# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 20:29:36 2022
#   Inital geometry file: a 79 line input string
#   Ligand name: N-(quinoxalin-2-ylcarbonyl)-D-serine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](NC(=O)c1cnc2ccccc2n1)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
 QDS  QDS  N-(quinoxalin-2-ylcarbonyl)-D-serine  D-peptide  29  19  .  2016-04-26  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QDS
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
 QDS  N1   N  N      0  -0.414  -6.5921  69.6379  23.5905
 QDS  C2   C  CR6    0   0.053  -5.9590  70.4686  22.8111
 QDS  C3   C  CR16   0  -0.086  -5.0895  71.4609  23.3326
 QDS  N4   N  N      0  -0.379  -4.8777  71.5879  24.6110
 QDS  C5   C  CR16   0  -0.295  -5.3163  70.8152  26.8310
 QDS  C6   C  CR16   0  -0.247  -5.9615  69.9434  27.6652
 QDS  C7   C  CR16   0  -0.248  -6.8308  68.9573  27.1481
 QDS  C8   C  CR16   0  -0.303  -7.0461  68.8544  25.8014
 QDS  C9   C  CR66   0   0.243  -6.3900  69.7403  24.9202
 QDS  C10  C  CR66   0   0.226  -5.5181  70.7298  25.4378
 QDS  C11  C  C      0   0.532  -6.1407  70.3587  21.3218
 QDS  O12  O  O      0  -0.481  -5.4990  71.0875  20.5751
 QDS  N    N  NH1    0  -0.621  -7.0280  69.4445  20.9405
 QDS  CA   C  CH1    0  -0.255  -7.2972  69.0850  19.5684
 QDS  C    C  C      0   0.423  -6.5143  67.7962  19.1634
 QDS  O    O  O      0  -0.599  -7.0962  67.0413  18.3547
 QDS  CB   C  CH2    0  -0.173  -8.7959  68.9624  19.3294
 QDS  OG   O  OH1    0  -0.673  -9.3590  67.8415  19.9709
 QDS  OXT  O  OC    -1  -0.575  -5.3899  67.6503  19.6619
 QDS  H3   H  HCR6   0   0.278  -4.5780  72.1439  22.6662
 QDS  H5   H  HCR6   0   0.272  -4.6469  71.5740  27.2148
 QDS  H6   H  HCR6   0   0.272  -5.8059  70.0043  28.7342
 QDS  H7   H  HCR6   0   0.272  -7.3252  68.2765  27.8281
 QDS  H8   H  HCR6   0   0.272  -7.7110  68.1065  25.3893
 QDS  H    H  HNH1   0   0.396  -7.4542  68.8866  21.6670
 QDS  HA   H  HCH1   0   0.255  -6.9302  69.9015  18.9393
 QDS  HB2  H  HCH2   0   0.219  -9.3013  69.8466  19.7246
 QDS  HB3  H  HCH2   0   0.200  -8.9793  68.9474  18.2495
 QDS  HG   H  HOH1   0   0.437  -8.9368  67.0767  19.5583

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
 QDS  N1   C2   aromatic  1.303  0.020  1.303
 QDS  N1   C9   aromatic  1.349  0.020  1.349
 QDS  C2   C3   aromatic  1.419  0.020  1.419
 QDS  C2   C11  single    1.504  0.020  1.504
 QDS  C3   N4   aromatic  1.302  0.020  1.302
 QDS  N4   C10  aromatic  1.353  0.020  1.353
 QDS  C5   C6   aromatic  1.368  0.020  1.368
 QDS  C5   C10  aromatic  1.410  0.020  1.410
 QDS  C6   C7   aromatic  1.413  0.020  1.413
 QDS  C7   C8   aromatic  1.368  0.020  1.368
 QDS  C8   C9   aromatic  1.411  0.020  1.411
 QDS  C9   C10  aromatic  1.417  0.020  1.417
 QDS  C11  O12  double    1.225  0.020  1.225
 QDS  C11  N    single    1.330  0.020  1.330
 QDS  N    CA   single    1.457  0.020  1.457
 QDS  CA   C    single    1.561  0.020  1.561
 QDS  CA   CB   single    1.537  0.020  1.537
 QDS  C    O    deloc     1.263  0.020  1.263
 QDS  C    OXT  deloc     1.238  0.020  1.238
 QDS  CB   OG   single    1.409  0.020  1.409
 QDS  C3   H3   single    0.930  0.020  1.080
 QDS  C5   H5   single    0.930  0.020  1.080
 QDS  C6   H6   single    0.930  0.020  1.080
 QDS  C7   H7   single    0.930  0.020  1.080
 QDS  C8   H8   single    0.930  0.020  1.080
 QDS  N    H    single    0.860  0.020  0.860
 QDS  CA   HA   single    0.970  0.020  0.970
 QDS  CB   HB2  single    0.970  0.020  1.090
 QDS  CB   HB3  single    0.970  0.020  1.090
 QDS  OG   HG   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
 QDS  C9   N1   C2   117.93  3.000
 QDS  C11  C2   C3   119.28  3.000
 QDS  C11  C2   N1   119.13  3.000
 QDS  C3   C2   N1   121.58  3.000
 QDS  H3   C3   N4   117.77  3.000
 QDS  H3   C3   C2   120.30  3.000
 QDS  N4   C3   C2   121.93  3.000
 QDS  C10  N4   C3   117.47  3.000
 QDS  H5   C5   C10  118.77  3.000
 QDS  H5   C5   C6   121.48  3.000
 QDS  C10  C5   C6   119.75  3.000
 QDS  H6   C6   C7   119.31  3.000
 QDS  H6   C6   C5   119.91  3.000
 QDS  C7   C6   C5   120.78  3.000
 QDS  H7   C7   C8   119.97  3.000
 QDS  H7   C7   C6   119.37  3.000
 QDS  C8   C7   C6   120.65  3.000
 QDS  H8   C8   C9   118.79  3.000
 QDS  H8   C8   C7   121.58  3.000
 QDS  C9   C8   C7   119.63  3.000
 QDS  C10  C9   C8   119.76  3.000
 QDS  C10  C9   N1   120.35  3.000
 QDS  C8   C9   N1   119.88  3.000
 QDS  C9   C10  C5   119.42  3.000
 QDS  C9   C10  N4   120.74  3.000
 QDS  C5   C10  N4   119.84  3.000
 QDS  N    C11  O12  125.72  3.000
 QDS  N    C11  C2   114.50  3.000
 QDS  O12  C11  C2   119.78  3.000
 QDS  H    N    CA   107.09  3.000
 QDS  H    N    C11  117.06  3.000
 QDS  CA   N    C11  124.61  3.000
 QDS  HA   CA   CB   107.69  3.000
 QDS  HA   CA   C    106.38  3.000
 QDS  CB   CA   C    108.98  3.000
 QDS  HA   CA   N    106.89  3.000
 QDS  CB   CA   N    112.16  3.000
 QDS  C    CA   N    114.36  3.000
 QDS  OXT  C    O    127.72  3.000
 QDS  OXT  C    CA   117.38  3.000
 QDS  O    C    CA   118.49  3.000
 QDS  HB3  CB   HB2  106.87  3.000
 QDS  HB3  CB   OG   111.78  3.000
 QDS  HB2  CB   OG   107.12  3.000
 QDS  HB3  CB   CA   108.70  3.000
 QDS  HB2  CB   CA   109.48  3.000
 QDS  OG   CB   CA   112.71  3.000
 QDS  HG   OG   CB   105.11  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
 QDS  CONST_01  N4   C3   C2   N1      0.00   0.0  0
 QDS  CONST_02  C7   C8   C9   N1    180.00   0.0  0
 QDS  CONST_03  N4   C10  C9   N1      0.00   0.0  0
 QDS  CONST_04  C5   C10  C9   N1    180.00   0.0  0
 QDS  CONST_05  C8   C9   N1   C2    180.00   0.0  0
 QDS  CONST_06  C10  C9   N1   C2      0.00   0.0  0
 QDS  CONST_07  C10  N4   C3   C2      0.00   0.0  0
 QDS  CONST_08  C9   N1   C2   C3      0.00   0.0  0
 QDS  CONST_09  C5   C10  N4   C3    180.00   0.0  0
 QDS  CONST_10  C9   C10  N4   C3      0.00   0.0  0
 QDS  CONST_11  C6   C5   C10  N4    180.00   0.0  0
 QDS  CONST_12  C8   C9   C10  N4    180.00   0.0  0
 QDS  CONST_13  C8   C7   C6   C5      0.00   0.0  0
 QDS  CONST_14  C8   C9   C10  C5      0.00   0.0  0
 QDS  CONST_15  C9   C10  C5   C6      0.00   0.0  0
 QDS  CONST_16  C9   C8   C7   C6      0.00   0.0  0
 QDS  CONST_17  C10  C5   C6   C7      0.00   0.0  0
 QDS  CONST_18  C10  C9   C8   C7      0.00   0.0  0
 QDS  CONST_19  C11  C2   C3   N4    180.00   0.0  0
 QDS  CONST_20  C11  C2   N1   C9    180.00   0.0  0
 QDS  CONST_21  H3   C3   C2   N1    180.00   0.0  0
 QDS  CONST_22  H8   C8   C9   N1      0.00   0.0  0
 QDS  CONST_23  H5   C5   C10  N4      0.00   0.0  0
 QDS  CONST_24  H7   C7   C6   C5    180.00   0.0  0
 QDS  CONST_25  H6   C6   C7   C8    180.00   0.0  0
 QDS  CONST_26  CA   N    C11  C2    180.00   0.0  0
 QDS  CONST_27  H    N    C11  C2      0.00   0.0  0
 QDS  CONST_28  CA   N    C11  O12     0.00   0.0  0
 QDS  Var_01    O12  C11  C2   N1   -176.25  30.0  2

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
 QDS  chir_01  CA  N  C  CB  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
 QDS  plan-1  N1   0.020
 QDS  plan-1  C2   0.020
 QDS  plan-1  C3   0.020
 QDS  plan-1  N4   0.020
 QDS  plan-1  C5   0.020
 QDS  plan-1  C6   0.020
 QDS  plan-1  C7   0.020
 QDS  plan-1  C8   0.020
 QDS  plan-1  C9   0.020
 QDS  plan-1  C10  0.020
 QDS  plan-1  C11  0.020
 QDS  plan-1  H3   0.020
 QDS  plan-1  H5   0.020
 QDS  plan-1  H6   0.020
 QDS  plan-1  H7   0.020
 QDS  plan-1  H8   0.020
 QDS  plan-2  C2   0.020
 QDS  plan-2  C11  0.020
 QDS  plan-2  O12  0.020
 QDS  plan-2  N    0.020
 QDS  plan-2  CA   0.020
 QDS  plan-2  H    0.020
 QDS  plan-3  CA   0.020
 QDS  plan-3  C    0.020
 QDS  plan-3  O    0.020
 QDS  plan-3  OXT  0.020

