# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 03:56:25 2022
#   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  60  29  .  2022-03-23  2022-03-23
;
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  -0.407  34.9730  20.9929  19.4995
 QTT  C1   C  CH3    0  -0.566  35.8388  19.8713  19.2066
 QTT  O1   O  OC    -1  -0.613  36.6440  18.4140  24.5384
 QTT  O2   O  O      0  -0.585  36.9139  18.6325  22.3386
 QTT  C2   C  CR16   0  -0.341  33.2321  25.6156  19.2197
 QTT  C3   C  CR16   0  -0.342  38.2994  24.9314  22.8860
 QTT  C4   C  CR16   0  -0.146  32.3461  24.7263  18.6361
 QTT  C5   C  CR16   0  -0.147  37.2741  25.0742  23.8058
 QTT  C6   C  CR6    0   0.225  34.5379  25.1973  19.4694
 QTT  C7   C  CR6    0   0.217  38.1974  23.9319  21.9216
 QTT  C8   C  CR16   0  -0.338  32.7847  23.4485  18.3234
 QTT  C9   C  CR16   0  -0.348  36.1844  24.2224  23.7322
 QTT  C10  C  CH2    0  -0.425  31.5772  19.5175  20.5548
 QTT  C11  C  CH2    0  -0.424  31.9080  19.1464  21.9932
 QTT  C12  C  CH2    0  -0.443  32.8469  19.6512  19.7224
 QTT  C13  C  CH2    0  -0.446  32.9086  20.1279  22.5910
 QTT  C15  C  CH2    0  -0.335  34.6428  21.7377  18.2997
 QTT  N2   N  N      0  -0.432  34.9518  23.9735  19.1563
 QTT  N3   N  N      0  -0.426  37.1477  23.1170  21.8581
 QTT  C17  C  C      0   0.389  36.5044  19.0118  23.4526
 QTT  C18  C  CR6    0   0.217  34.1021  23.1101  18.6063
 QTT  C19  C  CR6    0   0.217  36.1567  23.2548  22.7330
 QTT  C20  C  CH1    0  -0.073  33.8196  20.6756  20.3324
 QTT  C21  C  CH1    0  -0.066  34.1978  20.2046  21.7534
 QTT  N4   N  NT     0  -0.409  35.2739  20.9783  22.3611
 QTT  H2   H  HCH3   0   0.262  36.1638  19.3963  20.1308
 QTT  H3   H  HCH3   0   0.186  35.3860  19.1047  18.5610
 QTT  H4   H  HCH3   0   0.223  36.7334  20.2313  18.6936
 QTT  H6   H  HCR6   0   0.259  32.9231  26.6198  19.4785
 QTT  H7   H  HCR6   0   0.257  39.1657  25.5794  22.9107
 QTT  H8   H  HCR6   0   0.265  31.3258  25.0232  18.4294
 QTT  H9   H  HCR6   0   0.264  37.3257  25.8377  24.5717
 QTT  H10  H  HCR6   0   0.260  32.1197  22.7217  17.8751
 QTT  H11  H  HCR6   0   0.256  35.3672  24.3022  24.4372
 QTT  H12  H  HCH2   0   0.209  31.0310  20.4674  20.5411
 QTT  H13  H  HCH2   0   0.224  30.9126  18.7727  20.1098
 QTT  H14  H  HCH2   0   0.223  30.9995  19.1165  22.6000
 QTT  H15  H  HCH2   0   0.209  32.3327  18.1370  22.0189
 QTT  H16  H  HCH2   0   0.229  32.5877  19.9415  18.7009
 QTT  H17  H  HCH2   0   0.213  33.3357  18.6736  19.6541
 QTT  H18  H  HCH2   0   0.231  33.1426  19.8319  23.6165
 QTT  H19  H  HCH2   0   0.209  32.4440  21.1188  22.6538
 QTT  H20  H  HCH2   0   0.236  36.5806  21.0683  23.9546
 QTT  H21  H  HCH2   0   0.183  35.0656  20.3260  24.3799
 QTT  H22  H  HCH2   0   0.207  33.9418  21.2132  17.6317
 QTT  H23  H  HCH2   0   0.245  35.5675  21.8620  17.7294
 QTT  H24  H  HCH2   0   0.261  34.4060  22.7428  21.6941
 QTT  H25  H  HCH2   0   0.207  34.2770  22.5315  23.4293
 QTT  H26  H  HCH1   0   0.221  33.2536  21.6105  20.4331
 QTT  H27  H  HCH1   0   0.226  34.5825  19.1843  21.6639
 QTT  H29  H  HCH3   0   0.248  39.6489  22.7133  20.9175
 QTT  H30  H  HCH3   0   0.247  38.8603  23.8949  19.8868
 QTT  H31  H  HCH3   0   0.241  40.0994  24.4169  21.0311
 QTT  H32  H  HCH3   0   0.245  36.5143  26.0097  19.6586
 QTT  H33  H  HCH3   0   0.244  35.2243  27.1452  20.0873
 QTT  H34  H  HCH3   0   0.253  35.6561  25.8319  21.1792
 QTT  C14  C  CH2    0  -0.423  35.8103  20.3882  23.5704
 QTT  C16  C  CH2    0  -0.339  34.9453  22.3698  22.5678
 QTT  C02  C  CH3    0  -0.720  35.5351  26.1025  20.1273
 QTT  C01  C  CH3    0  -0.715  39.2646  23.7335  20.8876

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    1.507  0.020  1.507
 QTT  C15  N1   single    1.450  0.020  1.450
 QTT  C8   C18  aromatic  1.389  0.020  1.389
 QTT  C8   C4   aromatic  1.387  0.020  1.387
 QTT  C18  N2   aromatic  1.330  0.020  1.330
 QTT  C4   C2   aromatic  1.384  0.020  1.384
 QTT  C1   N1   single    1.447  0.020  1.447
 QTT  N2   C6   aromatic  1.329  0.020  1.329
 QTT  C2   C6   aromatic  1.394  0.020  1.394
 QTT  C6   C02  single    1.499  0.020  1.499
 QTT  N1   C20  single    1.458  0.020  1.458
 QTT  C12  C20  single    1.539  0.020  1.539
 QTT  C12  C10  single    1.524  0.020  1.524
 QTT  C20  C21  single    1.544  0.020  1.544
 QTT  C10  C11  single    1.522  0.020  1.522
 QTT  C01  C7   single    1.499  0.020  1.499
 QTT  O2   C17  deloc     1.246  0.020  1.246
 QTT  C21  N4   single    1.458  0.020  1.458
 QTT  C21  C13  single    1.539  0.020  1.539
 QTT  C7   N3   aromatic  1.330  0.020  1.330
 QTT  C7   C3   aromatic  1.393  0.020  1.393
 QTT  N3   C19  aromatic  1.329  0.020  1.329
 QTT  C11  C13  single    1.524  0.020  1.524
 QTT  N4   C16  single    1.445  0.020  1.445
 QTT  N4   C14  single    1.448  0.020  1.448
 QTT  C16  C19  single    1.509  0.020  1.509
 QTT  C3   C5   aromatic  1.385  0.020  1.385
 QTT  C19  C9   aromatic  1.391  0.020  1.391
 QTT  C17  C14  single    1.546  0.020  1.546
 QTT  C17  O1   deloc     1.247  0.020  1.247
 QTT  C5   C9   aromatic  1.385  0.020  1.385
 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  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  113.86  3.000
 QTT  C20  N1   C1   114.86  3.000
 QTT  C15  N1   C1   111.52  3.000
 QTT  H4   C1   H3   106.93  3.000
 QTT  H4   C1   H2   107.33  3.000
 QTT  H3   C1   H2   108.49  3.000
 QTT  H4   C1   N1   109.25  3.000
 QTT  H3   C1   N1   114.38  3.000
 QTT  H2   C1   N1   110.18  3.000
 QTT  H6   C2   C6   120.21  3.000
 QTT  H6   C2   C4   120.94  3.000
 QTT  C6   C2   C4   118.85  3.000
 QTT  H7   C3   C7   120.29  3.000
 QTT  H7   C3   C5   121.05  3.000
 QTT  C7   C3   C5   118.66  3.000
 QTT  H8   C4   C8   120.52  3.000
 QTT  H8   C4   C2   120.50  3.000
 QTT  C8   C4   C2   118.98  3.000
 QTT  H9   C5   C9   120.58  3.000
 QTT  H9   C5   C3   120.48  3.000
 QTT  C9   C5   C3   118.93  3.000
 QTT  C02  C6   N2   116.89  3.000
 QTT  C02  C6   C2   121.39  3.000
 QTT  N2   C6   C2   121.72  3.000
 QTT  C01  C7   N3   116.60  3.000
 QTT  N3   C7   C3   122.04  3.000
 QTT  C01  C7   C3   121.36  3.000
 QTT  H10  C8   C18  120.23  3.000
 QTT  H10  C8   C4   121.19  3.000
 QTT  C18  C8   C4   118.58  3.000
 QTT  H11  C9   C19  120.27  3.000
 QTT  H11  C9   C5   120.94  3.000
 QTT  C19  C9   C5   118.79  3.000
 QTT  H13  C10  H12  106.41  3.000
 QTT  H13  C10  C12  110.12  3.000
 QTT  H12  C10  C12  109.41  3.000
 QTT  H13  C10  C11  110.54  3.000
 QTT  H12  C10  C11  109.36  3.000
 QTT  C12  C10  C11  110.89  3.000
 QTT  H15  C11  H14  106.50  3.000
 QTT  H15  C11  C13  109.25  3.000
 QTT  H14  C11  C13  110.22  3.000
 QTT  H15  C11  C10  109.34  3.000
 QTT  H14  C11  C10  110.54  3.000
 QTT  C13  C11  C10  110.88  3.000
 QTT  H17  C12  H16  106.54  3.000
 QTT  H17  C12  C20  109.69  3.000
 QTT  H16  C12  C20  110.09  3.000
 QTT  H17  C12  C10  109.12  3.000
 QTT  H16  C12  C10  109.64  3.000
 QTT  C20  C12  C10  111.62  3.000
 QTT  H19  C13  H18  106.38  3.000
 QTT  H19  C13  C21  109.95  3.000
 QTT  H18  C13  C21  110.17  3.000
 QTT  H19  C13  C11  109.05  3.000
 QTT  H18  C13  C11  109.53  3.000
 QTT  C21  C13  C11  111.62  3.000
 QTT  H23  C15  H22  106.03  3.000
 QTT  H23  C15  C18  107.82  3.000
 QTT  H22  C15  C18  109.20  3.000
 QTT  H23  C15  N1   107.30  3.000
 QTT  H22  C15  N1   113.71  3.000
 QTT  C18  C15  N1   112.40  3.000
 QTT  C18  N2   C6   119.73  3.000
 QTT  C19  N3   C7   119.56  3.000
 QTT  C14  C17  O2   119.12  3.000
 QTT  C14  C17  O1   114.24  3.000
 QTT  O2   C17  O1   126.56  3.000
 QTT  N2   C18  C15  116.49  3.000
 QTT  N2   C18  C8   122.13  3.000
 QTT  C15  C18  C8   121.38  3.000
 QTT  N3   C19  C16  117.75  3.000
 QTT  C16  C19  C9   120.16  3.000
 QTT  N3   C19  C9   122.01  3.000
 QTT  H26  C20  C21  107.56  3.000
 QTT  H26  C20  C12  106.11  3.000
 QTT  C21  C20  C12  108.46  3.000
 QTT  H26  C20  N1   105.97  3.000
 QTT  C21  C20  N1   113.48  3.000
 QTT  C12  C20  N1   114.74  3.000
 QTT  H27  C21  N4   105.63  3.000
 QTT  H27  C21  C20  107.18  3.000
 QTT  N4   C21  C20  113.73  3.000
 QTT  H27  C21  C13  107.01  3.000
 QTT  N4   C21  C13  114.69  3.000
 QTT  C20  C21  C13  108.11  3.000
 QTT  C21  N4   C16  113.76  3.000
 QTT  C16  N4   C14  110.93  3.000
 QTT  C21  N4   C14  113.89  3.000
 QTT  H21  C14  H20  104.61  3.000
 QTT  H21  C14  N4   112.71  3.000
 QTT  H20  C14  N4   107.45  3.000
 QTT  H21  C14  C17  108.01  3.000
 QTT  H20  C14  C17  105.27  3.000
 QTT  N4   C14  C17  117.73  3.000
 QTT  H25  C16  H24  106.00  3.000
 QTT  H25  C16  N4   113.02  3.000
 QTT  H24  C16  N4   109.08  3.000
 QTT  H25  C16  C19  108.36  3.000
 QTT  H24  C16  C19  106.47  3.000
 QTT  N4   C16  C19  113.45  3.000
 QTT  H34  C02  H33  107.71  3.000
 QTT  H34  C02  H32  107.07  3.000
 QTT  H33  C02  H32  108.80  3.000
 QTT  H34  C02  C6   110.28  3.000
 QTT  H33  C02  C6   111.86  3.000
 QTT  H32  C02  C6   110.95  3.000
 QTT  H31  C01  H30  108.20  3.000
 QTT  H31  C01  H29  108.27  3.000
 QTT  H30  C01  H29  107.09  3.000
 QTT  H31  C01  C7   111.84  3.000
 QTT  H30  C01  C7   110.44  3.000
 QTT  H29  C01  C7   110.84  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  Var_01    C21  C13  C11  C10   -56.79  30.0  1
 QTT  Var_02    C20  C12  C10  C11   -56.36  30.0  1
 QTT  Var_03    C13  C11  C10  C12    53.74  30.0  1
 QTT  Var_04    C8   C18  C15  N1   -113.20  30.0  2
 QTT  Var_05    N4   C16  C19  C9   -135.75  30.0  2
 QTT  Var_06    C20  N1   C15  C18    65.09  30.0  3
 QTT  Var_07    C21  N4   C16  C19  -159.96  30.0  3
 QTT  Var_08    H32  C02  C6   C2   -139.28  30.0  2
 QTT  Var_09    H29  C01  C7   C3    123.58  30.0  2
 QTT  Var_10    H2   C1   N1   C20   -54.97  30.0  3
 QTT  Var_11    N4   C14  C17  O1   -163.13  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  C14  0.020

