# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 22:36:32 2020
#   Inital geometry file: a 157 line input string
#   Ligand name: N,N'-dimethyl-N-({3-[4-({trans-3-[2-(tetrahydro-2H-pyran-4-yl)ethoxy]cyclobutyl}oxy)phenyl]-1H-pyrazol-4-yl}methyl)ethane-1,2-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNCCN(C)Cc1c[nH]nc1c2ccc(O[C@H]3C[C@@H](C3)OCCC4CCOCC4)cc2
#
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
 49L  49L  N,N'-dimethyl-N-({3-[4-({trans-3-[2-(tetrahydro-2H-pyran-4-yl)ethoxy]cyclobutyl}oxy)phenyl]-1H-pyrazol-4-yl}methyl)ethane-1,2-diamine  ligand  70  32  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_49L
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
 49L  C1   C  CH2   0  -0.275  -5.3423   3.6750  -0.0940
 49L  O1   O  O2    0  -0.491   4.3867  -1.3998  -0.0650
 49L  C2   C  CH2   0  -0.281  -6.0303   2.4988   0.5854
 49L  N2   N  NR15  0  -0.427  -6.3904  -3.0737  -1.1719
 49L  C3   C  CH3   0  -0.528  -6.9676   1.4096  -1.3461
 49L  C4   C  CH2   0  -0.391  -6.3101   0.1156   0.5688
 49L  C5   C  CR5   0  -0.159  -6.0751  -1.1680  -0.1568
 49L  C6   C  CR15  0   0.003  -7.0353  -2.0141  -0.6640
 49L  C7   C  CR5   0   0.248  -4.8534  -1.8407  -0.4200
 49L  C8   C  CR6   0   0.020  -3.4865  -1.4479  -0.0609
 49L  N1   N  NT    0  -0.411  -6.0455   1.3016  -0.2356
 49L  N    N  NH1   0  -0.595  -5.2709   4.8025   0.8128
 49L  C    C  CH3   0  -0.516  -4.6587   5.9676   0.2087
 49L  N3   N  N     0  -0.302  -5.0746  -2.9932  -1.0371
 49L  C24  C  CR16  0  -0.315  -3.0972  -0.1063  -0.0139
 49L  C23  C  CR16  0  -0.344  -1.8055   0.2518   0.3243
 49L  C11  C  CR6   0   0.376  -0.8553  -0.7248   0.6244
 49L  C10  C  CR16  0  -0.362  -1.2261  -2.0677   0.5763
 49L  C9   C  CR16  0  -0.284  -2.5265  -2.4129   0.2365
 49L  O    O  O2    0  -0.479   0.3736  -0.2830   0.9584
 49L  C12  C  C     0  -0.021   1.3528  -1.2283   1.3510
 49L  C15  C  C     0  -0.515   2.0003  -1.9762   0.1676
 49L  C14  C  C     0   0.085   3.0998  -0.9102   0.1493
 49L  C13  C  C     0  -0.506   2.6841  -0.5021   1.5786
 49L  C17  C  CH2   0  -0.451   6.7352  -1.0277  -0.2605
 49L  C18  C  CH1   0  -0.257   7.8232  -0.0383  -0.6658
 49L  C22  C  CH2   0  -0.437   9.1719  -0.7371  -0.8307
 49L  C21  C  CH2   0  -0.180  10.2633   0.2624  -1.1768
 49L  O2   O  O2    0  -0.486  10.3587   1.2923  -0.2157
 49L  C20  C  CH2   0  -0.175   9.1510   2.0119  -0.0921
 49L  C19  C  CH2   0  -0.450   7.9876   1.1223   0.3171
 49L  H1   H  HCH2  0   0.191  -4.3542   3.3458  -0.4550
 49L  H2   H  HCH2  0   0.220  -5.9032   3.9924  -0.9778
 49L  H3   H  HCH2  0   0.226  -5.4761   2.2691   1.5011
 49L  H4   H  HCH2  0   0.200  -7.0433   2.7998   0.9013
 49L  H5   H  HNR5  0   0.419  -6.7990  -3.8727  -1.6290
 49L  H6   H  HCH3  0   0.239  -6.7139   2.2594  -1.9786
 49L  H7   H  HCH3  0   0.243  -6.9120   0.5185  -1.9701
 49L  H8   H  HCH3  0   0.190  -8.0129   1.5314  -1.0207
 49L  H9   H  HCH2  0   0.223  -7.3402   0.1186   0.9624
 49L  H10  H  HCH2  0   0.246  -5.6493   0.1499   1.4396
 49L  H11  H  HCR5  0   0.291  -8.1102  -1.9311  -0.6872
 49L  H13  H  HNH1  0   0.342  -4.7295   4.5342   1.6257
 49L  H15  H  HCH3  0   0.230  -4.5925   6.7735   0.9398
 49L  H16  H  HCH3  0   0.192  -3.6497   5.7923  -0.1904
 49L  H17  H  HCH3  0   0.221  -5.2769   6.3236  -0.6178
 49L  H18  H  HCR6  0   0.280  -3.8194   0.6655  -0.2573
 49L  H19  H  HCR6  0   0.255  -1.5219   1.2968   0.3561
 49L  H20  H  HCR6  0   0.279  -0.5208  -2.8568   0.8002
 49L  H21  H  HCR6  0   0.250  -2.7953  -3.4614   0.2129
 49L  H22  H  H     0   0.255   0.9754  -1.8387   2.1766
 49L  H23  H  H     0   0.252   2.3901  -2.9405   0.4981
 49L  H24  H  H     0   0.260   1.4106  -2.1214  -0.7380
 49L  H25  H  H     0   0.208   2.8645  -0.1099  -0.5654
 49L  H26  H  H     0   0.254   2.6390   0.5563   1.8364
 49L  H27  H  H     0   0.252   3.2790  -1.0285   2.3269
 49L  H28  H  HCH2  0   0.197   5.1766   0.2774  -0.9822
 49L  H29  H  HCH2  0   0.205   5.3249   0.2423   0.7754
 49L  H30  H  HCH2  0   0.222   7.0119  -1.5132   0.6810
 49L  H31  H  HCH2  0   0.230   6.6793  -1.8147  -1.0197
 49L  H32  H  HCH1  0   0.219   7.5462   0.3867  -1.6405
 49L  H33  H  HCH2  0   0.218   9.4334  -1.2550   0.0983
 49L  H34  H  HCH2  0   0.233   9.1171  -1.4966  -1.6153
 49L  H35  H  HCH2  0   0.232  11.2388  -0.2260  -1.2179
 49L  H36  H  HCH2  0   0.193  10.0675   0.6891  -2.1722
 49L  H37  H  HCH2  0   0.233   9.3207   2.7938   0.6504
 49L  H38  H  HCH2  0   0.192   8.9073   2.5092  -1.0433
 49L  H39  H  HCH2  0   0.236   7.0837   1.7356   0.3592
 49L  H40  H  HCH2  0   0.220   8.1558   0.7299   1.3264
 49L  C16  C  CH2   0  -0.142   5.3667  -0.3859  -0.1244

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
 49L  C    N    single    1.448  0.020  1.448
 49L  C17  C16  single    1.518  0.020  1.518
 49L  C17  C18  single    1.525  0.020  1.525
 49L  C16  O1   single    1.411  0.020  1.411
 49L  N    C1   single    1.449  0.020  1.449
 49L  C15  C12  single    1.542  0.020  1.542
 49L  C15  C14  single    1.532  0.020  1.532
 49L  C20  C19  single    1.521  0.020  1.521
 49L  C20  O2   single    1.411  0.020  1.411
 49L  C19  C18  single    1.530  0.020  1.530
 49L  O1   C14  single    1.393  0.020  1.393
 49L  C12  C13  single    1.534  0.020  1.534
 49L  C12  O    single    1.417  0.020  1.417
 49L  C18  C22  single    1.528  0.020  1.528
 49L  C1   C2   single    1.523  0.020  1.523
 49L  C14  C13  single    1.544  0.020  1.544
 49L  O2   C21  single    1.412  0.020  1.412
 49L  C21  C22  single    1.520  0.020  1.520
 49L  O    C11  single    1.348  0.020  1.348
 49L  C2   N1   single    1.452  0.020  1.452
 49L  C23  C11  aromatic  1.395  0.020  1.395
 49L  C23  C24  aromatic  1.382  0.020  1.382
 49L  C11  C10  aromatic  1.394  0.020  1.394
 49L  C24  C8   aromatic  1.398  0.020  1.398
 49L  C3   N1   single    1.447  0.020  1.447
 49L  N1   C4   single    1.457  0.020  1.457
 49L  C4   C5   single    1.493  0.020  1.493
 49L  C10  C9   aromatic  1.388  0.020  1.388
 49L  C8   C9   aromatic  1.393  0.020  1.393
 49L  C8   C7   single    1.467  0.020  1.467
 49L  C5   C7   aromatic  1.419  0.020  1.419
 49L  C5   C6   aromatic  1.377  0.020  1.377
 49L  C7   N3   aromatic  1.326  0.020  1.326
 49L  C6   N2   aromatic  1.340  0.020  1.340
 49L  N3   N2   aromatic  1.325  0.020  1.325
 49L  C1   H1   single    0.970  0.020  1.090
 49L  C1   H2   single    0.970  0.020  1.090
 49L  C2   H3   single    0.970  0.020  1.090
 49L  C2   H4   single    0.970  0.020  1.090
 49L  N2   H5   single    0.860  0.020  1.020
 49L  C3   H6   single    0.970  0.020  1.090
 49L  C3   H7   single    0.970  0.020  1.090
 49L  C3   H8   single    0.970  0.020  1.090
 49L  C4   H9   single    0.970  0.020  1.090
 49L  C4   H10  single    0.970  0.020  1.090
 49L  C6   H11  single    0.930  0.020  1.080
 49L  N    H13  single    0.890  0.020  1.040
 49L  C    H15  single    0.970  0.020  1.090
 49L  C    H16  single    0.970  0.020  1.090
 49L  C    H17  single    0.970  0.020  1.090
 49L  C24  H18  single    0.930  0.020  1.080
 49L  C23  H19  single    0.930  0.020  1.080
 49L  C10  H20  single    0.930  0.020  1.080
 49L  C9   H21  single    0.930  0.020  1.080
 49L  C12  H22  single    0.970  0.020  1.090
 49L  C15  H23  single    0.970  0.020  1.090
 49L  C15  H24  single    0.970  0.020  1.090
 49L  C14  H25  single    0.970  0.020  1.090
 49L  C13  H26  single    0.970  0.020  1.090
 49L  C13  H27  single    0.970  0.020  1.090
 49L  C16  H28  single    0.970  0.020  1.090
 49L  C16  H29  single    0.970  0.020  1.090
 49L  C17  H30  single    0.970  0.020  1.090
 49L  C17  H31  single    0.970  0.020  1.090
 49L  C18  H32  single    0.970  0.020  1.090
 49L  C22  H33  single    0.970  0.020  1.090
 49L  C22  H34  single    0.970  0.020  1.090
 49L  C21  H35  single    0.970  0.020  1.090
 49L  C21  H36  single    0.970  0.020  1.090
 49L  C20  H37  single    0.970  0.020  1.090
 49L  C20  H38  single    0.970  0.020  1.090
 49L  C19  H39  single    0.970  0.020  1.090
 49L  C19  H40  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
 49L  H2   C1   H1   106.37  3.000
 49L  H2   C1   N    107.77  3.000
 49L  H1   C1   N    113.15  3.000
 49L  H2   C1   C2   110.67  3.000
 49L  H1   C1   C2   108.70  3.000
 49L  N    C1   C2   110.13  3.000
 49L  C16  O1   C14  113.29  3.000
 49L  H4   C2   H3   106.42  3.000
 49L  H4   C2   N1   112.17  3.000
 49L  H3   C2   N1   107.77  3.000
 49L  H4   C2   C1   109.39  3.000
 49L  H3   C2   C1   107.85  3.000
 49L  N1   C2   C1   112.92  3.000
 49L  H5   N2   N3   119.81  3.000
 49L  H5   N2   C6   127.16  3.000
 49L  N3   N2   C6   113.03  3.000
 49L  H8   C3   H7   107.94  3.000
 49L  H8   C3   H6   107.84  3.000
 49L  H7   C3   H6   107.08  3.000
 49L  H8   C3   N1   112.71  3.000
 49L  H7   C3   N1   110.24  3.000
 49L  H6   C3   N1   110.81  3.000
 49L  H10  C4   H9   106.27  3.000
 49L  H10  C4   N1   107.71  3.000
 49L  H9   C4   N1   111.38  3.000
 49L  H10  C4   C5   108.59  3.000
 49L  H9   C4   C5   108.83  3.000
 49L  N1   C4   C5   113.76  3.000
 49L  C7   C5   C6   103.93  3.000
 49L  C6   C5   C4   126.70  3.000
 49L  C7   C5   C4   129.28  3.000
 49L  H11  C6   C5   130.98  3.000
 49L  H11  C6   N2   122.16  3.000
 49L  C5   C6   N2   106.86  3.000
 49L  N3   C7   C8   120.14  3.000
 49L  N3   C7   C5   110.78  3.000
 49L  C8   C7   C5   129.04  3.000
 49L  C9   C8   C24  117.76  3.000
 49L  C9   C8   C7   120.59  3.000
 49L  C24  C8   C7   121.65  3.000
 49L  C4   N1   C3   111.63  3.000
 49L  C4   N1   C2   111.16  3.000
 49L  C3   N1   C2   112.27  3.000
 49L  H13  N    C    108.78  3.000
 49L  H13  N    C1   108.81  3.000
 49L  C    N    C1   112.70  3.000
 49L  H17  C    H16  107.27  3.000
 49L  H17  C    H15  107.52  3.000
 49L  H16  C    H15  107.79  3.000
 49L  H17  C    N    109.80  3.000
 49L  H16  C    N    114.28  3.000
 49L  H15  C    N    109.92  3.000
 49L  C7   N3   N2   105.41  3.000
 49L  H18  C24  C23  119.52  3.000
 49L  H18  C24  C8   119.34  3.000
 49L  C23  C24  C8   121.14  3.000
 49L  H19  C23  C11  119.38  3.000
 49L  H19  C23  C24  120.11  3.000
 49L  C11  C23  C24  120.51  3.000
 49L  O    C11  C10  124.52  3.000
 49L  C10  C11  C23  119.06  3.000
 49L  O    C11  C23  116.41  3.000
 49L  H20  C10  C9   118.70  3.000
 49L  H20  C10  C11  121.48  3.000
 49L  C9   C10  C11  119.83  3.000
 49L  H21  C9   C10  118.62  3.000
 49L  H21  C9   C8   119.67  3.000
 49L  C10  C9   C8   121.71  3.000
 49L  C12  O    C11  118.70  3.000
 49L  H22  C12  C13  116.86  3.000
 49L  H22  C12  C15  116.96  3.000
 49L  C13  C12  C15   88.80  3.000
 49L  H22  C12  O    110.07  3.000
 49L  C13  C12  O    108.98  3.000
 49L  C15  C12  O    113.64  3.000
 49L  H24  C15  H23  109.09  3.000
 49L  H24  C15  C14  118.10  3.000
 49L  H23  C15  C14  111.23  3.000
 49L  H24  C15  C12  118.35  3.000
 49L  H23  C15  C12  110.24  3.000
 49L  C14  C15  C12   88.46  3.000
 49L  H25  C14  C13  110.62  3.000
 49L  H25  C14  C15  111.17  3.000
 49L  C13  C14  C15   88.83  3.000
 49L  H25  C14  O1   110.72  3.000
 49L  C13  C14  O1   118.95  3.000
 49L  C15  C14  O1   114.86  3.000
 49L  H27  C13  H26  109.19  3.000
 49L  H27  C13  C14  111.14  3.000
 49L  H26  C13  C14  119.13  3.000
 49L  H27  C13  C12  110.28  3.000
 49L  H26  C13  C12  117.32  3.000
 49L  C14  C13  C12   88.35  3.000
 49L  H31  C17  H30  106.89  3.000
 49L  H31  C17  C18  108.57  3.000
 49L  H30  C17  C18  109.62  3.000
 49L  H31  C17  C16  108.67  3.000
 49L  H30  C17  C16  109.77  3.000
 49L  C18  C17  C16  113.12  3.000
 49L  H32  C18  C19  107.68  3.000
 49L  H32  C18  C22  107.68  3.000
 49L  C19  C18  C22  108.75  3.000
 49L  H32  C18  C17  107.86  3.000
 49L  C22  C18  C17  111.20  3.000
 49L  C19  C18  C17  113.46  3.000
 49L  H34  C22  H33  106.99  3.000
 49L  H34  C22  C21  109.23  3.000
 49L  H33  C22  C21  109.43  3.000
 49L  H34  C22  C18  110.55  3.000
 49L  H33  C22  C18  109.60  3.000
 49L  C21  C22  C18  110.96  3.000
 49L  H36  C21  H35  107.36  3.000
 49L  H36  C21  O2   110.18  3.000
 49L  H35  C21  O2   106.95  3.000
 49L  H36  C21  C22  109.46  3.000
 49L  H35  C21  C22  110.86  3.000
 49L  O2   C21  C22  111.91  3.000
 49L  C20  O2   C21  111.94  3.000
 49L  H38  C20  H37  107.37  3.000
 49L  H38  C20  C19  109.12  3.000
 49L  H37  C20  C19  110.79  3.000
 49L  H38  C20  O2   110.13  3.000
 49L  H37  C20  O2   106.96  3.000
 49L  C19  C20  O2   112.33  3.000
 49L  H40  C19  H39  106.99  3.000
 49L  H40  C19  C20  109.87  3.000
 49L  H39  C19  C20  108.35  3.000
 49L  H40  C19  C18  109.67  3.000
 49L  H39  C19  C18  111.19  3.000
 49L  C20  C19  C18  110.68  3.000
 49L  H29  C16  H28  106.69  3.000
 49L  H29  C16  C17  110.47  3.000
 49L  H28  C16  C17  109.91  3.000
 49L  H29  C16  O1   110.49  3.000
 49L  H28  C16  O1   110.23  3.000
 49L  C17  C16  O1   109.03  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
 49L  CONST_01  C7   C5   C6   N2      0.00   0.0  0
 49L  CONST_02  C8   C7   N3   N2    180.00   0.0  0
 49L  CONST_03  C5   C7   N3   N2      0.00   0.0  0
 49L  CONST_06  N3   N2   C6   C5      0.00   0.0  0
 49L  CONST_07  C8   C7   C5   C6    180.00   0.0  0
 49L  CONST_08  N3   C7   C5   C6      0.00   0.0  0
 49L  CONST_09  C7   N3   N2   C6      0.00   0.0  0
 49L  CONST_10  C23  C24  C8   C7    180.00   0.0  0
 49L  CONST_11  C10  C9   C8   C7    180.00   0.0  0
 49L  CONST_12  C11  C23  C24  C8      0.00   0.0  0
 49L  CONST_13  C11  C10  C9   C8      0.00   0.0  0
 49L  CONST_16  C10  C11  C23  C24     0.00   0.0  0
 49L  CONST_17  C10  C9   C8   C24     0.00   0.0  0
 49L  CONST_18  C9   C10  C11  C23     0.00   0.0  0
 49L  CONST_19  C9   C8   C24  C23     0.00   0.0  0
 49L  CONST_20  C4   C5   C6   N2    180.00   0.0  0
 49L  CONST_21  C8   C7   C5   C4      0.00   0.0  0
 49L  CONST_22  N3   C7   C5   C4    180.00   0.0  0
 49L  CONST_23  O    C11  C23  C24   180.00   0.0  0
 49L  CONST_24  O    C11  C10  C9    180.00   0.0  0
 49L  CONST_25  H5   N2   C6   C5    180.00   0.0  0
 49L  CONST_26  H18  C24  C8   C7      0.00   0.0  0
 49L  CONST_27  H21  C9   C8   C7      0.00   0.0  0
 49L  CONST_28  H11  C6   C5   C7    180.00   0.0  0
 49L  CONST_29  H19  C23  C24  C8    180.00   0.0  0
 49L  CONST_30  H20  C10  C9   C8    180.00   0.0  0
 49L  Var_01    O2   C20  C19  C18   -55.89  30.0  1
 49L  Var_02    O2   C21  C22  C18    56.28  30.0  1
 49L  Var_03    C19  C20  O2   C21    59.36  30.0  1
 49L  Var_04    N1   C4   C5   C6   -104.42  30.0  2
 49L  Var_05    C18  C17  C16  O1    166.21  30.0  1
 49L  Var_06    C5   C4   N1   C2   -168.60  30.0  3
 49L  Var_07    C17  C16  O1   C14   176.02  30.0  2
 49L  Var_08    C3   N1   C2   C1    -72.26  30.0  3
 49L  Var_09    C    N    C1   C2   -178.36  30.0  2
 49L  Var_10    N    C1   C2   N1   -175.66  30.0  1
 49L  Var_11    H15  C    N    C1   -177.78  30.0  3
 49L  Var_12    H6   C3   N1   C2     58.49  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
 49L  chir_01  C12  C15  C13  O    negativ
 49L  chir_02  C14  O1   C13  C15  positiv
 49L  chir_03  C18  C22  C19  C17  positiv

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
 49L  plan-1  N2   0.020
 49L  plan-1  C4   0.020
 49L  plan-1  C5   0.020
 49L  plan-1  C6   0.020
 49L  plan-1  C7   0.020
 49L  plan-1  C8   0.020
 49L  plan-1  N3   0.020
 49L  plan-1  H5   0.020
 49L  plan-1  H11  0.020
 49L  plan-2  C7   0.020
 49L  plan-2  C8   0.020
 49L  plan-2  C24  0.020
 49L  plan-2  C23  0.020
 49L  plan-2  C11  0.020
 49L  plan-2  C10  0.020
 49L  plan-2  C9   0.020
 49L  plan-2  O    0.020
 49L  plan-2  H18  0.020
 49L  plan-2  H19  0.020
 49L  plan-2  H20  0.020
 49L  plan-2  H21  0.020

