# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 01:25:21 2020
#   Inital geometry file: a 157 line input string
#   Ligand name: N-benzyl-3-(2-cyano-6-propylpyrimidin-4-yl)-N-[2-(dimethylamino)ethyl]-5-(trifluoromethyl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCc1cc(nc(n1)C#N)c2cc(cc(c2)C(F)(F)F)C(=O)N(CCN(C)C)Cc3ccccc3
#
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
 O75  O75  N-benzyl-3-(2-cyano-6-propylpyrimidin-4-yl)-N-[2-(dimethylamino)ethyl]-5-(trifluoromethyl)benzamide  ligand  64  36  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_O75
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
 O75  C1    C  CR6   0   0.314  -2.9270  -0.2018   0.7565
 O75  N2    N  N     0  -0.428  -3.0517  -1.5099   0.9784
 O75  C3    C  CR6   0   0.361  -4.2089  -2.0476   0.6547
 O75  N4    N  N     0  -0.404  -5.2704  -1.4593   0.1399
 O75  C5    C  CR6   0   0.311  -5.1580  -0.1520  -0.0966
 O75  C6    C  CR16  0  -0.371  -3.9770   0.5188   0.1997
 O75  C7    C  CSP   0   0.043  -4.3326  -3.4681   0.9026
 O75  N8    N  NS    0  -0.218  -4.4320  -4.5963   1.0989
 O75  C9    C  CH2   0  -0.499  -6.3190   0.5376  -0.7335
 O75  C10   C  CH2   0  -0.428  -6.3705   0.2615  -2.2403
 O75  C11   C  CH3   0  -0.667  -7.5653   0.9342  -2.8983
 O75  C12   C  CR6   0   0.094  -1.6356   0.4160   1.1128
 O75  C13   C  CR16  0  -0.296  -0.4983  -0.3803   1.2345
 O75  C14   C  CR6   0  -0.033   0.7282   0.1898   1.5317
 O75  C15   C  CR16  0  -0.308   0.8228   1.5571   1.7641
 O75  C16   C  CR6   0  -0.147  -0.3120   2.3470   1.6741
 O75  C17   C  CR16  0  -0.347  -1.5355   1.7841   1.3385
 O75  C18   C  CT    0   1.062  -0.2477   3.8249   1.9155
 O75  F19   F  F     0  -0.311  -0.5201   4.5119   0.7978
 O75  F20   F  F     0  -0.309  -1.1401   4.2150   2.8331
 O75  F21   F  F     0  -0.299   0.9548   4.2216   2.3368
 O75  C22   C  C     0   0.532   1.9231  -0.6991   1.7130
 O75  O23   O  O     0  -0.478   1.9203  -1.5078   2.6291
 O75  N24   N  NT    0  -0.440   2.9499  -0.5351   0.8547
 O75  C25   C  CH2   0  -0.417   4.1791  -1.2952   1.0510
 O75  C26   C  CR6   0   0.122   4.3046  -2.4530   0.0939
 O75  C27   C  CR16  0  -0.302   5.2797  -2.4449  -0.8979
 O75  C28   C  CR16  0  -0.242   5.3914  -3.5023  -1.7932
 O75  C29   C  CR16  0  -0.265   4.5230  -4.5804  -1.7044
 O75  C30   C  CR16  0  -0.239   3.5447  -4.5969  -0.7163
 O75  C31   C  CR16  0  -0.297   3.4366  -3.5408   0.1762
 O75  C32   C  CH2   0  -0.326   2.8469   0.1963  -0.3987
 O75  C33   C  CH2   0  -0.266   3.6809   1.4737  -0.4164
 O75  N34   N  NT    0  -0.408   3.5359   2.1865  -1.6691
 O75  C35   C  CH3   0  -0.517   3.9307   3.5728  -1.5337
 O75  C36   C  CH3   0  -0.527   4.2544   1.5519  -2.7558
 O75  H6    H  HCR6  0   0.292  -3.8906   1.5734  -0.0191
 O75  H9    H  HCH2  0   0.262  -7.2414   0.1846  -0.2664
 O75  H9A   H  HCH2  0   0.255  -6.2507   1.6128  -0.5574
 O75  H10   H  HCH2  0   0.234  -5.4442   0.6113  -2.7035
 O75  H10A  H  HCH2  0   0.234  -6.4135  -0.8176  -2.4060
 O75  H11   H  HCH3  0   0.224  -8.5038   0.5644  -2.4830
 O75  H11A  H  HCH3  0   0.224  -7.5414   2.0153  -2.7530
 O75  H11B  H  HCH3  0   0.235  -7.5787   0.7447  -3.9716
 O75  H13   H  HCR6  0   0.279  -0.5751  -1.4474   1.0720
 O75  H15   H  HCR6  0   0.287   1.7773   1.9880   2.0339
 O75  H17   H  HCR6  0   0.286  -2.4165   2.4100   1.2783
 O75  H25   H  HCH2  0   0.275   5.0254  -0.6182   0.9236
 O75  H25A  H  HCH2  0   0.285   4.2076  -1.6438   2.0813
 O75  H27   H  HCR6  0   0.253   5.9600  -1.6042  -0.9726
 O75  H28   H  HCR6  0   0.258   6.1545  -3.4804  -2.5601
 O75  H29   H  HCR6  0   0.257   4.6071  -5.4057  -2.3996
 O75  H30   H  HCR6  0   0.257   2.8670  -5.4371  -0.6386
 O75  H31   H  HCR6  0   0.254   2.6755  -3.5666   0.9463
 O75  H32   H  HCH2  0   0.265   3.1545  -0.4813  -1.1985
 O75  H32A  H  HCH2  0   0.274   1.8076   0.4471  -0.6013
 O75  H33   H  HCH2  0   0.229   3.3300   2.1224   0.3888
 O75  H33A  H  HCH2  0   0.207   4.7375   1.2515  -0.1923
 O75  H35   H  HCH3  0   0.195   4.9923   3.7033  -1.2733
 O75  H35A  H  HCH3  0   0.235   3.7518   4.1030  -2.4702
 O75  H35B  H  HCH3  0   0.229   3.3360   4.0583  -0.7584
 O75  H36   H  HCH3  0   0.234   3.8929   0.5390  -2.9315
 O75  H36A  H  HCH3  0   0.238   4.0953   2.1130  -3.6776
 O75  H36B  H  HCH3  0   0.195   5.3402   1.4963  -2.5800

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
 O75  C1   C6    aromatic  1.390  0.020  1.390
 O75  N2   C1    aromatic  1.333  0.020  1.333
 O75  N2   C3    aromatic  1.316  0.020  1.316
 O75  C3   N4    aromatic  1.318  0.020  1.318
 O75  N4   C5    aromatic  1.333  0.020  1.333
 O75  C5   C9    single    1.493  0.020  1.493
 O75  C6   C5    aromatic  1.390  0.020  1.390
 O75  C7   C3    single    1.447  0.020  1.447
 O75  C7   N8    triple    1.149  0.020  1.149
 O75  C10  C9    single    1.533  0.020  1.533
 O75  C11  C10   single    1.521  0.020  1.521
 O75  C12  C1    single    1.475  0.020  1.475
 O75  C12  C13   aromatic  1.394  0.020  1.394
 O75  C14  C13   aromatic  1.385  0.020  1.385
 O75  C14  C22   single    1.500  0.020  1.500
 O75  C15  C14   aromatic  1.390  0.020  1.390
 O75  C16  C15   aromatic  1.386  0.020  1.386
 O75  C16  C17   aromatic  1.388  0.020  1.388
 O75  C17  C12   aromatic  1.390  0.020  1.390
 O75  C18  C16   single    1.499  0.020  1.499
 O75  C18  F21   single    1.334  0.020  1.334
 O75  F19  C18   single    1.340  0.020  1.340
 O75  F20  C18   single    1.338  0.020  1.338
 O75  C22  O23   double    1.222  0.020  1.222
 O75  N24  C22   single    1.348  0.020  1.348
 O75  N24  C32   single    1.455  0.020  1.455
 O75  C25  N24   single    1.458  0.020  1.458
 O75  C26  C25   single    1.507  0.020  1.507
 O75  C26  C27   aromatic  1.391  0.020  1.391
 O75  C28  C27   aromatic  1.390  0.020  1.390
 O75  C29  C28   aromatic  1.387  0.020  1.387
 O75  C30  C29   aromatic  1.391  0.020  1.391
 O75  C30  C31   aromatic  1.387  0.020  1.387
 O75  C31  C26   aromatic  1.394  0.020  1.394
 O75  C32  C33   single    1.526  0.020  1.526
 O75  N34  C33   single    1.449  0.020  1.449
 O75  N34  C35   single    1.448  0.020  1.448
 O75  C36  N34   single    1.449  0.020  1.449
 O75  C6   H6    single    0.930  0.020  1.080
 O75  C9   H9    single    0.970  0.020  1.090
 O75  C9   H9A   single    0.970  0.020  1.090
 O75  C10  H10   single    0.970  0.020  1.090
 O75  C10  H10A  single    0.970  0.020  1.090
 O75  C11  H11   single    0.970  0.020  1.090
 O75  C11  H11A  single    0.970  0.020  1.090
 O75  C11  H11B  single    0.970  0.020  1.090
 O75  C13  H13   single    0.930  0.020  1.080
 O75  C15  H15   single    0.930  0.020  1.080
 O75  C17  H17   single    0.930  0.020  1.080
 O75  C25  H25   single    0.970  0.020  1.090
 O75  C25  H25A  single    0.970  0.020  1.090
 O75  C27  H27   single    0.930  0.020  1.080
 O75  C28  H28   single    0.930  0.020  1.080
 O75  C29  H29   single    0.930  0.020  1.080
 O75  C30  H30   single    0.930  0.020  1.080
 O75  C31  H31   single    0.930  0.020  1.080
 O75  C32  H32   single    0.970  0.020  1.090
 O75  C32  H32A  single    0.970  0.020  1.090
 O75  C33  H33   single    0.970  0.020  1.090
 O75  C33  H33A  single    0.970  0.020  1.090
 O75  C35  H35   single    0.970  0.020  1.090
 O75  C35  H35A  single    0.970  0.020  1.090
 O75  C35  H35B  single    0.970  0.020  1.090
 O75  C36  H36   single    0.970  0.020  1.090
 O75  C36  H36A  single    0.970  0.020  1.090
 O75  C36  H36B  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
 O75  C12   C1   C6    122.75  3.000
 O75  C12   C1   N2    116.92  3.000
 O75  C6    C1   N2    120.32  3.000
 O75  C3    N2   C1    116.25  3.000
 O75  C7    C3   N4    115.86  3.000
 O75  C7    C3   N2    115.72  3.000
 O75  N4    C3   N2    128.43  3.000
 O75  C5    N4   C3    116.04  3.000
 O75  C9    C5   C6    121.92  3.000
 O75  C6    C5   N4    120.46  3.000
 O75  C9    C5   N4    117.58  3.000
 O75  H6    C6   C5    119.72  3.000
 O75  H6    C6   C1    121.78  3.000
 O75  C5    C6   C1    118.50  3.000
 O75  N8    C7   C3    180.00  3.000
 O75  H9A   C9   H9    107.58  3.000
 O75  H9A   C9   C10   109.76  3.000
 O75  H9    C9   C10   109.50  3.000
 O75  H9A   C9   C5    109.72  3.000
 O75  H9    C9   C5    108.96  3.000
 O75  C10   C9   C5    111.24  3.000
 O75  H10A  C10  H10   106.57  3.000
 O75  H10A  C10  C11   109.90  3.000
 O75  H10   C10  C11   109.93  3.000
 O75  H10A  C10  C9    109.16  3.000
 O75  H10   C10  C9    109.30  3.000
 O75  C11   C10  C9    111.84  3.000
 O75  H11B  C11  H11A  107.68  3.000
 O75  H11B  C11  H11   107.78  3.000
 O75  H11A  C11  H11   107.70  3.000
 O75  H11B  C11  C10   111.02  3.000
 O75  H11A  C11  C10   111.31  3.000
 O75  H11   C11  C10   111.18  3.000
 O75  C17   C12  C13   119.30  3.000
 O75  C17   C12  C1    120.95  3.000
 O75  C13   C12  C1    119.74  3.000
 O75  H13   C13  C14   120.08  3.000
 O75  H13   C13  C12   119.50  3.000
 O75  C14   C13  C12   120.41  3.000
 O75  C22   C14  C15   120.55  3.000
 O75  C15   C14  C13   120.07  3.000
 O75  C22   C14  C13   119.17  3.000
 O75  H15   C15  C16   120.79  3.000
 O75  H15   C15  C14   119.58  3.000
 O75  C16   C15  C14   119.61  3.000
 O75  C18   C16  C17   118.46  3.000
 O75  C18   C16  C15   121.10  3.000
 O75  C17   C16  C15   120.43  3.000
 O75  H17   C17  C16   119.76  3.000
 O75  H17   C17  C12   120.10  3.000
 O75  C16   C17  C12   120.12  3.000
 O75  F21   C18  F20   107.33  3.000
 O75  F20   C18  F19   106.68  3.000
 O75  F21   C18  F19   107.10  3.000
 O75  F20   C18  C16   111.67  3.000
 O75  F19   C18  C16   111.25  3.000
 O75  F21   C18  C16   112.49  3.000
 O75  N24   C22  O23   124.02  3.000
 O75  N24   C22  C14   117.23  3.000
 O75  O23   C22  C14   118.74  3.000
 O75  C32   N24  C25   115.96  3.000
 O75  C25   N24  C22   119.52  3.000
 O75  C32   N24  C22   123.76  3.000
 O75  H25A  C25  H25   106.80  3.000
 O75  H25A  C25  C26   110.67  3.000
 O75  H25   C25  C26   109.74  3.000
 O75  H25A  C25  N24   108.46  3.000
 O75  H25   C25  N24   108.33  3.000
 O75  C26   C25  N24   112.64  3.000
 O75  C31   C26  C27   118.89  3.000
 O75  C31   C26  C25   120.66  3.000
 O75  C27   C26  C25   120.44  3.000
 O75  H27   C27  C28   119.67  3.000
 O75  H27   C27  C26   119.58  3.000
 O75  C28   C27  C26   120.74  3.000
 O75  H28   C28  C29   120.17  3.000
 O75  H28   C28  C27   119.85  3.000
 O75  C29   C28  C27   119.98  3.000
 O75  H29   C29  C30   120.14  3.000
 O75  H29   C29  C28   120.19  3.000
 O75  C30   C29  C28   119.67  3.000
 O75  H30   C30  C31   119.75  3.000
 O75  H30   C30  C29   120.04  3.000
 O75  C31   C30  C29   120.21  3.000
 O75  H31   C31  C30   119.62  3.000
 O75  H31   C31  C26   119.87  3.000
 O75  C30   C31  C26   120.50  3.000
 O75  H32A  C32  H32   106.00  3.000
 O75  H32A  C32  C33   109.08  3.000
 O75  H32   C32  C33   110.91  3.000
 O75  H32A  C32  N24   110.12  3.000
 O75  H32   C32  N24   107.40  3.000
 O75  C33   C32  N24   113.09  3.000
 O75  H33A  C33  H33   106.13  3.000
 O75  H33A  C33  N34   111.76  3.000
 O75  H33   C33  N34   108.25  3.000
 O75  H33A  C33  C32   110.65  3.000
 O75  H33   C33  C32   108.25  3.000
 O75  N34   C33  C32   111.55  3.000
 O75  C36   N34  C35   110.75  3.000
 O75  C36   N34  C33   112.55  3.000
 O75  C35   N34  C33   111.29  3.000
 O75  H35B  C35  H35A  107.72  3.000
 O75  H35B  C35  H35   107.75  3.000
 O75  H35A  C35  H35   107.68  3.000
 O75  H35B  C35  N34   110.11  3.000
 O75  H35A  C35  N34   109.90  3.000
 O75  H35   C35  N34   113.49  3.000
 O75  H36B  C36  H36A  107.74  3.000
 O75  H36B  C36  H36   107.81  3.000
 O75  H36A  C36  H36   107.07  3.000
 O75  H36B  C36  N34   113.03  3.000
 O75  H36A  C36  N34   109.65  3.000
 O75  H36   C36  N34   111.31  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
 O75  CONST_01  N4   C5   C6   C1      0.00   0.0  0
 O75  CONST_02  N4   C3   N2   C1      0.00   0.0  0
 O75  CONST_03  C14  C13  C12  C1    180.00   0.0  0
 O75  CONST_04  C16  C17  C12  C1    180.00   0.0  0
 O75  CONST_05  C5   C6   C1   N2      0.00   0.0  0
 O75  CONST_08  C5   N4   C3   N2      0.00   0.0  0
 O75  CONST_09  C6   C1   N2   C3      0.00   0.0  0
 O75  CONST_10  C12  C1   N2   C3    180.00   0.0  0
 O75  CONST_11  C6   C5   N4   C3      0.00   0.0  0
 O75  CONST_12  C12  C1   C6   C5    180.00   0.0  0
 O75  CONST_15  C15  C14  C13  C12     0.00   0.0  0
 O75  CONST_16  C15  C16  C17  C12     0.00   0.0  0
 O75  CONST_17  C16  C17  C12  C13     0.00   0.0  0
 O75  CONST_18  C16  C15  C14  C13     0.00   0.0  0
 O75  CONST_19  C17  C12  C13  C14     0.00   0.0  0
 O75  CONST_20  C17  C16  C15  C14     0.00   0.0  0
 O75  CONST_21  C29  C28  C27  C26     0.00   0.0  0
 O75  CONST_22  C29  C30  C31  C26     0.00   0.0  0
 O75  CONST_23  C30  C31  C26  C27     0.00   0.0  0
 O75  CONST_24  C30  C29  C28  C27     0.00   0.0  0
 O75  CONST_25  C31  C26  C27  C28     0.00   0.0  0
 O75  CONST_26  C31  C30  C29  C28     0.00   0.0  0
 O75  CONST_27  C9   C5   C6   C1    180.00   0.0  0
 O75  CONST_28  C7   C3   N2   C1    180.00   0.0  0
 O75  CONST_29  C9   C5   N4   C3    180.00   0.0  0
 O75  CONST_30  C7   C3   N4   C5    180.00   0.0  0
 O75  CONST_31  C22  C14  C13  C12   180.00   0.0  0
 O75  CONST_32  C18  C16  C17  C12   180.00   0.0  0
 O75  CONST_33  C18  C16  C15  C14   180.00   0.0  0
 O75  CONST_34  C22  C14  C15  C16   180.00   0.0  0
 O75  CONST_35  C28  C27  C26  C25   180.00   0.0  0
 O75  CONST_36  C30  C31  C26  C25   180.00   0.0  0
 O75  CONST_37  H13  C13  C12  C1      0.00   0.0  0
 O75  CONST_38  H17  C17  C12  C1      0.00   0.0  0
 O75  CONST_39  H6   C6   C1   N2    180.00   0.0  0
 O75  CONST_40  H15  C15  C14  C13   180.00   0.0  0
 O75  CONST_41  H28  C28  C27  C26   180.00   0.0  0
 O75  CONST_42  H30  C30  C31  C26   180.00   0.0  0
 O75  CONST_43  H31  C31  C26  C27   180.00   0.0  0
 O75  CONST_44  H29  C29  C28  C27   180.00   0.0  0
 O75  CONST_45  H27  C27  C28  C29   180.00   0.0  0
 O75  CONST_47  C25  N24  C22  C14   180.00   0.0  0
 O75  CONST_48  C32  N24  C22  O23   180.00   0.0  0
 O75  CONST_49  C25  N24  C22  O23     0.00   0.0  0
 O75  Var_01    C10  C9   C5   N4    -77.93  30.0  2
 O75  Var_02    O23  C22  C14  C13   -62.96  30.0  2
 O75  Var_03    F21  C18  C16  C15    -6.08  30.0  3
 O75  Var_04    C27  C26  C25  N24   111.90  30.0  2
 O75  Var_05    C11  C10  C9   C5    178.81  30.0  1
 O75  Var_06    C26  C25  N24  C22   103.28  30.0  1
 O75  Var_07    C33  C32  N24  C22   113.72  30.0  3
 O75  Var_08    N34  C33  C32  N24  -179.01  30.0  3
 O75  Var_09    C35  N34  C33  C32   160.39  30.0  2
 O75  Var_10    H11  C11  C10  C9    -61.07  30.0  3
 O75  Var_11    H35  C35  N34  C33    63.04  30.0  3
 O75  Var_12    H36  C36  N34  C33    60.46  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
 O75  plan-1  C1   0.020
 O75  plan-1  N2   0.020
 O75  plan-1  C3   0.020
 O75  plan-1  N4   0.020
 O75  plan-1  C5   0.020
 O75  plan-1  C6   0.020
 O75  plan-1  C7   0.020
 O75  plan-1  N8   0.020
 O75  plan-1  C9   0.020
 O75  plan-1  C12  0.020
 O75  plan-1  H6   0.020
 O75  plan-2  C1   0.020
 O75  plan-2  C12  0.020
 O75  plan-2  C13  0.020
 O75  plan-2  C14  0.020
 O75  plan-2  C15  0.020
 O75  plan-2  C16  0.020
 O75  plan-2  C17  0.020
 O75  plan-2  C18  0.020
 O75  plan-2  C22  0.020
 O75  plan-2  H13  0.020
 O75  plan-2  H15  0.020
 O75  plan-2  H17  0.020
 O75  plan-3  C25  0.020
 O75  plan-3  C26  0.020
 O75  plan-3  C27  0.020
 O75  plan-3  C28  0.020
 O75  plan-3  C29  0.020
 O75  plan-3  C30  0.020
 O75  plan-3  C31  0.020
 O75  plan-3  H27  0.020
 O75  plan-3  H28  0.020
 O75  plan-3  H29  0.020
 O75  plan-3  H30  0.020
 O75  plan-3  H31  0.020
 O75  plan-4  C14  0.020
 O75  plan-4  C22  0.020
 O75  plan-4  O23  0.020
 O75  plan-4  N24  0.020
 O75  plan-4  C25  0.020
 O75  plan-4  C32  0.020

