# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 18:46:57 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: 3-(3-azaniumylpropanoylamino)propyl-dimethyl-azanium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[NH+](C)CCCNC(=O)CC[NH3+]
#
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
 9T8  9T8  3-(3-azaniumylpropanoylamino)propyl-dimethyl-azanium  ligand  33  12  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9T8
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
 9T8  C01   C  CH3   0  -0.543   4.3156   1.4877  -0.5136
 9T8  N02   N  NH1   0  -0.649  -0.8233   0.1355   0.0475
 9T8  C03   C  CH2   0  -0.291   2.8789  -0.4998  -0.1225
 9T8  C05   C  CH2   0  -0.233   0.4029  -0.6199  -0.0920
 9T8  C06   C  C     0   0.577  -2.0290  -0.4478   0.0326
 9T8  C07   C  CH2   0  -0.608  -3.2007   0.5049   0.1757
 9T8  C04   C  CH2   0  -0.529   1.6046   0.2968   0.0842
 9T8  N01   N  NT1   1  -0.511   4.1065   0.2510   0.2781
 9T8  C02   C  CH3   0  -0.537   5.3021  -0.6271   0.2174
 9T8  N03   N  NT3   1  -0.779  -5.6509   0.7213   0.1459
 9T8  C08   C  CH2   0  -0.297  -4.5159  -0.2295   0.0220
 9T8  O01   O  O     0  -0.494  -2.1814  -1.6553  -0.0797
 9T8  H006  H  HCH3  0   0.290   4.4063   1.2183  -1.5623
 9T8  H004  H  HCH3  0   0.295   3.4784   2.1622  -0.3714
 9T8  H005  H  HCH3  0   0.298   5.2272   1.9680  -0.1713
 9T8  HN02  H  HNH1  0   0.409  -0.7659   1.1401   0.1020
 9T8  H031  H  HCH2  0   0.299   2.8676  -1.4037   0.4854
 9T8  H032  H  HCH2  0   0.301   3.0111  -0.7870  -1.1655
 9T8  H052  H  HCH2  0   0.249   0.4325  -1.4162   0.6552
 9T8  H051  H  HCH2  0   0.246   0.4410  -1.1002  -1.0743
 9T8  H072  H  HCH2  0   0.300  -3.1469   0.9924   1.1537
 9T8  H071  H  HCH2  0   0.293  -3.1154   1.2972  -0.5731
 9T8  H042  H  HCH2  0   0.270   1.5908   0.7300   1.0884
 9T8  H041  H  HCH2  0   0.271   1.5412   1.1176  -0.6330
 9T8  HN01  H  HNT1  0   0.467   3.9905   0.5275   1.2539
 9T8  H001  H  HCH3  0   0.295   6.1646  -0.0686   0.5675
 9T8  H002  H  HCH3  0   0.295   5.1382  -1.4914   0.8537
 9T8  H003  H  HCH3  0   0.290   5.4551  -0.9418  -0.8109
 9T8  H1    H  HNT3  0   0.471  -5.6659   1.1891   1.0520
 9T8  H2    H  HNT3  0   0.471  -5.6238   1.4480  -0.5689
 9T8  HN03  H  HNT3  0   0.481  -6.5452   0.2421   0.0464
 9T8  H081  H  HCH2  0   0.301  -4.6081  -0.7003  -0.9528
 9T8  H082  H  HCH2  0   0.301  -4.6553  -0.9845   0.7904

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
 9T8  C01  N01   single  1.483  0.020  1.483
 9T8  N01  C03   single  1.494  0.020  1.494
 9T8  N01  C02   single  1.485  0.020  1.485
 9T8  C03  C04   single  1.517  0.020  1.517
 9T8  C04  C05   single  1.522  0.020  1.522
 9T8  C05  N02   single  1.447  0.020  1.447
 9T8  N02  C06   single  1.339  0.020  1.339
 9T8  C06  O01   double  1.222  0.020  1.222
 9T8  C06  C07   single  1.517  0.020  1.517
 9T8  C07  C08   single  1.514  0.020  1.514
 9T8  C08  N03   single  1.486  0.020  1.486
 9T8  C01  H006  single  0.970  0.020  1.090
 9T8  C01  H004  single  0.970  0.020  1.090
 9T8  C01  H005  single  0.970  0.020  1.090
 9T8  N02  HN02  single  0.860  0.020  1.020
 9T8  C03  H031  single  0.970  0.020  1.090
 9T8  C03  H032  single  0.970  0.020  1.090
 9T8  C05  H052  single  0.970  0.020  1.090
 9T8  C05  H051  single  0.970  0.020  1.090
 9T8  C07  H072  single  0.970  0.020  1.090
 9T8  C07  H071  single  0.970  0.020  1.090
 9T8  C04  H042  single  0.970  0.020  1.090
 9T8  C04  H041  single  0.970  0.020  1.090
 9T8  N01  HN01  single  0.890  0.020  1.040
 9T8  C02  H001  single  0.970  0.020  1.090
 9T8  C02  H002  single  0.970  0.020  1.090
 9T8  C02  H003  single  0.970  0.020  1.090
 9T8  N03  H1    single  0.890  0.020  1.040
 9T8  N03  H2    single  0.890  0.020  1.040
 9T8  N03  HN03  single  0.890  0.020  1.040
 9T8  C08  H081  single  0.970  0.020  1.090
 9T8  C08  H082  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
 9T8  H005  C01  H004  109.37  3.000
 9T8  H005  C01  H006  110.11  3.000
 9T8  H004  C01  H006  110.19  3.000
 9T8  H005  C01  N01   108.60  3.000
 9T8  H004  C01  N01   109.87  3.000
 9T8  H006  C01  N01   108.67  3.000
 9T8  HN02  N02  C06   119.08  3.000
 9T8  HN02  N02  C05   118.51  3.000
 9T8  C06   N02  C05   122.30  3.000
 9T8  H032  C03  H031  108.46  3.000
 9T8  H032  C03  N01   106.82  3.000
 9T8  H031  C03  N01   106.02  3.000
 9T8  H032  C03  C04   111.76  3.000
 9T8  H031  C03  C04   110.55  3.000
 9T8  N01   C03  C04   112.95  3.000
 9T8  H051  C05  H052  107.05  3.000
 9T8  H051  C05  C04   109.93  3.000
 9T8  H052  C05  C04   109.79  3.000
 9T8  H051  C05  N02   110.20  3.000
 9T8  H052  C05  N02   109.73  3.000
 9T8  C04   C05  N02   110.10  3.000
 9T8  O01   C06  C07   122.19  3.000
 9T8  C07   C06  N02   114.88  3.000
 9T8  O01   C06  N02   122.93  3.000
 9T8  H071  C07  H072  106.58  3.000
 9T8  H071  C07  C08   110.47  3.000
 9T8  H072  C07  C08   110.46  3.000
 9T8  H071  C07  C06   109.29  3.000
 9T8  H072  C07  C06   109.04  3.000
 9T8  C08   C07  C06   110.90  3.000
 9T8  H041  C04  H042  107.74  3.000
 9T8  H041  C04  C05   109.33  3.000
 9T8  H042  C04  C05   109.57  3.000
 9T8  H041  C04  C03   110.73  3.000
 9T8  H042  C04  C03   110.10  3.000
 9T8  C05   C04  C03   109.35  3.000
 9T8  HN01  N01  C02   106.90  3.000
 9T8  HN01  N01  C03   107.41  3.000
 9T8  C02   N01  C03   110.71  3.000
 9T8  HN01  N01  C01   107.48  3.000
 9T8  C02   N01  C01   110.97  3.000
 9T8  C03   N01  C01   113.07  3.000
 9T8  H003  C02  H002  110.21  3.000
 9T8  H003  C02  H001  110.03  3.000
 9T8  H002  C02  H001  109.91  3.000
 9T8  H003  C02  N01   108.87  3.000
 9T8  H002  C02  N01   108.98  3.000
 9T8  H001  C02  N01   108.81  3.000
 9T8  HN03  N03  H2    106.86  3.000
 9T8  HN03  N03  H1    106.82  3.000
 9T8  H2    N03  H1    107.24  3.000
 9T8  HN03  N03  C08   111.17  3.000
 9T8  H2    N03  C08   112.17  3.000
 9T8  H1    N03  C08   112.26  3.000
 9T8  H082  C08  H081  108.82  3.000
 9T8  H082  C08  N03   106.73  3.000
 9T8  H081  C08  N03   106.70  3.000
 9T8  H082  C08  C07   112.13  3.000
 9T8  H081  C08  C07   112.02  3.000
 9T8  N03   C08  C07   110.17  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
 9T8  CONST_01  O01   C06  N02  C05     0.00   0.0  0
 9T8  CONST_02  C07   C06  N02  C05   180.00   0.0  0
 9T8  CONST_03  HN02  N02  C06  C07     0.00   0.0  0
 9T8  Var_01    C04   C03  N01  C01   -61.87  30.0  3
 9T8  Var_02    C03   C04  C05  N02  -177.65  30.0  1
 9T8  Var_03    C08   C07  C06  N02   174.87  30.0  3
 9T8  Var_04    N01   C03  C04  C05  -169.29  30.0  1
 9T8  Var_05    C04   C05  N02  C06  -175.10  30.0  1
 9T8  Var_06    N03   C08  C07  C06  -179.21  30.0  3
 9T8  Var_07    H001  C02  N01  C01    56.78  30.0  3
 9T8  Var_08    H006  C01  N01  C03   -59.66  30.0  3
 9T8  Var_09    H1    N03  C08  C07   -60.30  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
 9T8  plan-1  N02   0.020
 9T8  plan-1  C05   0.020
 9T8  plan-1  C06   0.020
 9T8  plan-1  C07   0.020
 9T8  plan-1  O01   0.020
 9T8  plan-1  HN02  0.020

