# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 11:32:05 2020
#   Inital geometry file: a 61 line input string
#   Ligand name: 1-(naphthalen-1-yl)methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1cccc2ccccc12
#
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
 7CD  7CD  1-(naphthalen-1-yl)methanamine  ligand  23  12  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7CD
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
 7CD  C11  C  CR16  0  -0.332  -0.6445  -2.1586   0.1368
 7CD  C10  C  CR16  0  -0.244   0.6757  -2.4863   0.0173
 7CD  C12  C  CR66  0   0.112  -1.0538  -0.8055   0.0660
 7CD  C14  C  CR16  0  -0.315  -0.5200   1.5575  -0.1826
 7CD  C13  C  CR66  0   0.082  -0.0801   0.2127  -0.1195
 7CD  C15  C  CR16  0  -0.252  -1.8492   1.8706  -0.0807
 7CD  N06  N  NH2   0  -0.786   2.5441   1.7077   0.7201
 7CD  C08  C  CR6   0   0.103   1.2925  -0.1513  -0.2570
 7CD  C09  C  CR16  0  -0.328   1.6394  -1.4763  -0.1837
 7CD  C16  C  CR16  0  -0.261  -2.8123   0.8572   0.0973
 7CD  C17  C  CR16  0  -0.314  -2.4196  -0.4506   0.1721
 7CD  H1   H  HCR6  0   0.253  -1.3933  -2.9280   0.2816
 7CD  H2   H  HCR6  0   0.255   0.9893  -3.5208   0.0712
 7CD  H3   H  HCR6  0   0.254   0.2055   2.3507  -0.2927
 7CD  H4   H  HCR6  0   0.255  -2.1639   2.9050  -0.1323
 7CD  H7   H  HNH2  0   0.342   2.9627   1.1459   1.4509
 7CD  H8   H  HCH2  0   0.234   2.0744   1.5506  -1.2926
 7CD  H9   H  HCH2  0   0.227   3.2754   0.3795  -0.7988
 7CD  H10  H  HCR6  0   0.250   2.6805  -1.7588  -0.2885
 7CD  H11  H  HCR6  0   0.256  -3.8602   1.1165   0.1757
 7CD  H12  H  HCR6  0   0.254  -3.1535  -1.2359   0.3087
 7CD  H5   H  HNH2  0   0.351   3.2112   2.4417   0.5179
 7CD  C07  C  CH2   0  -0.396   2.3603   0.8887  -0.4704

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
 7CD  N06  C07  single    1.457  0.020  1.457
 7CD  C07  C08  single    1.506  0.020  1.506
 7CD  C14  C15  aromatic  1.369  0.020  1.369
 7CD  C14  C13  aromatic  1.416  0.020  1.416
 7CD  C15  C16  aromatic  1.409  0.020  1.409
 7CD  C08  C13  aromatic  1.427  0.020  1.427
 7CD  C08  C09  aromatic  1.372  0.020  1.372
 7CD  C13  C12  aromatic  1.421  0.020  1.421
 7CD  C16  C17  aromatic  1.368  0.020  1.368
 7CD  C09  C10  aromatic  1.410  0.020  1.410
 7CD  C12  C17  aromatic  1.415  0.020  1.415
 7CD  C12  C11  aromatic  1.415  0.020  1.415
 7CD  C10  C11  aromatic  1.365  0.020  1.365
 7CD  C11  H1   single    0.930  0.020  1.080
 7CD  C10  H2   single    0.930  0.020  1.080
 7CD  C14  H3   single    0.930  0.020  1.080
 7CD  C15  H4   single    0.930  0.020  1.080
 7CD  N06  H7   single    0.890  0.020  1.040
 7CD  C07  H8   single    0.970  0.020  1.090
 7CD  C07  H9   single    0.970  0.020  1.090
 7CD  C09  H10  single    0.930  0.020  1.080
 7CD  C16  H11  single    0.930  0.020  1.080
 7CD  C17  H12  single    0.930  0.020  1.080
 7CD  N06  H5   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
 7CD  H1   C11  C12  119.06  3.000
 7CD  H1   C11  C10  120.64  3.000
 7CD  C12  C11  C10  120.31  3.000
 7CD  H2   C10  C09  119.57  3.000
 7CD  H2   C10  C11  120.34  3.000
 7CD  C09  C10  C11  120.08  3.000
 7CD  C17  C12  C13  119.43  3.000
 7CD  C17  C12  C11  121.01  3.000
 7CD  C13  C12  C11  119.56  3.000
 7CD  H3   C14  C15  119.43  3.000
 7CD  H3   C14  C13  119.54  3.000
 7CD  C15  C14  C13  121.01  3.000
 7CD  C08  C13  C14  122.46  3.000
 7CD  C08  C13  C12  119.28  3.000
 7CD  C14  C13  C12  118.26  3.000
 7CD  H4   C15  C16  119.63  3.000
 7CD  H4   C15  C14  119.81  3.000
 7CD  C16  C15  C14  120.55  3.000
 7CD  H5   N06  H7   105.91  3.000
 7CD  H5   N06  C07  109.12  3.000
 7CD  H7   N06  C07  109.28  3.000
 7CD  C09  C08  C07  119.70  3.000
 7CD  C09  C08  C13  118.98  3.000
 7CD  C07  C08  C13  121.31  3.000
 7CD  H10  C09  C08  119.31  3.000
 7CD  H10  C09  C10  118.91  3.000
 7CD  C08  C09  C10  121.78  3.000
 7CD  H11  C16  C17  120.21  3.000
 7CD  H11  C16  C15  119.91  3.000
 7CD  C17  C16  C15  119.89  3.000
 7CD  H12  C17  C16  120.36  3.000
 7CD  H12  C17  C12  118.78  3.000
 7CD  C16  C17  C12  120.86  3.000
 7CD  H9   C07  H8   105.90  3.000
 7CD  H9   C07  C08  108.25  3.000
 7CD  H8   C07  C08  109.83  3.000
 7CD  H9   C07  N06  113.59  3.000
 7CD  H8   C07  N06  107.89  3.000
 7CD  C08  C07  N06  111.22  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
 7CD  CONST_01  C14  C13  C12  C11  180.00   0.0  0
 7CD  CONST_02  C08  C13  C12  C11    0.00   0.0  0
 7CD  CONST_03  C16  C17  C12  C11  180.00   0.0  0
 7CD  CONST_04  C08  C09  C10  C11    0.00   0.0  0
 7CD  CONST_05  C13  C08  C09  C10    0.00   0.0  0
 7CD  CONST_06  C13  C12  C11  C10    0.00   0.0  0
 7CD  CONST_07  C17  C12  C11  C10  180.00   0.0  0
 7CD  CONST_08  C15  C14  C13  C12    0.00   0.0  0
 7CD  CONST_09  C09  C08  C13  C12    0.00   0.0  0
 7CD  CONST_10  C15  C16  C17  C12    0.00   0.0  0
 7CD  CONST_11  C09  C10  C11  C12    0.00   0.0  0
 7CD  CONST_12  C17  C16  C15  C14    0.00   0.0  0
 7CD  CONST_13  C09  C08  C13  C14  180.00   0.0  0
 7CD  CONST_14  C17  C12  C13  C14    0.00   0.0  0
 7CD  CONST_15  C16  C15  C14  C13    0.00   0.0  0
 7CD  CONST_16  C16  C17  C12  C13    0.00   0.0  0
 7CD  CONST_17  C08  C13  C14  C15  180.00   0.0  0
 7CD  CONST_18  C17  C12  C13  C08  180.00   0.0  0
 7CD  CONST_19  C07  C08  C09  C10  180.00   0.0  0
 7CD  CONST_20  C07  C08  C13  C12  180.00   0.0  0
 7CD  CONST_21  C07  C08  C13  C14    0.00   0.0  0
 7CD  CONST_22  H12  C17  C12  C11    0.00   0.0  0
 7CD  CONST_23  H10  C09  C10  C11  180.00   0.0  0
 7CD  CONST_24  H3   C14  C13  C12  180.00   0.0  0
 7CD  CONST_25  H11  C16  C17  C12  180.00   0.0  0
 7CD  CONST_26  H2   C10  C11  C12  180.00   0.0  0
 7CD  CONST_27  H4   C15  C14  C13  180.00   0.0  0
 7CD  CONST_28  H1   C11  C12  C13  180.00   0.0  0
 7CD  Var_01    N06  C07  C08  C13   68.73  30.0  3
 7CD  Var_02    H7   N06  C07  C08   69.24  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
 7CD  plan-1  C11  0.020
 7CD  plan-1  C10  0.020
 7CD  plan-1  C12  0.020
 7CD  plan-1  C14  0.020
 7CD  plan-1  C13  0.020
 7CD  plan-1  C15  0.020
 7CD  plan-1  C08  0.020
 7CD  plan-1  C09  0.020
 7CD  plan-1  C16  0.020
 7CD  plan-1  C17  0.020
 7CD  plan-1  H1   0.020
 7CD  plan-1  H2   0.020
 7CD  plan-1  H3   0.020
 7CD  plan-1  H4   0.020
 7CD  plan-1  H10  0.020
 7CD  plan-1  H11  0.020
 7CD  plan-1  H12  0.020
 7CD  plan-1  C07  0.020

