# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 04:20:38 2021
#   Inital geometry file: a 85 line input string
#   Ligand name: methyl {4-[(pyridin-4-yl)methyl]phenyl}carbamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)Nc1ccc(Cc2ccncc2)cc1
#
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
 UVD  UVD  'methyl {4-[(pyridin-4-yl)methyl]phenyl}carbamate'  ligand  32  18  .  2022-03-23  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_UVD
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
 UVD  N1   N  N     0  -0.413  -23.9141  12.7475  25.8327
 UVD  C4   C  CR16  0  -0.284  -18.6512  13.9261  25.0221
 UVD  C5   C  CR6   0   0.136  -18.9303  13.3706  26.2682
 UVD  C6   C  CH2   0  -0.619  -19.6946  12.0765  26.3917
 UVD  C7   C  CR6   0   0.241  -21.1718  12.2911  26.1970
 UVD  C8   C  CR16  0  -0.388  -21.8046  11.9855  24.9984
 UVD  C10  C  CR16  0  -0.060  -23.3088  13.0388  26.9804
 UVD  C13  C  CR16  0  -0.298  -17.8267  15.2729  27.3029
 UVD  C    C  CH3   0  -0.416  -14.8402  19.6807  26.9418
 UVD  O    O  O2    0  -0.477  -15.6377  18.8146  26.1385
 UVD  C1   C  C     0   0.745  -16.1579  17.7450  26.7393
 UVD  C11  C  CR16  0  -0.364  -21.9584  12.8334  27.2090
 UVD  C12  C  CR16  0  -0.309  -18.5077  14.0657  27.3932
 UVD  C2   C  CR6   0   0.354  -17.5440  15.8137  26.0501
 UVD  C3   C  CR16  0  -0.327  -17.9700  15.1239  24.9114
 UVD  C9   C  CR16  0  -0.057  -23.1641  12.2310  24.8673
 UVD  O1   O  O     0  -0.494  -16.0040  17.4815  27.9105
 UVD  H1   H  HCR6  0   0.252  -18.9618  13.4161  24.1176
 UVD  H2   H  HCH2  0   0.275  -19.3297  11.3523  25.6608
 UVD  H3   H  HCH2  0   0.277  -19.5195  11.6481  27.3806
 UVD  H4   H  HCR6  0   0.264  -21.2551  11.5544  24.1712
 UVD  H5   H  HCR6  0   0.262  -23.9320  13.4558  27.7643
 UVD  H6   H  HCR6  0   0.276  -17.5260  15.7728  28.2090
 UVD  H7   H  HNH1  0   0.416  -16.8557  17.3507  24.8870
 UVD  H8   H  HCH3  0   0.252  -14.5456  20.4988  26.2910
 UVD  H9   H  HCH3  0   0.238  -15.4026  20.0782  27.7861
 UVD  H10  H  HCH3  0   0.238  -13.9473  19.1750  27.3090
 UVD  H11  H  HCR6  0   0.262  -21.5299  13.0941  28.1689
 UVD  H12  H  HCR6  0   0.252  -18.7108  13.6619  28.3782
 UVD  H13  H  HCR6  0   0.270  -17.7599  15.5283  23.9281
 UVD  H14  H  HCR6  0   0.262  -23.6672  11.9927  23.9363
 UVD  N    N  NH1   0  -0.766  -16.8723  17.0207  25.8406

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
 UVD  C3   C4   aromatic  1.382  0.020  1.382
 UVD  C3   C2   aromatic  1.398  0.020  1.398
 UVD  C9   C8   aromatic  1.388  0.020  1.388
 UVD  C9   N1   aromatic  1.327  0.020  1.327
 UVD  C4   C5   aromatic  1.393  0.020  1.393
 UVD  C8   C7   aromatic  1.389  0.020  1.389
 UVD  N    C2   single    1.397  0.020  1.397
 UVD  N    C1   single    1.358  0.020  1.358
 UVD  N1   C10  aromatic  1.330  0.020  1.330
 UVD  C2   C13  aromatic  1.394  0.020  1.394
 UVD  C5   C6   single    1.508  0.020  1.508
 UVD  C5   C12  aromatic  1.388  0.020  1.388
 UVD  C7   C6   single    1.505  0.020  1.505
 UVD  C7   C11  aromatic  1.392  0.020  1.392
 UVD  O    C1   single    1.332  0.020  1.332
 UVD  O    C    single    1.425  0.020  1.425
 UVD  C1   O1   double    1.210  0.020  1.210
 UVD  C10  C11  aromatic  1.385  0.020  1.385
 UVD  C13  C12  aromatic  1.389  0.020  1.389
 UVD  C4   H1   single    0.930  0.020  1.080
 UVD  C6   H2   single    0.970  0.020  1.090
 UVD  C6   H3   single    0.970  0.020  1.090
 UVD  C8   H4   single    0.930  0.020  1.080
 UVD  C10  H5   single    0.930  0.020  1.080
 UVD  C13  H6   single    0.930  0.020  1.080
 UVD  N    H7   single    0.860  0.020  1.020
 UVD  C    H8   single    0.970  0.020  1.090
 UVD  C    H9   single    0.970  0.020  1.090
 UVD  C    H10  single    0.970  0.020  1.090
 UVD  C11  H11  single    0.930  0.020  1.080
 UVD  C12  H12  single    0.930  0.020  1.080
 UVD  C3   H13  single    0.930  0.020  1.080
 UVD  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
 UVD  C9   N1   C10  117.12  3.000
 UVD  H1   C4   C3   118.82  3.000
 UVD  H1   C4   C5   120.11  3.000
 UVD  C3   C4   C5   121.07  3.000
 UVD  C12  C5   C6   121.17  3.000
 UVD  C12  C5   C4   117.67  3.000
 UVD  C6   C5   C4   121.14  3.000
 UVD  H3   C6   H2   107.01  3.000
 UVD  H3   C6   C7   109.30  3.000
 UVD  H2   C6   C7   109.63  3.000
 UVD  H3   C6   C5   109.25  3.000
 UVD  H2   C6   C5   110.18  3.000
 UVD  C7   C6   C5   111.37  3.000
 UVD  C11  C7   C8   117.10  3.000
 UVD  C11  C7   C6   121.07  3.000
 UVD  C8   C7   C6   121.82  3.000
 UVD  H4   C8   C9   119.70  3.000
 UVD  H4   C8   C7   121.03  3.000
 UVD  C9   C8   C7   119.26  3.000
 UVD  H5   C10  C11  119.86  3.000
 UVD  H5   C10  N1   116.51  3.000
 UVD  C11  C10  N1   123.63  3.000
 UVD  H6   C13  C2   121.29  3.000
 UVD  H6   C13  C12  119.03  3.000
 UVD  C2   C13  C12  119.68  3.000
 UVD  H10  C    H9   109.33  3.000
 UVD  H10  C    H8   109.22  3.000
 UVD  H9   C    H8   109.24  3.000
 UVD  H10  C    O    111.49  3.000
 UVD  H9   C    O    111.69  3.000
 UVD  H8   C    O    105.77  3.000
 UVD  C1   O    C    116.88  3.000
 UVD  O1   C1   O    124.16  3.000
 UVD  O1   C1   N    126.26  3.000
 UVD  O    C1   N    109.59  3.000
 UVD  H11  C11  C10  119.76  3.000
 UVD  H11  C11  C7   120.97  3.000
 UVD  C10  C11  C7   119.27  3.000
 UVD  H12  C12  C13  118.34  3.000
 UVD  H12  C12  C5   119.53  3.000
 UVD  C13  C12  C5   122.12  3.000
 UVD  C3   C2   N    116.79  3.000
 UVD  N    C2   C13  124.58  3.000
 UVD  C3   C2   C13  118.63  3.000
 UVD  H13  C3   C2   119.73  3.000
 UVD  H13  C3   C4   119.44  3.000
 UVD  C2   C3   C4   120.83  3.000
 UVD  H14  C9   C8   119.77  3.000
 UVD  H14  C9   N1   116.60  3.000
 UVD  C8   C9   N1   123.63  3.000
 UVD  H7   N    C2   115.60  3.000
 UVD  H7   N    C1   116.26  3.000
 UVD  C2   N    C1   127.93  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
 UVD  CONST_01  C7   C8   C9   N1      0.00   0.0  0
 UVD  CONST_02  C7   C11  C10  N1      0.00   0.0  0
 UVD  CONST_03  C13  C2   C3   C4      0.00   0.0  0
 UVD  CONST_04  C13  C12  C5   C4      0.00   0.0  0
 UVD  CONST_05  C2   C3   C4   C5      0.00   0.0  0
 UVD  CONST_06  C2   C13  C12  C5      0.00   0.0  0
 UVD  CONST_07  C10  N1   C9   C8      0.00   0.0  0
 UVD  CONST_08  C10  C11  C7   C8      0.00   0.0  0
 UVD  CONST_09  C9   C8   C7   C11     0.00   0.0  0
 UVD  CONST_10  C9   N1   C10  C11     0.00   0.0  0
 UVD  CONST_11  C3   C4   C5   C12     0.00   0.0  0
 UVD  CONST_12  C3   C2   C13  C12     0.00   0.0  0
 UVD  CONST_13  N    C2   C3   C4    180.00   0.0  0
 UVD  CONST_14  C3   C4   C5   C6    180.00   0.0  0
 UVD  CONST_15  C13  C12  C5   C6    180.00   0.0  0
 UVD  CONST_16  C9   C8   C7   C6    180.00   0.0  0
 UVD  CONST_17  C10  C11  C7   C6    180.00   0.0  0
 UVD  CONST_18  C12  C13  C2   N     180.00   0.0  0
 UVD  CONST_19  H4   C8   C9   N1    180.00   0.0  0
 UVD  CONST_20  H11  C11  C10  N1    180.00   0.0  0
 UVD  CONST_21  H12  C12  C5   C4    180.00   0.0  0
 UVD  CONST_22  H13  C3   C4   C5    180.00   0.0  0
 UVD  CONST_23  H6   C13  C12  C5    180.00   0.0  0
 UVD  CONST_24  H14  C9   C8   C7    180.00   0.0  0
 UVD  CONST_25  H5   C10  C11  C7    180.00   0.0  0
 UVD  CONST_26  H1   C4   C5   C12   180.00   0.0  0
 UVD  CONST_27  C1   N    C2   C13     0.00   0.0  0
 UVD  CONST_28  C3   C2   N    C1    180.00   0.0  0
 UVD  CONST_29  H7   N    C2   C13   180.00   0.0  0
 UVD  CONST_30  C2   N    C1   O     180.00   0.0  0
 UVD  CONST_31  O1   C1   N    C2      0.00   0.0  0
 UVD  Var_01    C7   C6   C5   C4    -78.10  30.0  2
 UVD  Var_02    C8   C7   C6   C5    101.43  30.0  2
 UVD  Var_03    H8   C    O    C1   -177.88  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
 UVD  plan-1  C4   0.020
 UVD  plan-1  C5   0.020
 UVD  plan-1  C6   0.020
 UVD  plan-1  C13  0.020
 UVD  plan-1  C12  0.020
 UVD  plan-1  C2   0.020
 UVD  plan-1  C3   0.020
 UVD  plan-1  H1   0.020
 UVD  plan-1  H6   0.020
 UVD  plan-1  H12  0.020
 UVD  plan-1  H13  0.020
 UVD  plan-1  N    0.020
 UVD  plan-2  N1   0.020
 UVD  plan-2  C6   0.020
 UVD  plan-2  C7   0.020
 UVD  plan-2  C8   0.020
 UVD  plan-2  C10  0.020
 UVD  plan-2  C11  0.020
 UVD  plan-2  C9   0.020
 UVD  plan-2  H4   0.020
 UVD  plan-2  H5   0.020
 UVD  plan-2  H11  0.020
 UVD  plan-2  H14  0.020
 UVD  plan-3  C1   0.020
 UVD  plan-3  C2   0.020
 UVD  plan-3  H7   0.020
 UVD  plan-3  N    0.020
 UVD  plan-4  O    0.020
 UVD  plan-4  C1   0.020
 UVD  plan-4  O1   0.020
 UVD  plan-4  N    0.020

