# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 21 11:08:22 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: (2Z,3R,4S,5R,6R)-2-[(4-aminobutyl)imino]-6-(hydroxymethyl)piperidine-3,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCCN=C1N[C@H](CO)[C@@H](O)[C@H](O)[C@@H]1O
#
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
 17B  17B  (2Z,3R,4S,5R,6R)-2-[(4-aminobutyl)imino]-6-(hydroxymethyl)piperidine-3,4,5-triol  ligand  38  17  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_17B
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
 17B  C8    C  CH2   0  -0.428  -4.1951   0.0435  -0.4213
 17B  C2    C  CH1   0  -0.061   1.5089   1.7034  -0.2095
 17B  C3    C  CH1   0   0.010   2.8095   0.9395  -0.3986
 17B  C4    C  CH1   0   0.041   2.7743  -0.3706   0.3768
 17B  C5    C  CH1   0  -0.115   1.6332  -1.2320  -0.1502
 17B  C6    C  CH2   0  -0.142   1.4138  -2.4553   0.7241
 17B  O2    O  OH1   0  -0.661   1.4140   2.1086   1.1373
 17B  O3    O  OH1   0  -0.673   3.9300   1.6671   0.0406
 17B  O4    O  OH1   0  -0.675   3.9643  -1.0992   0.2040
 17B  N5    N  NH1   0  -0.672   0.3956  -0.4707  -0.2095
 17B  O6    O  OH1   0  -0.673   0.3718  -3.2174   0.1542
 17B  N1    N  NH2   0  -0.801  -6.4213  -0.5586   0.4172
 17B  C7    C  CH2   0  -0.270  -5.1405   0.0376   0.7700
 17B  C10   C  CH2   0  -0.341  -1.9209   0.7199  -1.3162
 17B  C9    C  CH2   0  -0.431  -2.8475   0.6760  -0.1014
 17B  N2    N  N     0  -0.449  -0.7022   1.4471  -1.0509
 17B  C1    C  C     0   0.427   0.3123   0.8431  -0.5659
 17B  H8C1  H  HCH2  0   0.213  -4.0448  -0.9853  -0.7680
 17B  H8C2  H  HCH2  0   0.214  -4.6685   0.5822  -1.2482
 17B  H7C1  H  HCH2  0   0.187  -4.6439  -0.4587   1.6167
 17B  H7C2  H  HCH2  0   0.211  -5.3213   1.0691   1.0851
 17B  H9C1  H  HCH2  0   0.218  -2.9955   1.6982   0.2598
 17B  H9C2  H  HCH2  0   0.215  -2.3636   0.1282   0.7137
 17B  H2    H  HCH1  0   0.234   1.4953   2.5674  -0.8851
 17B  H3    H  HCH1  0   0.231   2.8938   0.6968  -1.4688
 17B  HA    H  HOH1  0   0.454   0.6130   2.6353   1.2285
 17B  H4    H  HCH1  0   0.216   2.5980  -0.1543   1.4410
 17B  HB    H  HOH1  0   0.460   4.1696   2.3074  -0.6359
 17B  H5    H  HCH1  0   0.242   1.9173  -1.5703  -1.1581
 17B  HC    H  HOH1  0   0.452   4.6979  -0.5139   0.4216
 17B  H6C1  H  HCH2  0   0.213   2.3451  -3.0283   0.7823
 17B  H6C2  H  HCH2  0   0.203   1.1625  -2.1222   1.7389
 17B  H6    H  HOH1  0   0.461   0.1018  -3.8860   0.7897
 17B  H1N1  H  HNH2  0   0.336  -6.2909  -1.5464   0.2347
 17B  H1N2  H  HNH2  0   0.345  -7.0467  -0.5103   1.2112
 17B  H101  H  HCH2  0   0.193  -1.7480  -0.3053  -1.6783
 17B  H102  H  HCH2  0   0.226  -2.4454   1.2313  -2.1281
 17B  H1N3  H  HNH1  0   0.390  -0.4059  -1.0459  -0.4230

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
 17B  C8   C7    single  1.521  0.020  1.521
 17B  C8   C9    single  1.523  0.020  1.523
 17B  C2   C3    single  1.520  0.020  1.520
 17B  C2   O2    single  1.410  0.020  1.410
 17B  C2   C1    single  1.516  0.020  1.516
 17B  C3   C4    single  1.523  0.020  1.523
 17B  C3   O3    single  1.406  0.020  1.406
 17B  C4   C5    single  1.524  0.020  1.524
 17B  C4   O4    single  1.406  0.020  1.406
 17B  C5   C6    single  1.520  0.020  1.520
 17B  C5   N5    single  1.454  0.020  1.454
 17B  C6   O6    single  1.411  0.020  1.411
 17B  N5   C1    single  1.364  0.020  1.364
 17B  N1   C7    single  1.456  0.020  1.456
 17B  C10  C9    single  1.528  0.020  1.528
 17B  C10  N2    single  1.444  0.020  1.444
 17B  N2   C1    double  1.276  0.020  1.276
 17B  C8   H8C1  single  0.970  0.020  1.090
 17B  C8   H8C2  single  0.970  0.020  1.090
 17B  C7   H7C1  single  0.970  0.020  1.090
 17B  C7   H7C2  single  0.970  0.020  1.090
 17B  C9   H9C1  single  0.970  0.020  1.090
 17B  C9   H9C2  single  0.970  0.020  1.090
 17B  C2   H2    single  0.970  0.020  1.090
 17B  C3   H3    single  0.970  0.020  1.090
 17B  O2   HA    single  0.850  0.020  0.980
 17B  C4   H4    single  0.970  0.020  1.090
 17B  O3   HB    single  0.850  0.020  0.980
 17B  C5   H5    single  0.970  0.020  1.090
 17B  O4   HC    single  0.850  0.020  0.980
 17B  C6   H6C1  single  0.970  0.020  1.090
 17B  C6   H6C2  single  0.970  0.020  1.090
 17B  O6   H6    single  0.850  0.020  0.980
 17B  N1   H1N1  single  0.890  0.020  1.040
 17B  N1   H1N2  single  0.890  0.020  1.040
 17B  N5   H1N3  single  0.890  0.020  1.040
 17B  C10  H101  single  0.970  0.020  1.090
 17B  C10  H102  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
 17B  H8C2  C8   H8C1  106.40  3.000
 17B  H8C2  C8   C9    109.70  3.000
 17B  H8C1  C8   C9    109.57  3.000
 17B  H8C2  C8   C7    108.95  3.000
 17B  H8C1  C8   C7    109.23  3.000
 17B  C9    C8   C7    112.78  3.000
 17B  H2    C2   C1    107.00  3.000
 17B  H2    C2   O2    111.18  3.000
 17B  C1    C2   O2    109.55  3.000
 17B  H2    C2   C3    109.26  3.000
 17B  C1    C2   C3    111.15  3.000
 17B  O2    C2   C3    108.72  3.000
 17B  H3    C3   O3    110.90  3.000
 17B  H3    C3   C4    107.89  3.000
 17B  O3    C3   C4    107.73  3.000
 17B  H3    C3   C2    107.30  3.000
 17B  O3    C3   C2    112.51  3.000
 17B  C4    C3   C2    110.44  3.000
 17B  H4    C4   O4    110.88  3.000
 17B  H4    C4   C5    109.01  3.000
 17B  O4    C4   C5    107.36  3.000
 17B  H4    C4   C3    109.09  3.000
 17B  O4    C4   C3    111.33  3.000
 17B  C5    C4   C3    109.12  3.000
 17B  H5    C5   N5    110.08  3.000
 17B  H5    C5   C6    108.47  3.000
 17B  N5    C5   C6    108.78  3.000
 17B  H5    C5   C4    107.29  3.000
 17B  N5    C5   C4    110.82  3.000
 17B  C6    C5   C4    111.36  3.000
 17B  H6C2  C6   H6C1  107.73  3.000
 17B  H6C2  C6   O6    111.61  3.000
 17B  H6C1  C6   O6    111.52  3.000
 17B  H6C2  C6   C5    108.71  3.000
 17B  H6C1  C6   C5    109.21  3.000
 17B  O6    C6   C5    108.00  3.000
 17B  HA    O2   C2    107.68  3.000
 17B  HB    O3   C3    108.86  3.000
 17B  HC    O4   C4    107.57  3.000
 17B  H1N3  N5   C1    116.44  3.000
 17B  H1N3  N5   C5    112.71  3.000
 17B  C1    N5   C5    124.54  3.000
 17B  H6    O6   C6    108.43  3.000
 17B  H1N2  N1   H1N1  105.51  3.000
 17B  H1N2  N1   C7    109.51  3.000
 17B  H1N1  N1   C7    109.24  3.000
 17B  H7C2  C7   H7C1  106.17  3.000
 17B  H7C2  C7   N1    108.09  3.000
 17B  H7C1  C7   N1    113.51  3.000
 17B  H7C2  C7   C8    108.95  3.000
 17B  H7C1  C7   C8    108.91  3.000
 17B  N1    C7   C8    111.01  3.000
 17B  H102  C10  H101  105.46  3.000
 17B  H102  C10  N2    107.80  3.000
 17B  H101  C10  N2    113.38  3.000
 17B  H102  C10  C9    108.23  3.000
 17B  H101  C10  C9    109.26  3.000
 17B  N2    C10  C9    112.35  3.000
 17B  H9C2  C9   H9C1  106.35  3.000
 17B  H9C2  C9   C10   109.76  3.000
 17B  H9C1  C9   C10   108.51  3.000
 17B  H9C2  C9   C8    109.86  3.000
 17B  H9C1  C9   C8    109.74  3.000
 17B  C10   C9   C8    112.43  3.000
 17B  C1    N2   C10   120.16  3.000
 17B  N2    C1   N5    127.14  3.000
 17B  N2    C1   C2    116.62  3.000
 17B  N5    C1   C2    115.91  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
 17B  CONST_03  H1N3  N5   C1  C2   180.00   0.0  0
 17B  CONST_04  C10   N2   C1  C2   180.00   0.0  0
 17B  CONST_05  C10   N2   C1  N5     0.00   0.0  0
 17B  Var_01    H101  C10  N2  C1   -36.27  30.0  1
 17B  Var_02    N2    C10  C9  C8   173.75  30.0  2
 17B  Var_03    C9    C8   C7  N1   179.24  30.0  2
 17B  Var_04    C10   C9   C8  C7  -178.09  30.0  3
 17B  Var_05    H1N1  N1   C7  C8    67.63  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
 17B  chir_01  C2  C3  O2  C1  positiv
 17B  chir_02  C3  O3  C2  C4  positiv
 17B  chir_03  C4  O4  C3  C5  negativ
 17B  chir_04  C5  N5  C4  C6  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
 17B  plan-1  C2    0.020
 17B  plan-1  C5    0.020
 17B  plan-1  N5    0.020
 17B  plan-1  C10   0.020
 17B  plan-1  N2    0.020
 17B  plan-1  C1    0.020
 17B  plan-1  H1N3  0.020

