# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 12 09:16:58 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: [(1R)-1-amino-4-methoxybutyl]boronic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCCC[C@H](N)B(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
 01L  01L  '[(1R)-1-amino-4-methoxybutyl]boronic acid'  peptide  24  10  .  2022-03-07  2022-03-07
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_01L
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
 01L  C1    C  CH3   0  -0.396   4.7383   0.4027  -0.2200
 01L  O2    O  O2    0  -0.488   3.5879  -0.2075   0.3025
 01L  C2    C  CH2   0  -0.123   2.4018   0.3506  -0.2104
 01L  C3    C  CH2   0  -0.451   1.2028  -0.3550   0.3895
 01L  C4    C  CH2   0  -0.470  -0.1082   0.2488  -0.0996
 01L  C5    C  CH1   0  -0.248  -1.3532  -0.4686   0.4421
 01L  B     B  B     0   0.504  -2.6534   0.3880   0.1143
 01L  O1A   O  OH1   0  -0.626  -3.4744  -0.0274  -0.8915
 01L  O1B   O  OH1   0  -0.631  -2.8640   1.5155   0.8561
 01L  N6    N  NH2   0  -0.810  -1.3614  -1.8601  -0.0282
 01L  H11A  H  HCH3  0   0.201   4.7802   1.4738   0.0141
 01L  H12A  H  HCH3  0   0.231   5.6103  -0.0795   0.2213
 01L  H13   H  HCH3  0   0.201   4.8012   0.2995  -1.3104
 01L  H21   H  HCH2  0   0.188   2.3559   1.4274   0.0137
 01L  H22A  H  HCH2  0   0.189   2.3777   0.2621  -1.3074
 01L  H31   H  HCH2  0   0.226   1.2338  -1.4177   0.1409
 01L  H32A  H  HCH2  0   0.215   1.2461  -0.2805   1.4810
 01L  H41   H  HCH2  0   0.227  -0.1437   1.3047   0.1852
 01L  H42   H  HCH2  0   0.213  -0.1331   0.2342  -1.1960
 01L  H5    H  HCH1  0   0.214  -1.2417  -0.5046   1.5339
 01L  HOA   H  HOH1  0   0.482  -4.2315   0.5381  -1.0737
 01L  HOB   H  HOH1  0   0.479  -3.6411   2.0316   0.6197
 01L  HN6   H  HNH2  0   0.342  -2.1432  -2.3508   0.3885
 01L  H2    H  HNH2  0   0.333  -1.5461  -1.8738  -1.0248

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
 01L  C1   O2    single  1.403  0.020  1.403
 01L  C1   H11A  single  0.970  0.020  1.090
 01L  C1   H12A  single  0.970  0.020  1.090
 01L  C1   H13   single  0.970  0.020  1.090
 01L  O2   C2    single  1.408  0.020  1.408
 01L  C2   C3    single  1.515  0.020  1.515
 01L  C2   H21   single  0.970  0.020  1.090
 01L  C2   H22A  single  0.970  0.020  1.090
 01L  C3   C4    single  1.524  0.020  1.524
 01L  C3   H31   single  0.970  0.020  1.090
 01L  C3   H32A  single  0.970  0.020  1.090
 01L  C4   C5    single  1.536  0.020  1.536
 01L  C4   H41   single  0.970  0.020  1.090
 01L  C4   H42   single  0.970  0.020  1.090
 01L  C5   B     single  1.591  0.020  1.591
 01L  C5   N6    single  1.469  0.020  1.469
 01L  C5   H5    single  0.970  0.020  1.090
 01L  B    O1A   single  1.363  0.020  1.363
 01L  B    O1B   single  1.366  0.020  1.366
 01L  O1A  HOA   single  0.850  0.020  0.980
 01L  O1B  HOB   single  0.850  0.020  0.980
 01L  N6   HN6   single  0.890  0.020  1.040
 01L  N6   H2    single  0.890  0.020  1.040

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
 01L  H13   C1   H12A  108.36  3.000
 01L  H13   C1   H11A  107.56  3.000
 01L  H12A  C1   H11A  108.36  3.000
 01L  H13   C1   O2    112.10  3.000
 01L  H12A  C1   O2    108.23  3.000
 01L  H11A  C1   O2    112.12  3.000
 01L  C2    O2   C1    112.50  3.000
 01L  H22A  C2   H21   106.30  3.000
 01L  H22A  C2   C3    109.87  3.000
 01L  H21   C2   C3    110.00  3.000
 01L  H22A  C2   O2    110.47  3.000
 01L  H21   C2   O2    110.41  3.000
 01L  C3    C2   O2    109.75  3.000
 01L  H32A  C3   H31   106.98  3.000
 01L  H32A  C3   C4    109.08  3.000
 01L  H31   C3   C4    109.69  3.000
 01L  H32A  C3   C2    109.38  3.000
 01L  H31   C3   C2    109.92  3.000
 01L  C4    C3   C2    111.67  3.000
 01L  H42   C4   H41   105.80  3.000
 01L  H42   C4   C5    109.15  3.000
 01L  H41   C4   C5    109.44  3.000
 01L  H42   C4   C3    109.58  3.000
 01L  H41   C4   C3    109.06  3.000
 01L  C5    C4   C3    113.53  3.000
 01L  H5    C5   N6    106.73  3.000
 01L  H5    C5   B     107.79  3.000
 01L  N6    C5   B     116.07  3.000
 01L  H5    C5   C4    106.48  3.000
 01L  N6    C5   C4    109.52  3.000
 01L  B     C5   C4    109.78  3.000
 01L  O1B   B    O1A   124.01  3.000
 01L  O1B   B    C5    117.29  3.000
 01L  O1A   B    C5    118.69  3.000
 01L  HOA   O1A  B     115.75  3.000
 01L  HOB   O1B  B     115.71  3.000
 01L  H2    N6   HN6   104.91  3.000
 01L  H2    N6   C5    109.18  3.000
 01L  HN6   N6   C5    109.37  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
 01L  Var_01  C3    C2  O2  C1  179.81  30.0  3
 01L  Var_02  C4    C3  C2  O2  177.99  30.0  3
 01L  Var_03  C5    C4  C3  C2  177.85  30.0  3
 01L  Var_04  H11A  C1  O2  C2   60.52  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
 01L  chir_01  C5  C4  B  N6  negativ

