# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 25 01:37:36 2021
#   Inital geometry file: a 144 line input string
#   Ligand name: 4-[(3-chloranyl-4-methoxy-phenyl)methylamino]-2-[(2~{S})-2-(hydroxymethyl)pyrrolidin-1-yl]-~{N}-(pyrimidin-2-ylmethyl)pyrimidine-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(CNc2nc(ncc2C(=O)NCc3ncccn3)N4CCC[C@H]4CO)cc1Cl
#
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
 E6L  E6L  4-[(3-chloranyl-4-methoxy-phenyl)methylamino]-2-[(2~{S})-2-(hydroxymethyl)pyrrolidin-1-yl]-~{N}-(pyrimidin-2-ylmethyl)pyrimidine-5-carboxamide  ligand  60  34  .  2022-07-24  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_E6L
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
 E6L  C11  C   CR6   0   0.571   0.1317  -28.5259  -26.1853
 E6L  C1   C   CH3   0  -0.406  -0.1769  -32.8542  -32.2327
 E6L  C3   C   CR6   0   0.445   0.2035  -32.5958  -29.9102
 E6L  C4   C   CR6   0  -0.149   0.0750  -33.0996  -28.6140
 E6L  C5   C   CR16  0  -0.251   0.5286  -32.3971  -27.5130
 E6L  C6   C   CR6   0   0.101   1.1352  -31.1570  -27.6713
 E6L  C7   C   CR16  0  -0.252   1.2631  -30.6483  -28.9568
 E6L  C8   C   CR16  0  -0.361   0.8060  -31.3495  -30.0632
 E6L  C9   C   CH2   0  -0.355   1.6698  -30.4040  -26.4761
 E6L  C13  C   CR6   0   0.638  -1.9594  -28.9389  -25.3614
 E6L  C15  C   CR16  0  -0.018  -1.4830  -26.8130  -25.9260
 E6L  C16  C   CR6   0  -0.286  -0.2018  -27.1434  -26.3461
 E6L  C17  C   C     0   0.616   0.7414  -26.1701  -26.9171
 E6L  C20  C   CH2   0  -0.351   1.1750  -23.9368  -27.7302
 E6L  C21  C   CR6   0   0.379   2.2843  -23.5517  -26.7831
 E6L  C23  C   CR16  0  -0.012   3.0269  -23.2331  -24.6731
 E6L  C24  C   CR16  0  -0.329   4.2508  -22.7960  -25.1503
 E6L  C25  C   CR16  0  -0.014   4.3894  -22.7626  -26.5266
 E6L  C28  C   CH2   0  -0.239  -4.1507  -29.4342  -24.3670
 E6L  C29  C   CH2   0  -0.484  -4.7638  -30.7572  -23.9220
 E6L  C30  C   CH2   0  -0.457  -3.5497  -31.6020  -23.5466
 E6L  C31  C   CH1   0  -0.095  -2.5120  -31.2182  -24.6018
 E6L  C32  C   CH2   0  -0.148  -2.6084  -32.0587  -25.8689
 E6L  N10  N   NH1   0  -0.672   1.3439  -29.0010  -26.4898
 E6L  N12  N   N     0  -0.509  -0.7605  -29.3916  -25.7186
 E6L  N14  N   N     0  -0.466  -2.3671  -27.6584  -25.4361
 E6L  N19  N   NH1   0  -0.654   0.2870  -24.9377  -27.2093
 E6L  N22  N   N     0  -0.369   2.0430  -23.6049  -25.4811
 E6L  N26  N   N     0  -0.381   3.4148  -23.1413  -27.3437
 E6L  N27  N   NT    0  -0.503  -2.8407  -29.8242  -24.8748
 E6L  O18  O   O     0  -0.487   1.9212  -26.4543  -27.1461
 E6L  O33  O   OH1   0  -0.646  -2.1838  -33.3647  -25.5464
 E6L  CL1  CL  CL    0  -0.099  -0.6958  -34.6384  -28.3989
 E6L  H1   H   HCH3  0   0.254  -0.6203  -33.6107  -32.8747
 E6L  H2   H   HCH3  0   0.217  -0.7287  -31.9189  -32.3542
 E6L  H3   H   HCH3  0   0.217   0.8606  -32.6976  -32.5382
 E6L  H4   H   HCR6  0   0.265   0.3899  -32.8110  -26.5218
 E6L  H5   H   HCR6  0   0.232   1.7231  -29.6805  -29.1149
 E6L  H6   H   HCR6  0   0.258   0.9300  -30.9135  -31.0450
 E6L  H7   H   HCH2  0   0.255   1.3068  -30.8657  -25.5574
 E6L  H8   H   HCH2  0   0.249   2.7586  -30.4736  -26.4582
 E6L  H9   H   HCR6  0   0.203  -1.8276  -25.7842  -25.9730
 E6L  H10  H   HCH2  0   0.271   1.6196  -24.2493  -28.6767
 E6L  H11  H   HCH2  0   0.249   0.5765  -23.0487  -27.9420
 E6L  H12  H   HCR6  0   0.245   2.8299  -23.2813  -23.6078
 E6L  H13  H   HCR6  0   0.245   5.0488  -22.4950  -24.4878
 E6L  H14  H   HCR6  0   0.245   5.3113  -22.4259  -26.9870
 E6L  H15  H   HCH2  0   0.226  -4.0466  -28.7405  -23.5281
 E6L  H16  H   HCH2  0   0.239  -4.7412  -28.9325  -25.1337
 E6L  H17  H   HCH2  0   0.239  -5.4637  -30.6254  -23.0980
 E6L  H18  H   HCH2  0   0.227  -5.3126  -31.2190  -24.7452
 E6L  H19  H   HCH2  0   0.256  -3.7547  -32.6720  -23.5348
 E6L  H20  H   HCH2  0   0.230  -3.1887  -31.3231  -22.5540
 E6L  H21  H   HCH1  0   0.253  -1.4912  -31.2908  -24.2196
 E6L  H22  H   HCH2  0   0.227  -1.9751  -31.6079  -26.6403
 E6L  H23  H   HCH2  0   0.177  -3.6417  -32.0488  -26.2426
 E6L  H24  H   HNH1  0   0.411   2.0124  -28.3260  -26.8349
 E6L  H25  H   HNH1  0   0.371  -0.6707  -24.6804  -27.0530
 E6L  H26  H   HOH1  0   0.427  -2.1470  -33.8820  -26.3560
 E6L  O2   O   O2    0  -0.442  -0.2686  -33.3516  -30.9101

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
 E6L  C1   O2   single    1.416  0.020  1.416
 E6L  O2   C3   single    1.339  0.020  1.339
 E6L  C3   C8   aromatic  1.393  0.020  1.393
 E6L  C3   C4   aromatic  1.397  0.020  1.397
 E6L  C8   C7   aromatic  1.387  0.020  1.387
 E6L  CL1  C4   single    1.734  0.020  1.734
 E6L  C4   C5   aromatic  1.383  0.020  1.383
 E6L  C7   C6   aromatic  1.388  0.020  1.388
 E6L  C5   C6   aromatic  1.389  0.020  1.389
 E6L  C6   C9   single    1.510  0.020  1.510
 E6L  C20  N19  single    1.436  0.020  1.436
 E6L  C20  C21  single    1.509  0.020  1.509
 E6L  N19  C17  single    1.346  0.020  1.346
 E6L  O18  C17  double    1.235  0.020  1.235
 E6L  C17  C16  single    1.471  0.020  1.471
 E6L  N26  C21  aromatic  1.327  0.020  1.327
 E6L  N26  C25  aromatic  1.327  0.020  1.327
 E6L  C21  N22  aromatic  1.325  0.020  1.325
 E6L  C9   N10  single    1.440  0.020  1.440
 E6L  N10  C11  single    1.337  0.020  1.337
 E6L  C16  C15  aromatic  1.388  0.020  1.388
 E6L  C16  C11  aromatic  1.431  0.020  1.431
 E6L  C15  N14  aromatic  1.318  0.020  1.318
 E6L  C11  N12  aromatic  1.328  0.020  1.328
 E6L  C25  C24  aromatic  1.384  0.020  1.384
 E6L  N22  C23  aromatic  1.326  0.020  1.326
 E6L  N14  C13  aromatic  1.346  0.020  1.346
 E6L  N12  C13  aromatic  1.330  0.020  1.330
 E6L  C13  N27  single    1.341  0.020  1.341
 E6L  C24  C23  aromatic  1.384  0.020  1.384
 E6L  C32  O33  single    1.411  0.020  1.411
 E6L  C32  C31  single    1.524  0.020  1.524
 E6L  N27  C28  single    1.458  0.020  1.458
 E6L  N27  C31  single    1.458  0.020  1.458
 E6L  C28  C29  single    1.525  0.020  1.525
 E6L  C31  C30  single    1.529  0.020  1.529
 E6L  C29  C30  single    1.526  0.020  1.526
 E6L  C1   H1   single    0.970  0.020  1.090
 E6L  C1   H2   single    0.970  0.020  1.090
 E6L  C1   H3   single    0.970  0.020  1.090
 E6L  C5   H4   single    0.930  0.020  1.080
 E6L  C7   H5   single    0.930  0.020  1.080
 E6L  C8   H6   single    0.930  0.020  1.080
 E6L  C9   H7   single    0.970  0.020  1.090
 E6L  C9   H8   single    0.970  0.020  1.090
 E6L  C15  H9   single    0.930  0.020  1.080
 E6L  C20  H10  single    0.970  0.020  1.090
 E6L  C20  H11  single    0.970  0.020  1.090
 E6L  C23  H12  single    0.930  0.020  1.080
 E6L  C24  H13  single    0.930  0.020  1.080
 E6L  C25  H14  single    0.930  0.020  1.080
 E6L  C28  H15  single    0.970  0.020  1.090
 E6L  C28  H16  single    0.970  0.020  1.090
 E6L  C29  H17  single    0.970  0.020  1.090
 E6L  C29  H18  single    0.970  0.020  1.090
 E6L  C30  H19  single    0.970  0.020  1.090
 E6L  C30  H20  single    0.970  0.020  1.090
 E6L  C31  H21  single    0.970  0.020  1.090
 E6L  C32  H22  single    0.970  0.020  1.090
 E6L  C32  H23  single    0.970  0.020  1.090
 E6L  N10  H24  single    0.860  0.020  1.020
 E6L  N19  H25  single    0.860  0.020  1.020
 E6L  O33  H26  single    0.850  0.020  0.980

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
 E6L  N12  C11  N10  117.23  3.000
 E6L  N12  C11  C16  120.85  3.000
 E6L  N10  C11  C16  121.93  3.000
 E6L  H3   C1   H2   109.01  3.000
 E6L  H3   C1   H1   108.79  3.000
 E6L  H2   C1   H1   108.91  3.000
 E6L  H3   C1   O2   111.90  3.000
 E6L  H2   C1   O2   111.83  3.000
 E6L  H1   C1   O2   106.31  3.000
 E6L  O2   C3   C8   125.13  3.000
 E6L  C8   C3   C4   117.68  3.000
 E6L  O2   C3   C4   117.18  3.000
 E6L  CL1  C4   C5   119.86  3.000
 E6L  C5   C4   C3   121.71  3.000
 E6L  CL1  C4   C3   118.43  3.000
 E6L  H4   C5   C6   120.08  3.000
 E6L  H4   C5   C4   119.51  3.000
 E6L  C6   C5   C4   120.40  3.000
 E6L  C9   C6   C7   121.16  3.000
 E6L  C9   C6   C5   120.61  3.000
 E6L  C7   C6   C5   118.21  3.000
 E6L  H5   C7   C8   118.36  3.000
 E6L  H5   C7   C6   120.11  3.000
 E6L  C8   C7   C6   121.52  3.000
 E6L  H6   C8   C7   118.85  3.000
 E6L  H6   C8   C3   120.67  3.000
 E6L  C7   C8   C3   120.48  3.000
 E6L  H8   C9   H7   106.94  3.000
 E6L  H8   C9   N10  106.74  3.000
 E6L  H7   C9   N10  110.19  3.000
 E6L  H8   C9   C6   109.53  3.000
 E6L  H7   C9   C6   109.74  3.000
 E6L  N10  C9   C6   113.45  3.000
 E6L  N27  C13  N14  116.70  3.000
 E6L  N27  C13  N12  117.72  3.000
 E6L  N14  C13  N12  125.58  3.000
 E6L  H9   C15  N14  114.27  3.000
 E6L  H9   C15  C16  120.35  3.000
 E6L  N14  C15  C16  125.38  3.000
 E6L  C17  C16  C15  123.49  3.000
 E6L  C15  C16  C11  114.27  3.000
 E6L  C17  C16  C11  122.24  3.000
 E6L  O18  C17  N19  119.54  3.000
 E6L  O18  C17  C16  122.17  3.000
 E6L  N19  C17  C16  118.29  3.000
 E6L  H11  C20  H10  106.74  3.000
 E6L  H11  C20  N19  107.36  3.000
 E6L  H10  C20  N19  111.53  3.000
 E6L  H11  C20  C21  108.50  3.000
 E6L  H10  C20  C21  108.55  3.000
 E6L  N19  C20  C21  113.88  3.000
 E6L  N26  C21  N22  125.64  3.000
 E6L  N22  C21  C20  118.21  3.000
 E6L  N26  C21  C20  116.11  3.000
 E6L  H12  C23  N22  116.82  3.000
 E6L  H12  C23  C24  120.88  3.000
 E6L  N22  C23  C24  122.30  3.000
 E6L  H13  C24  C25  121.97  3.000
 E6L  H13  C24  C23  121.99  3.000
 E6L  C25  C24  C23  116.04  3.000
 E6L  H14  C25  N26  116.85  3.000
 E6L  H14  C25  C24  121.00  3.000
 E6L  N26  C25  C24  122.14  3.000
 E6L  H16  C28  H15  107.41  3.000
 E6L  H16  C28  N27  111.40  3.000
 E6L  H15  C28  N27  110.57  3.000
 E6L  H16  C28  C29  112.76  3.000
 E6L  H15  C28  C29  111.39  3.000
 E6L  N27  C28  C29  103.34  3.000
 E6L  H18  C29  H17  107.37  3.000
 E6L  H18  C29  C30  110.56  3.000
 E6L  H17  C29  C30  113.09  3.000
 E6L  H18  C29  C28  110.43  3.000
 E6L  H17  C29  C28  111.98  3.000
 E6L  C30  C29  C28  103.44  3.000
 E6L  H20  C30  H19  107.65  3.000
 E6L  H20  C30  C31  109.80  3.000
 E6L  H19  C30  C31  112.44  3.000
 E6L  H20  C30  C29  110.18  3.000
 E6L  H19  C30  C29  113.37  3.000
 E6L  C31  C30  C29  103.37  3.000
 E6L  H21  C31  N27  109.86  3.000
 E6L  H21  C31  C32  108.26  3.000
 E6L  N27  C31  C32  110.94  3.000
 E6L  H21  C31  C30  112.09  3.000
 E6L  N27  C31  C30  102.49  3.000
 E6L  C32  C31  C30  113.11  3.000
 E6L  H23  C32  H22  107.50  3.000
 E6L  H23  C32  O33  111.66  3.000
 E6L  H22  C32  O33  111.59  3.000
 E6L  H23  C32  C31  109.72  3.000
 E6L  H22  C32  C31  108.79  3.000
 E6L  O33  C32  C31  107.55  3.000
 E6L  H24  N10  C9   120.27  3.000
 E6L  H24  N10  C11  116.11  3.000
 E6L  C9   N10  C11  123.30  3.000
 E6L  C13  N12  C11  118.55  3.000
 E6L  C15  N14  C13  115.33  3.000
 E6L  H25  N19  C20  117.89  3.000
 E6L  H25  N19  C17  121.54  3.000
 E6L  C20  N19  C17  120.56  3.000
 E6L  C23  N22  C21  116.88  3.000
 E6L  C25  N26  C21  116.99  3.000
 E6L  C31  N27  C28  113.15  3.000
 E6L  C31  N27  C13  123.44  3.000
 E6L  C28  N27  C13  122.71  3.000
 E6L  H26  O33  C32  108.49  3.000
 E6L  C3   O2   C1   118.44  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
 E6L  CONST_01  N14  C15  C16  C11     0.00   0.0  0
 E6L  CONST_02  N14  C13  N12  C11     0.00   0.0  0
 E6L  CONST_03  C6   C7   C8   C3      0.00   0.0  0
 E6L  CONST_04  C6   C5   C4   C3      0.00   0.0  0
 E6L  CONST_05  C7   C8   C3   C4      0.00   0.0  0
 E6L  CONST_06  C7   C6   C5   C4      0.00   0.0  0
 E6L  CONST_07  C8   C3   C4   C5      0.00   0.0  0
 E6L  CONST_08  C8   C7   C6   C5      0.00   0.0  0
 E6L  CONST_09  C16  C15  N14  C13     0.00   0.0  0
 E6L  CONST_10  C16  C11  N12  C13     0.00   0.0  0
 E6L  CONST_11  N12  C11  C16  C15     0.00   0.0  0
 E6L  CONST_12  N12  C13  N14  C15     0.00   0.0  0
 E6L  CONST_13  C24  C25  N26  C21     0.00   0.0  0
 E6L  CONST_14  C24  C23  N22  C21     0.00   0.0  0
 E6L  CONST_15  N26  C21  N22  C23     0.00   0.0  0
 E6L  CONST_16  N26  C25  C24  C23     0.00   0.0  0
 E6L  CONST_17  N22  C21  N26  C25     0.00   0.0  0
 E6L  CONST_18  N22  C23  C24  C25     0.00   0.0  0
 E6L  CONST_19  N27  C13  N12  C11   180.00   0.0  0
 E6L  CONST_20  N27  C13  N14  C15   180.00   0.0  0
 E6L  CONST_21  C9   C6   C5   C4    180.00   0.0  0
 E6L  CONST_22  O2   C3   C4   C5    180.00   0.0  0
 E6L  CONST_23  CL1  C4   C5   C6    180.00   0.0  0
 E6L  CONST_24  O2   C3   C8   C7    180.00   0.0  0
 E6L  CONST_25  CL1  C4   C3   C8    180.00   0.0  0
 E6L  CONST_26  C9   C6   C7   C8    180.00   0.0  0
 E6L  CONST_27  N10  C11  N12  C13   180.00   0.0  0
 E6L  CONST_28  N10  C11  C16  C15   180.00   0.0  0
 E6L  CONST_29  N14  C15  C16  C17   180.00   0.0  0
 E6L  CONST_30  N12  C11  C16  C17   180.00   0.0  0
 E6L  CONST_31  C25  N26  C21  C20   180.00   0.0  0
 E6L  CONST_32  C23  N22  C21  C20   180.00   0.0  0
 E6L  CONST_33  H9   C15  C16  C11   180.00   0.0  0
 E6L  CONST_34  H5   C7   C8   C3    180.00   0.0  0
 E6L  CONST_35  H4   C5   C4   C3    180.00   0.0  0
 E6L  CONST_36  H6   C8   C3   C4    180.00   0.0  0
 E6L  CONST_37  H14  C25  N26  C21   180.00   0.0  0
 E6L  CONST_38  H12  C23  N22  C21   180.00   0.0  0
 E6L  CONST_39  H13  C24  C23  N22   180.00   0.0  0
 E6L  CONST_40  C16  C11  N10  C9    180.00   0.0  0
 E6L  CONST_41  N12  C11  N10  C9      0.00   0.0  0
 E6L  CONST_42  H24  N10  C11  C16     0.00   0.0  0
 E6L  CONST_43  C20  N19  C17  C16   180.00   0.0  0
 E6L  CONST_44  H25  N19  C17  C16     0.00   0.0  0
 E6L  CONST_45  O18  C17  N19  C20     0.00   0.0  0
 E6L  Var_01    C29  C28  N27  C13  -179.39  30.0  1
 E6L  Var_02    N14  C13  N27  C28    -3.75  30.0  1
 E6L  Var_03    C31  C30  C29  C28   -37.97  30.0  1
 E6L  Var_04    N27  C28  C29  C30    28.61  30.0  1
 E6L  Var_05    C6   C9   N10  C11    76.27  30.0  2
 E6L  Var_06    N19  C17  C16  C11   170.68  30.0  2
 E6L  Var_07    C8   C3   O2   C1     -1.05  30.0  2
 E6L  Var_08    N10  C9   C6   C5   -136.11  30.0  2
 E6L  Var_09    N26  C21  C20  N19   150.92  30.0  2
 E6L  Var_10    C21  C20  N19  C17   -63.06  30.0  1
 E6L  Var_11    H1   C1   O2   C3   -179.47  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
 E6L  chir_01  C31  C32  N27  C30  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
 E6L  plan-1  C3   0.020
 E6L  plan-1  C4   0.020
 E6L  plan-1  C5   0.020
 E6L  plan-1  C6   0.020
 E6L  plan-1  C7   0.020
 E6L  plan-1  C8   0.020
 E6L  plan-1  C9   0.020
 E6L  plan-1  CL1  0.020
 E6L  plan-1  H4   0.020
 E6L  plan-1  H5   0.020
 E6L  plan-1  H6   0.020
 E6L  plan-1  O2   0.020
 E6L  plan-2  C11  0.020
 E6L  plan-2  C13  0.020
 E6L  plan-2  C15  0.020
 E6L  plan-2  C16  0.020
 E6L  plan-2  C17  0.020
 E6L  plan-2  N10  0.020
 E6L  plan-2  N12  0.020
 E6L  plan-2  N14  0.020
 E6L  plan-2  N27  0.020
 E6L  plan-2  H9   0.020
 E6L  plan-3  C20  0.020
 E6L  plan-3  C21  0.020
 E6L  plan-3  C23  0.020
 E6L  plan-3  C24  0.020
 E6L  plan-3  C25  0.020
 E6L  plan-3  N22  0.020
 E6L  plan-3  N26  0.020
 E6L  plan-3  H12  0.020
 E6L  plan-3  H13  0.020
 E6L  plan-3  H14  0.020
 E6L  plan-4  C11  0.020
 E6L  plan-4  C9   0.020
 E6L  plan-4  N10  0.020
 E6L  plan-4  H24  0.020
 E6L  plan-5  C16  0.020
 E6L  plan-5  C17  0.020
 E6L  plan-5  C20  0.020
 E6L  plan-5  N19  0.020
 E6L  plan-5  O18  0.020
 E6L  plan-5  H25  0.020

