# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 22:57:14 2021
#   Inital geometry file: a 75 line input string
#   Ligand name: (2-phenoxyphenyl)methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1ccccc1Oc2ccccc2
#
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
 SLY  SLY  (2-phenoxyphenyl)methanamine  ligand  28  15  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SLY
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
 SLY  C4   C  CR16  0  -0.270  25.5499  110.3903  13.0079
 SLY  C5   C  CR16  0  -0.293  26.2271  109.1861  12.8804
 SLY  C6   C  CR6   0   0.274  25.9306  108.1415  13.7426
 SLY  C7   C  CR6   0   0.367  26.2085  105.9885  12.8080
 SLY  C8   C  CR16  0  -0.338  25.0402  106.0777  12.0600
 SLY  C10  C  CR16  0  -0.273  25.4529  103.8681  11.1717
 SLY  N    N  NH2   0  -0.793  25.6747  107.0668  16.7399
 SLY  O    O  O2    0  -0.515  26.6491  106.9728  13.6413
 SLY  C1   C  CR6   0   0.066  24.9598  108.2590  14.7346
 SLY  C11  C  CR16  0  -0.247  26.6186  103.7928  11.9259
 SLY  C12  C  CR16  0  -0.331  27.0003  104.8451  12.7418
 SLY  C2   C  CR16  0  -0.313  24.2987  109.4795  14.8446
 SLY  C3   C  CR16  0  -0.243  24.5814  110.5368  13.9913
 SLY  C9   C  CR16  0  -0.247  24.6731  105.0122  11.2456
 SLY  H1   H  HCR6  0   0.262  25.7805  111.2095  12.3395
 SLY  H2   H  HCR6  0   0.271  26.9895  109.0596  12.1220
 SLY  H3   H  HCR6  0   0.278  24.4124  106.9580  12.1012
 SLY  H4   H  HCR6  0   0.254  25.1580  103.0445  10.5354
 SLY  H5   H  HNH2  0   0.352  25.4011  106.3602  17.4116
 SLY  H6   H  HNH2  0   0.344  26.5511  106.7432  16.3495
 SLY  H8   H  HCH2  0   0.245  23.7011  107.3184  16.1544
 SLY  H9   H  HCH2  0   0.214  24.5535  106.1896  15.1285
 SLY  H10  H  HCR6  0   0.260  27.2390  102.9070  11.8820
 SLY  H11  H  HCR6  0   0.267  27.9074  104.7865  13.3301
 SLY  H12  H  HCR6  0   0.257  23.5422  109.5969  15.6114
 SLY  H13  H  HCR6  0   0.258  24.0497  111.4732  14.0967
 SLY  H14  H  HCR6  0   0.261  23.7620  105.0858  10.6661
 SLY  C    C  CH2   0  -0.368  24.6678  107.1279  15.6857

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
 SLY  C10  C9   aromatic  1.386  0.020  1.386
 SLY  C10  C11  aromatic  1.391  0.020  1.391
 SLY  C9   C8   aromatic  1.391  0.020  1.391
 SLY  C11  C12  aromatic  1.385  0.020  1.385
 SLY  C8   C7   aromatic  1.390  0.020  1.390
 SLY  C5   C4   aromatic  1.387  0.020  1.387
 SLY  C5   C6   aromatic  1.386  0.020  1.386
 SLY  C4   C3   aromatic  1.388  0.020  1.388
 SLY  C12  C7   aromatic  1.392  0.020  1.392
 SLY  C7   O    single    1.363  0.020  1.363
 SLY  C6   O    single    1.376  0.020  1.376
 SLY  C6   C1   aromatic  1.393  0.020  1.393
 SLY  C3   C2   aromatic  1.388  0.020  1.388
 SLY  C2   C1   aromatic  1.392  0.020  1.392
 SLY  C1   C    single    1.506  0.020  1.506
 SLY  C    N    single    1.459  0.020  1.459
 SLY  C4   H1   single    0.930  0.020  1.080
 SLY  C5   H2   single    0.930  0.020  1.080
 SLY  C8   H3   single    0.930  0.020  1.080
 SLY  C10  H4   single    0.930  0.020  1.080
 SLY  N    H5   single    0.890  0.020  1.040
 SLY  N    H6   single    0.890  0.020  1.040
 SLY  C    H8   single    0.970  0.020  1.090
 SLY  C    H9   single    0.970  0.020  1.090
 SLY  C11  H10  single    0.930  0.020  1.080
 SLY  C12  H11  single    0.930  0.020  1.080
 SLY  C2   H12  single    0.930  0.020  1.080
 SLY  C3   H13  single    0.930  0.020  1.080
 SLY  C9   H14  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
 SLY  H1   C4   C3   120.43  3.000
 SLY  H1   C4   C5   119.75  3.000
 SLY  C3   C4   C5   119.82  3.000
 SLY  H2   C5   C6   119.88  3.000
 SLY  H2   C5   C4   120.62  3.000
 SLY  C6   C5   C4   119.50  3.000
 SLY  C1   C6   O    119.22  3.000
 SLY  C1   C6   C5   121.89  3.000
 SLY  O    C6   C5   118.86  3.000
 SLY  C12  C7   O    116.00  3.000
 SLY  O    C7   C8   123.66  3.000
 SLY  C12  C7   C8   120.33  3.000
 SLY  H3   C8   C9   119.51  3.000
 SLY  H3   C8   C7   121.29  3.000
 SLY  C9   C8   C7   119.20  3.000
 SLY  H4   C10  C9   120.42  3.000
 SLY  H4   C10  C11  120.42  3.000
 SLY  C9   C10  C11  119.16  3.000
 SLY  H6   N    H5   105.46  3.000
 SLY  H6   N    C    109.39  3.000
 SLY  H5   N    C    108.78  3.000
 SLY  C7   O    C6   119.33  3.000
 SLY  C2   C1   C    121.08  3.000
 SLY  C    C1   C6   121.43  3.000
 SLY  C2   C1   C6   117.46  3.000
 SLY  H10  C11  C12  119.19  3.000
 SLY  H10  C11  C10  120.19  3.000
 SLY  C12  C11  C10  120.62  3.000
 SLY  H11  C12  C11  120.65  3.000
 SLY  H11  C12  C7   119.67  3.000
 SLY  C11  C12  C7   119.68  3.000
 SLY  H12  C2   C3   119.66  3.000
 SLY  H12  C2   C1   118.84  3.000
 SLY  C3   C2   C1   121.50  3.000
 SLY  H13  C3   C2   119.96  3.000
 SLY  H13  C3   C4   120.22  3.000
 SLY  C2   C3   C4   119.83  3.000
 SLY  H14  C9   C10  120.07  3.000
 SLY  H14  C9   C8   118.93  3.000
 SLY  C10  C9   C8   121.00  3.000
 SLY  H9   C    H8   105.97  3.000
 SLY  H9   C    C1   109.98  3.000
 SLY  H8   C    C1   108.17  3.000
 SLY  H9   C    N    113.77  3.000
 SLY  H8   C    N    107.96  3.000
 SLY  C1   C    N    110.72  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
 SLY  CONST_01  C1   C6   C5   C4     0.00   0.0  0
 SLY  CONST_02  C1   C2   C3   C4     0.00   0.0  0
 SLY  CONST_03  C2   C3   C4   C5     0.00   0.0  0
 SLY  CONST_04  C2   C1   C6   C5     0.00   0.0  0
 SLY  CONST_05  C3   C4   C5   C6     0.00   0.0  0
 SLY  CONST_06  C3   C2   C1   C6     0.00   0.0  0
 SLY  CONST_07  C10  C9   C8   C7     0.00   0.0  0
 SLY  CONST_08  C10  C11  C12  C7     0.00   0.0  0
 SLY  CONST_09  C11  C10  C9   C8     0.00   0.0  0
 SLY  CONST_10  C11  C12  C7   C8     0.00   0.0  0
 SLY  CONST_11  C9   C10  C11  C12    0.00   0.0  0
 SLY  CONST_12  C9   C8   C7   C12    0.00   0.0  0
 SLY  CONST_13  O    C6   C5   C4   180.00   0.0  0
 SLY  CONST_14  C    C1   C6   C5   180.00   0.0  0
 SLY  CONST_15  C3   C2   C1   C    180.00   0.0  0
 SLY  CONST_16  C9   C8   C7   O    180.00   0.0  0
 SLY  CONST_17  C11  C12  C7   O    180.00   0.0  0
 SLY  CONST_18  C2   C1   C6   O    180.00   0.0  0
 SLY  CONST_19  H12  C2   C3   C4   180.00   0.0  0
 SLY  CONST_20  H13  C3   C4   C5   180.00   0.0  0
 SLY  CONST_21  H1   C4   C5   C6   180.00   0.0  0
 SLY  CONST_22  H14  C9   C8   C7   180.00   0.0  0
 SLY  CONST_23  H10  C11  C12  C7   180.00   0.0  0
 SLY  CONST_24  H4   C10  C9   C8   180.00   0.0  0
 SLY  CONST_25  H11  C12  C7   C8   180.00   0.0  0
 SLY  CONST_26  H3   C8   C9   C10  180.00   0.0  0
 SLY  CONST_27  H2   C5   C6   C1   180.00   0.0  0
 SLY  Var_01    C8   C7   O    C6    -1.51  30.0  2
 SLY  Var_02    C1   C6   O    C7    92.41  30.0  2
 SLY  Var_03    N    C    C1   C6    78.84  30.0  2
 SLY  Var_04    H5   N    C    C1   174.38  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
 SLY  plan-1  C4   0.020
 SLY  plan-1  C5   0.020
 SLY  plan-1  C6   0.020
 SLY  plan-1  O    0.020
 SLY  plan-1  C1   0.020
 SLY  plan-1  C2   0.020
 SLY  plan-1  C3   0.020
 SLY  plan-1  H1   0.020
 SLY  plan-1  H2   0.020
 SLY  plan-1  H12  0.020
 SLY  plan-1  H13  0.020
 SLY  plan-1  C    0.020
 SLY  plan-2  C7   0.020
 SLY  plan-2  C8   0.020
 SLY  plan-2  C10  0.020
 SLY  plan-2  O    0.020
 SLY  plan-2  C11  0.020
 SLY  plan-2  C12  0.020
 SLY  plan-2  C9   0.020
 SLY  plan-2  H3   0.020
 SLY  plan-2  H4   0.020
 SLY  plan-2  H10  0.020
 SLY  plan-2  H11  0.020
 SLY  plan-2  H14  0.020

