# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 05:53:25 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: [(1R)-1-(acetylamino)-2-naphthalen-1-ylethyl](trihydroxy)borate(1-)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H](Cc1cccc2ccccc12)[B-](O)(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
 SRB  SRB  '[(1R)-1-(acetylamino)-2-naphthalen-1-ylethyl](trihydroxy)borate(1-)'  ligand  37  20  .  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_SRB
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
 SRB  C1    C  CR6    0   0.179  -0.9271   0.5325   0.9235
 SRB  C2    C  CR66   0   0.061  -1.7921  -0.4417   0.3414
 SRB  C3    C  CR66   0   0.112  -3.1526  -0.1125   0.0891
 SRB  C4    C  CR16   0  -0.347  -3.6357   1.1715   0.4333
 SRB  C5    C  CR16   0  -0.245  -2.8000   2.0820   1.0157
 SRB  C6    C  CR16   0  -0.342  -1.4521   1.7551   1.2581
 SRB  C7    C  CR16   0  -0.352  -1.3497  -1.7491   0.0158
 SRB  C8    C  CR16   0  -0.264  -2.2017  -2.6674  -0.5376
 SRB  C9    C  CR16   0  -0.262  -3.5452  -2.3309  -0.8000
 SRB  C10   C  CR16   0  -0.316  -4.0068  -1.0815  -0.4903
 SRB  C7'   C  CH2    0  -0.572   0.5185   0.2245   1.1891
 SRB  C8'   C  CH1    0  -0.250   1.4165   0.1603  -0.0659
 SRB  C9'   C  CH3    0  -0.777   4.4575  -1.9010   0.9569
 SRB  N     N  NH1    0  -0.627   2.7253  -0.3469   0.3244
 SRB  O     O  O      0  -0.527   2.1885  -2.5327   0.5667
 SRB  B     B  B     -1   0.457   1.5976   1.6097  -0.8670
 SRB  H4    H  HCR6   0   0.246  -4.6738   1.4144   0.2395
 SRB  H5    H  HCR6   0   0.249  -3.1682   3.0609   1.2955
 SRB  H6    H  HCR6   0   0.235  -0.8157   2.4958   1.7288
 SRB  H7    H  HCR6   0   0.270  -0.3225  -2.0311   0.2098
 SRB  H8    H  HCR6   0   0.251  -1.8434  -3.6606  -0.7769
 SRB  H9    H  HCR6   0   0.252  -4.2084  -3.0645  -1.2404
 SRB  H10   H  HCR6   0   0.249  -5.0401  -0.8172  -0.6824
 SRB  H7'1  H  HCH2   0   0.228   0.5807  -0.7212   1.7373
 SRB  H7'2  H  HCH2   0   0.224   0.9193   0.9815   1.8697
 SRB  H8'   H  HCH1   0   0.190   0.9791  -0.5716  -0.7548
 SRB  H9'1  H  HCH3   0   0.255   4.8528  -2.6778   0.3025
 SRB  H9'2  H  HCH3   0   0.242   5.1049  -1.0287   0.8852
 SRB  H9'3  H  HCH3   0   0.257   4.5103  -2.2818   1.9774
 SRB  HN    H  HNH1   0   0.386   3.4845   0.3138   0.3367
 SRB  HOB1  H  H      0   0.419   2.7597   0.7500  -2.2629
 SRB  HOB2  H  H      0   0.421   0.3747   2.6700  -2.0392
 SRB  HOB3  H  H      0   0.420   1.1600   2.8831   0.6162
 SRB  C     C  C      0   0.507   3.0153  -1.6205   0.5977
 SRB  O1B   O  OB     0  -0.746   2.7754   1.5650  -1.7562
 SRB  O2B   O  OB     0  -0.734   0.3401   1.8169  -1.5963
 SRB  O3B   O  OB     0  -0.747   1.9151   2.7219   0.0471

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
 SRB  C1   C2    aromatic  1.427  0.020  1.427
 SRB  C1   C6    aromatic  1.372  0.020  1.372
 SRB  C1   C7'   single    1.502  0.020  1.502
 SRB  C2   C3    aromatic  1.422  0.020  1.422
 SRB  C2   C7    aromatic  1.418  0.020  1.418
 SRB  C3   C4    aromatic  1.414  0.020  1.414
 SRB  C3   C10   aromatic  1.416  0.020  1.416
 SRB  C4   C5    aromatic  1.366  0.020  1.366
 SRB  C4   H4    single    0.930  0.020  1.080
 SRB  C5   C6    aromatic  1.408  0.020  1.408
 SRB  C5   H5    single    0.930  0.020  1.080
 SRB  C6   H6    single    0.930  0.020  1.080
 SRB  C7   C8    aromatic  1.369  0.020  1.369
 SRB  C7   H7    single    0.930  0.020  1.080
 SRB  C8   C9    aromatic  1.410  0.020  1.410
 SRB  C8   H8    single    0.930  0.020  1.080
 SRB  C9   C10   aromatic  1.367  0.020  1.367
 SRB  C9   H9    single    0.930  0.020  1.080
 SRB  C10  H10   single    0.930  0.020  1.080
 SRB  C7'  C8'   single    1.545  0.020  1.545
 SRB  C7'  H7'1  single    0.970  0.020  1.090
 SRB  C7'  H7'2  single    0.970  0.020  1.090
 SRB  C8'  N     single    1.457  0.020  1.457
 SRB  C8'  B     single    1.666  0.020  1.666
 SRB  C8'  H8'   single    0.970  0.020  1.090
 SRB  C9'  C     single    1.513  0.020  1.513
 SRB  C9'  H9'1  single    0.970  0.020  1.090
 SRB  C9'  H9'2  single    0.970  0.020  1.090
 SRB  C9'  H9'3  single    0.970  0.020  1.090
 SRB  C    N     single    1.335  0.020  1.335
 SRB  C    O     double    1.231  0.020  1.231
 SRB  N    HN    single    0.860  0.020  1.020
 SRB  O1B  B     single    1.476  0.020  1.476
 SRB  O1B  HOB1  single    0.850  0.020  0.980
 SRB  O2B  B     single    1.468  0.020  1.468
 SRB  O2B  HOB2  single    0.850  0.020  0.980
 SRB  O3B  B     single    1.474  0.020  1.474
 SRB  O3B  HOB3  single    0.850  0.020  0.980

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
 SRB  C7'   C1   C6    120.53  3.000
 SRB  C7'   C1   C2    121.04  3.000
 SRB  C6    C1   C2    118.42  3.000
 SRB  C7    C2   C3    118.10  3.000
 SRB  C7    C2   C1    122.28  3.000
 SRB  C3    C2   C1    119.62  3.000
 SRB  C10   C3   C4    120.99  3.000
 SRB  C10   C3   C2    119.42  3.000
 SRB  C4    C3   C2    119.58  3.000
 SRB  H4    C4   C5    120.85  3.000
 SRB  H4    C4   C3    119.16  3.000
 SRB  C5    C4   C3    119.98  3.000
 SRB  H5    C5   C6    119.41  3.000
 SRB  H5    C5   C4    120.31  3.000
 SRB  C6    C5   C4    120.28  3.000
 SRB  H6    C6   C5    118.56  3.000
 SRB  H6    C6   C1    119.35  3.000
 SRB  C5    C6   C1    122.09  3.000
 SRB  H7    C7   C8    119.21  3.000
 SRB  H7    C7   C2    119.66  3.000
 SRB  C8    C7   C2    121.13  3.000
 SRB  H8    C8   C9    119.56  3.000
 SRB  H8    C8   C7    119.90  3.000
 SRB  C9    C8   C7    120.54  3.000
 SRB  H9    C9   C10   120.30  3.000
 SRB  H9    C9   C8    119.86  3.000
 SRB  C10   C9   C8    119.84  3.000
 SRB  H10   C10  C9    120.29  3.000
 SRB  H10   C10  C3    118.74  3.000
 SRB  C9    C10  C3    120.96  3.000
 SRB  H7'2  C7'  H7'1  105.39  3.000
 SRB  H7'2  C7'  C8'   108.74  3.000
 SRB  H7'1  C7'  C8'   109.75  3.000
 SRB  H7'2  C7'  C1    108.71  3.000
 SRB  H7'1  C7'  C1    108.69  3.000
 SRB  C8'   C7'  C1    115.12  3.000
 SRB  H8'   C8'  B     108.79  3.000
 SRB  H8'   C8'  N     107.12  3.000
 SRB  B     C8'  N     109.51  3.000
 SRB  H8'   C8'  C7'   107.85  3.000
 SRB  B     C8'  C7'   114.69  3.000
 SRB  N     C8'  C7'   108.61  3.000
 SRB  H9'3  C9'  H9'2  108.22  3.000
 SRB  H9'3  C9'  H9'1  107.19  3.000
 SRB  H9'2  C9'  H9'1  108.41  3.000
 SRB  H9'3  C9'  C     109.46  3.000
 SRB  H9'2  C9'  C     113.75  3.000
 SRB  H9'1  C9'  C     109.59  3.000
 SRB  HN    N    C     117.39  3.000
 SRB  HN    N    C8'   116.90  3.000
 SRB  C     N    C8'   125.61  3.000
 SRB  O3B   B    O2B   112.70  3.000
 SRB  O3B   B    O1B   102.97  3.000
 SRB  O2B   B    O1B   112.85  3.000
 SRB  O3B   B    C8'   112.44  3.000
 SRB  O2B   B    C8'   105.57  3.000
 SRB  O1B   B    C8'   110.48  3.000
 SRB  O     C    N     123.77  3.000
 SRB  O     C    C9'   120.58  3.000
 SRB  N     C    C9'   115.65  3.000
 SRB  HOB1  O1B  B     109.31  3.000
 SRB  HOB2  O2B  B     108.85  3.000
 SRB  HOB3  O3B  B     108.98  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
 SRB  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 SRB  CONST_02  C10   C3   C2   C1    180.00   0.0  0
 SRB  CONST_03  C8    C7   C2   C1    180.00   0.0  0
 SRB  CONST_04  C4    C5   C6   C1      0.00   0.0  0
 SRB  CONST_05  C5    C6   C1   C2      0.00   0.0  0
 SRB  CONST_06  C5    C4   C3   C2      0.00   0.0  0
 SRB  CONST_07  C9    C10  C3   C2      0.00   0.0  0
 SRB  CONST_08  C9    C8   C7   C2      0.00   0.0  0
 SRB  CONST_09  C6    C1   C2   C3      0.00   0.0  0
 SRB  CONST_10  C8    C7   C2   C3      0.00   0.0  0
 SRB  CONST_11  C6    C5   C4   C3      0.00   0.0  0
 SRB  CONST_12  C8    C9   C10  C3      0.00   0.0  0
 SRB  CONST_13  C7    C2   C3   C4    180.00   0.0  0
 SRB  CONST_14  C9    C10  C3   C4    180.00   0.0  0
 SRB  CONST_15  C10   C3   C4   C5    180.00   0.0  0
 SRB  CONST_16  C7    C2   C1   C6    180.00   0.0  0
 SRB  CONST_17  C10   C3   C2   C7      0.00   0.0  0
 SRB  CONST_18  C10   C9   C8   C7      0.00   0.0  0
 SRB  CONST_19  C7'   C1   C2   C3    180.00   0.0  0
 SRB  CONST_20  C7'   C1   C6   C5    180.00   0.0  0
 SRB  CONST_21  C7'   C1   C2   C7      0.00   0.0  0
 SRB  CONST_22  H7    C7   C2   C1      0.00   0.0  0
 SRB  CONST_23  H5    C5   C6   C1    180.00   0.0  0
 SRB  CONST_24  H6    C6   C1   C2    180.00   0.0  0
 SRB  CONST_25  H4    C4   C3   C2    180.00   0.0  0
 SRB  CONST_26  H10   C10  C3   C2    180.00   0.0  0
 SRB  CONST_27  H8    C8   C7   C2    180.00   0.0  0
 SRB  CONST_28  H9    C9   C10  C3    180.00   0.0  0
 SRB  CONST_29  C9'   C    N    C8'   180.00   0.0  0
 SRB  CONST_30  O     C    N    C8'     0.00   0.0  0
 SRB  CONST_31  HN    N    C    C9'     0.00   0.0  0
 SRB  Var_01    C8'   C7'  C1   C2     73.04  30.0  2
 SRB  Var_02    H9'1  C9'  C    N    -125.31  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
 SRB  chir_01  C8'  C7'  N  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
 SRB  plan-1  C1   0.020
 SRB  plan-1  C2   0.020
 SRB  plan-1  C3   0.020
 SRB  plan-1  C4   0.020
 SRB  plan-1  C5   0.020
 SRB  plan-1  C6   0.020
 SRB  plan-1  C7   0.020
 SRB  plan-1  C8   0.020
 SRB  plan-1  C9   0.020
 SRB  plan-1  C10  0.020
 SRB  plan-1  C7'  0.020
 SRB  plan-1  H4   0.020
 SRB  plan-1  H5   0.020
 SRB  plan-1  H6   0.020
 SRB  plan-1  H7   0.020
 SRB  plan-1  H8   0.020
 SRB  plan-1  H9   0.020
 SRB  plan-1  H10  0.020
 SRB  plan-2  C8'  0.020
 SRB  plan-2  C9'  0.020
 SRB  plan-2  N    0.020
 SRB  plan-2  O    0.020
 SRB  plan-2  HN   0.020
 SRB  plan-2  C    0.020

