# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 07:19:27 2021
#   Inital geometry file: a 99 line input string
#   Ligand name: N-(4-methoxypyridin-2-yl)-2-(naphthalen-2-yl)acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccnc(NC(=O)Cc2ccc3ccccc3c2)c1
#
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
 UGS  UGS  N-(4-methoxypyridin-2-yl)-2-(naphthalen-2-yl)acetamide  ligand  38  22  .  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_UGS
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
 UGS  N1   N  NH1   0  -0.716  10.9867   3.2050  21.9086
 UGS  C4   C  CR6   0   0.493  10.6573   1.8543  21.9768
 UGS  C5   C  C     0   0.565  10.7376   4.2087  22.7919
 UGS  C6   C  CH2   0  -0.699  11.3305   5.5396  22.3613
 UGS  C7   C  CR6   0   0.160  10.7444   6.6953  23.1115
 UGS  C8   C  CR16  0  -0.283   9.4212   7.1125  22.8293
 UGS  C10  C  CR66  0   0.098   9.5836   8.8631  24.4893
 UGS  C13  C  CR16  0  -0.258  11.0828  10.2053  26.4365
 UGS  C15  C  CR66  0   0.137  10.9103   8.4540  24.7774
 UGS  C17  C  CR16  0  -0.479   9.9457   1.2771  23.0189
 UGS  O1   O  O     0  -0.447  10.1233   4.0675  23.8298
 UGS  N    N  N     0  -0.466  11.0983   1.1679  20.9230
 UGS  C3   C  CR16  0  -0.061  10.8365  -0.1282  20.8816
 UGS  C2   C  CR16  0  -0.454  10.1389  -0.8211  21.8558
 UGS  C1   C  CR6   0   0.491   9.6845  -0.0917  22.9536
 UGS  O    O  O2    0  -0.458   9.0018  -0.6092  23.9758
 UGS  C    C  CH3   0  -0.441   8.6995  -1.9949  23.9622
 UGS  C16  C  CR16  0  -0.389  11.4623   7.3604  24.0686
 UGS  C9   C  CR16  0  -0.302   8.8576   8.1624  23.4962
 UGS  C14  C  CR16  0  -0.315  11.6431   9.1515  25.7663
 UGS  C12  C  CR16  0  -0.259   9.7629  10.6119  26.1492
 UGS  C11  C  CR16  0  -0.310   9.0307   9.9553  25.1969
 UGS  H1   H  HNH1  0   0.412  11.5037   3.4425  21.0737
 UGS  H2   H  HCH2  0   0.311  12.4110   5.4867  22.5247
 UGS  H3   H  HCH2  0   0.294  11.1923   5.6677  21.2839
 UGS  H4   H  HCR6  0   0.253   8.8513   6.5924  22.0684
 UGS  H5   H  HCR6  0   0.258  11.6528  10.7314  27.1911
 UGS  H6   H  HCR6  0   0.293   9.5940   1.8529  23.8595
 UGS  H7   H  HCR6  0   0.269  11.2055  -0.6622  20.0131
 UGS  H8   H  HCR6  0   0.289   9.9690  -1.8815  21.7407
 UGS  H9   H  HCH3  0   0.265   8.1480  -2.1963  24.8765
 UGS  H10  H  HCH3  0   0.236   8.0767  -2.2639  23.1062
 UGS  H11  H  HCH3  0   0.236   9.6048  -2.6058  23.9519
 UGS  H12  H  HCR6  0   0.251  12.4779   7.0538  24.2943
 UGS  H13  H  HCR6  0   0.255   7.8442   8.4709  23.2692
 UGS  H14  H  HCR6  0   0.255  12.6572   8.8400  25.9864
 UGS  H15  H  HCR6  0   0.258   9.3311  11.4466  26.6859
 UGS  H16  H  HCR6  0   0.255   8.0166  10.2659  24.9753

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
 UGS  C3   N    aromatic  1.323  0.020  1.323
 UGS  C3   C2   aromatic  1.384  0.020  1.384
 UGS  N    C4   aromatic  1.333  0.020  1.333
 UGS  C2   C1   aromatic  1.394  0.020  1.394
 UGS  C4   N1   single    1.392  0.020  1.392
 UGS  C4   C17  aromatic  1.388  0.020  1.388
 UGS  N1   C5   single    1.360  0.020  1.360
 UGS  C8   C9   aromatic  1.366  0.020  1.366
 UGS  C8   C7   aromatic  1.416  0.020  1.416
 UGS  C6   C5   single    1.519  0.020  1.519
 UGS  C6   C7   single    1.497  0.020  1.497
 UGS  C1   C17  aromatic  1.395  0.020  1.395
 UGS  C1   O    single    1.334  0.020  1.334
 UGS  C9   C10  aromatic  1.416  0.020  1.416
 UGS  C5   O1   double    1.214  0.020  1.214
 UGS  C7   C16  aromatic  1.369  0.020  1.369
 UGS  C    O    single    1.418  0.020  1.418
 UGS  C10  C11  aromatic  1.414  0.020  1.414
 UGS  C10  C15  aromatic  1.418  0.020  1.418
 UGS  C16  C15  aromatic  1.415  0.020  1.415
 UGS  C11  C12  aromatic  1.369  0.020  1.369
 UGS  C15  C14  aromatic  1.415  0.020  1.415
 UGS  C12  C13  aromatic  1.411  0.020  1.411
 UGS  C14  C13  aromatic  1.369  0.020  1.369
 UGS  N1   H1   single    0.860  0.020  1.020
 UGS  C6   H2   single    0.970  0.020  1.090
 UGS  C6   H3   single    0.970  0.020  1.090
 UGS  C8   H4   single    0.930  0.020  1.080
 UGS  C13  H5   single    0.930  0.020  1.080
 UGS  C17  H6   single    0.930  0.020  1.080
 UGS  C3   H7   single    0.930  0.020  1.080
 UGS  C2   H8   single    0.930  0.020  1.080
 UGS  C    H9   single    0.970  0.020  1.090
 UGS  C    H10  single    0.970  0.020  1.090
 UGS  C    H11  single    0.970  0.020  1.090
 UGS  C16  H12  single    0.930  0.020  1.080
 UGS  C9   H13  single    0.930  0.020  1.080
 UGS  C14  H14  single    0.930  0.020  1.080
 UGS  C12  H15  single    0.930  0.020  1.080
 UGS  C11  H16  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
 UGS  H1   N1   C5   117.19  3.000
 UGS  H1   N1   C4   112.94  3.000
 UGS  C5   N1   C4   129.86  3.000
 UGS  N    C4   C17  123.32  3.000
 UGS  C17  C4   N1   124.18  3.000
 UGS  N    C4   N1   112.50  3.000
 UGS  O1   C5   C6   122.79  3.000
 UGS  O1   C5   N1   124.19  3.000
 UGS  C6   C5   N1   113.01  3.000
 UGS  H3   C6   H2   106.11  3.000
 UGS  H3   C6   C7   110.71  3.000
 UGS  H2   C6   C7   110.43  3.000
 UGS  H3   C6   C5   109.42  3.000
 UGS  H2   C6   C5   107.51  3.000
 UGS  C7   C6   C5   112.42  3.000
 UGS  C16  C7   C8   119.10  3.000
 UGS  C16  C7   C6   121.34  3.000
 UGS  C8   C7   C6   119.56  3.000
 UGS  H4   C8   C9   119.66  3.000
 UGS  H4   C8   C7   119.35  3.000
 UGS  C9   C8   C7   120.99  3.000
 UGS  C11  C10  C9   122.20  3.000
 UGS  C11  C10  C15  119.15  3.000
 UGS  C9   C10  C15  118.65  3.000
 UGS  H5   C13  C12  119.65  3.000
 UGS  H5   C13  C14  120.01  3.000
 UGS  C12  C13  C14  120.34  3.000
 UGS  C14  C15  C16  121.94  3.000
 UGS  C14  C15  C10  118.98  3.000
 UGS  C16  C15  C10  119.09  3.000
 UGS  H6   C17  C1   119.97  3.000
 UGS  H6   C17  C4   122.06  3.000
 UGS  C1   C17  C4   117.97  3.000
 UGS  C3   N    C4   117.63  3.000
 UGS  H7   C3   C2   119.26  3.000
 UGS  H7   C3   N    116.11  3.000
 UGS  C2   C3   N    124.62  3.000
 UGS  H8   C2   C1   123.11  3.000
 UGS  H8   C2   C3   119.72  3.000
 UGS  C1   C2   C3   117.17  3.000
 UGS  O    C1   C2   124.56  3.000
 UGS  O    C1   C17  116.14  3.000
 UGS  C2   C1   C17  119.29  3.000
 UGS  C    O    C1   118.74  3.000
 UGS  H11  C    H10  109.11  3.000
 UGS  H11  C    H9   108.96  3.000
 UGS  H10  C    H9   108.93  3.000
 UGS  H11  C    O    111.71  3.000
 UGS  H10  C    O    111.70  3.000
 UGS  H9   C    O    106.33  3.000
 UGS  H12  C16  C15  118.65  3.000
 UGS  H12  C16  C7   119.95  3.000
 UGS  C15  C16  C7   121.40  3.000
 UGS  H13  C9   C10  119.05  3.000
 UGS  H13  C9   C8   120.18  3.000
 UGS  C10  C9   C8   120.76  3.000
 UGS  H14  C14  C15  119.02  3.000
 UGS  H14  C14  C13  120.33  3.000
 UGS  C15  C14  C13  120.65  3.000
 UGS  H15  C12  C11  120.10  3.000
 UGS  H15  C12  C13  119.64  3.000
 UGS  C11  C12  C13  120.26  3.000
 UGS  H16  C11  C12  120.36  3.000
 UGS  H16  C11  C10  119.01  3.000
 UGS  C12  C11  C10  120.63  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
 UGS  CONST_01  C2   C3   N    C4     0.00   0.0  0
 UGS  CONST_02  C2   C1   C17  C4     0.00   0.0  0
 UGS  CONST_03  C10  C9   C8   C7     0.00   0.0  0
 UGS  CONST_04  C10  C15  C16  C7     0.00   0.0  0
 UGS  CONST_05  C14  C15  C16  C7   180.00   0.0  0
 UGS  CONST_06  C11  C10  C9   C8   180.00   0.0  0
 UGS  CONST_07  C15  C10  C9   C8     0.00   0.0  0
 UGS  CONST_08  C15  C16  C7   C8     0.00   0.0  0
 UGS  CONST_09  C13  C12  C11  C10    0.00   0.0  0
 UGS  CONST_10  C13  C14  C15  C10    0.00   0.0  0
 UGS  CONST_11  C16  C15  C14  C13  180.00   0.0  0
 UGS  CONST_12  C12  C11  C10  C15    0.00   0.0  0
 UGS  CONST_13  C12  C13  C14  C15    0.00   0.0  0
 UGS  CONST_14  C3   N    C4   C17    0.00   0.0  0
 UGS  CONST_15  C3   C2   C1   C17    0.00   0.0  0
 UGS  CONST_16  C1   C2   C3   N      0.00   0.0  0
 UGS  CONST_17  C1   C17  C4   N      0.00   0.0  0
 UGS  CONST_18  C9   C8   C7   C16    0.00   0.0  0
 UGS  CONST_19  C9   C10  C15  C16    0.00   0.0  0
 UGS  CONST_20  C11  C10  C15  C16  180.00   0.0  0
 UGS  CONST_21  C12  C11  C10  C9   180.00   0.0  0
 UGS  CONST_22  C14  C15  C10  C9   180.00   0.0  0
 UGS  CONST_23  C11  C10  C15  C14    0.00   0.0  0
 UGS  CONST_24  C11  C12  C13  C14    0.00   0.0  0
 UGS  CONST_25  C3   N    C4   N1   180.00   0.0  0
 UGS  CONST_26  C1   C17  C4   N1   180.00   0.0  0
 UGS  CONST_27  O    C1   C17  C4   180.00   0.0  0
 UGS  CONST_28  C9   C8   C7   C6   180.00   0.0  0
 UGS  CONST_29  C15  C16  C7   C6   180.00   0.0  0
 UGS  CONST_30  O    C1   C2   C3   180.00   0.0  0
 UGS  CONST_31  H7   C3   N    C4   180.00   0.0  0
 UGS  CONST_32  H13  C9   C8   C7   180.00   0.0  0
 UGS  CONST_33  H12  C16  C7   C8   180.00   0.0  0
 UGS  CONST_34  H4   C8   C9   C10  180.00   0.0  0
 UGS  CONST_35  H15  C12  C11  C10  180.00   0.0  0
 UGS  CONST_36  H14  C14  C15  C10  180.00   0.0  0
 UGS  CONST_37  H16  C11  C12  C13  180.00   0.0  0
 UGS  CONST_38  H5   C13  C14  C15  180.00   0.0  0
 UGS  CONST_39  H8   C2   C1   C17  180.00   0.0  0
 UGS  CONST_40  H6   C17  C4   N    180.00   0.0  0
 UGS  CONST_41  N    C4   N1   C5   180.00   0.0  0
 UGS  CONST_42  C17  C4   N1   C5     0.00   0.0  0
 UGS  CONST_43  H1   N1   C4   C17  180.00   0.0  0
 UGS  CONST_44  C6   C5   N1   C4   180.00   0.0  0
 UGS  CONST_45  O1   C5   N1   C4     0.00   0.0  0
 UGS  Var_01    C8   C7   C6   C5   -72.76  30.0  2
 UGS  Var_02    C7   C6   C5   N1   163.94  30.0  1
 UGS  Var_03    H9   C    O    C1   179.96  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
 UGS  plan-1  N1   0.020
 UGS  plan-1  C4   0.020
 UGS  plan-1  C17  0.020
 UGS  plan-1  N    0.020
 UGS  plan-1  C3   0.020
 UGS  plan-1  C2   0.020
 UGS  plan-1  C1   0.020
 UGS  plan-1  O    0.020
 UGS  plan-1  H6   0.020
 UGS  plan-1  H7   0.020
 UGS  plan-1  H8   0.020
 UGS  plan-2  C6   0.020
 UGS  plan-2  C7   0.020
 UGS  plan-2  C8   0.020
 UGS  plan-2  C10  0.020
 UGS  plan-2  C13  0.020
 UGS  plan-2  C15  0.020
 UGS  plan-2  C16  0.020
 UGS  plan-2  C9   0.020
 UGS  plan-2  C14  0.020
 UGS  plan-2  C12  0.020
 UGS  plan-2  C11  0.020
 UGS  plan-2  H4   0.020
 UGS  plan-2  H5   0.020
 UGS  plan-2  H12  0.020
 UGS  plan-2  H13  0.020
 UGS  plan-2  H14  0.020
 UGS  plan-2  H15  0.020
 UGS  plan-2  H16  0.020
 UGS  plan-3  N1   0.020
 UGS  plan-3  C4   0.020
 UGS  plan-3  C5   0.020
 UGS  plan-3  C6   0.020
 UGS  plan-3  O1   0.020
 UGS  plan-3  H1   0.020

