# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 01:41:47 2022
#   Inital geometry file: a 113 line input string
#   Ligand name: N~2~-{[5-(dimethylamino)naphthalen-1-yl]sulfonyl}-L-asparagine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)c1cccc2c1cccc2[S](=O)(=O)N[C@@H](CC(N)=O)C(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
 9DN  9DN  N~2~-{[5-(dimethylamino)naphthalen-1-yl]sulfonyl}-L-asparagine  L-peptide  43  25  .  2012-08-28  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9DN
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
 9DN  N     N  NC1    0  -0.746  53.4543  33.2803  76.3079
 9DN  CA    C  CH1    0  -0.243  54.6256  33.0005  77.1324
 9DN  C     C  C      0   0.453  54.1312  32.7876  78.5941
 9DN  O     O  O      0  -0.583  52.8986  32.6921  78.7497
 9DN  CB    C  CH2    0  -0.541  55.6348  34.1493  77.0389
 9DN  CG    C  C      0   0.510  56.9538  33.9290  77.7499
 9DN  OD1   O  O      0  -0.493  57.4070  34.7327  78.5511
 9DN  ND2   N  NH2    0  -0.803  57.6348  32.8331  77.3665
 9DN  OXT   O  OC    -1  -0.569  55.0207  32.7252  79.4534
 9DN  S1    S  S      0   1.365  53.3116  32.6191  74.8145
 9DN  O2    O  OS     0  -0.649  53.8067  31.2474  74.7658
 9DN  O3    O  OS     0  -0.665  51.9347  32.8461  74.3917
 9DN  N1    N  NT     0  -0.490  56.1708  37.8180  72.1313
 9DN  C1    C  CR6    0  -0.279  54.4260  33.6080  73.8435
 9DN  C2    C  CR16   0  -0.247  55.4700  32.9477  73.2509
 9DN  C3    C  CR16   0  -0.245  56.3870  33.6507  72.4547
 9DN  C4    C  CR16   0  -0.292  56.2678  35.0034  72.3097
 9DN  C5    C  CR66   0   0.042  55.2301  35.7230  72.9460
 9DN  C6    C  CR66   0   0.184  54.2458  35.0156  73.6936
 9DN  C7    C  CR16   0  -0.352  53.1514  35.7351  74.2293
 9DN  C8    C  CR16   0  -0.232  53.0541  37.0825  74.0222
 9DN  C9    C  CR16   0  -0.337  54.0443  37.7941  73.3257
 9DN  C10   C  CR6    0   0.293  55.1407  37.1462  72.8089
 9DN  C11   C  CH3    0  -0.544  55.8169  39.0772  71.5121
 9DN  C12   C  CH3    0  -0.541  57.4151  37.9305  72.8809
 9DN  H     H  HNC1   0   0.406  52.6164  33.1215  76.8789
 9DN  H111  H  HCH3   0   0.210  55.6549  39.8935  72.2287
 9DN  H112  H  HCH3   0   0.248  56.6288  39.3812  70.8510
 9DN  H113  H  HCH3   0   0.246  54.9166  38.9656  70.9089
 9DN  H121  H  HCH3   0   0.240  58.2188  38.2336  72.2094
 9DN  H122  H  HCH3   0   0.220  57.3444  38.6726  73.6868
 9DN  H123  H  HCH3   0   0.251  57.6965  36.9793  73.3280
 9DN  H2    H  HCR6   0   0.285  55.5929  31.8823  73.3826
 9DN  H3    H  HCR6   0   0.268  57.1831  33.1130  71.9585
 9DN  H4    H  HCR6   0   0.276  56.9665  35.5354  71.6791
 9DN  H7    H  HCR6   0   0.253  52.3781  35.2353  74.7893
 9DN  H8    H  HCR6   0   0.261  52.2067  37.6224  74.4247
 9DN  H9    H  HCR6   0   0.267  53.9385  38.8654  73.2218
 9DN  HA    H  HCH1   0   0.255  55.0939  32.0589  76.8221
 9DN  HB1C  H  HCH2   0   0.270  55.8672  34.3373  75.9862
 9DN  HB2C  H  HCH2   0   0.254  55.1825  35.0620  77.4274
 9DN  HD21  H  HNH2   0   0.402  57.2786  32.1871  76.6843
 9DN  HD22  H  HNH2   0   0.394  58.5269  32.6186  77.7805

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
 9DN  S1   O2    double    1.459  0.020  1.459
 9DN  S1   O3    double    1.458  0.020  1.458
 9DN  S1   C1    single    1.778  0.020  1.778
 9DN  S1   N     single    1.640  0.020  1.640
 9DN  OXT  C     deloc     1.238  0.020  1.238
 9DN  N1   C10   single    1.404  0.020  1.404
 9DN  N1   C11   single    1.447  0.020  1.447
 9DN  N1   C12   single    1.457  0.020  1.457
 9DN  C1   C2    aromatic  1.370  0.020  1.370
 9DN  C1   C6    aromatic  1.427  0.020  1.427
 9DN  C2   C3    aromatic  1.403  0.020  1.403
 9DN  C3   C4    aromatic  1.366  0.020  1.366
 9DN  C4   C5    aromatic  1.414  0.020  1.414
 9DN  C5   C6    aromatic  1.424  0.020  1.424
 9DN  C5   C10   aromatic  1.433  0.020  1.433
 9DN  C6   C7    aromatic  1.415  0.020  1.415
 9DN  C7   C8    aromatic  1.367  0.020  1.367
 9DN  C8   C9    aromatic  1.404  0.020  1.404
 9DN  C9   C10   aromatic  1.374  0.020  1.374
 9DN  N    CA    single    1.458  0.019  1.458
 9DN  CA   C     single    1.525  0.021  1.525
 9DN  CA   CB    single    1.530  0.020  1.530
 9DN  C    O     deloc     1.231  0.020  1.231
 9DN  CB   CG    single    1.514  0.020  1.514
 9DN  CG   OD1   double    1.222  0.020  1.222
 9DN  CG   ND2   single    1.346  0.020  1.346
 9DN  N    H     single    0.860  0.020  0.860
 9DN  C11  H111  single    0.970  0.020  1.090
 9DN  C11  H112  single    0.970  0.020  1.090
 9DN  C11  H113  single    0.970  0.020  1.090
 9DN  C12  H121  single    0.970  0.020  1.090
 9DN  C12  H122  single    0.970  0.020  1.090
 9DN  C12  H123  single    0.970  0.020  1.090
 9DN  C2   H2    single    0.930  0.020  1.080
 9DN  C3   H3    single    0.930  0.020  1.080
 9DN  C4   H4    single    0.930  0.020  1.080
 9DN  C7   H7    single    0.930  0.020  1.080
 9DN  C8   H8    single    0.930  0.020  1.080
 9DN  C9   H9    single    0.930  0.020  1.080
 9DN  CA   HA    single    0.970  0.020  0.970
 9DN  CB   HB1C  single    0.970  0.020  1.090
 9DN  CB   HB2C  single    0.970  0.020  1.090
 9DN  ND2  HD21  single    0.860  0.020  1.020
 9DN  ND2  HD22  single    0.860  0.020  1.020

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
 9DN  H     N    S1    111.92  3.000
 9DN  H     N    CA    114.00  3.000
 9DN  S1    N    CA    120.47  3.000
 9DN  HA    CA   CB    109.00  3.000
 9DN  HA    CA   C     109.00  3.000
 9DN  CB    CA   C     110.10  1.900
 9DN  HA    CA   N     110.00  3.000
 9DN  CB    CA   N     110.50  1.700
 9DN  C     CA   N     111.00  2.800
 9DN  OXT   C    O     128.32  3.000
 9DN  O     C    CA    120.80  1.700
 9DN  OXT   C    CA    115.47  3.000
 9DN  HB2C  CB   HB1C  106.68  3.000
 9DN  HB2C  CB   CG    108.41  3.000
 9DN  HB1C  CB   CG    106.96  3.000
 9DN  HB2C  CB   CA    109.43  3.000
 9DN  HB1C  CB   CA    109.11  3.000
 9DN  CG    CB   CA    115.85  3.000
 9DN  ND2   CG   OD1   122.31  3.000
 9DN  ND2   CG   CB    115.17  3.000
 9DN  OD1   CG   CB    122.35  3.000
 9DN  HD22  ND2  HD21  117.16  3.000
 9DN  HD22  ND2  CG    120.32  3.000
 9DN  HD21  ND2  CG    122.51  3.000
 9DN  C1    S1   O3    110.30  3.000
 9DN  C1    S1   O2    106.97  3.000
 9DN  O3    S1   O2    117.20  3.000
 9DN  C1    S1   N     102.62  3.000
 9DN  O3    S1   N     106.47  3.000
 9DN  O2    S1   N     112.33  3.000
 9DN  C12   N1   C11   111.21  3.000
 9DN  C12   N1   C10   114.53  3.000
 9DN  C11   N1   C10   116.32  3.000
 9DN  C6    C1   C2    121.75  3.000
 9DN  C6    C1   S1    121.78  3.000
 9DN  C2    C1   S1    116.47  3.000
 9DN  H2    C2   C3    119.26  3.000
 9DN  H2    C2   C1    120.61  3.000
 9DN  C3    C2   C1    120.13  3.000
 9DN  H3    C3   C4    120.54  3.000
 9DN  H3    C3   C2    119.50  3.000
 9DN  C4    C3   C2    119.96  3.000
 9DN  H4    C4   C5    119.10  3.000
 9DN  H4    C4   C3    119.54  3.000
 9DN  C5    C4   C3    121.35  3.000
 9DN  C10   C5   C6    120.04  3.000
 9DN  C10   C5   C4    120.55  3.000
 9DN  C6    C5   C4    119.38  3.000
 9DN  C7    C6   C5    118.73  3.000
 9DN  C7    C6   C1    124.02  3.000
 9DN  C5    C6   C1    117.25  3.000
 9DN  H7    C7   C8    119.01  3.000
 9DN  H7    C7   C6    121.05  3.000
 9DN  C8    C7   C6    119.93  3.000
 9DN  H8    C8   C9    118.94  3.000
 9DN  H8    C8   C7    119.41  3.000
 9DN  C9    C8   C7    121.64  3.000
 9DN  H9    C9   C10   120.59  3.000
 9DN  H9    C9   C8    118.72  3.000
 9DN  C10   C9   C8    120.68  3.000
 9DN  C9    C10  C5    118.82  3.000
 9DN  C9    C10  N1    122.77  3.000
 9DN  C5    C10  N1    118.41  3.000
 9DN  H113  C11  H112  107.96  3.000
 9DN  H113  C11  H111  108.39  3.000
 9DN  H112  C11  H111  107.36  3.000
 9DN  H113  C11  N1    110.48  3.000
 9DN  H112  C11  N1    108.66  3.000
 9DN  H111  C11  N1    113.80  3.000
 9DN  H123  C12  H122  107.82  3.000
 9DN  H123  C12  H121  107.79  3.000
 9DN  H122  C12  H121  108.16  3.000
 9DN  H123  C12  N1    111.39  3.000
 9DN  H122  C12  N1    112.01  3.000
 9DN  H121  C12  N1    109.52  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
 9DN  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 9DN  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 9DN  CONST_03  C10   C5   C6   C1    180.00   0.0  0
 9DN  CONST_04  C8    C7   C6   C1    180.00   0.0  0
 9DN  CONST_05  C5    C6   C1   C2      0.00   0.0  0
 9DN  CONST_06  C7    C6   C1   C2    180.00   0.0  0
 9DN  CONST_07  C5    C4   C3   C2      0.00   0.0  0
 9DN  CONST_08  C6    C1   C2   C3      0.00   0.0  0
 9DN  CONST_09  C6    C5   C4   C3      0.00   0.0  0
 9DN  CONST_10  C10   C5   C4   C3    180.00   0.0  0
 9DN  CONST_11  C7    C6   C5   C4    180.00   0.0  0
 9DN  CONST_12  C9    C10  C5   C4    180.00   0.0  0
 9DN  CONST_13  C8    C7   C6   C5      0.00   0.0  0
 9DN  CONST_14  C8    C9   C10  C5      0.00   0.0  0
 9DN  CONST_15  C9    C10  C5   C6      0.00   0.0  0
 9DN  CONST_16  C9    C8   C7   C6      0.00   0.0  0
 9DN  CONST_17  C10   C5   C6   C7      0.00   0.0  0
 9DN  CONST_18  C10   C9   C8   C7      0.00   0.0  0
 9DN  CONST_19  C3    C2   C1   S1    180.00   0.0  0
 9DN  CONST_20  C5    C6   C1   S1    180.00   0.0  0
 9DN  CONST_21  C7    C6   C1   S1      0.00   0.0  0
 9DN  CONST_22  C4    C5   C10  N1      0.00   0.0  0
 9DN  CONST_23  C6    C5   C10  N1    180.00   0.0  0
 9DN  CONST_24  C8    C9   C10  N1    180.00   0.0  0
 9DN  CONST_25  H3    C3   C2   C1    180.00   0.0  0
 9DN  CONST_26  H7    C7   C6   C1      0.00   0.0  0
 9DN  CONST_27  H4    C4   C3   C2    180.00   0.0  0
 9DN  CONST_28  H2    C2   C3   C4    180.00   0.0  0
 9DN  CONST_29  H9    C9   C10  C5    180.00   0.0  0
 9DN  CONST_30  H8    C8   C7   C6    180.00   0.0  0
 9DN  CONST_35  HD21  ND2  CG   CB      0.00   0.0  0
 9DN  CONST_36  HD22  ND2  CG   CB    180.00   0.0  0
 9DN  Var_01    C2    C1   S1   N     119.08  30.0  2
 9DN  Var_02    C1    S1   N    CA    -76.33  30.0  2
 9DN  Var_03    H111  C11  N1   C10    72.50  30.0  3
 9DN  Var_04    H121  C12  N1   C10   166.09  30.0  3
 9DN  Var_05    OD1   CG   CB   CA   -127.62  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
 9DN  chir_01  CA  N  C  CB  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
 9DN  plan-1  S1    0.020
 9DN  plan-1  N1    0.020
 9DN  plan-1  C1    0.020
 9DN  plan-1  C2    0.020
 9DN  plan-1  C3    0.020
 9DN  plan-1  C4    0.020
 9DN  plan-1  C5    0.020
 9DN  plan-1  C6    0.020
 9DN  plan-1  C7    0.020
 9DN  plan-1  C8    0.020
 9DN  plan-1  C9    0.020
 9DN  plan-1  C10   0.020
 9DN  plan-1  H2    0.020
 9DN  plan-1  H3    0.020
 9DN  plan-1  H4    0.020
 9DN  plan-1  H7    0.020
 9DN  plan-1  H8    0.020
 9DN  plan-1  H9    0.020
 9DN  plan-2  CB    0.020
 9DN  plan-2  CG    0.020
 9DN  plan-2  OD1   0.020
 9DN  plan-2  ND2   0.020
 9DN  plan-2  HD21  0.020
 9DN  plan-2  HD22  0.020
 9DN  plan-3  N1    0.020
 9DN  plan-3  C10   0.020
 9DN  plan-3  C11   0.020
 9DN  plan-3  C12   0.020
 9DN  plan-4  CA    0.020
 9DN  plan-4  C     0.020
 9DN  plan-4  O     0.020
 9DN  plan-4  OXT   0.020

