# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 12 09:03:21 2020
#   Inital geometry file: a 47 line input string
#   Ligand name: 1-(2,5-dichlorophenyl)methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1cc(Cl)ccc1Cl
#
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
 01V  01V  1-(2,5-dichlorophenyl)methanamine  ligand  17  10  .  2021-07-27  2021-07-27  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_01V
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
 01V  N'    N   NH2   0  -0.783  -2.1646  -2.1155  -0.7632
 01V  CA'   C   CH2   0  -0.366  -1.5165  -1.7654   0.4903
 01V  CB'   C   CR6   0   0.193  -0.5481  -0.6351   0.2716
 01V  CG'   C   CR6   0  -0.094  -0.9615   0.6762   0.0446
 01V  CD'   C   CR16  0  -0.203  -0.0528   1.6967  -0.1855
 01V  CE'   C   CR16  0  -0.237   1.3061   1.4227  -0.2075
 01V  CDB   C   CR6   0  -0.018   1.7286   0.1232   0.0112
 01V  CGB   C   CR16  0  -0.274   0.8181  -0.8941   0.2488
 01V  CL1   CL  CL    0  -0.121  -2.6475   1.0716   0.0743
 01V  CL2   CL  CL    0  -0.125   3.4216  -0.2412  -0.0124
 01V  HN'   H   HNH2  0   0.344  -1.5075  -2.6060  -1.3565
 01V  HA11  H   HCH2  0   0.243  -2.2864  -1.4556   1.1993
 01V  HA12  H   HCH2  0   0.227  -0.9765  -2.5954   0.9617
 01V  HD'   H   HCR6  0   0.288  -0.3979   2.7084  -0.3498
 01V  HE'   H   HCR6  0   0.288   2.0164   2.2175  -0.3879
 01V  HG'   H   HCR6  0   0.282   1.1659  -1.9049   0.4219
 01V  H2    H   HNH2  0   0.354  -2.9161  -2.7675  -0.5794

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
 01V  N'   CA'   single    1.454  0.020  1.454
 01V  N'   HN'   single    0.890  0.020  1.040
 01V  CA'  CB'   single    1.504  0.020  1.504
 01V  CA'  HA11  single    0.970  0.020  1.090
 01V  CA'  HA12  single    0.970  0.020  1.090
 01V  CB'  CG'   aromatic  1.394  0.020  1.394
 01V  CB'  CGB   aromatic  1.391  0.020  1.391
 01V  CG'  CD'   aromatic  1.386  0.020  1.386
 01V  CG'  CL1   single    1.732  0.020  1.732
 01V  CD'  CE'   aromatic  1.386  0.020  1.386
 01V  CD'  HD'   single    0.930  0.020  1.080
 01V  CE'  CDB   aromatic  1.384  0.020  1.384
 01V  CE'  HE'   single    0.930  0.020  1.080
 01V  CDB  CGB   aromatic  1.386  0.020  1.386
 01V  CDB  CL2   single    1.732  0.020  1.732
 01V  CGB  HG'   single    0.930  0.020  1.080
 01V  N'   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
 01V  H2    N'   HN'   106.05  3.000
 01V  H2    N'   CA'   109.25  3.000
 01V  HN'   N'   CA'   109.43  3.000
 01V  HA12  CA'  HA11  106.43  3.000
 01V  HA12  CA'  CB'   108.31  3.000
 01V  HA11  CA'  CB'   109.59  3.000
 01V  HA12  CA'  N'    114.07  3.000
 01V  HA11  CA'  N'    108.29  3.000
 01V  CB'   CA'  N'    110.03  3.000
 01V  CGB   CB'  CG'   117.65  3.000
 01V  CGB   CB'  CA'   119.65  3.000
 01V  CG'   CB'  CA'   122.67  3.000
 01V  CL1   CG'  CD'   118.24  3.000
 01V  CL1   CG'  CB'   120.05  3.000
 01V  CD'   CG'  CB'   121.70  3.000
 01V  HD'   CD'  CE'   119.69  3.000
 01V  HD'   CD'  CG'   120.32  3.000
 01V  CE'   CD'  CG'   119.99  3.000
 01V  HE'   CE'  CDB   121.07  3.000
 01V  HE'   CE'  CD'   120.08  3.000
 01V  CDB   CE'  CD'   118.84  3.000
 01V  CL2   CDB  CGB   119.35  3.000
 01V  CL2   CDB  CE'   119.60  3.000
 01V  CGB   CDB  CE'   121.05  3.000
 01V  HG'   CGB  CDB   120.11  3.000
 01V  HG'   CGB  CB'   119.13  3.000
 01V  CDB   CGB  CB'   120.76  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
 01V  CONST_01  CE'  CD'  CG'  CB'    0.00   0.0  0
 01V  CONST_02  CE'  CDB  CGB  CB'    0.00   0.0  0
 01V  CONST_03  CDB  CGB  CB'  CG'    0.00   0.0  0
 01V  CONST_04  CDB  CE'  CD'  CG'    0.00   0.0  0
 01V  CONST_05  CGB  CB'  CG'  CD'    0.00   0.0  0
 01V  CONST_06  CGB  CDB  CE'  CD'    0.00   0.0  0
 01V  CONST_07  CD'  CG'  CB'  CA'  180.00   0.0  0
 01V  CONST_08  CDB  CGB  CB'  CA'  180.00   0.0  0
 01V  CONST_09  CL2  CDB  CGB  CB'  180.00   0.0  0
 01V  CONST_10  CL2  CDB  CE'  CD'  180.00   0.0  0
 01V  CONST_11  CL1  CG'  CD'  CE'  180.00   0.0  0
 01V  CONST_12  CL1  CG'  CB'  CGB  180.00   0.0  0
 01V  CONST_13  HD'  CD'  CG'  CB'  180.00   0.0  0
 01V  CONST_14  HG'  CGB  CB'  CG'  180.00   0.0  0
 01V  CONST_15  HE'  CE'  CD'  CG'  180.00   0.0  0
 01V  Var_01    CG'  CB'  CA'  N'    73.01  30.0  2
 01V  Var_02    HN'  N'   CA'  CB'   73.41  30.0  3

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
 01V  plan-1  CA'  0.020
 01V  plan-1  CB'  0.020
 01V  plan-1  CG'  0.020
 01V  plan-1  CD'  0.020
 01V  plan-1  CE'  0.020
 01V  plan-1  CDB  0.020
 01V  plan-1  CGB  0.020
 01V  plan-1  CL1  0.020
 01V  plan-1  CL2  0.020
 01V  plan-1  HD'  0.020
 01V  plan-1  HE'  0.020
 01V  plan-1  HG'  0.020

