# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 07:29:35 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: ~{N}-oxidanyl-3-[1-(phenylsulfanylmethyl)-1,2,3-triazol-4-yl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ONC(=O)c1cccc(c1)c2cn(CSc3ccccc3)nn2
#
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
 GM5  GM5  ~{N}-oxidanyl-3-[1-(phenylsulfanylmethyl)-1,2,3-triazol-4-yl]benzamide  ligand  37  23  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GM5
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
 GM5  C6   C  CR16  0  -0.258   5.9224   0.0536  -1.4625
 GM5  C5   C  CR16  0  -0.242   7.2703  -0.2396  -1.3258
 GM5  C4   C  CR16  0  -0.263   7.8368  -0.3741  -0.0642
 GM5  C2   C  CR16  0  -0.252   5.6988   0.1181   0.9367
 GM5  C10  C  CR5   0   0.165  -0.8530   0.2411   0.4303
 GM5  C12  C  CR16  0  -0.291  -4.8449   1.6942   0.1953
 GM5  C13  C  CR6   0  -0.039  -4.5850   0.3342   0.0411
 GM5  C14  C  CR16  0  -0.315  -3.2797  -0.1351   0.1321
 GM5  C15  C  CR6   0   0.087  -2.2216   0.7424   0.3502
 GM5  C16  C  CR16  0  -0.327  -2.4936   2.1037   0.4938
 GM5  C17  C  CR16  0  -0.221  -3.7948   2.5716   0.4229
 GM5  C1   C  CR6   0  -0.119   5.1300   0.2351  -0.3292
 GM5  C3   C  CR16  0  -0.239   7.0451  -0.1991   1.0614
 GM5  N7   N  NR5   0  -0.275   1.2471  -0.0654   0.7185
 GM5  N8   N  N     0  -0.073   0.7382  -1.2060   0.2761
 GM5  N9   N  N     0  -0.314  -0.5200  -1.0330   0.1082
 GM5  C11  C  CR15  0  -0.067   0.2970   0.8792   0.8265
 GM5  N19  N  NH1   0  -0.383  -6.7544  -0.1816  -0.8135
 GM5  O20  O  OH1   0  -0.538  -7.7385  -1.0465  -1.1886
 GM5  O21  O  O     0  -0.458  -5.5790  -1.8207   0.2140
 GM5  S22  S  S2    0   0.070   3.4356   0.6523  -0.5941
 GM5  C23  C  CH2   0  -0.411   2.6578   0.0641   0.9484
 GM5  H1   H  HCR6  0   0.269   5.4870   0.1344  -2.4509
 GM5  H2   H  HCR6  0   0.264   7.8761  -0.3770  -2.2119
 GM5  H3   H  HCR6  0   0.261   8.8869  -0.6126   0.0396
 GM5  H4   H  HCR6  0   0.272   5.1111   0.2740   1.8316
 GM5  H5   H  HCR6  0   0.269  -5.8573   2.0760   0.1652
 GM5  H6   H  HCR6  0   0.262  -3.0871  -1.1946   0.0282
 GM5  H7   H  HCR6  0   0.262  -1.6868   2.8066   0.6587
 GM5  H8   H  HCR6  0   0.270  -3.9930   3.6274   0.5488
 GM5  H9   H  HCR6  0   0.264   7.4743  -0.2998   2.0498
 GM5  H10  H  HCR5  0   0.323   0.5063   1.8768   1.1739
 GM5  H11  H  HNH1  0   0.419  -6.6975   0.6487  -1.3866
 GM5  H12  H  HOH1  0   0.480  -8.4598  -0.9144  -0.5599
 GM5  H13  H  HCH2  0   0.318   2.8147   0.7658   1.7634
 GM5  H14  H  HCH2  0   0.327   3.0592  -0.9099   1.2208
 GM5  C18  C  C     0   0.501  -5.6692  -0.6712  -0.1756

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
 GM5  C17  C12  aromatic  1.387  0.020  1.387
 GM5  C17  C16  aromatic  1.385  0.020  1.385
 GM5  C12  C13  aromatic  1.393  0.020  1.393
 GM5  C16  C15  aromatic  1.396  0.020  1.396
 GM5  N19  O20  single    1.363  0.020  1.363
 GM5  N19  C18  single    1.351  0.020  1.351
 GM5  C13  C18  single    1.494  0.020  1.494
 GM5  C13  C14  aromatic  1.390  0.020  1.390
 GM5  C18  O21  double    1.217  0.020  1.217
 GM5  C15  C14  aromatic  1.392  0.020  1.392
 GM5  C15  C10  single    1.460  0.020  1.460
 GM5  C10  N9   aromatic  1.356  0.020  1.356
 GM5  C10  C11  aromatic  1.374  0.020  1.374
 GM5  N9   N8   aromatic  1.281  0.020  1.281
 GM5  C11  N7   aromatic  1.344  0.020  1.344
 GM5  N8   N7   aromatic  1.325  0.020  1.325
 GM5  N7   C23  single    1.435  0.020  1.435
 GM5  C23  S22  single    1.825  0.020  1.825
 GM5  S22  C1   single    1.765  0.020  1.765
 GM5  C6   C1   aromatic  1.395  0.020  1.395
 GM5  C6   C5   aromatic  1.386  0.020  1.386
 GM5  C1   C2   aromatic  1.393  0.020  1.393
 GM5  C5   C4   aromatic  1.389  0.020  1.389
 GM5  C2   C3   aromatic  1.389  0.020  1.389
 GM5  C4   C3   aromatic  1.387  0.020  1.387
 GM5  C6   H1   single    0.930  0.020  1.080
 GM5  C5   H2   single    0.930  0.020  1.080
 GM5  C4   H3   single    0.930  0.020  1.080
 GM5  C2   H4   single    0.930  0.020  1.080
 GM5  C12  H5   single    0.930  0.020  1.080
 GM5  C14  H6   single    0.930  0.020  1.080
 GM5  C16  H7   single    0.930  0.020  1.080
 GM5  C17  H8   single    0.930  0.020  1.080
 GM5  C3   H9   single    0.930  0.020  1.080
 GM5  C11  H10  single    0.930  0.020  1.080
 GM5  N19  H11  single    0.890  0.020  1.040
 GM5  O20  H12  single    0.850  0.020  0.980
 GM5  C23  H13  single    0.970  0.020  1.090
 GM5  C23  H14  single    0.970  0.020  1.090

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
 GM5  H1   C6   C1   120.23  3.000
 GM5  H1   C6   C5   119.78  3.000
 GM5  C1   C6   C5   119.99  3.000
 GM5  H2   C5   C4   120.19  3.000
 GM5  H2   C5   C6   119.37  3.000
 GM5  C4   C5   C6   120.43  3.000
 GM5  H3   C4   C3   120.26  3.000
 GM5  H3   C4   C5   120.28  3.000
 GM5  C3   C4   C5   119.46  3.000
 GM5  H4   C2   C3   119.02  3.000
 GM5  H4   C2   C1   121.19  3.000
 GM5  C3   C2   C1   119.79  3.000
 GM5  C11  C10  N9   107.43  3.000
 GM5  C11  C10  C15  129.88  3.000
 GM5  N9   C10  C15  122.68  3.000
 GM5  H5   C12  C17  119.31  3.000
 GM5  H5   C12  C13  121.05  3.000
 GM5  C17  C12  C13  119.63  3.000
 GM5  C18  C13  C14  117.62  3.000
 GM5  C14  C13  C12  119.84  3.000
 GM5  C18  C13  C12  122.51  3.000
 GM5  H6   C14  C15  119.81  3.000
 GM5  H6   C14  C13  119.44  3.000
 GM5  C15  C14  C13  120.75  3.000
 GM5  C16  C15  C14  118.88  3.000
 GM5  C14  C15  C10  120.32  3.000
 GM5  C16  C15  C10  120.80  3.000
 GM5  H7   C16  C17  119.26  3.000
 GM5  H7   C16  C15  120.24  3.000
 GM5  C17  C16  C15  120.50  3.000
 GM5  H8   C17  C16  119.74  3.000
 GM5  H8   C17  C12  119.85  3.000
 GM5  C16  C17  C12  120.40  3.000
 GM5  S22  C1   C2   123.25  3.000
 GM5  C2   C1   C6   119.71  3.000
 GM5  S22  C1   C6   117.01  3.000
 GM5  H9   C3   C2   119.20  3.000
 GM5  H9   C3   C4   120.19  3.000
 GM5  C2   C3   C4   120.61  3.000
 GM5  C23  N7   C11  128.21  3.000
 GM5  C23  N7   N8   120.57  3.000
 GM5  C11  N7   N8   111.12  3.000
 GM5  N9   N8   N7   107.74  3.000
 GM5  N8   N9   C10  109.69  3.000
 GM5  H10  C11  N7   122.65  3.000
 GM5  H10  C11  C10  133.33  3.000
 GM5  N7   C11  C10  104.01  3.000
 GM5  H11  N19  O20  113.96  3.000
 GM5  H11  N19  C18  121.36  3.000
 GM5  O20  N19  C18  118.69  3.000
 GM5  H12  O20  N19  105.86  3.000
 GM5  C23  S22  C1   101.90  3.000
 GM5  H14  C23  H13  109.69  3.000
 GM5  H14  C23  S22  110.06  3.000
 GM5  H13  C23  S22  111.36  3.000
 GM5  H14  C23  N7   108.78  3.000
 GM5  H13  C23  N7   108.68  3.000
 GM5  S22  C23  N7   108.22  3.000
 GM5  O21  C18  N19  123.58  3.000
 GM5  O21  C18  C13  122.36  3.000
 GM5  N19  C18  C13  114.04  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
 GM5  CONST_01  C3   C2   C1   C6      0.00   0.0  0
 GM5  CONST_02  C3   C4   C5   C6      0.00   0.0  0
 GM5  CONST_03  C2   C1   C6   C5      0.00   0.0  0
 GM5  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 GM5  CONST_05  C1   C6   C5   C4      0.00   0.0  0
 GM5  CONST_06  C1   C2   C3   C4      0.00   0.0  0
 GM5  CONST_07  C17  C16  C15  C10   180.00   0.0  0
 GM5  CONST_08  C13  C14  C15  C10   180.00   0.0  0
 GM5  CONST_09  N7   N8   N9   C10     0.00   0.0  0
 GM5  CONST_10  N8   N7   C11  C10     0.00   0.0  0
 GM5  CONST_11  C15  C16  C17  C12     0.00   0.0  0
 GM5  CONST_12  C15  C14  C13  C12     0.00   0.0  0
 GM5  CONST_13  C16  C17  C12  C13     0.00   0.0  0
 GM5  CONST_14  C16  C15  C14  C13     0.00   0.0  0
 GM5  CONST_15  C17  C12  C13  C14     0.00   0.0  0
 GM5  CONST_16  C17  C16  C15  C14     0.00   0.0  0
 GM5  CONST_17  N9   C10  C15  C14     0.00   0.0  0
 GM5  CONST_18  C11  C10  C15  C14   180.00   0.0  0
 GM5  CONST_19  N8   N9   C10  C15   180.00   0.0  0
 GM5  CONST_20  N7   C11  C10  C15   180.00   0.0  0
 GM5  CONST_21  N9   C10  C15  C16   180.00   0.0  0
 GM5  CONST_22  C11  C10  C15  C16     0.00   0.0  0
 GM5  CONST_23  N9   C10  C11  N7      0.00   0.0  0
 GM5  CONST_24  C11  C10  N9   N8      0.00   0.0  0
 GM5  CONST_25  C11  N7   N8   N9      0.00   0.0  0
 GM5  CONST_26  S22  C1   C6   C5    180.00   0.0  0
 GM5  CONST_27  C23  N7   C11  C10   180.00   0.0  0
 GM5  CONST_28  C18  C13  C14  C15   180.00   0.0  0
 GM5  CONST_29  C18  C13  C12  C17   180.00   0.0  0
 GM5  CONST_30  S22  C1   C2   C3    180.00   0.0  0
 GM5  CONST_31  C23  N7   N8   N9    180.00   0.0  0
 GM5  CONST_32  H4   C2   C1   C6    180.00   0.0  0
 GM5  CONST_33  H3   C4   C5   C6    180.00   0.0  0
 GM5  CONST_34  H9   C3   C4   C5    180.00   0.0  0
 GM5  CONST_35  H1   C6   C5   C4    180.00   0.0  0
 GM5  CONST_36  H7   C16  C15  C10     0.00   0.0  0
 GM5  CONST_37  H6   C14  C15  C10     0.00   0.0  0
 GM5  CONST_38  H8   C17  C12  C13   180.00   0.0  0
 GM5  CONST_39  H5   C12  C13  C14   180.00   0.0  0
 GM5  CONST_40  H10  C11  C10  C15     0.00   0.0  0
 GM5  CONST_41  H2   C5   C6   C1    180.00   0.0  0
 GM5  CONST_42  O20  N19  C18  C13   180.00   0.0  0
 GM5  CONST_44  O21  C18  N19  O20     0.00   0.0  0
 GM5  Var_01    N19  C18  C13  C12    29.46  30.0  2
 GM5  Var_02    N7   C23  S22  C1   -161.59  30.0  1
 GM5  Var_03    S22  C23  N7   N8     89.99  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
 GM5  plan-1  C10  0.020
 GM5  plan-1  C15  0.020
 GM5  plan-1  N7   0.020
 GM5  plan-1  N8   0.020
 GM5  plan-1  N9   0.020
 GM5  plan-1  C11  0.020
 GM5  plan-1  C23  0.020
 GM5  plan-1  H10  0.020
 GM5  plan-2  C6   0.020
 GM5  plan-2  C5   0.020
 GM5  plan-2  C4   0.020
 GM5  plan-2  C2   0.020
 GM5  plan-2  C1   0.020
 GM5  plan-2  C3   0.020
 GM5  plan-2  S22  0.020
 GM5  plan-2  H1   0.020
 GM5  plan-2  H2   0.020
 GM5  plan-2  H3   0.020
 GM5  plan-2  H4   0.020
 GM5  plan-2  H9   0.020
 GM5  plan-3  C10  0.020
 GM5  plan-3  C12  0.020
 GM5  plan-3  C13  0.020
 GM5  plan-3  C14  0.020
 GM5  plan-3  C15  0.020
 GM5  plan-3  C16  0.020
 GM5  plan-3  C17  0.020
 GM5  plan-3  H5   0.020
 GM5  plan-3  H6   0.020
 GM5  plan-3  H7   0.020
 GM5  plan-3  H8   0.020
 GM5  plan-3  C18  0.020
 GM5  plan-4  C13  0.020
 GM5  plan-4  N19  0.020
 GM5  plan-4  O20  0.020
 GM5  plan-4  O21  0.020
 GM5  plan-4  H11  0.020
 GM5  plan-4  C18  0.020

