# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 11:32:40 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: [(1S)-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
 SRD  SRD  '[(1S)-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_SRD
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
 SRD  C1    C  CR6    0   0.171  -0.9560  -0.6136   0.8730
 SRD  C2    C  CR66   0   0.057  -1.8394   0.3811   0.3574
 SRD  C3    C  CR66   0   0.114  -3.1968   0.0457   0.0902
 SRD  C4    C  CR16   0  -0.347  -3.6581  -1.2630   0.3591
 SRD  C5    C  CR16   0  -0.252  -2.8036  -2.1949   0.8787
 SRD  C6    C  CR16   0  -0.313  -1.4590  -1.8643   1.1286
 SRD  C7    C  CR16   0  -0.356  -1.4207   1.7131   0.1065
 SRD  C8    C  CR16   0  -0.265  -2.2894   2.6472  -0.3913
 SRD  C9    C  CR16   0  -0.263  -3.6286   2.3051  -0.6694
 SRD  C10   C  CR16   0  -0.316  -4.0685   1.0329  -0.4301
 SRD  C7'   C  CH2    0  -0.563   0.4848  -0.3006   1.1608
 SRD  C8'   C  CH1    0  -0.267   1.3953  -0.1260  -0.0771
 SRD  C9'   C  CH3    0  -0.776   4.2884   2.0611   1.1068
 SRD  N     N  NH1    0  -0.619   2.6601   0.4498   0.3586
 SRD  O     O  O      0  -0.528   2.0328   2.6165   0.5578
 SRD  B     B  B     -1   0.456   1.7507  -1.5179  -0.9116
 SRD  H4    H  HCR6   0   0.245  -4.6935  -1.5098   0.1560
 SRD  H5    H  HCR6   0   0.247  -3.1547  -3.1956   1.0973
 SRD  H6    H  HCR6   0   0.231  -0.8008  -2.6253   1.5301
 SRD  H7    H  HCR6   0   0.276  -0.3975   2.0010   0.3124
 SRD  H8    H  HCR6   0   0.250  -1.9478   3.6583  -0.5741
 SRD  H9    H  HCR6   0   0.252  -4.3051   3.0518  -1.0656
 SRD  H10   H  HCR6   0   0.248  -5.0979   0.7628  -0.6346
 SRD  H7'1  H  HCH2   0   0.220   0.8957  -1.0944   1.7922
 SRD  H7'2  H  HCH2   0   0.225   0.5287   0.6074   1.7718
 SRD  H8'   H  HCH1   0   0.189   0.9193   0.6007  -0.7454
 SRD  H9'1  H  HCH3   0   0.256   4.2572   2.4458   2.1269
 SRD  H9'2  H  HCH3   0   0.241   4.9668   1.2102   1.0825
 SRD  H9'3  H  HCH3   0   0.255   4.7022   2.8490   0.4777
 SRD  HN    H  HNH1   0   0.382   3.4156  -0.2035   0.4925
 SRD  HOB1  H  H      0   0.419   2.0486  -2.7172   0.6726
 SRD  HOB2  H  H      0   0.424   0.6629  -2.8929  -1.8523
 SRD  HOB3  H  H      0   0.419   2.2485  -0.5014  -2.5614
 SRD  C     C  C      0   0.503   2.8847   1.7315   0.6493
 SRD  O1B   O  OB     0  -0.752   2.5679  -2.4266  -0.0805
 SRD  O2B   O  OB     0  -0.725   0.4749  -2.1097  -1.3262
 SRD  O3B   O  OB     0  -0.738   2.6338  -1.2192  -2.0541

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
 SRD  C1   C2    aromatic  1.427  0.020  1.427
 SRD  C1   C6    aromatic  1.372  0.020  1.372
 SRD  C1   C7'   single    1.502  0.020  1.502
 SRD  C2   C3    aromatic  1.423  0.020  1.423
 SRD  C2   C7    aromatic  1.419  0.020  1.419
 SRD  C3   C4    aromatic  1.413  0.020  1.413
 SRD  C3   C10   aromatic  1.416  0.020  1.416
 SRD  C4   C5    aromatic  1.367  0.020  1.367
 SRD  C4   H4    single    0.930  0.020  1.080
 SRD  C5   C6    aromatic  1.407  0.020  1.407
 SRD  C5   H5    single    0.930  0.020  1.080
 SRD  C6   H6    single    0.930  0.020  1.080
 SRD  C7   C8    aromatic  1.369  0.020  1.369
 SRD  C7   H7    single    0.930  0.020  1.080
 SRD  C8   C9    aromatic  1.410  0.020  1.410
 SRD  C8   H8    single    0.930  0.020  1.080
 SRD  C9   C10   aromatic  1.367  0.020  1.367
 SRD  C9   H9    single    0.930  0.020  1.080
 SRD  C10  H10   single    0.930  0.020  1.080
 SRD  C7'  C8'   single    1.547  0.020  1.547
 SRD  C7'  H7'1  single    0.970  0.020  1.090
 SRD  C7'  H7'2  single    0.970  0.020  1.090
 SRD  C8'  N     single    1.456  0.020  1.456
 SRD  C8'  B     single    1.661  0.020  1.661
 SRD  C8'  H8'   single    0.970  0.020  1.090
 SRD  C9'  C     single    1.513  0.020  1.513
 SRD  C9'  H9'1  single    0.970  0.020  1.090
 SRD  C9'  H9'2  single    0.970  0.020  1.090
 SRD  C9'  H9'3  single    0.970  0.020  1.090
 SRD  C    N     single    1.333  0.020  1.333
 SRD  C    O     double    1.232  0.020  1.232
 SRD  N    HN    single    0.860  0.020  1.020
 SRD  O1B  B     single    1.478  0.020  1.478
 SRD  O1B  HOB1  single    0.850  0.020  0.980
 SRD  O2B  B     single    1.466  0.020  1.466
 SRD  O2B  HOB2  single    0.850  0.020  0.980
 SRD  O3B  B     single    1.475  0.020  1.475
 SRD  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
 SRD  C7'   C1   C6    120.39  3.000
 SRD  C7'   C1   C2    121.18  3.000
 SRD  C6    C1   C2    118.42  3.000
 SRD  C7    C2   C3    118.00  3.000
 SRD  C7    C2   C1    122.40  3.000
 SRD  C3    C2   C1    119.60  3.000
 SRD  C10   C3   C4    120.96  3.000
 SRD  C10   C3   C2    119.45  3.000
 SRD  C4    C3   C2    119.58  3.000
 SRD  H4    C4   C5    120.88  3.000
 SRD  H4    C4   C3    119.15  3.000
 SRD  C5    C4   C3    119.97  3.000
 SRD  H5    C5   C6    119.42  3.000
 SRD  H5    C5   C4    120.27  3.000
 SRD  C6    C5   C4    120.31  3.000
 SRD  H6    C6   C5    118.77  3.000
 SRD  H6    C6   C1    119.13  3.000
 SRD  C5    C6   C1    122.10  3.000
 SRD  H7    C7   C8    119.16  3.000
 SRD  H7    C7   C2    119.67  3.000
 SRD  C8    C7   C2    121.17  3.000
 SRD  H8    C8   C9    119.54  3.000
 SRD  H8    C8   C7    119.88  3.000
 SRD  C9    C8   C7    120.58  3.000
 SRD  H9    C9   C10   120.32  3.000
 SRD  H9    C9   C8    119.89  3.000
 SRD  C10   C9   C8    119.79  3.000
 SRD  H10   C10  C9    120.30  3.000
 SRD  H10   C10  C3    118.71  3.000
 SRD  C9    C10  C3    121.00  3.000
 SRD  H7'2  C7'  H7'1  105.33  3.000
 SRD  H7'2  C7'  C8'   109.23  3.000
 SRD  H7'1  C7'  C8'   108.82  3.000
 SRD  H7'2  C7'  C1    108.54  3.000
 SRD  H7'1  C7'  C1    108.63  3.000
 SRD  C8'   C7'  C1    115.78  3.000
 SRD  H8'   C8'  B     110.01  3.000
 SRD  H8'   C8'  N     107.30  3.000
 SRD  B     C8'  N     107.20  3.000
 SRD  H8'   C8'  C7'   107.89  3.000
 SRD  B     C8'  C7'   115.68  3.000
 SRD  N     C8'  C7'   108.45  3.000
 SRD  H9'3  C9'  H9'2  108.40  3.000
 SRD  H9'3  C9'  H9'1  107.20  3.000
 SRD  H9'2  C9'  H9'1  108.33  3.000
 SRD  H9'3  C9'  C     109.59  3.000
 SRD  H9'2  C9'  C     113.66  3.000
 SRD  H9'1  C9'  C     109.46  3.000
 SRD  HN    N    C     117.90  3.000
 SRD  HN    N    C8'   115.75  3.000
 SRD  C     N    C8'   126.27  3.000
 SRD  O3B   B    O2B   112.57  3.000
 SRD  O3B   B    O1B   103.24  3.000
 SRD  O2B   B    O1B   113.08  3.000
 SRD  O3B   B    C8'   110.34  3.000
 SRD  O2B   B    C8'   107.10  3.000
 SRD  O1B   B    C8'   110.55  3.000
 SRD  O     C    N     123.91  3.000
 SRD  O     C    C9'   120.51  3.000
 SRD  N     C    C9'   115.58  3.000
 SRD  HOB1  O1B  B     109.16  3.000
 SRD  HOB2  O2B  B     108.25  3.000
 SRD  HOB3  O3B  B     108.70  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
 SRD  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 SRD  CONST_02  C10   C3   C2   C1    180.00   0.0  0
 SRD  CONST_03  C8    C7   C2   C1    180.00   0.0  0
 SRD  CONST_04  C4    C5   C6   C1      0.00   0.0  0
 SRD  CONST_05  C5    C6   C1   C2      0.00   0.0  0
 SRD  CONST_06  C5    C4   C3   C2      0.00   0.0  0
 SRD  CONST_07  C9    C10  C3   C2      0.00   0.0  0
 SRD  CONST_08  C9    C8   C7   C2      0.00   0.0  0
 SRD  CONST_09  C6    C1   C2   C3      0.00   0.0  0
 SRD  CONST_10  C8    C7   C2   C3      0.00   0.0  0
 SRD  CONST_11  C6    C5   C4   C3      0.00   0.0  0
 SRD  CONST_12  C8    C9   C10  C3      0.00   0.0  0
 SRD  CONST_13  C7    C2   C3   C4    180.00   0.0  0
 SRD  CONST_14  C9    C10  C3   C4    180.00   0.0  0
 SRD  CONST_15  C10   C3   C4   C5    180.00   0.0  0
 SRD  CONST_16  C7    C2   C1   C6    180.00   0.0  0
 SRD  CONST_17  C10   C3   C2   C7      0.00   0.0  0
 SRD  CONST_18  C10   C9   C8   C7      0.00   0.0  0
 SRD  CONST_19  C7'   C1   C2   C3    180.00   0.0  0
 SRD  CONST_20  C7'   C1   C6   C5    180.00   0.0  0
 SRD  CONST_21  C7'   C1   C2   C7      0.00   0.0  0
 SRD  CONST_22  H7    C7   C2   C1      0.00   0.0  0
 SRD  CONST_23  H5    C5   C6   C1    180.00   0.0  0
 SRD  CONST_24  H6    C6   C1   C2    180.00   0.0  0
 SRD  CONST_25  H4    C4   C3   C2    180.00   0.0  0
 SRD  CONST_26  H10   C10  C3   C2    180.00   0.0  0
 SRD  CONST_27  H8    C8   C7   C2    180.00   0.0  0
 SRD  CONST_28  H9    C9   C10  C3    180.00   0.0  0
 SRD  CONST_29  C9'   C    N    C8'   180.00   0.0  0
 SRD  CONST_30  O     C    N    C8'     0.00   0.0  0
 SRD  CONST_31  HN    N    C    C9'     0.00   0.0  0
 SRD  Var_01    C8'   C7'  C1   C2    -72.74  30.0  2
 SRD  Var_02    H9'1  C9'  C    N    -117.62  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
 SRD  chir_01  C8'  C7'  N  B  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
 SRD  plan-1  C1   0.020
 SRD  plan-1  C2   0.020
 SRD  plan-1  C3   0.020
 SRD  plan-1  C4   0.020
 SRD  plan-1  C5   0.020
 SRD  plan-1  C6   0.020
 SRD  plan-1  C7   0.020
 SRD  plan-1  C8   0.020
 SRD  plan-1  C9   0.020
 SRD  plan-1  C10  0.020
 SRD  plan-1  C7'  0.020
 SRD  plan-1  H4   0.020
 SRD  plan-1  H5   0.020
 SRD  plan-1  H6   0.020
 SRD  plan-1  H7   0.020
 SRD  plan-1  H8   0.020
 SRD  plan-1  H9   0.020
 SRD  plan-1  H10  0.020
 SRD  plan-2  C8'  0.020
 SRD  plan-2  C9'  0.020
 SRD  plan-2  N    0.020
 SRD  plan-2  O    0.020
 SRD  plan-2  HN   0.020
 SRD  plan-2  C    0.020

