# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 22:24:21 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: (2S)-3-amino-2-{[(4-cyclohexylbutoxy)carbonyl]amino}propanethioic S-acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[C@H](NC(=O)OCCCCC1CCCCC1)C(S)=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
 HJA  HJA  '(2S)-3-amino-2-{[(4-cyclohexylbutoxy)carbonyl]amino}propanethioic S-acid'  ligand  46  20  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_HJA
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
 HJA  N01   N  NH2   0  -0.790   5.0375   2.9406  -0.0272
 HJA  C02   C  CH2   0  -0.295   5.3749   1.6201   0.4666
 HJA  C03   C  CH1   0  -0.180   4.4610   0.5697  -0.1731
 HJA  N04   N  NH1   0  -0.661   3.1068   0.7867   0.2445
 HJA  C05   C  C     0   0.761   2.0870   0.1391  -0.3658
 HJA  O06   O  O     0  -0.512   2.2114  -0.5424  -1.3613
 HJA  O07   O  O2    0  -0.482   0.9354   0.3709   0.2574
 HJA  C08   C  CH2   0  -0.155  -0.2471  -0.2355  -0.2767
 HJA  C09   C  CH2   0  -0.463  -1.4295   0.2939   0.5054
 HJA  C18   C  C     0   0.237   4.9277  -0.8364   0.1985
 HJA  O20   O  O     0  -0.355   4.3959  -1.5218   1.0251
 HJA  C10   C  CH2   0  -0.437  -2.7435  -0.2870  -0.0041
 HJA  C11   C  CH2   0  -0.402  -3.9460   0.2695   0.7493
 HJA  C12   C  CH1   0  -0.221  -5.2969  -0.2925   0.3088
 HJA  C13   C  CH2   0  -0.413  -6.4043   0.1719   1.2560
 HJA  C14   C  CH2   0  -0.431  -7.7767  -0.3525   0.8469
 HJA  C15   C  CH2   0  -0.428  -8.1109   0.0291  -0.5911
 HJA  C16   C  CH2   0  -0.427  -7.0198  -0.4405  -1.5467
 HJA  C17   C  CH2   0  -0.422  -5.6489   0.0851  -1.1310
 HJA  H012  H  HNH2  0   0.348   4.1631   3.2517   0.3757
 HJA  H1    H  HNH2  0   0.361   5.7362   3.5980   0.2935
 HJA  H021  H  HCH2  0   0.255   6.4047   1.4013   0.1845
 HJA  H022  H  HCH2  0   0.225   5.3207   1.5139   1.5597
 HJA  H031  H  HCH1  0   0.289   4.5339   0.6837  -1.2582
 HJA  H041  H  HNH1  0   0.405   2.9459   1.1634   1.1671
 HJA  H082  H  HCH2  0   0.229  -0.3499   0.0090  -1.3367
 HJA  H081  H  HCH2  0   0.229  -0.1769  -1.3230  -0.1882
 HJA  H092  H  HCH2  0   0.230  -1.3095   0.0572   1.5665
 HJA  H091  H  HCH2  0   0.229  -1.4593   1.3845   0.4231
 HJA  H101  H  HCH2  0   0.223  -2.8389  -0.0773  -1.0734
 HJA  H102  H  HCH2  0   0.217  -2.7283  -1.3779   0.0927
 HJA  H112  H  HCH2  0   0.216  -3.8147   0.0687   1.8185
 HJA  H111  H  HCH2  0   0.206  -3.9625   1.3614   0.6483
 HJA  H121  H  HCH1  0   0.200  -5.2431  -1.3892   0.3686
 HJA  H132  H  HCH2  0   0.221  -6.1722  -0.1406   2.2784
 HJA  H131  H  HCH2  0   0.202  -6.4233   1.2688   1.2662
 HJA  H141  H  HCH2  0   0.206  -7.7882  -1.4444   0.9411
 HJA  H142  H  HCH2  0   0.223  -8.5428   0.0252   1.5290
 HJA  H152  H  HCH2  0   0.224  -9.0765  -0.3926  -0.8817
 HJA  H151  H  HCH2  0   0.206  -8.2129   1.1177  -0.6642
 HJA  H161  H  HCH2  0   0.206  -6.9991  -1.5360  -1.5590
 HJA  H162  H  HCH2  0   0.224  -7.2470  -0.1255  -2.5683
 HJA  H172  H  HCH2  0   0.201  -5.6391   1.1789  -1.2190
 HJA  H171  H  HCH2  0   0.227  -4.8877  -0.2866  -1.8217
 HJA  S1    S  S2    0  -0.188   6.3650  -1.3390  -0.7212
 HJA  H2    H  HSH1  0   0.262   6.5390  -2.5108  -0.0991

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
 HJA  O06  C05   double  1.213  0.020  1.213
 HJA  C05  N04   single  1.354  0.020  1.354
 HJA  C05  O07   single  1.330  0.020  1.330
 HJA  N04  C03   single  1.434  0.020  1.434
 HJA  O07  C08   single  1.432  0.020  1.432
 HJA  C08  C09   single  1.513  0.020  1.513
 HJA  C03  C02   single  1.532  0.020  1.532
 HJA  C03  C18   single  1.527  0.020  1.527
 HJA  C10  C09   single  1.524  0.020  1.524
 HJA  C10  C11   single  1.524  0.020  1.524
 HJA  C02  N01   single  1.450  0.020  1.450
 HJA  C16  C17   single  1.526  0.020  1.526
 HJA  C16  C15   single  1.525  0.020  1.525
 HJA  C17  C12   single  1.530  0.020  1.530
 HJA  C18  O20   double  1.198  0.020  1.198
 HJA  C12  C11   single  1.528  0.020  1.528
 HJA  C12  C13   single  1.529  0.020  1.529
 HJA  C15  C14   single  1.525  0.020  1.525
 HJA  C13  C14   single  1.525  0.020  1.525
 HJA  N01  H012  single  0.890  0.020  1.040
 HJA  N01  H1    single  0.890  0.020  1.040
 HJA  C02  H021  single  0.970  0.020  1.090
 HJA  C02  H022  single  0.970  0.020  1.090
 HJA  C03  H031  single  0.970  0.020  1.090
 HJA  N04  H041  single  0.890  0.020  1.040
 HJA  C08  H082  single  0.970  0.020  1.090
 HJA  C08  H081  single  0.970  0.020  1.090
 HJA  C09  H092  single  0.970  0.020  1.090
 HJA  C09  H091  single  0.970  0.020  1.090
 HJA  C10  H101  single  0.970  0.020  1.090
 HJA  C10  H102  single  0.970  0.020  1.090
 HJA  C11  H112  single  0.970  0.020  1.090
 HJA  C11  H111  single  0.970  0.020  1.090
 HJA  C12  H121  single  0.970  0.020  1.090
 HJA  C13  H132  single  0.970  0.020  1.090
 HJA  C13  H131  single  0.970  0.020  1.090
 HJA  C14  H141  single  0.970  0.020  1.090
 HJA  C14  H142  single  0.970  0.020  1.090
 HJA  C15  H152  single  0.970  0.020  1.090
 HJA  C15  H151  single  0.970  0.020  1.090
 HJA  C16  H161  single  0.970  0.020  1.090
 HJA  C16  H162  single  0.970  0.020  1.090
 HJA  C17  H172  single  0.970  0.020  1.090
 HJA  C17  H171  single  0.970  0.020  1.090
 HJA  C18  S1    single  1.779  0.020  1.779
 HJA  S1   H2    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
 HJA  H1    N01  H012  105.71  3.000
 HJA  H1    N01  C02   108.86  3.000
 HJA  H012  N01  C02   110.22  3.000
 HJA  H022  C02  H021  106.53  3.000
 HJA  H022  C02  C03   108.63  3.000
 HJA  H021  C02  C03   108.54  3.000
 HJA  H022  C02  N01   114.53  3.000
 HJA  H021  C02  N01   108.34  3.000
 HJA  C03   C02  N01   110.08  3.000
 HJA  H031  C03  C18   108.48  3.000
 HJA  H031  C03  N04   109.65  3.000
 HJA  C18   C03  N04   110.92  3.000
 HJA  H031  C03  C02   107.64  3.000
 HJA  C18   C03  C02   110.32  3.000
 HJA  N04   C03  C02   109.76  3.000
 HJA  H041  N04  C05   118.07  3.000
 HJA  H041  N04  C03   118.25  3.000
 HJA  C05   N04  C03   120.53  3.000
 HJA  O07   C05  O06   124.86  3.000
 HJA  O07   C05  N04   110.97  3.000
 HJA  O06   C05  N04   124.17  3.000
 HJA  C08   O07  C05   117.80  3.000
 HJA  H081  C08  H082  107.89  3.000
 HJA  H081  C08  C09   110.87  3.000
 HJA  H082  C08  C09   110.46  3.000
 HJA  H081  C08  O07   109.75  3.000
 HJA  H082  C08  O07   110.16  3.000
 HJA  C09   C08  O07   107.71  3.000
 HJA  H091  C09  H092  106.96  3.000
 HJA  H091  C09  C10   109.34  3.000
 HJA  H092  C09  C10   109.66  3.000
 HJA  H091  C09  C08   109.33  3.000
 HJA  H092  C09  C08   109.88  3.000
 HJA  C10   C09  C08   111.56  3.000
 HJA  S1    C18  O20   123.62  3.000
 HJA  S1    C18  C03   112.41  3.000
 HJA  O20   C18  C03   123.97  3.000
 HJA  H102  C10  H101  106.17  3.000
 HJA  H102  C10  C11   109.32  3.000
 HJA  H101  C10  C11   110.15  3.000
 HJA  H102  C10  C09   109.75  3.000
 HJA  H101  C10  C09   109.20  3.000
 HJA  C11   C10  C09   112.07  3.000
 HJA  H111  C11  H112  105.90  3.000
 HJA  H111  C11  C12   109.05  3.000
 HJA  H112  C11  C12   108.65  3.000
 HJA  H111  C11  C10   109.26  3.000
 HJA  H112  C11  C10   108.71  3.000
 HJA  C12   C11  C10   114.88  3.000
 HJA  H121  C12  C17   107.98  3.000
 HJA  H121  C12  C13   107.73  3.000
 HJA  C17   C12  C13   109.96  3.000
 HJA  H121  C12  C11   107.93  3.000
 HJA  C13   C12  C11   110.48  3.000
 HJA  C17   C12  C11   112.58  3.000
 HJA  H131  C13  H132  106.30  3.000
 HJA  H131  C13  C14   109.31  3.000
 HJA  H132  C13  C14   110.08  3.000
 HJA  H131  C13  C12   108.78  3.000
 HJA  H132  C13  C12   109.78  3.000
 HJA  C14   C13  C12   112.40  3.000
 HJA  H142  C14  H141  106.46  3.000
 HJA  H142  C14  C15   110.39  3.000
 HJA  H141  C14  C15   109.16  3.000
 HJA  H142  C14  C13   110.15  3.000
 HJA  H141  C14  C13   109.21  3.000
 HJA  C15   C14  C13   111.36  3.000
 HJA  H151  C15  H152  106.46  3.000
 HJA  H151  C15  C16   109.32  3.000
 HJA  H152  C15  C16   110.29  3.000
 HJA  H151  C15  C14   109.39  3.000
 HJA  H152  C15  C14   110.35  3.000
 HJA  C16   C15  C14   110.92  3.000
 HJA  H162  C16  H161  106.35  3.000
 HJA  H162  C16  C17   110.01  3.000
 HJA  H161  C16  C17   109.29  3.000
 HJA  H162  C16  C15   110.39  3.000
 HJA  H161  C16  C15   109.18  3.000
 HJA  C17   C16  C15   111.48  3.000
 HJA  H171  C17  H172  106.38  3.000
 HJA  H171  C17  C16   109.65  3.000
 HJA  H172  C17  C16   109.23  3.000
 HJA  H171  C17  C12   110.53  3.000
 HJA  H172  C17  C12   108.63  3.000
 HJA  C16   C17  C12   112.22  3.000
 HJA  H2    S1   C18    96.44  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
 HJA  Var_01  C15   C16  C17  C12    55.51  30.0  1
 HJA  Var_02  C15   C14  C13  C12   -55.47  30.0  1
 HJA  Var_03  C16   C15  C14  C13    54.92  30.0  1
 HJA  Var_04  C17   C16  C15  C14   -55.01  30.0  1
 HJA  Var_05  C12   C11  C10  C09  -178.79  30.0  3
 HJA  Var_06  O06   C05  N04  C03    -7.63  30.0  1
 HJA  Var_07  C09   C08  O07  C05  -173.96  30.0  3
 HJA  Var_08  C10   C09  C08  O07   179.38  30.0  3
 HJA  Var_09  C11   C10  C09  C08  -178.34  30.0  2
 HJA  Var_10  H012  N01  C02  C03    73.04  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
 HJA  chir_01  C03  N04  C02  C18  negativ
 HJA  chir_02  C12  C17  C11  C13  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
 HJA  plan-1  N04  0.020
 HJA  plan-1  C05  0.020
 HJA  plan-1  O06  0.020
 HJA  plan-1  O07  0.020
 HJA  plan-2  C03  0.020
 HJA  plan-2  C18  0.020
 HJA  plan-2  O20  0.020
 HJA  plan-2  S1   0.020

