# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 09:14:37 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: N-({4-[(2-amino-6-ethyl-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidin-5-yl)sulfanyl]phenyl}carbonyl)-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1sc2N=C(N)NC(=O)c2c1Sc3ccc(cc3)C(=O)N[C@@H](CCC(O)=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
 GHC  GHC  'N-({4-[(2-amino-6-ethyl-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidin-5-yl)sulfanyl]phenyl}carbonyl)-L-glutamic acid'  L-peptide  50  32  .  2022-09-22  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_GHC
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
 GHC  C4    C  CR56   0  -0.016   5.0762  -0.2425   0.2309
 GHC  C5    C  CR56   0  -0.006   4.0031   0.0606  -0.5854
 GHC  C6    C  CR6    0   0.536   3.4911  -0.9844  -1.4262
 GHC  N1    N  NR16   0  -0.717   4.2001  -2.1753  -1.2729
 GHC  C3    C  CR5    0  -0.160   4.2978   2.1236   0.4654
 GHC  N3    N  N      0  -0.498   5.7215  -1.4113   0.3348
 GHC  C29   C  CH3    0  -0.654   3.1236   3.5877   2.1239
 GHC  S4    S  S2     0   0.218   5.5497   1.1371   1.1615
 GHC  C2    C  CR6    0   0.701   5.2563  -2.3652  -0.4352
 GHC  O6    O  O      0  -0.451   2.5582  -0.9255  -2.2060
 GHC  C1    C  CR5    0  -0.134   3.5646   1.4180  -0.4372
 GHC  SAT   S  S2     0   0.102   2.2403   2.1444  -1.3283
 GHC  CAZ   C  CR6    0  -0.101   0.8234   1.4103  -0.5755
 GHC  CAJ   C  CR16   0  -0.220   0.8586   0.7667   0.6582
 GHC  CAL   C  CR16   0  -0.265  -0.3082   0.2658   1.2093
 GHC  CAI   C  CR16   0  -0.257  -0.3895   1.5356  -1.2491
 GHC  CAK   C  CR16   0  -0.280  -1.5497   1.0242  -0.6925
 GHC  CBA   C  CR6    0  -0.051  -1.5245   0.3776   0.5415
 GHC  CAX   C  C      0   0.532  -2.7573  -0.1493   1.2009
 GHC  OAE   O  O      0  -0.504  -2.8416  -0.1969   2.4234
 GHC  NAS   N  NH1    0  -0.631  -3.7506  -0.5194   0.3823
 GHC  CAP   C  CH1    0  -0.187  -4.9694  -1.1207   0.8752
 GHC  CAW   C  C      0   0.410  -4.7555  -2.5653   1.3959
 GHC  OAG   O  OC    -1  -0.619  -5.7057  -3.0302   2.0577
 GHC  OAD   O  O      0  -0.599  -3.6943  -3.1391   1.0986
 GHC  CBG   C  CH2    0  -0.448  -6.0344  -1.0957  -0.2218
 GHC  CAN   C  CH2    0  -0.579  -6.4155   0.3048  -0.6738
 GHC  CAV   C  C      0   0.413  -7.5213   0.3798  -1.7420
 GHC  OAF   O  OC    -1  -0.634  -7.8720   1.5299  -2.0825
 GHC  OAC   O  O      0  -0.608  -7.9775  -0.6916  -2.1875
 GHC  H13   H  HCH2   0   0.257   5.0620   3.9526   1.2441
 GHC  H13A  H  HCH2   0   0.257   3.7295   4.1319   0.1281
 GHC  HN1   H  HNR6   0   0.426   3.8882  -2.9481  -1.8473
 GHC  HN2   H  HNH2   0   0.419   5.5414  -4.3081  -1.0438
 GHC  HN2A  H  HNH2   0   0.418   6.6341  -3.7229   0.1500
 GHC  H29   H  HCH3   0   0.232   2.1454   3.2057   1.8326
 GHC  H29A  H  HCH3   0   0.229   3.4777   2.9983   2.9700
 GHC  H29B  H  HCH3   0   0.241   2.9982   4.6167   2.4609
 GHC  HAJ   H  HCR6   0   0.271   1.7901   0.6605   1.1983
 GHC  HAL   H  HCR6   0   0.260  -0.2678  -0.2221   2.1742
 GHC  HAI   H  HCR6   0   0.269  -0.4349   2.0390  -2.2069
 GHC  HAK   H  HCR6   0   0.259  -2.4814   1.1593  -1.2277
 GHC  HNAS  H  HNH1   0   0.391  -3.5308  -0.6648  -0.5906
 GHC  HAP   H  HCH1   0   0.227  -5.3263  -0.5126   1.7121
 GHC  HBG   H  HCH2   0   0.211  -5.6869  -1.6863  -1.0765
 GHC  HBGA  H  HCH2   0   0.228  -6.9155  -1.6102   0.1620
 GHC  HAN   H  HCH2   0   0.219  -6.7352   0.8945   0.1936
 GHC  HANA  H  HCH2   0   0.222  -5.5391   0.8339  -1.0637
 GHC  C13   C  CH2    0  -0.494   4.1020   3.5224   0.9522
 GHC  N2    N  NH2    0  -0.831   5.8081  -3.5793  -0.4048

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
 GHC  N3   C4    single    1.339  0.020  1.339
 GHC  C4   C5    aromatic  1.382  0.020  1.382
 GHC  C4   S4    aromatic  1.730  0.020  1.730
 GHC  C6   C5    single    1.436  0.020  1.436
 GHC  C5   C1    aromatic  1.434  0.020  1.434
 GHC  N1   C6    single    1.394  0.020  1.394
 GHC  O6   C6    double    1.217  0.020  1.217
 GHC  C3   C13   single    1.494  0.020  1.494
 GHC  C13  C29   single    1.528  0.020  1.528
 GHC  C13  H13   single    0.970  0.020  1.090
 GHC  C13  H13A  single    0.970  0.020  1.090
 GHC  C2   N1    single    1.361  0.020  1.361
 GHC  N1   HN1   single    0.860  0.020  1.020
 GHC  N2   C2    single    1.334  0.020  1.334
 GHC  N2   HN2   single    0.860  0.020  1.020
 GHC  N2   HN2A  single    0.860  0.020  1.020
 GHC  S4   C3    aromatic  1.739  0.020  1.739
 GHC  C1   C3    aromatic  1.360  0.020  1.360
 GHC  C2   N3    double    1.311  0.020  1.311
 GHC  C29  H29   single    0.970  0.020  1.090
 GHC  C29  H29A  single    0.970  0.020  1.090
 GHC  C29  H29B  single    0.970  0.020  1.090
 GHC  C1   SAT   single    1.754  0.020  1.754
 GHC  CAZ  SAT   single    1.765  0.020  1.765
 GHC  CAJ  CAZ   aromatic  1.392  0.020  1.392
 GHC  CAZ  CAI   aromatic  1.393  0.020  1.393
 GHC  CAL  CAJ   aromatic  1.384  0.020  1.384
 GHC  CAJ  HAJ   single    0.930  0.020  1.080
 GHC  CAL  CBA   aromatic  1.392  0.020  1.392
 GHC  CAL  HAL   single    0.930  0.020  1.080
 GHC  CAK  CAI   aromatic  1.385  0.020  1.385
 GHC  CAI  HAI   single    0.930  0.020  1.080
 GHC  CBA  CAK   aromatic  1.393  0.020  1.393
 GHC  CAK  HAK   single    0.930  0.020  1.080
 GHC  CBA  CAX   single    1.494  0.020  1.494
 GHC  NAS  CAX   single    1.339  0.020  1.339
 GHC  CAX  OAE   double    1.226  0.020  1.226
 GHC  CAP  NAS   single    1.446  0.020  1.446
 GHC  NAS  HNAS  single    0.890  0.020  1.040
 GHC  CBG  CAP   single    1.529  0.020  1.529
 GHC  CAW  CAP   single    1.550  0.020  1.550
 GHC  CAP  HAP   single    0.970  0.020  1.090
 GHC  OAD  CAW   deloc     1.242  0.020  1.242
 GHC  CAW  OAG   deloc     1.248  0.020  1.248
 GHC  CAN  CBG   single    1.520  0.020  1.520
 GHC  CBG  HBG   single    0.970  0.020  1.090
 GHC  CBG  HBGA  single    0.970  0.020  1.090
 GHC  CAV  CAN   single    1.539  0.020  1.539
 GHC  CAN  HAN   single    0.970  0.020  1.090
 GHC  CAN  HANA  single    0.970  0.020  1.090
 GHC  OAC  CAV   deloc     1.247  0.020  1.247
 GHC  CAV  OAF   deloc     1.250  0.020  1.250

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
 GHC  S4    C4   N3    121.49  3.000
 GHC  S4    C4   C5    110.81  3.000
 GHC  N3    C4   C5    127.70  3.000
 GHC  C1    C5   C6    129.82  3.000
 GHC  C1    C5   C4    112.58  3.000
 GHC  C6    C5   C4    117.59  3.000
 GHC  O6    C6   N1    120.10  3.000
 GHC  O6    C6   C5    127.83  3.000
 GHC  N1    C6   C5    112.08  3.000
 GHC  HN1   N1   C2    118.80  3.000
 GHC  HN1   N1   C6    115.66  3.000
 GHC  C2    N1   C6    125.54  3.000
 GHC  C1    C3   S4    111.06  3.000
 GHC  C1    C3   C13   129.14  3.000
 GHC  S4    C3   C13   119.67  3.000
 GHC  C2    N3   C4    114.73  3.000
 GHC  H29B  C29  H29A  107.93  3.000
 GHC  H29B  C29  H29   108.08  3.000
 GHC  H29A  C29  H29   108.03  3.000
 GHC  H29B  C29  C13   110.56  3.000
 GHC  H29A  C29  C13   111.35  3.000
 GHC  H29   C29  C13   110.78  3.000
 GHC  C3    S4   C4     92.29  3.000
 GHC  N3    C2   N2    120.13  3.000
 GHC  N3    C2   N1    122.36  3.000
 GHC  N2    C2   N1    117.51  3.000
 GHC  SAT   C1   C3    121.96  3.000
 GHC  SAT   C1   C5    124.78  3.000
 GHC  C3    C1   C5    113.25  3.000
 GHC  CAZ   SAT  C1    102.55  3.000
 GHC  CAI   CAZ  CAJ   119.48  3.000
 GHC  CAI   CAZ  SAT   117.09  3.000
 GHC  CAJ   CAZ  SAT   123.38  3.000
 GHC  HAJ   CAJ  CAL   119.44  3.000
 GHC  HAJ   CAJ  CAZ   120.64  3.000
 GHC  CAL   CAJ  CAZ   119.93  3.000
 GHC  HAL   CAL  CBA   119.77  3.000
 GHC  HAL   CAL  CAJ   119.13  3.000
 GHC  CBA   CAL  CAJ   121.10  3.000
 GHC  HAI   CAI  CAK   119.47  3.000
 GHC  HAI   CAI  CAZ   120.40  3.000
 GHC  CAK   CAI  CAZ   120.13  3.000
 GHC  HAK   CAK  CBA   120.74  3.000
 GHC  HAK   CAK  CAI   118.43  3.000
 GHC  CBA   CAK  CAI   120.81  3.000
 GHC  CAX   CBA  CAK   122.66  3.000
 GHC  CAX   CBA  CAL   118.75  3.000
 GHC  CAK   CBA  CAL   118.54  3.000
 GHC  NAS   CAX  OAE   123.20  3.000
 GHC  OAE   CAX  CBA   120.69  3.000
 GHC  NAS   CAX  CBA   116.08  3.000
 GHC  HNAS  NAS  CAP   116.93  3.000
 GHC  HNAS  NAS  CAX   117.91  3.000
 GHC  CAP   NAS  CAX   122.13  3.000
 GHC  HAP   CAP  CBG   108.21  3.000
 GHC  HAP   CAP  CAW   107.81  3.000
 GHC  CBG   CAP  CAW   110.62  3.000
 GHC  HAP   CAP  NAS   107.74  3.000
 GHC  CAW   CAP  NAS   112.69  3.000
 GHC  CBG   CAP  NAS   109.62  3.000
 GHC  OAD   CAW  OAG   127.25  3.000
 GHC  OAG   CAW  CAP   114.85  3.000
 GHC  OAD   CAW  CAP   117.89  3.000
 GHC  HBGA  CBG  HBG   106.05  3.000
 GHC  HBGA  CBG  CAN   109.68  3.000
 GHC  HBG   CBG  CAN   110.14  3.000
 GHC  HBGA  CBG  CAP   107.61  3.000
 GHC  HBG   CBG  CAP   109.27  3.000
 GHC  CAN   CBG  CAP   113.76  3.000
 GHC  HANA  CAN  HAN   104.78  3.000
 GHC  HANA  CAN  CAV   107.71  3.000
 GHC  HAN   CAN  CAV   108.26  3.000
 GHC  HANA  CAN  CBG   110.50  3.000
 GHC  HAN   CAN  CBG   109.47  3.000
 GHC  CAV   CAN  CBG   115.55  3.000
 GHC  OAC   CAV  OAF   126.22  3.000
 GHC  OAF   CAV  CAN   115.82  3.000
 GHC  OAC   CAV  CAN   117.97  3.000
 GHC  H13A  C13  H13   106.38  3.000
 GHC  H13A  C13  C29   109.69  3.000
 GHC  H13   C13  C29   109.95  3.000
 GHC  H13A  C13  C3    108.78  3.000
 GHC  H13   C13  C3    109.93  3.000
 GHC  C29   C13  C3    111.96  3.000
 GHC  HN2A  N2   HN2   117.73  3.000
 GHC  HN2A  N2   C2    118.85  3.000
 GHC  HN2   N2   C2    122.38  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
 GHC  CONST_01  C3    C1   C5   C4      0.00   0.0  0
 GHC  CONST_02  C1    C3   S4   C4      0.00   0.0  0
 GHC  CONST_03  C3    S4   C4   C5      0.00   0.0  0
 GHC  CONST_04  S4    C3   C1   C5      0.00   0.0  0
 GHC  CONST_05  C1    C5   C4   S4      0.00   0.0  0
 GHC  CONST_06  CBA   CAL  CAJ  CAZ     0.00   0.0  0
 GHC  CONST_07  CBA   CAK  CAI  CAZ     0.00   0.0  0
 GHC  CONST_08  CAK   CAI  CAZ  CAJ     0.00   0.0  0
 GHC  CONST_09  CAK   CBA  CAL  CAJ     0.00   0.0  0
 GHC  CONST_10  CAI   CAZ  CAJ  CAL     0.00   0.0  0
 GHC  CONST_11  CAI   CAK  CBA  CAL     0.00   0.0  0
 GHC  CONST_12  N1    C2   N3   C4      0.00   0.0  0
 GHC  CONST_13  C2    N1   C6   C5      0.00   0.0  0
 GHC  CONST_14  N3    C2   N1   C6      0.00   0.0  0
 GHC  CONST_15  SAT   C1   C5   C4    180.00   0.0  0
 GHC  CONST_16  C13   C3   S4   C4    180.00   0.0  0
 GHC  CONST_17  C13   C3   C1   C5    180.00   0.0  0
 GHC  CONST_18  SAT   C1   C5   C6      0.00   0.0  0
 GHC  CONST_19  SAT   C1   C3   S4    180.00   0.0  0
 GHC  CONST_20  CAL   CAJ  CAZ  SAT   180.00   0.0  0
 GHC  CONST_21  CAK   CAI  CAZ  SAT   180.00   0.0  0
 GHC  CONST_22  CAX   CBA  CAL  CAJ   180.00   0.0  0
 GHC  CONST_23  CAX   CBA  CAK  CAI   180.00   0.0  0
 GHC  CONST_24  N2    C2   N3   C4    180.00   0.0  0
 GHC  CONST_25  N2    C2   N1   C6    180.00   0.0  0
 GHC  CONST_26  O6    C6   N1   C2    180.00   0.0  0
 GHC  CONST_27  HAL   CAL  CAJ  CAZ   180.00   0.0  0
 GHC  CONST_28  HAK   CAK  CAI  CAZ   180.00   0.0  0
 GHC  CONST_29  HAI   CAI  CAZ  CAJ   180.00   0.0  0
 GHC  CONST_30  HAJ   CAJ  CAZ  CAI   180.00   0.0  0
 GHC  CONST_31  HN1   N1   C6   C5    180.00   0.0  0
 GHC  CONST_32  HN2   N2   C2   N1      0.00   0.0  0
 GHC  CONST_33  HN2A  N2   C2   N1    180.00   0.0  0
 GHC  CONST_34  CAP   NAS  CAX  CBA   180.00   0.0  0
 GHC  CONST_36  CAP   NAS  CAX  OAE     0.00   0.0  0
 GHC  Var_01    CAJ   CAZ  SAT  C1     16.74  30.0  2
 GHC  Var_02    S4    C3   C13  C29   -89.51  30.0  1
 GHC  Var_03    NAS   CAX  CBA  CAL  -153.97  30.0  2
 GHC  Var_04    H29   C29  C13  C3    -60.25  30.0  3
 GHC  Var_05    CAV   CAN  CBG  CAP  -177.90  30.0  1
 GHC  Var_06    OAC   CAV  CAN  CBG    -2.70  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
 GHC  chir_01  CAP  NAS  CBG  CAW  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
 GHC  plan-1  SAT   0.020
 GHC  plan-1  CAZ   0.020
 GHC  plan-1  CAJ   0.020
 GHC  plan-1  CAL   0.020
 GHC  plan-1  CAI   0.020
 GHC  plan-1  CAK   0.020
 GHC  plan-1  CBA   0.020
 GHC  plan-1  CAX   0.020
 GHC  plan-1  HAJ   0.020
 GHC  plan-1  HAL   0.020
 GHC  plan-1  HAI   0.020
 GHC  plan-1  HAK   0.020
 GHC  plan-2  C4    0.020
 GHC  plan-2  C5    0.020
 GHC  plan-2  C6    0.020
 GHC  plan-2  N1    0.020
 GHC  plan-2  C3    0.020
 GHC  plan-2  N3    0.020
 GHC  plan-2  S4    0.020
 GHC  plan-2  C2    0.020
 GHC  plan-2  O6    0.020
 GHC  plan-2  C1    0.020
 GHC  plan-2  SAT   0.020
 GHC  plan-2  HN1   0.020
 GHC  plan-2  HN2   0.020
 GHC  plan-2  HN2A  0.020
 GHC  plan-2  C13   0.020
 GHC  plan-2  N2    0.020
 GHC  plan-3  CBA   0.020
 GHC  plan-3  CAX   0.020
 GHC  plan-3  OAE   0.020
 GHC  plan-3  NAS   0.020
 GHC  plan-3  CAP   0.020
 GHC  plan-3  HNAS  0.020
 GHC  plan-4  CAP   0.020
 GHC  plan-4  CAW   0.020
 GHC  plan-4  OAG   0.020
 GHC  plan-4  OAD   0.020
 GHC  plan-5  CAN   0.020
 GHC  plan-5  CAV   0.020
 GHC  plan-5  OAF   0.020
 GHC  plan-5  OAC   0.020

