# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar  9 18:37:52 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: 1-(1-phenylcyclopentyl)methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCC1(CCCC1)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
 007  007  1-(1-phenylcyclopentyl)methanamine  ligand  30  13  .  2021-07-27  2022-07-21
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_007
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
 007  C1    C  CH2   0  -0.436  -1.2503  -0.6766   1.5071
 007  C2    C  CH2   0  -0.449  -1.1466  -0.2028   2.9514
 007  C3    C  CT    0  -0.134   0.0189  -0.1222   0.8284
 007  C4    C  CH2   0  -0.440  -0.6252   1.2280   2.8133
 007  C5    C  CH2   0  -0.436   0.2448   1.2365   1.5399
 007  C6    C  CR6   0   0.148  -0.1069  -0.0154  -0.6774
 007  C7    C  CR16  0  -0.316  -0.8861  -0.9217  -1.3984
 007  C8    C  CR16  0  -0.314   0.6020   0.9464  -1.3992
 007  C9    C  CR16  0  -0.240  -0.9709  -0.8584  -2.7831
 007  C10   C  CR16  0  -0.240   0.5218   1.0132  -2.7843
 007  C11   C  CR16  0  -0.277  -0.2685   0.1122  -3.4845
 007  C12   C  CH2   0  -0.263   1.1811  -1.0928   1.1365
 007  N13   N  NH2   0  -0.793   2.4593  -0.6243   0.6375
 007  H1C1  H  HCH2  0   0.230  -2.1398  -0.2435   1.0386
 007  H1C2  H  HCH2  0   0.230  -1.3397  -1.7621   1.4173
 007  H2C1  H  HCH2  0   0.232  -2.0959  -0.2575   3.4857
 007  H2C2  H  HCH2  0   0.219  -0.4378  -0.8215   3.5072
 007  H4C1  H  HCH2  0   0.222  -1.4696   1.9081   2.6856
 007  H4C2  H  HCH2  0   0.228  -0.0845   1.5653   3.6985
 007  H5C1  H  HCH2  0   0.232   1.3040   1.3753   1.7577
 007  H5C2  H  HCH2  0   0.228  -0.0473   2.0688   0.8979
 007  H7    H  HCR6  0   0.246  -1.4396  -1.6929  -0.8765
 007  H8    H  HCR6  0   0.252   1.2297   1.6577  -0.8776
 007  H9    H  HCR6  0   0.250  -1.5874  -1.5715  -3.3156
 007  H10   H  HCR6  0   0.250   1.0815   1.7718  -3.3170
 007  H11   H  HCR6  0   0.251  -0.3356   0.1656  -4.5635
 007  H121  H  HCH2  0   0.201   0.8961  -2.0845   0.7548
 007  H122  H  HCH2  0   0.227   1.2704  -1.1949   2.2210
 007  H131  H  HNH2  0   0.350   3.1976  -1.2073   1.0083
 007  H132  H  HNH2  0   0.344   2.5028  -0.7313  -0.3678

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
 007  C1   C2    single    1.524  0.020  1.524
 007  C1   C3    single    1.542  0.020  1.542
 007  C1   H1C1  single    0.970  0.020  1.090
 007  C1   H1C2  single    0.970  0.020  1.090
 007  C2   C4    single    1.529  0.020  1.529
 007  C2   H2C1  single    0.970  0.020  1.090
 007  C2   H2C2  single    0.970  0.020  1.090
 007  C3   C5    single    1.550  0.020  1.550
 007  C3   C6    single    1.515  0.020  1.515
 007  C3   C12   single    1.545  0.020  1.545
 007  C4   C5    single    1.542  0.020  1.542
 007  C4   H4C1  single    0.970  0.020  1.090
 007  C4   H4C2  single    0.970  0.020  1.090
 007  C5   H5C1  single    0.970  0.020  1.090
 007  C5   H5C2  single    0.970  0.020  1.090
 007  C6   C7    aromatic  1.396  0.020  1.396
 007  C6   C8    aromatic  1.396  0.020  1.396
 007  C7   C9    aromatic  1.389  0.020  1.389
 007  C7   H7    single    0.930  0.020  1.080
 007  C8   C10   aromatic  1.389  0.020  1.389
 007  C8   H8    single    0.930  0.020  1.080
 007  C9   C11   aromatic  1.388  0.020  1.388
 007  C9   H9    single    0.930  0.020  1.080
 007  C10  C11   aromatic  1.388  0.020  1.388
 007  C10  H10   single    0.930  0.020  1.080
 007  C11  H11   single    0.930  0.020  1.080
 007  C12  N13   single    1.450  0.020  1.450
 007  C12  H121  single    0.970  0.020  1.090
 007  C12  H122  single    0.970  0.020  1.090
 007  N13  H131  single    0.890  0.020  1.040
 007  N13  H132  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
 007  H1C2  C1   H1C1  106.94  3.000
 007  H1C2  C1   C3    112.84  3.000
 007  H1C1  C1   C3    109.76  3.000
 007  H1C2  C1   C2    113.10  3.000
 007  H1C1  C1   C2    109.75  3.000
 007  C3    C1   C2    104.44  3.000
 007  H2C2  C2   H2C1  106.68  3.000
 007  H2C2  C2   C4    110.77  3.000
 007  H2C1  C2   C4    112.83  3.000
 007  H2C2  C2   C1    110.50  3.000
 007  H2C1  C2   C1    112.92  3.000
 007  C4    C2   C1    103.21  3.000
 007  C12   C3   C6    107.75  3.000
 007  C12   C3   C5    110.45  3.000
 007  C6    C3   C5    113.99  3.000
 007  C12   C3   C1    107.79  3.000
 007  C6    C3   C1    113.23  3.000
 007  C5    C3   C1    103.47  3.000
 007  H4C2  C4   H4C1  106.60  3.000
 007  H4C2  C4   C5    112.88  3.000
 007  H4C1  C4   C5    109.65  3.000
 007  H4C2  C4   C2    112.65  3.000
 007  H4C1  C4   C2    109.26  3.000
 007  C5    C4   C2    105.79  3.000
 007  H5C2  C5   H5C1  106.29  3.000
 007  H5C2  C5   C4    109.82  3.000
 007  H5C1  C5   C4    112.57  3.000
 007  H5C2  C5   C3    111.07  3.000
 007  H5C1  C5   C3    110.17  3.000
 007  C4    C5   C3    106.97  3.000
 007  C8    C6   C7    117.63  3.000
 007  C8    C6   C3    121.36  3.000
 007  C7    C6   C3    120.93  3.000
 007  H7    C7   C9    118.79  3.000
 007  H7    C7   C6    119.91  3.000
 007  C9    C7   C6    121.30  3.000
 007  H8    C8   C10   118.84  3.000
 007  H8    C8   C6    119.87  3.000
 007  C10   C8   C6    121.29  3.000
 007  H9    C9   C11   120.01  3.000
 007  H9    C9   C7    119.68  3.000
 007  C11   C9   C7    120.31  3.000
 007  H10   C10  C11   120.06  3.000
 007  H10   C10  C8    119.63  3.000
 007  C11   C10  C8    120.31  3.000
 007  H11   C11  C10   120.41  3.000
 007  H11   C11  C9    120.45  3.000
 007  C10   C11  C9    119.15  3.000
 007  H122  C12  H121  106.33  3.000
 007  H122  C12  N13   107.44  3.000
 007  H121  C12  N13   113.59  3.000
 007  H122  C12  C3    108.54  3.000
 007  H121  C12  C3    107.59  3.000
 007  N13   C12  C3    113.05  3.000
 007  H132  N13  H131  105.79  3.000
 007  H132  N13  C12   110.22  3.000
 007  H131  N13  C12   109.34  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
 007  CONST_01  C11   C9   C7   C6    0.00   0.0  0
 007  CONST_02  C11   C10  C8   C6    0.00   0.0  0
 007  CONST_03  C10   C8   C6   C7    0.00   0.0  0
 007  CONST_04  C10   C11  C9   C7    0.00   0.0  0
 007  CONST_05  C9    C7   C6   C8    0.00   0.0  0
 007  CONST_06  C9    C11  C10  C8    0.00   0.0  0
 007  CONST_07  C9    C7   C6   C3  180.00   0.0  0
 007  CONST_08  C10   C8   C6   C3  180.00   0.0  0
 007  CONST_09  H7    C7   C6   C3    0.00   0.0  0
 007  CONST_10  H8    C8   C6   C3    0.00   0.0  0
 007  CONST_11  H9    C9   C7   C6  180.00   0.0  0
 007  CONST_12  H10   C10  C8   C6  180.00   0.0  0
 007  CONST_13  H11   C11  C9   C7  180.00   0.0  0
 007  Var_01    C5    C4   C2   C1  -30.78  30.0  1
 007  Var_02    C3    C5   C4   C2    9.49  30.0  1
 007  Var_03    C4    C2   C1   C3   40.80  30.0  1
 007  Var_04    H131  N13  C12  C3  169.89  30.0  3

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
 007  chir_01  C3  C5  C6  C1  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
 007  plan-1  C3   0.020
 007  plan-1  C6   0.020
 007  plan-1  C7   0.020
 007  plan-1  C8   0.020
 007  plan-1  C9   0.020
 007  plan-1  C10  0.020
 007  plan-1  C11  0.020
 007  plan-1  H7   0.020
 007  plan-1  H8   0.020
 007  plan-1  H9   0.020
 007  plan-1  H10  0.020
 007  plan-1  H11  0.020

