# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 14:27:30 2022
#   Inital geometry file: a 117 line input string
#   Ligand name: [(1S)-1-(acetylamino)-2-naphthalen-1-ylethyl](dihydroxy)(L-serinato-kappaO~3~)borate(1-)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@H](Cc1cccc2ccccc12)[B-](O)(O)OC[C@H](N)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
 SBD  SBD  '[(1S)-1-(acetylamino)-2-naphthalen-1-ylethyl](dihydroxy)(L-serinato-kappaO~3~)borate(1-)'  D-peptide  47  26  .  2016-05-13  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_SBD
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
 SBD  N     N  NH2    0  -0.805  16.8743   4.0144  27.1470
 SBD  CA    C  CH1    0  -0.255  18.0945   3.3359  26.7324
 SBD  CB    C  CH2    0  -0.059  18.2557   3.4697  25.2220
 SBD  O3    O  OC2    0  -0.562  17.1686   2.8732  24.5831
 SBD  C     C  C      0   0.399  19.3246   3.8657  27.5069
 SBD  O     O  O      0  -0.613  20.4439   3.5355  27.0617
 SBD  OXT   O  OC    -1  -0.607  19.1076   4.5382  28.5350
 SBD  N13   N  NH1    0  -0.613  15.1985   1.9941  21.4508
 SBD  C12   C  CH1    0  -0.263  15.4847   2.3376  22.8470
 SBD  C11   C  CH2    0  -0.552  14.2829   3.0552  23.4894
 SBD  C1    C  CR6    0   0.125  13.0175   2.2406  23.4866
 SBD  C10   C  CR66   0   0.071  11.9989   2.3807  22.4963
 SBD  C5    C  CR66   0   0.118  10.8615   1.5236  22.5354
 SBD  C2    C  CR16   0  -0.334  12.8527   1.2826  24.4607
 SBD  C3    C  CR16   0  -0.237  11.7292   0.4381  24.5019
 SBD  C4    C  CR16   0  -0.344  10.7499   0.5517  23.5548
 SBD  O1    O  OB     0  -0.726  18.0384   2.3995  22.4182
 SBD  O2    O  OB     0  -0.776  16.9070   4.5313  22.8512
 SBD  B     B  B     -1   0.523  16.9525   3.0971  23.1465
 SBD  O15   O  O      0  -0.537  15.4627   4.0285  20.4801
 SBD  C16   C  CH3    0  -0.766  14.7224   2.2339  19.1012
 SBD  C9    C  CR16   0  -0.341  12.0580   3.3531  21.4655
 SBD  C8    C  CR16   0  -0.255  11.0655   3.4623  20.5296
 SBD  C7    C  CR16   0  -0.262   9.9492   2.6027  20.5675
 SBD  C6    C  CR16   0  -0.311   9.8525   1.6585  21.5509
 SBD  H     H  HNH2   0   0.323  16.8274   4.0230  28.1564
 SBD  H2    H  HNH2   0   0.327  16.0742   3.4905  26.8189
 SBD  HA    H  HCH1   0   0.173  18.0589   2.2514  26.9532
 SBD  HB2   H  HCH2   0   0.140  18.3405   4.5418  24.9827
 SBD  HB3   H  HCH2   0   0.146  19.2057   3.0072  24.9261
 SBD  HN3   H  HNH1   0   0.384  14.8901   1.0535  21.2665
 SBD  H12   H  HCH1   0   0.188  15.5627   1.3614  23.3375
 SBD  H111  H  HCH2   0   0.243  14.5551   3.2625  24.5259
 SBD  H112  H  HCH2   0   0.218  14.1336   4.0312  23.0247
 SBD  HC2   H  HCR6   0   0.240  13.6164   1.1725  25.2227
 SBD  H3    H  HCR6   0   0.248  11.6442  -0.3004  25.2890
 SBD  H4    H  HCR6   0   0.246   9.8794  -0.0930  23.5749
 SBD  HO1   H  H      0   0.412  18.0032   2.6385  21.4895
 SBD  HO2   H  H      0   0.425  16.3728   4.6235  22.0527
 SBD  H161  H  HCH3   0   0.254  15.3979   2.5415  18.3041
 SBD  H162  H  HCH3   0   0.243  14.6641   1.1469  19.1094
 SBD  H163  H  HCH3   0   0.257  13.7324   2.6239  18.8594
 SBD  H9    H  HCR6   0   0.250  12.9004   4.0276  21.4129
 SBD  H8    H  HCR6   0   0.252  11.1372   4.2155  19.7555
 SBD  H7    H  HCR6   0   0.251   9.1714   2.6965  19.8207
 SBD  H6    H  HCR6   0   0.249   8.9951   0.9968  21.5907
 SBD  C14   C  C      0   0.514  15.1739   2.8290  20.4144

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
 SBD  N    CA    single    1.458  0.019  1.458
 SBD  N    H     single    0.860  0.020  0.860
 SBD  N    H2    single    0.890  0.020  1.040
 SBD  CA   CB    single    1.521  0.033  1.521
 SBD  CA   C     single    1.525  0.021  1.525
 SBD  CA   HA    single    0.970  0.020  0.970
 SBD  CB   O3    single    1.395  0.020  1.395
 SBD  CB   HB2   single    0.970  0.020  1.090
 SBD  CB   HB3   single    0.970  0.020  1.090
 SBD  O3   B     single    1.470  0.020  1.470
 SBD  C    O     deloc     1.231  0.020  1.231
 SBD  C    OXT   deloc     1.248  0.020  1.248
 SBD  N13  C12   single    1.466  0.020  1.466
 SBD  N13  C14   single    1.331  0.020  1.331
 SBD  N13  HN3   single    0.860  0.020  1.020
 SBD  C12  C11   single    1.540  0.020  1.540
 SBD  C12  B     single    1.680  0.020  1.680
 SBD  C12  H12   single    0.970  0.020  1.090
 SBD  C11  C1    single    1.505  0.020  1.505
 SBD  C11  H111  single    0.970  0.020  1.090
 SBD  C11  H112  single    0.970  0.020  1.090
 SBD  C1   C10   aromatic  1.427  0.020  1.427
 SBD  C1   C2    aromatic  1.376  0.020  1.376
 SBD  C10  C5    aromatic  1.425  0.020  1.425
 SBD  C10  C9    aromatic  1.418  0.020  1.418
 SBD  C5   C4    aromatic  1.413  0.020  1.413
 SBD  C5   C6    aromatic  1.416  0.020  1.416
 SBD  C2   C3    aromatic  1.406  0.020  1.406
 SBD  C2   HC2   single    0.930  0.020  1.080
 SBD  C3   C4    aromatic  1.367  0.020  1.367
 SBD  C3   H3    single    0.930  0.020  1.080
 SBD  C4   H4    single    0.930  0.020  1.080
 SBD  O1   B     single    1.482  0.020  1.482
 SBD  O1   HO1   single    0.850  0.020  0.980
 SBD  O2   B     single    1.465  0.020  1.465
 SBD  O2   HO2   single    0.850  0.020  0.980
 SBD  C14  O15   double    1.236  0.020  1.236
 SBD  C14  C16   single    1.511  0.020  1.511
 SBD  C16  H161  single    0.970  0.020  1.090
 SBD  C16  H162  single    0.970  0.020  1.090
 SBD  C16  H163  single    0.970  0.020  1.090
 SBD  C9   C8    aromatic  1.369  0.020  1.369
 SBD  C9   H9    single    0.930  0.020  1.080
 SBD  C8   C7    aromatic  1.409  0.020  1.409
 SBD  C8   H8    single    0.930  0.020  1.080
 SBD  C7   C6    aromatic  1.367  0.020  1.367
 SBD  C7   H7    single    0.930  0.020  1.080
 SBD  C6   H6    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
 SBD  H2    N    H     106.97  3.000
 SBD  H2    N    CA    109.22  3.000
 SBD  H     N    CA    114.00  3.000
 SBD  HA    CA   C     110.00  3.000
 SBD  HA    CA   CB    109.00  3.000
 SBD  C     CA   CB    110.50  1.500
 SBD  HA    CA   N     110.00  3.000
 SBD  C     CA   N     111.00  2.800
 SBD  CB    CA   N     110.40  1.500
 SBD  HB3   CB   HB2   106.56  3.000
 SBD  HB3   CB   O3    111.78  3.000
 SBD  HB2   CB   O3    112.12  3.000
 SBD  HB3   CB   CA    108.76  3.000
 SBD  HB2   CB   CA    107.98  3.000
 SBD  O3    CB   CA    109.50  3.000
 SBD  B     O3   CB    119.81  3.000
 SBD  OXT   C    O     126.31  3.000
 SBD  OXT   C    CA    120.80  1.700
 SBD  O     C    CA    120.80  1.700
 SBD  HN3   N13  C14   115.96  3.000
 SBD  HN3   N13  C12   116.93  3.000
 SBD  C14   N13  C12   126.74  3.000
 SBD  H12   C12  B     105.12  3.000
 SBD  H12   C12  C11   106.51  3.000
 SBD  B     C12  C11   113.39  3.000
 SBD  H12   C12  N13   103.39  3.000
 SBD  B     C12  N13   116.51  3.000
 SBD  C11   C12  N13   110.74  3.000
 SBD  H112  C11  H111  105.59  3.000
 SBD  H112  C11  C1    111.61  3.000
 SBD  H111  C11  C1    108.31  3.000
 SBD  H112  C11  C12   110.23  3.000
 SBD  H111  C11  C12   106.86  3.000
 SBD  C1    C11  C12   113.77  3.000
 SBD  C2    C1   C10   118.29  3.000
 SBD  C2    C1   C11   118.44  3.000
 SBD  C10   C1   C11   123.24  3.000
 SBD  C9    C10  C5    117.75  3.000
 SBD  C9    C10  C1    122.80  3.000
 SBD  C5    C10  C1    119.44  3.000
 SBD  C6    C5   C4    120.72  3.000
 SBD  C6    C5   C10   119.50  3.000
 SBD  C4    C5   C10   119.78  3.000
 SBD  HC2   C2   C3    118.76  3.000
 SBD  HC2   C2   C1    118.93  3.000
 SBD  C3    C2   C1    122.31  3.000
 SBD  H3    C3   C4    120.27  3.000
 SBD  H3    C3   C2    119.59  3.000
 SBD  C4    C3   C2    120.14  3.000
 SBD  H4    C4   C3    120.88  3.000
 SBD  H4    C4   C5    119.09  3.000
 SBD  C3    C4   C5    120.03  3.000
 SBD  HO1   O1   B     109.36  3.000
 SBD  HO2   O2   B     106.11  3.000
 SBD  O2    B    O1    112.62  3.000
 SBD  O2    B    C12   112.31  3.000
 SBD  O1    B    C12   109.87  3.000
 SBD  O2    B    O3    110.53  3.000
 SBD  O1    B    O3    107.51  3.000
 SBD  C12   B    O3    103.53  3.000
 SBD  H163  C16  H162  108.05  3.000
 SBD  H163  C16  H161  107.43  3.000
 SBD  H162  C16  H161  108.70  3.000
 SBD  H163  C16  C14   108.84  3.000
 SBD  H162  C16  C14   113.75  3.000
 SBD  H161  C16  C14   109.85  3.000
 SBD  H9    C9   C8    118.84  3.000
 SBD  H9    C9   C10   119.73  3.000
 SBD  C8    C9   C10   121.43  3.000
 SBD  H8    C8   C7    119.75  3.000
 SBD  H8    C8   C9    119.77  3.000
 SBD  C7    C8   C9    120.49  3.000
 SBD  H7    C7   C6    120.37  3.000
 SBD  H7    C7   C8    119.85  3.000
 SBD  C6    C7   C8    119.78  3.000
 SBD  H6    C6   C7    120.28  3.000
 SBD  H6    C6   C5    118.69  3.000
 SBD  C7    C6   C5    121.04  3.000
 SBD  C16   C14  O15   119.89  3.000
 SBD  C16   C14  N13   115.80  3.000
 SBD  O15   C14  N13   124.28  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
 SBD  CONST_01  C4    C5   C10  C1      0.00   0.0  0
 SBD  CONST_02  C6    C5   C10  C1    180.00   0.0  0
 SBD  CONST_03  C8    C9   C10  C1    180.00   0.0  0
 SBD  CONST_04  C4    C3   C2   C1      0.00   0.0  0
 SBD  CONST_05  C3    C2   C1   C10     0.00   0.0  0
 SBD  CONST_06  C3    C4   C5   C10     0.00   0.0  0
 SBD  CONST_07  C7    C6   C5   C10     0.00   0.0  0
 SBD  CONST_08  C7    C8   C9   C10     0.00   0.0  0
 SBD  CONST_09  C2    C1   C10  C5      0.00   0.0  0
 SBD  CONST_10  C8    C9   C10  C5      0.00   0.0  0
 SBD  CONST_11  C2    C3   C4   C5      0.00   0.0  0
 SBD  CONST_12  C8    C7   C6   C5      0.00   0.0  0
 SBD  CONST_13  C9    C10  C1   C2    180.00   0.0  0
 SBD  CONST_14  C6    C5   C4   C3    180.00   0.0  0
 SBD  CONST_15  C9    C10  C5   C4    180.00   0.0  0
 SBD  CONST_16  C7    C6   C5   C4    180.00   0.0  0
 SBD  CONST_17  C6    C5   C10  C9      0.00   0.0  0
 SBD  CONST_18  C6    C7   C8   C9      0.00   0.0  0
 SBD  CONST_19  C5    C10  C1   C11   180.00   0.0  0
 SBD  CONST_20  C9    C10  C1   C11     0.00   0.0  0
 SBD  CONST_21  C3    C2   C1   C11   180.00   0.0  0
 SBD  CONST_22  H9    C9   C10  C1      0.00   0.0  0
 SBD  CONST_23  H3    C3   C2   C1    180.00   0.0  0
 SBD  CONST_24  HC2   C2   C1   C10   180.00   0.0  0
 SBD  CONST_25  H4    C4   C5   C10   180.00   0.0  0
 SBD  CONST_26  H6    C6   C5   C10   180.00   0.0  0
 SBD  CONST_27  H8    C8   C9   C10   180.00   0.0  0
 SBD  CONST_28  H7    C7   C6   C5    180.00   0.0  0
 SBD  CONST_29  O15   C14  N13  C12     0.00   0.0  0
 SBD  CONST_30  C16   C14  N13  C12   180.00   0.0  0
 SBD  CONST_31  HN3   N13  C14  O15   180.00   0.0  0
 SBD  Var_01    C10   C1   C11  C12   -96.92  30.0  2
 SBD  Var_02    C12   B    O3   CB   -174.56  30.0  3
 SBD  Var_03    H161  C16  C14  N13  -133.95  30.0  3
 SBD  Var_04    HB2   CB   O3   B      48.14  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
 SBD  chir_01  CA   N    CB   C  negativ
 SBD  chir_02  C12  N13  C11  B  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
 SBD  plan-1  C11  0.020
 SBD  plan-1  C1   0.020
 SBD  plan-1  C10  0.020
 SBD  plan-1  C5   0.020
 SBD  plan-1  C2   0.020
 SBD  plan-1  C3   0.020
 SBD  plan-1  C4   0.020
 SBD  plan-1  C9   0.020
 SBD  plan-1  C8   0.020
 SBD  plan-1  C7   0.020
 SBD  plan-1  C6   0.020
 SBD  plan-1  HC2  0.020
 SBD  plan-1  H3   0.020
 SBD  plan-1  H4   0.020
 SBD  plan-1  H9   0.020
 SBD  plan-1  H8   0.020
 SBD  plan-1  H7   0.020
 SBD  plan-1  H6   0.020
 SBD  plan-2  N13  0.020
 SBD  plan-2  C12  0.020
 SBD  plan-2  O15  0.020
 SBD  plan-2  C16  0.020
 SBD  plan-2  HN3  0.020
 SBD  plan-2  C14  0.020
 SBD  plan-3  CA   0.020
 SBD  plan-3  C    0.020
 SBD  plan-3  O    0.020
 SBD  plan-3  OXT  0.020

