# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 03:29:30 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  39  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 OK
;

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  OC    -1  -0.592  85.4755  7.2974  28.0228
 SM4  C22   C  C      0   0.406  85.0356  8.3635  27.5447
 SM4  O23   O  O      0  -0.616  85.7067  9.2781  27.0226
 SM4  C21   C  C1     0  -0.445  83.5434  8.6018  27.5881
 SM4  CAU   C  C1     0  -0.254  82.6743  7.7037  28.0563
 SM4  CAR   C  CR6    0   0.178  81.2214  7.8499  28.1692
 SM4  CAQ   C  CR16   0  -0.350  80.4972  6.8187  28.7682
 SM4  CAS   C  CR16   0  -0.339  80.5256  8.9812  27.7290
 SM4  CAN   C  CR16   0  -0.219  79.1572  9.0709  27.9068
 SM4  CAM   C  CR16   0  -0.360  78.4558  8.0436  28.5308
 SM4  CAL   C  CR6    0   0.108  79.1226  6.9030  28.9645
 SM4  CAK   C  CH1    0  -0.327  78.3528  5.7603  29.5908
 SM4  B     B  B      0   0.535  77.8302  4.7514  28.4641
 SM4  OAT   O  OH1    0  -0.612  77.3866  5.1926  27.2600
 SM4  OAO   O  OH1    0  -0.619  77.8225  3.4270  28.7487
 SM4  N     N  NH1    0  -0.639  79.1072  5.0721  30.6107
 SM4  CAH   C  C      0   0.531  79.4683  5.6655  31.7628
 SM4  OAI   O  O      0  -0.474  79.0500  6.7556  32.1133
 SM4  CAG   C  CH2    0  -0.638  80.4890  4.8804  32.5789
 SM4  CAE   C  CR5    0  -0.152  81.8015  4.8679  31.8639
 SM4  CAF   C  CR15   0  -0.239  82.3933  3.8360  31.1982
 SM4  CAC   C  CR15   0  -0.188  83.5876  4.2181  30.5252
 SM4  CAB   C  CR15   0  -0.473  83.8835  5.5353  30.6909
 SM4  SAD   S  S2     0   0.214  82.7138  6.3192  31.6696
 SM4  H21   H  H      0   0.226  83.2006  9.5627  27.2141
 SM4  HAU   H  H      0   0.252  83.0735  6.7620  28.4195
 SM4  HAQ   H  HCR6   0   0.240  81.0326  5.9394  29.1090
 SM4  HAS   H  HCR6   0   0.247  81.0526  9.7994  27.2554
 SM4  HAN   H  HCR6   0   0.258  78.6290  9.9541  27.5711
 SM4  HAM   H  HCR6   0   0.263  77.3896  8.1479  28.7005
 SM4  HAK   H  HCH1   0   0.282  77.4479  6.1815  30.0490
 SM4  HOAT  H  HOH1   0   0.486  77.4796  6.1417  27.1240
 SM4  HOAO  H  HOH1   0   0.494  77.5099  2.8685  28.0283
 SM4  HN    H  HNH1   0   0.402  79.5266  4.1842  30.3855
 SM4  HAG1  H  HCH2   0   0.290  80.5710  5.3374  33.5653
 SM4  HAG2  H  HCH2   0   0.294  80.1532  3.8507  32.7202
 SM4  HAF   H  HCR5   0   0.266  81.9863  2.8337  31.1852
 SM4  HAC   H  HCR5   0   0.266  84.1930  3.5419  29.9389
 SM4  HAB   H  HCR5   0   0.300  84.6975  6.0966  30.2566

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   deloc     1.248  0.020  1.248
 SM4  C22  O23   deloc     1.249  0.020  1.249
 SM4  C22  C21   single    1.512  0.020  1.512
 SM4  C21  CAU   double    1.335  0.020  1.335
 SM4  C21  H21   single    0.930  0.020  1.080
 SM4  CAU  CAR   single    1.465  0.020  1.465
 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  1.383  0.020  1.383
 SM4  CAS  HAS   single    0.930  0.020  1.080
 SM4  CAN  CAM   aromatic  1.392  0.020  1.392
 SM4  CAN  HAN   single    0.930  0.020  1.080
 SM4  CAM  CAL   aromatic  1.391  0.020  1.391
 SM4  CAM  HAM   single    0.930  0.020  1.080
 SM4  CAL  CAK   single    1.513  0.020  1.513
 SM4  CAK  B     single    1.600  0.020  1.600
 SM4  CAK  N     single    1.443  0.020  1.443
 SM4  CAK  HAK   single    0.970  0.020  1.090
 SM4  B    OAT   single    1.357  0.020  1.357
 SM4  B    OAO   single    1.355  0.020  1.355
 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    1.525  0.020  1.525
 SM4  CAG  CAE   single    1.495  0.020  1.495
 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  C21   C22  O23   115.28  3.000
 SM4  C21   C22  O24   118.13  3.000
 SM4  O23   C22  O24   126.59  3.000
 SM4  H21   C21  CAU   120.69  3.000
 SM4  H21   C21  C22   116.16  3.000
 SM4  CAU   C21  C22   123.15  3.000
 SM4  HAU   CAU  CAR   115.20  3.000
 SM4  HAU   CAU  C21   117.50  3.000
 SM4  CAR   CAU  C21   127.29  3.000
 SM4  CAS   CAR  CAQ   118.33  3.000
 SM4  CAQ   CAR  CAU   118.31  3.000
 SM4  CAS   CAR  CAU   123.36  3.000
 SM4  HAQ   CAQ  CAL   119.51  3.000
 SM4  HAQ   CAQ  CAR   118.55  3.000
 SM4  CAL   CAQ  CAR   121.92  3.000
 SM4  HAS   CAS  CAN   119.28  3.000
 SM4  HAS   CAS  CAR   120.44  3.000
 SM4  CAN   CAS  CAR   120.27  3.000
 SM4  HAN   CAN  CAM   119.70  3.000
 SM4  HAN   CAN  CAS   119.73  3.000
 SM4  CAM   CAN  CAS   120.57  3.000
 SM4  HAM   CAM  CAL   120.09  3.000
 SM4  HAM   CAM  CAN   119.64  3.000
 SM4  CAL   CAM  CAN   120.25  3.000
 SM4  CAK   CAL  CAM   120.30  3.000
 SM4  CAK   CAL  CAQ   121.02  3.000
 SM4  CAM   CAL  CAQ   118.65  3.000
 SM4  HAK   CAK  N     108.59  3.000
 SM4  HAK   CAK  B     105.46  3.000
 SM4  N     CAK  B     111.57  3.000
 SM4  HAK   CAK  CAL   107.59  3.000
 SM4  N     CAK  CAL   112.74  3.000
 SM4  B     CAK  CAL   110.54  3.000
 SM4  OAO   B    OAT   120.16  3.000
 SM4  OAO   B    CAK   118.06  3.000
 SM4  OAT   B    CAK   121.77  3.000
 SM4  HOAT  OAT  B     114.46  3.000
 SM4  HOAO  OAO  B     114.30  3.000
 SM4  HN    N    CAH   117.93  3.000
 SM4  HN    N    CAK   118.68  3.000
 SM4  CAH   N    CAK   122.35  3.000
 SM4  CAG   CAH  OAI   122.43  3.000
 SM4  CAG   CAH  N     114.27  3.000
 SM4  OAI   CAH  N     123.27  3.000
 SM4  HAG2  CAG  HAG1  107.53  3.000
 SM4  HAG2  CAG  CAE   108.90  3.000
 SM4  HAG1  CAG  CAE   111.73  3.000
 SM4  HAG2  CAG  CAH   110.42  3.000
 SM4  HAG1  CAG  CAH   108.60  3.000
 SM4  CAE   CAG  CAH   109.64  3.000
 SM4  SAD   CAE  CAF   110.63  3.000
 SM4  SAD   CAE  CAG   120.74  3.000
 SM4  CAF   CAE  CAG   128.40  3.000
 SM4  HAF   CAF  CAC   123.97  3.000
 SM4  HAF   CAF  CAE   122.95  3.000
 SM4  CAC   CAF  CAE   113.08  3.000
 SM4  HAC   CAC  CAB   123.38  3.000
 SM4  HAC   CAC  CAF   123.97  3.000
 SM4  CAB   CAC  CAF   112.64  3.000
 SM4  HAB   CAB  SAD   120.41  3.000
 SM4  HAB   CAB  CAC   128.19  3.000
 SM4  SAD   CAB  CAC   111.33  3.000
 SM4  CAB   SAD  CAE    92.32  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  Var_01    CAS  CAR  CAU  C21     2.84  30.0  2
 SM4  Var_02    CAF  CAE  CAG  CAH  -106.55  30.0  2
 SM4  Var_03    CAR  CAU  C21  C22   178.47   0.0  2
 SM4  Var_04    CAE  CAG  CAH  N      68.42  30.0  3
 SM4  Var_05    CAU  C21  C22  O24    -3.13  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-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

