# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  1 15:36:39 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: N-[(5S)-5-amino-5-carboxypentanoyl]-L-cysteinyl-D-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](NC(=O)[C@H](CS)NC(=O)CCC[C@H](N)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
 W05  W05  N-[(5S)-5-amino-5-carboxypentanoyl]-L-cysteinyl-D-alanine  ligand  43  22  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_W05
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
 W05  C1    C  C     0   0.517  6.3062   8.9575  -0.1499
 W05  C2    C  CH1   0  -0.224  5.2105   8.5061   0.8069
 W05  C3    C  CH2   0  -0.424  5.3104   6.9937   1.0525
 W05  C4    C  CH2   0  -0.440  5.0958   6.1367  -0.1904
 W05  C7    C  CH2   0  -0.574  5.1457   4.6548   0.1560
 W05  C10   C  C     0   0.574  4.9217   3.7578  -1.0417
 W05  N11   N  NH1   0  -0.636  5.5920   2.5922  -1.0046
 W05  C12   C  CH1   0  -0.194  5.4929   1.5942  -2.0297
 W05  C13   C  C     0   0.554  5.8148   0.2315  -1.4218
 W05  N14   N  NH2   0  -0.782  3.8808   8.8771   0.3822
 W05  O15   O  O     0  -0.499  4.1723   4.0585  -1.9601
 W05  C16   C  CH2   0  -0.576  6.4207   1.8896  -3.2161
 W05  S17   S  S2    0  -0.228  8.1804   1.9416  -2.7707
 W05  O18   O  O     0  -0.473  6.3133   0.1188  -0.3137
 W05  O19   O  OH1   0  -0.593  7.5177   8.8201   0.3783
 W05  O20   O  O     0  -0.441  6.1156   9.3822  -1.2621
 W05  N29   N  NH1   0  -0.639  5.5420  -0.8077  -2.2222
 W05  C30   C  CH1   0  -0.200  5.8592  -2.1693  -1.8652
 W05  C31   C  C     0   0.551  4.8639  -3.0910  -2.5406
 W05  C32   C  CH3   0  -0.656  7.2953  -2.5425  -2.2434
 W05  O42   O  O     0  -0.432  4.0730  -2.7431  -3.3800
 W05  O43   O  OH1   0  -0.585  4.9876  -4.3324  -2.1052
 W05  H2    H  HCH1  0   0.283  5.4052   8.9970   1.7656
 W05  H3C1  H  HCH2  0   0.242  4.5557   6.7433   1.8021
 W05  H3C2  H  HCH2  0   0.238  6.2796   6.7599   1.4984
 W05  H4C1  H  HCH2  0   0.232  4.1308   6.3666  -0.6453
 W05  H4C2  H  HCH2  0   0.235  5.8606   6.3539  -0.9421
 W05  H7C1  H  HCH2  0   0.253  6.0974   4.4111   0.6342
 W05  H7C2  H  HCH2  0   0.273  4.3674   4.4237   0.8915
 W05  H11   H  HNH1  0   0.400  6.2200   2.4023  -0.2390
 W05  H12   H  HCH1  0   0.304  4.4687   1.5762  -2.4157
 W05  H141  H  HNH2  0   0.347  3.7156   8.5844  -0.5725
 W05  H142  H  HNH2  0   0.355  3.7836   9.8842   0.3821
 W05  H161  H  HCH2  0   0.289  6.2680   1.1803  -4.0288
 W05  H162  H  HCH2  0   0.306  6.1814   2.8763  -3.6106
 W05  H19   H  HOH1  0   0.480  8.1929   9.0881  -0.2633
 W05  H29   H  HNH1  0   0.409  5.1030  -0.6463  -3.1167
 W05  H30   H  HCH1  0   0.300  5.7368  -2.2807  -0.7850
 W05  H321  H  HCH3  0   0.253  7.9876  -1.8598  -1.7530
 W05  H322  H  HCH3  0   0.252  7.5408  -3.5527  -1.9217
 W05  H323  H  HCH3  0   0.241  7.4460  -2.4712  -3.3206
 W05  H43   H  HOH1  0   0.490  4.3613  -4.9143  -2.5620
 W05  HS1   H  HSH1  0   0.218  8.4124   0.6232  -2.7814

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
 W05  C1   C2    single  1.523  0.020  1.523
 W05  C1   O19   single  1.329  0.020  1.329
 W05  C1   O20   double  1.206  0.020  1.206
 W05  C2   C3    single  1.535  0.020  1.535
 W05  C2   N14   single  1.444  0.020  1.444
 W05  C2   H2    single  0.970  0.020  1.090
 W05  C3   C4    single  1.525  0.020  1.525
 W05  C3   H3C1  single  0.970  0.020  1.090
 W05  C3   H3C2  single  0.970  0.020  1.090
 W05  C4   C7    single  1.523  0.020  1.523
 W05  C4   H4C1  single  0.970  0.020  1.090
 W05  C4   H4C2  single  0.970  0.020  1.090
 W05  C7   C10   single  1.513  0.020  1.513
 W05  C7   H7C1  single  0.970  0.020  1.090
 W05  C7   H7C2  single  0.970  0.020  1.090
 W05  C10  N11   single  1.345  0.020  1.345
 W05  C10  O15   double  1.223  0.020  1.223
 W05  N11  C12   single  1.434  0.020  1.434
 W05  N11  H11   single  0.860  0.020  1.020
 W05  C12  C13   single  1.526  0.020  1.526
 W05  C12  C16   single  1.535  0.020  1.535
 W05  C12  H12   single  0.970  0.020  1.090
 W05  C13  O18   double  1.220  0.020  1.220
 W05  C13  N29   single  1.340  0.020  1.340
 W05  N14  H141  single  0.890  0.020  1.040
 W05  N14  H142  single  0.890  0.020  1.040
 W05  C16  S17   single  1.816  0.020  1.816
 W05  C16  H161  single  0.970  0.020  1.090
 W05  C16  H162  single  0.970  0.020  1.090
 W05  O19  H19   single  0.850  0.020  0.980
 W05  N29  C30   single  1.443  0.020  1.443
 W05  N29  H29   single  0.860  0.020  1.020
 W05  C30  C31   single  1.515  0.020  1.515
 W05  C30  C32   single  1.531  0.020  1.531
 W05  C30  H30   single  0.970  0.020  1.090
 W05  C31  O42   double  1.205  0.020  1.205
 W05  C31  O43   single  1.321  0.020  1.321
 W05  C32  H321  single  0.970  0.020  1.090
 W05  C32  H322  single  0.970  0.020  1.090
 W05  C32  H323  single  0.970  0.020  1.090
 W05  O43  H43   single  0.850  0.020  0.980
 W05  HS1  S17   single  1.200  0.020  1.300

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
 W05  O20   C1   O19   123.18  3.000
 W05  O20   C1   C2    124.76  3.000
 W05  O19   C1   C2    112.06  3.000
 W05  H2    C2   N14   107.82  3.000
 W05  H2    C2   C3    106.87  3.000
 W05  N14   C2   C3    111.09  3.000
 W05  H2    C2   C1    106.82  3.000
 W05  N14   C2   C1    113.67  3.000
 W05  C3    C2   C1    110.22  3.000
 W05  H3C2  C3   H3C1  106.48  3.000
 W05  H3C2  C3   C4    109.72  3.000
 W05  H3C1  C3   C4    109.46  3.000
 W05  H3C2  C3   C2    109.50  3.000
 W05  H3C1  C3   C2    106.88  3.000
 W05  C4    C3   C2    114.46  3.000
 W05  H4C2  C4   H4C1  106.85  3.000
 W05  H4C2  C4   C7    109.06  3.000
 W05  H4C1  C4   C7    109.19  3.000
 W05  H4C2  C4   C3    110.49  3.000
 W05  H4C1  C4   C3    110.23  3.000
 W05  C7    C4   C3    110.91  3.000
 W05  H7C2  C7   H7C1  106.14  3.000
 W05  H7C2  C7   C10   107.53  3.000
 W05  H7C1  C7   C10   110.07  3.000
 W05  H7C2  C7   C4    109.56  3.000
 W05  H7C1  C7   C4    110.19  3.000
 W05  C10   C7   C4    113.08  3.000
 W05  O15   C10  N11   122.63  3.000
 W05  O15   C10  C7    122.64  3.000
 W05  N11   C10  C7    114.72  3.000
 W05  H11   N11  C12   117.05  3.000
 W05  H11   N11  C10   119.64  3.000
 W05  C12   N11  C10   123.29  3.000
 W05  H12   C12  C16   107.23  3.000
 W05  H12   C12  C13   108.85  3.000
 W05  C16   C12  C13   110.62  3.000
 W05  H12   C12  N11   109.16  3.000
 W05  C16   C12  N11   112.14  3.000
 W05  C13   C12  N11   108.79  3.000
 W05  N29   C13  O18   123.65  3.000
 W05  N29   C13  C12   114.30  3.000
 W05  O18   C13  C12   122.02  3.000
 W05  H142  N14  H141  105.79  3.000
 W05  H142  N14  C2    110.13  3.000
 W05  H141  N14  C2    110.69  3.000
 W05  H162  C16  H161  106.79  3.000
 W05  H162  C16  S17   106.01  3.000
 W05  H161  C16  S17   109.73  3.000
 W05  H162  C16  C12   108.75  3.000
 W05  H161  C16  C12   111.50  3.000
 W05  S17   C16  C12   113.68  3.000
 W05  HS1   S17  C16    97.92  3.000
 W05  H19   O19  C1    110.09  3.000
 W05  H29   N29  C30   117.76  3.000
 W05  H29   N29  C13   119.60  3.000
 W05  C30   N29  C13   122.64  3.000
 W05  H30   C30  C32   108.92  3.000
 W05  H30   C30  C31   107.76  3.000
 W05  C32   C30  C31   110.95  3.000
 W05  H30   C30  N29   108.43  3.000
 W05  C32   C30  N29   112.03  3.000
 W05  C31   C30  N29   108.62  3.000
 W05  O43   C31  O42   124.22  3.000
 W05  O43   C31  C30   111.29  3.000
 W05  O42   C31  C30   124.48  3.000
 W05  H323  C32  H322  108.77  3.000
 W05  H323  C32  H321  108.43  3.000
 W05  H322  C32  H321  107.79  3.000
 W05  H323  C32  C30   110.96  3.000
 W05  H322  C32  C30   111.40  3.000
 W05  H321  C32  C30   109.40  3.000
 W05  H43   O43  C31   110.38  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
 W05  CONST_01  C12  N11  C10  C7    180.00   0.0  0
 W05  CONST_02  O15  C10  N11  C12     0.00   0.0  0
 W05  CONST_03  C30  N29  C13  C12   180.00   0.0  0
 W05  CONST_04  C30  N29  C13  O18     0.00   0.0  0
 W05  CONST_05  H11  N11  C10  C7      0.00   0.0  0
 W05  CONST_06  H29  N29  C13  C12     0.00   0.0  0
 W05  CONST_07  H19  O19  C1   C2    180.00   0.0  0
 W05  CONST_08  H43  O43  C31  C30   180.00   0.0  0
 W05  Var_01    C7   C4   C3   C2   -177.28  30.0  3
 W05  Var_02    C10  C7   C4   C3    179.32  30.0  3
 W05  Var_03    N11  C10  C7   C4    147.15  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
 W05  chir_01  C2   C1   C3   N14  positiv
 W05  chir_02  C12  N11  C13  C16  positiv
 W05  chir_03  C30  N29  C31  C32  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
 W05  plan-1  C7   0.020
 W05  plan-1  C10  0.020
 W05  plan-1  N11  0.020
 W05  plan-1  C12  0.020
 W05  plan-1  O15  0.020
 W05  plan-1  H11  0.020
 W05  plan-2  C12  0.020
 W05  plan-2  C13  0.020
 W05  plan-2  O18  0.020
 W05  plan-2  N29  0.020
 W05  plan-2  C30  0.020
 W05  plan-2  H29  0.020
 W05  plan-3  C1   0.020
 W05  plan-3  C2   0.020
 W05  plan-3  O19  0.020
 W05  plan-3  O20  0.020
 W05  plan-3  H19  0.020
 W05  plan-4  C30  0.020
 W05  plan-4  C31  0.020
 W05  plan-4  O42  0.020
 W05  plan-4  O43  0.020
 W05  plan-4  H43  0.020

