# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 09:28:33 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: N-({4-[(2-amino-6-methyl-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: Cc1sc2N=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
 GHW  GHW  'N-({4-[(2-amino-6-methyl-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidin-5-yl)sulfanyl]phenyl}carbonyl)-L-glutamic acid'  L-peptide  47  31  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT (side chain)
;

data_comp_GHW
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
 GHW  C4    C  CR56   0  -0.016   5.2336  -0.1754   0.2819
 GHW  C5    C  CR56   0  -0.007   4.1270   0.2146  -0.4465
 GHW  C6    C  CR6    0   0.536   3.5594  -0.7390  -1.3566
 GHW  N1    N  NR16   0  -0.717   4.2578  -1.9462  -1.3542
 GHW  C3    C  CR5    0  -0.171   4.5000   2.1652   0.7810
 GHW  N3    N  N      0  -0.499   5.8634  -1.3564   0.2451
 GHW  S4    S  S2     0   0.214   5.7722   1.1033   1.3162
 GHW  C2    C  CR6    0   0.701   5.3503  -2.2260  -0.5920
 GHW  O6    O  O      0  -0.449   2.5903  -0.5950  -2.0791
 GHW  C1    C  CR5    0  -0.126   3.7174   1.5584  -0.1519
 GHW  SAT   S  S2     0   0.097   2.3955   2.3885  -0.9497
 GHW  CAZ   C  CR6    0  -0.093   0.9753   1.5744  -0.2922
 GHW  CAJ   C  CR16   0  -0.257  -0.2242   1.7304  -0.9819
 GHW  CAL   C  CR16   0  -0.280  -1.3870   1.1612  -0.4909
 GHW  CAI   C  CR16   0  -0.219   0.9961   0.8446   0.8922
 GHW  CAK   C  CR16   0  -0.263  -0.1719   0.2813   1.3759
 GHW  CBA   C  CR6    0  -0.051  -1.3761   0.4223   0.6907
 GHW  CAX   C  C      0   0.533  -2.6107  -0.1773   1.2820
 GHW  OAE   O  O      0  -0.505  -2.7057  -0.3453   2.4932
 GHW  NAS   N  NH1    0  -0.631  -3.5924  -0.4763   0.4218
 GHW  CAP   C  CH1    0  -0.189  -4.8088  -1.1356   0.8401
 GHW  CAW   C  C      0   0.412  -4.5846  -2.6280   1.1974
 GHW  OAG   O  O      0  -0.599  -3.5050  -3.1482   0.8688
 GHW  OAD   O  OC    -1  -0.619  -5.5443  -3.1794   1.7734
 GHW  CBG   C  CH2    0  -0.447  -5.8739  -0.9942  -0.2484
 GHW  CAN   C  CH2    0  -0.577  -6.2404   0.4483  -0.5594
 GHW  CAV   C  C      0   0.412  -7.3521   0.6434  -1.6061
 GHW  OXT   O  OC    -1  -0.634  -7.6366   1.8285  -1.8822
 GHW  OAC   O  O      0  -0.608  -7.8813  -0.3738  -2.0957
 GHW  H13   H  HCH3   0   0.259   4.4937   3.5237   2.4360
 GHW  H13A  H  HCH3   0   0.262   5.1990   4.1821   0.9650
 GHW  H13B  H  HCH3   0   0.260   3.4511   3.9864   1.0879
 GHW  HN1   H  HNR6   0   0.426   3.9066  -2.6575  -1.9829
 GHW  HN2   H  HNH2   0   0.418   5.5050  -4.1474  -1.3080
 GHW  HN2A  H  HNH2   0   0.418   6.6769  -3.6826  -0.1354
 GHW  HAJ   H  HCR6   0   0.268  -0.2570   2.3012  -1.9016
 GHW  HAL   H  HCR6   0   0.255  -2.3083   1.3217  -1.0368
 GHW  HAI   H  HCR6   0   0.267   1.9184   0.7197   1.4443
 GHW  HAK   H  HCR6   0   0.259  -0.1438  -0.2767   2.3025
 GHW  HNAS  H  HNH1   0   0.391  -3.3636  -0.5199  -0.5587
 GHW  HAP   H  HCH1   0   0.228  -5.1705  -0.6265   1.7384
 GHW  HBG   H  HCH2   0   0.211  -5.5327  -1.5019  -1.1572
 GHW  HBGA  H  HCH2   0   0.228  -6.7590  -1.5351   0.0867
 GHW  HAN   H  HCH2   0   0.220  -6.5498   0.9524   0.3642
 GHW  HANA  H  HCH2   0   0.219  -5.3597   1.0033  -0.8999
 GHW  C13   C  CH3    0  -0.709   4.4073   3.5369   1.3493
 GHW  N2    N  NH2    0  -0.831   5.9078  -3.4293  -0.7315

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
 GHW  N3   C4    single    1.339  0.020  1.339
 GHW  C4   C5    aromatic  1.381  0.020  1.381
 GHW  C4   S4    aromatic  1.731  0.020  1.731
 GHW  C6   C5    single    1.435  0.020  1.435
 GHW  C5   C1    aromatic  1.435  0.020  1.435
 GHW  N1   C6    single    1.395  0.020  1.395
 GHW  C6   O6    double    1.217  0.020  1.217
 GHW  C3   C13   single    1.488  0.020  1.488
 GHW  C13  H13   single    0.970  0.020  1.090
 GHW  C13  H13A  single    0.970  0.020  1.090
 GHW  C13  H13B  single    0.970  0.020  1.090
 GHW  C2   N1    single    1.361  0.020  1.361
 GHW  N1   HN1   single    0.860  0.020  1.020
 GHW  N2   C2    single    1.334  0.020  1.334
 GHW  N2   HN2   single    0.860  0.020  1.020
 GHW  N2   HN2A  single    0.860  0.020  1.020
 GHW  S4   C3    aromatic  1.741  0.020  1.741
 GHW  C1   C3    aromatic  1.360  0.020  1.360
 GHW  C2   N3    double    1.312  0.020  1.312
 GHW  C1   SAT   single    1.753  0.020  1.753
 GHW  CAZ  SAT   single    1.764  0.020  1.764
 GHW  CAI  CAZ   aromatic  1.391  0.020  1.391
 GHW  CAZ  CAJ   aromatic  1.392  0.020  1.392
 GHW  CAL  CAJ   aromatic  1.385  0.020  1.385
 GHW  CAJ  HAJ   single    0.930  0.020  1.080
 GHW  CBA  CAL   aromatic  1.394  0.020  1.394
 GHW  CAL  HAL   single    0.930  0.020  1.080
 GHW  CAK  CAI   aromatic  1.384  0.020  1.384
 GHW  CAI  HAI   single    0.930  0.020  1.080
 GHW  CAK  CBA   aromatic  1.393  0.020  1.393
 GHW  CAK  HAK   single    0.930  0.020  1.080
 GHW  CAX  CBA   single    1.494  0.020  1.494
 GHW  NAS  CAX   single    1.339  0.020  1.339
 GHW  CAX  OAE   double    1.226  0.020  1.226
 GHW  CAP  NAS   single    1.445  0.020  1.445
 GHW  NAS  HNAS  single    0.890  0.020  1.040
 GHW  CBG  CAP   single    1.529  0.020  1.529
 GHW  CAW  CAP   single    1.551  0.020  1.551
 GHW  CAP  HAP   single    0.970  0.020  1.090
 GHW  OAG  CAW   deloc     1.243  0.020  1.243
 GHW  CAW  OAD   deloc     1.248  0.020  1.248
 GHW  CAN  CBG   single    1.520  0.020  1.520
 GHW  CBG  HBG   single    0.970  0.020  1.090
 GHW  CBG  HBGA  single    0.970  0.020  1.090
 GHW  CAV  CAN   single    1.539  0.020  1.539
 GHW  CAN  HAN   single    0.970  0.020  1.090
 GHW  CAN  HANA  single    0.970  0.020  1.090
 GHW  OAC  CAV   deloc     1.247  0.020  1.247
 GHW  CAV  OXT   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
 GHW  S4    C4   N3    121.45  3.000
 GHW  S4    C4   C5    110.85  3.000
 GHW  N3    C4   C5    127.70  3.000
 GHW  C1    C5   C6    129.74  3.000
 GHW  C1    C5   C4    112.63  3.000
 GHW  C6    C5   C4    117.62  3.000
 GHW  O6    C6   N1    120.14  3.000
 GHW  O6    C6   C5    127.78  3.000
 GHW  N1    C6   C5    112.08  3.000
 GHW  HN1   N1   C2    118.81  3.000
 GHW  HN1   N1   C6    115.68  3.000
 GHW  C2    N1   C6    125.51  3.000
 GHW  C1    C3   S4    111.04  3.000
 GHW  C1    C3   C13   129.59  3.000
 GHW  S4    C3   C13   119.36  3.000
 GHW  C2    N3   C4    114.72  3.000
 GHW  C3    S4   C4     92.26  3.000
 GHW  N3    C2   N2    120.10  3.000
 GHW  N3    C2   N1    122.35  3.000
 GHW  N2    C2   N1    117.55  3.000
 GHW  SAT   C1   C3    122.32  3.000
 GHW  SAT   C1   C5    124.41  3.000
 GHW  C3    C1   C5    113.21  3.000
 GHW  CAZ   SAT  C1    102.65  3.000
 GHW  CAI   CAZ  CAJ   119.56  3.000
 GHW  CAJ   CAZ  SAT   117.21  3.000
 GHW  CAI   CAZ  SAT   123.18  3.000
 GHW  HAJ   CAJ  CAL   119.50  3.000
 GHW  HAJ   CAJ  CAZ   120.39  3.000
 GHW  CAL   CAJ  CAZ   120.11  3.000
 GHW  HAL   CAL  CBA   120.84  3.000
 GHW  HAL   CAL  CAJ   118.34  3.000
 GHW  CBA   CAL  CAJ   120.81  3.000
 GHW  HAI   CAI  CAK   119.61  3.000
 GHW  HAI   CAI  CAZ   120.50  3.000
 GHW  CAK   CAI  CAZ   119.89  3.000
 GHW  HAK   CAK  CBA   119.74  3.000
 GHW  HAK   CAK  CAI   119.15  3.000
 GHW  CBA   CAK  CAI   121.11  3.000
 GHW  CAX   CBA  CAK   118.62  3.000
 GHW  CAX   CBA  CAL   122.81  3.000
 GHW  CAK   CBA  CAL   118.52  3.000
 GHW  NAS   CAX  OAE   123.16  3.000
 GHW  OAE   CAX  CBA   120.64  3.000
 GHW  NAS   CAX  CBA   116.17  3.000
 GHW  HNAS  NAS  CAP   116.93  3.000
 GHW  HNAS  NAS  CAX   117.92  3.000
 GHW  CAP   NAS  CAX   122.20  3.000
 GHW  HAP   CAP  CBG   108.12  3.000
 GHW  HAP   CAP  CAW   107.84  3.000
 GHW  CBG   CAP  CAW   110.71  3.000
 GHW  HAP   CAP  NAS   107.67  3.000
 GHW  CAW   CAP  NAS   112.58  3.000
 GHW  CBG   CAP  NAS   109.75  3.000
 GHW  OAD   CAW  OAG   127.25  3.000
 GHW  OAD   CAW  CAP   114.87  3.000
 GHW  OAG   CAW  CAP   117.87  3.000
 GHW  HBGA  CBG  HBG   106.14  3.000
 GHW  HBGA  CBG  CAN   109.75  3.000
 GHW  HBG   CBG  CAN   110.19  3.000
 GHW  HBGA  CBG  CAP   107.51  3.000
 GHW  HBG   CBG  CAP   109.30  3.000
 GHW  CAN   CBG  CAP   113.65  3.000
 GHW  HANA  CAN  HAN   104.82  3.000
 GHW  HANA  CAN  CAV   107.76  3.000
 GHW  HAN   CAN  CAV   108.09  3.000
 GHW  HANA  CAN  CBG   110.52  3.000
 GHW  HAN   CAN  CBG   109.38  3.000
 GHW  CAV   CAN  CBG   115.68  3.000
 GHW  OAC   CAV  OXT   126.18  3.000
 GHW  OXT   CAV  CAN   115.78  3.000
 GHW  OAC   CAV  CAN   118.04  3.000
 GHW  H13B  C13  H13A  107.98  3.000
 GHW  H13B  C13  H13   108.31  3.000
 GHW  H13A  C13  H13   107.50  3.000
 GHW  H13B  C13  C3    110.10  3.000
 GHW  H13A  C13  C3    111.43  3.000
 GHW  H13   C13  C3    111.39  3.000
 GHW  HN2A  N2   HN2   117.82  3.000
 GHW  HN2A  N2   C2    119.02  3.000
 GHW  HN2   N2   C2    122.48  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
 GHW  CONST_01  C3    C1   C5   C4      0.00   0.0  0
 GHW  CONST_02  C1    C3   S4   C4      0.00   0.0  0
 GHW  CONST_03  C3    S4   C4   C5      0.00   0.0  0
 GHW  CONST_04  S4    C3   C1   C5      0.00   0.0  0
 GHW  CONST_05  C1    C5   C4   S4      0.00   0.0  0
 GHW  CONST_06  CBA   CAK  CAI  CAZ     0.00   0.0  0
 GHW  CONST_07  CBA   CAL  CAJ  CAZ     0.00   0.0  0
 GHW  CONST_08  CAK   CAI  CAZ  CAJ     0.00   0.0  0
 GHW  CONST_09  CAK   CBA  CAL  CAJ     0.00   0.0  0
 GHW  CONST_10  CAI   CAZ  CAJ  CAL     0.00   0.0  0
 GHW  CONST_11  CAI   CAK  CBA  CAL     0.00   0.0  0
 GHW  CONST_12  N1    C2   N3   C4      0.00   0.0  0
 GHW  CONST_13  C2    N1   C6   C5      0.00   0.0  0
 GHW  CONST_14  N3    C2   N1   C6      0.00   0.0  0
 GHW  CONST_15  SAT   C1   C5   C4    180.00   0.0  0
 GHW  CONST_16  C13   C3   S4   C4    180.00   0.0  0
 GHW  CONST_17  C13   C3   C1   C5    180.00   0.0  0
 GHW  CONST_18  SAT   C1   C5   C6      0.00   0.0  0
 GHW  CONST_19  SAT   C1   C3   S4    180.00   0.0  0
 GHW  CONST_20  CAK   CAI  CAZ  SAT   180.00   0.0  0
 GHW  CONST_21  CAL   CAJ  CAZ  SAT   180.00   0.0  0
 GHW  CONST_22  CAX   CBA  CAL  CAJ   180.00   0.0  0
 GHW  CONST_23  CAX   CBA  CAK  CAI   180.00   0.0  0
 GHW  CONST_24  N2    C2   N3   C4    180.00   0.0  0
 GHW  CONST_25  N2    C2   N1   C6    180.00   0.0  0
 GHW  CONST_26  O6    C6   N1   C2    180.00   0.0  0
 GHW  CONST_27  HAK   CAK  CAI  CAZ   180.00   0.0  0
 GHW  CONST_28  HAL   CAL  CAJ  CAZ   180.00   0.0  0
 GHW  CONST_29  HAI   CAI  CAZ  CAJ   180.00   0.0  0
 GHW  CONST_30  HAJ   CAJ  CAZ  CAI   180.00   0.0  0
 GHW  CONST_31  HN1   N1   C6   C5    180.00   0.0  0
 GHW  CONST_32  HN2   N2   C2   N1      0.00   0.0  0
 GHW  CONST_33  HN2A  N2   C2   N1    180.00   0.0  0
 GHW  CONST_34  CAP   NAS  CAX  CBA   180.00   0.0  0
 GHW  CONST_36  CAP   NAS  CAX  OAE     0.00   0.0  0
 GHW  Var_01    CAI   CAZ  SAT  C1     20.10  30.0  1
 GHW  Var_02    NAS   CAX  CBA  CAL    27.20  30.0  2
 GHW  Var_03    H13   C13  C3   S4    -47.28  30.0  2
 GHW  Var_04    CAV   CAN  CBG  CAP  -177.49  30.0  2
 GHW  Var_05    OAC   CAV  CAN  CBG     1.37  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
 GHW  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
 GHW  plan-1  SAT   0.020
 GHW  plan-1  CAZ   0.020
 GHW  plan-1  CAJ   0.020
 GHW  plan-1  CAL   0.020
 GHW  plan-1  CAI   0.020
 GHW  plan-1  CAK   0.020
 GHW  plan-1  CBA   0.020
 GHW  plan-1  CAX   0.020
 GHW  plan-1  HAJ   0.020
 GHW  plan-1  HAL   0.020
 GHW  plan-1  HAI   0.020
 GHW  plan-1  HAK   0.020
 GHW  plan-2  C4    0.020
 GHW  plan-2  C5    0.020
 GHW  plan-2  C6    0.020
 GHW  plan-2  N1    0.020
 GHW  plan-2  C3    0.020
 GHW  plan-2  N3    0.020
 GHW  plan-2  S4    0.020
 GHW  plan-2  C2    0.020
 GHW  plan-2  O6    0.020
 GHW  plan-2  C1    0.020
 GHW  plan-2  SAT   0.020
 GHW  plan-2  HN1   0.020
 GHW  plan-2  HN2   0.020
 GHW  plan-2  HN2A  0.020
 GHW  plan-2  C13   0.020
 GHW  plan-2  N2    0.020
 GHW  plan-3  CBA   0.020
 GHW  plan-3  CAX   0.020
 GHW  plan-3  OAE   0.020
 GHW  plan-3  NAS   0.020
 GHW  plan-3  CAP   0.020
 GHW  plan-3  HNAS  0.020
 GHW  plan-4  CAP   0.020
 GHW  plan-4  CAW   0.020
 GHW  plan-4  OAG   0.020
 GHW  plan-4  OAD   0.020
 GHW  plan-5  CAN   0.020
 GHW  plan-5  CAV   0.020
 GHW  plan-5  OXT   0.020
 GHW  plan-5  OAC   0.020

