C  C    N02   single  1.342  0.020  1.342
 Q9C  C    C08   single  1.511  0.020  1.511
 Q9C  C01  N01   single  1.450  0.020  1.450
 Q9C  N01  C03   single  1.450  0.020  1.450
 Q9C  N01  HN01  single  0.890  0.020  1.040
 Q9C  C04  N02   single  1.448  0.020  1.448
 Q9C  N02  HN02  single  0.860  0.020  1.020
 Q9C  C01  C05   single  1.520  0.020  1.520
 Q9C  C01  H01   single  0.970  0.020  1.090
 Q9C  C01  H01A  single  0.970  0.020  1.090
 Q9C  C02  C05   single  1.521  0.020  1.521
 Q9C  C02  H02   single  0.970  0.020  1.090
 Q9C  C02  H02A  single  0.970  0.020  1.090
 Q9C  C06  C03   single  1.521  0.020  1.521
 Q9C  C03  H03   single  0.970  0.020  1.090
 Q9C  C03  H03A  single  0.970  0.020  1.090
 Q9C  C04  C07   single  1.520  0.020  1.520
 Q9C  C04  H04   single  0.970  0.020  1.090
 Q9C  C04  H04A  single  0.970  0.020  1.090
 Q9C  C05  H05   single  0.970  0.020  1.090
 Q9C  C05  H05A  single  0.970  0.020  1.090
 Q9C  C06  C07   single  1.523  0.020  1.523
 Q9C  C06  H06   single  0.970  0.020  1.090
 Q9C  C06  H06A  single  0.970  0.020  1.090
 Q9C  C07  H07   single  0.970  0.020  1.090
 Q9C  C07  H07A  single  0.970  0.020  1.090
 Q9C  C08  H08   single  0.970  0.020  1.090
 Q9C  C08  H08A  single  0.970  0.020  1.090
 Q9C  C08  H08B  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
 Q9C  HNA   N    HN    105.43  3.000
 Q9C  HNA   N    C02   109.01  3.000
 Q9C  HN    N    C02   109.44  3.000
 Q9C  C08   C    N02   114.77  3.000
 Q9C  C08   C    O     122.90  3.000
 Q9C  N02   C    O     122.33  3.000
 Q9C  HN01  N01  C03   108.67  3.000
 Q9C  HN01  N01  C01   108.65  3.000
 Q9C  C03   N01  C01   112.90  3.000
 Q9C  HN02  N02  C04   118.03  3.000
 Q9C  HN02  N02  C     118.62  3.000
 Q9C  C04   N02  C     123.34  3.000
 Q9C  H01A  C01  H01   105.99  3.000
 Q9C  H01A  C01  C05   109.28  3.000
 Q9C  H01   C01  C05   109.29  3.000
 Q9C  H01A  C01  N01   108.10  3.000
 Q9C  H01   C01  N01   112.46  3.000
 Q9C  C05   C01  N01   111.53  3.000
 Q9C  H02A  C02  H02   106.20  3.000
 Q9C  H02A  C02  C05   109.10  3.000
 Q9C  H02   C02  C05   108.89  3.000
 Q9C  H02A  C02  N     108.22  3.000
 Q9C  H02   C02  N     113.40  3.000
 Q9C  C05   C02  N     110.87  3.000
 Q9C  H03A  C03  H03   106.03  3.000
 Q9C  H03A  C03  C06   109.24  3.000
 Q9C  H03   C03  C06   109.10  3.000
 Q9C  H03A  C03  N01   112.55  3.000
 Q9C  H03   C03  N01   108.18  3.000
 Q9C  C06   C03  N01   111.54  3.000
 Q9C  H04A  C04  H04   106.81  3.000
 Q9C  H04A  C04  C07   109.69  3.000
 Q9C  H04   C04  C07   109.69  3.000
 Q9C  H04A  C04  N02   109.94  3.000
 Q9C  H04   C04  N02   110.16  3.000
 Q9C  C07   C04  N02   110.49  3.000
 Q9C  H05A  C05  H05   106.76  3.000
 Q9C  H05A  C05  C02   109.01  3.000
 Q9C  H05   C05  C02   109.69  3.000
 Q9C  H05A  C05  C01   109.86  3.000
 Q9C  H05   C05  C01   109.07  3.000
 Q9C  C02   C05  C01   112.30  3.000
 Q9C  H06A  C06  H06   106.61  3.000
 Q9C  H06A  C06  C07   109.95  3.000
 Q9C  H06   C06  C07   109.43  3.000
 Q9C  H06A  C06  C03   109.14  3.000
 Q9C  H06   C06  C03   109.44  3.000
 Q9C  C07   C06  C03   112.11  3.000
 Q9C  H07A  C07  H07   106.70  3.000
 Q9C  H07A  C07  C06   109.48  3.000
 Q9C  H07   C07  C06   109.62  3.000
 Q9C  H07A  C07  C04   109.41  3.000
 Q9C  H07   C07  C04   109.44  3.000
 Q9C  C06   C07  C04   112.05  3.000
 Q9C  H08B  C08  H08A  108.64  3.000
 Q9C  H08B  C08  H08   107.35  3.000
 Q9C  H08A  C08  H08   108.72  3.000
 Q9C  H08B  C08  C     110.85  3.000
 Q9C  H08A  C08  C     110.43  3.000
 Q9C  H08   C08  C     110.77  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
 Q9C  CONST_01  C04   N02  C    O       0.00   0.0  0
 Q9C  CONST_02  C08   C    N02  C04   180.00   0.0  0
 Q9C  CONST_03  HN02  N02  C    O     180.00   0.0  0
 Q9C  Var_01    C01   C05  C02  N     179.44  30.0  3
 Q9C  Var_02    C07   C04  N02  C     178.49  30.0  1
 Q9C  Var_03    C02   C05  C01  N01  -179.76  30.0  3
 Q9C  Var_04    C07   C06  C03  N01   179.51  30.0  1
 Q9C  Var_05    C06   C07  C04  N02   179.81  30.0  3
 Q9C  Var_06    C06   C03  N01  C01   179.84  30.0  3
 Q9C  Var_07    C05   C01  N01  C03  -179.71  30.0  1
 Q9C  Var_08    C04   C07  C06  C03  -179.67  30.0  3
 Q9C  Var_09    H08   C08  C    O    -120.64  30.0  3
 Q9C  Var_10    HN    N    C02  C05   177.92  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
 Q9C  plan-1  C     0.020
 Q9C  plan-1  O     0.020
 Q9C  plan-1  N02   0.020
 Q9C  plan-1  C04   0.020
 Q9C  plan-1  C08   0.020
 Q9C  plan-1  HN02  0.020

