# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 04:15:42 2020
#   Inital geometry file: a 67 line input string
#   Ligand name: (2~{S})-2-[(6-azanyl-5-chloranyl-pyridin-3-yl)methyl]-3-selanyl-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncc(C[C@H](C[SeH])C(O)=O)cc1Cl
#
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
 9B3  9B3  '(2~{S})-2-[(6-azanyl-5-chloranyl-pyridin-3-yl)methyl]-3-selanyl-propanoic acid'  ligand  25  15  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9B3
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
 9B3  C1   C   CR16   0  -0.135   2.1255  -0.2802   0.7942
 9B3  C2   C   CR6    0  -0.168   3.3470  -0.1751   0.1691
 9B3  CL1  CL  CL     0  -0.130   4.4872  -1.4806   0.2605
 9B3  C3   C   CR6    0   0.475   3.6754   0.9865  -0.5515
 9B3  N1   N   NH2    0  -0.826   4.8504   1.1155  -1.2307
 9B3  N2   N   N      0  -0.451   2.8055   1.9880  -0.6214
 9B3  C4   C   CR16   0  -0.101   1.6309   1.8787  -0.0123
 9B3  C5   C   CR6    0   0.009   1.2176   0.7747   0.7169
 9B3  C6   C   CH2    0  -0.483  -0.1392   0.7246   1.3572
 9B3  C7   C   CH1    0  -0.344  -1.2439   0.3239   0.3753
 9B3  C8   C   C      0   0.436  -1.1023  -1.1114  -0.1704
 9B3  O1   O   OC    -1  -0.604  -1.6537  -1.3232  -1.2716
 9B3  O2   O   O      0  -0.587  -0.5155  -1.9487   0.5394
 9B3  C9   C   CH2    0  -0.572  -2.5975   0.4630   1.0674
 9B3  SE1  SE  SE     0  -0.205  -4.0881   0.0313  -0.1548
 9B3  H1   H   HCR6   0   0.274   1.8692  -1.1776   1.3403
 9B3  H2   H   HNH2   0   0.387   5.6369   0.5675  -0.9242
 9B3  H3   H   HNH2   0   0.387   5.0899   2.0566  -1.4971
 9B3  H4   H   HCR6   0   0.252   0.9713   2.7370  -0.1070
 9B3  H5   H   HCH2   0   0.238  -0.1283   0.0333   2.2018
 9B3  H6   H   HCH2   0   0.236  -0.3748   1.7122   1.7653
 9B3  H7   H   HCH1   0   0.229  -1.2229   1.0213  -0.4695
 9B3  H9   H   HCH2   0   0.258  -2.6495  -0.1975   1.9353
 9B3  H10  H   HCH2   0   0.270  -2.7447   1.4878   1.4108
 9B3  H11  H   H      0   0.158  -5.0878   0.7169   0.6590

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
 9B3  N2   C4   aromatic  1.328  0.020  1.328
 9B3  N2   C3   aromatic  1.328  0.020  1.328
 9B3  C4   C5   aromatic  1.386  0.020  1.386
 9B3  N1   C3   single    1.363  0.020  1.363
 9B3  C3   C2   aromatic  1.406  0.020  1.406
 9B3  C5   C6   single    1.501  0.020  1.501
 9B3  C5   C1   aromatic  1.394  0.020  1.394
 9B3  C6   C7   single    1.531  0.020  1.531
 9B3  C2   C1   aromatic  1.376  0.020  1.376
 9B3  C2   CL1  single    1.736  0.020  1.736
 9B3  C7   C9   single    1.527  0.020  1.527
 9B3  C7   C8   single    1.542  0.020  1.542
 9B3  C9   SE1  single    1.975  0.020  1.975
 9B3  C8   O2   deloc     1.245  0.020  1.245
 9B3  C8   O1   deloc     1.250  0.020  1.250
 9B3  C1   H1   single    0.929  0.020  1.085
 9B3  N1   H2   single    0.868  0.020  1.013
 9B3  N1   H3   single    0.868  0.020  1.013
 9B3  C4   H4   single    0.929  0.020  1.085
 9B3  C6   H5   single    0.939  0.020  1.096
 9B3  C6   H6   single    0.939  0.020  1.096
 9B3  C7   H7   single    0.939  0.020  1.096
 9B3  C9   H9   single    0.939  0.020  1.096
 9B3  C9   H10  single    0.939  0.020  1.096
 9B3  SE1  H11  single    1.444  0.020  1.000

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
 9B3  H1   C1   C5   120.11  3.000
 9B3  H1   C1   C2   120.21  3.000
 9B3  C5   C1   C2   119.68  3.000
 9B3  C3   C2   CL1  119.67  3.000
 9B3  CL1  C2   C1   120.11  3.000
 9B3  C3   C2   C1   120.22  3.000
 9B3  N2   C3   N1   117.83  3.000
 9B3  N1   C3   C2   122.34  3.000
 9B3  N2   C3   C2   119.80  3.000
 9B3  H3   N1   H2   113.80  3.000
 9B3  H3   N1   C3   115.17  3.000
 9B3  H2   N1   C3   118.06  3.000
 9B3  C4   N2   C3   119.55  3.000
 9B3  H4   C4   C5   119.60  3.000
 9B3  H4   C4   N2   115.59  3.000
 9B3  C5   C4   N2   124.80  3.000
 9B3  C6   C5   C4   121.37  3.000
 9B3  C6   C5   C1   122.67  3.000
 9B3  C4   C5   C1   115.96  3.000
 9B3  H6   C6   H5   106.57  3.000
 9B3  H6   C6   C7   108.66  3.000
 9B3  H5   C6   C7   109.73  3.000
 9B3  H6   C6   C5   108.88  3.000
 9B3  H5   C6   C5   110.01  3.000
 9B3  C7   C6   C5   112.78  3.000
 9B3  H7   C7   C9   107.97  3.000
 9B3  H7   C7   C8   108.53  3.000
 9B3  C9   C7   C8   109.07  3.000
 9B3  H7   C7   C6   108.30  3.000
 9B3  C8   C7   C6   113.84  3.000
 9B3  C9   C7   C6   108.97  3.000
 9B3  O2   C8   O1   126.62  3.000
 9B3  O1   C8   C7   115.41  3.000
 9B3  O2   C8   C7   117.88  3.000
 9B3  H10  C9   H9   108.16  3.000
 9B3  H10  C9   SE1  107.35  3.000
 9B3  H9   C9   SE1  108.89  3.000
 9B3  H10  C9   C7   110.37  3.000
 9B3  H9   C9   C7   110.33  3.000
 9B3  SE1  C9   C7   111.63  3.000
 9B3  H11  SE1  C9    93.97  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
 9B3  CONST_01  N2  C4  C5  C1     0.00   0.0  0
 9B3  CONST_02  N2  C3  C2  C1     0.00   0.0  0
 9B3  CONST_03  C4  N2  C3  C2     0.00   0.0  0
 9B3  CONST_04  C4  C5  C1  C2     0.00   0.0  0
 9B3  CONST_05  C5  C4  N2  C3     0.00   0.0  0
 9B3  CONST_06  C5  C1  C2  C3     0.00   0.0  0
 9B3  CONST_07  N1  C3  C2  C1   180.00   0.0  0
 9B3  CONST_08  C6  C5  C1  C2   180.00   0.0  0
 9B3  CONST_09  N2  C3  C2  CL1  180.00   0.0  0
 9B3  CONST_10  C5  C1  C2  CL1  180.00   0.0  0
 9B3  CONST_11  C4  N2  C3  N1   180.00   0.0  0
 9B3  CONST_12  C6  C5  C4  N2   180.00   0.0  0
 9B3  CONST_13  H4  C4  C5  C1   180.00   0.0  0
 9B3  CONST_14  H1  C1  C2  C3   180.00   0.0  0
 9B3  Var_01    C7  C6  C5  C1   -97.28  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
 9B3  chir_01  C7  C6  C9  C8  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
 9B3  plan-1  C1   0.020
 9B3  plan-1  C2   0.020
 9B3  plan-1  CL1  0.020
 9B3  plan-1  C3   0.020
 9B3  plan-1  N1   0.020
 9B3  plan-1  N2   0.020
 9B3  plan-1  C4   0.020
 9B3  plan-1  C5   0.020
 9B3  plan-1  C6   0.020
 9B3  plan-1  H1   0.020
 9B3  plan-1  H4   0.020
 9B3  plan-2  C3   0.020
 9B3  plan-2  N1   0.020
 9B3  plan-2  H2   0.020
 9B3  plan-2  H3   0.020
 9B3  plan-3  C7   0.020
 9B3  plan-3  C8   0.020
 9B3  plan-3  O1   0.020
 9B3  plan-3  O2   0.020

