# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 10:06:11 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: (2~{R})-2-methyl-~{N}-(phenylmethyl)-3-sulfanyl-propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](CS)C(=O)NCc1ccccc1
#
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
 9DU  9DU  (2~{R})-2-methyl-~{N}-(phenylmethyl)-3-sulfanyl-propanamide  ligand  29  14  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_9DU
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
 9DU  CAJ  C  CR16  0  -0.283  -2.8863  -0.6871  -1.0628
 9DU  CAK  C  CR16  0  -0.241  -4.0176  -0.1549  -1.6644
 9DU  CAL  C  CR16  0  -0.264  -4.8387   0.7151  -0.9569
 9DU  CAN  C  CR16  0  -0.242  -4.5226   1.0479   0.3531
 9DU  CAM  C  CR16  0  -0.291  -3.3887   0.5137   0.9521
 9DU  CAI  C  CR6   0   0.051  -2.5621  -0.3592   0.2520
 9DU  CAH  C  CH2   0  -0.319  -1.3182  -0.9124   0.8894
 9DU  NAG  N  NH1   0  -0.630  -0.1607  -0.1447   0.4656
 9DU  CAD  C  C     0   0.582   1.0946  -0.5178   0.7482
 9DU  OAE  O  O     0  -0.503   1.3561  -1.5512   1.3499
 9DU  CAC  C  CH1   0  -0.378   2.1822   0.4403   0.2868
 9DU  CAF  C  CH3   0  -0.652   2.8357   1.0800   1.5113
 9DU  CAB  C  CH2   0  -0.537   3.1741  -0.3352  -0.5787
 9DU  SAA  S  S2    0  -0.256   4.3979   0.8169  -1.2909
 9DU  H1   H  HCR6  0   0.255  -2.2517  -1.3680  -1.6178
 9DU  H2   H  HCR6  0   0.258  -4.2601  -0.4211  -2.6850
 9DU  H3   H  HCR6  0   0.258  -5.7223   1.1293  -1.4247
 9DU  H4   H  HCR6  0   0.258  -5.1584   1.7230   0.9111
 9DU  H5   H  HCR6  0   0.254  -3.1463   0.7761   1.9751
 9DU  H6   H  HCH2  0   0.254  -1.4113  -0.8871   1.9785
 9DU  H7   H  HCH2  0   0.257  -1.1794  -1.9572   0.6048
 9DU  H8   H  HNH1  0   0.405  -0.3188   0.7337  -0.0010
 9DU  H9   H  HCH1  0   0.264   1.7329   1.2288  -0.3245
 9DU  H10  H  HCH3  0   0.233   3.3383   0.3305   2.1231
 9DU  H11  H  HCH3  0   0.244   3.5743   1.8259   1.2194
 9DU  H12  H  HCH3  0   0.244   2.0926   1.5832   2.1306
 9DU  H13  H  HCH2  0   0.270   3.6873  -1.0899   0.0161
 9DU  H14  H  HCH2  0   0.282   2.6512  -0.8339  -1.3950
 9DU  H15  H  HSH1  0   0.227   5.0581  -0.0799  -2.0305

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
 9DU  CAL  CAK  aromatic  1.390  0.020  1.390
 9DU  CAL  CAN  aromatic  1.388  0.020  1.388
 9DU  CAK  CAJ  aromatic  1.387  0.020  1.387
 9DU  CAN  CAM  aromatic  1.389  0.020  1.389
 9DU  CAJ  CAI  aromatic  1.393  0.020  1.393
 9DU  CAM  CAI  aromatic  1.391  0.020  1.391
 9DU  CAI  CAH  single    1.503  0.020  1.503
 9DU  CAH  NAG  single    1.452  0.020  1.452
 9DU  NAG  CAD  single    1.340  0.020  1.340
 9DU  CAD  OAE  double    1.224  0.020  1.224
 9DU  CAD  CAC  single    1.521  0.020  1.521
 9DU  SAA  CAB  single    1.826  0.020  1.826
 9DU  CAB  CAC  single    1.528  0.020  1.528
 9DU  CAC  CAF  single    1.528  0.020  1.528
 9DU  CAJ  H1   single    0.930  0.020  1.080
 9DU  CAK  H2   single    0.930  0.020  1.080
 9DU  CAL  H3   single    0.930  0.020  1.080
 9DU  CAN  H4   single    0.930  0.020  1.080
 9DU  CAM  H5   single    0.930  0.020  1.080
 9DU  CAH  H6   single    0.970  0.020  1.090
 9DU  CAH  H7   single    0.970  0.020  1.090
 9DU  NAG  H8   single    0.860  0.020  1.020
 9DU  CAC  H9   single    0.970  0.020  1.090
 9DU  CAF  H10  single    0.970  0.020  1.090
 9DU  CAF  H11  single    0.970  0.020  1.090
 9DU  CAF  H12  single    0.970  0.020  1.090
 9DU  CAB  H13  single    0.970  0.020  1.090
 9DU  CAB  H14  single    0.970  0.020  1.090
 9DU  SAA  H15  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
 9DU  H1   CAJ  CAI  119.66  3.000
 9DU  H1   CAJ  CAK  119.77  3.000
 9DU  CAI  CAJ  CAK  120.57  3.000
 9DU  H2   CAK  CAL  120.12  3.000
 9DU  H2   CAK  CAJ  119.81  3.000
 9DU  CAL  CAK  CAJ  120.07  3.000
 9DU  H3   CAL  CAN  120.14  3.000
 9DU  H3   CAL  CAK  120.12  3.000
 9DU  CAN  CAL  CAK  119.74  3.000
 9DU  H4   CAN  CAM  119.80  3.000
 9DU  H4   CAN  CAL  120.16  3.000
 9DU  CAM  CAN  CAL  120.04  3.000
 9DU  H5   CAM  CAI  119.62  3.000
 9DU  H5   CAM  CAN  119.77  3.000
 9DU  CAI  CAM  CAN  120.61  3.000
 9DU  CAH  CAI  CAM  120.61  3.000
 9DU  CAH  CAI  CAJ  120.40  3.000
 9DU  CAM  CAI  CAJ  118.97  3.000
 9DU  H7   CAH  H6   107.01  3.000
 9DU  H7   CAH  NAG  109.18  3.000
 9DU  H6   CAH  NAG  110.27  3.000
 9DU  H7   CAH  CAI  110.30  3.000
 9DU  H6   CAH  CAI  110.08  3.000
 9DU  NAG  CAH  CAI  109.95  3.000
 9DU  H8   NAG  CAD  119.19  3.000
 9DU  H8   NAG  CAH  118.12  3.000
 9DU  CAD  NAG  CAH  122.55  3.000
 9DU  CAC  CAD  OAE  121.88  3.000
 9DU  CAC  CAD  NAG  115.50  3.000
 9DU  OAE  CAD  NAG  122.62  3.000
 9DU  H9   CAC  CAB  108.41  3.000
 9DU  H9   CAC  CAF  108.76  3.000
 9DU  CAB  CAC  CAF  112.88  3.000
 9DU  H9   CAC  CAD  109.25  3.000
 9DU  CAF  CAC  CAD  109.05  3.000
 9DU  CAB  CAC  CAD  108.44  3.000
 9DU  H12  CAF  H11  107.34  3.000
 9DU  H12  CAF  H10  108.22  3.000
 9DU  H11  CAF  H10  107.97  3.000
 9DU  H12  CAF  CAC  110.91  3.000
 9DU  H11  CAF  CAC  111.21  3.000
 9DU  H10  CAF  CAC  111.04  3.000
 9DU  H14  CAB  H13  108.54  3.000
 9DU  H14  CAB  SAA  108.55  3.000
 9DU  H13  CAB  SAA  109.54  3.000
 9DU  H14  CAB  CAC  110.19  3.000
 9DU  H13  CAB  CAC  110.38  3.000
 9DU  SAA  CAB  CAC  109.62  3.000
 9DU  H15  SAA  CAB   97.10  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
 9DU  CONST_01  CAN  CAL  CAK  CAJ     0.00   0.0  0
 9DU  CONST_02  CAN  CAM  CAI  CAJ     0.00   0.0  0
 9DU  CONST_03  CAM  CAN  CAL  CAK     0.00   0.0  0
 9DU  CONST_04  CAM  CAI  CAJ  CAK     0.00   0.0  0
 9DU  CONST_05  CAI  CAJ  CAK  CAL     0.00   0.0  0
 9DU  CONST_06  CAI  CAM  CAN  CAL     0.00   0.0  0
 9DU  CONST_07  CAH  CAI  CAJ  CAK   180.00   0.0  0
 9DU  CONST_08  CAH  CAI  CAM  CAN   180.00   0.0  0
 9DU  CONST_09  H3   CAL  CAK  CAJ   180.00   0.0  0
 9DU  CONST_10  H5   CAM  CAI  CAJ   180.00   0.0  0
 9DU  CONST_11  H4   CAN  CAL  CAK   180.00   0.0  0
 9DU  CONST_12  H1   CAJ  CAK  CAL   180.00   0.0  0
 9DU  CONST_13  H2   CAK  CAL  CAN   180.00   0.0  0
 9DU  CONST_14  OAE  CAD  NAG  CAH     0.00   0.0  0
 9DU  CONST_15  CAC  CAD  NAG  CAH   180.00   0.0  0
 9DU  CONST_16  H8   NAG  CAD  OAE   180.00   0.0  0
 9DU  Var_01    NAG  CAH  CAI  CAJ    80.19  30.0  2
 9DU  Var_02    CAD  NAG  CAH  CAI  -171.54  30.0  3

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
 9DU  chir_01  CAC  CAD  CAB  CAF  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
 9DU  plan-1  CAJ  0.020
 9DU  plan-1  CAK  0.020
 9DU  plan-1  CAL  0.020
 9DU  plan-1  CAN  0.020
 9DU  plan-1  CAM  0.020
 9DU  plan-1  CAI  0.020
 9DU  plan-1  CAH  0.020
 9DU  plan-1  H1   0.020
 9DU  plan-1  H2   0.020
 9DU  plan-1  H3   0.020
 9DU  plan-1  H4   0.020
 9DU  plan-1  H5   0.020
 9DU  plan-2  CAH  0.020
 9DU  plan-2  NAG  0.020
 9DU  plan-2  CAD  0.020
 9DU  plan-2  OAE  0.020
 9DU  plan-2  CAC  0.020
 9DU  plan-2  H8   0.020

