# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 06:44:33 2021
#   Inital geometry file: a 142 line input string
#   Ligand name: 2-[[(1~{S},2~{S})-2-[methyl-[(6-methylpyridin-2-yl)methyl]amino]cyclohexyl]-[(6-methylpyridin-2-yl)methyl]amino]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(Cc1cccc(C)n1)[C@H]2CCCC[C@@H]2N(CC(O)=O)Cc3cccc(C)n3
#
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
 QTT  QTT  '2-[[(1~{S},2~{S})-2-[methyl-[(6-methylpyridin-2-yl)methyl]amino]cyclohexyl]-[(6-methylpyridin-2-yl)methyl]amino]ethanoic acid'  ligand  61  29  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QTT
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
 QTT  N1   N  NT    0  -0.390  34.6332  20.9949  19.3328
 QTT  C1   C  CH3   0  -0.545  35.5505  19.9602  18.9197
 QTT  O1   O  OH1   0  -0.607  38.1454  20.0967  23.9352
 QTT  O2   O  O     0  -0.446  37.6887  19.5307  21.8283
 QTT  C2   C  CR16  0  -0.340  33.3539  25.7078  19.6686
 QTT  C3   C  CR16  0  -0.357  38.1771  24.8885  22.8623
 QTT  C4   C  CR16  0  -0.154  32.2724  24.8780  19.4296
 QTT  C5   C  CR16  0  -0.144  36.8986  25.4058  23.0218
 QTT  C6   C  CR6   0   0.232  34.6370  25.2381  19.3922
 QTT  C7   C  CR6   0   0.234  38.3180  23.5409  22.5560
 QTT  C8   C  CR16  0  -0.341  32.5013  23.6035  18.9326
 QTT  C9   C  CR16  0  -0.345  35.8118  24.5685  22.8617
 QTT  C10  C  CH2   0  -0.428  31.4603  19.2655  20.6343
 QTT  C11  C  CH2   0  -0.428  31.9309  18.9027  22.0362
 QTT  C12  C  CH2   0  -0.442  32.6465  19.4794  19.7002
 QTT  C13  C  CH2   0  -0.443  32.9271  19.9288  22.5642
 QTT  C15  C  CH2   0  -0.360  34.1428  21.8090  18.2383
 QTT  N2   N  N     0  -0.432  34.8479  24.0096  18.9307
 QTT  N3   N  N     0  -0.432  37.2620  22.7422  22.3955
 QTT  C17  C  C     0   0.580  37.3307  19.9828  22.8853
 QTT  C18  C  CR6   0   0.241  33.8131  23.2020  18.7110
 QTT  C19  C  CR6   0   0.244  36.0410  23.2330  22.5336
 QTT  C20  C  CH1   0  -0.086  33.5901  20.5659  20.2451
 QTT  C21  C  CH1   0  -0.073  34.1247  20.1019  21.6118
 QTT  N4   N  NT    0  -0.390  35.1910  20.9401  22.1340
 QTT  H2   H  HCH3  0   0.256  36.0097  19.5014  19.7930
 QTT  H3   H  HCH3  0   0.185  35.1034  19.1670  18.3025
 QTT  H4   H  HCH3  0   0.224  36.3567  20.4069  18.3350
 QTT  H5   H  HOH1  0   0.470  39.0276  19.7776  23.6961
 QTT  H6   H  HCR6  0   0.258  33.2094  26.7087  20.0533
 QTT  H7   H  HCR6  0   0.256  39.0503  25.5173  22.9773
 QTT  H8   H  HCR6  0   0.267  31.2644  25.2187  19.6276
 QTT  H9   H  HCR6  0   0.263  36.7553  26.4516  23.2615
 QTT  H10  H  HCR6  0   0.260  31.6802  22.9277  18.7297
 QTT  H11  H  HCR6  0   0.252  34.8001  24.9369  22.9754
 QTT  H12  H  HCH2  0   0.211  30.8660  20.1853  20.6733
 QTT  H13  H  HCH2  0   0.228  30.8020  18.4886  20.2381
 QTT  H14  H  HCH2  0   0.228  31.0813  18.8178  22.7179
 QTT  H15  H  HCH2  0   0.212  32.4106  17.9181  22.0108
 QTT  H16  H  HCH2  0   0.231  32.2843  19.7571  18.7067
 QTT  H17  H  HCH2  0   0.214  33.1927  18.5376  19.5811
 QTT  H18  H  HCH2  0   0.231  33.2792  19.6233  23.5538
 QTT  H19  H  HCH2  0   0.215  32.4253  20.8932  22.6998
 QTT  H20  H  HCH2  0   0.254  35.9028  20.9936  24.1258
 QTT  H21  H  HCH2  0   0.272  35.4326  19.4188  23.5646
 QTT  H22  H  HCH2  0   0.209  33.2729  21.3776  17.7184
 QTT  H23  H  HCH2  0   0.245  34.9364  21.8876  17.4923
 QTT  H24  H  HCH2  0   0.280  34.3570  22.6907  21.4194
 QTT  H25  H  HCH2  0   0.214  34.1478  22.4973  23.1480
 QTT  H26  H  HCH1  0   0.223  32.9590  21.4450  20.4289
 QTT  H27  H  HCH1  0   0.225  34.5679  19.1075  21.4713
 QTT  H29  H  HCH3  0   0.245  39.6622  22.1351  21.6544
 QTT  H30  H  HCH3  0   0.242  40.4327  23.6479  22.1635
 QTT  H31  H  HCH3  0   0.247  39.9719  22.4419  23.3566
 QTT  H32  H  HCH3  0   0.251  36.6274  25.5742  20.1091
 QTT  H33  H  HCH3  0   0.250  36.2477  26.4110  18.6088
 QTT  H34  H  HCH3  0   0.238  35.6035  27.0128  20.1350
 QTT  C02  C  CH3   0  -0.716  35.8423  26.1091  19.5767
 QTT  C14  C  CH2   0  -0.432  35.9073  20.3539  23.2389
 QTT  C16  C  CH2   0  -0.333  34.8556  22.3259  22.3188
 QTT  C01  C  CH3   0  -0.720  39.6714  22.9115  22.4176

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
 QTT  C15  C18  single    1.508  0.020  1.508
 QTT  C15  N1   single    1.450  0.020  1.450
 QTT  C8   C18  aromatic  1.390  0.020  1.390
 QTT  C8   C4   aromatic  1.387  0.020  1.387
 QTT  C18  N2   aromatic  1.331  0.020  1.331
 QTT  C4   C2   aromatic  1.384  0.020  1.384
 QTT  C1   N1   single    1.443  0.020  1.443
 QTT  N2   C6   aromatic  1.329  0.020  1.329
 QTT  C2   C6   aromatic  1.394  0.020  1.394
 QTT  C6   C02  single    1.498  0.020  1.498
 QTT  N1   C20  single    1.451  0.020  1.451
 QTT  C12  C20  single    1.539  0.020  1.539
 QTT  C12  C10  single    1.525  0.020  1.525
 QTT  C20  C21  single    1.539  0.020  1.539
 QTT  C10  C11  single    1.523  0.020  1.523
 QTT  C01  C7   single    1.499  0.020  1.499
 QTT  O2   C17  double    1.204  0.020  1.204
 QTT  C21  N4   single    1.453  0.020  1.453
 QTT  C21  C13  single    1.540  0.020  1.540
 QTT  C7   N3   aromatic  1.334  0.020  1.334
 QTT  C7   C3   aromatic  1.389  0.020  1.389
 QTT  N3   C19  aromatic  1.323  0.020  1.323
 QTT  C11  C13  single    1.524  0.020  1.524
 QTT  N4   C16  single    1.438  0.020  1.438
 QTT  N4   C14  single    1.441  0.020  1.441
 QTT  C16  C19  single    1.508  0.020  1.508
 QTT  C3   C5   aromatic  1.388  0.020  1.388
 QTT  C19  C9   aromatic  1.394  0.020  1.394
 QTT  C17  C14  single    1.513  0.020  1.513
 QTT  C17  O1   single    1.334  0.020  1.334
 QTT  C5   C9   aromatic  1.381  0.020  1.381
 QTT  C1   H2   single    0.970  0.020  1.090
 QTT  C1   H3   single    0.970  0.020  1.090
 QTT  C1   H4   single    0.970  0.020  1.090
 QTT  O1   H5   single    0.850  0.020  0.980
 QTT  C2   H6   single    0.930  0.020  1.080
 QTT  C3   H7   single    0.930  0.020  1.080
 QTT  C4   H8   single    0.930  0.020  1.080
 QTT  C5   H9   single    0.930  0.020  1.080
 QTT  C8   H10  single    0.930  0.020  1.080
 QTT  C9   H11  single    0.930  0.020  1.080
 QTT  C10  H12  single    0.970  0.020  1.090
 QTT  C10  H13  single    0.970  0.020  1.090
 QTT  C11  H14  single    0.970  0.020  1.090
 QTT  C11  H15  single    0.970  0.020  1.090
 QTT  C12  H16  single    0.970  0.020  1.090
 QTT  C12  H17  single    0.970  0.020  1.090
 QTT  C13  H18  single    0.970  0.020  1.090
 QTT  C13  H19  single    0.970  0.020  1.090
 QTT  C14  H20  single    0.970  0.020  1.090
 QTT  C14  H21  single    0.970  0.020  1.090
 QTT  C15  H22  single    0.970  0.020  1.090
 QTT  C15  H23  single    0.970  0.020  1.090
 QTT  C16  H24  single    0.970  0.020  1.090
 QTT  C16  H25  single    0.970  0.020  1.090
 QTT  C20  H26  single    0.970  0.020  1.090
 QTT  C21  H27  single    0.970  0.020  1.090
 QTT  C01  H29  single    0.970  0.020  1.090
 QTT  C01  H30  single    0.970  0.020  1.090
 QTT  C01  H31  single    0.970  0.020  1.090
 QTT  C02  H32  single    0.970  0.020  1.090
 QTT  C02  H33  single    0.970  0.020  1.090
 QTT  C02  H34  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
 QTT  C20  N1   C15  113.43  3.000
 QTT  C20  N1   C1   115.15  3.000
 QTT  C15  N1   C1   113.68  3.000
 QTT  H4   C1   H3   107.14  3.000
 QTT  H4   C1   H2   106.90  3.000
 QTT  H3   C1   H2   108.53  3.000
 QTT  H4   C1   N1   109.23  3.000
 QTT  H3   C1   N1   114.79  3.000
 QTT  H2   C1   N1   109.93  3.000
 QTT  H5   O1   C17  109.51  3.000
 QTT  H6   C2   C6   120.33  3.000
 QTT  H6   C2   C4   120.78  3.000
 QTT  C6   C2   C4   118.88  3.000
 QTT  H7   C3   C7   120.35  3.000
 QTT  H7   C3   C5   120.95  3.000
 QTT  C7   C3   C5   118.69  3.000
 QTT  H8   C4   C8   120.57  3.000
 QTT  H8   C4   C2   120.49  3.000
 QTT  C8   C4   C2   118.94  3.000
 QTT  H9   C5   C9   120.48  3.000
 QTT  H9   C5   C3   120.48  3.000
 QTT  C9   C5   C3   119.04  3.000
 QTT  C02  C6   N2   116.90  3.000
 QTT  C02  C6   C2   121.34  3.000
 QTT  N2   C6   C2   121.75  3.000
 QTT  C01  C7   N3   116.90  3.000
 QTT  N3   C7   C3   121.82  3.000
 QTT  C01  C7   C3   121.28  3.000
 QTT  H10  C8   C18  120.38  3.000
 QTT  H10  C8   C4   121.03  3.000
 QTT  C18  C8   C4   118.59  3.000
 QTT  H11  C9   C19  120.28  3.000
 QTT  H11  C9   C5   121.12  3.000
 QTT  C19  C9   C5   118.59  3.000
 QTT  H13  C10  H12  106.44  3.000
 QTT  H13  C10  C12  110.26  3.000
 QTT  H12  C10  C12  109.03  3.000
 QTT  H13  C10  C11  110.52  3.000
 QTT  H12  C10  C11  109.56  3.000
 QTT  C12  C10  C11  110.91  3.000
 QTT  H15  C11  H14  106.57  3.000
 QTT  H15  C11  C13  109.07  3.000
 QTT  H14  C11  C13  110.15  3.000
 QTT  H15  C11  C10  109.16  3.000
 QTT  H14  C11  C10  110.65  3.000
 QTT  C13  C11  C10  111.13  3.000
 QTT  H17  C12  H16  106.55  3.000
 QTT  H17  C12  C20  109.87  3.000
 QTT  H16  C12  C20  110.22  3.000
 QTT  H17  C12  C10  109.51  3.000
 QTT  H16  C12  C10  109.54  3.000
 QTT  C20  C12  C10  111.05  3.000
 QTT  H19  C13  H18  106.33  3.000
 QTT  H19  C13  C21  109.50  3.000
 QTT  H18  C13  C21  109.91  3.000
 QTT  H19  C13  C11  109.64  3.000
 QTT  H18  C13  C11  109.62  3.000
 QTT  C21  C13  C11  111.70  3.000
 QTT  H23  C15  H22  106.25  3.000
 QTT  H23  C15  C18  107.86  3.000
 QTT  H22  C15  C18  109.71  3.000
 QTT  H23  C15  N1   108.08  3.000
 QTT  H22  C15  N1   113.80  3.000
 QTT  C18  C15  N1   110.87  3.000
 QTT  C18  N2   C6   119.66  3.000
 QTT  C19  N3   C7   119.73  3.000
 QTT  C14  C17  O2   125.24  3.000
 QTT  C14  C17  O1   111.70  3.000
 QTT  O2   C17  O1   122.79  3.000
 QTT  N2   C18  C15  116.26  3.000
 QTT  N2   C18  C8   122.16  3.000
 QTT  C15  C18  C8   121.56  3.000
 QTT  N3   C19  C16  119.17  3.000
 QTT  C16  C19  C9   118.72  3.000
 QTT  N3   C19  C9   122.12  3.000
 QTT  H26  C20  C21  107.00  3.000
 QTT  H26  C20  C12  105.80  3.000
 QTT  C21  C20  C12  108.33  3.000
 QTT  H26  C20  N1   106.37  3.000
 QTT  C21  C20  N1   113.44  3.000
 QTT  C12  C20  N1   115.28  3.000
 QTT  H27  C21  N4   105.80  3.000
 QTT  H27  C21  C20  107.44  3.000
 QTT  N4   C21  C20  113.58  3.000
 QTT  H27  C21  C13  106.94  3.000
 QTT  N4   C21  C13  114.41  3.000
 QTT  C20  C21  C13  108.24  3.000
 QTT  C21  N4   C16  115.52  3.000
 QTT  C16  N4   C14  114.17  3.000
 QTT  C21  N4   C14  113.92  3.000
 QTT  H34  C02  H33  107.85  3.000
 QTT  H34  C02  H32  108.37  3.000
 QTT  H33  C02  H32  107.54  3.000
 QTT  H34  C02  C6   111.67  3.000
 QTT  H33  C02  C6   110.50  3.000
 QTT  H32  C02  C6   110.77  3.000
 QTT  H21  C14  H20  104.82  3.000
 QTT  H21  C14  N4   111.03  3.000
 QTT  H20  C14  N4   112.44  3.000
 QTT  H21  C14  C17  105.50  3.000
 QTT  H20  C14  C17  109.69  3.000
 QTT  N4   C14  C17  112.84  3.000
 QTT  H25  C16  H24  105.92  3.000
 QTT  H25  C16  N4   113.32  3.000
 QTT  H24  C16  N4   108.84  3.000
 QTT  H25  C16  C19  107.68  3.000
 QTT  H24  C16  C19  106.00  3.000
 QTT  N4   C16  C19  114.50  3.000
 QTT  H31  C01  H30  107.39  3.000
 QTT  H31  C01  H29  107.36  3.000
 QTT  H30  C01  H29  108.94  3.000
 QTT  H31  C01  C7   110.46  3.000
 QTT  H30  C01  C7   111.64  3.000
 QTT  H29  C01  C7   110.89  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
 QTT  CONST_01  C18  C8   C4   C2      0.00   0.0  0
 QTT  CONST_02  C18  N2   C6   C2      0.00   0.0  0
 QTT  CONST_03  C19  N3   C7   C3      0.00   0.0  0
 QTT  CONST_04  C19  C9   C5   C3      0.00   0.0  0
 QTT  CONST_05  N2   C18  C8   C4      0.00   0.0  0
 QTT  CONST_06  N2   C6   C2   C4      0.00   0.0  0
 QTT  CONST_07  N3   C7   C3   C5      0.00   0.0  0
 QTT  CONST_08  N3   C19  C9   C5      0.00   0.0  0
 QTT  CONST_09  C8   C18  N2   C6      0.00   0.0  0
 QTT  CONST_10  C8   C4   C2   C6      0.00   0.0  0
 QTT  CONST_11  C9   C19  N3   C7      0.00   0.0  0
 QTT  CONST_12  C9   C5   C3   C7      0.00   0.0  0
 QTT  CONST_13  C15  C18  C8   C4    180.00   0.0  0
 QTT  CONST_14  C02  C6   C2   C4    180.00   0.0  0
 QTT  CONST_15  C01  C7   C3   C5    180.00   0.0  0
 QTT  CONST_16  C16  C19  C9   C5    180.00   0.0  0
 QTT  CONST_17  C15  C18  N2   C6    180.00   0.0  0
 QTT  CONST_18  C16  C19  N3   C7    180.00   0.0  0
 QTT  CONST_19  C02  C6   N2   C18   180.00   0.0  0
 QTT  CONST_20  C01  C7   N3   C19   180.00   0.0  0
 QTT  CONST_21  H10  C8   C4   C2    180.00   0.0  0
 QTT  CONST_22  H11  C9   C5   C3    180.00   0.0  0
 QTT  CONST_23  H8   C4   C2   C6    180.00   0.0  0
 QTT  CONST_24  H9   C5   C3   C7    180.00   0.0  0
 QTT  CONST_25  H6   C2   C4   C8    180.00   0.0  0
 QTT  CONST_26  H7   C3   C5   C9    180.00   0.0  0
 QTT  CONST_27  H5   O1   C17  O2      0.00   0.0  0
 QTT  Var_01    C21  C13  C11  C10   -55.64  30.0  1
 QTT  Var_02    C20  C12  C10  C11   -56.95  30.0  1
 QTT  Var_03    C13  C11  C10  C12    53.42  30.0  1
 QTT  Var_04    C8   C18  C15  N1   -102.68  30.0  2
 QTT  Var_05    N4   C16  C19  C9   -173.34  30.0  2
 QTT  Var_06    C20  N1   C15  C18    74.93  30.0  3
 QTT  Var_07    C21  N4   C16  C19  -165.82  30.0  3
 QTT  Var_08    H32  C02  C6   C2    133.30  30.0  2
 QTT  Var_09    H29  C01  C7   C3   -145.80  30.0  2
 QTT  Var_10    H2   C1   N1   C20   -56.41  30.0  3
 QTT  Var_11    N4   C14  C17  O1    148.32  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
 QTT  chir_01  C20  N1  C12  C21  negativ
 QTT  chir_02  C21  N4  C13  C20  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
 QTT  plan-1  C3   0.020
 QTT  plan-1  C5   0.020
 QTT  plan-1  C7   0.020
 QTT  plan-1  C9   0.020
 QTT  plan-1  N3   0.020
 QTT  plan-1  C19  0.020
 QTT  plan-1  H7   0.020
 QTT  plan-1  H9   0.020
 QTT  plan-1  H11  0.020
 QTT  plan-1  C16  0.020
 QTT  plan-1  C01  0.020
 QTT  plan-2  C2   0.020
 QTT  plan-2  C4   0.020
 QTT  plan-2  C6   0.020
 QTT  plan-2  C8   0.020
 QTT  plan-2  C15  0.020
 QTT  plan-2  N2   0.020
 QTT  plan-2  C18  0.020
 QTT  plan-2  H6   0.020
 QTT  plan-2  H8   0.020
 QTT  plan-2  H10  0.020
 QTT  plan-2  C02  0.020
 QTT  plan-3  O1   0.020
 QTT  plan-3  O2   0.020
 QTT  plan-3  C17  0.020
 QTT  plan-3  H5   0.020
 QTT  plan-3  C14  0.020

