# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 21 13:10:44 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: 4-{3-[2-amino-5-(2-methoxyethoxy)pyrimidin-4-yl]-1H-indol-5-yl}-2-methylbut-3-yn-2-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCCOc1cnc(N)nc1c2c[nH]c3ccc(cc23)C#CC(C)(C)O
#
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
 13V  13V  4-{3-[2-amino-5-(2-methoxyethoxy)pyrimidin-4-yl]-1H-indol-5-yl}-2-methylbut-3-yn-2-ol  ligand  49  27  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_13V
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
 13V  N3   N  NH2   0  -0.831  -0.1418   4.0126  -0.5438
 13V  C15  C  CR6   0   0.512   0.8882   3.1401  -0.3487
 13V  N2   N  N     0  -0.481   0.5958   1.8418  -0.3877
 13V  N4   N  N     0  -0.448   2.0899   3.6485  -0.1033
 13V  C16  C  CR16  0  -0.151   3.0589   2.7746   0.1546
 13V  C17  C  CR6   0   0.267   2.8579   1.4077   0.1599
 13V  O2   O  O2    0  -0.477   3.7949   0.4863   0.4533
 13V  C18  C  CH2   0  -0.217   5.1550   0.8732   0.4960
 13V  C19  C  CH2   0  -0.162   5.9759  -0.3642   0.7482
 13V  O3   O  O2    0  -0.480   5.8149  -1.2604  -0.3192
 13V  C20  C  CH3   0  -0.394   6.5066  -2.4673  -0.1207
 13V  C14  C  CR6   0   0.140   1.5588   0.9583  -0.1515
 13V  C11  C  CR5   0  -0.066   1.1951  -0.4465  -0.2265
 13V  C10  C  CR15  0  -0.041   2.0341  -1.5382  -0.3270
 13V  N1   N  NR15  0  -0.680   1.3040  -2.6727  -0.4195
 13V  C12  C  CR56  0   0.079  -0.1479  -0.9768  -0.2577
 13V  C9   C  CR56  0   0.355  -0.0273  -2.3777  -0.3719
 13V  C8   C  CR16  0  -0.292  -1.1277  -3.2300  -0.4089
 13V  C7   C  CR16  0  -0.316  -2.3777  -2.6598  -0.3224
 13V  C13  C  CR16  0  -0.414  -1.4262  -0.4219  -0.1697
 13V  C6   C  CR6   0  -0.139  -2.5346  -1.2619  -0.1968
 13V  C5   C  CSP   0   0.140  -3.8480  -0.7149  -0.0841
 13V  C4   C  CSP   0   0.124  -4.9624  -0.2702   0.0295
 13V  C1   C  CT    0  -0.002  -6.3229   0.2641   0.1664
 13V  C3   C  CH3   0  -0.668  -6.2968   1.7874   0.0177
 13V  C2   C  CH3   0  -0.670  -7.2289  -0.3638  -0.8962
 13V  O1   O  OH1   0  -0.669  -6.7499  -0.1052   1.4691
 13V  H1   H  HNH2  0   0.385  -0.9463   3.6517  -1.0287
 13V  H2   H  HNH2  0   0.384   0.1133   4.9517  -0.8000
 13V  H3   H  HCR6  0   0.281   4.0351   3.1979   0.3666
 13V  H4   H  HCH2  0   0.234   5.4491   1.3513  -0.4457
 13V  H5   H  HCH2  0   0.234   5.3409   1.5859   1.3067
 13V  H6   H  HCH2  0   0.218   7.0250  -0.0576   0.8609
 13V  H7   H  HCH2  0   0.212   5.6735  -0.8222   1.7005
 13V  H8   H  HCH3  0   0.207   7.5872  -2.3109  -0.0203
 13V  H9   H  HCH3  0   0.206   6.1584  -2.9975   0.7735
 13V  H10  H  HCH3  0   0.235   6.3301  -3.1024  -0.9878
 13V  H11  H  HCR5  0   0.297   3.1091  -1.5877  -0.3615
 13V  H12  H  HNR5  0   0.420   1.6945  -3.5968  -0.5088
 13V  H13  H  HCR6  0   0.270  -1.0074  -4.3019  -0.4971
 13V  H14  H  HCR6  0   0.256  -3.2565  -3.2899  -0.3463
 13V  H15  H  HCR6  0   0.258  -1.5553   0.6466  -0.0830
 13V  H16  H  HCH3  0   0.235  -5.9424   2.0795  -0.9704
 13V  H17  H  HCH3  0   0.238  -7.3035   2.1913   0.1456
 13V  H18  H  HCH3  0   0.243  -5.6459   2.2412   0.7650
 13V  H19  H  HCH3  0   0.242  -7.2354  -1.4504  -0.8112
 13V  H20  H  HCH3  0   0.238  -8.2529  -0.0026  -0.7766
 13V  H21  H  HCH3  0   0.236  -6.8979  -0.0991  -1.8999
 13V  H22  H  HOH1  0   0.451  -7.6525   0.2142   1.5839

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
 13V  C20  O3   single    1.405  0.020  1.405
 13V  O3   C19  single    1.403  0.020  1.403
 13V  C19  C18  single    1.506  0.020  1.506
 13V  C18  O2   single    1.415  0.020  1.415
 13V  N1   C10  aromatic  1.352  0.020  1.352
 13V  N1   C9   aromatic  1.364  0.020  1.364
 13V  C10  C11  aromatic  1.380  0.020  1.380
 13V  C8   C9   aromatic  1.392  0.020  1.392
 13V  C8   C7   aromatic  1.377  0.020  1.377
 13V  C9   C12  aromatic  1.411  0.020  1.411
 13V  O2   C17  single    1.346  0.020  1.346
 13V  C11  C12  aromatic  1.444  0.020  1.444
 13V  C11  C14  single    1.453  0.020  1.453
 13V  C7   C6   aromatic  1.412  0.020  1.412
 13V  C17  C14  aromatic  1.409  0.020  1.409
 13V  C17  C16  aromatic  1.382  0.020  1.382
 13V  C12  C13  aromatic  1.396  0.020  1.396
 13V  C14  N2   aromatic  1.328  0.020  1.328
 13V  C16  N4   aromatic  1.330  0.020  1.330
 13V  C6   C13  aromatic  1.391  0.020  1.391
 13V  C6   C5   single    1.427  0.020  1.427
 13V  N2   C15  aromatic  1.331  0.020  1.331
 13V  N4   C15  aromatic  1.328  0.020  1.328
 13V  C5   C4   triple    1.205  0.020  1.205
 13V  C15  N3   single    1.364  0.020  1.364
 13V  O1   C1   single    1.420  0.020  1.420
 13V  C2   C1   single    1.531  0.020  1.531
 13V  C4   C1   single    1.468  0.020  1.468
 13V  C1   C3   single    1.531  0.020  1.531
 13V  N3   H1   single    0.890  0.020  1.040
 13V  N3   H2   single    0.890  0.020  1.040
 13V  C16  H3   single    0.930  0.020  1.080
 13V  C18  H4   single    0.970  0.020  1.090
 13V  C18  H5   single    0.970  0.020  1.090
 13V  C19  H6   single    0.970  0.020  1.090
 13V  C19  H7   single    0.970  0.020  1.090
 13V  C20  H8   single    0.970  0.020  1.090
 13V  C20  H9   single    0.970  0.020  1.090
 13V  C20  H10  single    0.970  0.020  1.090
 13V  C10  H11  single    0.930  0.020  1.080
 13V  N1   H12  single    0.860  0.020  1.020
 13V  C8   H13  single    0.930  0.020  1.080
 13V  C7   H14  single    0.930  0.020  1.080
 13V  C13  H15  single    0.930  0.020  1.080
 13V  C3   H16  single    0.970  0.020  1.090
 13V  C3   H17  single    0.970  0.020  1.090
 13V  C3   H18  single    0.970  0.020  1.090
 13V  C2   H19  single    0.970  0.020  1.090
 13V  C2   H20  single    0.970  0.020  1.090
 13V  C2   H21  single    0.970  0.020  1.090
 13V  O1   H22  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
 13V  H2   N3   H1   114.50  3.000
 13V  H2   N3   C15  116.23  3.000
 13V  H1   N3   C15  116.31  3.000
 13V  N4   C15  N2   125.28  3.000
 13V  N4   C15  N3   117.71  3.000
 13V  N2   C15  N3   116.98  3.000
 13V  C14  N2   C15  118.96  3.000
 13V  C16  N4   C15  116.33  3.000
 13V  H3   C16  C17  121.08  3.000
 13V  H3   C16  N4   115.91  3.000
 13V  C17  C16  N4   123.01  3.000
 13V  C14  C17  O2   118.12  3.000
 13V  C14  C17  C16  116.66  3.000
 13V  O2   C17  C16  125.21  3.000
 13V  C18  O2   C17  119.24  3.000
 13V  H5   C18  H4   107.85  3.000
 13V  H5   C18  C19  108.55  3.000
 13V  H4   C18  C19  110.85  3.000
 13V  H5   C18  O2   111.31  3.000
 13V  H4   C18  O2   110.57  3.000
 13V  C19  C18  O2   107.72  3.000
 13V  H7   C19  H6   106.87  3.000
 13V  H7   C19  O3   111.19  3.000
 13V  H6   C19  O3   111.46  3.000
 13V  H7   C19  C18  109.73  3.000
 13V  H6   C19  C18  107.95  3.000
 13V  O3   C19  C18  109.56  3.000
 13V  C20  O3   C19  112.62  3.000
 13V  H10  C20  H9   108.42  3.000
 13V  H10  C20  H8   108.41  3.000
 13V  H9   C20  H8   107.90  3.000
 13V  H10  C20  O3   107.97  3.000
 13V  H9   C20  O3   111.98  3.000
 13V  H8   C20  O3   112.06  3.000
 13V  C11  C14  C17  123.39  3.000
 13V  C17  C14  N2   119.70  3.000
 13V  C11  C14  N2   116.90  3.000
 13V  C12  C11  C10  105.85  3.000
 13V  C12  C11  C14  126.08  3.000
 13V  C10  C11  C14  128.04  3.000
 13V  H11  C10  N1   119.89  3.000
 13V  H11  C10  C11  130.20  3.000
 13V  N1   C10  C11  109.90  3.000
 13V  H12  N1   C9   125.43  3.000
 13V  H12  N1   C10  124.51  3.000
 13V  C9   N1   C10  110.06  3.000
 13V  C13  C12  C9   118.56  3.000
 13V  C13  C12  C11  134.75  3.000
 13V  C9   C12  C11  106.67  3.000
 13V  C8   C9   C12  122.85  3.000
 13V  C12  C9   N1   107.51  3.000
 13V  C8   C9   N1   129.63  3.000
 13V  H13  C8   C7   121.09  3.000
 13V  H13  C8   C9   121.37  3.000
 13V  C7   C8   C9   117.54  3.000
 13V  H14  C7   C6   119.23  3.000
 13V  H14  C7   C8   119.67  3.000
 13V  C6   C7   C8   121.10  3.000
 13V  H15  C13  C6   120.26  3.000
 13V  H15  C13  C12  120.52  3.000
 13V  C6   C13  C12  119.23  3.000
 13V  C5   C6   C13  120.02  3.000
 13V  C5   C6   C7   119.25  3.000
 13V  C13  C6   C7   120.73  3.000
 13V  C4   C5   C6   180.00  3.000
 13V  C1   C4   C5   180.00  3.000
 13V  O1   C1   C2   110.62  3.000
 13V  C2   C1   C3   110.54  3.000
 13V  O1   C1   C3   110.68  3.000
 13V  C3   C1   C4   109.71  3.000
 13V  C2   C1   C4   109.54  3.000
 13V  O1   C1   C4   105.64  3.000
 13V  H18  C3   H17  108.43  3.000
 13V  H18  C3   H16  108.42  3.000
 13V  H17  C3   H16  107.87  3.000
 13V  H18  C3   C1   110.97  3.000
 13V  H17  C3   C1   109.93  3.000
 13V  H16  C3   C1   111.13  3.000
 13V  H21  C2   H20  107.78  3.000
 13V  H21  C2   H19  108.41  3.000
 13V  H20  C2   H19  108.39  3.000
 13V  H21  C2   C1   111.10  3.000
 13V  H20  C2   C1   110.07  3.000
 13V  H19  C2   C1   111.00  3.000
 13V  H22  O1   C1   107.74  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
 13V  CONST_01  C11  C14  N2   C15   180.00   0.0  0
 13V  CONST_02  C17  C14  N2   C15     0.00   0.0  0
 13V  CONST_03  C17  C16  N4   C15     0.00   0.0  0
 13V  CONST_05  C12  C11  C14  N2      0.00   0.0  0
 13V  CONST_06  C16  C17  C14  N2      0.00   0.0  0
 13V  CONST_07  C16  N4   C15  N2      0.00   0.0  0
 13V  CONST_08  C14  C17  C16  N4      0.00   0.0  0
 13V  CONST_09  C14  N2   C15  N4      0.00   0.0  0
 13V  CONST_10  C11  C14  C17  C16   180.00   0.0  0
 13V  CONST_12  C12  C11  C14  C17   180.00   0.0  0
 13V  CONST_13  N1   C10  C11  C14   180.00   0.0  0
 13V  CONST_14  C9   C12  C11  C14   180.00   0.0  0
 13V  CONST_15  C13  C12  C11  C14     0.00   0.0  0
 13V  CONST_16  C9   N1   C10  C11     0.00   0.0  0
 13V  CONST_17  N1   C9   C12  C11     0.00   0.0  0
 13V  CONST_18  C8   C9   C12  C11   180.00   0.0  0
 13V  CONST_19  C6   C13  C12  C11   180.00   0.0  0
 13V  CONST_20  C8   C9   N1   C10   180.00   0.0  0
 13V  CONST_21  C12  C9   N1   C10     0.00   0.0  0
 13V  CONST_22  C9   C12  C11  C10     0.00   0.0  0
 13V  CONST_23  C13  C12  C11  C10   180.00   0.0  0
 13V  CONST_24  C12  C11  C10  N1      0.00   0.0  0
 13V  CONST_25  C7   C8   C9   N1    180.00   0.0  0
 13V  CONST_26  C13  C12  C9   N1    180.00   0.0  0
 13V  CONST_27  C7   C8   C9   C12     0.00   0.0  0
 13V  CONST_28  C7   C6   C13  C12     0.00   0.0  0
 13V  CONST_29  C6   C7   C8   C9      0.00   0.0  0
 13V  CONST_30  C6   C13  C12  C9      0.00   0.0  0
 13V  CONST_31  C13  C12  C9   C8      0.00   0.0  0
 13V  CONST_32  C13  C6   C7   C8      0.00   0.0  0
 13V  CONST_33  C14  N2   C15  N3    180.00   0.0  0
 13V  CONST_34  C16  N4   C15  N3    180.00   0.0  0
 13V  CONST_35  O2   C17  C14  N2    180.00   0.0  0
 13V  CONST_36  O2   C17  C16  N4    180.00   0.0  0
 13V  CONST_37  C11  C14  C17  O2      0.00   0.0  0
 13V  CONST_38  C5   C6   C13  C12   180.00   0.0  0
 13V  CONST_39  C5   C6   C7   C8    180.00   0.0  0
 13V  CONST_40  H3   C16  N4   C15   180.00   0.0  0
 13V  CONST_41  H11  C10  C11  C14     0.00   0.0  0
 13V  CONST_42  H12  N1   C10  C11   180.00   0.0  0
 13V  CONST_43  H15  C13  C12  C11     0.00   0.0  0
 13V  CONST_44  H13  C8   C9   N1      0.00   0.0  0
 13V  CONST_45  H14  C7   C8   C9    180.00   0.0  0
 13V  Var_01    C14  C17  O2   C18   166.96  30.0  2
 13V  Var_02    C19  C18  O2   C17  -176.10  30.0  1
 13V  Var_03    O3   C19  C18  O2     62.83  30.0  2
 13V  Var_04    O1   C1   C4   C5     79.62  30.0  3
 13V  Var_05    H8   C20  O3   C19   -60.72  30.0  3
 13V  Var_06    H19  C2   C1   C4     57.72  30.0  3
 13V  Var_07    H16  C3   C1   C4     62.17  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
 13V  plan-1  N3   0.020
 13V  plan-1  C15  0.020
 13V  plan-1  N2   0.020
 13V  plan-1  N4   0.020
 13V  plan-1  C16  0.020
 13V  plan-1  C17  0.020
 13V  plan-1  O2   0.020
 13V  plan-1  C14  0.020
 13V  plan-1  C11  0.020
 13V  plan-1  H3   0.020
 13V  plan-2  C14  0.020
 13V  plan-2  C11  0.020
 13V  plan-2  C10  0.020
 13V  plan-2  N1   0.020
 13V  plan-2  C12  0.020
 13V  plan-2  C9   0.020
 13V  plan-2  C8   0.020
 13V  plan-2  C7   0.020
 13V  plan-2  C13  0.020
 13V  plan-2  C6   0.020
 13V  plan-2  C5   0.020
 13V  plan-2  C4   0.020
 13V  plan-2  H11  0.020
 13V  plan-2  H12  0.020
 13V  plan-2  H13  0.020
 13V  plan-2  H14  0.020
 13V  plan-2  H15  0.020
 13V  plan-3  N3   0.020
 13V  plan-3  C15  0.020
 13V  plan-3  H1   0.020
 13V  plan-3  H2   0.020

