# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 26 09:12:36 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: N-benzoyl-D-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](NC(=O)c1ccccc1)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
 S2D  S2D  'N-benzoyl-D-alanine      '  D-peptide  25  14  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_S2D
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
 S2D  O2    O  O     0  -0.488   0.1981  -2.0950   0.1511
 S2D  C4    C  C     0   0.545   0.3105  -0.8832   0.0226
 S2D  C27   C  CR6   0  -0.030   1.6547  -0.2301  -0.0193
 S2D  C32   C  CR16  0  -0.269   2.7206  -0.8848   0.5946
 S2D  C31   C  CR16  0  -0.242   3.9886  -0.3256   0.5805
 S2D  C30   C  CR16  0  -0.251   4.2089   0.8851  -0.0646
 S2D  C29   C  CR16  0  -0.240   3.1555   1.5337  -0.6942
 S2D  C28   C  CR16  0  -0.296   1.8830   0.9809  -0.6703
 S2D  N1    N  NH1   0  -0.657  -0.7477  -0.0606  -0.0720
 S2D  C2    C  CH1   0  -0.196  -2.1048  -0.5453  -0.1064
 S2D  C3    C  CH3   0  -0.654  -2.5369  -0.9490  -1.5192
 S2D  C1    C  C     0   0.548  -3.0176   0.5267   0.4542
 S2D  O1    O  O     0  -0.433  -2.6682   1.6447   0.7365
 S2D  OXT   O  OH1   0  -0.585  -4.2574   0.0856   0.5788
 S2D  H1    H  HNH1  0   0.408  -0.6083   0.9366  -0.1199
 S2D  H32   H  HCR6  0   0.260   2.5540  -1.8304   1.0932
 S2D  H28   H  HCR6  0   0.261   1.0838   1.4936  -1.1909
 S2D  H31   H  HCR6  0   0.263   4.8068  -0.8358   1.0713
 S2D  H30   H  HCR6  0   0.265   5.2003   1.3186  -0.0820
 S2D  H29   H  HCR6  0   0.265   3.3238   2.4690  -1.2111
 S2D  H2    H  HCH1  0   0.297  -2.1800  -1.4177   0.5482
 S2D  H3C1  H  HCH3  0   0.253  -1.8668  -1.7201  -1.8953
 S2D  H3C2  H  HCH3  0   0.248  -3.5478  -1.3525  -1.5272
 S2D  H3C3  H  HCH3  0   0.240  -2.4937  -0.0960  -2.1962
 S2D  HXT   H  HOH1  0   0.489  -4.8335   0.7916   0.9093

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
 S2D  O2   C4    double    1.224  0.020  1.224
 S2D  C4   C27   single    1.495  0.020  1.495
 S2D  C4   N1    single    1.344  0.020  1.344
 S2D  C27  C32   aromatic  1.393  0.020  1.393
 S2D  C27  C28   aromatic  1.394  0.020  1.394
 S2D  C32  C31   aromatic  1.386  0.020  1.386
 S2D  C32  H32   single    0.930  0.020  1.080
 S2D  C31  C30   aromatic  1.389  0.020  1.389
 S2D  C31  H31   single    0.930  0.020  1.080
 S2D  C30  C29   aromatic  1.388  0.020  1.388
 S2D  C30  H30   single    0.930  0.020  1.080
 S2D  C29  C28   aromatic  1.388  0.020  1.388
 S2D  C29  H29   single    0.930  0.020  1.080
 S2D  C28  H28   single    0.930  0.020  1.080
 S2D  N1   C2    single    1.441  0.020  1.441
 S2D  N1   H1    single    0.860  0.020  1.020
 S2D  C2   C3    single    1.532  0.020  1.532
 S2D  C2   C1    single    1.516  0.020  1.516
 S2D  C2   H2    single    0.970  0.020  1.090
 S2D  C3   H3C1  single    0.970  0.020  1.090
 S2D  C3   H3C2  single    0.970  0.020  1.090
 S2D  C3   H3C3  single    0.970  0.020  1.090
 S2D  C1   O1    double    1.205  0.020  1.205
 S2D  C1   OXT   single    1.322  0.020  1.322
 S2D  OXT  HXT   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
 S2D  N1    C4   C27   116.02  3.000
 S2D  N1    C4   O2    122.78  3.000
 S2D  C27   C4   O2    121.20  3.000
 S2D  C28   C27  C32   119.26  3.000
 S2D  C28   C27  C4    122.68  3.000
 S2D  C32   C27  C4    118.04  3.000
 S2D  H32   C32  C31   119.89  3.000
 S2D  H32   C32  C27   119.73  3.000
 S2D  C31   C32  C27   120.38  3.000
 S2D  H31   C31  C30   120.11  3.000
 S2D  H31   C31  C32   119.80  3.000
 S2D  C30   C31  C32   120.09  3.000
 S2D  H30   C30  C29   120.05  3.000
 S2D  H30   C30  C31   120.12  3.000
 S2D  C29   C30  C31   119.83  3.000
 S2D  H29   C29  C28   119.69  3.000
 S2D  H29   C29  C30   120.17  3.000
 S2D  C28   C29  C30   120.13  3.000
 S2D  H28   C28  C29   118.68  3.000
 S2D  H28   C28  C27   121.00  3.000
 S2D  C29   C28  C27   120.29  3.000
 S2D  H1    N1   C2    117.50  3.000
 S2D  H1    N1   C4    120.00  3.000
 S2D  C2    N1   C4    122.50  3.000
 S2D  H2    C2   C1    107.55  3.000
 S2D  H2    C2   C3    108.82  3.000
 S2D  C1    C2   C3    110.96  3.000
 S2D  H2    C2   N1    108.59  3.000
 S2D  C1    C2   N1    108.69  3.000
 S2D  C3    C2   N1    112.10  3.000
 S2D  H3C3  C3   H3C2  108.81  3.000
 S2D  H3C3  C3   H3C1  108.39  3.000
 S2D  H3C2  C3   H3C1  107.85  3.000
 S2D  H3C3  C3   C2    110.82  3.000
 S2D  H3C2  C3   C2    111.50  3.000
 S2D  H3C1  C3   C2    109.37  3.000
 S2D  OXT   C1   O1    124.03  3.000
 S2D  OXT   C1   C2    111.33  3.000
 S2D  O1    C1   C2    124.64  3.000
 S2D  HXT   OXT  C1    110.27  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
 S2D  CONST_01  C30  C31  C32  C27    0.00   0.0  0
 S2D  CONST_02  C30  C29  C28  C27    0.00   0.0  0
 S2D  CONST_03  C29  C28  C27  C32    0.00   0.0  0
 S2D  CONST_04  C29  C30  C31  C32    0.00   0.0  0
 S2D  CONST_05  C28  C27  C32  C31    0.00   0.0  0
 S2D  CONST_06  C28  C29  C30  C31    0.00   0.0  0
 S2D  CONST_07  C31  C32  C27  C4   180.00   0.0  0
 S2D  CONST_08  C29  C28  C27  C4   180.00   0.0  0
 S2D  CONST_09  H31  C31  C32  C27  180.00   0.0  0
 S2D  CONST_10  H29  C29  C28  C27  180.00   0.0  0
 S2D  CONST_11  H28  C28  C27  C32  180.00   0.0  0
 S2D  CONST_12  H30  C30  C31  C32  180.00   0.0  0
 S2D  CONST_13  H32  C32  C31  C30  180.00   0.0  0
 S2D  CONST_14  C2   N1   C4   C27  180.00   0.0  0
 S2D  CONST_15  H1   N1   C4   C27    0.00   0.0  0
 S2D  CONST_16  C2   N1   C4   O2     0.00   0.0  0
 S2D  CONST_17  HXT  OXT  C1   C2   180.00   0.0  0
 S2D  Var_01    C32  C27  C4   O2   -24.87  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
 S2D  chir_01  C2  N1  C3  C1  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
 S2D  plan-1  C4   0.020
 S2D  plan-1  C27  0.020
 S2D  plan-1  C32  0.020
 S2D  plan-1  C31  0.020
 S2D  plan-1  C30  0.020
 S2D  plan-1  C29  0.020
 S2D  plan-1  C28  0.020
 S2D  plan-1  H32  0.020
 S2D  plan-1  H28  0.020
 S2D  plan-1  H31  0.020
 S2D  plan-1  H30  0.020
 S2D  plan-1  H29  0.020
 S2D  plan-2  O2   0.020
 S2D  plan-2  C4   0.020
 S2D  plan-2  C27  0.020
 S2D  plan-2  N1   0.020
 S2D  plan-2  C2   0.020
 S2D  plan-2  H1   0.020
 S2D  plan-3  C2   0.020
 S2D  plan-3  C1   0.020
 S2D  plan-3  O1   0.020
 S2D  plan-3  OXT  0.020
 S2D  plan-3  HXT  0.020

