# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 00:15:01 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: {(R)-phenyl[(thiophen-2-ylacetyl)amino]methyl}boronic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OB(O)[C@@H](NC(=O)Cc1sccc1)c2ccccc2
#
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
 SM3  SM3  '{(R)-phenyl[(thiophen-2-ylacetyl)amino]methyl}boronic acid'  ligand  33  19  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_SM3
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
 SM3  CAF   C  CR15  0  -0.218  -0.3852   1.8522  -2.9812
 SM3  CAC   C  CR15  0  -0.183  -1.6009   2.1353  -3.6622
 SM3  CAB   C  CR15  0  -0.468  -2.2564   1.0068  -4.0475
 SM3  SAD   S  S2    0   0.223  -1.4044  -0.4048  -3.5820
 SM3  CAE   C  CR5   0  -0.146  -0.1420   0.5166  -2.8616
 SM3  CAG   C  CH2   0  -0.656   1.0325  -0.1335  -2.2052
 SM3  CAH   C  C     0   0.683   0.6880  -0.7031  -0.8651
 SM3  OAI   O  O     0  -0.487  -0.3449  -1.4027  -0.6984
 SM3  NAJ   N  NH1   0  -0.582   1.4541  -0.5115   0.1790
 SM3  CAK   C  CH1   0  -0.422   0.9790  -1.1477   1.3943
 SM3  B     B  B     0   0.565  -0.4112  -1.9326   0.8865
 SM3  OAT   O  OH1   0  -0.676  -1.6403  -1.5078   1.4254
 SM3  OAO   O  OH1   0  -0.677  -0.3662  -3.3439   0.8561
 SM3  CAL   C  CR6   0   0.115   0.7358  -0.1587   2.4945
 SM3  CAQ   C  CR16  0  -0.325   0.2520   1.1246   2.2417
 SM3  CAM   C  CR16  0  -0.311   0.9231  -0.5453   3.8209
 SM3  CAN   C  CR16  0  -0.241   0.6332   0.3207   4.8650
 SM3  CAS   C  CR16  0  -0.273   0.1525   1.5976   4.6023
 SM3  CAR   C  CR16  0  -0.237  -0.0342   1.9955   3.2860
 SM3  HAF   H  HCR5  0   0.268   0.2864   2.6096  -2.6007
 SM3  HAC   H  HCR5  0   0.268  -1.9666   3.1331  -3.8563
 SM3  HAB   H  HCR5  0   0.297  -3.1926   0.9280  -4.5781
 SM3  HAG1  H  HCH2  0   0.310   1.8392   0.5923  -2.1020
 SM3  HAG2  H  HCH2  0   0.325   1.4233  -0.9541  -2.8149
 SM3  HAJ   H  HNH1  0   0.419   2.2975   0.0419   0.1302
 SM3  HAK   H  HCH1  0   0.260   1.7292  -1.8714   1.7276
 SM3  HAT   H  HOH1  0   0.455  -1.6320  -0.5878   1.7016
 SM3  HAO   H  HOH1  0   0.450   0.5114  -3.6793   0.6613
 SM3  HAQ   H  HCR6  0   0.250   0.1055   1.4636   1.2226
 SM3  HAM   H  HCR6  0   0.249   1.3034  -1.5367   4.0390
 SM3  HAN   H  HCR6  0   0.256   0.7885  -0.0011   5.8868
 SM3  HAS   H  HCR6  0   0.254  -0.0696   2.2760   5.4158
 SM3  HAR   H  HCR6  0   0.256  -0.4058   2.9879   3.0651

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
 SM3  CAF  CAC   aromatic  1.422  0.020  1.422
 SM3  CAF  CAE   aromatic  1.363  0.020  1.363
 SM3  CAF  HAF   single    0.930  0.020  1.080
 SM3  CAC  CAB   aromatic  1.361  0.020  1.361
 SM3  CAC  HAC   single    0.930  0.020  1.080
 SM3  CAB  SAD   aromatic  1.713  0.020  1.713
 SM3  CAB  HAB   single    0.930  0.020  1.080
 SM3  SAD  CAE   aromatic  1.721  0.020  1.721
 SM3  CAE  CAG   single    1.494  0.020  1.494
 SM3  CAG  CAH   single    1.496  0.020  1.496
 SM3  CAG  HAG1  single    0.970  0.020  1.090
 SM3  CAG  HAG2  single    0.970  0.020  1.090
 SM3  CAH  OAI   double    1.259  0.020  1.259
 SM3  CAH  NAJ   single    1.309  0.020  1.309
 SM3  NAJ  CAK   single    1.452  0.020  1.452
 SM3  NAJ  HAJ   single    0.860  0.020  1.020
 SM3  CAK  B     single    1.675  0.020  1.675
 SM3  CAK  CAL   single    1.499  0.020  1.499
 SM3  CAK  HAK   single    0.970  0.020  1.090
 SM3  B    OAT   single    1.408  0.020  1.408
 SM3  B    OAO   single    1.412  0.020  1.412
 SM3  OAT  HAT   single    0.850  0.020  0.980
 SM3  OAO  HAO   single    0.850  0.020  0.980
 SM3  CAL  CAQ   aromatic  1.395  0.020  1.395
 SM3  CAL  CAM   aromatic  1.394  0.020  1.394
 SM3  CAQ  CAR   aromatic  1.390  0.020  1.390
 SM3  CAQ  HAQ   single    0.930  0.020  1.080
 SM3  CAM  CAN   aromatic  1.387  0.020  1.387
 SM3  CAM  HAM   single    0.930  0.020  1.080
 SM3  CAN  CAS   aromatic  1.389  0.020  1.389
 SM3  CAN  HAN   single    0.930  0.020  1.080
 SM3  CAS  CAR   aromatic  1.388  0.020  1.388
 SM3  CAS  HAS   single    0.930  0.020  1.080
 SM3  CAR  HAR   single    0.930  0.020  1.080

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
 SM3  HAF   CAF  CAE   123.00  3.000
 SM3  HAF   CAF  CAC   124.06  3.000
 SM3  CAE   CAF  CAC   112.94  3.000
 SM3  HAC   CAC  CAB   123.51  3.000
 SM3  HAC   CAC  CAF   124.01  3.000
 SM3  CAB   CAC  CAF   112.48  3.000
 SM3  HAB   CAB  SAD   120.33  3.000
 SM3  HAB   CAB  CAC   128.15  3.000
 SM3  SAD   CAB  CAC   111.52  3.000
 SM3  CAE   SAD  CAB    92.14  3.000
 SM3  CAG   CAE  SAD   121.84  3.000
 SM3  CAG   CAE  CAF   127.24  3.000
 SM3  SAD   CAE  CAF   110.92  3.000
 SM3  HAG2  CAG  HAG1  106.72  3.000
 SM3  HAG2  CAG  CAH   107.20  3.000
 SM3  HAG1  CAG  CAH   109.82  3.000
 SM3  HAG2  CAG  CAE   111.23  3.000
 SM3  HAG1  CAG  CAE   109.49  3.000
 SM3  CAH   CAG  CAE   112.21  3.000
 SM3  NAJ   CAH  OAI   117.13  3.000
 SM3  NAJ   CAH  CAG   121.59  3.000
 SM3  OAI   CAH  CAG   121.28  3.000
 SM3  HAJ   NAJ  CAK   123.63  3.000
 SM3  HAJ   NAJ  CAH   122.03  3.000
 SM3  CAK   NAJ  CAH   114.33  3.000
 SM3  HAK   CAK  CAL   108.90  3.000
 SM3  HAK   CAK  B     110.57  3.000
 SM3  CAL   CAK  B     113.39  3.000
 SM3  HAK   CAK  NAJ   108.69  3.000
 SM3  CAL   CAK  NAJ   112.23  3.000
 SM3  B     CAK  NAJ   102.90  3.000
 SM3  OAO   B    OAT   109.73  3.000
 SM3  OAO   B    CAK   116.64  3.000
 SM3  OAT   B    CAK   117.85  3.000
 SM3  HAT   OAT  B     113.05  3.000
 SM3  HAO   OAO  B     112.51  3.000
 SM3  CAM   CAL  CAQ   118.30  3.000
 SM3  CAM   CAL  CAK   119.57  3.000
 SM3  CAQ   CAL  CAK   122.03  3.000
 SM3  HAQ   CAQ  CAR   118.86  3.000
 SM3  HAQ   CAQ  CAL   120.34  3.000
 SM3  CAR   CAQ  CAL   120.80  3.000
 SM3  HAM   CAM  CAN   119.53  3.000
 SM3  HAM   CAM  CAL   119.48  3.000
 SM3  CAN   CAM  CAL   120.99  3.000
 SM3  HAN   CAN  CAS   120.08  3.000
 SM3  HAN   CAN  CAM   119.67  3.000
 SM3  CAS   CAN  CAM   120.24  3.000
 SM3  HAS   CAS  CAR   120.37  3.000
 SM3  HAS   CAS  CAN   120.33  3.000
 SM3  CAR   CAS  CAN   119.30  3.000
 SM3  HAR   CAR  CAS   120.17  3.000
 SM3  HAR   CAR  CAQ   119.47  3.000
 SM3  CAS   CAR  CAQ   120.36  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
 SM3  CONST_01  SAD  CAB  CAC  CAF    0.00   0.0  0
 SM3  CONST_02  CAB  SAD  CAE  CAF    0.00   0.0  0
 SM3  CONST_03  SAD  CAE  CAF  CAC    0.00   0.0  0
 SM3  CONST_04  CAE  SAD  CAB  CAC    0.00   0.0  0
 SM3  CONST_05  CAE  CAF  CAC  CAB    0.00   0.0  0
 SM3  CONST_06  CAS  CAR  CAQ  CAL    0.00   0.0  0
 SM3  CONST_07  CAS  CAN  CAM  CAL    0.00   0.0  0
 SM3  CONST_08  CAN  CAM  CAL  CAQ    0.00   0.0  0
 SM3  CONST_09  CAN  CAS  CAR  CAQ    0.00   0.0  0
 SM3  CONST_10  CAR  CAQ  CAL  CAM    0.00   0.0  0
 SM3  CONST_11  CAR  CAS  CAN  CAM    0.00   0.0  0
 SM3  CONST_12  CAG  CAE  CAF  CAC  180.00   0.0  0
 SM3  CONST_13  CAG  CAE  SAD  CAB  180.00   0.0  0
 SM3  CONST_14  CAR  CAQ  CAL  CAK  180.00   0.0  0
 SM3  CONST_15  CAN  CAM  CAL  CAK  180.00   0.0  0
 SM3  CONST_16  HAB  CAB  CAC  CAF  180.00   0.0  0
 SM3  CONST_17  HAF  CAF  CAC  CAB  180.00   0.0  0
 SM3  CONST_18  HAC  CAC  CAB  SAD  180.00   0.0  0
 SM3  CONST_19  HAR  CAR  CAQ  CAL  180.00   0.0  0
 SM3  CONST_20  HAN  CAN  CAM  CAL  180.00   0.0  0
 SM3  CONST_21  HAM  CAM  CAL  CAQ  180.00   0.0  0
 SM3  CONST_22  HAS  CAS  CAR  CAQ  180.00   0.0  0
 SM3  CONST_23  HAQ  CAQ  CAL  CAM  180.00   0.0  0
 SM3  CONST_24  CAK  NAJ  CAH  CAG  180.00   0.0  0
 SM3  CONST_25  CAK  NAJ  CAH  OAI    0.00   0.0  0
 SM3  CONST_26  HAJ  NAJ  CAH  CAG    0.00   0.0  0
 SM3  Var_01    CAH  CAG  CAE  CAF  104.28  30.0  2
 SM3  Var_02    OAI  CAH  CAG  CAE   46.84  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
 SM3  chir_01  CAK  NAJ  B  CAL  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
 SM3  plan-1  CAF  0.020
 SM3  plan-1  CAC  0.020
 SM3  plan-1  CAB  0.020
 SM3  plan-1  SAD  0.020
 SM3  plan-1  CAE  0.020
 SM3  plan-1  CAG  0.020
 SM3  plan-1  HAF  0.020
 SM3  plan-1  HAC  0.020
 SM3  plan-1  HAB  0.020
 SM3  plan-2  CAK  0.020
 SM3  plan-2  CAL  0.020
 SM3  plan-2  CAQ  0.020
 SM3  plan-2  CAM  0.020
 SM3  plan-2  CAN  0.020
 SM3  plan-2  CAS  0.020
 SM3  plan-2  CAR  0.020
 SM3  plan-2  HAQ  0.020
 SM3  plan-2  HAM  0.020
 SM3  plan-2  HAN  0.020
 SM3  plan-2  HAS  0.020
 SM3  plan-2  HAR  0.020
 SM3  plan-3  CAG  0.020
 SM3  plan-3  CAH  0.020
 SM3  plan-3  OAI  0.020
 SM3  plan-3  NAJ  0.020
 SM3  plan-3  CAK  0.020
 SM3  plan-3  HAJ  0.020

