# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 06:48:41 2020
#   Inital geometry file: a 68 line input string
#   Ligand name: 3-(1-benzothiophen-3-yl)-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1csc2ccccc12)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
 4OG  4OG  3-(1-benzothiophen-3-yl)-L-alanine  L-peptide  26  15  .  2022-09-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_4OG
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
 4OG  C4   C  CR56  0  -0.220  -2.3721  -0.2781   0.1041
 4OG  C5   C  CR16  0  -0.252  -2.2549   2.4141  -0.4736
 4OG  C6   C  CR16  0  -0.274  -3.4645   1.8298  -0.0755
 4OG  C7   C  CR16  0  -0.274  -3.5344   0.4816   0.2163
 4OG  C8   C  CR16  0  -0.346  -1.1059   1.6576  -0.5785
 4OG  C9   C  CR56  0   0.189  -1.1473   0.2886  -0.2885
 4OG  N    N  NH2   0  -0.768   1.6752   0.9464   1.3120
 4OG  CA   C  CH1   0  -0.195   2.2182  -0.1166   0.5078
 4OG  CB   C  CH2   0  -0.556   1.3298  -0.3852  -0.7220
 4OG  C1   C  CR5   0   0.244  -0.0870  -0.6856  -0.3437
 4OG  C2   C  CR15  0  -0.560  -0.5285  -1.9195  -0.0059
 4OG  S3   S  S2    0   0.200  -2.2088  -1.9773   0.4023
 4OG  C    C  C     0   0.516   3.6482   0.1337   0.0421
 4OG  O1   O  O     0  -0.435   4.2198   1.1912   0.1289
 4OG  O2   O  OH1   0  -0.593   4.1993  -0.9535  -0.4848
 4OG  H1   H  HCR6  0   0.258  -2.2234   3.4720  -0.6988
 4OG  H2   H  HCR6  0   0.260  -4.3543   2.4405   0.0019
 4OG  H3   H  HCR6  0   0.267  -4.4684   0.0284   0.5223
 4OG  H4   H  HCR6  0   0.245  -0.1789   2.1218  -0.8908
 4OG  H6   H  HNH2  0   0.343   1.7000   1.8244   0.8083
 4OG  H8   H  HCH1  0   0.281   2.2292  -1.0301   1.1114
 4OG  H9   H  HCH2  0   0.261   1.3654   0.4812  -1.3886
 4OG  H10  H  HCH2  0   0.279   1.7405  -1.2230  -1.2853
 4OG  H11  H  HCR5  0   0.294   0.0548  -2.8288   0.0258
 4OG  H12  H  HOH1  0   0.482   5.0947  -0.7568  -0.7989
 4OG  H5   H  HNH2  0   0.356   2.2351   1.0811   2.1439

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
 4OG  C6  C7   aromatic  1.381  0.020  1.381
 4OG  C6  C5   aromatic  1.401  0.020  1.401
 4OG  C7  C4   aromatic  1.393  0.020  1.393
 4OG  C5  C8   aromatic  1.380  0.020  1.380
 4OG  C4  S3   aromatic  1.733  0.020  1.733
 4OG  C4  C9   aromatic  1.405  0.020  1.405
 4OG  S3  C2   aromatic  1.730  0.020  1.730
 4OG  C8  C9   aromatic  1.400  0.020  1.400
 4OG  C9  C1   aromatic  1.441  0.020  1.441
 4OG  C2  C1   aromatic  1.353  0.020  1.353
 4OG  C1  CB   single    1.497  0.020  1.497
 4OG  CB  CA   single    1.530  0.020  1.530
 4OG  O1  C    double    1.205  0.020  1.205
 4OG  CA  C    single    1.525  0.021  1.525
 4OG  CA  N    single    1.458  0.019  1.458
 4OG  C   O2   single    1.328  0.020  1.328
 4OG  C5  H1   single    0.930  0.020  1.080
 4OG  C6  H2   single    0.930  0.020  1.080
 4OG  C7  H3   single    0.930  0.020  1.080
 4OG  C8  H4   single    0.930  0.020  1.080
 4OG  N   H5   single    0.890  0.020  1.040
 4OG  N   H6   single    0.890  0.020  1.040
 4OG  CA  H8   single    0.970  0.020  1.090
 4OG  CB  H9   single    0.970  0.020  1.090
 4OG  CB  H10  single    0.970  0.020  1.090
 4OG  C2  H11  single    0.930  0.020  1.080
 4OG  O2  H12  single    0.850  0.020  0.980

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
 4OG  S3   C4  C9  111.18  3.000
 4OG  C9   C4  C7  121.99  3.000
 4OG  S3   C4  C7  126.83  3.000
 4OG  H1   C5  C8  119.73  3.000
 4OG  H1   C5  C6  119.47  3.000
 4OG  C8   C5  C6  120.79  3.000
 4OG  H2   C6  C7  119.61  3.000
 4OG  H2   C6  C5  119.67  3.000
 4OG  C7   C6  C5  120.72  3.000
 4OG  H3   C7  C6  120.81  3.000
 4OG  H3   C7  C4  120.96  3.000
 4OG  C6   C7  C4  118.23  3.000
 4OG  H4   C8  C9  120.29  3.000
 4OG  H4   C8  C5  119.99  3.000
 4OG  C9   C8  C5  119.72  3.000
 4OG  C1   C9  C8  129.15  3.000
 4OG  C1   C9  C4  112.29  3.000
 4OG  C8   C9  C4  118.55  3.000
 4OG  H6   N   H5  106.26  3.000
 4OG  H6   N   CA  110.68  3.000
 4OG  H5   N   CA  110.42  3.000
 4OG  H8   CA  C   107.21  3.000
 4OG  H8   CA  CB  107.48  3.000
 4OG  C    CA  CB  110.10  1.900
 4OG  H8   CA  N   108.18  3.000
 4OG  C    CA  N   111.00  2.800
 4OG  CB   CA  N   110.50  1.700
 4OG  H10  CB  H9  106.36  3.000
 4OG  H10  CB  C1  109.45  3.000
 4OG  H9   CB  C1  110.11  3.000
 4OG  H10  CB  CA  109.22  3.000
 4OG  H9   CB  CA  109.24  3.000
 4OG  C1   CB  CA  112.27  3.000
 4OG  C2   C1  CB  123.70  3.000
 4OG  CB   C1  C9  124.78  3.000
 4OG  C2   C1  C9  111.52  3.000
 4OG  H11  C2  S3  119.28  3.000
 4OG  H11  C2  C1  126.75  3.000
 4OG  S3   C2  C1  113.97  3.000
 4OG  C2   S3  C4   91.04  3.000
 4OG  O2   C   O1  123.38  3.000
 4OG  O2   C   CA  112.09  3.000
 4OG  O1   C   CA  124.53  3.000
 4OG  H12  O2  C   110.24  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
 4OG  CONST_01  C5   C6  C7  C4    0.00   0.0  0
 4OG  CONST_02  C1   C2  S3  C4    0.00   0.0  0
 4OG  CONST_03  C5   C8  C9  C4    0.00   0.0  0
 4OG  CONST_04  C2   C1  C9  C4    0.00   0.0  0
 4OG  CONST_05  C1   C9  C8  C5  180.00   0.0  0
 4OG  CONST_06  S3   C4  C7  C6  180.00   0.0  0
 4OG  CONST_07  C9   C4  C7  C6    0.00   0.0  0
 4OG  CONST_08  C9   C8  C5  C6    0.00   0.0  0
 4OG  CONST_09  C8   C5  C6  C7    0.00   0.0  0
 4OG  CONST_10  C2   S3  C4  C7  180.00   0.0  0
 4OG  CONST_11  C8   C9  C4  C7    0.00   0.0  0
 4OG  CONST_12  C1   C9  C4  C7  180.00   0.0  0
 4OG  CONST_13  S3   C4  C9  C8  180.00   0.0  0
 4OG  CONST_14  C2   C1  C9  C8  180.00   0.0  0
 4OG  CONST_15  C2   S3  C4  C9    0.00   0.0  0
 4OG  CONST_16  S3   C2  C1  C9    0.00   0.0  0
 4OG  CONST_17  S3   C4  C9  C1    0.00   0.0  0
 4OG  CONST_18  CB   C1  C9  C4  180.00   0.0  0
 4OG  CONST_19  CB   C1  C9  C8    0.00   0.0  0
 4OG  CONST_20  S3   C2  C1  CB  180.00   0.0  0
 4OG  CONST_21  H2   C6  C7  C4  180.00   0.0  0
 4OG  CONST_22  H11  C2  S3  C4  180.00   0.0  0
 4OG  CONST_23  H4   C8  C9  C4  180.00   0.0  0
 4OG  CONST_24  H3   C7  C6  C5  180.00   0.0  0
 4OG  CONST_25  H1   C5  C6  C7  180.00   0.0  0
 4OG  CONST_26  H12  O2  C   CA  180.00   0.0  0
 4OG  Var_01    CA   CB  C1  C9   94.50  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
 4OG  chir_01  CA  CB  C  N  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
 4OG  plan-1  C4   0.020
 4OG  plan-1  C5   0.020
 4OG  plan-1  C6   0.020
 4OG  plan-1  C7   0.020
 4OG  plan-1  C8   0.020
 4OG  plan-1  C9   0.020
 4OG  plan-1  CB   0.020
 4OG  plan-1  C1   0.020
 4OG  plan-1  C2   0.020
 4OG  plan-1  S3   0.020
 4OG  plan-1  H1   0.020
 4OG  plan-1  H2   0.020
 4OG  plan-1  H3   0.020
 4OG  plan-1  H4   0.020
 4OG  plan-1  H11  0.020
 4OG  plan-2  CA   0.020
 4OG  plan-2  C    0.020
 4OG  plan-2  O1   0.020
 4OG  plan-2  O2   0.020
 4OG  plan-2  H12  0.020

