# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 16 19:55:17 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: N-{[(1R)-1-carboxy-2-(methylsulfanyl)ethyl]carbamoyl}-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSC[C@H](NC(=O)N[C@@H](CCC(O)=O)C(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
 MUD  MUD  'N-{[(1R)-1-carboxy-2-(methylsulfanyl)ethyl]carbamoyl}-L-glutamic acid'  ligand  36  20  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_MUD
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
 MUD  O3    O  OH1   0  -0.596  -4.9473  -2.5110   1.4708
 MUD  C2    C  C     0   0.554  -4.7610  -1.2174   1.2300
 MUD  O1    O  O     0  -0.443  -5.5187  -0.3604   1.6111
 MUD  C4    C  CH2   0  -0.576  -3.5069  -0.9752   0.4368
 MUD  C5    C  CH2   0  -0.464  -3.2689   0.4968   0.1417
 MUD  C6    C  CH1   0  -0.189  -2.0102   0.6994  -0.7071
 MUD  C7    C  C     0   0.544  -1.8729   2.1645  -1.1003
 MUD  O8    O  O     0  -0.432  -1.0823   2.9293  -0.6130
 MUD  O9    O  OH1   0  -0.591  -2.7525   2.4999  -2.0331
 MUD  N10   N  NH1   0  -0.681  -0.8506   0.2444   0.0058
 MUD  C11   C  C     0   0.768   0.3432   0.1397  -0.6420
 MUD  O20   O  O     0  -0.531   0.4487   0.2647  -1.8543
 MUD  N12   N  NH1   0  -0.675   1.4124  -0.1188   0.1625
 MUD  C13   C  CH1   0  -0.190   2.6779  -0.4463  -0.4246
 MUD  C17   C  C     0   0.551   2.6341  -1.8054  -1.1179
 MUD  O18   O  OH1   0  -0.590   3.6942  -1.9825  -1.8922
 MUD  O19   O  O     0  -0.427   1.7615  -2.6176  -0.9652
 MUD  C14   C  CH2   0  -0.576   3.7704  -0.4540   0.6428
 MUD  S15   S  S2    0  -0.019   3.8002   1.1518   1.4888
 MUD  C16   C  CH3   0  -0.766   5.3161   0.9359   2.4468
 MUD  HO3   H  HOH1  0   0.480  -5.7599  -2.6372   1.9834
 MUD  H4    H  HCH2  0   0.288  -2.6675  -1.4110   0.9850
 MUD  H4A   H  HCH2  0   0.287  -3.5751  -1.5442  -0.4955
 MUD  H5    H  HCH2  0   0.272  -4.1239   0.9076  -0.3951
 MUD  H5A   H  HCH2  0   0.257  -3.1784   1.0638   1.0719
 MUD  H6    H  HCH1  0   0.291  -2.1169   0.1144  -1.6244
 MUD  HO9   H  HOH1  0   0.485  -2.6761   3.4426  -2.2451
 MUD  HN10  H  HNH1  0   0.398  -0.8380   0.4058   1.0019
 MUD  HN12  H  HNH1  0   0.399   1.2399  -0.4520   1.0990
 MUD  H13   H  HCH1  0   0.301   2.9332   0.3081  -1.1730
 MUD  HO18  H  HOH1  0   0.486   3.6712  -2.8604  -2.3029
 MUD  H14   H  HCH2  0   0.281   3.5982  -1.2512   1.3708
 MUD  H14A  H  HCH2  0   0.296   4.7384  -0.6279   0.1736
 MUD  H16   H  HCH3  0   0.265   5.2444   0.0726   3.1063
 MUD  H16A  H  HCH3  0   0.264   6.1849   0.8279   1.7991
 MUD  H16B  H  HCH3  0   0.277   5.4438   1.8288   3.0562

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
 MUD  C2   O3    single  1.329  0.020  1.329
 MUD  O3   HO3   single  0.850  0.020  0.980
 MUD  O1   C2    double  1.206  0.020  1.206
 MUD  C2   C4    single  1.504  0.020  1.504
 MUD  C4   C5    single  1.520  0.020  1.520
 MUD  C4   H4    single  0.970  0.020  1.090
 MUD  C4   H4A   single  0.970  0.020  1.090
 MUD  C5   C6    single  1.532  0.020  1.532
 MUD  C5   H5    single  0.970  0.020  1.090
 MUD  C5   H5A   single  0.970  0.020  1.090
 MUD  C7   C6    single  1.523  0.020  1.523
 MUD  C6   N10   single  1.435  0.020  1.435
 MUD  C6   H6    single  0.970  0.020  1.090
 MUD  O8   C7    double  1.203  0.020  1.203
 MUD  C7   O9    single  1.325  0.020  1.325
 MUD  O9   HO9   single  0.850  0.020  0.980
 MUD  N10  C11   single  1.362  0.020  1.362
 MUD  N10  HN10  single  0.890  0.020  1.040
 MUD  O20  C11   double  1.223  0.020  1.223
 MUD  C11  N12   single  1.363  0.020  1.363
 MUD  N12  C13   single  1.433  0.020  1.433
 MUD  N12  HN12  single  0.890  0.020  1.040
 MUD  C14  C13   single  1.527  0.020  1.527
 MUD  C13  C17   single  1.526  0.020  1.526
 MUD  C13  H13   single  0.970  0.020  1.090
 MUD  C17  O19   double  1.202  0.020  1.202
 MUD  C17  O18   single  1.325  0.020  1.325
 MUD  O18  HO18  single  0.850  0.020  0.980
 MUD  C14  S15   single  1.815  0.020  1.815
 MUD  C14  H14   single  0.970  0.020  1.090
 MUD  C14  H14A  single  0.970  0.020  1.090
 MUD  C16  S15   single  1.806  0.020  1.806
 MUD  C16  H16   single  0.970  0.020  1.090
 MUD  C16  H16A  single  0.970  0.020  1.090
 MUD  C16  H16B  single  0.970  0.020  1.090

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
 MUD  HO3   O3   C2    109.89  3.000
 MUD  C4    C2   O1    125.20  3.000
 MUD  C4    C2   O3    111.67  3.000
 MUD  O1    C2   O3    123.13  3.000
 MUD  H4A   C4   H4    105.53  3.000
 MUD  H4A   C4   C5    110.36  3.000
 MUD  H4    C4   C5    111.30  3.000
 MUD  H4A   C4   C2    108.28  3.000
 MUD  H4    C4   C2    108.16  3.000
 MUD  C5    C4   C2    112.89  3.000
 MUD  H5A   C5   H5    106.78  3.000
 MUD  H5A   C5   C6    109.56  3.000
 MUD  H5    C5   C6    108.77  3.000
 MUD  H5A   C5   C4    110.49  3.000
 MUD  H5    C5   C4    109.74  3.000
 MUD  C6    C5   C4    111.37  3.000
 MUD  H6    C6   N10   109.02  3.000
 MUD  H6    C6   C7    107.88  3.000
 MUD  N10   C6   C7    111.12  3.000
 MUD  H6    C6   C5    108.30  3.000
 MUD  N10   C6   C5    110.29  3.000
 MUD  C7    C6   C5    110.15  3.000
 MUD  O9    C7   O8    124.09  3.000
 MUD  O9    C7   C6    111.42  3.000
 MUD  O8    C7   C6    124.48  3.000
 MUD  HO9   O9   C7    110.35  3.000
 MUD  HN10  N10  C11   118.08  3.000
 MUD  HN10  N10  C6    116.72  3.000
 MUD  C11   N10  C6    119.75  3.000
 MUD  N12   C11  O20   122.46  3.000
 MUD  N12   C11  N10   114.92  3.000
 MUD  O20   C11  N10   122.61  3.000
 MUD  HN12  N12  C13   117.12  3.000
 MUD  HN12  N12  C11   118.45  3.000
 MUD  C13   N12  C11   119.63  3.000
 MUD  H13   C13  C14   108.35  3.000
 MUD  H13   C13  C17   108.07  3.000
 MUD  C14   C13  C17   109.48  3.000
 MUD  H13   C13  N12   109.21  3.000
 MUD  C17   C13  N12   111.36  3.000
 MUD  C14   C13  N12   110.28  3.000
 MUD  O19   C17  O18   124.40  3.000
 MUD  O18   C17  C13   111.20  3.000
 MUD  O19   C17  C13   124.39  3.000
 MUD  HO18  O18  C17   110.47  3.000
 MUD  H14A  C14  H14   108.07  3.000
 MUD  H14A  C14  S15   109.10  3.000
 MUD  H14   C14  S15   109.71  3.000
 MUD  H14A  C14  C13   109.59  3.000
 MUD  H14   C14  C13   110.88  3.000
 MUD  S15   C14  C13   109.45  3.000
 MUD  C16   S15  C14    98.93  3.000
 MUD  H16B  C16  H16A  108.71  3.000
 MUD  H16B  C16  H16   108.60  3.000
 MUD  H16A  C16  H16   109.52  3.000
 MUD  H16B  C16  S15   107.30  3.000
 MUD  H16A  C16  S15   111.47  3.000
 MUD  H16   C16  S15   111.15  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
 MUD  CONST_01  O20   C11  N10  C6      0.00   0.0  0
 MUD  CONST_02  C13   N12  C11  O20     0.00   0.0  0
 MUD  CONST_03  N12   C11  N10  C6    180.00   0.0  0
 MUD  CONST_04  C13   N12  C11  N10   180.00   0.0  0
 MUD  CONST_07  HO3   O3   C2   O1      0.00   0.0  0
 MUD  CONST_08  HO9   O9   C7   C6    180.00   0.0  0
 MUD  CONST_09  HO18  O18  C17  C13   180.00   0.0  0
 MUD  Var_01    C5    C4   C2   O3    179.82  30.0  3
 MUD  Var_02    C6    C5   C4   C2   -178.06  30.0  3
 MUD  Var_03    H16   C16  S15  C14   -58.88  30.0  3
 MUD  Var_04    H14   C14  S15  C16    67.19  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
 MUD  chir_01  C6   C5   C7   N10  negativ
 MUD  chir_02  C13  N12  C14  C17  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
 MUD  plan-1  C6    0.020
 MUD  plan-1  N10   0.020
 MUD  plan-1  C11   0.020
 MUD  plan-1  O20   0.020
 MUD  plan-1  N12   0.020
 MUD  plan-1  C13   0.020
 MUD  plan-1  HN10  0.020
 MUD  plan-1  HN12  0.020
 MUD  plan-2  O3    0.020
 MUD  plan-2  C2    0.020
 MUD  plan-2  O1    0.020
 MUD  plan-2  C4    0.020
 MUD  plan-2  HO3   0.020
 MUD  plan-3  C6    0.020
 MUD  plan-3  C7    0.020
 MUD  plan-3  O8    0.020
 MUD  plan-3  O9    0.020
 MUD  plan-3  HO9   0.020
 MUD  plan-4  C13   0.020
 MUD  plan-4  C17   0.020
 MUD  plan-4  O18   0.020
 MUD  plan-4  O19   0.020
 MUD  plan-4  HO18  0.020

