# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 03:30:01 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: 3-(2,2'-bipyridin-5-yl)-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccc(nc1)c2ccccn2)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
 BP5  BP5  3-(2,2'-bipyridin-5-yl)-L-alanine  L-peptide  30  18  .  2022-07-24  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_BP5
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
 BP5  C9    C  CR6    0   0.075  -1.1006  -0.0377   0.6479
 BP5  C8    C  CR16   0  -0.185  -0.4128   1.1704   0.6886
 BP5  C7    C  CR16   0  -0.296   0.9561   1.1919   0.4856
 BP5  C6    C  CR6    0   0.187   1.6195  -0.0078   0.2377
 BP5  C5    C  CR16   0  -0.323   5.7857  -0.0294  -0.3822
 BP5  C4    C  CR16   0  -0.074   5.0425   1.1201  -0.1572
 BP5  C3    C  CR6    0   0.198   3.0847  -0.0488   0.0152
 BP5  C2    C  CR16   0  -0.305   3.7446  -1.2576  -0.2041
 BP5  C1    C  CR16   0  -0.153   5.1143  -1.2427  -0.4056
 BP5  C12   C  CH2    0  -0.525  -2.5823  -0.1390   0.8217
 BP5  C11   C  CR16   0  -0.122  -0.3375  -1.1749   0.3957
 BP5  N1    N  N      0  -0.434   3.7318   1.1147   0.0360
 BP5  N2    N  N      0  -0.433   0.9708  -1.1687   0.1974
 BP5  C13   C  CH1    0  -0.204  -3.3491   0.1082  -0.4900
 BP5  C14   C  C      0   0.383  -4.8384  -0.2672  -0.2729
 BP5  O1    O  OC    -1  -0.621  -5.0739  -1.4823  -0.1104
 BP5  O2    O  O      0  -0.603  -5.6701   0.6607  -0.2575
 BP5  N     N  NH2    0  -0.775  -3.0990   1.4581  -0.9579
 BP5  H8    H  HCR6   0   0.253  -0.9450   2.0907   0.8902
 BP5  H7    H  HCR6   0   0.262   1.5078   2.1206   0.5185
 BP5  H2    H  HCR6   0   0.268   3.1892  -2.1841  -0.2145
 BP5  H1    H  HCR6   0   0.273   5.6497  -2.1670  -0.5788
 BP5  H121  H  HCH2   0   0.247  -2.8373  -1.1324   1.1939
 BP5  H122  H  HCH2   0   0.240  -2.9216   0.5812   1.5732
 BP5  H11   H  HCR6   0   0.249  -0.8230  -2.1463   0.3568
 BP5  H13   H  HCH1   0   0.223  -2.9420  -0.5837  -1.2361
 BP5  HN1   H  HNH2   0   0.338  -3.4551   1.5499  -1.9015
 BP5  HN2   H  HNH2   0   0.325  -3.6684   2.0915  -0.4075
 BP5  H5    H  HCR6   0   0.272   6.8547   0.0302  -0.5324
 BP5  H4    H  HCR6   0   0.262   5.5291   2.0891  -0.1325

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
 BP5  C9   C12   single    1.495  0.020  1.495
 BP5  C9   C8    aromatic  1.391  0.020  1.391
 BP5  C9   C11   aromatic  1.393  0.020  1.393
 BP5  C8   C7    aromatic  1.384  0.020  1.384
 BP5  C8   H8    single    0.930  0.020  1.080
 BP5  C7   C6    aromatic  1.393  0.020  1.393
 BP5  C7   H7    single    0.930  0.020  1.080
 BP5  C6   N2    aromatic  1.330  0.020  1.330
 BP5  C6   C3    single    1.483  0.020  1.483
 BP5  C5   C1    aromatic  1.387  0.020  1.387
 BP5  C5   C4    aromatic  1.387  0.020  1.387
 BP5  C5   H5    single    0.930  0.020  1.080
 BP5  C4   N1    aromatic  1.325  0.020  1.325
 BP5  C4   H4    single    0.930  0.020  1.080
 BP5  C3   C2    aromatic  1.395  0.020  1.395
 BP5  C3   N1    aromatic  1.331  0.020  1.331
 BP5  C2   C1    aromatic  1.385  0.020  1.385
 BP5  C2   H2    single    0.930  0.020  1.080
 BP5  C1   H1    single    0.930  0.020  1.080
 BP5  C12  C13   single    1.539  0.020  1.539
 BP5  C12  H121  single    0.970  0.020  1.090
 BP5  C12  H122  single    0.970  0.020  1.090
 BP5  C11  N2    aromatic  1.323  0.020  1.323
 BP5  C11  H11   single    0.930  0.020  1.080
 BP5  C13  C14   single    1.551  0.020  1.551
 BP5  C13  N     single    1.450  0.020  1.450
 BP5  C13  H13   single    0.970  0.020  1.090
 BP5  C14  O2    deloc     1.246  0.020  1.246
 BP5  C14  O1    deloc     1.248  0.020  1.248
 BP5  N    HN1   single    0.890  0.020  1.040
 BP5  N    HN2   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
 BP5  C11   C9   C12   120.58  3.000
 BP5  C11   C9   C8    116.34  3.000
 BP5  C12   C9   C8    123.06  3.000
 BP5  H8    C8   C7    120.04  3.000
 BP5  H8    C8   C9    120.07  3.000
 BP5  C7    C8   C9    119.89  3.000
 BP5  H7    C7   C6    120.15  3.000
 BP5  H7    C7   C8    120.92  3.000
 BP5  C6    C7   C8    118.93  3.000
 BP5  N2    C6   C3    116.95  3.000
 BP5  C3    C6   C7    121.41  3.000
 BP5  N2    C6   C7    121.64  3.000
 BP5  H5    C5   C1    121.64  3.000
 BP5  H5    C5   C4    120.44  3.000
 BP5  C1    C5   C4    117.92  3.000
 BP5  H4    C4   N1    116.38  3.000
 BP5  H4    C4   C5    120.24  3.000
 BP5  N1    C4   C5    123.38  3.000
 BP5  N1    C3   C2    122.00  3.000
 BP5  N1    C3   C6    116.99  3.000
 BP5  C2    C3   C6    121.01  3.000
 BP5  H2    C2   C1    121.09  3.000
 BP5  H2    C2   C3    120.11  3.000
 BP5  C1    C2   C3    118.80  3.000
 BP5  H1    C1   C2    120.24  3.000
 BP5  H1    C1   C5    120.69  3.000
 BP5  C2    C1   C5    119.07  3.000
 BP5  H122  C12  H121  107.00  3.000
 BP5  H122  C12  C13   108.96  3.000
 BP5  H121  C12  C13   108.70  3.000
 BP5  H122  C12  C9    110.02  3.000
 BP5  H121  C12  C9    109.44  3.000
 BP5  C13   C12  C9    112.56  3.000
 BP5  H11   C11  N2    116.14  3.000
 BP5  H11   C11  C9    119.45  3.000
 BP5  N2    C11  C9    124.41  3.000
 BP5  C3    N1   C4    118.83  3.000
 BP5  C11   N2   C6    118.79  3.000
 BP5  H13   C13  N     107.70  3.000
 BP5  H13   C13  C14   107.40  3.000
 BP5  N     C13  C14   115.85  3.000
 BP5  H13   C13  C12   107.08  3.000
 BP5  N     C13  C12   109.78  3.000
 BP5  C14   C13  C12   108.67  3.000
 BP5  O2    C14  O1    126.67  3.000
 BP5  O1    C14  C13   115.78  3.000
 BP5  O2    C14  C13   117.54  3.000
 BP5  HN2   N    HN1   104.57  3.000
 BP5  HN2   N    C13   108.03  3.000
 BP5  HN1   N    C13   108.92  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
 BP5  CONST_01  C6   C7   C8   C9     0.00   0.0  0
 BP5  CONST_02  C6   N2   C11  C9     0.00   0.0  0
 BP5  CONST_03  N2   C11  C9   C8     0.00   0.0  0
 BP5  CONST_04  N2   C6   C7   C8     0.00   0.0  0
 BP5  CONST_05  C3   C6   C7   C8   180.00   0.0  0
 BP5  CONST_06  C11  C9   C8   C7     0.00   0.0  0
 BP5  CONST_07  C11  N2   C6   C7     0.00   0.0  0
 BP5  CONST_08  C2   C3   C6   C7   180.00   0.0  0
 BP5  CONST_09  N1   C3   C6   C7     0.00   0.0  0
 BP5  CONST_10  C1   C2   C3   C6   180.00   0.0  0
 BP5  CONST_11  C4   N1   C3   C6   180.00   0.0  0
 BP5  CONST_12  C3   C2   C1   C5     0.00   0.0  0
 BP5  CONST_13  C3   N1   C4   C5     0.00   0.0  0
 BP5  CONST_14  C2   C1   C5   C4     0.00   0.0  0
 BP5  CONST_15  C2   C3   N1   C4     0.00   0.0  0
 BP5  CONST_16  C11  N2   C6   C3   180.00   0.0  0
 BP5  CONST_17  N2   C6   C3   C2     0.00   0.0  0
 BP5  CONST_18  N1   C4   C5   C1     0.00   0.0  0
 BP5  CONST_19  N1   C3   C2   C1     0.00   0.0  0
 BP5  CONST_20  N2   C6   C3   N1   180.00   0.0  0
 BP5  CONST_21  C12  C9   C8   C7   180.00   0.0  0
 BP5  CONST_22  N2   C11  C9   C12  180.00   0.0  0
 BP5  CONST_23  H7   C7   C8   C9   180.00   0.0  0
 BP5  CONST_24  H11  C11  C9   C8   180.00   0.0  0
 BP5  CONST_25  H8   C8   C7   C6   180.00   0.0  0
 BP5  CONST_26  H2   C2   C3   C6     0.00   0.0  0
 BP5  CONST_27  H1   C1   C5   C4   180.00   0.0  0
 BP5  CONST_28  H4   C4   N1   C3   180.00   0.0  0
 BP5  CONST_29  H5   C5   C1   C2   180.00   0.0  0
 BP5  Var_01    C13  C12  C9   C8    84.25  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
 BP5  chir_01  C13  C12  C14  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
 BP5  plan-1  C9   0.020
 BP5  plan-1  C8   0.020
 BP5  plan-1  C7   0.020
 BP5  plan-1  C6   0.020
 BP5  plan-1  C3   0.020
 BP5  plan-1  C12  0.020
 BP5  plan-1  C11  0.020
 BP5  plan-1  N2   0.020
 BP5  plan-1  H8   0.020
 BP5  plan-1  H7   0.020
 BP5  plan-1  H11  0.020
 BP5  plan-2  C6   0.020
 BP5  plan-2  C5   0.020
 BP5  plan-2  C4   0.020
 BP5  plan-2  C3   0.020
 BP5  plan-2  C2   0.020
 BP5  plan-2  C1   0.020
 BP5  plan-2  N1   0.020
 BP5  plan-2  H2   0.020
 BP5  plan-2  H1   0.020
 BP5  plan-2  H5   0.020
 BP5  plan-2  H4   0.020
 BP5  plan-3  C13  0.020
 BP5  plan-3  C14  0.020
 BP5  plan-3  O1   0.020
 BP5  plan-3  O2   0.020

