# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 14:10:16 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: (2R)-2-benzyl-3-iodopropanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@H](CI)Cc1ccccc1
#
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
 BIP  BIP  '(2R)-2-benzyl-3-iodopropanoic acid'  ligand  23  13  .  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_BIP
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
 BIP  C1   C  C      0   0.417   2.2396   0.1039   0.7841
 BIP  O1   O  O      0  -0.605   2.4911  -1.0190   1.2625
 BIP  O2   O  OC    -1  -0.605   2.8634   1.1625   0.9862
 BIP  C2   C  CH1    0  -0.330   1.0579   0.1731  -0.2096
 BIP  C3   C  CH2    0  -0.584  -0.1319  -0.6378   0.2443
 BIP  I    I  I      0  -0.096  -0.9813   0.1477   2.1033
 BIP  C    C  CH2    0  -0.517   1.5388  -0.3686  -1.5750
 BIP  C1'  C  CR6    0   0.131   0.5355  -0.1756  -2.6779
 BIP  C2'  C  CR16   0  -0.305   0.3500   1.0849  -3.2452
 BIP  C3'  C  CR16   0  -0.240  -0.5901   1.2874  -4.2452
 BIP  C4'  C  CR16   0  -0.274  -1.3666   0.2268  -4.6974
 BIP  C5'  C  CR16   0  -0.241  -1.1910  -1.0333  -4.1426
 BIP  C6'  C  CR16   0  -0.313  -0.2460  -1.2306  -3.1427
 BIP  H2   H  HCH1   0   0.233   0.7610   1.2163  -0.3486
 BIP  H31  H  HCH2   0   0.291  -0.9602  -0.6168  -0.4604
 BIP  H32  H  HCH2   0   0.282   0.1376  -1.6668   0.4702
 BIP  H1   H  HCH2   0   0.258   2.4636   0.1542  -1.8353
 BIP  H2A  H  HCH2   0   0.247   1.7925  -1.4267  -1.4751
 BIP  H2'  H  HCR6   0   0.245   0.9546   1.9174  -2.9026
 BIP  H3'  H  HCR6   0   0.252  -0.7147   2.2732  -4.6752
 BIP  H4'  H  HCR6   0   0.253  -2.1002   0.3808  -5.4781
 BIP  H5'  H  HCR6   0   0.253  -1.7898  -1.8663  -4.4884
 BIP  H6'  H  HCR6   0   0.248  -0.1144  -2.2201  -2.7201

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
 BIP  C1   O1   deloc     1.246  0.020  1.246
 BIP  C1   O2   deloc     1.245  0.020  1.245
 BIP  C1   C2   single    1.546  0.020  1.546
 BIP  C2   C3   single    1.510  0.020  1.510
 BIP  C2   C    single    1.546  0.020  1.546
 BIP  C2   H2   single    0.970  0.020  1.090
 BIP  C3   I    single    2.190  0.020  2.190
 BIP  C3   H31  single    0.970  0.020  1.090
 BIP  C3   H32  single    0.970  0.020  1.090
 BIP  C    C1'  single    1.503  0.020  1.503
 BIP  C    H1   single    0.970  0.020  1.090
 BIP  C    H2A  single    0.970  0.020  1.090
 BIP  C1'  C2'  aromatic  1.395  0.020  1.395
 BIP  C1'  C6'  aromatic  1.393  0.020  1.393
 BIP  C2'  C3'  aromatic  1.387  0.020  1.387
 BIP  C2'  H2'  single    0.930  0.020  1.080
 BIP  C3'  C4'  aromatic  1.390  0.020  1.390
 BIP  C3'  H3'  single    0.930  0.020  1.080
 BIP  C4'  C5'  aromatic  1.388  0.020  1.388
 BIP  C4'  H4'  single    0.930  0.020  1.080
 BIP  C5'  C6'  aromatic  1.390  0.020  1.390
 BIP  C5'  H5'  single    0.930  0.020  1.080
 BIP  C6'  H6'  single    0.930  0.020  1.080

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
 BIP  C2   C1   O2   116.70  3.000
 BIP  C2   C1   O1   116.20  3.000
 BIP  O2   C1   O1   127.06  3.000
 BIP  H2   C2   C    107.85  3.000
 BIP  H2   C2   C3   109.68  3.000
 BIP  C    C2   C3   108.82  3.000
 BIP  H2   C2   C1   109.39  3.000
 BIP  C    C2   C1   108.32  3.000
 BIP  C3   C2   C1   112.65  3.000
 BIP  H32  C3   H31  109.97  3.000
 BIP  H32  C3   I    105.02  3.000
 BIP  H31  C3   I    104.34  3.000
 BIP  H32  C3   C2   112.05  3.000
 BIP  H31  C3   C2   113.26  3.000
 BIP  I    C3   C2   111.61  3.000
 BIP  H2A  C    H1   106.76  3.000
 BIP  H2A  C    C1'  110.27  3.000
 BIP  H1   C    C1'  109.17  3.000
 BIP  H2A  C    C2   109.32  3.000
 BIP  H1   C    C2   107.80  3.000
 BIP  C1'  C    C2   113.29  3.000
 BIP  C6'  C1'  C2'  118.31  3.000
 BIP  C6'  C1'  C    121.47  3.000
 BIP  C2'  C1'  C    120.21  3.000
 BIP  H2'  C2'  C3'  119.57  3.000
 BIP  H2'  C2'  C1'  119.41  3.000
 BIP  C3'  C2'  C1'  121.01  3.000
 BIP  H3'  C3'  C4'  120.08  3.000
 BIP  H3'  C3'  C2'  119.81  3.000
 BIP  C4'  C3'  C2'  120.11  3.000
 BIP  H4'  C4'  C5'  120.22  3.000
 BIP  H4'  C4'  C3'  120.31  3.000
 BIP  C5'  C4'  C3'  119.47  3.000
 BIP  H5'  C5'  C6'  119.77  3.000
 BIP  H5'  C5'  C4'  120.06  3.000
 BIP  C6'  C5'  C4'  120.16  3.000
 BIP  H6'  C6'  C5'  119.51  3.000
 BIP  H6'  C6'  C1'  119.55  3.000
 BIP  C5'  C6'  C1'  120.94  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
 BIP  CONST_01  C4'  C3'  C2'  C1'    0.00   0.0  0
 BIP  CONST_02  C4'  C5'  C6'  C1'    0.00   0.0  0
 BIP  CONST_03  C5'  C6'  C1'  C2'    0.00   0.0  0
 BIP  CONST_04  C5'  C4'  C3'  C2'    0.00   0.0  0
 BIP  CONST_05  C6'  C1'  C2'  C3'    0.00   0.0  0
 BIP  CONST_06  C6'  C5'  C4'  C3'    0.00   0.0  0
 BIP  CONST_07  C3'  C2'  C1'  C    180.00   0.0  0
 BIP  CONST_08  C5'  C6'  C1'  C    180.00   0.0  0
 BIP  CONST_09  H3'  C3'  C2'  C1'  180.00   0.0  0
 BIP  CONST_10  H5'  C5'  C6'  C1'  180.00   0.0  0
 BIP  CONST_11  H6'  C6'  C1'  C2'  180.00   0.0  0
 BIP  CONST_12  H4'  C4'  C3'  C2'  180.00   0.0  0
 BIP  CONST_13  H2'  C2'  C3'  C4'  180.00   0.0  0
 BIP  Var_01    C2'  C1'  C    C2    75.57  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
 BIP  chir_01  C2  C1  C3  C  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
 BIP  plan-1  C    0.020
 BIP  plan-1  C1'  0.020
 BIP  plan-1  C2'  0.020
 BIP  plan-1  C3'  0.020
 BIP  plan-1  C4'  0.020
 BIP  plan-1  C5'  0.020
 BIP  plan-1  C6'  0.020
 BIP  plan-1  H2'  0.020
 BIP  plan-1  H3'  0.020
 BIP  plan-1  H4'  0.020
 BIP  plan-1  H5'  0.020
 BIP  plan-1  H6'  0.020
 BIP  plan-2  C1   0.020
 BIP  plan-2  O1   0.020
 BIP  plan-2  O2   0.020
 BIP  plan-2  C2   0.020

