# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 13:58:07 2020
#   Inital geometry file: a 150 line input string
#   Ligand name: N-(3-tert-butylphenyl)-4-methyl-3-[6-(morpholin-4-yl)pyrimidin-4-yl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(cc1c2cc(ncn2)N3CCOCC3)C(=O)Nc4cccc(c4)C(C)(C)C
#
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
 92D  92D  N-(3-tert-butylphenyl)-4-methyl-3-[6-(morpholin-4-yl)pyrimidin-4-yl]benzamide  ligand  62  32  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_92D
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
 92D  C1   C  CR6   0   0.083   1.5654  -3.2952   0.7400
 92D  C2   C  CH3   0  -0.735   2.7441  -4.1927   0.9745
 92D  C3   C  CR16  0  -0.284   0.3006  -3.7036   1.1523
 92D  C11  C  CR16  0  -0.220  -6.6634  -1.1880  -0.4578
 92D  C12  C  CR16  0  -0.359  -6.9332   0.1737  -0.3721
 92D  C13  C  CR6   0   0.215  -5.9032   1.0797  -0.1455
 92D  C14  C  CR16  0  -0.387  -4.6000   0.5933  -0.0073
 92D  C15  C  CR16  0  -0.308   0.5652  -1.2187   0.0043
 92D  C16  C  CR6   0   0.048   1.6863  -2.0257   0.1517
 92D  C17  C  CR6   0   0.217   2.9916  -1.5038  -0.3174
 92D  C18  C  CR16  0  -0.432   3.4103  -0.2478   0.0624
 92D  C19  C  CR6   0   0.588   4.6480   0.2089  -0.4392
 92D  C21  C  CH2   0  -0.322   6.3513   1.9242  -0.8085
 92D  C22  C  CH2   0  -0.191   7.1955   2.7444   0.1473
 92D  C24  C  CH2   0  -0.183   5.3675   3.2398   1.4763
 92D  C25  C  CH2   0  -0.324   4.4324   2.4326   0.5919
 92D  C27  C  CR16  0   0.050   4.8549  -1.7697  -1.5437
 92D  C29  C  CT    0  -0.174  -6.1379   2.5846  -0.0372
 92D  C30  C  CH3   0  -0.632  -5.3162   3.3076  -1.1128
 92D  N20  N  NT    0  -0.510   5.1759   1.4113  -0.1223
 92D  N8   N  NH1   0  -0.763  -3.0516  -1.3303   0.0491
 92D  C31  C  CH3   0  -0.665  -7.6083   2.9562  -0.2275
 92D  C6   C  C     0   0.526  -1.8504  -0.7210   0.2027
 92D  C5   C  CR6   0  -0.037  -0.6983  -1.6514   0.3940
 92D  N26  N  N     0  -0.476   5.3540  -0.5832  -1.2562
 92D  C4   C  CR16  0  -0.286  -0.8197  -2.9070   0.9790
 92D  C32  C  CH3   0  -0.630  -5.6921   3.0671   1.3496
 92D  C10  C  CR16  0  -0.376  -5.3758  -1.6640  -0.3195
 92D  O7   O  O     0  -0.462  -1.6869   0.4877   0.1797
 92D  C9   C  CR6   0   0.401  -4.3264  -0.7687  -0.0924
 92D  N28  N  N     0  -0.442   3.7148  -2.2881  -1.1288
 92D  O23  O  O2    0  -0.481   6.4491   3.7757   0.7526
 92D  H1   H  HCH3  0   0.258   3.1353  -4.5890   0.0387
 92D  H2   H  HCH3  0   0.246   3.5633  -3.6604   1.4585
 92D  H3   H  HCH3  0   0.248   2.4654  -5.0310   1.6112
 92D  H4   H  HCR6  0   0.261   0.1901  -4.6666   1.6350
 92D  H5   H  HCR6  0   0.256  -7.4717  -1.8861  -0.6332
 92D  H6   H  HCR6  0   0.250  -7.9543   0.5095  -0.4857
 92D  H7   H  HCR6  0   0.272  -3.7925   1.2861   0.1631
 92D  H8   H  HCR6  0   0.263   0.6746  -0.2409  -0.4480
 92D  H9   H  HCR6  0   0.283   2.7966   0.3422   0.7252
 92D  H10  H  HCH2  0   0.239   6.0428   2.5403  -1.6622
 92D  H11  H  HCH2  0   0.276   6.9408   1.0981  -1.1957
 92D  H12  H  HCH2  0   0.210   7.6274   2.0833   0.9117
 92D  H13  H  HCH2  0   0.246   8.0165   3.2082  -0.4005
 92D  H14  H  HCH2  0   0.248   4.8173   4.0723   1.9162
 92D  H15  H  HCH2  0   0.211   5.7295   2.6015   2.2945
 92D  H16  H  HCH2  0   0.269   3.6761   1.9880   1.2335
 92D  H17  H  HCH2  0   0.246   3.9183   3.0897  -0.1196
 92D  H18  H  HCR6  0   0.252   5.4530  -2.3872  -2.2068
 92D  H19  H  HCH3  0   0.229  -5.6094   2.9880  -2.1142
 92D  H20  H  HCH3  0   0.228  -5.4709   4.3863  -1.0439
 92D  H21  H  HCH3  0   0.229  -4.2467   3.1241  -1.0028
 92D  H22  H  HNH1  0   0.421  -3.0344  -2.3351  -0.0337
 92D  H23  H  HCH3  0   0.230  -8.2468   2.5085   0.5361
 92D  H24  H  HCH3  0   0.237  -7.7237   4.0386  -0.1545
 92D  H25  H  HCH3  0   0.230  -7.9866   2.6531  -1.2059
 92D  H26  H  HCR6  0   0.264  -1.7733  -3.2722   1.3395
 92D  H27  H  HCH3  0   0.228  -4.6279   2.8974   1.5152
 92D  H28  H  HCH3  0   0.227  -5.8729   4.1388   1.4543
 92D  H29  H  HCH3  0   0.228  -6.2404   2.5549   2.1423
 92D  H30  H  HCR6  0   0.267  -5.1805  -2.7282  -0.3852

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
 92D  C2   C1   single    1.500  0.020  1.500
 92D  C21  C22  single    1.516  0.020  1.516
 92D  C21  N20  single    1.454  0.020  1.454
 92D  C22  O23  single    1.410  0.020  1.410
 92D  O23  C24  single    1.407  0.020  1.407
 92D  N20  C25  single    1.451  0.020  1.451
 92D  N20  C19  single    1.351  0.020  1.351
 92D  C25  C24  single    1.519  0.020  1.519
 92D  N26  C19  aromatic  1.339  0.020  1.339
 92D  N26  C27  aromatic  1.319  0.020  1.319
 92D  C19  C18  aromatic  1.411  0.020  1.411
 92D  C1   C3   aromatic  1.392  0.020  1.392
 92D  C1   C16  aromatic  1.404  0.020  1.404
 92D  C27  N28  aromatic  1.319  0.020  1.319
 92D  C18  C17  aromatic  1.377  0.020  1.377
 92D  C3   C4   aromatic  1.386  0.020  1.386
 92D  N28  C17  aromatic  1.340  0.020  1.340
 92D  C17  C16  single    1.482  0.020  1.482
 92D  C16  C15  aromatic  1.389  0.020  1.389
 92D  C4   C5   aromatic  1.391  0.020  1.391
 92D  C15  C5   aromatic  1.391  0.020  1.391
 92D  C5   C6   single    1.493  0.020  1.493
 92D  C6   N8   single    1.356  0.020  1.356
 92D  C6   O7   double    1.220  0.020  1.220
 92D  N8   C9   single    1.400  0.020  1.400
 92D  C9   C10  aromatic  1.398  0.020  1.398
 92D  C9   C14  aromatic  1.392  0.020  1.392
 92D  C10  C11  aromatic  1.380  0.020  1.380
 92D  C14  C13  aromatic  1.398  0.020  1.398
 92D  C11  C12  aromatic  1.391  0.020  1.391
 92D  C13  C12  aromatic  1.390  0.020  1.390
 92D  C13  C29  single    1.527  0.020  1.527
 92D  C30  C29  single    1.535  0.020  1.535
 92D  C29  C31  single    1.528  0.020  1.528
 92D  C29  C32  single    1.535  0.020  1.535
 92D  C2   H1   single    0.970  0.020  1.090
 92D  C2   H2   single    0.970  0.020  1.090
 92D  C2   H3   single    0.970  0.020  1.090
 92D  C3   H4   single    0.930  0.020  1.080
 92D  C11  H5   single    0.930  0.020  1.080
 92D  C12  H6   single    0.930  0.020  1.080
 92D  C14  H7   single    0.930  0.020  1.080
 92D  C15  H8   single    0.930  0.020  1.080
 92D  C18  H9   single    0.930  0.020  1.080
 92D  C21  H10  single    0.970  0.020  1.090
 92D  C21  H11  single    0.970  0.020  1.090
 92D  C22  H12  single    0.970  0.020  1.090
 92D  C22  H13  single    0.970  0.020  1.090
 92D  C24  H14  single    0.970  0.020  1.090
 92D  C24  H15  single    0.970  0.020  1.090
 92D  C25  H16  single    0.970  0.020  1.090
 92D  C25  H17  single    0.970  0.020  1.090
 92D  C27  H18  single    0.930  0.020  1.080
 92D  C30  H19  single    0.970  0.020  1.090
 92D  C30  H20  single    0.970  0.020  1.090
 92D  C30  H21  single    0.970  0.020  1.090
 92D  N8   H22  single    0.860  0.020  1.020
 92D  C31  H23  single    0.970  0.020  1.090
 92D  C31  H24  single    0.970  0.020  1.090
 92D  C31  H25  single    0.970  0.020  1.090
 92D  C4   H26  single    0.930  0.020  1.080
 92D  C32  H27  single    0.970  0.020  1.090
 92D  C32  H28  single    0.970  0.020  1.090
 92D  C32  H29  single    0.970  0.020  1.090
 92D  C10  H30  single    0.930  0.020  1.080

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
 92D  C16  C1   C3   117.88  3.000
 92D  C16  C1   C2   122.60  3.000
 92D  C3   C1   C2   119.49  3.000
 92D  H3   C2   H2   107.98  3.000
 92D  H3   C2   H1   108.32  3.000
 92D  H2   C2   H1   106.81  3.000
 92D  H3   C2   C1   110.54  3.000
 92D  H2   C2   C1   111.57  3.000
 92D  H1   C2   C1   111.45  3.000
 92D  H4   C3   C4   118.98  3.000
 92D  H4   C3   C1   119.07  3.000
 92D  C4   C3   C1   121.94  3.000
 92D  H5   C11  C10  119.38  3.000
 92D  H5   C11  C12  119.78  3.000
 92D  C10  C11  C12  120.84  3.000
 92D  H6   C12  C13  120.97  3.000
 92D  H6   C12  C11  118.74  3.000
 92D  C13  C12  C11  120.29  3.000
 92D  C29  C13  C14  118.64  3.000
 92D  C29  C13  C12  122.68  3.000
 92D  C14  C13  C12  118.69  3.000
 92D  H7   C14  C9   119.45  3.000
 92D  H7   C14  C13  119.38  3.000
 92D  C9   C14  C13  121.18  3.000
 92D  H8   C15  C5   119.31  3.000
 92D  H8   C15  C16  119.16  3.000
 92D  C5   C15  C16  121.51  3.000
 92D  C17  C16  C15  118.21  3.000
 92D  C15  C16  C1   120.00  3.000
 92D  C17  C16  C1   121.79  3.000
 92D  N28  C17  C18  122.44  3.000
 92D  N28  C17  C16  117.44  3.000
 92D  C18  C17  C16  120.11  3.000
 92D  H9   C18  C19  122.70  3.000
 92D  H9   C18  C17  119.68  3.000
 92D  C19  C18  C17  117.62  3.000
 92D  N26  C19  N20  117.62  3.000
 92D  N26  C19  C18  119.19  3.000
 92D  N20  C19  C18  123.18  3.000
 92D  H11  C21  H10  107.60  3.000
 92D  H11  C21  N20  109.79  3.000
 92D  H10  C21  N20  109.75  3.000
 92D  H11  C21  C22  109.51  3.000
 92D  H10  C21  C22  110.08  3.000
 92D  N20  C21  C22  110.08  3.000
 92D  H13  C22  H12  108.02  3.000
 92D  H13  C22  O23  107.65  3.000
 92D  H12  C22  O23  110.46  3.000
 92D  H13  C22  C21  109.43  3.000
 92D  H12  C22  C21  109.38  3.000
 92D  O23  C22  C21  111.82  3.000
 92D  H15  C24  H14  108.01  3.000
 92D  H15  C24  O23  110.54  3.000
 92D  H14  C24  O23  107.73  3.000
 92D  H15  C24  C25  109.12  3.000
 92D  H14  C24  C25  109.27  3.000
 92D  O23  C24  C25  112.09  3.000
 92D  H17  C25  H16  107.58  3.000
 92D  H17  C25  N20  110.04  3.000
 92D  H16  C25  N20  111.05  3.000
 92D  H17  C25  C24  110.36  3.000
 92D  H16  C25  C24  107.58  3.000
 92D  N20  C25  C24  110.19  3.000
 92D  H18  C27  N28  116.40  3.000
 92D  H18  C27  N26  115.87  3.000
 92D  N28  C27  N26  127.73  3.000
 92D  C32  C29  C31  108.40  3.000
 92D  C32  C29  C30  109.25  3.000
 92D  C31  C29  C30  108.26  3.000
 92D  C32  C29  C13  109.23  3.000
 92D  C31  C29  C13  112.25  3.000
 92D  C30  C29  C13  109.41  3.000
 92D  H21  C30  H20  107.38  3.000
 92D  H21  C30  H19  107.86  3.000
 92D  H20  C30  H19  108.00  3.000
 92D  H21  C30  C29  112.03  3.000
 92D  H20  C30  C29  110.20  3.000
 92D  H19  C30  C29  111.19  3.000
 92D  C25  N20  C21  113.45  3.000
 92D  C25  N20  C19  122.80  3.000
 92D  C21  N20  C19  121.27  3.000
 92D  H22  N8   C9   114.01  3.000
 92D  H22  N8   C6   116.24  3.000
 92D  C9   N8   C6   129.64  3.000
 92D  H25  C31  H24  107.38  3.000
 92D  H25  C31  H23  108.08  3.000
 92D  H24  C31  H23  107.35  3.000
 92D  H25  C31  C29  112.17  3.000
 92D  H24  C31  C29  109.55  3.000
 92D  H23  C31  C29  112.09  3.000
 92D  O7   C6   C5   121.09  3.000
 92D  O7   C6   N8   124.19  3.000
 92D  C5   C6   N8   114.71  3.000
 92D  C4   C5   C6   123.31  3.000
 92D  C6   C5   C15  118.11  3.000
 92D  C4   C5   C15  118.55  3.000
 92D  C27  N26  C19  117.75  3.000
 92D  H26  C4   C5   121.43  3.000
 92D  H26  C4   C3   118.46  3.000
 92D  C5   C4   C3   120.08  3.000
 92D  H29  C32  H28  107.93  3.000
 92D  H29  C32  H27  107.88  3.000
 92D  H28  C32  H27  107.45  3.000
 92D  H29  C32  C29  111.27  3.000
 92D  H28  C32  C29  110.32  3.000
 92D  H27  C32  C29  111.83  3.000
 92D  H30  C10  C9   120.23  3.000
 92D  H30  C10  C11  120.05  3.000
 92D  C9   C10  C11  119.72  3.000
 92D  C10  C9   N8   116.29  3.000
 92D  C10  C9   C14  119.29  3.000
 92D  N8   C9   C14  124.42  3.000
 92D  C27  N28  C17  115.26  3.000
 92D  C24  O23  C22  110.44  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
 92D  CONST_01  C5   C4   C3   C1      0.00   0.0  0
 92D  CONST_04  C5   C15  C16  C1      0.00   0.0  0
 92D  CONST_05  C17  C16  C1   C3    180.00   0.0  0
 92D  CONST_06  C15  C16  C1   C3      0.00   0.0  0
 92D  CONST_07  C15  C5   C4   C3      0.00   0.0  0
 92D  CONST_08  C14  C9   C10  C11     0.00   0.0  0
 92D  CONST_09  C14  C13  C12  C11     0.00   0.0  0
 92D  CONST_10  C9   C10  C11  C12     0.00   0.0  0
 92D  CONST_11  C9   C14  C13  C12     0.00   0.0  0
 92D  CONST_12  C10  C9   C14  C13     0.00   0.0  0
 92D  CONST_13  C10  C11  C12  C13     0.00   0.0  0
 92D  CONST_16  C4   C3   C1   C16     0.00   0.0  0
 92D  CONST_17  C19  C18  C17  C16   180.00   0.0  0
 92D  CONST_18  C27  N28  C17  C16   180.00   0.0  0
 92D  CONST_19  C4   C5   C15  C16     0.00   0.0  0
 92D  CONST_20  N26  C19  C18  C17     0.00   0.0  0
 92D  CONST_21  N26  C27  N28  C17     0.00   0.0  0
 92D  CONST_22  C5   C15  C16  C17   180.00   0.0  0
 92D  CONST_23  C27  N26  C19  C18     0.00   0.0  0
 92D  CONST_24  C27  N28  C17  C18     0.00   0.0  0
 92D  CONST_25  N28  C27  N26  C19     0.00   0.0  0
 92D  CONST_26  N28  C17  C18  C19     0.00   0.0  0
 92D  CONST_27  N20  C19  C18  C17   180.00   0.0  0
 92D  CONST_28  N20  C19  N26  C27   180.00   0.0  0
 92D  CONST_29  C4   C3   C1   C2    180.00   0.0  0
 92D  CONST_30  C17  C16  C1   C2      0.00   0.0  0
 92D  CONST_31  C15  C16  C1   C2    180.00   0.0  0
 92D  CONST_32  C6   C5   C4   C3    180.00   0.0  0
 92D  CONST_33  N8   C9   C10  C11   180.00   0.0  0
 92D  CONST_34  C29  C13  C12  C11   180.00   0.0  0
 92D  CONST_35  N8   C9   C14  C13   180.00   0.0  0
 92D  CONST_36  C6   C5   C15  C16   180.00   0.0  0
 92D  CONST_37  C9   C14  C13  C29   180.00   0.0  0
 92D  CONST_38  H26  C4   C3   C1    180.00   0.0  0
 92D  CONST_39  H8   C15  C16  C1    180.00   0.0  0
 92D  CONST_40  H30  C10  C11  C12   180.00   0.0  0
 92D  CONST_41  H7   C14  C13  C12   180.00   0.0  0
 92D  CONST_42  H5   C11  C12  C13   180.00   0.0  0
 92D  CONST_43  H6   C12  C13  C14   180.00   0.0  0
 92D  CONST_44  H4   C3   C1   C16   180.00   0.0  0
 92D  CONST_45  H9   C18  C17  C16     0.00   0.0  0
 92D  CONST_46  H18  C27  N28  C17   180.00   0.0  0
 92D  CONST_47  C9   N8   C6   C5    180.00   0.0  0
 92D  CONST_48  C6   N8   C9   C14     0.00   0.0  0
 92D  CONST_49  C10  C9   N8   C6    180.00   0.0  0
 92D  CONST_50  H22  N8   C9   C14   180.00   0.0  0
 92D  CONST_51  C9   N8   C6   O7      0.00   0.0  0
 92D  Var_01    C21  N20  C19  C18  -170.90  30.0  1
 92D  Var_02    C22  C21  N20  C19  -146.41  30.0  1
 92D  Var_03    C24  C25  N20  C19   147.19  30.0  1
 92D  Var_04    C25  C24  O23  C22   -59.24  30.0  1
 92D  Var_05    O23  C22  C21  N20   -55.01  30.0  1
 92D  Var_06    O23  C24  C25  N20    54.21  30.0  1
 92D  Var_07    H12  C22  O23  C24   -62.40  30.0  1
 92D  Var_08    C30  C29  C13  C12  -121.10  30.0  2
 92D  Var_09    N8   C6   C5   C15   153.30  30.0  2
 92D  Var_10    H1   C2   C1   C3    111.31  30.0  2
 92D  Var_11    H19  C30  C29  C13    60.54  30.0  3
 92D  Var_12    H23  C31  C29  C13    61.67  30.0  3
 92D  Var_13    H27  C32  C29  C13    61.73  30.0  3

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
 92D  plan-1  C1   0.020
 92D  plan-1  C2   0.020
 92D  plan-1  C3   0.020
 92D  plan-1  C15  0.020
 92D  plan-1  C16  0.020
 92D  plan-1  C17  0.020
 92D  plan-1  C6   0.020
 92D  plan-1  C5   0.020
 92D  plan-1  C4   0.020
 92D  plan-1  H4   0.020
 92D  plan-1  H8   0.020
 92D  plan-1  H26  0.020
 92D  plan-2  C16  0.020
 92D  plan-2  C17  0.020
 92D  plan-2  C18  0.020
 92D  plan-2  C19  0.020
 92D  plan-2  C27  0.020
 92D  plan-2  N20  0.020
 92D  plan-2  N26  0.020
 92D  plan-2  N28  0.020
 92D  plan-2  H9   0.020
 92D  plan-2  H18  0.020
 92D  plan-3  C11  0.020
 92D  plan-3  C12  0.020
 92D  plan-3  C13  0.020
 92D  plan-3  C14  0.020
 92D  plan-3  C29  0.020
 92D  plan-3  N8   0.020
 92D  plan-3  C10  0.020
 92D  plan-3  C9   0.020
 92D  plan-3  H5   0.020
 92D  plan-3  H6   0.020
 92D  plan-3  H7   0.020
 92D  plan-3  H30  0.020
 92D  plan-4  N8   0.020
 92D  plan-4  C6   0.020
 92D  plan-4  C5   0.020
 92D  plan-4  O7   0.020
 92D  plan-4  C9   0.020
 92D  plan-4  H22  0.020

