# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 05:27:33 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: 2-[4-(aminomethyl)-2-chloranyl-phenyl]phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1ccc(c(Cl)c1)c2ccccc2O
#
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
 A9K  A9K  2-[4-(aminomethyl)-2-chloranyl-phenyl]phenol  ligand  28  16  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A9K
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
 A9K  C1   C   CR6   0   0.059  -2.8798  -0.6637  -0.0807
 A9K  C2   C   CR16  0  -0.279  -2.1157  -1.8069   0.1330
 A9K  C3   C   CR16  0  -0.296  -0.7321  -1.7451   0.1287
 A9K  C4   C   CR6   0   0.163  -0.0566  -0.5437  -0.0783
 A9K  C5   C   CR6   0  -0.092  -0.8375   0.5892  -0.2904
 A9K  C6   C   CR16  0  -0.235  -2.2227   0.5428  -0.2928
 A9K  CL   CL  CL    0  -0.136  -0.0679   2.1136  -0.5981
 A9K  C    C   CH2   0  -0.330  -4.3853  -0.7494  -0.1182
 A9K  N    N   NH2   0  -0.795  -5.0203   0.5071   0.2285
 A9K  C7   C   CR6   0  -0.066   1.4216  -0.5146  -0.0933
 A9K  C12  C   CR6   0   0.339   2.1384   0.1363   0.9168
 A9K  O    O   OH1   0  -0.618   1.4336   0.7341   1.8943
 A9K  C11  C   CR16  0  -0.380   3.5302   0.1347   0.8946
 A9K  C10  C   CR16  0  -0.249   4.2114  -0.5200  -0.1211
 A9K  C9   C   CR16  0  -0.275   3.5134  -1.1813  -1.1212
 A9K  C8   C   CR16  0  -0.272   2.1255  -1.1731  -1.0959
 A9K  H1   H   HCR6  0   0.252  -2.6055  -2.7563   0.3144
 A9K  H2   H   HCR6  0   0.257  -0.1544  -2.6437   0.3057
 A9K  H3   H   HCR6  0   0.269  -2.7976   1.4435  -0.4607
 A9K  H4   H   HCH2  0   0.248  -4.6842  -1.0073  -1.1384
 A9K  H5   H   HCH2  0   0.219  -4.6990  -1.5974   0.5051
 A9K  H6   H   HNH2  0   0.358  -6.0124   0.4443   0.0436
 A9K  H7   H   HNH2  0   0.347  -4.9284   0.6724   1.2229
 A9K  H9   H   HOH1  0   0.475   2.0281   1.1429   2.5333
 A9K  H10  H   HCR6  0   0.270   4.0826   0.6401   1.6788
 A9K  H11  H   HCR6  0   0.260   5.2938  -0.5123  -0.1235
 A9K  H12  H   HCR6  0   0.254   4.0400  -1.6938  -1.9147
 A9K  H13  H   HCR6  0   0.254   1.5693  -1.6777  -1.8764

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
 A9K  O    C12  single    1.345  0.020  1.345
 A9K  N    C    single    1.450  0.020  1.450
 A9K  C12  C11  aromatic  1.392  0.020  1.392
 A9K  C12  C7   aromatic  1.399  0.020  1.399
 A9K  CL   C5   single    1.735  0.020  1.735
 A9K  C6   C5   aromatic  1.386  0.020  1.386
 A9K  C6   C1   aromatic  1.390  0.020  1.390
 A9K  C11  C10  aromatic  1.387  0.020  1.387
 A9K  C    C1   single    1.508  0.020  1.508
 A9K  C5   C4   aromatic  1.392  0.020  1.392
 A9K  C1   C2   aromatic  1.392  0.020  1.392
 A9K  C4   C3   aromatic  1.394  0.020  1.394
 A9K  C4   C7   single    1.479  0.020  1.479
 A9K  C2   C3   aromatic  1.385  0.020  1.385
 A9K  C7   C8   aromatic  1.391  0.020  1.391
 A9K  C10  C9   aromatic  1.387  0.020  1.387
 A9K  C8   C9   aromatic  1.388  0.020  1.388
 A9K  C2   H1   single    0.930  0.020  1.080
 A9K  C3   H2   single    0.930  0.020  1.080
 A9K  C6   H3   single    0.930  0.020  1.080
 A9K  C    H4   single    0.970  0.020  1.090
 A9K  C    H5   single    0.970  0.020  1.090
 A9K  N    H6   single    0.890  0.020  1.040
 A9K  N    H7   single    0.890  0.020  1.040
 A9K  O    H9   single    0.850  0.020  0.980
 A9K  C11  H10  single    0.930  0.020  1.080
 A9K  C10  H11  single    0.930  0.020  1.080
 A9K  C9   H12  single    0.930  0.020  1.080
 A9K  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
 A9K  C    C1   C6   121.15  3.000
 A9K  C    C1   C2   120.35  3.000
 A9K  C6   C1   C2   118.48  3.000
 A9K  H1   C2   C3   119.42  3.000
 A9K  H1   C2   C1   119.82  3.000
 A9K  C3   C2   C1   120.76  3.000
 A9K  H2   C3   C4   118.76  3.000
 A9K  H2   C3   C2   119.69  3.000
 A9K  C4   C3   C2   121.54  3.000
 A9K  C7   C4   C5   122.90  3.000
 A9K  C7   C4   C3   120.20  3.000
 A9K  C5   C4   C3   116.88  3.000
 A9K  CL   C5   C6   118.19  3.000
 A9K  C6   C5   C4   122.25  3.000
 A9K  CL   C5   C4   119.54  3.000
 A9K  H3   C6   C5   120.24  3.000
 A9K  H3   C6   C1   119.68  3.000
 A9K  C5   C6   C1   120.08  3.000
 A9K  H5   C    H4   105.62  3.000
 A9K  H5   C    N    114.10  3.000
 A9K  H4   C    N    107.92  3.000
 A9K  H5   C    C1   108.35  3.000
 A9K  H4   C    C1   108.01  3.000
 A9K  N    C    C1   112.45  3.000
 A9K  H7   N    H6   106.19  3.000
 A9K  H7   N    C    109.67  3.000
 A9K  H6   N    C    109.40  3.000
 A9K  C8   C7   C12  118.77  3.000
 A9K  C8   C7   C4   120.27  3.000
 A9K  C12  C7   C4   120.93  3.000
 A9K  C11  C12  O    122.41  3.000
 A9K  C11  C12  C7   120.02  3.000
 A9K  O    C12  C7   117.57  3.000
 A9K  H9   O    C12  110.31  3.000
 A9K  H10  C11  C10  119.96  3.000
 A9K  H10  C11  C12  119.83  3.000
 A9K  C10  C11  C12  120.21  3.000
 A9K  H11  C10  C9   120.32  3.000
 A9K  H11  C10  C11  119.30  3.000
 A9K  C9   C10  C11  120.38  3.000
 A9K  H12  C9   C8   120.20  3.000
 A9K  H12  C9   C10  120.65  3.000
 A9K  C8   C9   C10  119.15  3.000
 A9K  H13  C8   C9   119.83  3.000
 A9K  H13  C8   C7   118.70  3.000
 A9K  C9   C8   C7   121.46  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
 A9K  CONST_01  C4   C5   C6   C1     0.00   0.0  0
 A9K  CONST_02  C4   C3   C2   C1     0.00   0.0  0
 A9K  CONST_03  C5   C6   C1   C2     0.00   0.0  0
 A9K  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 A9K  CONST_05  C7   C4   C3   C2   180.00   0.0  0
 A9K  CONST_06  C6   C5   C4   C3     0.00   0.0  0
 A9K  CONST_09  C6   C1   C2   C3     0.00   0.0  0
 A9K  CONST_10  C11  C12  C7   C4   180.00   0.0  0
 A9K  CONST_11  C9   C8   C7   C4   180.00   0.0  0
 A9K  CONST_14  C7   C4   C5   C6   180.00   0.0  0
 A9K  CONST_15  C10  C11  C12  C7     0.00   0.0  0
 A9K  CONST_16  C10  C9   C8   C7     0.00   0.0  0
 A9K  CONST_17  C9   C10  C11  C12    0.00   0.0  0
 A9K  CONST_18  C9   C8   C7   C12    0.00   0.0  0
 A9K  CONST_19  C8   C7   C12  C11    0.00   0.0  0
 A9K  CONST_20  C8   C9   C10  C11    0.00   0.0  0
 A9K  CONST_21  CL   C5   C6   C1   180.00   0.0  0
 A9K  CONST_22  CL   C5   C4   C3   180.00   0.0  0
 A9K  CONST_23  C    C1   C2   C3   180.00   0.0  0
 A9K  CONST_24  O    C12  C7   C4     0.00   0.0  0
 A9K  CONST_25  C    C1   C6   C5   180.00   0.0  0
 A9K  CONST_26  C7   C4   C5   CL     0.00   0.0  0
 A9K  CONST_27  C10  C11  C12  O    180.00   0.0  0
 A9K  CONST_28  C8   C7   C12  O    180.00   0.0  0
 A9K  CONST_29  H2   C3   C2   C1   180.00   0.0  0
 A9K  CONST_30  H3   C6   C1   C2   180.00   0.0  0
 A9K  CONST_31  H1   C2   C3   C4   180.00   0.0  0
 A9K  CONST_32  H13  C8   C7   C4     0.00   0.0  0
 A9K  CONST_33  H10  C11  C12  C7   180.00   0.0  0
 A9K  CONST_34  H12  C9   C8   C7   180.00   0.0  0
 A9K  CONST_35  H11  C10  C11  C12  180.00   0.0  0
 A9K  Var_01    N    C    C1   C2   154.99  30.0  2
 A9K  Var_02    H6   N    C    C1   170.79  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
 A9K  plan-1  C1   0.020
 A9K  plan-1  C2   0.020
 A9K  plan-1  C3   0.020
 A9K  plan-1  C4   0.020
 A9K  plan-1  C5   0.020
 A9K  plan-1  C6   0.020
 A9K  plan-1  CL   0.020
 A9K  plan-1  C    0.020
 A9K  plan-1  C7   0.020
 A9K  plan-1  H1   0.020
 A9K  plan-1  H2   0.020
 A9K  plan-1  H3   0.020
 A9K  plan-2  C4   0.020
 A9K  plan-2  C7   0.020
 A9K  plan-2  C12  0.020
 A9K  plan-2  O    0.020
 A9K  plan-2  C11  0.020
 A9K  plan-2  C10  0.020
 A9K  plan-2  C9   0.020
 A9K  plan-2  C8   0.020
 A9K  plan-2  H10  0.020
 A9K  plan-2  H11  0.020
 A9K  plan-2  H12  0.020
 A9K  plan-2  H13  0.020

