# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 08:24:46 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: (2S)-1-amino-3-[(5-nitroquinolin-8-yl)amino]propan-2-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[C@H](O)CNc1ccc(c2cccnc12)[N+]([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
 3B3  3B3  (2S)-1-amino-3-[(5-nitroquinolin-8-yl)amino]propan-2-ol  ligand  33  19  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3B3
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
 3B3  C1    C  CR16   0  -0.180  -2.9754   1.5452  -0.0791
 3B3  C2    C  CR16   0  -0.311  -2.4764   2.8202  -0.0925
 3B3  C3    C  CR16   0  -0.064  -1.0909   3.0179  -0.0556
 3B3  N4    N  N      0  -0.440  -0.2483   2.0189  -0.0324
 3B3  C4A   C  CR66   0   0.135  -0.7152   0.7608  -0.0310
 3B3  C4B   C  CR6    0   0.396   0.3002  -0.2711  -0.0340
 3B3  N5    N  NH1    0  -0.657   1.5752   0.1070  -0.0347
 3B3  C6    C  CH2    0  -0.286   2.6973  -0.7962   0.0162
 3B3  C8A   C  CR16   0  -0.395  -0.1101  -1.6030  -0.0421
 3B3  C9    C  CR16   0  -0.287  -1.4564  -1.9163  -0.0502
 3B3  C10   C  CR6    0   0.163  -2.4475  -0.9500  -0.0354
 3B3  C1A   C  CR66   0   0.078  -2.0942   0.4377  -0.0335
 3B3  CB    C  CH1    0  -0.018   3.9991  -0.0398  -0.2187
 3B3  CA    C  CH2    0  -0.294   5.1892  -0.9846  -0.1348
 3B3  N     N  NH2    0  -0.799   6.4197  -0.2907  -0.4695
 3B3  O     O  O      0  -0.416  -4.6833  -0.6363   0.3141
 3B3  OXT   O  O     -1  -0.414  -4.0230  -2.5782  -0.2564
 3B3  N1    N  N      1   0.324  -3.7967  -1.4111   0.0051
 3B3  O16   O  OH1    0  -0.661   4.1263   1.0590   0.6613
 3B3  H1    H  HCR6   0   0.285  -4.0417   1.4053  -0.1090
 3B3  H2    H  HCR6   0   0.280  -3.1448   3.6689  -0.1315
 3B3  H3    H  HCR6   0   0.273  -0.6748   4.0188  -0.0529
 3B3  H5    H  HNH1   0   0.400   1.7450   1.0994   0.0582
 3B3  H6C1  H  HCH2   0   0.253   2.5924  -1.5641  -0.7547
 3B3  H6C2  H  HCH2   0   0.243   2.7280  -1.3172   0.9826
 3B3  H8A   H  HCR6   0   0.287   0.6118  -2.4064  -0.0287
 3B3  H9    H  HCR6   0   0.297  -1.7300  -2.9615  -0.0452
 3B3  HB    H  HCH1   0   0.240   3.9738   0.3953  -1.2225
 3B3  HAC1  H  HCH2   0   0.230   5.0379  -1.7901  -0.8573
 3B3  HAC2  H  HCH2   0   0.198   5.1970  -1.4579   0.8601
 3B3  HN1   H  HNH2   0   0.341   6.6207   0.4019   0.2402
 3B3  HN2   H  HNH2   0   0.351   7.1912  -0.9440  -0.4429
 3B3  H16   H  HOH1   0   0.449   4.1694   0.7256   1.5655

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
 3B3  C1   C2    aromatic  1.369  0.020  1.369
 3B3  C1   C1A   aromatic  1.416  0.020  1.416
 3B3  C1   H1    single    0.930  0.020  1.080
 3B3  C2   C3    aromatic  1.400  0.020  1.400
 3B3  C2   H2    single    0.930  0.020  1.080
 3B3  C3   N4    aromatic  1.307  0.020  1.307
 3B3  C3   H3    single    0.930  0.020  1.080
 3B3  N4   C4A   aromatic  1.342  0.020  1.342
 3B3  C4A  C4B   aromatic  1.448  0.020  1.448
 3B3  C4A  C1A   aromatic  1.416  0.020  1.416
 3B3  C4B  N5    single    1.330  0.020  1.330
 3B3  C4B  C8A   aromatic  1.394  0.020  1.394
 3B3  N5   C6    single    1.441  0.020  1.441
 3B3  N5   H5    single    0.860  0.020  1.020
 3B3  C6   CB    single    1.524  0.020  1.524
 3B3  C6   H6C1  single    0.970  0.020  1.090
 3B3  C6   H6C2  single    0.970  0.020  1.090
 3B3  C8A  C9    aromatic  1.382  0.020  1.382
 3B3  C8A  H8A   single    0.930  0.020  1.080
 3B3  C9   C10   aromatic  1.384  0.020  1.384
 3B3  C9   H9    single    0.930  0.020  1.080
 3B3  C10  C1A   aromatic  1.432  0.020  1.432
 3B3  C10  N1    single    1.426  0.020  1.426
 3B3  CB   CA    single    1.522  0.020  1.522
 3B3  CB   O16   single    1.413  0.020  1.413
 3B3  CB   HB    single    0.970  0.020  1.090
 3B3  CA   N     single    1.452  0.020  1.452
 3B3  CA   HAC1  single    0.970  0.020  1.090
 3B3  CA   HAC2  single    0.970  0.020  1.090
 3B3  N    HN1   single    0.890  0.020  1.040
 3B3  N    HN2   single    0.890  0.020  1.040
 3B3  O    N1    double    1.217  0.020  1.217
 3B3  OXT  N1    single    1.217  0.020  1.217
 3B3  O16  H16   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
 3B3  H1    C1   C1A   121.06  3.000
 3B3  H1    C1   C2    118.82  3.000
 3B3  C1A   C1   C2    120.12  3.000
 3B3  H2    C2   C3    120.13  3.000
 3B3  H2    C2   C1    120.40  3.000
 3B3  C3    C2   C1    119.46  3.000
 3B3  H3    C3   N4    117.28  3.000
 3B3  H3    C3   C2    120.69  3.000
 3B3  N4    C3   C2    122.04  3.000
 3B3  C4A   N4   C3    119.49  3.000
 3B3  C1A   C4A  C4B   121.35  3.000
 3B3  C1A   C4A  N4    123.54  3.000
 3B3  C4B   C4A  N4    115.10  3.000
 3B3  C8A   C4B  N5    123.64  3.000
 3B3  C8A   C4B  C4A   118.34  3.000
 3B3  N5    C4B  C4A   118.02  3.000
 3B3  H5    N5   C6    118.76  3.000
 3B3  H5    N5   C4B   116.10  3.000
 3B3  C6    N5   C4B   124.62  3.000
 3B3  H6C2  C6   H6C1  106.86  3.000
 3B3  H6C2  C6   CB    110.32  3.000
 3B3  H6C1  C6   CB    108.78  3.000
 3B3  H6C2  C6   N5    110.50  3.000
 3B3  H6C1  C6   N5    109.91  3.000
 3B3  CB    C6   N5    110.40  3.000
 3B3  H8A   C8A  C9    118.84  3.000
 3B3  H8A   C8A  C4B   120.93  3.000
 3B3  C9    C8A  C4B   120.22  3.000
 3B3  H9    C9   C10   119.60  3.000
 3B3  H9    C9   C8A   117.77  3.000
 3B3  C10   C9   C8A   122.62  3.000
 3B3  N1    C10  C1A   123.14  3.000
 3B3  N1    C10  C9    116.86  3.000
 3B3  C1A   C10  C9    119.99  3.000
 3B3  C10   C1A  C4A   117.47  3.000
 3B3  C10   C1A  C1    127.18  3.000
 3B3  C4A   C1A  C1    115.31  3.000
 3B3  HB    CB   O16   105.32  3.000
 3B3  HB    CB   CA    108.39  3.000
 3B3  O16   CB   CA    112.20  3.000
 3B3  HB    CB   C6    108.61  3.000
 3B3  O16   CB   C6    111.52  3.000
 3B3  CA    CB   C6    110.57  3.000
 3B3  HAC2  CA   HAC1  106.35  3.000
 3B3  HAC2  CA   N     114.04  3.000
 3B3  HAC1  CA   N     108.50  3.000
 3B3  HAC2  CA   CB    108.79  3.000
 3B3  HAC1  CA   CB    108.24  3.000
 3B3  N     CA   CB    110.69  3.000
 3B3  HN2   N    HN1   105.79  3.000
 3B3  HN2   N    CA    109.38  3.000
 3B3  HN1   N    CA    109.51  3.000
 3B3  OXT   N1   O     121.96  3.000
 3B3  OXT   N1   C10   118.66  3.000
 3B3  O     N1   C10   119.37  3.000
 3B3  H16   O16  CB    108.60  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
 3B3  CONST_01  N4   C3   C2   C1     0.00   0.0  0
 3B3  CONST_02  N4   C4A  C1A  C1     0.00   0.0  0
 3B3  CONST_03  C4B  C4A  C1A  C1   180.00   0.0  0
 3B3  CONST_04  C9   C10  C1A  C1   180.00   0.0  0
 3B3  CONST_05  C4A  C1A  C1   C2     0.00   0.0  0
 3B3  CONST_06  C10  C1A  C1   C2   180.00   0.0  0
 3B3  CONST_07  C4A  N4   C3   C2     0.00   0.0  0
 3B3  CONST_08  C1A  C1   C2   C3     0.00   0.0  0
 3B3  CONST_09  C4B  C4A  N4   C3   180.00   0.0  0
 3B3  CONST_10  C1A  C4A  N4   C3     0.00   0.0  0
 3B3  CONST_11  C8A  C4B  C4A  N4   180.00   0.0  0
 3B3  CONST_12  C10  C1A  C4A  N4   180.00   0.0  0
 3B3  CONST_13  C9   C8A  C4B  C4A    0.00   0.0  0
 3B3  CONST_14  C9   C10  C1A  C4A    0.00   0.0  0
 3B3  CONST_15  C10  C1A  C4A  C4B    0.00   0.0  0
 3B3  CONST_16  C10  C9   C8A  C4B    0.00   0.0  0
 3B3  CONST_17  C1A  C4A  C4B  C8A    0.00   0.0  0
 3B3  CONST_18  C1A  C10  C9   C8A    0.00   0.0  0
 3B3  CONST_19  N1   C10  C1A  C1     0.00   0.0  0
 3B3  CONST_20  N5   C4B  C4A  N4     0.00   0.0  0
 3B3  CONST_21  N1   C10  C1A  C4A  180.00   0.0  0
 3B3  CONST_22  C1A  C4A  C4B  N5   180.00   0.0  0
 3B3  CONST_23  C9   C8A  C4B  N5   180.00   0.0  0
 3B3  CONST_24  N1   C10  C9   C8A  180.00   0.0  0
 3B3  CONST_25  H3   C3   C2   C1   180.00   0.0  0
 3B3  CONST_26  H1   C1   C2   C3   180.00   0.0  0
 3B3  CONST_27  H2   C2   C3   N4   180.00   0.0  0
 3B3  CONST_28  H8A  C8A  C4B  C4A  180.00   0.0  0
 3B3  CONST_29  H9   C9   C8A  C4B  180.00   0.0  0
 3B3  CONST_30  C6   N5   C4B  C4A  180.00   0.0  0
 3B3  CONST_31  C8A  C4B  N5   C6     0.00   0.0  0
 3B3  CONST_34  O    N1   C10  C1A    0.00   0.0  0
 3B3  CONST_35  OXT  N1   C10  C1A  180.00   0.0  0
 3B3  CONST_36  H5   N5   C4B  C4A    0.00   0.0  0
 3B3  Var_01    CB   C6   N5   C4B  171.20  30.0  3
 3B3  Var_02    HN1  N    CA   CB    66.69  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
 3B3  chir_01  CB  C6  CA  O16  positiv

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
 3B3  plan-1  C1   0.020
 3B3  plan-1  C2   0.020
 3B3  plan-1  C3   0.020
 3B3  plan-1  N4   0.020
 3B3  plan-1  C4A  0.020
 3B3  plan-1  C4B  0.020
 3B3  plan-1  N5   0.020
 3B3  plan-1  C8A  0.020
 3B3  plan-1  C9   0.020
 3B3  plan-1  C10  0.020
 3B3  plan-1  C1A  0.020
 3B3  plan-1  N1   0.020
 3B3  plan-1  H1   0.020
 3B3  plan-1  H2   0.020
 3B3  plan-1  H3   0.020
 3B3  plan-1  H8A  0.020
 3B3  plan-1  H9   0.020
 3B3  plan-2  C4B  0.020
 3B3  plan-2  N5   0.020
 3B3  plan-2  C6   0.020
 3B3  plan-2  H5   0.020
 3B3  plan-3  C10  0.020
 3B3  plan-3  O    0.020
 3B3  plan-3  OXT  0.020
 3B3  plan-3  N1   0.020

