# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 09:33:51 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: (2R,4S)-2-[(1R)-1-{[(6S)-6-amino-6-carboxyhexanoyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(C)S[C@@H](N[C@H]1C(O)=O)[C@H](NC(=O)CCCC[C@H](N)C(O)=O)C=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
 HJ3  HJ3  '(2R,4S)-2-[(1R)-1-{[(6S)-6-amino-6-carboxyhexanoyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid'  ligand  48  25  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_HJ3
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
 HJ3  O11   O  O      0  -0.494   0.9113  -0.7140   1.9889
 HJ3  C10   C  C      0   0.573   0.8074  -0.6172   0.7759
 HJ3  CA1   C  CH2    0  -0.586   1.9961  -0.6849  -0.1550
 HJ3  CB1   C  CH2    0  -0.415   3.2546  -0.0566   0.4286
 HJ3  N9    N  NH1    0  -0.640  -0.3854  -0.4386   0.1670
 HJ3  C6    C  CH1    0  -0.198  -1.6287  -0.5322   0.8761
 HJ3  C7    C  C1     0   0.181  -2.0451  -1.9770   1.0834
 HJ3  O8    O  O      0  -0.364  -1.3287  -2.9186   0.8714
 HJ3  C5    C  CR15   0  -0.206  -2.7244   0.2584   0.1647
 HJ3  S1    S  S2     0  -0.050  -3.3770  -0.6986  -1.3001
 HJ3  N4    N  NR15   0  -0.562  -3.8433   0.5512   1.0101
 HJ3  C3    C  CR15   0  -0.210  -5.0534   0.7356   0.2253
 HJ3  C12   C  C      0   0.435  -5.1420   2.1452  -0.3966
 HJ3  O14   O  OC    -1  -0.612  -6.2850   2.6387  -0.4491
 HJ3  O13   O  O      0  -0.586  -4.0853   2.6661  -0.8004
 HJ3  C2    C  CR5    0  -0.197  -5.1327  -0.4041  -0.8397
 HJ3  C16   C  CH3    0  -0.628  -5.7136  -1.6684  -0.2112
 HJ3  C15   C  CH3    0  -0.637  -5.9296  -0.0437  -2.0872
 HJ3  HA1   H  HCH2   0   0.268   2.1776  -1.7444  -0.3673
 HJ3  HA1A  H  HCH2   0   0.251   1.7543  -0.2219  -1.1151
 HJ3  C121  C  CH2    0  -0.407   4.4457  -0.1765  -0.5136
 HJ3  HB1   H  HCH2   0   0.220   3.0646   0.9984   0.6490
 HJ3  HB1A  H  HCH2   0   0.222   3.4972  -0.5326   1.3816
 HJ3  HN9   H  HNH1   0   0.401  -0.4127  -0.4628  -0.8410
 HJ3  H6    H  HCH1   0   0.309  -1.4966  -0.0915   1.8725
 HJ3  H7    H  H      0   0.196  -3.0595  -2.1170   1.4941
 HJ3  H5    H  HCR5   0   0.297  -2.3035   1.1819  -0.2248
 HJ3  HN4   H  HNR5   0   0.357  -3.9974  -0.1875   1.6857
 HJ3  H3    H  HCR5   0   0.250  -5.9031   0.6134   0.9016
 HJ3  H16   H  HCH3   0   0.226  -5.1898  -1.9530   0.7017
 HJ3  H16A  H  HCH3   0   0.233  -6.7649  -1.5134   0.0438
 HJ3  H16B  H  HCH3   0   0.239  -5.6571  -2.5127  -0.8990
 HJ3  H15   H  HCH3   0   0.234  -5.9638  -0.8879  -2.7770
 HJ3  H15A  H  HCH3   0   0.234  -6.9568   0.2076  -1.8198
 HJ3  H15B  H  HCH3   0   0.239  -5.4963   0.8031  -2.6166
 HJ3  C13   C  CH2    0  -0.415   5.7043   0.4701   0.0478
 HJ3  H18   H  HCH2   0   0.215   4.6444  -1.2304  -0.7230
 HJ3  H19   H  HCH2   0   0.204   4.2011   0.2876  -1.4760
 HJ3  H20   H  HCH2   0   0.215   5.5282   1.5380   0.1978
 HJ3  H21   H  HCH2   0   0.202   5.9167   0.0513   1.0400
 HJ3  C14   C  CH1    0  -0.212   6.9398   0.2947  -0.8401
 HJ3  N3    N  NH2    0  -0.786   7.2556  -1.1202  -0.9734
 HJ3  H22   H  HCH1   0   0.204   6.6810   0.6688  -1.8383
 HJ3  C151  C  C      0   0.383   8.0883   1.1803  -0.2966
 HJ3  O6    O  O      0  -0.610   9.0535   0.6073   0.2478
 HJ3  H24   H  HNH2   0   0.333   7.9856  -1.2280  -1.6676
 HJ3  H25   H  HNH2   0   0.321   7.6895  -1.4201  -0.1071
 HJ3  O5    O  OC    -1  -0.625   7.9382   2.4135  -0.4288

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
 HJ3  O11   C10   double  1.221  0.020  1.221
 HJ3  C10   CA1   single  1.511  0.020  1.511
 HJ3  CA1   CB1   single  1.523  0.020  1.523
 HJ3  CA1   HA1   single  0.970  0.020  1.090
 HJ3  CA1   HA1A  single  0.970  0.020  1.090
 HJ3  CB1   C121  single  1.523  0.020  1.523
 HJ3  CB1   HB1   single  0.970  0.020  1.090
 HJ3  CB1   HB1A  single  0.970  0.020  1.090
 HJ3  N9    C10   single  1.351  0.020  1.351
 HJ3  N9    HN9   single  0.890  0.020  1.040
 HJ3  C6    N9    single  1.434  0.020  1.434
 HJ3  C6    C5    single  1.527  0.020  1.527
 HJ3  C6    H6    single  0.970  0.020  1.090
 HJ3  C7    C6    single  1.518  0.020  1.518
 HJ3  C7    O8    double  1.202  0.020  1.202
 HJ3  C7    H7    single  0.930  0.020  1.080
 HJ3  C5    S1    single  1.867  0.020  1.867
 HJ3  C5    H5    single  0.970  0.020  1.090
 HJ3  S1    C2    single  1.839  0.020  1.839
 HJ3  N4    C5    single  1.433  0.020  1.433
 HJ3  N4    C3    single  1.454  0.020  1.454
 HJ3  N4    HN4   single  0.890  0.020  1.040
 HJ3  C3    C2    single  1.562  0.020  1.562
 HJ3  C3    H3    single  0.970  0.020  1.090
 HJ3  C12   C3    single  1.543  0.020  1.543
 HJ3  C12   O14   deloc   1.246  0.020  1.246
 HJ3  O13   C12   deloc   1.245  0.020  1.245
 HJ3  C2    C15   single  1.524  0.020  1.524
 HJ3  C2    C16   single  1.527  0.020  1.527
 HJ3  C16   H16   single  0.970  0.020  1.090
 HJ3  C16   H16A  single  0.970  0.020  1.090
 HJ3  C16   H16B  single  0.970  0.020  1.090
 HJ3  C15   H15   single  0.970  0.020  1.090
 HJ3  C15   H15A  single  0.970  0.020  1.090
 HJ3  C15   H15B  single  0.970  0.020  1.090
 HJ3  C121  C13   single  1.522  0.020  1.522
 HJ3  C121  H18   single  0.970  0.020  1.090
 HJ3  C121  H19   single  0.970  0.020  1.090
 HJ3  C13   H20   single  0.970  0.020  1.090
 HJ3  C13   H21   single  0.970  0.020  1.090
 HJ3  C13   C14   single  1.532  0.020  1.532
 HJ3  C14   C151  single  1.549  0.020  1.549
 HJ3  C14   N3    single  1.456  0.020  1.456
 HJ3  C14   H22   single  0.970  0.020  1.090
 HJ3  O5    C151  deloc   1.249  0.020  1.249
 HJ3  C151  O6    deloc   1.247  0.020  1.247
 HJ3  N3    H24   single  0.890  0.020  1.040
 HJ3  N3    H25   single  0.890  0.020  1.040

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
 HJ3  N9    C10   CA1   115.01  3.000
 HJ3  N9    C10   O11   122.22  3.000
 HJ3  CA1   C10   O11   122.77  3.000
 HJ3  HA1A  CA1   HA1   106.03  3.000
 HJ3  HA1A  CA1   CB1   110.16  3.000
 HJ3  HA1   CA1   CB1   109.65  3.000
 HJ3  HA1A  CA1   C10   110.37  3.000
 HJ3  HA1   CA1   C10   107.03  3.000
 HJ3  CB1   CA1   C10   113.30  3.000
 HJ3  HB1A  CB1   HB1   106.43  3.000
 HJ3  HB1A  CB1   C121  109.37  3.000
 HJ3  HB1   CB1   C121  109.64  3.000
 HJ3  HB1A  CB1   CA1   109.75  3.000
 HJ3  HB1   CB1   CA1   109.36  3.000
 HJ3  C121  CB1   CA1   112.12  3.000
 HJ3  HN9   N9    C6    117.98  3.000
 HJ3  C6    N9    C10   122.26  3.000
 HJ3  HN9   N9    C10   118.10  3.000
 HJ3  H6    C6    C5    107.55  3.000
 HJ3  H6    C6    C7    106.93  3.000
 HJ3  C5    C6    C7    111.07  3.000
 HJ3  C7    C6    N9    111.56  3.000
 HJ3  H6    C6    N9    108.57  3.000
 HJ3  C5    C6    N9    110.97  3.000
 HJ3  H7    C7    O8    120.95  3.000
 HJ3  H7    C7    C6    115.08  3.000
 HJ3  O8    C7    C6    123.93  3.000
 HJ3  H5    C5    N4    109.89  3.000
 HJ3  N4    C5    S1    107.14  3.000
 HJ3  H5    C5    S1    106.83  3.000
 HJ3  N4    C5    C6    113.04  3.000
 HJ3  H5    C5    C6    109.20  3.000
 HJ3  S1    C5    C6    110.54  3.000
 HJ3  C2    S1    C5     93.16  3.000
 HJ3  HN4   N4    C3    109.03  3.000
 HJ3  HN4   N4    C5    111.31  3.000
 HJ3  C3    N4    C5    110.94  3.000
 HJ3  H3    C3    C2    107.51  3.000
 HJ3  H3    C3    C12   107.87  3.000
 HJ3  C2    C3    C12   112.88  3.000
 HJ3  C12   C3    N4    112.41  3.000
 HJ3  H3    C3    N4    107.39  3.000
 HJ3  C2    C3    N4    108.53  3.000
 HJ3  O13   C12   O14   126.80  3.000
 HJ3  O13   C12   C3    117.64  3.000
 HJ3  O14   C12   C3    115.56  3.000
 HJ3  C15   C2    C16   109.50  3.000
 HJ3  C16   C2    C3    110.05  3.000
 HJ3  C15   C2    C3    114.35  3.000
 HJ3  C16   C2    S1    109.50  3.000
 HJ3  C15   C2    S1    109.41  3.000
 HJ3  C3    C2    S1    103.84  3.000
 HJ3  H16B  C16   H16A  107.87  3.000
 HJ3  H16B  C16   H16   107.52  3.000
 HJ3  H16A  C16   H16   107.68  3.000
 HJ3  H16B  C16   C2    111.21  3.000
 HJ3  H16A  C16   C2    110.17  3.000
 HJ3  H16   C16   C2    112.21  3.000
 HJ3  H15B  C15   H15A  108.35  3.000
 HJ3  H15B  C15   H15   107.87  3.000
 HJ3  H15A  C15   H15   107.69  3.000
 HJ3  H15B  C15   C2    111.96  3.000
 HJ3  H15A  C15   C2    110.27  3.000
 HJ3  H15   C15   C2    110.56  3.000
 HJ3  H19   C121  H18   106.30  3.000
 HJ3  H19   C121  C13   109.17  3.000
 HJ3  H18   C121  C13   109.27  3.000
 HJ3  H19   C121  CB1   109.59  3.000
 HJ3  H18   C121  CB1   109.67  3.000
 HJ3  C13   C121  CB1   112.64  3.000
 HJ3  C14   C13   H21   108.92  3.000
 HJ3  C14   C13   H20   108.76  3.000
 HJ3  H21   C13   H20   106.26  3.000
 HJ3  C14   C13   C121  113.86  3.000
 HJ3  H21   C13   C121  109.35  3.000
 HJ3  H20   C13   C121  109.42  3.000
 HJ3  C151  C14   H22   107.41  3.000
 HJ3  H22   C14   N3    107.42  3.000
 HJ3  C151  C14   N3    115.28  3.000
 HJ3  H22   C14   C13   107.35  3.000
 HJ3  N3    C14   C13   109.84  3.000
 HJ3  C151  C14   C13   109.22  3.000
 HJ3  H25   N3    H24   104.21  3.000
 HJ3  H25   N3    C14   107.57  3.000
 HJ3  H24   N3    C14   108.81  3.000
 HJ3  O6    C151  O5    126.34  3.000
 HJ3  O6    C151  C14   117.66  3.000
 HJ3  O5    C151  C14   115.99  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
 HJ3  CONST_01  C6    N9    C10   O11    0.00   0.0  0
 HJ3  CONST_02  C6    N9    C10   CA1  180.00   0.0  0
 HJ3  CONST_03  HN9   N9    C10   O11  180.00   0.0  0
 HJ3  Var_01    C3    C2    S1    C5    14.24  30.0  1
 HJ3  Var_02    H15   C15   C2    S1    65.29  30.0  3
 HJ3  Var_03    H16   C16   C2    S1    61.45  30.0  3
 HJ3  Var_04    CB1   CA1   C10   O11  -35.04  30.0  3
 HJ3  Var_05    C121  CB1   CA1   C10  178.28  30.0  3
 HJ3  Var_06    C13   C121  CB1   CA1  178.97  30.0  3
 HJ3  Var_07    C14   C13   C121  CB1  176.61  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
 HJ3  chir_01  C6   N9   C5    C7   negativ
 HJ3  chir_02  C5   S1   N4    C6   negativ
 HJ3  chir_03  C3   N4   C2    C12  positiv
 HJ3  chir_04  C14  C13  C151  N3   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
 HJ3  plan-1  O11   0.020
 HJ3  plan-1  C10   0.020
 HJ3  plan-1  CA1   0.020
 HJ3  plan-1  N9    0.020
 HJ3  plan-1  C6    0.020
 HJ3  plan-1  HN9   0.020
 HJ3  plan-2  C3    0.020
 HJ3  plan-2  C12   0.020
 HJ3  plan-2  O14   0.020
 HJ3  plan-2  O13   0.020
 HJ3  plan-3  C14   0.020
 HJ3  plan-3  C151  0.020
 HJ3  plan-3  O6    0.020
 HJ3  plan-3  O5    0.020
 HJ3  plan-4  C6    0.020
 HJ3  plan-4  C7    0.020
 HJ3  plan-4  O8    0.020
 HJ3  plan-4  H7    0.020

