# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 06:34:55 2021
#   Inital geometry file: a 108 line input string
#   Ligand name: ~{N}4-[3-(4-methoxyphenyl)-[1,2,3]triazolo[4,5-d]pyrimidin-5-yl]cyclohexane-1,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1)n2nnc3cnc(N[C@H]4CC[C@H](N)CC4)nc23
#
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
 OYB  OYB  ~{N}4-[3-(4-methoxyphenyl)-[1,2,3]triazolo[4,5-d]pyrimidin-5-yl]cyclohexane-1,4-diamine  ligand  46  25  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_OYB
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
 OYB  C1   C  CR6   0   0.617  -35.4929  4.6407  -31.0051
 OYB  C3   C  CR16  0  -0.021  -34.6395  2.8679  -32.2010
 OYB  N6   N  N     0  -0.484  -35.1390  4.1959  -29.7998
 OYB  C9   C  CR6   0   0.315  -33.9533  2.5371  -27.4614
 OYB  C10  C  CR16  0  -0.272  -32.8408  2.1545  -26.7292
 OYB  C11  C  CR16  0  -0.340  -34.9513  3.4370  -25.4744
 OYB  C12  C  CR16  0  -0.275  -35.0148  3.1778  -26.8289
 OYB  C14  C  CR6   0   0.390  -33.8368  3.0493  -24.7267
 OYB  C15  C  CR16  0  -0.380  -32.7829  2.3979  -25.3645
 OYB  C19  C  CH3   0  -0.439  -32.7487  2.9978  -22.6201
 OYB  C20  C  CH2   0  -0.454  -36.8477  8.0193  -30.3790
 OYB  C21  C  CH2   0  -0.434  -37.3893  8.8577  -29.2263
 OYB  C22  C  CH1   0  -0.072  -38.6577  8.2615  -28.6261
 OYB  C24  C  CH2   0  -0.441  -37.8760  5.9695  -29.3568
 OYB  N25  N  NH2   0  -0.795  -39.1536  9.1257  -27.5643
 OYB  N2   N  N     0  -0.462  -35.2624  4.0167  -32.1980
 OYB  C4   C  CR56  0   0.007  -34.2232  2.3023  -30.9925
 OYB  C5   C  CR56  0   0.542  -34.5129  3.0347  -29.8474
 OYB  N7   N  NR5   0  -0.499  -34.0031  2.2805  -28.8476
 OYB  N8   N  N     0  -0.287  -33.5671  1.1660  -30.6317
 OYB  N13  N  N     0  -0.074  -33.4451  1.1623  -29.3666
 OYB  O16  O  O2    0  -0.467  -33.8663  3.3421  -23.4166
 OYB  N17  N  NH1   0  -0.663  -36.1272  5.8151  -31.0921
 OYB  C18  C  CH1   0  -0.044  -36.6055  6.5748  -29.9540
 OYB  C23  C  CH2   0  -0.448  -38.3963  6.8156  -28.2002
 OYB  H1   H  HCR6  0   0.294  -34.4657  2.3862  -33.1572
 OYB  H2   H  HCR6  0   0.280  -32.0076  1.6651  -27.2146
 OYB  H3   H  HCR6  0   0.273  -35.7758  3.9377  -24.9833
 OYB  H4   H  HCR6  0   0.283  -35.8908  3.4780  -27.3865
 OYB  H5   H  HCR6  0   0.288  -31.9028  2.0797  -24.8232
 OYB  H6   H  HCH3  0   0.262  -32.9750  3.3316  -21.6109
 OYB  H7   H  HCH3  0   0.231  -32.5762  1.9189  -22.6037
 OYB  H8   H  HCH3  0   0.231  -31.8376  3.4969  -22.9598
 OYB  H9   H  HCH2  0   0.246  -35.9200  8.4552  -30.7572
 OYB  H10  H  HCH2  0   0.222  -37.5666  8.0334  -31.2070
 OYB  H11  H  HCH2  0   0.213  -36.6260  8.9333  -28.4417
 OYB  H12  H  HCH2  0   0.236  -37.5861  9.8753  -29.5710
 OYB  H13  H  HCH1  0   0.211  -39.4247  8.2462  -29.4112
 OYB  H14  H  HCH2  0   0.216  -38.6378  5.9062  -30.1421
 OYB  H15  H  HCH2  0   0.244  -37.6784  4.9491  -29.0212
 OYB  H16  H  HNH2  0   0.341  -39.9966  8.7245  -27.1703
 OYB  H17  H  HNH2  0   0.332  -38.4822  9.1436  -26.8040
 OYB  H19  H  HNH1  0   0.394  -36.4403  6.0830  -32.0121
 OYB  H20  H  HCH1  0   0.240  -35.8213  6.5606  -29.1906
 OYB  H21  H  HCH2  0   0.231  -39.3128  6.3731  -27.8002
 OYB  H22  H  HCH2  0   0.209  -37.6647  6.8147  -27.3825

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
 OYB  C3   N2   aromatic  1.307  0.020  1.307
 OYB  C3   C4   aromatic  1.398  0.020  1.398
 OYB  N2   C1   aromatic  1.366  0.020  1.366
 OYB  N17  C1   single    1.338  0.020  1.338
 OYB  N17  C18  single    1.450  0.020  1.450
 OYB  C4   N8   aromatic  1.361  0.020  1.361
 OYB  C4   C5   aromatic  1.390  0.020  1.390
 OYB  C1   N6   aromatic  1.333  0.020  1.333
 OYB  N8   N13  aromatic  1.271  0.020  1.271
 OYB  C20  C18  single    1.525  0.020  1.525
 OYB  C20  C21  single    1.525  0.020  1.525
 OYB  C18  C24  single    1.529  0.020  1.529
 OYB  N6   C5   aromatic  1.320  0.020  1.320
 OYB  C5   N7   aromatic  1.352  0.020  1.352
 OYB  C24  C23  single    1.525  0.020  1.525
 OYB  N13  N7   aromatic  1.353  0.020  1.353
 OYB  C21  C22  single    1.525  0.020  1.525
 OYB  N7   C9   single    1.411  0.020  1.411
 OYB  C22  C23  single    1.530  0.020  1.530
 OYB  C22  N25  single    1.456  0.020  1.456
 OYB  C9   C10  aromatic  1.386  0.020  1.386
 OYB  C9   C12  aromatic  1.392  0.020  1.392
 OYB  C10  C15  aromatic  1.387  0.020  1.387
 OYB  C12  C11  aromatic  1.381  0.020  1.381
 OYB  C15  C14  aromatic  1.393  0.020  1.393
 OYB  C11  C14  aromatic  1.397  0.020  1.397
 OYB  C14  O16  single    1.343  0.020  1.343
 OYB  O16  C19  single    1.415  0.020  1.415
 OYB  C3   H1   single    0.930  0.020  1.080
 OYB  C10  H2   single    0.930  0.020  1.080
 OYB  C11  H3   single    0.930  0.020  1.080
 OYB  C12  H4   single    0.930  0.020  1.080
 OYB  C15  H5   single    0.930  0.020  1.080
 OYB  C19  H6   single    0.970  0.020  1.090
 OYB  C19  H7   single    0.970  0.020  1.090
 OYB  C19  H8   single    0.970  0.020  1.090
 OYB  C20  H9   single    0.970  0.020  1.090
 OYB  C20  H10  single    0.970  0.020  1.090
 OYB  C21  H11  single    0.970  0.020  1.090
 OYB  C21  H12  single    0.970  0.020  1.090
 OYB  C22  H13  single    0.970  0.020  1.090
 OYB  C24  H14  single    0.970  0.020  1.090
 OYB  C24  H15  single    0.970  0.020  1.090
 OYB  N25  H16  single    0.890  0.020  1.040
 OYB  N25  H17  single    0.890  0.020  1.040
 OYB  N17  H19  single    0.860  0.020  1.020
 OYB  C18  H20  single    0.970  0.020  1.090
 OYB  C23  H21  single    0.970  0.020  1.090
 OYB  C23  H22  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
 OYB  N17  C1   N2   115.11  3.000
 OYB  N17  C1   N6   118.55  3.000
 OYB  N2   C1   N6   126.34  3.000
 OYB  H1   C3   C4   122.33  3.000
 OYB  H1   C3   N2   117.95  3.000
 OYB  C4   C3   N2   119.72  3.000
 OYB  C5   N6   C1   112.77  3.000
 OYB  N7   C9   C12  120.22  3.000
 OYB  C12  C9   C10  119.95  3.000
 OYB  N7   C9   C10  119.83  3.000
 OYB  H2   C10  C15  119.26  3.000
 OYB  H2   C10  C9   120.42  3.000
 OYB  C15  C10  C9   120.32  3.000
 OYB  H3   C11  C14  119.55  3.000
 OYB  H3   C11  C12  119.80  3.000
 OYB  C14  C11  C12  120.65  3.000
 OYB  H4   C12  C11  119.42  3.000
 OYB  H4   C12  C9   120.76  3.000
 OYB  C11  C12  C9   119.81  3.000
 OYB  O16  C14  C15  124.41  3.000
 OYB  O16  C14  C11  116.37  3.000
 OYB  C15  C14  C11  119.22  3.000
 OYB  H5   C15  C14  121.61  3.000
 OYB  H5   C15  C10  118.35  3.000
 OYB  C14  C15  C10  120.04  3.000
 OYB  H8   C19  H7   108.90  3.000
 OYB  H8   C19  H6   108.78  3.000
 OYB  H7   C19  H6   108.80  3.000
 OYB  H8   C19  O16  111.86  3.000
 OYB  H7   C19  O16  111.93  3.000
 OYB  H6   C19  O16  106.47  3.000
 OYB  H10  C20  H9   106.86  3.000
 OYB  H10  C20  C18  109.06  3.000
 OYB  H9   C20  C18  109.85  3.000
 OYB  H10  C20  C21  109.32  3.000
 OYB  H9   C20  C21  110.12  3.000
 OYB  C18  C20  C21  111.51  3.000
 OYB  H12  C21  H11  106.67  3.000
 OYB  H12  C21  C22  109.80  3.000
 OYB  H11  C21  C22  108.91  3.000
 OYB  H12  C21  C20  109.74  3.000
 OYB  H11  C21  C20  109.35  3.000
 OYB  C22  C21  C20  112.21  3.000
 OYB  H13  C22  C23  107.78  3.000
 OYB  H13  C22  N25  106.97  3.000
 OYB  C23  C22  N25  114.59  3.000
 OYB  H13  C22  C21  107.77  3.000
 OYB  N25  C22  C21  109.77  3.000
 OYB  C23  C22  C21  109.70  3.000
 OYB  H15  C24  H14  106.98  3.000
 OYB  H15  C24  C23  110.31  3.000
 OYB  H14  C24  C23  109.78  3.000
 OYB  H15  C24  C18  109.85  3.000
 OYB  H14  C24  C18  108.70  3.000
 OYB  C23  C24  C18  111.12  3.000
 OYB  H17  N25  H16  105.44  3.000
 OYB  H17  N25  C22  109.36  3.000
 OYB  H16  N25  C22  109.38  3.000
 OYB  C3   N2   C1   118.95  3.000
 OYB  N8   C4   C5   108.79  3.000
 OYB  C5   C4   C3   115.91  3.000
 OYB  N8   C4   C3   135.30  3.000
 OYB  N7   C5   C4   103.69  3.000
 OYB  N7   C5   N6   130.00  3.000
 OYB  C4   C5   N6   126.31  3.000
 OYB  N13  N7   C5   109.44  3.000
 OYB  N13  N7   C9   120.84  3.000
 OYB  C5   N7   C9   129.68  3.000
 OYB  N13  N8   C4   108.22  3.000
 OYB  N8   N13  N7   109.86  3.000
 OYB  C19  O16  C14  118.61  3.000
 OYB  H19  N17  C18  118.35  3.000
 OYB  H19  N17  C1   116.10  3.000
 OYB  C18  N17  C1   124.44  3.000
 OYB  H20  C18  N17  107.72  3.000
 OYB  H20  C18  C24  108.53  3.000
 OYB  N17  C18  C24  111.93  3.000
 OYB  H20  C18  C20  108.69  3.000
 OYB  C24  C18  C20  110.61  3.000
 OYB  N17  C18  C20  109.27  3.000
 OYB  H22  C23  H21  106.61  3.000
 OYB  H22  C23  C24  109.72  3.000
 OYB  H21  C23  C24  109.82  3.000
 OYB  H22  C23  C22  108.79  3.000
 OYB  H21  C23  C22  109.94  3.000
 OYB  C24  C23  C22  111.81  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
 OYB  CONST_01  C4   C3   N2   C1     0.00   0.0  0
 OYB  CONST_02  C4   C5   N6   C1     0.00   0.0  0
 OYB  CONST_03  N7   C5   N6   C1   180.00   0.0  0
 OYB  CONST_04  N6   C1   N2   C3     0.00   0.0  0
 OYB  CONST_05  N13  N8   C4   C3   180.00   0.0  0
 OYB  CONST_06  N6   C5   C4   C3     0.00   0.0  0
 OYB  CONST_07  N7   C5   C4   C3   180.00   0.0  0
 OYB  CONST_08  N8   C4   C5   N6   180.00   0.0  0
 OYB  CONST_09  N13  N7   C5   N6   180.00   0.0  0
 OYB  CONST_10  C9   N7   C5   N6     0.00   0.0  0
 OYB  CONST_11  C4   C5   N7   C9   180.00   0.0  0
 OYB  CONST_12  N8   N13  N7   C9   180.00   0.0  0
 OYB  CONST_13  C14  C15  C10  C9     0.00   0.0  0
 OYB  CONST_14  C14  C11  C12  C9     0.00   0.0  0
 OYB  CONST_17  C11  C12  C9   C10    0.00   0.0  0
 OYB  CONST_18  C11  C14  C15  C10    0.00   0.0  0
 OYB  CONST_19  N7   C9   C12  C11  180.00   0.0  0
 OYB  CONST_22  C15  C10  C9   C12    0.00   0.0  0
 OYB  CONST_23  C15  C14  C11  C12    0.00   0.0  0
 OYB  CONST_24  N7   C9   C10  C15  180.00   0.0  0
 OYB  CONST_25  N8   C4   C3   N2   180.00   0.0  0
 OYB  CONST_26  C5   C4   C3   N2     0.00   0.0  0
 OYB  CONST_27  C5   N6   C1   N2     0.00   0.0  0
 OYB  CONST_28  N7   N13  N8   C4     0.00   0.0  0
 OYB  CONST_29  N13  N7   C5   C4     0.00   0.0  0
 OYB  CONST_30  N13  N8   C4   C5     0.00   0.0  0
 OYB  CONST_31  N8   N13  N7   C5     0.00   0.0  0
 OYB  CONST_32  N8   C4   C5   N7     0.00   0.0  0
 OYB  CONST_33  N17  C1   N2   C3   180.00   0.0  0
 OYB  CONST_34  O16  C14  C15  C10  180.00   0.0  0
 OYB  CONST_35  O16  C14  C11  C12  180.00   0.0  0
 OYB  CONST_36  N17  C1   N6   C5   180.00   0.0  0
 OYB  CONST_37  C18  N17  C1   N6     0.00   0.0  0
 OYB  CONST_38  C18  N17  C1   N2   180.00   0.0  0
 OYB  CONST_39  H1   C3   N2   C1   180.00   0.0  0
 OYB  CONST_40  H5   C15  C10  C9   180.00   0.0  0
 OYB  CONST_41  H3   C11  C12  C9   180.00   0.0  0
 OYB  CONST_42  H4   C12  C9   C10  180.00   0.0  0
 OYB  CONST_43  H2   C10  C9   C12  180.00   0.0  0
 OYB  CONST_44  H19  N17  C1   N6   180.00   0.0  0
 OYB  Var_01    C18  C20  C21  C22  -55.60  30.0  1
 OYB  Var_02    C18  C24  C23  C22   56.75  30.0  1
 OYB  Var_03    H6   C19  O16  C14  179.29  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 OYB  chir_01  C22  C21  C23  N25  negativ
 OYB  chir_02  C18  N17  C20  C24  negativ

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
 OYB  plan-1  C9   0.020
 OYB  plan-1  C10  0.020
 OYB  plan-1  C11  0.020
 OYB  plan-1  C12  0.020
 OYB  plan-1  C14  0.020
 OYB  plan-1  C15  0.020
 OYB  plan-1  N7   0.020
 OYB  plan-1  O16  0.020
 OYB  plan-1  H2   0.020
 OYB  plan-1  H3   0.020
 OYB  plan-1  H4   0.020
 OYB  plan-1  H5   0.020
 OYB  plan-2  C1   0.020
 OYB  plan-2  C3   0.020
 OYB  plan-2  N6   0.020
 OYB  plan-2  C9   0.020
 OYB  plan-2  N2   0.020
 OYB  plan-2  C4   0.020
 OYB  plan-2  C5   0.020
 OYB  plan-2  N7   0.020
 OYB  plan-2  N8   0.020
 OYB  plan-2  N13  0.020
 OYB  plan-2  N17  0.020
 OYB  plan-2  H1   0.020
 OYB  plan-3  C1   0.020
 OYB  plan-3  N17  0.020
 OYB  plan-3  C18  0.020
 OYB  plan-3  H19  0.020

