# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 14:42:40 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: 1-(2-chlorobiphenyl-4-yl)methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1ccc(c(Cl)c1)c2ccccc2
#
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
 54E  54E  1-(2-chlorobiphenyl-4-yl)methanamine  ligand  27  15  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_54E
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
 54E  CL   CL  CL    0  -0.134   0.0388   2.0006   1.0477
 54E  C3   C   CR6   0  -0.105  -0.6990   0.6027   0.3255
 54E  C2   C   CR16  0  -0.235  -2.0843   0.5689   0.2615
 54E  C4   C   CR6   0   0.139   0.0915  -0.4509  -0.1276
 54E  C5   C   CR16  0  -0.299  -0.5808  -1.5619  -0.6399
 54E  C6   C   CR16  0  -0.275  -1.9618  -1.6121  -0.7031
 54E  C1   C   CR6   0   0.058  -2.7342  -0.5413  -0.2615
 54E  C    C   CH2   0  -0.328  -4.2371  -0.5915  -0.3774
 54E  N    N   NH2   0  -0.796  -4.8990   0.3419   0.5123
 54E  C7   C   CR6   0   0.063   1.5695  -0.4496  -0.0734
 54E  C12  C   CR16  0  -0.285   2.3172   0.5223  -0.7379
 54E  C11  C   CR16  0  -0.244   3.7034   0.4850  -0.7103
 54E  C10  C   CR16  0  -0.263   4.3630  -0.5212  -0.0149
 54E  C9   C   CR16  0  -0.242   3.6271  -1.4944   0.6465
 54E  C8   C   CR16  0  -0.294   2.2393  -1.4597   0.6149
 54E  H1   H   HCR6  0   0.271  -2.6641   1.4036   0.6309
 54E  H2   H   HCR6  0   0.260  -0.0003  -2.4007  -1.0030
 54E  H3   H   HCR6  0   0.254  -2.4437  -2.4951  -1.1050
 54E  H4   H   HCH2  0   0.250  -4.5067  -0.3252  -1.4035
 54E  H5   H   HCH2  0   0.221  -4.5555  -1.6347  -0.2476
 54E  H6   H   HNH2  0   0.359  -5.8807   0.3890   0.2749
 54E  H7   H   HNH2  0   0.347  -4.8558  -0.0009   1.4639
 54E  H9   H   HCR6  0   0.254   1.8147   1.3039  -1.2934
 54E  H10  H   HCR6  0   0.258   4.2701   1.2419  -1.2368
 54E  H11  H   HCR6  0   0.258   5.4448  -0.5471   0.0076
 54E  H12  H   HCR6  0   0.258   4.1315  -2.2832   1.1893
 54E  H13  H   HCR6  0   0.255   1.6713  -2.2204   1.1362

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
 54E  C5   C6   aromatic  1.383  0.020  1.383
 54E  C5   C4   aromatic  1.396  0.020  1.396
 54E  C6   C1   aromatic  1.392  0.020  1.392
 54E  C11  C12  aromatic  1.387  0.020  1.387
 54E  C11  C10  aromatic  1.390  0.020  1.390
 54E  C12  C7   aromatic  1.395  0.020  1.395
 54E  C10  C9   aromatic  1.388  0.020  1.388
 54E  C7   C8   aromatic  1.394  0.020  1.394
 54E  C7   C4   single    1.479  0.020  1.479
 54E  C9   C8   aromatic  1.389  0.020  1.389
 54E  C4   C3   aromatic  1.393  0.020  1.393
 54E  C1   C    single    1.508  0.020  1.508
 54E  C1   C2   aromatic  1.389  0.020  1.389
 54E  C    N    single    1.449  0.020  1.449
 54E  C3   C2   aromatic  1.387  0.020  1.387
 54E  C3   CL   single    1.738  0.020  1.738
 54E  C2   H1   single    0.930  0.020  1.080
 54E  C5   H2   single    0.930  0.020  1.080
 54E  C6   H3   single    0.930  0.020  1.080
 54E  C    H4   single    0.970  0.020  1.090
 54E  C    H5   single    0.970  0.020  1.090
 54E  N    H6   single    0.890  0.020  1.040
 54E  N    H7   single    0.890  0.020  1.040
 54E  C12  H9   single    0.930  0.020  1.080
 54E  C11  H10  single    0.930  0.020  1.080
 54E  C10  H11  single    0.930  0.020  1.080
 54E  C9   H12  single    0.930  0.020  1.080
 54E  C8   H13  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
 54E  C4   C3   C2   122.23  3.000
 54E  C2   C3   CL   117.57  3.000
 54E  C4   C3   CL   120.18  3.000
 54E  H1   C2   C1   119.66  3.000
 54E  H1   C2   C3   120.06  3.000
 54E  C1   C2   C3   120.28  3.000
 54E  C7   C4   C5   119.70  3.000
 54E  C7   C4   C3   123.68  3.000
 54E  C5   C4   C3   116.62  3.000
 54E  H2   C5   C6   119.46  3.000
 54E  H2   C5   C4   118.77  3.000
 54E  C6   C5   C4   121.76  3.000
 54E  H3   C6   C1   119.86  3.000
 54E  H3   C6   C5   119.38  3.000
 54E  C1   C6   C5   120.76  3.000
 54E  C    C1   C6   120.19  3.000
 54E  C    C1   C2   121.46  3.000
 54E  C6   C1   C2   118.34  3.000
 54E  H5   C    H4   105.71  3.000
 54E  H5   C    N    114.00  3.000
 54E  H4   C    N    107.85  3.000
 54E  H5   C    C1   108.14  3.000
 54E  H4   C    C1   108.03  3.000
 54E  N    C    C1   112.73  3.000
 54E  H7   N    H6   106.14  3.000
 54E  H7   N    C    109.85  3.000
 54E  H6   N    C    109.22  3.000
 54E  C8   C7   C12  118.86  3.000
 54E  C8   C7   C4   119.85  3.000
 54E  C12  C7   C4   121.26  3.000
 54E  H9   C12  C11  119.57  3.000
 54E  H9   C12  C7   119.92  3.000
 54E  C11  C12  C7   120.50  3.000
 54E  H10  C11  C10  120.08  3.000
 54E  H10  C11  C12  119.66  3.000
 54E  C10  C11  C12  120.25  3.000
 54E  H11  C10  C9   120.22  3.000
 54E  H11  C10  C11  120.14  3.000
 54E  C9   C10  C11  119.64  3.000
 54E  H12  C9   C8   119.70  3.000
 54E  H12  C9   C10  120.19  3.000
 54E  C8   C9   C10  120.10  3.000
 54E  H13  C8   C9   119.71  3.000
 54E  H13  C8   C7   119.65  3.000
 54E  C9   C8   C7   120.64  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
 54E  CONST_01  C6   C5   C4   C3     0.00   0.0  0
 54E  CONST_04  C6   C1   C2   C3     0.00   0.0  0
 54E  CONST_05  C5   C6   C1   C2     0.00   0.0  0
 54E  CONST_06  C5   C4   C3   C2     0.00   0.0  0
 54E  CONST_07  C7   C4   C3   C2   180.00   0.0  0
 54E  CONST_08  C1   C6   C5   C4     0.00   0.0  0
 54E  CONST_09  C11  C12  C7   C4   180.00   0.0  0
 54E  CONST_10  C9   C8   C7   C4   180.00   0.0  0
 54E  CONST_11  C1   C2   C3   C4     0.00   0.0  0
 54E  CONST_14  C7   C4   C5   C6   180.00   0.0  0
 54E  CONST_15  C10  C11  C12  C7     0.00   0.0  0
 54E  CONST_16  C10  C9   C8   C7     0.00   0.0  0
 54E  CONST_17  C9   C10  C11  C12    0.00   0.0  0
 54E  CONST_18  C9   C8   C7   C12    0.00   0.0  0
 54E  CONST_19  C8   C7   C12  C11    0.00   0.0  0
 54E  CONST_20  C8   C9   C10  C11    0.00   0.0  0
 54E  CONST_21  C5   C4   C3   CL   180.00   0.0  0
 54E  CONST_22  C7   C4   C3   CL     0.00   0.0  0
 54E  CONST_23  C1   C2   C3   CL   180.00   0.0  0
 54E  CONST_24  C    C1   C2   C3   180.00   0.0  0
 54E  CONST_25  C    C1   C6   C5   180.00   0.0  0
 54E  CONST_26  H2   C5   C4   C3   180.00   0.0  0
 54E  CONST_27  H3   C6   C1   C2   180.00   0.0  0
 54E  CONST_28  H9   C12  C7   C4     0.00   0.0  0
 54E  CONST_29  H13  C8   C7   C4     0.00   0.0  0
 54E  CONST_30  H1   C2   C3   C4   180.00   0.0  0
 54E  CONST_31  H10  C11  C12  C7   180.00   0.0  0
 54E  CONST_32  H12  C9   C8   C7   180.00   0.0  0
 54E  CONST_33  H11  C10  C11  C12  180.00   0.0  0
 54E  Var_01    N    C    C1   C2   -21.10  30.0  2
 54E  Var_02    H6   N    C    C1   169.66  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
 54E  plan-1  CL   0.020
 54E  plan-1  C3   0.020
 54E  plan-1  C2   0.020
 54E  plan-1  C4   0.020
 54E  plan-1  C5   0.020
 54E  plan-1  C6   0.020
 54E  plan-1  C1   0.020
 54E  plan-1  C    0.020
 54E  plan-1  C7   0.020
 54E  plan-1  H1   0.020
 54E  plan-1  H2   0.020
 54E  plan-1  H3   0.020
 54E  plan-2  C4   0.020
 54E  plan-2  C7   0.020
 54E  plan-2  C12  0.020
 54E  plan-2  C11  0.020
 54E  plan-2  C10  0.020
 54E  plan-2  C9   0.020
 54E  plan-2  C8   0.020
 54E  plan-2  H9   0.020
 54E  plan-2  H10  0.020
 54E  plan-2  H11  0.020
 54E  plan-2  H12  0.020
 54E  plan-2  H13  0.020

