# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 11:59:07 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: (2~{S})-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
 R59  R59  '(2~{S})-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 PERFECT
;

data_comp_R59
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
 R59  C21  C  CH3    0  -0.652  -3.5764  -0.4207   1.0836
 R59  C14  C  CR16   0  -0.270   1.9771   2.8445   1.5189
 R59  C13  C  CR16   0  -0.287   2.6345   3.5909   0.5261
 R59  C12  C  CR16   0  -0.306   3.1681   2.9805  -0.5925
 R59  C16  C  C      0   0.584  -1.5853  -0.6734  -0.3569
 R59  C15  C  CR16   0  -0.383   1.8395   1.4750   1.4060
 R59  C02  C  CH1    0  -0.194   0.3914  -2.0433   0.0870
 R59  C03  C  C      0   0.411  -0.1421  -3.3448   0.7470
 R59  C06  C  CH2    0  -0.574   1.8236  -1.7303   0.5378
 R59  C07  C  CR5    0   0.041   2.4167  -0.5410  -0.1441
 R59  C08  C  CR56   0   0.034   2.3660   0.8261   0.2826
 R59  C09  C  CR56   0   0.349   3.0277   1.5971  -0.7007
 R59  C11  C  CR15   0  -0.087   3.0895  -0.5368  -1.3337
 R59  C18  C  CH1    0  -0.392  -2.5228   0.3442   0.2771
 R59  C19  C  CH2    0  -0.535  -3.1302   1.2295  -0.8043
 R59  N10  N  NR15   0  -0.687   3.4513   0.7385  -1.6708
 R59  O04  O  OC    -1  -0.615   0.5650  -4.3557   0.5625
 R59  O05  O  O      0  -0.583  -1.2069  -3.2753   1.3829
 R59  S20  S  S2     0  -0.261  -4.1555   2.5262  -0.0274
 R59  H1   H  HCH3   0   0.230  -4.2214  -0.9998   0.4218
 R59  H2   H  HCH3   0   0.247  -3.0992  -1.1126   1.7777
 R59  H3   H  HCH3   0   0.240  -4.2047   0.2560   1.6619
 R59  H6   H  HCR6   0   0.256   3.6783   3.5550  -1.3555
 R59  H7   H  HCR6   0   0.234   1.3382   0.9157   2.1873
 R59  H8   H  HCH1   0   0.245   0.4143  -2.2047  -0.9936
 R59  H9   H  HCH2   0   0.237   1.8416  -1.5849   1.6240
 R59  H10  H  HCH2   0   0.254   2.4299  -2.6144   0.3423
 R59  H11  H  HCR5   0   0.277   3.3430  -1.3646  -1.9783
 R59  H12  H  HCH1   0   0.255  -1.9506   0.9803   0.9610
 R59  H13  H  HCH2   0   0.279  -2.3445   1.7145  -1.3835
 R59  H14  H  HCH2   0   0.267  -3.7443   0.6385  -1.4824
 R59  H16  H  HNR5   0   0.406   3.9698   0.9916  -2.4947
 R59  H18  H  HSH1   0   0.226  -4.4065   3.2266  -1.1382
 R59  N01  N  NH1    0  -0.607  -0.4650  -0.9106   0.3364
 R59  H4   H  HCR6   0   0.244   1.5726   3.3541   2.3840
 R59  H15  H  HNH1   0   0.383  -0.4008  -0.4936   1.2515
 R59  O17  O  O      0  -0.511  -1.8612  -1.2308  -1.4125
 R59  H5   H  HCR6   0   0.246   2.7273   4.6632   0.6420

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
 R59  O05  C03  deloc     1.242  0.020  1.242
 R59  O04  C03  deloc     1.247  0.020  1.247
 R59  S20  C19  single    1.827  0.020  1.827
 R59  C03  C02  single    1.554  0.020  1.554
 R59  C02  N01  single    1.442  0.020  1.442
 R59  C02  C06  single    1.534  0.020  1.534
 R59  C19  C18  single    1.524  0.020  1.524
 R59  N01  C16  single    1.339  0.020  1.339
 R59  C16  O17  double    1.225  0.020  1.225
 R59  C16  C18  single    1.522  0.020  1.522
 R59  C18  C21  single    1.532  0.020  1.532
 R59  C11  C07  aromatic  1.367  0.020  1.367
 R59  C11  N10  aromatic  1.368  0.020  1.368
 R59  C06  C07  single    1.494  0.020  1.494
 R59  C07  C08  aromatic  1.433  0.020  1.433
 R59  N10  C09  aromatic  1.363  0.020  1.363
 R59  C08  C09  aromatic  1.414  0.020  1.414
 R59  C08  C15  aromatic  1.400  0.020  1.400
 R59  C09  C12  aromatic  1.395  0.020  1.395
 R59  C15  C14  aromatic  1.381  0.020  1.381
 R59  C12  C13  aromatic  1.382  0.020  1.382
 R59  C14  C13  aromatic  1.405  0.020  1.405
 R59  C21  H1   single    0.970  0.020  1.090
 R59  C21  H2   single    0.970  0.020  1.090
 R59  C21  H3   single    0.970  0.020  1.090
 R59  C14  H4   single    0.930  0.020  1.080
 R59  C13  H5   single    0.930  0.020  1.080
 R59  C12  H6   single    0.930  0.020  1.080
 R59  C15  H7   single    0.930  0.020  1.080
 R59  C02  H8   single    0.970  0.020  1.090
 R59  C06  H9   single    0.970  0.020  1.090
 R59  C06  H10  single    0.970  0.020  1.090
 R59  C11  H11  single    0.930  0.020  1.080
 R59  C18  H12  single    0.970  0.020  1.090
 R59  C19  H13  single    0.970  0.020  1.090
 R59  C19  H14  single    0.970  0.020  1.090
 R59  N01  H15  single    0.890  0.020  1.040
 R59  N10  H16  single    0.860  0.020  1.020
 R59  S20  H18  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
 R59  H3   C21  H2   107.98  3.000
 R59  H3   C21  H1   108.11  3.000
 R59  H2   C21  H1   107.95  3.000
 R59  H3   C21  C18  111.47  3.000
 R59  H2   C21  C18  110.56  3.000
 R59  H1   C21  C18  110.64  3.000
 R59  H4   C14  C15  119.67  3.000
 R59  H4   C14  C13  119.30  3.000
 R59  C15  C14  C13  121.04  3.000
 R59  H5   C13  C12  119.42  3.000
 R59  H5   C13  C14  119.38  3.000
 R59  C12  C13  C14  121.20  3.000
 R59  H6   C12  C09  121.27  3.000
 R59  H6   C12  C13  121.20  3.000
 R59  C09  C12  C13  117.53  3.000
 R59  O17  C16  N01  123.65  3.000
 R59  O17  C16  C18  121.62  3.000
 R59  N01  C16  C18  114.72  3.000
 R59  H7   C15  C08  120.88  3.000
 R59  H7   C15  C14  119.93  3.000
 R59  C08  C15  C14  119.19  3.000
 R59  H8   C02  N01  107.43  3.000
 R59  H8   C02  C06  107.53  3.000
 R59  N01  C02  C06  110.09  3.000
 R59  H8   C02  C03  107.67  3.000
 R59  C06  C02  C03  111.51  3.000
 R59  N01  C02  C03  112.38  3.000
 R59  O05  C03  O04  127.37  3.000
 R59  O04  C03  C02  114.92  3.000
 R59  O05  C03  C02  117.71  3.000
 R59  H10  C06  H9   106.04  3.000
 R59  H10  C06  C07  110.07  3.000
 R59  H9   C06  C07  109.89  3.000
 R59  H10  C06  C02  107.53  3.000
 R59  H9   C06  C02  109.49  3.000
 R59  C07  C06  C02  113.52  3.000
 R59  C11  C07  C08  105.88  3.000
 R59  C08  C07  C06  127.56  3.000
 R59  C11  C07  C06  126.53  3.000
 R59  C09  C08  C07  107.25  3.000
 R59  C09  C08  C15  118.77  3.000
 R59  C07  C08  C15  133.98  3.000
 R59  N10  C09  C08  107.28  3.000
 R59  C08  C09  C12  122.28  3.000
 R59  N10  C09  C12  130.45  3.000
 R59  H11  C11  N10  120.39  3.000
 R59  H11  C11  C07  129.27  3.000
 R59  N10  C11  C07  110.34  3.000
 R59  H12  C18  C19  108.30  3.000
 R59  H12  C18  C16  109.06  3.000
 R59  C19  C18  C16  109.78  3.000
 R59  H12  C18  C21  108.70  3.000
 R59  C16  C18  C21  108.01  3.000
 R59  C19  C18  C21  112.93  3.000
 R59  H14  C19  H13  108.49  3.000
 R59  H14  C19  S20  109.48  3.000
 R59  H13  C19  S20  108.35  3.000
 R59  H14  C19  C18  110.57  3.000
 R59  H13  C19  C18  110.38  3.000
 R59  S20  C19  C18  109.53  3.000
 R59  H16  N10  C11  124.95  3.000
 R59  H16  N10  C09  125.78  3.000
 R59  C11  N10  C09  109.25  3.000
 R59  H18  S20  C19   97.12  3.000
 R59  H15  N01  C02  116.39  3.000
 R59  H15  N01  C16  116.76  3.000
 R59  C02  N01  C16  123.14  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
 R59  CONST_01  C07  C08  C15  C14  180.00   0.0  0
 R59  CONST_02  C09  C08  C15  C14    0.00   0.0  0
 R59  CONST_03  C09  C12  C13  C14    0.00   0.0  0
 R59  CONST_04  N10  C09  C12  C13  180.00   0.0  0
 R59  CONST_05  C08  C09  C12  C13    0.00   0.0  0
 R59  CONST_06  C08  C15  C14  C13    0.00   0.0  0
 R59  CONST_07  C11  N10  C09  C12  180.00   0.0  0
 R59  CONST_08  C07  C08  C09  C12  180.00   0.0  0
 R59  CONST_09  C15  C08  C09  C12    0.00   0.0  0
 R59  CONST_10  C15  C14  C13  C12    0.00   0.0  0
 R59  CONST_11  C11  C07  C08  C15  180.00   0.0  0
 R59  CONST_12  N10  C09  C08  C15  180.00   0.0  0
 R59  CONST_13  C09  N10  C11  C07    0.00   0.0  0
 R59  CONST_14  N10  C09  C08  C07    0.00   0.0  0
 R59  CONST_15  N10  C11  C07  C08    0.00   0.0  0
 R59  CONST_16  C11  N10  C09  C08    0.00   0.0  0
 R59  CONST_17  C11  C07  C08  C09    0.00   0.0  0
 R59  CONST_18  C06  C07  C08  C15    0.00   0.0  0
 R59  CONST_19  N10  C11  C07  C06  180.00   0.0  0
 R59  CONST_20  C09  C08  C07  C06  180.00   0.0  0
 R59  CONST_21  H6   C12  C13  C14  180.00   0.0  0
 R59  CONST_22  H7   C15  C14  C13  180.00   0.0  0
 R59  CONST_23  H16  N10  C09  C12    0.00   0.0  0
 R59  CONST_24  H4   C14  C13  C12  180.00   0.0  0
 R59  CONST_25  H5   C13  C14  C15  180.00   0.0  0
 R59  CONST_26  H11  C11  C07  C08  180.00   0.0  0
 R59  CONST_27  O17  C16  N01  C02    0.00   0.0  0
 R59  CONST_29  H15  N01  C16  C18    0.00   0.0  0
 R59  Var_01    C11  C07  C06  C02  -87.43  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
 R59  chir_01  C02  C03  N01  C06  negativ
 R59  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
 R59  plan-1  C14  0.020
 R59  plan-1  C13  0.020
 R59  plan-1  C12  0.020
 R59  plan-1  C15  0.020
 R59  plan-1  C06  0.020
 R59  plan-1  C07  0.020
 R59  plan-1  C08  0.020
 R59  plan-1  C09  0.020
 R59  plan-1  C11  0.020
 R59  plan-1  N10  0.020
 R59  plan-1  H6   0.020
 R59  plan-1  H7   0.020
 R59  plan-1  H11  0.020
 R59  plan-1  H16  0.020
 R59  plan-1  H4   0.020
 R59  plan-1  H5   0.020
 R59  plan-2  C16  0.020
 R59  plan-2  C02  0.020
 R59  plan-2  C18  0.020
 R59  plan-2  N01  0.020
 R59  plan-2  H15  0.020
 R59  plan-2  O17  0.020
 R59  plan-3  C02  0.020
 R59  plan-3  C03  0.020
 R59  plan-3  O04  0.020
 R59  plan-3  O05  0.020

