# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 14:14:35 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 5-{[2-(acetylamino)ethyl]amino}naphthalene-1-sulfonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)NCCNc1cccc2c1cccc2[S](O)(=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
 AEN  AEN  '5-{[2-(acetylamino)ethyl]amino}naphthalene-1-sulfonic acid'  ligand  36  21  .  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_AEN
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
 AEN  C1    C  CR6    0  -0.296   0.6218  -0.0428  -2.9224
 AEN  C2    C  CR16   0  -0.274   1.9861  -0.0139  -2.8093
 AEN  C3    C  CR16   0  -0.246   2.5967   0.0806  -1.5484
 AEN  C4    C  CR16   0  -0.305   1.8308   0.1167  -0.4175
 AEN  C5    C  CR6    0   0.332  -0.3793   0.0680   0.7067
 AEN  C6    C  CR16   0  -0.373  -1.7529   0.0933   0.5890
 AEN  C7    C  CR16   0  -0.234  -2.3587   0.0851  -0.6770
 AEN  C8    C  CR16   0  -0.369  -1.6272   0.0292  -1.8294
 AEN  C9    C  CR66   0   0.157  -0.2111   0.0103  -1.7651
 AEN  C10   C  CR66   0   0.022   0.4200   0.0595  -0.4882
 AEN  C1'   C  CH3    0  -0.776  -0.7377  -0.0501   7.9468
 AEN  C2'   C  C      0   0.525   0.2122   0.0735   6.7821
 AEN  O2'   O  O      0  -0.510   1.4138   0.2507   6.9382
 AEN  N3'   N  NH1    0  -0.636  -0.3456  -0.0248   5.5657
 AEN  C4'   C  CH2    0  -0.264   0.4220   0.0701   4.3454
 AEN  C5'   C  CH2    0  -0.319  -0.5139  -0.0004   3.1497
 AEN  N6'   N  NH1    0  -0.694   0.2533   0.0864   1.9318
 AEN  S     S  S      0   1.419  -0.0834  -0.1518  -4.5745
 AEN  O1S   O  OS     0  -0.736   1.0649  -0.2278  -5.4934
 AEN  O2S   O  OS     0  -0.754  -0.8991  -1.3791  -4.5714
 AEN  O3S   O  OS    -1  -0.755  -0.8763   1.0784  -4.7476
 AEN  H2    H  HCR6   0   0.270   2.6064  -0.0534  -3.6933
 AEN  H3    H  HCR6   0   0.261   3.6750   0.1294  -1.4777
 AEN  H4    H  HCR6   0   0.251   2.3286   0.2142   0.5380
 AEN  H6    H  HCR6   0   0.271  -2.3866   0.1025   1.4646
 AEN  H7    H  HCR6   0   0.255  -3.4397   0.1039  -0.7334
 AEN  H8    H  HCR6   0   0.245  -2.1410   0.0076  -2.7764
 AEN  H1'1  H  HCH3   0   0.266  -0.4585  -0.9122   8.5528
 AEN  H1'2  H  HCH3   0   0.265  -0.6516   0.8324   8.5800
 AEN  H1'3  H  HCH3   0   0.248  -1.7787  -0.1615   7.6503
 AEN  HN'3  H  HNH1   0   0.404  -1.3376  -0.1831   5.4972
 AEN  H4'1  H  HCH2   0   0.247   0.9795   1.0093   4.3186
 AEN  H4'2  H  HCH2   0   0.241   1.1531  -0.7429   4.2929
 AEN  H5'1  H  HCH2   0   0.230  -1.1114  -0.9220   3.2015
 AEN  H5'2  H  HCH2   0   0.248  -1.2138   0.8378   3.1949
 AEN  HN'6  H  HNH1   0   0.385   1.1084  -0.4478   1.9657

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
 AEN  C1   C2    aromatic  1.369  0.020  1.369
 AEN  C1   C9    aromatic  1.427  0.020  1.427
 AEN  C1   S     single    1.800  0.020  1.800
 AEN  C2   C3    aromatic  1.404  0.020  1.404
 AEN  C2   H2    single    0.930  0.020  1.080
 AEN  C3   C4    aromatic  1.366  0.020  1.366
 AEN  C3   H3    single    0.930  0.020  1.080
 AEN  C4   C10   aromatic  1.414  0.020  1.414
 AEN  C4   H4    single    0.930  0.020  1.080
 AEN  C5   C6    aromatic  1.379  0.020  1.379
 AEN  C5   C10   aromatic  1.438  0.020  1.438
 AEN  C5   N6'   single    1.379  0.020  1.379
 AEN  C6   C7    aromatic  1.403  0.020  1.403
 AEN  C6   H6    single    0.930  0.020  1.080
 AEN  C7   C8    aromatic  1.366  0.020  1.366
 AEN  C7   H7    single    0.930  0.020  1.080
 AEN  C8   C9    aromatic  1.418  0.020  1.418
 AEN  C8   H8    single    0.930  0.020  1.080
 AEN  C9   C10   aromatic  1.425  0.020  1.425
 AEN  C1'  C2'   single    1.508  0.020  1.508
 AEN  C1'  H1'1  single    0.970  0.020  1.090
 AEN  C1'  H1'2  single    0.970  0.020  1.090
 AEN  C1'  H1'3  single    0.970  0.020  1.090
 AEN  C2'  O2'   double    1.225  0.020  1.225
 AEN  C2'  N3'   single    1.342  0.020  1.342
 AEN  N3'  C4'   single    1.445  0.020  1.445
 AEN  N3'  HN'3  single    0.860  0.020  1.020
 AEN  C4'  C5'   single    1.520  0.020  1.520
 AEN  C4'  H4'1  single    0.970  0.020  1.090
 AEN  C4'  H4'2  single    0.970  0.020  1.090
 AEN  C5'  N6'   single    1.442  0.020  1.442
 AEN  C5'  H5'1  single    0.970  0.020  1.090
 AEN  C5'  H5'2  single    0.970  0.020  1.090
 AEN  N6'  HN'6  single    0.890  0.020  1.040
 AEN  S    O1S   deloc     1.473  0.020  1.473
 AEN  S    O2S   deloc     1.474  0.020  1.474
 AEN  S    O3S   deloc     1.474  0.020  1.474

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
 AEN  S     C1   C9    121.20  3.000
 AEN  S     C1   C2    117.88  3.000
 AEN  C9    C1   C2    120.92  3.000
 AEN  H2    C2   C3    119.17  3.000
 AEN  H2    C2   C1    120.24  3.000
 AEN  C3    C2   C1    120.59  3.000
 AEN  H3    C3   C4    120.24  3.000
 AEN  H3    C3   C2    119.68  3.000
 AEN  C4    C3   C2    120.08  3.000
 AEN  H4    C4   C10   120.47  3.000
 AEN  H4    C4   C3    118.39  3.000
 AEN  C10   C4   C3    121.13  3.000
 AEN  N6'   C5   C10   118.91  3.000
 AEN  N6'   C5   C6    122.18  3.000
 AEN  C10   C5   C6    118.88  3.000
 AEN  H6    C6   C7    118.54  3.000
 AEN  H6    C6   C5    121.00  3.000
 AEN  C7    C6   C5    120.45  3.000
 AEN  H7    C7   C8    119.43  3.000
 AEN  H7    C7   C6    118.54  3.000
 AEN  C8    C7   C6    122.01  3.000
 AEN  H8    C8   C9    121.05  3.000
 AEN  H8    C8   C7    119.13  3.000
 AEN  C9    C8   C7    119.82  3.000
 AEN  C10   C9   C8    118.85  3.000
 AEN  C10   C9   C1    118.00  3.000
 AEN  C8    C9   C1    123.15  3.000
 AEN  C9    C10  C5    119.91  3.000
 AEN  C9    C10  C4    119.22  3.000
 AEN  C5    C10  C4    120.87  3.000
 AEN  H1'3  C1'  H1'2  108.47  3.000
 AEN  H1'3  C1'  H1'1  108.39  3.000
 AEN  H1'2  C1'  H1'1  107.30  3.000
 AEN  H1'3  C1'  C2'   113.61  3.000
 AEN  H1'2  C1'  C2'   109.43  3.000
 AEN  H1'1  C1'  C2'   109.44  3.000
 AEN  N3'   C2'  O2'   122.28  3.000
 AEN  N3'   C2'  C1'   115.61  3.000
 AEN  O2'   C2'  C1'   122.11  3.000
 AEN  HN'3  N3'  C4'   118.44  3.000
 AEN  HN'3  N3'  C2'   118.87  3.000
 AEN  C4'   N3'  C2'   122.69  3.000
 AEN  H4'2  C4'  H4'1  107.24  3.000
 AEN  H4'2  C4'  C5'   109.82  3.000
 AEN  H4'1  C4'  C5'   109.56  3.000
 AEN  H4'2  C4'  N3'   110.28  3.000
 AEN  H4'1  C4'  N3'   110.38  3.000
 AEN  C5'   C4'  N3'   109.53  3.000
 AEN  H5'2  C5'  H5'1  107.03  3.000
 AEN  H5'2  C5'  N6'   109.23  3.000
 AEN  H5'1  C5'  N6'   112.30  3.000
 AEN  H5'2  C5'  C4'   109.04  3.000
 AEN  H5'1  C5'  C4'   109.66  3.000
 AEN  N6'   C5'  C4'   109.51  3.000
 AEN  HN'6  N6'  C5'   113.00  3.000
 AEN  HN'6  N6'  C5    114.31  3.000
 AEN  C5'   N6'  C5    120.36  3.000
 AEN  O3S   S    O2S   113.43  3.000
 AEN  O3S   S    O1S   112.91  3.000
 AEN  O2S   S    O1S   112.95  3.000
 AEN  O3S   S    C1    105.55  3.000
 AEN  O2S   S    C1    105.39  3.000
 AEN  O1S   S    C1    105.69  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
 AEN  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 AEN  CONST_02  C7    C8   C9   C1    180.00   0.0  0
 AEN  CONST_03  C4    C10  C9   C1      0.00   0.0  0
 AEN  CONST_04  C5    C10  C9   C1    180.00   0.0  0
 AEN  CONST_05  C8    C9   C1   C2    180.00   0.0  0
 AEN  CONST_06  C10   C9   C1   C2      0.00   0.0  0
 AEN  CONST_07  C10   C4   C3   C2      0.00   0.0  0
 AEN  CONST_08  C9    C1   C2   C3      0.00   0.0  0
 AEN  CONST_09  C5    C10  C4   C3    180.00   0.0  0
 AEN  CONST_10  C9    C10  C4   C3      0.00   0.0  0
 AEN  CONST_11  C6    C5   C10  C4    180.00   0.0  0
 AEN  CONST_12  C8    C9   C10  C4    180.00   0.0  0
 AEN  CONST_13  C8    C7   C6   C5      0.00   0.0  0
 AEN  CONST_14  C8    C9   C10  C5      0.00   0.0  0
 AEN  CONST_15  C9    C10  C5   C6      0.00   0.0  0
 AEN  CONST_16  C9    C8   C7   C6      0.00   0.0  0
 AEN  CONST_17  C10   C5   C6   C7      0.00   0.0  0
 AEN  CONST_18  C10   C9   C8   C7      0.00   0.0  0
 AEN  CONST_19  S     C1   C2   C3    180.00   0.0  0
 AEN  CONST_20  N6'   C5   C10  C4      0.00   0.0  0
 AEN  CONST_21  N6'   C5   C6   C7    180.00   0.0  0
 AEN  CONST_22  S     C1   C9   C8      0.00   0.0  0
 AEN  CONST_23  N6'   C5   C10  C9    180.00   0.0  0
 AEN  CONST_24  S     C1   C9   C10   180.00   0.0  0
 AEN  CONST_25  H3    C3   C2   C1    180.00   0.0  0
 AEN  CONST_26  H8    C8   C9   C1      0.00   0.0  0
 AEN  CONST_27  H4    C4   C3   C2    180.00   0.0  0
 AEN  CONST_28  H2    C2   C3   C4    180.00   0.0  0
 AEN  CONST_29  H7    C7   C6   C5    180.00   0.0  0
 AEN  CONST_30  H6    C6   C7   C8    180.00   0.0  0
 AEN  CONST_31  C5'   N6'  C5   C6      0.00   0.0  0
 AEN  CONST_32  C5'   N6'  C5   C10   180.00   0.0  0
 AEN  CONST_34  C4'   N3'  C2'  C1'   180.00   0.0  0
 AEN  CONST_35  C4'   N3'  C2'  O2'     0.00   0.0  0
 AEN  CONST_36  HN'3  N3'  C2'  C1'     0.00   0.0  0
 AEN  Var_01    O1S   S    C1   C2      1.64  30.0  2
 AEN  Var_02    C4'   C5'  N6'  C5   -178.86  30.0  1
 AEN  Var_03    C5'   C4'  N3'  C2'  -176.73  30.0  3
 AEN  Var_04    N6'   C5'  C4'  N3'  -179.67  30.0  3
 AEN  Var_05    H1'1  C1'  C2'  O2'   -61.22  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
 AEN  plan-1  C1    0.020
 AEN  plan-1  C2    0.020
 AEN  plan-1  C3    0.020
 AEN  plan-1  C4    0.020
 AEN  plan-1  C5    0.020
 AEN  plan-1  C6    0.020
 AEN  plan-1  C7    0.020
 AEN  plan-1  C8    0.020
 AEN  plan-1  C9    0.020
 AEN  plan-1  C10   0.020
 AEN  plan-1  N6'   0.020
 AEN  plan-1  S     0.020
 AEN  plan-1  H2    0.020
 AEN  plan-1  H3    0.020
 AEN  plan-1  H4    0.020
 AEN  plan-1  H6    0.020
 AEN  plan-1  H7    0.020
 AEN  plan-1  H8    0.020
 AEN  plan-2  C1'   0.020
 AEN  plan-2  C2'   0.020
 AEN  plan-2  O2'   0.020
 AEN  plan-2  N3'   0.020
 AEN  plan-2  C4'   0.020
 AEN  plan-2  HN'3  0.020
 AEN  plan-3  C5    0.020
 AEN  plan-3  C5'   0.020
 AEN  plan-3  N6'   0.020
 AEN  plan-3  HN'6  0.020

