# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 14:59:38 2022
#   Inital geometry file: a 103 line input string
#   Ligand name: S-[2-oxo-2-(1,10-phenanthrolin-5-ylamino)ethyl]-L-cysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CSCC(=O)Nc1cc2cccnc2c3ncccc13)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
 NPH  NPH  S-[2-oxo-2-(1,10-phenanthrolin-5-ylamino)ethyl]-L-cysteine  L-peptide  40  25  .  2012-08-28  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_NPH
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
 NPH  N    N  NH2    0  -0.805  23.5025  14.0136  -50.0881
 NPH  CA   C  CH1    0  -0.236  22.9128  14.3237  -48.7966
 NPH  CB   C  CH2    0  -0.517  23.5898  15.5395  -48.1806
 NPH  SG   S  S2     0  -0.028  25.3150  15.1402  -47.7562
 NPH  CD   C  CH2    0  -0.683  25.8629  16.7915  -47.2671
 NPH  CE   C  C      0   0.544  27.2294  16.7208  -46.6204
 NPH  OZ   O  O      0  -0.440  27.6242  15.7366  -46.0318
 NPH  NZ   N  NH1    0  -0.755  27.9421  17.8742  -46.7334
 NPH  C6   C  CR6    0   0.322  29.1590  18.1279  -46.0808
 NPH  C5   C  CR16   0  -0.370  30.1975  17.2619  -46.1636
 NPH  C6A  C  CR66   0   0.024  29.2809  19.3336  -45.3016
 NPH  C4A  C  CR6    0   0.069  31.4211  17.5144  -45.4788
 NPH  C10  C  CR66   0   0.151  30.4954  19.6289  -44.6454
 NPH  C7   C  CR16   0  -0.177  28.2252  20.2494  -45.1466
 NPH  C4   C  C1     0  -0.187  32.4964  16.6110  -45.5390
 NPH  C1A  C  CR6    0   0.147  31.5946  18.6899  -44.7257
 NPH  N10  N  N      0  -0.403  30.6688  20.7449  -43.9235
 NPH  C8   C  CR16   0  -0.311  28.4189  21.3844  -44.4024
 NPH  C3   C  C1     0  -0.317  33.6544  16.9035  -44.8673
 NPH  N1   N  N      0  -0.400  32.7345  18.9675  -44.0762
 NPH  C9   C  CR16   0  -0.079  29.6720  21.5901  -43.8139
 NPH  C2   C  C1     0  -0.081  33.7207  18.1043  -44.1462
 NPH  C    C  C      0   0.427  21.3764  14.5442  -48.9265
 NPH  O    O  O      0  -0.595  20.8283  14.0388  -49.9242
 NPH  OXT  O  OC    -1  -0.598  20.8232  15.1603  -47.9970
 NPH  H    H  HNH2   0   0.337  22.8396  13.4469  -50.6007
 NPH  H2   H  HNH2   0   0.332  24.3407  13.4600  -49.9731
 NPH  HA   H  HCH1   0   0.209  23.0164  13.4901  -48.0789
 NPH  HB2  H  HCH2   0   0.247  23.5784  16.3698  -48.8906
 NPH  HB3  H  HCH2   0   0.258  23.0718  15.8453  -47.2735
 NPH  HD2  H  HCH2   0   0.290  25.8611  17.4649  -48.1265
 NPH  HD3  H  HCH2   0   0.307  25.1653  17.2055  -46.5319
 NPH  HZ   H  HNH1   0   0.419  27.5169  18.6355  -47.2414
 NPH  H5   H  HCR6   0   0.276  30.1216  16.3646  -46.7628
 NPH  H7   H  HCR6   0   0.267  27.2592  20.0656  -45.5975
 NPH  H4   H  H      0   0.276  32.3986  15.6963  -46.1108
 NPH  H8   H  HCR6   0   0.277  27.6263  22.1063  -44.2640
 NPH  H3   H  H      0   0.274  34.5033  16.2342  -44.8858
 NPH  H9   H  HCR6   0   0.266  29.8529  22.4831  -43.2252
 NPH  HC2  H  H      0   0.264  34.6274  18.3584  -43.6076

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
 NPH  N    CA   single    1.458  0.019  1.458
 NPH  N    H    single    0.860  0.020  0.860
 NPH  N    H2   single    0.890  0.020  1.040
 NPH  CA   CB   single    1.530  0.020  1.530
 NPH  CA   C    single    1.525  0.021  1.525
 NPH  CA   HA   single    0.970  0.020  0.970
 NPH  CB   SG   single    1.821  0.020  1.821
 NPH  CB   HB2  single    0.970  0.020  1.090
 NPH  CB   HB3  single    0.970  0.020  1.090
 NPH  SG   CD   single    1.807  0.020  1.807
 NPH  CD   CE   single    1.513  0.020  1.513
 NPH  CD   HD2  single    0.970  0.020  1.090
 NPH  CD   HD3  single    0.970  0.020  1.090
 NPH  CE   OZ   double    1.213  0.020  1.213
 NPH  CE   NZ   single    1.361  0.020  1.361
 NPH  NZ   C6   single    1.404  0.020  1.404
 NPH  NZ   HZ   single    0.860  0.020  1.020
 NPH  C6   C5   aromatic  1.355  0.020  1.355
 NPH  C6   C6A  aromatic  1.441  0.020  1.441
 NPH  C5   C4A  aromatic  1.425  0.020  1.425
 NPH  C5   H5   single    0.930  0.020  1.080
 NPH  C6A  C10  aromatic  1.412  0.020  1.412
 NPH  C6A  C7   aromatic  1.406  0.020  1.406
 NPH  C4A  C4   aromatic  1.406  0.020  1.406
 NPH  C4A  C1A  aromatic  1.407  0.020  1.407
 NPH  C10  C1A  aromatic  1.448  0.020  1.448
 NPH  C10  N10  aromatic  1.340  0.020  1.340
 NPH  C7   C8   aromatic  1.371  0.020  1.371
 NPH  C7   H7   single    0.930  0.020  1.080
 NPH  C4   C3   aromatic  1.370  0.020  1.370
 NPH  C4   H4   single    0.930  0.020  1.080
 NPH  C1A  N1   aromatic  1.341  0.020  1.341
 NPH  N10  C9   aromatic  1.312  0.020  1.312
 NPH  C8   C9   aromatic  1.400  0.020  1.400
 NPH  C8   H8   single    0.930  0.020  1.080
 NPH  C3   C2   aromatic  1.402  0.020  1.402
 NPH  C3   H3   single    0.930  0.020  1.080
 NPH  N1   C2   aromatic  1.312  0.020  1.312
 NPH  C9   H9   single    0.930  0.020  1.080
 NPH  C2   HC2  single    0.930  0.020  1.080
 NPH  C    O    deloc     1.231  0.020  1.231
 NPH  C    OXT  deloc     1.245  0.020  1.245

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
 NPH  H2   N    H    107.10  3.000
 NPH  H2   N    CA   110.62  3.000
 NPH  H    N    CA   114.00  3.000
 NPH  HA   CA   C    109.00  3.000
 NPH  HA   CA   CB   109.00  3.000
 NPH  C    CA   CB   110.10  1.900
 NPH  HA   CA   N    110.00  3.000
 NPH  C    CA   N    111.00  2.800
 NPH  CB   CA   N    110.50  1.700
 NPH  HB3  CB   HB2  108.85  3.000
 NPH  HB3  CB   SG   108.56  3.000
 NPH  HB2  CB   SG   109.15  3.000
 NPH  HB3  CB   CA   110.49  3.000
 NPH  HB2  CB   CA   109.84  3.000
 NPH  SG   CB   CA   109.92  3.000
 NPH  CD   SG   CB    98.62  3.000
 NPH  HD3  CD   HD2  107.12  3.000
 NPH  HD3  CD   CE   107.82  3.000
 NPH  HD2  CD   CE   111.51  3.000
 NPH  HD3  CD   SG   109.52  3.000
 NPH  HD2  CD   SG   110.49  3.000
 NPH  CE   CD   SG   110.28  3.000
 NPH  NZ   CE   OZ   123.90  3.000
 NPH  NZ   CE   CD   113.44  3.000
 NPH  OZ   CE   CD   122.63  3.000
 NPH  HZ   NZ   C6   117.57  3.000
 NPH  HZ   NZ   CE   117.43  3.000
 NPH  C6   NZ   CE   124.65  3.000
 NPH  C6A  C6   C5   120.21  3.000
 NPH  C6A  C6   NZ   118.42  3.000
 NPH  C5   C6   NZ   121.37  3.000
 NPH  H5   C5   C4A  118.27  3.000
 NPH  H5   C5   C6   120.68  3.000
 NPH  C4A  C5   C6   121.04  3.000
 NPH  C7   C6A  C10  117.29  3.000
 NPH  C7   C6A  C6   122.77  3.000
 NPH  C10  C6A  C6   119.95  3.000
 NPH  C1A  C4A  C4   117.74  3.000
 NPH  C1A  C4A  C5   120.76  3.000
 NPH  C4   C4A  C5   121.50  3.000
 NPH  N10  C10  C1A  118.14  3.000
 NPH  N10  C10  C6A  122.40  3.000
 NPH  C1A  C10  C6A  119.45  3.000
 NPH  H7   C7   C8   119.54  3.000
 NPH  H7   C7   C6A  120.92  3.000
 NPH  C8   C7   C6A  119.54  3.000
 NPH  H4   C4   C3   121.02  3.000
 NPH  H4   C4   C4A  119.75  3.000
 NPH  C3   C4   C4A  119.23  3.000
 NPH  N1   C1A  C10  118.96  3.000
 NPH  N1   C1A  C4A  122.49  3.000
 NPH  C10  C1A  C4A  118.55  3.000
 NPH  C9   N10  C10  118.90  3.000
 NPH  H8   C8   C9   120.29  3.000
 NPH  H8   C8   C7   121.25  3.000
 NPH  C9   C8   C7   118.46  3.000
 NPH  H3   C3   C2   120.12  3.000
 NPH  H3   C3   C4   121.54  3.000
 NPH  C2   C3   C4   118.34  3.000
 NPH  C2   N1   C1A  118.47  3.000
 NPH  H9   C9   C8   119.90  3.000
 NPH  H9   C9   N10  116.69  3.000
 NPH  C8   C9   N10  123.41  3.000
 NPH  HC2  C2   N1   116.59  3.000
 NPH  HC2  C2   C3   119.69  3.000
 NPH  N1   C2   C3   123.72  3.000
 NPH  OXT  C    O    127.11  3.000
 NPH  OXT  C    CA   116.50  3.000
 NPH  O    C    CA   120.80  1.700

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
 NPH  CONST_01  C4   C4A  C5   C6   180.00   0.0  0
 NPH  CONST_02  C1A  C4A  C5   C6     0.00   0.0  0
 NPH  CONST_03  C1A  C10  C6A  C6     0.00   0.0  0
 NPH  CONST_04  N10  C10  C6A  C6   180.00   0.0  0
 NPH  CONST_05  C8   C7   C6A  C6   180.00   0.0  0
 NPH  CONST_06  C10  C6A  C6   C5     0.00   0.0  0
 NPH  CONST_07  C7   C6A  C6   C5   180.00   0.0  0
 NPH  CONST_08  C3   C4   C4A  C5   180.00   0.0  0
 NPH  CONST_09  C10  C1A  C4A  C5     0.00   0.0  0
 NPH  CONST_10  N1   C1A  C4A  C5   180.00   0.0  0
 NPH  CONST_11  C4A  C5   C6   C6A    0.00   0.0  0
 NPH  CONST_12  C4A  C1A  C10  C6A    0.00   0.0  0
 NPH  CONST_13  N1   C1A  C10  C6A  180.00   0.0  0
 NPH  CONST_14  C9   N10  C10  C6A    0.00   0.0  0
 NPH  CONST_15  C9   C8   C7   C6A    0.00   0.0  0
 NPH  CONST_16  C2   C3   C4   C4A    0.00   0.0  0
 NPH  CONST_17  N10  C10  C1A  C4A  180.00   0.0  0
 NPH  CONST_18  C2   N1   C1A  C4A    0.00   0.0  0
 NPH  CONST_19  C8   C7   C6A  C10    0.00   0.0  0
 NPH  CONST_20  C4   C4A  C1A  C10  180.00   0.0  0
 NPH  CONST_21  C2   N1   C1A  C10  180.00   0.0  0
 NPH  CONST_22  C8   C9   N10  C10    0.00   0.0  0
 NPH  CONST_23  C1A  C10  C6A  C7   180.00   0.0  0
 NPH  CONST_24  N10  C10  C6A  C7     0.00   0.0  0
 NPH  CONST_25  N10  C9   C8   C7     0.00   0.0  0
 NPH  CONST_26  N1   C1A  C4A  C4     0.00   0.0  0
 NPH  CONST_27  N1   C2   C3   C4     0.00   0.0  0
 NPH  CONST_28  C3   C4   C4A  C1A    0.00   0.0  0
 NPH  CONST_29  C9   N10  C10  C1A  180.00   0.0  0
 NPH  CONST_30  C3   C2   N1   C1A    0.00   0.0  0
 NPH  CONST_31  N1   C1A  C10  N10    0.00   0.0  0
 NPH  CONST_32  C4A  C5   C6   NZ   180.00   0.0  0
 NPH  CONST_33  C10  C6A  C6   NZ   180.00   0.0  0
 NPH  CONST_34  C7   C6A  C6   NZ     0.00   0.0  0
 NPH  CONST_35  H7   C7   C6A  C6     0.00   0.0  0
 NPH  CONST_36  H4   C4   C4A  C5     0.00   0.0  0
 NPH  CONST_37  H5   C5   C6   C6A  180.00   0.0  0
 NPH  CONST_38  H8   C8   C7   C6A  180.00   0.0  0
 NPH  CONST_39  H3   C3   C4   C4A  180.00   0.0  0
 NPH  CONST_40  H9   C9   N10  C10  180.00   0.0  0
 NPH  CONST_41  HC2  C2   C3   C4   180.00   0.0  0
 NPH  CONST_45  C6   NZ   CE   CD   180.00   0.0  0
 NPH  CONST_46  C6   NZ   CE   OZ     0.00   0.0  0
 NPH  Var_01    CE   CD   SG   CB   169.99  30.0  3
 NPH  Var_02    OZ   CE   CD   SG   -27.87  30.0  3
 NPH  Var_03    HB2  CB   SG   CD    52.81  30.0  1

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
 NPH  chir_01  CA  N  CB  C  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
 NPH  plan-1  NZ   0.020
 NPH  plan-1  C6   0.020
 NPH  plan-1  C5   0.020
 NPH  plan-1  C6A  0.020
 NPH  plan-1  C4A  0.020
 NPH  plan-1  C10  0.020
 NPH  plan-1  C7   0.020
 NPH  plan-1  C4   0.020
 NPH  plan-1  C1A  0.020
 NPH  plan-1  N10  0.020
 NPH  plan-1  C8   0.020
 NPH  plan-1  C3   0.020
 NPH  plan-1  N1   0.020
 NPH  plan-1  C9   0.020
 NPH  plan-1  C2   0.020
 NPH  plan-1  H5   0.020
 NPH  plan-1  H7   0.020
 NPH  plan-1  H4   0.020
 NPH  plan-1  H8   0.020
 NPH  plan-1  H3   0.020
 NPH  plan-1  H9   0.020
 NPH  plan-1  HC2  0.020
 NPH  plan-2  CD   0.020
 NPH  plan-2  CE   0.020
 NPH  plan-2  OZ   0.020
 NPH  plan-2  NZ   0.020
 NPH  plan-2  C6   0.020
 NPH  plan-2  HZ   0.020
 NPH  plan-3  CA   0.020
 NPH  plan-3  C    0.020
 NPH  plan-3  O    0.020
 NPH  plan-3  OXT  0.020

