# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 28 23:09:04 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: (2E)-3-(3-{(R)-(dihydroxyboranyl)[(thiophen-2-ylacetyl)amino]methyl}phenyl)prop-2-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OB(O)[C@@H](NC(=O)Cc1sccc1)c2cccc(/C=C/C(O)=O)c2
#
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
 SM4  SM4  '(2E)-3-(3-{(R)-(dihydroxyboranyl)[(thiophen-2-ylacetyl)amino]methyl}phenyl)prop-2-enoic acid'  ligand  40  24  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SM4
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
 SM4  O24   O  OH1   0  -0.506  85.3115   6.9714  27.6832
 SM4  C22   C  C     0   0.469  84.9421   8.1893  27.2998
 SM4  O23   O  O     0  -0.448  85.7221   9.0054  26.8620
 SM4  C21   C  C1    0  -0.375  83.5068   8.4619  27.4477
 SM4  CAU   C  C1    0  -0.297  82.6277   7.5923  27.9602
 SM4  CAR   C  CR6   0   0.170  81.1970   7.8171  28.1478
 SM4  CAQ   C  CR16  0  -0.374  80.4489   6.8020  28.7442
 SM4  CAS   C  CR16  0  -0.283  80.5503   8.9980  27.7694
 SM4  CAN   C  CR16  0  -0.180  79.1963   9.1487  28.0025
 SM4  CAM   C  CR16  0  -0.303  78.4686   8.1342  28.6154
 SM4  CAL   C  CR6   0   0.032  79.0874   6.9468  28.9877
 SM4  CAK   C  CH1   0  -0.301  78.2864   5.8161  29.6005
 SM4  B     B  B     0   0.674  77.7734   4.8642  28.4228
 SM4  OAT   O  OH1   0  -0.659  77.0385   5.3377  27.3853
 SM4  OAO   O  OH1   0  -0.753  78.1138   3.5548  28.4731
 SM4  N     N  NH1   0  -0.587  79.0434   5.0779  30.5806
 SM4  CAH   C  C     0   0.535  79.4911   5.6420  31.7165
 SM4  OAI   O  O     0  -0.485  79.1676   6.7593  32.0798
 SM4  CAG   C  CH2   0  -0.626  80.5036   4.7977  32.4773
 SM4  CAE   C  CR5   0  -0.213  81.8295   4.9027  31.7927
 SM4  CAF   C  CR15  0  -0.128  82.4669   3.9640  31.0373
 SM4  CAC   C  CR15  0  -0.242  83.6747   4.4411  30.4566
 SM4  CAB   C  CR15  0  -0.402  83.9339   5.7361  30.7821
 SM4  SAD   S  S2    0   0.169  82.7086   6.3867  31.7897
 SM4  HO24  H  HOH1  0   0.500  86.2666   6.8668  27.5652
 SM4  H21   H  H     0   0.292  83.2056   9.4463  27.1120
 SM4  HAU   H  H     0   0.262  82.9808   6.6213  28.2910
 SM4  HAQ   H  HCR6  0   0.262  80.9521   5.8886  29.0423
 SM4  HAS   H  HCR6  0   0.252  81.0988   9.8051  27.3021
 SM4  HAN   H  HCR6  0   0.266  78.7017  10.0682  27.7185
 SM4  HAM   H  HCR6  0   0.275  77.4160   8.2857  28.8280
 SM4  HAK   H  HCH1  0   0.309  77.3996   6.2497  30.0791
 SM4  HOAT  H  HOH1  0   0.440  76.8466   6.2794  27.4152
 SM4  HOAO  H  HOH1  0   0.467  77.7989   3.0259  27.7321
 SM4  HN    H  HNH1  0   0.417  79.3444   4.1427  30.3586
 SM4  HAG1  H  HCH2  0   0.268  80.5552   5.1504  33.5075
 SM4  HAG2  H  HCH2  0   0.295  80.2008   3.7493  32.5008
 SM4  HAF   H  HCR5  0   0.273  82.0855   2.9610  30.9005
 SM4  HAC   H  HCR5  0   0.234  84.3197   3.8452  29.8273
 SM4  HAB   H  HCR5  0   0.303  84.7704   6.3446  30.4762

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
 SM4  O24  C22   single    1.329  0.020  1.329
 SM4  O24  HO24  single    0.850  0.020  0.980
 SM4  C22  O23   double    1.211  0.020  1.211
 SM4  C22  C21   single    1.468  0.020  1.468
 SM4  C21  CAU   double    1.339  0.020  1.339
 SM4  C21  H21   single    0.930  0.020  1.080
 SM4  CAU  CAR   single    1.460  0.020  1.460
 SM4  CAU  HAU   single    0.930  0.020  1.080
 SM4  CAR  CAS   aromatic  1.399  0.020  1.399
 SM4  CAR  CAQ   aromatic  1.395  0.020  1.395
 SM4  CAQ  CAL   aromatic  1.391  0.020  1.391
 SM4  CAQ  HAQ   single    0.930  0.020  1.080
 SM4  CAS  CAN   aromatic  1.382  0.020  1.382
 SM4  CAS  HAS   single    0.930  0.020  1.080
 SM4  CAN  CAM   aromatic  1.391  0.020  1.391
 SM4  CAN  HAN   single    0.930  0.020  1.080
 SM4  CAM  CAL   aromatic  1.390  0.020  1.390
 SM4  CAM  HAM   single    0.930  0.020  1.080
 SM4  CAL  CAK   single    1.515  0.020  1.515
 SM4  CAK  B     single    1.599  0.020  1.599
 SM4  CAK  N     single    1.442  0.020  1.442
 SM4  CAK  HAK   single    0.970  0.020  1.090
 SM4  B    OAT   single    1.357  0.020  1.357
 SM4  B    OAO   single    1.354  0.020  1.354
 SM4  OAT  HOAT  single    0.850  0.020  0.980
 SM4  OAO  HOAO  single    0.850  0.020  0.980
 SM4  N    CAH   single    1.345  0.020  1.345
 SM4  N    HN    single    0.860  0.020  1.020
 SM4  CAH  OAI   double    1.219  0.020  1.219
 SM4  CAH  CAG   single    1.522  0.020  1.522
 SM4  CAG  CAE   single    1.496  0.020  1.496
 SM4  CAG  HAG1  single    0.970  0.020  1.090
 SM4  CAG  HAG2  single    0.970  0.020  1.090
 SM4  CAE  CAF   aromatic  1.363  0.020  1.363
 SM4  CAE  SAD   aromatic  1.725  0.020  1.725
 SM4  CAF  CAC   aromatic  1.423  0.020  1.423
 SM4  CAF  HAF   single    0.930  0.020  1.080
 SM4  CAC  CAB   aromatic  1.360  0.020  1.360
 SM4  CAC  HAC   single    0.930  0.020  1.080
 SM4  CAB  SAD   aromatic  1.715  0.020  1.715
 SM4  CAB  HAB   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
 SM4  HO24  O24  C22   109.76  3.000
 SM4  C21   C22  O23   122.75  3.000
 SM4  C21   C22  O24   114.37  3.000
 SM4  O23   C22  O24   122.88  3.000
 SM4  H21   C21  CAU   121.78  3.000
 SM4  H21   C21  C22   114.17  3.000
 SM4  CAU   C21  C22   124.05  3.000
 SM4  HAU   CAU  CAR   114.68  3.000
 SM4  HAU   CAU  C21   118.97  3.000
 SM4  CAR   CAU  C21   126.34  3.000
 SM4  CAS   CAR  CAQ   118.83  3.000
 SM4  CAQ   CAR  CAU   117.92  3.000
 SM4  CAS   CAR  CAU   123.25  3.000
 SM4  HAQ   CAQ  CAL   119.59  3.000
 SM4  HAQ   CAQ  CAR   118.79  3.000
 SM4  CAL   CAQ  CAR   121.61  3.000
 SM4  HAS   CAS  CAN   119.22  3.000
 SM4  HAS   CAS  CAR   120.82  3.000
 SM4  CAN   CAS  CAR   119.96  3.000
 SM4  HAN   CAN  CAM   119.76  3.000
 SM4  HAN   CAN  CAS   119.75  3.000
 SM4  CAM   CAN  CAS   120.49  3.000
 SM4  HAM   CAM  CAL   119.93  3.000
 SM4  HAM   CAM  CAN   119.49  3.000
 SM4  CAL   CAM  CAN   120.55  3.000
 SM4  CAK   CAL  CAM   120.70  3.000
 SM4  CAK   CAL  CAQ   120.71  3.000
 SM4  CAM   CAL  CAQ   118.56  3.000
 SM4  HAK   CAK  N     109.28  3.000
 SM4  HAK   CAK  B     107.30  3.000
 SM4  N     CAK  B     111.37  3.000
 SM4  HAK   CAK  CAL   107.99  3.000
 SM4  N     CAK  CAL   112.30  3.000
 SM4  B     CAK  CAL   108.42  3.000
 SM4  OAO   B    OAT   120.14  3.000
 SM4  OAO   B    CAK   117.89  3.000
 SM4  OAT   B    CAK   121.95  3.000
 SM4  HOAT  OAT  B     115.22  3.000
 SM4  HOAO  OAO  B     114.85  3.000
 SM4  HN    N    CAH   118.43  3.000
 SM4  HN    N    CAK   118.84  3.000
 SM4  CAH   N    CAK   122.29  3.000
 SM4  CAG   CAH  OAI   122.42  3.000
 SM4  CAG   CAH  N     114.26  3.000
 SM4  OAI   CAH  N     123.23  3.000
 SM4  HAG2  CAG  HAG1  107.67  3.000
 SM4  HAG2  CAG  CAE   108.85  3.000
 SM4  HAG1  CAG  CAE   111.58  3.000
 SM4  HAG2  CAG  CAH   111.04  3.000
 SM4  HAG1  CAG  CAH   108.93  3.000
 SM4  CAE   CAG  CAH   108.78  3.000
 SM4  SAD   CAE  CAF   110.68  3.000
 SM4  SAD   CAE  CAG   120.86  3.000
 SM4  CAF   CAE  CAG   128.30  3.000
 SM4  HAF   CAF  CAC   123.97  3.000
 SM4  HAF   CAF  CAE   122.94  3.000
 SM4  CAC   CAF  CAE   113.09  3.000
 SM4  HAC   CAC  CAB   123.42  3.000
 SM4  HAC   CAC  CAF   124.03  3.000
 SM4  CAB   CAC  CAF   112.55  3.000
 SM4  HAB   CAB  SAD   120.45  3.000
 SM4  HAB   CAB  CAC   128.09  3.000
 SM4  SAD   CAB  CAC   111.45  3.000
 SM4  CAB   SAD  CAE    92.22  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
 SM4  CONST_01  CAM   CAN  CAS  CAR     0.00   0.0  0
 SM4  CONST_02  CAM   CAL  CAQ  CAR     0.00   0.0  0
 SM4  CONST_03  CAN   CAS  CAR  CAQ     0.00   0.0  0
 SM4  CONST_04  CAN   CAM  CAL  CAQ     0.00   0.0  0
 SM4  CONST_05  CAL   CAQ  CAR  CAS     0.00   0.0  0
 SM4  CONST_06  CAL   CAM  CAN  CAS     0.00   0.0  0
 SM4  CONST_07  CAB   CAC  CAF  CAE     0.00   0.0  0
 SM4  CONST_08  CAC   CAB  SAD  CAE     0.00   0.0  0
 SM4  CONST_09  CAB   SAD  CAE  CAF     0.00   0.0  0
 SM4  CONST_10  SAD   CAB  CAC  CAF     0.00   0.0  0
 SM4  CONST_11  SAD   CAE  CAF  CAC     0.00   0.0  0
 SM4  CONST_12  CAN   CAS  CAR  CAU   180.00   0.0  0
 SM4  CONST_13  CAL   CAQ  CAR  CAU   180.00   0.0  0
 SM4  CONST_14  CAK   CAL  CAQ  CAR   180.00   0.0  0
 SM4  CONST_15  CAK   CAL  CAM  CAN   180.00   0.0  0
 SM4  CONST_16  CAC   CAF  CAE  CAG   180.00   0.0  0
 SM4  CONST_17  CAB   SAD  CAE  CAG   180.00   0.0  0
 SM4  CONST_18  HAN   CAN  CAS  CAR   180.00   0.0  0
 SM4  CONST_19  HAS   CAS  CAR  CAQ   180.00   0.0  0
 SM4  CONST_20  HAM   CAM  CAL  CAQ   180.00   0.0  0
 SM4  CONST_21  HAQ   CAQ  CAR  CAS   180.00   0.0  0
 SM4  CONST_22  HAC   CAC  CAF  CAE   180.00   0.0  0
 SM4  CONST_23  HAB   CAB  SAD  CAE   180.00   0.0  0
 SM4  CONST_24  HAF   CAF  CAC  CAB   180.00   0.0  0
 SM4  CONST_25  OAI   CAH  N    CAK     0.00   0.0  0
 SM4  CONST_26  CAG   CAH  N    CAK   180.00   0.0  0
 SM4  CONST_27  HN    N    CAH  OAI   180.00   0.0  0
 SM4  CONST_28  HO24  O24  C22  O23     0.00   0.0  0
 SM4  Var_01    CAS   CAR  CAU  C21     1.69  30.0  2
 SM4  Var_02    CAF   CAE  CAG  CAH  -106.95  30.0  2
 SM4  Var_03    CAR   CAU  C21  C22   179.06   0.0  2
 SM4  Var_04    CAE   CAG  CAH  N      76.99  30.0  3
 SM4  Var_05    CAU   C21  C22  O24     1.97  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
 SM4  chir_01  CAK  CAL  B  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
 SM4  plan-1  CAG   0.020
 SM4  plan-1  CAE   0.020
 SM4  plan-1  CAF   0.020
 SM4  plan-1  CAC   0.020
 SM4  plan-1  CAB   0.020
 SM4  plan-1  SAD   0.020
 SM4  plan-1  HAF   0.020
 SM4  plan-1  HAC   0.020
 SM4  plan-1  HAB   0.020
 SM4  plan-2  CAU   0.020
 SM4  plan-2  CAR   0.020
 SM4  plan-2  CAQ   0.020
 SM4  plan-2  CAS   0.020
 SM4  plan-2  CAN   0.020
 SM4  plan-2  CAM   0.020
 SM4  plan-2  CAL   0.020
 SM4  plan-2  CAK   0.020
 SM4  plan-2  HAQ   0.020
 SM4  plan-2  HAS   0.020
 SM4  plan-2  HAN   0.020
 SM4  plan-2  HAM   0.020
 SM4  plan-3  CAK   0.020
 SM4  plan-3  N     0.020
 SM4  plan-3  CAH   0.020
 SM4  plan-3  OAI   0.020
 SM4  plan-3  CAG   0.020
 SM4  plan-3  HN    0.020
 SM4  plan-4  O24   0.020
 SM4  plan-4  C22   0.020
 SM4  plan-4  O23   0.020
 SM4  plan-4  C21   0.020
 SM4  plan-4  HO24  0.020
 SM4  plan-5  C22   0.020
 SM4  plan-5  C21   0.020
 SM4  plan-5  CAU   0.020
 SM4  plan-5  CAR   0.020
 SM4  plan-5  H21   0.020
 SM4  plan-5  HAU   0.020

