# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 17 04:09:12 2020
#   Inital geometry file: a 67 line input string
#   Ligand name: 5-aminonaphthalene-2-sulfonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cccc2cc(ccc12)[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
 N2M  N2M  '5-aminonaphthalene-2-sulfonic acid'  ligand  24  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 PERFECT
;

data_comp_N2M
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
 N2M  S    S  S     0   1.467   5.4982  -4.5896  -1.2084
 N2M  O1S  O  OS    0  -0.710   5.2740  -5.3714  -2.5836
 N2M  O2S  O  OS    0  -0.632   6.2246  -3.3622  -1.4580
 N2M  O3S  O  OS    0  -0.641   6.0519  -5.5958  -0.3304
 N2M  C1   C  CR16  0  -0.296   3.4120  -2.9214  -0.7277
 N2M  C2   C  CR6   0  -0.237   3.8569  -4.2123  -0.6903
 N2M  C3   C  CR16  0  -0.230   3.0424  -5.2650  -0.2249
 N2M  C4   C  CR16  0  -0.290   1.7702  -4.9833   0.1818
 N2M  C5   C  CR6   0   0.269  -0.0759  -3.3582   0.5692
 N2M  C6   C  CR16  0  -0.337  -0.4852  -2.0378   0.5541
 N2M  C7   C  CR16  0  -0.249   0.3683  -1.0102   0.1276
 N2M  C8   C  CR16  0  -0.343   1.6392  -1.2784  -0.3045
 N2M  C9   C  CR66  0   0.119   2.0998  -2.6124  -0.3001
 N2M  C10  C  CR66  0   0.072   1.2564  -3.6645   0.1483
 N2M  N    N  NH2   0  -0.857  -0.9037  -4.3530   1.0359
 N2M  H1S  H  H     0   0.504   5.0386  -4.7763  -3.3146
 N2M  H3   H  HCR6  0   0.286   3.4128  -6.2799  -0.1794
 N2M  H4   H  HCR6  0   0.263   1.1643  -5.7994   0.5516
 N2M  H6   H  HCR6  0   0.264  -1.4902  -1.7914   0.8751
 N2M  H7   H  HCR6  0   0.261   0.0018   0.0082   0.1347
 N2M  H8   H  HCR6  0   0.255   2.2943  -0.4863  -0.6433
 N2M  HN1  H  HNH2  0   0.389  -0.8244  -5.2550   0.5944
 N2M  HN2  H  HNH2  0   0.386  -1.8706  -4.0860   1.1336
 N2M  H1   H  HCR6  0   0.285   4.0491  -2.1170  -1.0729

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
 N2M  S    O1S  single    1.598  0.020  1.598
 N2M  S    O2S  double    1.448  0.020  1.448
 N2M  S    O3S  double    1.446  0.020  1.446
 N2M  S    C2   single    1.762  0.020  1.762
 N2M  O1S  H1S  single    0.850  0.020  0.980
 N2M  C1   C2   aromatic  1.366  0.020  1.366
 N2M  C1   C9   aromatic  1.414  0.020  1.414
 N2M  C1   H1   single    0.930  0.020  1.080
 N2M  C2   C3   aromatic  1.410  0.020  1.410
 N2M  C3   C4   aromatic  1.365  0.020  1.365
 N2M  C3   H3   single    0.930  0.020  1.080
 N2M  C4   C10  aromatic  1.416  0.020  1.416
 N2M  C4   H4   single    0.930  0.020  1.080
 N2M  C5   C6   aromatic  1.382  0.020  1.382
 N2M  C5   C10  aromatic  1.430  0.020  1.430
 N2M  C5   N    single    1.376  0.020  1.376
 N2M  C6   C7   aromatic  1.402  0.020  1.402
 N2M  C6   H6   single    0.930  0.020  1.080
 N2M  C7   C8   aromatic  1.369  0.020  1.369
 N2M  C7   H7   single    0.930  0.020  1.080
 N2M  C8   C9   aromatic  1.411  0.020  1.411
 N2M  C8   H8   single    0.930  0.020  1.080
 N2M  C9   C10  aromatic  1.421  0.020  1.421
 N2M  N    HN1  single    0.890  0.020  1.040
 N2M  N    HN2  single    0.890  0.020  1.040

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
 N2M  C2   S    O3S  109.10  3.000
 N2M  C2   S    O2S  109.66  3.000
 N2M  O3S  S    O2S  120.17  3.000
 N2M  C2   S    O1S  103.13  3.000
 N2M  O3S  S    O1S  103.65  3.000
 N2M  O2S  S    O1S  109.68  3.000
 N2M  H1S  O1S  S    112.45  3.000
 N2M  H1   C1   C9   118.69  3.000
 N2M  H1   C1   C2   121.28  3.000
 N2M  C9   C1   C2   120.03  3.000
 N2M  C3   C2   C1   121.77  3.000
 N2M  C3   C2   S    118.37  3.000
 N2M  C1   C2   S    119.85  3.000
 N2M  H3   C3   C4   120.02  3.000
 N2M  H3   C3   C2   121.12  3.000
 N2M  C4   C3   C2   118.86  3.000
 N2M  H4   C4   C10  120.50  3.000
 N2M  H4   C4   C3   117.93  3.000
 N2M  C10  C4   C3   121.57  3.000
 N2M  N    C5   C10  120.36  3.000
 N2M  N    C5   C6   121.07  3.000
 N2M  C10  C5   C6   118.50  3.000
 N2M  H6   C6   C7   119.21  3.000
 N2M  H6   C6   C5   119.25  3.000
 N2M  C7   C6   C5   121.53  3.000
 N2M  H7   C7   C8   120.05  3.000
 N2M  H7   C7   C6   118.78  3.000
 N2M  C8   C7   C6   121.17  3.000
 N2M  H8   C8   C9   119.68  3.000
 N2M  H8   C8   C7   121.16  3.000
 N2M  C9   C8   C7   119.16  3.000
 N2M  C10  C9   C8   120.47  3.000
 N2M  C10  C9   C1   118.97  3.000
 N2M  C8   C9   C1   120.56  3.000
 N2M  C9   C10  C5   119.15  3.000
 N2M  C9   C10  C4   118.80  3.000
 N2M  C5   C10  C4   122.05  3.000
 N2M  HN2  N    HN1  110.81  3.000
 N2M  HN2  N    C5   114.75  3.000
 N2M  HN1  N    C5   116.84  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
 N2M  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 N2M  CONST_02  C7   C8   C9   C1    180.00   0.0  0
 N2M  CONST_03  C4   C10  C9   C1      0.00   0.0  0
 N2M  CONST_04  C5   C10  C9   C1    180.00   0.0  0
 N2M  CONST_05  C8   C9   C1   C2    180.00   0.0  0
 N2M  CONST_06  C10  C9   C1   C2      0.00   0.0  0
 N2M  CONST_07  C10  C4   C3   C2      0.00   0.0  0
 N2M  CONST_08  C9   C1   C2   C3      0.00   0.0  0
 N2M  CONST_09  C5   C10  C4   C3    180.00   0.0  0
 N2M  CONST_10  C9   C10  C4   C3      0.00   0.0  0
 N2M  CONST_11  C6   C5   C10  C4    180.00   0.0  0
 N2M  CONST_12  C8   C9   C10  C4    180.00   0.0  0
 N2M  CONST_13  C8   C7   C6   C5      0.00   0.0  0
 N2M  CONST_14  C8   C9   C10  C5      0.00   0.0  0
 N2M  CONST_15  C9   C10  C5   C6      0.00   0.0  0
 N2M  CONST_16  C9   C8   C7   C6      0.00   0.0  0
 N2M  CONST_17  C10  C5   C6   C7      0.00   0.0  0
 N2M  CONST_18  C10  C9   C8   C7      0.00   0.0  0
 N2M  CONST_19  C9   C1   C2   S     180.00   0.0  0
 N2M  CONST_20  C4   C3   C2   S     180.00   0.0  0
 N2M  CONST_21  N    C5   C10  C4      0.00   0.0  0
 N2M  CONST_22  N    C5   C6   C7    180.00   0.0  0
 N2M  CONST_23  N    C5   C10  C9    180.00   0.0  0
 N2M  CONST_24  H3   C3   C2   C1    180.00   0.0  0
 N2M  CONST_25  H8   C8   C9   C1      0.00   0.0  0
 N2M  CONST_26  H4   C4   C3   C2    180.00   0.0  0
 N2M  CONST_27  H1   C1   C2   C3    180.00   0.0  0
 N2M  CONST_28  H7   C7   C6   C5    180.00   0.0  0
 N2M  CONST_29  H6   C6   C7   C8    180.00   0.0  0
 N2M  CONST_31  HN2  N    C5   C6      0.00   0.0  0
 N2M  Var_01    C1   C2   S    O1S  -109.37  30.0  2

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
 N2M  plan-1  S    0.020
 N2M  plan-1  C1   0.020
 N2M  plan-1  C2   0.020
 N2M  plan-1  C3   0.020
 N2M  plan-1  C4   0.020
 N2M  plan-1  C5   0.020
 N2M  plan-1  C6   0.020
 N2M  plan-1  C7   0.020
 N2M  plan-1  C8   0.020
 N2M  plan-1  C9   0.020
 N2M  plan-1  C10  0.020
 N2M  plan-1  N    0.020
 N2M  plan-1  H3   0.020
 N2M  plan-1  H4   0.020
 N2M  plan-1  H6   0.020
 N2M  plan-1  H7   0.020
 N2M  plan-1  H8   0.020
 N2M  plan-1  H1   0.020
 N2M  plan-2  C5   0.020
 N2M  plan-2  N    0.020
 N2M  plan-2  HN1  0.020
 N2M  plan-2  HN2  0.020

