# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 10:27:52 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: (2~{R})-3-(1~{H}-indol-3-yl)-2-[[(2~{S})-2-methyl-3-sulfanyl-propanoyl]amino]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](CS)C(=O)N[C@H](Cc1c[nH]c2ccccc12)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
 R38  R38  '(2~{R})-3-(1~{H}-indol-3-yl)-2-[[(2~{S})-2-methyl-3-sulfanyl-propanoyl]amino]propanoic acid'  ligand  38  21  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_R38
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
 R38  N01  N  NH1    0  -0.603   0.9138  -1.0537   0.4357
 R38  C02  C  CH1    0  -0.207  -0.1219  -2.0205   0.1759
 R38  C03  C  C      0   0.413   0.3866  -3.4834   0.1791
 R38  O04  O  OC    -1  -0.615  -0.5004  -4.3477   0.0285
 R38  O05  O  O      0  -0.592   1.6057  -3.6738   0.3196
 R38  C06  C  CH2    0  -0.565  -1.2688  -1.8262   1.1840
 R38  C07  C  CR5    0   0.045  -1.7673  -0.4221   1.2230
 R38  C08  C  CR56   0   0.043  -2.4857   0.2642   0.1908
 R38  C09  C  CR56   0   0.355  -2.6822   1.5937   0.6285
 R38  N10  N  NR15   0  -0.692  -2.1097   1.7028   1.8607
 R38  C11  C  CR15   0  -0.096  -1.5616   0.4979   2.2108
 R38  C12  C  CR16   0  -0.306  -3.3620   2.5345  -0.1439
 R38  C13  C  CR16   0  -0.287  -3.8449   2.1238  -1.3722
 R38  C14  C  CR16   0  -0.271  -3.6605   0.8071  -1.8267
 R38  C15  C  CR16   0  -0.374  -2.9871  -0.1218  -1.0573
 R38  C16  C  C      0   0.575   1.4590  -0.2556  -0.4857
 R38  O17  O  O      0  -0.512   1.2304  -0.3411  -1.6872
 R38  C18  C  CH1    0  -0.385   2.3565   0.8404   0.0734
 R38  C19  C  CH2    0  -0.535   3.5698   1.0199  -0.8317
 R38  S20  S  S2     0  -0.262   4.7066   2.2476  -0.0990
 R38  C21  C  CH3    0  -0.657   1.5173   2.1141   0.2095
 R38  H1   H  HNH1   0   0.385   1.1897  -0.9210   1.3956
 R38  H2   H  HCH1   0   0.250  -0.5063  -1.8080  -0.8247
 R38  H4   H  HCH2   0   0.244  -2.0700  -2.5171   0.9180
 R38  H5   H  HCH2   0   0.240  -0.9272  -2.1198   2.1820
 R38  H6   H  HNR5   0   0.404  -2.0891   2.5317   2.4296
 R38  H7   H  HCR5   0   0.276  -1.0554   0.3815   3.1569
 R38  H8   H  HCR6   0   0.255  -3.5081   3.5500   0.2025
 R38  H9   H  HCR6   0   0.246  -4.3772   2.8305  -1.9959
 R38  H10  H  HCR6   0   0.243  -4.0531   0.5214  -2.7941
 R38  H11  H  HCR6   0   0.235  -2.8511  -1.1357  -1.4153
 R38  H12  H  HCH1   0   0.257   2.7089   0.5479   1.0679
 R38  H13  H  HCH2   0   0.279   4.1046   0.0761  -0.9363
 R38  H14  H  HCH2   0   0.266   3.2622   1.3536  -1.8215
 R38  H15  H  HSH1   0   0.225   5.7209   2.0637  -0.9503
 R38  H16  H  HCH3   0   0.240   2.0856   2.9179   0.6774
 R38  H17  H  HCH3   0   0.230   1.1777   2.4618  -0.7669
 R38  H18  H  HCH3   0   0.253   0.6367   1.9297   0.8258

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
 R38  C13  C14  aromatic  1.405  0.020  1.405
 R38  C13  C12  aromatic  1.382  0.020  1.382
 R38  C14  C15  aromatic  1.381  0.020  1.381
 R38  C12  C09  aromatic  1.394  0.020  1.394
 R38  C21  C18  single    1.531  0.020  1.531
 R38  C15  C08  aromatic  1.399  0.020  1.399
 R38  C09  C08  aromatic  1.413  0.020  1.413
 R38  C09  N10  aromatic  1.363  0.020  1.363
 R38  C08  C07  aromatic  1.433  0.020  1.433
 R38  N10  C11  aromatic  1.369  0.020  1.369
 R38  C07  C11  aromatic  1.365  0.020  1.365
 R38  C07  C06  single    1.491  0.020  1.491
 R38  C06  C02  single    1.539  0.020  1.539
 R38  C18  C16  single    1.523  0.020  1.523
 R38  C18  C19  single    1.524  0.020  1.524
 R38  O17  C16  double    1.226  0.020  1.226
 R38  C16  N01  single    1.335  0.020  1.335
 R38  N01  C02  single    1.440  0.020  1.440
 R38  C02  C03  single    1.549  0.020  1.549
 R38  C19  S20  single    1.827  0.020  1.827
 R38  C03  O05  deloc     1.242  0.020  1.242
 R38  C03  O04  deloc     1.248  0.020  1.248
 R38  N01  H1   single    0.860  0.020  1.020
 R38  C02  H2   single    0.970  0.020  1.090
 R38  C06  H4   single    0.970  0.020  1.090
 R38  C06  H5   single    0.970  0.020  1.090
 R38  N10  H6   single    0.860  0.020  1.020
 R38  C11  H7   single    0.930  0.020  1.080
 R38  C12  H8   single    0.930  0.020  1.080
 R38  C13  H9   single    0.930  0.020  1.080
 R38  C14  H10  single    0.930  0.020  1.080
 R38  C15  H11  single    0.930  0.020  1.080
 R38  C18  H12  single    0.970  0.020  1.090
 R38  C19  H13  single    0.970  0.020  1.090
 R38  C19  H14  single    0.970  0.020  1.090
 R38  S20  H15  single    1.200  0.020  1.300
 R38  C21  H16  single    0.970  0.020  1.090
 R38  C21  H17  single    0.970  0.020  1.090
 R38  C21  H18  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
 R38  H1   N01  C16  117.83  3.000
 R38  H1   N01  C02  117.20  3.000
 R38  C16  N01  C02  124.77  3.000
 R38  H2   C02  C06  108.24  3.000
 R38  H2   C02  C03  107.52  3.000
 R38  C06  C02  C03  111.26  3.000
 R38  H2   C02  N01  106.71  3.000
 R38  C03  C02  N01  113.42  3.000
 R38  C06  C02  N01  109.45  3.000
 R38  O05  C03  O04  127.26  3.000
 R38  O04  C03  C02  114.88  3.000
 R38  O05  C03  C02  117.86  3.000
 R38  H5   C06  H4   106.35  3.000
 R38  H5   C06  C07  109.46  3.000
 R38  H4   C06  C07  110.94  3.000
 R38  H5   C06  C02  109.30  3.000
 R38  H4   C06  C02  107.92  3.000
 R38  C07  C06  C02  112.66  3.000
 R38  C11  C07  C08  105.90  3.000
 R38  C11  C07  C06  127.10  3.000
 R38  C08  C07  C06  126.88  3.000
 R38  C15  C08  C09  119.07  3.000
 R38  C09  C08  C07  107.28  3.000
 R38  C15  C08  C07  133.64  3.000
 R38  C12  C09  N10  130.66  3.000
 R38  N10  C09  C08  107.27  3.000
 R38  C12  C09  C08  122.07  3.000
 R38  H6   N10  C11  124.93  3.000
 R38  H6   N10  C09  125.88  3.000
 R38  C11  N10  C09  109.20  3.000
 R38  H7   C11  N10  120.45  3.000
 R38  H7   C11  C07  129.21  3.000
 R38  N10  C11  C07  110.34  3.000
 R38  H8   C12  C13  121.05  3.000
 R38  H8   C12  C09  121.43  3.000
 R38  C13  C12  C09  117.52  3.000
 R38  H9   C13  C14  119.34  3.000
 R38  H9   C13  C12  119.32  3.000
 R38  C14  C13  C12  121.34  3.000
 R38  H10  C14  C15  119.82  3.000
 R38  H10  C14  C13  119.26  3.000
 R38  C15  C14  C13  120.92  3.000
 R38  H11  C15  C14  120.41  3.000
 R38  H11  C15  C08  120.51  3.000
 R38  C14  C15  C08  119.08  3.000
 R38  C18  C16  O17  121.32  3.000
 R38  O17  C16  N01  123.94  3.000
 R38  C18  C16  N01  114.67  3.000
 R38  H12  C18  C21  108.53  3.000
 R38  H12  C18  C19  108.34  3.000
 R38  C21  C18  C19  113.02  3.000
 R38  H12  C18  C16  109.32  3.000
 R38  C19  C18  C16  109.63  3.000
 R38  C21  C18  C16  107.95  3.000
 R38  H14  C19  H13  108.47  3.000
 R38  H14  C19  S20  109.54  3.000
 R38  H13  C19  S20  108.37  3.000
 R38  H14  C19  C18  110.55  3.000
 R38  H13  C19  C18  110.22  3.000
 R38  S20  C19  C18  109.66  3.000
 R38  H15  S20  C19   97.14  3.000
 R38  H18  C21  H17  107.96  3.000
 R38  H18  C21  H16  107.65  3.000
 R38  H17  C21  H16  108.16  3.000
 R38  H18  C21  C18  110.61  3.000
 R38  H17  C21  C18  110.87  3.000
 R38  H16  C21  C18  111.45  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
 R38  CONST_01  C14  C15  C08  C07  180.00   0.0  0
 R38  CONST_02  C12  C09  C08  C07  180.00   0.0  0
 R38  CONST_03  N10  C09  C08  C07    0.00   0.0  0
 R38  CONST_04  C09  N10  C11  C07    0.00   0.0  0
 R38  CONST_05  C13  C14  C15  C08    0.00   0.0  0
 R38  CONST_06  C13  C12  C09  C08    0.00   0.0  0
 R38  CONST_07  C11  N10  C09  C08    0.00   0.0  0
 R38  CONST_08  N10  C11  C07  C08    0.00   0.0  0
 R38  CONST_09  C14  C13  C12  C09    0.00   0.0  0
 R38  CONST_10  C14  C15  C08  C09    0.00   0.0  0
 R38  CONST_11  C11  C07  C08  C09    0.00   0.0  0
 R38  CONST_12  C13  C12  C09  N10  180.00   0.0  0
 R38  CONST_13  C15  C08  C09  N10  180.00   0.0  0
 R38  CONST_14  C12  C09  N10  C11  180.00   0.0  0
 R38  CONST_15  C15  C08  C07  C11  180.00   0.0  0
 R38  CONST_16  C15  C14  C13  C12    0.00   0.0  0
 R38  CONST_17  C15  C08  C09  C12    0.00   0.0  0
 R38  CONST_18  C15  C08  C07  C06    0.00   0.0  0
 R38  CONST_19  C09  C08  C07  C06  180.00   0.0  0
 R38  CONST_20  N10  C11  C07  C06  180.00   0.0  0
 R38  CONST_21  H11  C15  C08  C07    0.00   0.0  0
 R38  CONST_22  H6   N10  C11  C07  180.00   0.0  0
 R38  CONST_23  H10  C14  C15  C08  180.00   0.0  0
 R38  CONST_24  H8   C12  C09  C08  180.00   0.0  0
 R38  CONST_25  H7   C11  C07  C08  180.00   0.0  0
 R38  CONST_26  H9   C13  C12  C09  180.00   0.0  0
 R38  CONST_27  C18  C16  N01  C02  180.00   0.0  0
 R38  CONST_28  O17  C16  N01  C02    0.00   0.0  0
 R38  CONST_29  H1   N01  C16  O17  180.00   0.0  0
 R38  Var_01    C08  C07  C06  C02   68.63  30.0  2

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
 R38  chir_01  C02  C06  N01  C03  negativ
 R38  chir_02  C18  C19  C16  C21  positiv

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
 R38  plan-1  C06  0.020
 R38  plan-1  C07  0.020
 R38  plan-1  C08  0.020
 R38  plan-1  C09  0.020
 R38  plan-1  N10  0.020
 R38  plan-1  C11  0.020
 R38  plan-1  C12  0.020
 R38  plan-1  C13  0.020
 R38  plan-1  C14  0.020
 R38  plan-1  C15  0.020
 R38  plan-1  H6   0.020
 R38  plan-1  H7   0.020
 R38  plan-1  H8   0.020
 R38  plan-1  H9   0.020
 R38  plan-1  H10  0.020
 R38  plan-1  H11  0.020
 R38  plan-2  N01  0.020
 R38  plan-2  C02  0.020
 R38  plan-2  C16  0.020
 R38  plan-2  O17  0.020
 R38  plan-2  C18  0.020
 R38  plan-2  H1   0.020
 R38  plan-3  C02  0.020
 R38  plan-3  C03  0.020
 R38  plan-3  O04  0.020
 R38  plan-3  O05  0.020

