# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 17:48:24 2022
#   Inital geometry file: a 79 line input string
#   Ligand name: (3R)-3-[(3S)-3-hydroxy-2-oxo-2,3-dihydro-1H-indol-3-yl]-L-serine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]([C@@H](O)[C@]1(O)C(=O)Nc2ccccc12)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
 R4K  R4K  (3R)-3-[(3S)-3-hydroxy-2-oxo-2,3-dihydro-1H-indol-3-yl]-L-serine  L-peptide  29  18  .  2012-08-28  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_R4K
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
 R4K  C50  C  CR56   0   0.097  59.1634  -138.1569  39.1954
 R4K  C51  C  CR16   0  -0.322  58.5869  -137.9346  40.4283
 R4K  C52  C  CR16   0  -0.266  57.3116  -137.3713  40.4854
 R4K  C53  C  CR16   0  -0.259  56.6386  -137.0403  39.3167
 R4K  C54  C  CR16   0  -0.310  57.2103  -137.2628  38.0659
 R4K  C55  C  CR56   0   0.375  58.4726  -137.8248  38.0310
 R4K  N31  N  NR15   0  -0.746  59.2344  -138.1600  36.9207
 R4K  C32  C  CR5    0   0.571  60.4497  -138.6551  37.2709
 R4K  O33  O  O      0  -0.449  61.3005  -139.0808  36.5200
 R4K  N    N  NH2    0  -0.791  61.5893  -136.1929  37.8538
 R4K  CA   C  CH1    0  -0.230  61.6997  -136.5086  39.2720
 R4K  C    C  C      0   0.400  62.9636  -135.9100  39.9407
 R4K  O    O  O      0  -0.612  64.0424  -136.1651  39.3643
 R4K  CB   C  CH1    0   0.051  61.7175  -138.0240  39.4208
 R4K  O34  O  OH1    0  -0.659  61.8025  -138.3149  40.7934
 R4K  C29  C  CR5    0  -0.015  60.4933  -138.7357  38.8121
 R4K  O30  O  OH1    0  -0.654  60.5197  -140.1060  39.1725
 R4K  H51  H  HCR6   0   0.250  59.1135  -138.1852  41.3391
 R4K  H52  H  HCR6   0   0.251  56.8456  -137.1897  41.4448
 R4K  H53  H  HCR6   0   0.256  55.6500  -136.6030  39.3730
 R4K  H31  H  HNR5   0   0.406  58.9463  -138.0108  35.9655
 R4K  HA   H  HCH1   0   0.216  60.8086  -136.1219  39.7739
 R4K  HB2  H  HCH1   0   0.200  62.6028  -138.4086  38.8860
 R4K  H34  H  HOH1   0   0.444  61.7698  -139.2720  40.8987
 R4K  H30  H  HOH1   0   0.452  61.2747  -140.5237  38.7362
 R4K  H54  H  HCR6   0   0.264  56.6808  -137.0068  37.1576
 R4K  OXT  O  OC    -1  -0.600  62.8034  -135.2269  40.9693
 R4K  H    H  HNH2   0   0.349  61.3626  -135.2125  37.7431
 R4K  H2   H  HNH2   0   0.333  62.5041  -136.3147  37.4334

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
 R4K  C50  C51  aromatic  1.379  0.020  1.379
 R4K  C50  C55  aromatic  1.394  0.020  1.394
 R4K  C50  C29  single    1.500  0.020  1.500
 R4K  C51  C52  aromatic  1.395  0.020  1.395
 R4K  C51  H51  single    0.930  0.020  1.080
 R4K  C52  C53  aromatic  1.389  0.020  1.389
 R4K  C52  H52  single    0.930  0.020  1.080
 R4K  C53  C54  aromatic  1.393  0.020  1.393
 R4K  C53  H53  single    0.930  0.020  1.080
 R4K  C54  C55  aromatic  1.382  0.020  1.382
 R4K  C55  N31  single    1.388  0.020  1.388
 R4K  N31  C32  single    1.358  0.020  1.358
 R4K  N31  H31  single    0.860  0.020  1.020
 R4K  C32  O33  double    1.212  0.020  1.212
 R4K  C32  C29  single    1.544  0.020  1.544
 R4K  N    CA   single    1.458  0.019  1.458
 R4K  N    H    single    0.860  0.020  0.860
 R4K  CA   C    single    1.525  0.021  1.525
 R4K  CA   CB   single    1.530  0.020  1.530
 R4K  CA   HA   single    0.970  0.020  0.970
 R4K  C    O    deloc     1.231  0.020  1.231
 R4K  CB   O34  single    1.406  0.020  1.406
 R4K  CB   C29  single    1.541  0.020  1.541
 R4K  CB   HB2  single    0.970  0.020  1.090
 R4K  O34  H34  single    0.850  0.020  0.980
 R4K  C29  O30  single    1.417  0.020  1.417
 R4K  O30  H30  single    0.850  0.020  0.980
 R4K  C54  H54  single    0.930  0.020  1.080
 R4K  N    H2   single    0.890  0.020  1.040
 R4K  C    OXT  deloc     1.245  0.020  1.245

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
 R4K  C29  C50  C55  108.53  3.000
 R4K  C29  C50  C51  131.39  3.000
 R4K  C55  C50  C51  120.08  3.000
 R4K  H51  C51  C52  120.27  3.000
 R4K  H51  C51  C50  120.80  3.000
 R4K  C52  C51  C50  118.93  3.000
 R4K  H52  C52  C53  119.84  3.000
 R4K  H52  C52  C51  119.85  3.000
 R4K  C53  C52  C51  120.32  3.000
 R4K  H53  C53  C54  119.08  3.000
 R4K  H53  C53  C52  119.69  3.000
 R4K  C54  C53  C52  121.24  3.000
 R4K  H54  C54  C55  121.46  3.000
 R4K  H54  C54  C53  121.00  3.000
 R4K  C55  C54  C53  117.54  3.000
 R4K  N31  C55  C54  128.30  3.000
 R4K  N31  C55  C50  109.80  3.000
 R4K  C54  C55  C50  121.89  3.000
 R4K  H31  N31  C32  123.62  3.000
 R4K  H31  N31  C55  124.41  3.000
 R4K  C32  N31  C55  111.90  3.000
 R4K  C29  C32  O33  125.47  3.000
 R4K  C29  C32  N31  107.56  3.000
 R4K  O33  C32  N31  126.61  3.000
 R4K  H2   N    H    105.84  3.000
 R4K  H2   N    CA   108.01  3.000
 R4K  H    N    CA   114.00  3.000
 R4K  HA   CA   CB   109.00  3.000
 R4K  HA   CA   C    109.00  3.000
 R4K  CB   CA   C    110.10  1.900
 R4K  HA   CA   N    110.00  3.000
 R4K  CB   CA   N    110.50  1.700
 R4K  C    CA   N    111.00  2.800
 R4K  OXT  C    O    127.17  3.000
 R4K  OXT  C    CA   117.60  3.000
 R4K  O    C    CA   120.80  1.700
 R4K  HB2  CB   C29  106.55  3.000
 R4K  HB2  CB   O34  110.65  3.000
 R4K  C29  CB   O34  109.76  3.000
 R4K  HB2  CB   CA   107.99  3.000
 R4K  C29  CB   CA   114.31  3.000
 R4K  O34  CB   CA   107.58  3.000
 R4K  H34  O34  CB   108.07  3.000
 R4K  O30  C29  CB   109.34  3.000
 R4K  O30  C29  C32  107.75  3.000
 R4K  CB   C29  C32  113.11  3.000
 R4K  O30  C29  C50  108.94  3.000
 R4K  CB   C29  C50  115.15  3.000
 R4K  C32  C29  C50  102.12  3.000
 R4K  H30  O30  C29  108.52  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
 R4K  CONST_01  C53  C52  C51  C50    0.00  0.0  0
 R4K  CONST_02  C53  C54  C55  C50    0.00  0.0  0
 R4K  CONST_03  C54  C55  C50  C51    0.00  0.0  0
 R4K  CONST_04  C54  C53  C52  C51    0.00  0.0  0
 R4K  CONST_05  C55  C50  C51  C52    0.00  0.0  0
 R4K  CONST_06  C55  C54  C53  C52    0.00  0.0  0
 R4K  CONST_07  C29  C32  N31  C55    0.00  0.0  0
 R4K  CONST_08  O33  C32  N31  C55  180.00  0.0  0
 R4K  CONST_09  H52  C52  C51  C50  180.00  0.0  0
 R4K  CONST_10  H54  C54  C55  C50  180.00  0.0  0
 R4K  CONST_11  H53  C53  C52  C51  180.00  0.0  0
 R4K  CONST_12  H51  C51  C52  C53  180.00  0.0  0
 R4K  CONST_13  H31  N31  C32  C29  180.00  0.0  0

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
 R4K  chir_01  CA   N    C    CB   positiv
 R4K  chir_02  CB   O34  CA   C29  positiv
 R4K  chir_03  C29  C50  C32  CB   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
 R4K  plan-1  C50  0.020
 R4K  plan-1  C51  0.020
 R4K  plan-1  C52  0.020
 R4K  plan-1  C53  0.020
 R4K  plan-1  C54  0.020
 R4K  plan-1  C55  0.020
 R4K  plan-1  N31  0.020
 R4K  plan-1  C32  0.020
 R4K  plan-1  O33  0.020
 R4K  plan-1  C29  0.020
 R4K  plan-1  H51  0.020
 R4K  plan-1  H52  0.020
 R4K  plan-1  H53  0.020
 R4K  plan-1  H31  0.020
 R4K  plan-1  H54  0.020
 R4K  plan-2  CA   0.020
 R4K  plan-2  C    0.020
 R4K  plan-2  O    0.020
 R4K  plan-2  OXT  0.020

