# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 07:51:57 2020
#   Inital geometry file: a 144 line input string
#   Ligand name: N-{(3S)-1-[2-(methylamino)pyrimidin-4-yl]pyrrolidin-3-yl}-N'-{4-[(morpholin-4-yl)methyl]-3-(trifluoromethyl)phenyl}urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1nccc(n1)N2CC[C@@H](C2)NC(=O)Nc3ccc(CN4CCOCC4)c(c3)C(F)(F)F
#
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
 66X  66X  N-{(3S)-1-[2-(methylamino)pyrimidin-4-yl]pyrrolidin-3-yl}-N'-{4-[(morpholin-4-yl)methyl]-3-(trifluoromethyl)phenyl}urea  ligand  62  34  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_66X
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
 66X  C14  C  CH2   0  -0.251   4.5912  -0.1848  -0.0495
 66X  C5   C  CR16  0  -0.028   9.2964   0.6619  -0.5993
 66X  C6   C  CR16  0  -0.462   8.0261   1.0321  -0.9628
 66X  C11  C  CH2   0  -0.473   3.7459   1.7137  -1.2404
 66X  C7   C  CR6   0   0.563   6.9758   0.3089  -0.3502
 66X  C10  C  CH2   0  -0.280   5.2451   1.6518  -1.4916
 66X  C12  C  CR15  0  -0.104   3.3971   0.2670  -0.8899
 66X  C3   C  CR6   0   0.578   8.5176  -0.9370   0.7791
 66X  C1   C  CH3   0  -0.507  10.0657  -2.3666   2.0423
 66X  N4   N  N     0  -0.498   9.5799  -0.3113   0.2650
 66X  N8   N  N     0  -0.535   7.2348  -0.6696   0.5140
 66X  N9   N  NR5   0  -0.510   5.6869   0.5789  -0.6109
 66X  N15  N  NH1   0  -0.697   2.1563   0.0771  -0.1859
 66X  C16  C  C     0   0.747   0.9684   0.0490  -0.8407
 66X  O17  O  O     0  -0.514   0.8803   0.0441  -2.0587
 66X  N18  N  NH1   0  -0.796  -0.1183   0.0040  -0.0010
 66X  C19  C  CR6   0   0.396  -1.4632   0.0570  -0.3541
 66X  C20  C  CR16  0  -0.290  -1.9703  -0.2589  -1.6115
 66X  C21  C  CR16  0  -0.304  -3.3372  -0.1893  -1.8280
 66X  C22  C  CR6   0   0.117  -4.2508   0.1812  -0.8491
 66X  C23  C  CH2   0  -0.357  -5.7152   0.2198  -1.2097
 66X  N24  N  NT    0  -0.414  -6.5212  -0.6089  -0.3445
 66X  C25  C  CH2   0  -0.299  -7.9382  -0.3522  -0.4969
 66X  C26  C  CH2   0  -0.188  -8.7203  -1.1872   0.4986
 66X  O27  O  O2    0  -0.487  -8.4487  -2.5634   0.3480
 66X  C28  C  CH2   0  -0.185  -7.0687  -2.8183   0.4958
 66X  C29  C  CH2   0  -0.295  -6.2414  -2.0224  -0.4953
 66X  C30  C  CR6   0  -0.248  -3.7301   0.4952   0.4139
 66X  C31  C  CR16  0  -0.388  -2.3638   0.4289   0.6455
 66X  C32  C  CT    0   1.063  -4.5941   0.8842   1.5839
 66X  F33  F  F     0  -0.306  -5.6396   1.6434   1.2476
 66X  F34  F  F     0  -0.309  -5.0605  -0.1825   2.2448
 66X  F35  F  F     0  -0.314  -3.9017   1.6008   2.4871
 66X  H1   H  HCH2  0   0.234   4.4417   0.0540   1.0107
 66X  H2   H  HCH2  0   0.257   4.7671  -1.2577  -0.1236
 66X  H3   H  HCR6  0   0.255  10.1479   1.1804  -1.0290
 66X  H4   H  HCR6  0   0.266   7.8596   1.8234  -1.6772
 66X  H5   H  HCH2  0   0.244   3.5294   2.3597  -0.3859
 66X  H6   H  HCH2  0   0.261   3.1912   2.0871  -2.0996
 66X  H7   H  HCH2  0   0.242   5.4682   1.4173  -2.5374
 66X  H8   H  HCH2  0   0.253   5.7402   2.5939  -1.2494
 66X  H9   H  HCR5  0   0.269   3.3700  -0.3286  -1.8043
 66X  H10  H  HNH1  0   0.389   7.9495  -2.4244   2.0097
 66X  H11  H  HCH3  0   0.245   9.9582  -3.1672   2.7691
 66X  H12  H  HCH3  0   0.227  10.6411  -2.7486   1.1967
 66X  H13  H  HCH3  0   0.229  10.6435  -1.5642   2.5030
 66X  H14  H  HNH1  0   0.397   2.1678   0.2418   0.8090
 66X  H15  H  HNH1  0   0.411   0.0623   0.0770   0.9888
 66X  H16  H  HCR6  0   0.280  -1.3238  -0.5659  -2.4170
 66X  H17  H  HCR6  0   0.260  -3.7102  -0.4511  -2.8107
 66X  H18  H  HCH2  0   0.255  -6.0881   1.2449  -1.1510
 66X  H19  H  HCH2  0   0.223  -5.8150  -0.0730  -2.2682
 66X  H21  H  HCH2  0   0.239  -8.1383   0.7046  -0.3039
 66X  H22  H  HCH2  0   0.195  -8.2913  -0.5701  -1.5205
 66X  H23  H  HCH2  0   0.200  -8.4707  -0.8568   1.5167
 66X  H24  H  HCH2  0   0.234  -9.7921  -1.0463   0.3497
 66X  H25  H  HCH2  0   0.200  -6.7407  -2.5695   1.5147
 66X  H26  H  HCH2  0   0.234  -6.9148  -3.8874   0.3416
 66X  H27  H  HCH2  0   0.195  -6.4472  -2.3733  -1.5226
 66X  H28  H  HCH2  0   0.243  -5.1844  -2.2130  -0.2960
 66X  H29  H  HCR6  0   0.281  -1.9665   0.6813   1.6202
 66X  N2   N  NH1   0  -0.646   8.7501  -1.9301   1.6573

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
 66X  C1   N2   single    1.439  0.020  1.439
 66X  N2   C3   single    1.346  0.020  1.346
 66X  C3   N4   aromatic  1.336  0.020  1.336
 66X  C3   N8   aromatic  1.337  0.020  1.337
 66X  N4   C5   aromatic  1.332  0.020  1.332
 66X  N8   C7   aromatic  1.331  0.020  1.331
 66X  C5   C6   aromatic  1.372  0.020  1.372
 66X  C7   C6   aromatic  1.415  0.020  1.415
 66X  C7   N9   single    1.342  0.020  1.342
 66X  C10  N9   single    1.457  0.020  1.457
 66X  C10  C11  single    1.521  0.020  1.521
 66X  N9   C14  single    1.449  0.020  1.449
 66X  C11  C12  single    1.529  0.020  1.529
 66X  C14  C12  single    1.529  0.020  1.529
 66X  C12  N15  single    1.439  0.020  1.439
 66X  N15  C16  single    1.357  0.020  1.357
 66X  O17  C16  double    1.221  0.020  1.221
 66X  C16  N18  single    1.374  0.020  1.374
 66X  N18  C19  single    1.392  0.020  1.392
 66X  C19  C31  aromatic  1.396  0.020  1.396
 66X  C19  C20  aromatic  1.392  0.020  1.392
 66X  C31  C30  aromatic  1.387  0.020  1.387
 66X  C20  C21  aromatic  1.386  0.020  1.386
 66X  F33  C32  single    1.335  0.020  1.335
 66X  C30  C32  single    1.506  0.020  1.506
 66X  C30  C22  aromatic  1.402  0.020  1.402
 66X  F34  C32  single    1.339  0.020  1.339
 66X  C32  F35  single    1.345  0.020  1.345
 66X  C21  C22  aromatic  1.389  0.020  1.389
 66X  C22  C23  single    1.509  0.020  1.509
 66X  C23  N24  single    1.444  0.020  1.444
 66X  N24  C25  single    1.448  0.020  1.448
 66X  N24  C29  single    1.449  0.020  1.449
 66X  C25  C26  single    1.517  0.020  1.517
 66X  C29  C28  single    1.517  0.020  1.517
 66X  C26  O27  single    1.411  0.020  1.411
 66X  C28  O27  single    1.411  0.020  1.411
 66X  C14  H1   single    0.970  0.020  1.090
 66X  C14  H2   single    0.970  0.020  1.090
 66X  C5   H3   single    0.930  0.020  1.080
 66X  C6   H4   single    0.930  0.020  1.080
 66X  C11  H5   single    0.970  0.020  1.090
 66X  C11  H6   single    0.970  0.020  1.090
 66X  C10  H7   single    0.970  0.020  1.090
 66X  C10  H8   single    0.970  0.020  1.090
 66X  C12  H9   single    0.970  0.020  1.090
 66X  N2   H10  single    0.860  0.020  1.020
 66X  C1   H11  single    0.970  0.020  1.090
 66X  C1   H12  single    0.970  0.020  1.090
 66X  C1   H13  single    0.970  0.020  1.090
 66X  N15  H14  single    0.860  0.020  1.020
 66X  N18  H15  single    0.860  0.020  1.020
 66X  C20  H16  single    0.930  0.020  1.080
 66X  C21  H17  single    0.930  0.020  1.080
 66X  C23  H18  single    0.970  0.020  1.090
 66X  C23  H19  single    0.970  0.020  1.090
 66X  C25  H21  single    0.970  0.020  1.090
 66X  C25  H22  single    0.970  0.020  1.090
 66X  C26  H23  single    0.970  0.020  1.090
 66X  C26  H24  single    0.970  0.020  1.090
 66X  C28  H25  single    0.970  0.020  1.090
 66X  C28  H26  single    0.970  0.020  1.090
 66X  C29  H27  single    0.970  0.020  1.090
 66X  C29  H28  single    0.970  0.020  1.090
 66X  C31  H29  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
 66X  H2   C14  H1   107.58  3.000
 66X  H2   C14  N9   111.75  3.000
 66X  H1   C14  N9   111.27  3.000
 66X  H2   C14  C12  112.32  3.000
 66X  H1   C14  C12  111.14  3.000
 66X  N9   C14  C12  102.83  3.000
 66X  H3   C5   N4   116.03  3.000
 66X  H3   C5   C6   119.50  3.000
 66X  N4   C5   C6   124.47  3.000
 66X  H4   C6   C7   123.17  3.000
 66X  H4   C6   C5   121.07  3.000
 66X  C7   C6   C5   115.76  3.000
 66X  H6   C11  H5   108.26  3.000
 66X  H6   C11  C12  112.90  3.000
 66X  H5   C11  C12  109.57  3.000
 66X  H6   C11  C10  112.69  3.000
 66X  H5   C11  C10  110.39  3.000
 66X  C12  C11  C10  102.96  3.000
 66X  N9   C7   N8   117.44  3.000
 66X  N9   C7   C6   121.73  3.000
 66X  N8   C7   C6   120.83  3.000
 66X  H8   C10  H7   107.72  3.000
 66X  H8   C10  N9   111.35  3.000
 66X  H7   C10  N9   110.98  3.000
 66X  H8   C10  C11  112.04  3.000
 66X  H7   C10  C11  111.55  3.000
 66X  N9   C10  C11  103.24  3.000
 66X  H9   C12  N15  108.45  3.000
 66X  H9   C12  C11  109.26  3.000
 66X  N15  C12  C11  115.70  3.000
 66X  H9   C12  C14  108.58  3.000
 66X  N15  C12  C14  111.45  3.000
 66X  C11  C12  C14  103.15  3.000
 66X  N8   C3   N4   126.38  3.000
 66X  N8   C3   N2   116.28  3.000
 66X  N4   C3   N2   117.34  3.000
 66X  H13  C1   H12  107.77  3.000
 66X  H13  C1   H11  108.17  3.000
 66X  H12  C1   H11  108.20  3.000
 66X  H13  C1   N2   111.98  3.000
 66X  H12  C1   N2   112.39  3.000
 66X  H11  C1   N2   108.19  3.000
 66X  C3   N4   C5   115.00  3.000
 66X  C3   N8   C7   117.55  3.000
 66X  C10  N9   C7   123.83  3.000
 66X  C10  N9   C14  113.15  3.000
 66X  C7   N9   C14  123.02  3.000
 66X  H14  N15  C16  119.31  3.000
 66X  H14  N15  C12  116.82  3.000
 66X  C16  N15  C12  121.43  3.000
 66X  N18  C16  O17  123.53  3.000
 66X  N18  C16  N15  113.46  3.000
 66X  O17  C16  N15  123.00  3.000
 66X  H15  N18  C19  114.78  3.000
 66X  H15  N18  C16  117.11  3.000
 66X  C19  N18  C16  127.45  3.000
 66X  C31  C19  C20  118.18  3.000
 66X  C20  C19  N18  124.93  3.000
 66X  C31  C19  N18  116.88  3.000
 66X  H16  C20  C21  119.30  3.000
 66X  H16  C20  C19  121.42  3.000
 66X  C21  C20  C19  119.28  3.000
 66X  H17  C21  C22  118.50  3.000
 66X  H17  C21  C20  117.99  3.000
 66X  C22  C21  C20  123.50  3.000
 66X  C30  C22  C23  124.77  3.000
 66X  C23  C22  C21  118.47  3.000
 66X  C30  C22  C21  116.76  3.000
 66X  H19  C23  H18  105.66  3.000
 66X  H19  C23  N24  111.85  3.000
 66X  H18  C23  N24  108.41  3.000
 66X  H19  C23  C22  108.09  3.000
 66X  H18  C23  C22  110.03  3.000
 66X  N24  C23  C22  112.58  3.000
 66X  C29  N24  C25  110.55  3.000
 66X  C29  N24  C23  112.94  3.000
 66X  C25  N24  C23  112.42  3.000
 66X  H22  C25  H21  107.21  3.000
 66X  H22  C25  C26  109.56  3.000
 66X  H21  C25  C26  108.79  3.000
 66X  H22  C25  N24  112.05  3.000
 66X  H21  C25  N24  109.39  3.000
 66X  C26  C25  N24  109.76  3.000
 66X  H24  C26  H23  108.10  3.000
 66X  H24  C26  O27  107.49  3.000
 66X  H23  C26  O27  110.39  3.000
 66X  H24  C26  C25  110.24  3.000
 66X  H23  C26  C25  108.99  3.000
 66X  O27  C26  C25  111.58  3.000
 66X  C28  O27  C26  110.69  3.000
 66X  H26  C28  H25  108.11  3.000
 66X  H26  C28  C29  110.18  3.000
 66X  H25  C28  C29  108.92  3.000
 66X  H26  C28  O27  107.47  3.000
 66X  H25  C28  O27  110.37  3.000
 66X  C29  C28  O27  111.73  3.000
 66X  H28  C29  H27  107.13  3.000
 66X  H28  C29  C28  108.48  3.000
 66X  H27  C29  C28  109.83  3.000
 66X  H28  C29  N24  109.76  3.000
 66X  H27  C29  N24  111.76  3.000
 66X  C28  C29  N24  109.79  3.000
 66X  C32  C30  C31  116.60  3.000
 66X  C32  C30  C22  123.02  3.000
 66X  C31  C30  C22  120.37  3.000
 66X  H29  C31  C30  120.05  3.000
 66X  H29  C31  C19  118.04  3.000
 66X  C30  C31  C19  121.91  3.000
 66X  F35  C32  F34  105.81  3.000
 66X  F35  C32  F33  105.63  3.000
 66X  F34  C32  F33  107.74  3.000
 66X  F35  C32  C30  111.35  3.000
 66X  F34  C32  C30  112.19  3.000
 66X  F33  C32  C30  113.61  3.000
 66X  H10  N2   C1   119.05  3.000
 66X  H10  N2   C3   117.01  3.000
 66X  C1   N2   C3   123.82  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
 66X  CONST_01  N8   C3   N4   C5      0.00   0.0  0
 66X  CONST_02  N8   C7   C6   C5      0.00   0.0  0
 66X  CONST_03  C3   N4   C5   C6      0.00   0.0  0
 66X  CONST_04  C3   N8   C7   C6      0.00   0.0  0
 66X  CONST_05  N4   C3   N8   C7      0.00   0.0  0
 66X  CONST_06  N4   C5   C6   C7      0.00   0.0  0
 66X  CONST_07  C22  C30  C31  C19     0.00   0.0  0
 66X  CONST_08  C22  C21  C20  C19     0.00   0.0  0
 66X  CONST_09  C30  C31  C19  C20     0.00   0.0  0
 66X  CONST_10  C30  C22  C21  C20     0.00   0.0  0
 66X  CONST_11  C31  C19  C20  C21     0.00   0.0  0
 66X  CONST_12  C31  C30  C22  C21     0.00   0.0  0
 66X  CONST_13  N9   C7   C6   C5    180.00   0.0  0
 66X  CONST_14  N9   C7   N8   C3    180.00   0.0  0
 66X  CONST_15  N2   C3   N4   C5    180.00   0.0  0
 66X  CONST_16  N2   C3   N8   C7    180.00   0.0  0
 66X  CONST_17  C30  C31  C19  N18   180.00   0.0  0
 66X  CONST_18  C21  C20  C19  N18   180.00   0.0  0
 66X  CONST_19  C32  C30  C31  C19   180.00   0.0  0
 66X  CONST_20  C23  C22  C21  C20   180.00   0.0  0
 66X  CONST_21  C32  C30  C22  C21   180.00   0.0  0
 66X  CONST_22  C31  C30  C22  C23   180.00   0.0  0
 66X  CONST_23  H3   C5   C6   C7    180.00   0.0  0
 66X  CONST_24  H4   C6   C5   N4    180.00   0.0  0
 66X  CONST_25  H17  C21  C20  C19   180.00   0.0  0
 66X  CONST_26  H29  C31  C19  C20   180.00   0.0  0
 66X  CONST_27  H16  C20  C21  C22   180.00   0.0  0
 66X  CONST_28  N4   C3   N2   C1      0.00   0.0  0
 66X  CONST_29  N8   C3   N2   C1    180.00   0.0  0
 66X  CONST_32  H10  N2   C3   N4    180.00   0.0  0
 66X  CONST_33  H15  N18  C19  C20   180.00   0.0  0
 66X  CONST_34  O17  C16  N15  C12     0.00   0.0  0
 66X  CONST_35  C19  N18  C16  O17     0.00   0.0  0
 66X  CONST_36  C19  N18  C16  N15   180.00   0.0  0
 66X  CONST_37  N18  C16  N15  C12   180.00   0.0  0
 66X  CONST_38  H14  N15  C16  O17   180.00   0.0  0
 66X  Var_01    N8   C7   N9   C14    -3.17  30.0  1
 66X  Var_02    C11  C10  N9   C14    11.25  30.0  1
 66X  Var_03    C12  C14  N9   C7   -166.60  30.0  1
 66X  Var_04    N9   C10  C11  C12   -30.46  30.0  1
 66X  Var_05    O27  C26  C25  N24   -57.18  30.0  1
 66X  Var_06    O27  C28  C29  N24    56.72  30.0  1
 66X  Var_07    C28  C29  N24  C25   -56.14  30.0  1
 66X  Var_08    C29  N24  C25  C26    56.38  30.0  1
 66X  Var_09    C29  C28  O27  C26   -57.42  30.0  1
 66X  Var_10    N24  C23  C22  C21   123.94  30.0  2
 66X  Var_11    C25  N24  C23  C22   167.42  30.0  3
 66X  Var_12    F33  C32  C30  C22   -37.60  30.0  2
 66X  Var_13    H11  C1   N2   C3    179.23  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
 66X  chir_01  C12  C11  C14  N15  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
 66X  plan-1  C5   0.020
 66X  plan-1  C6   0.020
 66X  plan-1  C7   0.020
 66X  plan-1  C3   0.020
 66X  plan-1  N4   0.020
 66X  plan-1  N8   0.020
 66X  plan-1  N9   0.020
 66X  plan-1  H3   0.020
 66X  plan-1  H4   0.020
 66X  plan-1  N2   0.020
 66X  plan-2  N18  0.020
 66X  plan-2  C19  0.020
 66X  plan-2  C20  0.020
 66X  plan-2  C21  0.020
 66X  plan-2  C22  0.020
 66X  plan-2  C23  0.020
 66X  plan-2  C30  0.020
 66X  plan-2  C31  0.020
 66X  plan-2  C32  0.020
 66X  plan-2  H16  0.020
 66X  plan-2  H17  0.020
 66X  plan-2  H29  0.020
 66X  plan-3  C12  0.020
 66X  plan-3  N15  0.020
 66X  plan-3  C16  0.020
 66X  plan-3  O17  0.020
 66X  plan-3  N18  0.020
 66X  plan-3  C19  0.020
 66X  plan-3  H14  0.020
 66X  plan-3  H15  0.020
 66X  plan-4  C3   0.020
 66X  plan-4  C1   0.020
 66X  plan-4  H10  0.020
 66X  plan-4  N2   0.020

