# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 21:25:14 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: 3-[(3-{[3-(methylamino)propyl]amino}propyl)amino]propane-1,1-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNCCCNCCCNCCC(O)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
 NBA  NBA  3-[(3-{[3-(methylamino)propyl]amino}propyl)amino]propane-1,1-diol  ligand  40  15  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_NBA
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
 NBA  O4    O  OH1   0  -0.670   0.9102  -0.1714  -7.3094
 NBA  C4    C  CH1   0   0.266   0.0928   0.3258  -6.2886
 NBA  C5    C  CH2   0  -0.520   0.6137  -0.2331  -4.9759
 NBA  C6    C  CH2   0  -0.251  -0.1991   0.2291  -3.7754
 NBA  N7    N  NH1   0  -0.601   0.4456  -0.1680  -2.5390
 NBA  C8    C  CH2   0  -0.247  -0.3355   0.1605  -1.3617
 NBA  C9    C  CH2   0  -0.469   0.4398  -0.1281  -0.0858
 NBA  C10   C  CH2   0  -0.250  -0.3922   0.1232   1.1615
 NBA  N11   N  NH1   0  -0.600   0.3753  -0.1152   2.3689
 NBA  C12   C  CH2   0  -0.250  -0.3945   0.1108   3.5772
 NBA  C13   C  CH2   0  -0.466   0.4451  -0.1118   4.8249
 NBA  C14   C  CH2   0  -0.252  -0.3552   0.1073   6.0987
 NBA  N15   N  NH1   0  -0.593   0.4527  -0.1128   7.2820
 NBA  C16   C  CH3   0  -0.517  -0.2837   0.1170   8.5075
 NBA  O4L   O  OH1   0  -0.665  -1.2599   0.0310  -6.5037
 NBA  HO4   H  HOH1  0   0.453   0.6989   0.2910  -8.1275
 NBA  HC4   H  HCH1  0   0.198   0.1321   1.4220  -6.2606
 NBA  HC51  H  HCH2  0   0.235   1.6530   0.0868  -4.8550
 NBA  HC52  H  HCH2  0   0.234   0.6228  -1.3277  -5.0159
 NBA  HC61  H  HCH2  0   0.218  -1.1924  -0.2255  -3.8040
 NBA  HC62  H  HCH2  0   0.189  -0.3605   1.3185  -3.8331
 NBA  HN7   H  HNH1  0   0.335   1.3403   0.3050  -2.4772
 NBA  HC81  H  HCH2  0   0.212  -1.2480  -0.4449  -1.3773
 NBA  HC82  H  HCH2  0   0.184  -0.6654   1.2124  -1.3544
 NBA  HC91  H  HCH2  0   0.217   1.3342   0.5054  -0.0599
 NBA  HC92  H  HCH2  0   0.222   0.7853  -1.1651  -0.0931
 NBA  H101  H  HCH2  0   0.214  -1.2501  -0.5572   1.1638
 NBA  H102  H  HCH2  0   0.185  -0.8121   1.1421   1.1253
 NBA  HN11  H  HNH1  0   0.334   1.1730   0.5112   2.3725
 NBA  H121  H  HCH2  0   0.213  -1.2367  -0.5893   3.5797
 NBA  H122  H  HCH2  0   0.184  -0.8381   1.1199   3.6100
 NBA  H131  H  HCH2  0   0.217   1.3008   0.5734   4.8130
 NBA  H132  H  HCH2  0   0.222   0.8517  -1.1265   4.8171
 NBA  H141  H  HCH2  0   0.212  -1.1936  -0.5974   6.1235
 NBA  H142  H  HCH2  0   0.183  -0.8064   1.1138   6.0795
 NBA  HN51  H  HNH1  0   0.339   1.2460   0.5164   7.2565
 NBA  H161  H  HCH3  0   0.230   0.3795   0.0097   9.3660
 NBA  H162  H  HCH3  0   0.191  -0.7564   1.1077   8.5689
 NBA  H163  H  HCH3  0   0.220  -1.0767  -0.6267   8.6108
 NBA  HOL4  H  HOH1  0   0.444  -1.3913  -0.9201  -6.4071

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
 NBA  O4   C4    single  1.399  0.020  1.399
 NBA  O4   HO4   single  0.850  0.020  0.980
 NBA  C4   C5    single  1.519  0.020  1.519
 NBA  C4   O4L   single  1.401  0.020  1.401
 NBA  C4   HC4   single  0.970  0.020  1.090
 NBA  C5   C6    single  1.522  0.020  1.522
 NBA  C5   HC51  single  0.970  0.020  1.090
 NBA  C5   HC52  single  0.970  0.020  1.090
 NBA  C6   N7    single  1.450  0.020  1.450
 NBA  C6   HC61  single  0.970  0.020  1.090
 NBA  C6   HC62  single  0.970  0.020  1.090
 NBA  N7   C8    single  1.451  0.020  1.451
 NBA  N7   HN7   single  0.890  0.020  1.040
 NBA  C8   C9    single  1.521  0.020  1.521
 NBA  C8   HC81  single  0.970  0.020  1.090
 NBA  C8   HC82  single  0.970  0.020  1.090
 NBA  C9   C10   single  1.520  0.020  1.520
 NBA  C9   HC91  single  0.970  0.020  1.090
 NBA  C9   HC92  single  0.970  0.020  1.090
 NBA  C10  N11   single  1.450  0.020  1.450
 NBA  C10  H101  single  0.970  0.020  1.090
 NBA  C10  H102  single  0.970  0.020  1.090
 NBA  N11  C12   single  1.450  0.020  1.450
 NBA  N11  HN11  single  0.890  0.020  1.040
 NBA  C12  C13   single  1.520  0.020  1.520
 NBA  C12  H121  single  0.970  0.020  1.090
 NBA  C12  H122  single  0.970  0.020  1.090
 NBA  C13  C14   single  1.520  0.020  1.520
 NBA  C13  H131  single  0.970  0.020  1.090
 NBA  C13  H132  single  0.970  0.020  1.090
 NBA  C14  N15   single  1.450  0.020  1.450
 NBA  C14  H141  single  0.970  0.020  1.090
 NBA  C14  H142  single  0.970  0.020  1.090
 NBA  N15  C16   single  1.448  0.020  1.448
 NBA  N15  HN51  single  0.890  0.020  1.040
 NBA  C16  H161  single  0.970  0.020  1.090
 NBA  C16  H162  single  0.970  0.020  1.090
 NBA  C16  H163  single  0.970  0.020  1.090
 NBA  O4L  HOL4  single  0.850  0.020  0.980

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
 NBA  HO4   O4   C4    108.72  3.000
 NBA  HC4   C4   O4L   104.40  3.000
 NBA  HC4   C4   C5    109.47  3.000
 NBA  O4L   C4   C5    112.73  3.000
 NBA  HC4   C4   O4    110.65  3.000
 NBA  O4L   C4   O4    112.16  3.000
 NBA  C5    C4   O4    107.43  3.000
 NBA  HC52  C5   HC51  106.76  3.000
 NBA  HC52  C5   C6    109.68  3.000
 NBA  HC51  C5   C6    109.35  3.000
 NBA  HC52  C5   C4    109.82  3.000
 NBA  HC51  C5   C4    108.28  3.000
 NBA  C6    C5   C4    112.76  3.000
 NBA  HC62  C6   HC61  106.06  3.000
 NBA  HC62  C6   N7    112.35  3.000
 NBA  HC61  C6   N7    108.21  3.000
 NBA  HC62  C6   C5    109.69  3.000
 NBA  HC61  C6   C5    109.79  3.000
 NBA  N7    C6   C5    110.62  3.000
 NBA  HN7   N7   C8    108.67  3.000
 NBA  HN7   N7   C6    108.46  3.000
 NBA  C8    N7   C6    113.00  3.000
 NBA  HC82  C8   HC81  106.16  3.000
 NBA  HC82  C8   C9    109.15  3.000
 NBA  HC81  C8   C9    109.38  3.000
 NBA  HC82  C8   N7    112.49  3.000
 NBA  HC81  C8   N7    108.18  3.000
 NBA  C9    C8   N7    111.31  3.000
 NBA  HC92  C9   HC91  106.89  3.000
 NBA  HC92  C9   C10   109.59  3.000
 NBA  HC91  C9   C10   109.37  3.000
 NBA  HC92  C9   C8    109.61  3.000
 NBA  HC91  C9   C8    109.03  3.000
 NBA  C10   C9   C8    112.21  3.000
 NBA  H102  C10  H101  106.02  3.000
 NBA  H102  C10  N11   112.37  3.000
 NBA  H101  C10  N11   108.10  3.000
 NBA  H102  C10  C9    109.53  3.000
 NBA  H101  C10  C9    109.14  3.000
 NBA  N11   C10  C9    111.49  3.000
 NBA  HN11  N11  C12   108.56  3.000
 NBA  HN11  N11  C10   108.52  3.000
 NBA  C12   N11  C10   112.77  3.000
 NBA  H122  C12  H121  106.00  3.000
 NBA  H122  C12  C13   109.38  3.000
 NBA  H121  C12  C13   109.22  3.000
 NBA  H122  C12  N11   112.38  3.000
 NBA  H121  C12  N11   108.08  3.000
 NBA  C13   C12  N11   111.58  3.000
 NBA  H132  C13  H131  106.84  3.000
 NBA  H132  C13  C14   109.61  3.000
 NBA  H131  C13  C14   109.26  3.000
 NBA  H132  C13  C12   109.61  3.000
 NBA  H131  C13  C12   109.31  3.000
 NBA  C14   C13  C12   112.07  3.000
 NBA  H142  C14  H141  105.92  3.000
 NBA  H142  C14  N15   112.38  3.000
 NBA  H141  C14  N15   108.08  3.000
 NBA  H142  C14  C13   109.40  3.000
 NBA  H141  C14  C13   109.21  3.000
 NBA  N15   C14  C13   111.64  3.000
 NBA  HN51  N15  C16   108.73  3.000
 NBA  HN51  N15  C14   108.76  3.000
 NBA  C16   N15  C14   112.54  3.000
 NBA  H163  C16  H162  107.24  3.000
 NBA  H163  C16  H161  107.47  3.000
 NBA  H162  C16  H161  107.83  3.000
 NBA  H163  C16  N15   109.95  3.000
 NBA  H162  C16  N15   114.13  3.000
 NBA  H161  C16  N15   109.96  3.000
 NBA  HOL4  O4L  C4    108.88  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
 NBA  Var_01  C6    C5   C4   O4   -179.70  30.0  3
 NBA  Var_02  N7    C6   C5   C4   -171.74  30.0  3
 NBA  Var_03  C8    N7   C6   C5   -175.73  30.0  3
 NBA  Var_04  C9    C8   N7   C6   -173.61  30.0  3
 NBA  Var_05  C10   C9   C8   N7   -176.27  30.0  3
 NBA  Var_06  N11   C10  C9   C8   -178.15  30.0  3
 NBA  Var_07  C12   N11  C10  C9   -179.74  30.0  3
 NBA  Var_08  C13   C12  N11  C10  -178.54  30.0  3
 NBA  Var_09  C14   C13  C12  N11  -179.37  30.0  3
 NBA  Var_10  N15   C14  C13  C12   179.76  30.0  3
 NBA  Var_11  C16   N15  C14  C13   178.84  30.0  3
 NBA  Var_12  H161  C16  N15  C14  -175.98  30.0  3

