# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 04:05:11 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  33  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  OC    -1  -0.635  -5.2350  -2.5776   0.8996
 MUD  C2    C  C      0   0.410  -4.9068  -1.3718   0.9238
 MUD  O1    O  O      0  -0.610  -5.5246  -0.4533   1.4983
 MUD  C4    C  CH2    0  -0.575  -3.6142  -1.0121   0.1708
 MUD  C5    C  CH2    0  -0.445  -3.2537   0.4645   0.1527
 MUD  C6    C  CH1    0  -0.180  -1.9835   0.7808  -0.6392
 MUD  C7    C  C      0   0.401  -1.7996   2.3136  -0.7595
 MUD  O8    O  O      0  -0.601  -0.8962   2.8446  -0.0895
 MUD  O9    O  OC    -1  -0.625  -2.6119   2.8897  -1.5137
 MUD  N10   N  NH1    0  -0.667  -0.8582   0.1167  -0.0209
 MUD  C11   C  C      0   0.740   0.3621   0.1344  -0.6199
 MUD  O20   O  O      0  -0.561   0.5104   0.3944  -1.8100
 MUD  N12   N  NH1    0  -0.660   1.4108  -0.1601   0.2059
 MUD  C13   C  CH1    0  -0.207   2.6686  -0.5930  -0.3497
 MUD  C17   C  C      0   0.415   2.6573  -2.0594  -0.8636
 MUD  O18   O  OC    -1  -0.617   3.7268  -2.4496  -1.3737
 MUD  O19   O  O      0  -0.590   1.6071  -2.7065  -0.7222
 MUD  C14   C  CH2    0  -0.557   3.7722  -0.4126   0.6844
 MUD  S15   S  S2     0  -0.041   3.7788   1.2987   1.2972
 MUD  C16   C  CH3    0  -0.768   5.4163   1.3379   2.0620
 MUD  H4    H  HCH2   0   0.223  -2.7958  -1.5982   0.6020
 MUD  H4A   H  HCH2   0   0.214  -3.7065  -1.3753  -0.8596
 MUD  H5    H  HCH2   0   0.222  -4.0718   1.0361  -0.2860
 MUD  H5A   H  HCH2   0   0.206  -3.1393   0.8366   1.1768
 MUD  H6    H  HCH1   0   0.216  -2.1089   0.3781  -1.6487
 MUD  HN10  H  HNH1   0   0.367  -0.8606   0.1299   0.9880
 MUD  HN12  H  HNH1   0   0.368   1.1665  -0.6097   1.0763
 MUD  H13   H  HCH1   0   0.247   2.9003   0.0561  -1.1971
 MUD  H14   H  HCH2   0   0.255   3.6404  -1.0984   1.5266
 MUD  H14A  H  HCH2   0   0.270   4.7360  -0.6294   0.2259
 MUD  H16   H  HCH3   0   0.257   5.5050   0.5944   2.8533
 MUD  H16A  H  HCH3   0   0.256   6.2023   1.1739   1.3256
 MUD  H16B  H  HCH3   0   0.268   5.5514   2.3250   2.5014

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    deloc   1.250  0.020  1.250
 MUD  O1   C2    deloc   1.247  0.020  1.247
 MUD  C2   C4    single  1.539  0.020  1.539
 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  1.530  0.020  1.530
 MUD  C5   H5    single  0.970  0.020  1.090
 MUD  C5   H5A   single  0.970  0.020  1.090
 MUD  C7   C6    single  1.548  0.020  1.548
 MUD  C6   N10   single  1.445  0.020  1.445
 MUD  C6   H6    single  0.970  0.020  1.090
 MUD  O8   C7    deloc   1.244  0.020  1.244
 MUD  C7   O9    deloc   1.249  0.020  1.249
 MUD  N10  C11   single  1.359  0.020  1.359
 MUD  N10  HN10  single  0.890  0.020  1.040
 MUD  O20  C11   double  1.227  0.020  1.227
 MUD  C11  N12   single  1.367  0.020  1.367
 MUD  N12  C13   single  1.442  0.020  1.442
 MUD  N12  HN12  single  0.890  0.020  1.040
 MUD  C14  C13   single  1.523  0.020  1.523
 MUD  C13  C17   single  1.554  0.020  1.554
 MUD  C13  H13   single  0.970  0.020  1.090
 MUD  C17  O19   deloc   1.242  0.020  1.242
 MUD  C17  O18   deloc   1.248  0.020  1.248
 MUD  C14  S15   single  1.818  0.020  1.818
 MUD  C14  H14   single  0.970  0.020  1.090
 MUD  C14  H14A  single  0.970  0.020  1.090
 MUD  C16  S15   single  1.808  0.020  1.808
 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  C4    C2   O1    118.00  3.000
 MUD  C4    C2   O3    115.89  3.000
 MUD  O1    C2   O3    126.11  3.000
 MUD  H4A   C4   H4    104.82  3.000
 MUD  H4A   C4   C5    109.30  3.000
 MUD  H4    C4   C5    110.32  3.000
 MUD  H4A   C4   C2    108.16  3.000
 MUD  H4    C4   C2    108.06  3.000
 MUD  C5    C4   C2    115.61  3.000
 MUD  H5A   C5   H5    106.04  3.000
 MUD  H5A   C5   C6    109.08  3.000
 MUD  H5    C5   C6    107.84  3.000
 MUD  H5A   C5   C4    110.09  3.000
 MUD  H5    C5   C4    109.64  3.000
 MUD  C6    C5   C4    113.82  3.000
 MUD  H6    C6   N10   108.35  3.000
 MUD  H6    C6   C7    107.83  3.000
 MUD  N10   C6   C7    113.30  3.000
 MUD  H6    C6   C5    107.84  3.000
 MUD  N10   C6   C5    109.27  3.000
 MUD  C7    C6   C5    110.09  3.000
 MUD  O9    C7   O8    126.91  3.000
 MUD  O9    C7   C6    115.23  3.000
 MUD  O8    C7   C6    117.84  3.000
 MUD  HN10  N10  C11   116.26  3.000
 MUD  HN10  N10  C6    114.82  3.000
 MUD  C11   N10  C6    120.29  3.000
 MUD  N12   C11  O20   122.60  3.000
 MUD  N12   C11  N10   114.81  3.000
 MUD  O20   C11  N10   122.58  3.000
 MUD  HN12  N12  C13   114.19  3.000
 MUD  HN12  N12  C11   115.54  3.000
 MUD  C13   N12  C11   120.08  3.000
 MUD  H13   C13  C14   107.62  3.000
 MUD  H13   C13  C17   107.80  3.000
 MUD  C14   C13  C17   109.97  3.000
 MUD  H13   C13  N12   107.80  3.000
 MUD  C17   C13  N12   113.86  3.000
 MUD  C14   C13  N12   109.57  3.000
 MUD  O19   C17  O18   127.49  3.000
 MUD  O18   C17  C13   115.10  3.000
 MUD  O19   C17  C13   117.41  3.000
 MUD  H14A  C14  H14   107.81  3.000
 MUD  H14A  C14  S15   109.04  3.000
 MUD  H14   C14  S15   109.34  3.000
 MUD  H14A  C14  C13   109.37  3.000
 MUD  H14   C14  C13   111.17  3.000
 MUD  S15   C14  C13   110.06  3.000
 MUD  C16   S15  C14    99.58  3.000
 MUD  H16B  C16  H16A  108.64  3.000
 MUD  H16B  C16  H16   108.39  3.000
 MUD  H16A  C16  H16   109.23  3.000
 MUD  H16B  C16  S15   107.63  3.000
 MUD  H16A  C16  S15   111.36  3.000
 MUD  H16   C16  S15   111.48  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
 MUD  Var_01  C5   C4   C2   O3    177.42  30.0  3
 MUD  Var_02  C6   C5   C4   C2   -178.38  30.0  3
 MUD  Var_03  H16  C16  S15  C14   -60.03  30.0  3
 MUD  Var_04  H14  C14  S15  C16    73.90  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-3  C6    0.020
 MUD  plan-3  C7    0.020
 MUD  plan-3  O8    0.020
 MUD  plan-3  O9    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

