# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 16 16:30:11 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: 3-(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1nc(N)nc(N)c1OCCCOc2ccccc2CCC(O)=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
 MMV  MMV  '3-(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)propanoic acid'  ligand  50  26  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MMV
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
 MMV  C1   C  CR6   0   0.435  -4.0463  -0.7478  -1.2961
 MMV  N2   N  N     0  -0.501  -5.3239  -0.5719  -1.6101
 MMV  C3   C  CR6   0   0.510  -6.1220  -0.0926  -0.6552
 MMV  N4   N  N     0  -0.497  -5.7681   0.2066   0.5902
 MMV  C5   C  CR6   0   0.212  -4.4805   0.0337   0.9108
 MMV  C6   C  CR6   0   0.127  -3.5662  -0.4367  -0.0063
 MMV  N7   N  NH2   0  -0.822  -3.2147  -1.2137  -2.2514
 MMV  N8   N  NH2   0  -0.825  -7.4139   0.1402  -1.0049
 MMV  C9   C  CH2   0  -0.497  -4.1049   0.3116   2.3366
 MMV  C10  C  CH3   0  -0.661  -4.4168  -0.8904   3.2284
 MMV  O11  O  O2    0  -0.499  -2.2486  -0.6421   0.2948
 MMV  C12  C  CH2   0  -0.157  -1.4096   0.4769   0.0176
 MMV  C13  C  CH2   0  -0.500   0.0241   0.0689   0.2848
 MMV  C14  C  CH2   0  -0.176   0.9664   1.2325   0.0499
 MMV  O15  O  O2    0  -0.470   2.2842   0.7635   0.2647
 MMV  C16  C  CR6   0   0.356   3.3242   1.6035   0.0879
 MMV  C17  C  CR6   0   0.024   4.5992   1.0396   0.2562
 MMV  C18  C  CR16  0  -0.300   5.7061   1.8595   0.0890
 MMV  C19  C  CR16  0  -0.270   5.5802   3.2053  -0.2390
 MMV  C20  C  CR16  0  -0.257   4.3155   3.7427  -0.4031
 MMV  C21  C  CR16  0  -0.377   3.1856   2.9487  -0.2411
 MMV  C22  C  CH2   0  -0.500   4.7638  -0.4217   0.5726
 MMV  C23  C  CH2   0  -0.578   4.5225  -1.2903  -0.6588
 MMV  C24  C  C     0   0.552   4.6806  -2.7610  -0.3921
 MMV  O25  O  OH1   0  -0.597   4.4498  -3.4862  -1.4830
 MMV  O26  O  O     0  -0.445   4.9786  -3.2490   0.6695
 MMV  H1   H  HNH2  0   0.398  -2.3351  -1.6174  -1.9773
 MMV  H2   H  HNH2  0   0.392  -3.6339  -1.6056  -3.0780
 MMV  H3   H  HNH2  0   0.385  -8.0781   0.2507  -0.2581
 MMV  H4   H  HNH2  0   0.386  -7.7605  -0.3232  -1.8273
 MMV  H5   H  HCH2  0   0.245  -3.0485   0.5643   2.4253
 MMV  H6   H  HCH2  0   0.245  -4.6729   1.1780   2.6796
 MMV  H7   H  HCH3  0   0.228  -5.4743  -1.1501   3.1801
 MMV  H8   H  HCH3  0   0.228  -3.8407  -1.7651   2.9247
 MMV  H9   H  HCH3  0   0.236  -4.1709  -0.6718   4.2675
 MMV  H10  H  HCH2  0   0.225  -1.5307   0.7966  -1.0240
 MMV  H11  H  HCH2  0   0.222  -1.6948   1.3242   0.6522
 MMV  H12  H  HCH2  0   0.246   0.1204  -0.2775   1.3169
 MMV  H13  H  HCH2  0   0.244   0.2986  -0.7605  -0.3724
 MMV  H14  H  HCH2  0   0.225   0.8578   1.6132  -0.9725
 MMV  H15  H  HCH2  0   0.226   0.7338   2.0559   0.7348
 MMV  H16  H  HCR6  0   0.248   6.6933   1.4317   0.2206
 MMV  H17  H  HCR6  0   0.250   6.4611   3.8208  -0.3635
 MMV  H18  H  HCR6  0   0.256   4.1931   4.7876  -0.6577
 MMV  H19  H  HCR6  0   0.277   2.2093   3.3946  -0.3756
 MMV  H20  H  HCH2  0   0.253   5.7770  -0.5892   0.9413
 MMV  H21  H  HCH2  0   0.251   4.0866  -0.7218   1.3745
 MMV  H22  H  HCH2  0   0.286   3.5200  -1.1232  -1.0603
 MMV  H23  H  HCH2  0   0.285   5.2128  -1.0123  -1.4610
 MMV  H24  H  HOH1  0   0.478   4.5562  -4.4278  -1.2820

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
 MMV  N8   C3   single    1.359  0.020  1.359
 MMV  C3   N4   aromatic  1.329  0.020  1.329
 MMV  C3   N2   aromatic  1.334  0.020  1.334
 MMV  N4   C5   aromatic  1.338  0.020  1.338
 MMV  N2   C1   aromatic  1.327  0.020  1.327
 MMV  C10  C9   single    1.529  0.020  1.529
 MMV  C5   C9   single    1.500  0.020  1.500
 MMV  C5   C6   aromatic  1.378  0.020  1.378
 MMV  O26  C24  double    1.206  0.020  1.206
 MMV  O25  C24  single    1.330  0.020  1.330
 MMV  C1   C6   aromatic  1.411  0.020  1.411
 MMV  C1   N7   single    1.349  0.020  1.349
 MMV  C24  C23  single    1.503  0.020  1.503
 MMV  C6   O11  single    1.367  0.020  1.367
 MMV  C23  C22  single    1.526  0.020  1.526
 MMV  O11  C12  single    1.426  0.020  1.426
 MMV  C12  C13  single    1.514  0.020  1.514
 MMV  C22  C17  single    1.504  0.020  1.504
 MMV  C17  C18  aromatic  1.388  0.020  1.388
 MMV  C17  C16  aromatic  1.404  0.020  1.404
 MMV  C18  C19  aromatic  1.391  0.020  1.391
 MMV  O15  C16  single    1.349  0.020  1.349
 MMV  O15  C14  single    1.415  0.020  1.415
 MMV  C13  C14  single    1.516  0.020  1.516
 MMV  C16  C21  aromatic  1.392  0.020  1.392
 MMV  C19  C20  aromatic  1.384  0.020  1.384
 MMV  C21  C20  aromatic  1.390  0.020  1.390
 MMV  N7   H1   single    0.890  0.020  1.040
 MMV  N7   H2   single    0.890  0.020  1.040
 MMV  N8   H3   single    0.890  0.020  1.040
 MMV  N8   H4   single    0.890  0.020  1.040
 MMV  C9   H5   single    0.970  0.020  1.090
 MMV  C9   H6   single    0.970  0.020  1.090
 MMV  C10  H7   single    0.970  0.020  1.090
 MMV  C10  H8   single    0.970  0.020  1.090
 MMV  C10  H9   single    0.970  0.020  1.090
 MMV  C12  H10  single    0.970  0.020  1.090
 MMV  C12  H11  single    0.970  0.020  1.090
 MMV  C13  H12  single    0.970  0.020  1.090
 MMV  C13  H13  single    0.970  0.020  1.090
 MMV  C14  H14  single    0.970  0.020  1.090
 MMV  C14  H15  single    0.970  0.020  1.090
 MMV  C18  H16  single    0.930  0.020  1.080
 MMV  C19  H17  single    0.930  0.020  1.080
 MMV  C20  H18  single    0.930  0.020  1.080
 MMV  C21  H19  single    0.930  0.020  1.080
 MMV  C22  H20  single    0.970  0.020  1.090
 MMV  C22  H21  single    0.970  0.020  1.090
 MMV  C23  H22  single    0.970  0.020  1.090
 MMV  C23  H23  single    0.970  0.020  1.090
 MMV  O25  H24  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
 MMV  N7   C1   C6   120.90  3.000
 MMV  N7   C1   N2   118.13  3.000
 MMV  C6   C1   N2   120.97  3.000
 MMV  C3   N2   C1   117.02  3.000
 MMV  N8   C3   N4   117.13  3.000
 MMV  N4   C3   N2   126.34  3.000
 MMV  N8   C3   N2   116.51  3.000
 MMV  C5   N4   C3   116.86  3.000
 MMV  C9   C5   C6   121.98  3.000
 MMV  C6   C5   N4   121.54  3.000
 MMV  C9   C5   N4   116.40  3.000
 MMV  O11  C6   C5   122.97  3.000
 MMV  O11  C6   C1   119.75  3.000
 MMV  C5   C6   C1   117.26  3.000
 MMV  H2   N7   H1   115.58  3.000
 MMV  H2   N7   C1   117.34  3.000
 MMV  H1   N7   C1   118.98  3.000
 MMV  H4   N8   H3   115.49  3.000
 MMV  H4   N8   C3   117.34  3.000
 MMV  H3   N8   C3   117.12  3.000
 MMV  H6   C9   H5   107.15  3.000
 MMV  H6   C9   C10  109.55  3.000
 MMV  H5   C9   C10  109.43  3.000
 MMV  H6   C9   C5   108.38  3.000
 MMV  H5   C9   C5   111.28  3.000
 MMV  C10  C9   C5   110.95  3.000
 MMV  H9   C10  H8   107.89  3.000
 MMV  H9   C10  H7   107.99  3.000
 MMV  H8   C10  H7   108.00  3.000
 MMV  H9   C10  C9   110.64  3.000
 MMV  H8   C10  C9   111.13  3.000
 MMV  H7   C10  C9   111.06  3.000
 MMV  C12  O11  C6   113.98  3.000
 MMV  H11  C12  H10  107.21  3.000
 MMV  H11  C12  C13  110.63  3.000
 MMV  H10  C12  C13  110.54  3.000
 MMV  H11  C12  O11  109.93  3.000
 MMV  H10  C12  O11  110.40  3.000
 MMV  C13  C12  O11  108.14  3.000
 MMV  H13  C13  H12  107.76  3.000
 MMV  H13  C13  C14  109.46  3.000
 MMV  H12  C13  C14  109.57  3.000
 MMV  H13  C13  C12  109.64  3.000
 MMV  H12  C13  C12  109.60  3.000
 MMV  C14  C13  C12  110.76  3.000
 MMV  H15  C14  H14  107.51  3.000
 MMV  H15  C14  O15  110.59  3.000
 MMV  H14  C14  O15  110.42  3.000
 MMV  H15  C14  C13  110.36  3.000
 MMV  H14  C14  C13  110.46  3.000
 MMV  O15  C14  C13  107.52  3.000
 MMV  C16  O15  C14  119.46  3.000
 MMV  C21  C16  C17  120.45  3.000
 MMV  C21  C16  O15  123.80  3.000
 MMV  C17  C16  O15  115.75  3.000
 MMV  C22  C17  C18  120.80  3.000
 MMV  C18  C17  C16  118.20  3.000
 MMV  C22  C17  C16  120.98  3.000
 MMV  H16  C18  C19  119.53  3.000
 MMV  H16  C18  C17  118.60  3.000
 MMV  C19  C18  C17  121.87  3.000
 MMV  H17  C19  C20  120.63  3.000
 MMV  H17  C19  C18  120.26  3.000
 MMV  C20  C19  C18  119.10  3.000
 MMV  H18  C20  C21  119.13  3.000
 MMV  H18  C20  C19  120.40  3.000
 MMV  C21  C20  C19  120.47  3.000
 MMV  H19  C21  C20  118.92  3.000
 MMV  H19  C21  C16  121.17  3.000
 MMV  C20  C21  C16  119.91  3.000
 MMV  H21  C22  H20  106.60  3.000
 MMV  H21  C22  C23  109.77  3.000
 MMV  H20  C22  C23  109.39  3.000
 MMV  H21  C22  C17  110.71  3.000
 MMV  H20  C22  C17  108.78  3.000
 MMV  C23  C22  C17  111.46  3.000
 MMV  H23  C23  H22  105.70  3.000
 MMV  H23  C23  C24  108.20  3.000
 MMV  H22  C23  C24  108.14  3.000
 MMV  H23  C23  C22  110.32  3.000
 MMV  H22  C23  C22  110.76  3.000
 MMV  C24  C23  C22  113.40  3.000
 MMV  O26  C24  O25  122.98  3.000
 MMV  O25  C24  C23  111.69  3.000
 MMV  O26  C24  C23  125.32  3.000
 MMV  H24  O25  C24  109.92  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
 MMV  CONST_01  N4   C3   N2   C1      0.00   0.0  0
 MMV  CONST_02  N4   C5   C6   C1      0.00   0.0  0
 MMV  CONST_03  C5   N4   C3   N2      0.00   0.0  0
 MMV  CONST_04  C5   C6   C1   N2      0.00   0.0  0
 MMV  CONST_05  C6   C5   N4   C3      0.00   0.0  0
 MMV  CONST_06  C6   C1   N2   C3      0.00   0.0  0
 MMV  CONST_07  C19  C18  C17  C16     0.00   0.0  0
 MMV  CONST_08  C19  C20  C21  C16     0.00   0.0  0
 MMV  CONST_09  C20  C19  C18  C17     0.00   0.0  0
 MMV  CONST_10  C20  C21  C16  C17     0.00   0.0  0
 MMV  CONST_11  C21  C16  C17  C18     0.00   0.0  0
 MMV  CONST_12  C21  C20  C19  C18     0.00   0.0  0
 MMV  CONST_13  N8   C3   N2   C1    180.00   0.0  0
 MMV  CONST_14  C9   C5   C6   C1    180.00   0.0  0
 MMV  CONST_15  O11  C6   C1   N2    180.00   0.0  0
 MMV  CONST_16  C9   C5   N4   C3    180.00   0.0  0
 MMV  CONST_17  N7   C1   N2   C3    180.00   0.0  0
 MMV  CONST_18  O11  C6   C5   N4    180.00   0.0  0
 MMV  CONST_19  N8   C3   N4   C5    180.00   0.0  0
 MMV  CONST_20  N7   C1   C6   C5    180.00   0.0  0
 MMV  CONST_21  C18  C17  C16  O15   180.00   0.0  0
 MMV  CONST_22  C20  C21  C16  O15   180.00   0.0  0
 MMV  CONST_23  C22  C17  C18  C19   180.00   0.0  0
 MMV  CONST_24  C22  C17  C16  C21   180.00   0.0  0
 MMV  CONST_25  H16  C18  C17  C16   180.00   0.0  0
 MMV  CONST_26  H18  C20  C21  C16   180.00   0.0  0
 MMV  CONST_27  H17  C19  C18  C17   180.00   0.0  0
 MMV  CONST_28  H19  C21  C16  C17   180.00   0.0  0
 MMV  CONST_32  H2   N7   C1   N2      0.00   0.0  0
 MMV  CONST_33  H24  O25  C24  C23   180.00   0.0  0
 MMV  Var_01    C10  C9   C5   N4     82.17  30.0  2
 MMV  Var_02    C17  C16  O15  C14  -176.91  30.0  2
 MMV  Var_03    C23  C22  C17  C16    75.48  30.0  2
 MMV  Var_04    C13  C12  O11  C6   -175.22  30.0  3
 MMV  Var_05    C24  C23  C22  C17   179.81  30.0  1
 MMV  Var_06    H7   C10  C9   C5    -58.33  30.0  3
 MMV  Var_07    H14  C14  O15  C16    57.88  30.0  3
 MMV  Var_08    C14  C13  C12  O11  -178.21  30.0  3
 MMV  Var_09    O15  C14  C13  C12  -177.66  30.0  3
 MMV  Var_10    O26  C24  C23  C22    -0.63  30.0  2

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
 MMV  plan-1  C1   0.020
 MMV  plan-1  N2   0.020
 MMV  plan-1  C3   0.020
 MMV  plan-1  N4   0.020
 MMV  plan-1  C5   0.020
 MMV  plan-1  C6   0.020
 MMV  plan-1  N7   0.020
 MMV  plan-1  N8   0.020
 MMV  plan-1  C9   0.020
 MMV  plan-1  O11  0.020
 MMV  plan-2  O15  0.020
 MMV  plan-2  C16  0.020
 MMV  plan-2  C17  0.020
 MMV  plan-2  C18  0.020
 MMV  plan-2  C19  0.020
 MMV  plan-2  C20  0.020
 MMV  plan-2  C21  0.020
 MMV  plan-2  C22  0.020
 MMV  plan-2  H16  0.020
 MMV  plan-2  H17  0.020
 MMV  plan-2  H18  0.020
 MMV  plan-2  H19  0.020
 MMV  plan-3  C1   0.020
 MMV  plan-3  N7   0.020
 MMV  plan-3  H1   0.020
 MMV  plan-3  H2   0.020
 MMV  plan-4  C3   0.020
 MMV  plan-4  N8   0.020
 MMV  plan-4  H3   0.020
 MMV  plan-4  H4   0.020
 MMV  plan-5  C23  0.020
 MMV  plan-5  C24  0.020
 MMV  plan-5  O25  0.020
 MMV  plan-5  O26  0.020
 MMV  plan-5  H24  0.020

