# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 19:54:45 2022
#   Inital geometry file: a 99 line input string
#   Ligand name: ~{N}-[[3-[(4-methylphenyl)methoxy]phenyl]methyl]-1~{H}-1,2,3,4-tetrazol-5-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(COc2cccc(CNc3[nH]nnn3)c2)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
 Y9A  Y9A  ~{N}-[[3-[(4-methylphenyl)methoxy]phenyl]methyl]-1~{H}-1,2,3,4-tetrazol-5-amine  ligand  39  22  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_Y9A
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
 Y9A  C1   C  CH3   0  -0.719  -15.5349  25.5853  -10.3679
 Y9A  C2   C  CR6   0   0.087  -15.9790  24.1940  -10.0231
 Y9A  C3   C  CR16  0  -0.284  -15.0614  23.2247   -9.6218
 Y9A  C4   C  CR16  0  -0.264  -15.4641  21.9306   -9.3273
 Y9A  C5   C  CR6   0   0.021  -16.8030  21.5667   -9.4305
 Y9A  C6   C  CR16  0  -0.277  -17.7229  22.5285   -9.8321
 Y9A  C12  C  CR16  0  -0.335  -16.0918  17.9325  -13.4228
 Y9A  C13  C  CR6   0   0.089  -16.9079  19.0121  -13.1211
 Y9A  C14  C  CR16  0  -0.393  -17.0231  19.4561  -11.8044
 Y9A  C15  C  CH2   0  -0.332  -17.6301  19.7386  -14.2259
 Y9A  C16  C  CR5   0   0.746  -19.6845  21.0616  -14.4380
 Y9A  C10  C  CR16  0  -0.359  -15.4880  17.7373  -11.0977
 Y9A  C11  C  CR16  0  -0.224  -15.3818  17.3037  -12.4054
 Y9A  C7   C  CR16  0  -0.284  -17.3177  23.8242  -10.1197
 Y9A  C8   C  CH2   0  -0.258  -17.2642  20.1792   -9.0692
 Y9A  C9   C  CR6   0   0.410  -16.3185  18.8175  -10.7898
 Y9A  N1   N  NH1   0  -0.665  -18.9763  20.0938  -13.8323
 Y9A  N2   N  NR15  0  -0.515  -19.2149  21.9979  -15.2712
 Y9A  N3   N  N     0  -0.135  -21.2502  22.3673  -15.0176
 Y9A  N4   N  N     0  -0.407  -20.9764  21.2899  -14.2798
 Y9A  N5   N  N     0  -0.098  -20.2243  22.8080  -15.6147
 Y9A  O1   O  O2    0  -0.478  -16.3756  19.1604   -9.4856
 Y9A  H1   H  HCH3  0   0.247  -15.3237  25.6747  -11.4356
 Y9A  H2   H  HCH3  0   0.243  -16.3020  26.3213  -10.1287
 Y9A  H3   H  HCH3  0   0.243  -14.6251  25.8588   -9.8343
 Y9A  H4   H  HCR6  0   0.245  -14.0136  23.4873   -9.5324
 Y9A  H5   H  HCR6  0   0.249  -14.7244  21.2037   -9.0144
 Y9A  H6   H  HCR6  0   0.252  -18.7704  22.2634   -9.9248
 Y9A  H7   H  HCR6  0   0.250  -16.0088  17.5809  -14.4437
 Y9A  H8   H  HCR6  0   0.281  -17.6668  20.3002  -11.5977
 Y9A  H9   H  HCH2  0   0.264  -17.6203  19.1320  -15.1371
 Y9A  H10  H  HCH2  0   0.267  -17.0788  20.6552  -14.4509
 Y9A  H11  H  HCR6  0   0.262  -14.9417  17.2408  -10.3054
 Y9A  H12  H  HCR6  0   0.256  -14.7451  16.4591  -12.6350
 Y9A  H13  H  HCR6  0   0.246  -18.0546  24.5563  -10.4289
 Y9A  H14  H  HCH2  0   0.244  -18.2750  20.0016   -9.4529
 Y9A  H15  H  HCH2  0   0.272  -17.3145  20.0742   -7.9838
 Y9A  H16  H  HNH1  0   0.408  -19.5350  19.3642  -13.4154
 Y9A  H17  H  HNR5  0   0.444  -18.2863  22.1544  -15.6348

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
 Y9A  N5   N2   aromatic  1.339  0.020  1.339
 Y9A  N5   N3   aromatic  1.266  0.020  1.266
 Y9A  N2   C16  aromatic  1.338  0.020  1.338
 Y9A  N3   N4   aromatic  1.334  0.020  1.334
 Y9A  C16  N4   aromatic  1.321  0.020  1.321
 Y9A  C16  N1   single    1.344  0.020  1.344
 Y9A  C15  N1   single    1.447  0.020  1.447
 Y9A  C15  C13  single    1.507  0.020  1.507
 Y9A  C12  C13  aromatic  1.387  0.020  1.387
 Y9A  C12  C11  aromatic  1.391  0.020  1.391
 Y9A  C13  C14  aromatic  1.394  0.020  1.394
 Y9A  C11  C10  aromatic  1.382  0.020  1.382
 Y9A  C14  C9   aromatic  1.391  0.020  1.391
 Y9A  C10  C9   aromatic  1.397  0.020  1.397
 Y9A  C9   O1   single    1.350  0.020  1.350
 Y9A  C8   O1   single    1.415  0.020  1.415
 Y9A  C8   C5   single    1.506  0.020  1.506
 Y9A  C5   C4   aromatic  1.391  0.020  1.391
 Y9A  C5   C6   aromatic  1.390  0.020  1.390
 Y9A  C4   C3   aromatic  1.387  0.020  1.387
 Y9A  C6   C7   aromatic  1.388  0.020  1.388
 Y9A  C3   C2   aromatic  1.394  0.020  1.394
 Y9A  C7   C2   aromatic  1.392  0.020  1.392
 Y9A  C2   C1   single    1.501  0.020  1.501
 Y9A  C1   H1   single    0.970  0.020  1.090
 Y9A  C1   H2   single    0.970  0.020  1.090
 Y9A  C1   H3   single    0.970  0.020  1.090
 Y9A  C3   H4   single    0.930  0.020  1.080
 Y9A  C4   H5   single    0.930  0.020  1.080
 Y9A  C6   H6   single    0.930  0.020  1.080
 Y9A  C12  H7   single    0.930  0.020  1.080
 Y9A  C14  H8   single    0.930  0.020  1.080
 Y9A  C15  H9   single    0.970  0.020  1.090
 Y9A  C15  H10  single    0.970  0.020  1.090
 Y9A  C10  H11  single    0.930  0.020  1.080
 Y9A  C11  H12  single    0.930  0.020  1.080
 Y9A  C7   H13  single    0.930  0.020  1.080
 Y9A  C8   H14  single    0.970  0.020  1.090
 Y9A  C8   H15  single    0.970  0.020  1.090
 Y9A  N1   H16  single    0.890  0.020  1.040
 Y9A  N2   H17  single    0.860  0.020  1.020

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
 Y9A  H3   C1   H2   108.11  3.000
 Y9A  H3   C1   H1   107.26  3.000
 Y9A  H2   C1   H1   107.19  3.000
 Y9A  H3   C1   C2   111.55  3.000
 Y9A  H2   C1   C2   111.56  3.000
 Y9A  H1   C1   C2   110.96  3.000
 Y9A  C7   C2   C3   117.92  3.000
 Y9A  C7   C2   C1   121.00  3.000
 Y9A  C3   C2   C1   121.08  3.000
 Y9A  H4   C3   C4   119.29  3.000
 Y9A  H4   C3   C2   119.44  3.000
 Y9A  C4   C3   C2   121.26  3.000
 Y9A  H5   C4   C5   120.20  3.000
 Y9A  H5   C4   C3   119.29  3.000
 Y9A  C5   C4   C3   120.51  3.000
 Y9A  C8   C5   C6   120.27  3.000
 Y9A  C6   C5   C4   118.51  3.000
 Y9A  C8   C5   C4   121.19  3.000
 Y9A  H6   C6   C7   119.51  3.000
 Y9A  H6   C6   C5   119.65  3.000
 Y9A  C7   C6   C5   120.84  3.000
 Y9A  H7   C12  C11  120.24  3.000
 Y9A  H7   C12  C13  120.20  3.000
 Y9A  C11  C12  C13  119.56  3.000
 Y9A  C15  C13  C14  119.96  3.000
 Y9A  C14  C13  C12  120.13  3.000
 Y9A  C15  C13  C12  119.87  3.000
 Y9A  H8   C14  C9   121.37  3.000
 Y9A  H8   C14  C13  118.57  3.000
 Y9A  C9   C14  C13  120.06  3.000
 Y9A  H10  C15  H9   106.79  3.000
 Y9A  H10  C15  N1   108.63  3.000
 Y9A  H9   C15  N1   111.77  3.000
 Y9A  H10  C15  C13  108.27  3.000
 Y9A  H9   C15  C13  109.81  3.000
 Y9A  N1   C15  C13  111.40  3.000
 Y9A  N4   C16  N2   107.26  3.000
 Y9A  N4   C16  N1   125.86  3.000
 Y9A  N2   C16  N1   126.84  3.000
 Y9A  H11  C10  C9   119.56  3.000
 Y9A  H11  C10  C11  120.64  3.000
 Y9A  C9   C10  C11  119.80  3.000
 Y9A  H12  C11  C10  119.40  3.000
 Y9A  H12  C11  C12  119.86  3.000
 Y9A  C10  C11  C12  120.74  3.000
 Y9A  H13  C7   C6   119.43  3.000
 Y9A  H13  C7   C2   119.61  3.000
 Y9A  C6   C7   C2   120.96  3.000
 Y9A  H15  C8   H14  106.86  3.000
 Y9A  H15  C8   O1   104.61  3.000
 Y9A  H14  C8   O1   111.08  3.000
 Y9A  H15  C8   C5   109.95  3.000
 Y9A  H14  C8   C5   110.35  3.000
 Y9A  O1   C8   C5   113.61  3.000
 Y9A  O1   C9   C10  115.76  3.000
 Y9A  O1   C9   C14  124.54  3.000
 Y9A  C10  C9   C14  119.70  3.000
 Y9A  H16  N1   C16  114.53  3.000
 Y9A  H16  N1   C15  116.75  3.000
 Y9A  C16  N1   C15  123.00  3.000
 Y9A  H17  N2   N5   120.48  3.000
 Y9A  H17  N2   C16  130.96  3.000
 Y9A  N5   N2   C16  108.56  3.000
 Y9A  N5   N3   N4   112.06  3.000
 Y9A  N3   N4   C16  105.90  3.000
 Y9A  N3   N5   N2   106.21  3.000
 Y9A  C9   O1   C8   119.60  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
 Y9A  CONST_01  C5   C4   C3   C2     0.00   0.0  0
 Y9A  CONST_02  C5   C6   C7   C2     0.00   0.0  0
 Y9A  CONST_03  C6   C5   C4   C3     0.00   0.0  0
 Y9A  CONST_04  C6   C7   C2   C3     0.00   0.0  0
 Y9A  CONST_05  C7   C6   C5   C4     0.00   0.0  0
 Y9A  CONST_06  C7   C2   C3   C4     0.00   0.0  0
 Y9A  CONST_07  C9   C14  C13  C12    0.00   0.0  0
 Y9A  CONST_08  C9   C10  C11  C12    0.00   0.0  0
 Y9A  CONST_09  C10  C11  C12  C13    0.00   0.0  0
 Y9A  CONST_10  C10  C9   C14  C13    0.00   0.0  0
 Y9A  CONST_11  C11  C12  C13  C14    0.00   0.0  0
 Y9A  CONST_12  C11  C10  C9   C14    0.00   0.0  0
 Y9A  CONST_13  N3   N5   N2   C16    0.00   0.0  0
 Y9A  CONST_14  N5   N3   N4   C16    0.00   0.0  0
 Y9A  CONST_15  N4   N3   N5   N2     0.00   0.0  0
 Y9A  CONST_16  N3   N4   C16  N2     0.00   0.0  0
 Y9A  CONST_17  N5   N2   C16  N4     0.00   0.0  0
 Y9A  CONST_18  C4   C3   C2   C1   180.00   0.0  0
 Y9A  CONST_19  C6   C7   C2   C1   180.00   0.0  0
 Y9A  CONST_20  C8   C5   C4   C3   180.00   0.0  0
 Y9A  CONST_21  O1   C9   C14  C13  180.00   0.0  0
 Y9A  CONST_22  C11  C12  C13  C15  180.00   0.0  0
 Y9A  CONST_23  C9   C14  C13  C15  180.00   0.0  0
 Y9A  CONST_24  O1   C9   C10  C11  180.00   0.0  0
 Y9A  CONST_25  C8   C5   C6   C7   180.00   0.0  0
 Y9A  CONST_26  N5   N2   C16  N1   180.00   0.0  0
 Y9A  CONST_27  N3   N4   C16  N1   180.00   0.0  0
 Y9A  CONST_28  H5   C4   C3   C2   180.00   0.0  0
 Y9A  CONST_29  H6   C6   C7   C2   180.00   0.0  0
 Y9A  CONST_30  H13  C7   C2   C3   180.00   0.0  0
 Y9A  CONST_31  H4   C3   C4   C5   180.00   0.0  0
 Y9A  CONST_32  H8   C14  C13  C12  180.00   0.0  0
 Y9A  CONST_33  H11  C10  C11  C12  180.00   0.0  0
 Y9A  CONST_34  H12  C11  C12  C13  180.00   0.0  0
 Y9A  CONST_35  H7   C12  C13  C14  180.00   0.0  0
 Y9A  CONST_36  H17  N2   N5   N3   180.00   0.0  0
 Y9A  CONST_37  N2   C16  N1   C15    0.00   0.0  0
 Y9A  CONST_38  N4   C16  N1   C15  180.00   0.0  0
 Y9A  CONST_39  H16  N1   C16  N2   180.00   0.0  0
 Y9A  Var_01    O1   C8   C5   C4   -39.85  30.0  2
 Y9A  Var_02    N1   C15  C13  C12  139.76  30.0  2
 Y9A  Var_03    C16  N1   C15  C13  159.60  30.0  3
 Y9A  Var_04    H1   C1   C2   C3    91.89  30.0  2

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
 Y9A  plan-1  C16  0.020
 Y9A  plan-1  N1   0.020
 Y9A  plan-1  N2   0.020
 Y9A  plan-1  N3   0.020
 Y9A  plan-1  N4   0.020
 Y9A  plan-1  N5   0.020
 Y9A  plan-1  H17  0.020
 Y9A  plan-2  C1   0.020
 Y9A  plan-2  C2   0.020
 Y9A  plan-2  C3   0.020
 Y9A  plan-2  C4   0.020
 Y9A  plan-2  C5   0.020
 Y9A  plan-2  C6   0.020
 Y9A  plan-2  C7   0.020
 Y9A  plan-2  C8   0.020
 Y9A  plan-2  H4   0.020
 Y9A  plan-2  H5   0.020
 Y9A  plan-2  H6   0.020
 Y9A  plan-2  H13  0.020
 Y9A  plan-3  C12  0.020
 Y9A  plan-3  C13  0.020
 Y9A  plan-3  C14  0.020
 Y9A  plan-3  C15  0.020
 Y9A  plan-3  C10  0.020
 Y9A  plan-3  C11  0.020
 Y9A  plan-3  C9   0.020
 Y9A  plan-3  O1   0.020
 Y9A  plan-3  H7   0.020
 Y9A  plan-3  H8   0.020
 Y9A  plan-3  H11  0.020
 Y9A  plan-3  H12  0.020
 Y9A  plan-4  C15  0.020
 Y9A  plan-4  C16  0.020
 Y9A  plan-4  N1   0.020
 Y9A  plan-4  H16  0.020

