# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 06:43:06 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: 5-{[(2S)-2-cyclopropyl-7,8-dimethoxy-2H-chromen-5-yl]methyl}pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(Cc2cnc(N)nc2N)c3C=C[C@@H](Oc3c1OC)C4CC4
#
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
 I2H  I2H  5-{[(2S)-2-cyclopropyl-7,8-dimethoxy-2H-chromen-5-yl]methyl}pyrimidine-2,4-diamine  ligand  48  26  .  2022-09-22  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_I2H
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
 I2H  N7   N  NH2   0  -0.832  -2.0343   1.4354   1.2057
 I2H  C6   C  CR6   0   0.466  -2.7297   0.5590   0.4528
 I2H  N5   N  N     0  -0.506  -3.6676  -0.1463   1.0792
 I2H  C3   C  CR6   0   0.529  -4.4055  -0.9835   0.3542
 I2H  N4   N  NH2   0  -0.823  -5.3822  -1.6623   1.0063
 I2H  N2   N  N     0  -0.484  -4.2937  -1.1890  -0.9578
 I2H  C1   C  CR16  0  -0.088  -3.3457  -0.4761  -1.5603
 I2H  C8   C  CR6   0  -0.044  -2.5087   0.4215  -0.9386
 I2H  C9   C  CH2   0  -0.620  -1.4737   1.1964  -1.7092
 I2H  C10  C  CR6   0   0.079  -0.0651   1.0709  -1.1744
 I2H  C21  C  CR16  0  -0.512   0.5996   2.2232  -0.7581
 I2H  C18  C  CR6   0   0.331   1.8738   2.1533  -0.2005
 I2H  O19  O  O2    0  -0.459   2.5810   3.2126   0.2212
 I2H  C20  C  CH3   0  -0.439   1.9972   4.4973   0.1198
 I2H  C11  C  CR6   0  -0.022   0.5537  -0.1713  -1.0492
 I2H  C12  C  CR6   0   0.293   1.8179  -0.2361  -0.4485
 I2H  O13  O  O2    0  -0.486   2.4574  -1.4105  -0.2914
 I2H  C15  C  CR6   0   0.157   2.4828   0.9052  -0.0213
 I2H  O16  O  O2    0  -0.480   3.6928   0.8140   0.5886
 I2H  C17  C  CH3   0  -0.409   4.8019   0.8561  -0.2997
 I2H  C27  C  C1    0  -0.207  -0.0055  -1.4276  -1.5273
 I2H  C28  C  C1    0  -0.273   0.5367  -2.5859  -1.1557
 I2H  C14  C  CH1   0  -0.041   1.6851  -2.6061  -0.1940
 I2H  C24  C  CH1   0  -0.249   1.2210  -2.8849   1.2219
 I2H  C26  C  CH2   0  -0.488   1.9394  -2.3528   2.4217
 I2H  C25  C  CH2   0  -0.488   0.5569  -1.8642   2.0892
 I2H  H1   H  HNH2  0   0.411  -1.1583   1.8055   0.8783
 I2H  H2   H  HNH2  0   0.390  -2.1376   1.3723   2.2050
 I2H  H3   H  HNH2  0   0.386  -5.3214  -1.7188   2.0084
 I2H  H4   H  HNH2  0   0.387  -5.7698  -2.4675   0.5453
 I2H  H5   H  HCR6  0   0.253  -3.2410  -0.6360  -2.6309
 I2H  H6   H  HCH2  0   0.272  -1.5064   0.8639  -2.7514
 I2H  H7   H  HCH2  0   0.275  -1.7369   2.2581  -1.7333
 I2H  H8   H  HCR6  0   0.287   0.1022   3.1771  -0.8792
 I2H  H9   H  HCH3  0   0.263   2.7294   5.1989   0.5112
 I2H  H10  H  HCH3  0   0.231   1.7732   4.7641  -0.9160
 I2H  H11  H  HCH3  0   0.230   1.0813   4.5755   0.7110
 I2H  H12  H  HCH3  0   0.222   4.8217   1.7822  -0.8794
 I2H  H13  H  HCH3  0   0.237   5.7035   0.8076   0.3085
 I2H  H14  H  HCH3  0   0.222   4.8004   0.0092  -0.9899
 I2H  H15  H  H     0   0.249  -0.8363  -1.4072  -2.2185
 I2H  H17  H  H     0   0.261   0.1574  -3.5350  -1.5120
 I2H  H19  H  HCH1  0   0.262   2.3828  -3.3993  -0.4745
 I2H  H20  H  HCH1  0   0.264   0.8343  -3.8956   1.3144
 I2H  H21  H  HCH2  0   0.251   2.0658  -3.0090   3.2735
 I2H  H22  H  HCH2  0   0.248   2.7607  -1.6660   2.2597
 I2H  H23  H  HCH2  0   0.247   0.4452  -0.8485   1.7321
 I2H  H24  H  HCH2  0   0.250  -0.2665  -2.1983   2.7080

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
 I2H  N7   C6   single    1.349  0.020  1.349
 I2H  C25  C26  single    1.503  0.020  1.503
 I2H  C25  C24  single    1.495  0.020  1.495
 I2H  N5   C6   aromatic  1.330  0.020  1.330
 I2H  N5   C3   aromatic  1.331  0.020  1.331
 I2H  C6   C8   aromatic  1.416  0.020  1.416
 I2H  C28  C27  double    1.332  0.020  1.332
 I2H  C28  C14  single    1.498  0.020  1.498
 I2H  C27  C11  single    1.456  0.020  1.456
 I2H  N4   C3   single    1.356  0.020  1.356
 I2H  C26  C24  single    1.496  0.020  1.496
 I2H  C3   N2   aromatic  1.333  0.020  1.333
 I2H  C8   C9   single    1.505  0.020  1.505
 I2H  C8   C1   aromatic  1.376  0.020  1.376
 I2H  C24  C14  single    1.516  0.020  1.516
 I2H  C9   C10  single    1.512  0.020  1.512
 I2H  C14  O13  single    1.427  0.020  1.427
 I2H  N2   C1   aromatic  1.330  0.020  1.330
 I2H  C11  C10  aromatic  1.393  0.020  1.393
 I2H  C11  C12  aromatic  1.401  0.020  1.401
 I2H  C10  C21  aromatic  1.394  0.020  1.394
 I2H  O13  C12  single    1.346  0.020  1.346
 I2H  C12  C15  aromatic  1.388  0.020  1.388
 I2H  C21  C18  aromatic  1.393  0.020  1.393
 I2H  C15  C18  aromatic  1.400  0.020  1.400
 I2H  C15  O16  single    1.358  0.020  1.358
 I2H  C18  O19  single    1.342  0.020  1.342
 I2H  C17  O16  single    1.422  0.020  1.422
 I2H  O19  C20  single    1.415  0.020  1.415
 I2H  N7   H1   single    0.890  0.020  1.040
 I2H  N7   H2   single    0.890  0.020  1.040
 I2H  N4   H3   single    0.890  0.020  1.040
 I2H  N4   H4   single    0.890  0.020  1.040
 I2H  C1   H5   single    0.930  0.020  1.080
 I2H  C9   H6   single    0.970  0.020  1.090
 I2H  C9   H7   single    0.970  0.020  1.090
 I2H  C21  H8   single    0.930  0.020  1.080
 I2H  C20  H9   single    0.970  0.020  1.090
 I2H  C20  H10  single    0.970  0.020  1.090
 I2H  C20  H11  single    0.970  0.020  1.090
 I2H  C17  H12  single    0.970  0.020  1.090
 I2H  C17  H13  single    0.970  0.020  1.090
 I2H  C17  H14  single    0.970  0.020  1.090
 I2H  C27  H15  single    0.930  0.020  1.080
 I2H  C28  H17  single    0.930  0.020  1.080
 I2H  C14  H19  single    0.970  0.020  1.090
 I2H  C24  H20  single    0.970  0.020  1.090
 I2H  C26  H21  single    0.970  0.020  1.090
 I2H  C26  H22  single    0.970  0.020  1.090
 I2H  C25  H23  single    0.970  0.020  1.090
 I2H  C25  H24  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
 I2H  H2   N7   H1   115.83  3.000
 I2H  H2   N7   C6   117.43  3.000
 I2H  H1   N7   C6   120.43  3.000
 I2H  C8   C6   N5   121.43  3.000
 I2H  C8   C6   N7   122.10  3.000
 I2H  N5   C6   N7   116.44  3.000
 I2H  C3   N5   C6   117.90  3.000
 I2H  N2   C3   N4   117.16  3.000
 I2H  N2   C3   N5   125.93  3.000
 I2H  N4   C3   N5   116.88  3.000
 I2H  H4   N4   H3   115.79  3.000
 I2H  H4   N4   C3   117.25  3.000
 I2H  H3   N4   C3   117.63  3.000
 I2H  C1   N2   C3   115.03  3.000
 I2H  H5   C1   C8   118.83  3.000
 I2H  H5   C1   N2   115.83  3.000
 I2H  C8   C1   N2   125.34  3.000
 I2H  C9   C8   C1   121.53  3.000
 I2H  C1   C8   C6   114.37  3.000
 I2H  C9   C8   C6   124.09  3.000
 I2H  H7   C9   H6   105.46  3.000
 I2H  H7   C9   C10  108.21  3.000
 I2H  H6   C9   C10  109.84  3.000
 I2H  H7   C9   C8   110.21  3.000
 I2H  H6   C9   C8   108.09  3.000
 I2H  C10  C9   C8   114.64  3.000
 I2H  C11  C10  C21  119.89  3.000
 I2H  C21  C10  C9   118.77  3.000
 I2H  C11  C10  C9   121.30  3.000
 I2H  H8   C21  C18  120.63  3.000
 I2H  H8   C21  C10  118.41  3.000
 I2H  C18  C21  C10  120.96  3.000
 I2H  C15  C18  O19  115.74  3.000
 I2H  O19  C18  C21  124.64  3.000
 I2H  C15  C18  C21  119.60  3.000
 I2H  C20  O19  C18  118.49  3.000
 I2H  H11  C20  H10  108.87  3.000
 I2H  H11  C20  H9   108.88  3.000
 I2H  H10  C20  H9   108.78  3.000
 I2H  H11  C20  O19  111.84  3.000
 I2H  H10  C20  O19  111.97  3.000
 I2H  H9   C20  O19  106.40  3.000
 I2H  C27  C11  C12  116.58  3.000
 I2H  C12  C11  C10  118.71  3.000
 I2H  C27  C11  C10  124.70  3.000
 I2H  C15  C12  O13  116.98  3.000
 I2H  C15  C12  C11  121.74  3.000
 I2H  O13  C12  C11  121.26  3.000
 I2H  C14  O13  C12  118.81  3.000
 I2H  O16  C15  C12  120.64  3.000
 I2H  O16  C15  C18  120.32  3.000
 I2H  C12  C15  C18  119.02  3.000
 I2H  C17  O16  C15  114.36  3.000
 I2H  H14  C17  H13  108.63  3.000
 I2H  H14  C17  H12  108.77  3.000
 I2H  H13  C17  H12  108.61  3.000
 I2H  H14  C17  O16  111.76  3.000
 I2H  H13  C17  O16  107.20  3.000
 I2H  H12  C17  O16  111.76  3.000
 I2H  H15  C27  C28  120.52  3.000
 I2H  H15  C27  C11  119.27  3.000
 I2H  C28  C27  C11  120.17  3.000
 I2H  H17  C28  C14  117.92  3.000
 I2H  H17  C28  C27  121.87  3.000
 I2H  C14  C28  C27  120.20  3.000
 I2H  H19  C14  C24  107.56  3.000
 I2H  H19  C14  C28  109.53  3.000
 I2H  C24  C14  C28  111.56  3.000
 I2H  H19  C14  O13  104.19  3.000
 I2H  C24  C14  O13  112.56  3.000
 I2H  C28  C14  O13  111.09  3.000
 I2H  H20  C24  C25  115.33  3.000
 I2H  H20  C24  C26  115.70  3.000
 I2H  C25  C24  C26   60.35  3.000
 I2H  H20  C24  C14  111.08  3.000
 I2H  C26  C24  C14  122.45  3.000
 I2H  C25  C24  C14  123.53  3.000
 I2H  H22  C26  H21  114.43  3.000
 I2H  H22  C26  C25  117.27  3.000
 I2H  H21  C26  C25  118.57  3.000
 I2H  H22  C26  C24  118.02  3.000
 I2H  H21  C26  C24  118.13  3.000
 I2H  C25  C26  C24   59.79  3.000
 I2H  H24  C25  H23  113.55  3.000
 I2H  H24  C25  C26  118.20  3.000
 I2H  H23  C25  C26  118.22  3.000
 I2H  H24  C25  C24  117.30  3.000
 I2H  H23  C25  C24  119.68  3.000
 I2H  C26  C25  C24   59.86  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
 I2H  CONST_01  N2   C3   N5   C6      0.00   0.0  0
 I2H  CONST_02  N2   C1   C8   C6      0.00   0.0  0
 I2H  CONST_03  C1   C8   C6   N5      0.00   0.0  0
 I2H  CONST_04  C1   N2   C3   N5      0.00   0.0  0
 I2H  CONST_05  C8   C6   N5   C3      0.00   0.0  0
 I2H  CONST_06  C8   C1   N2   C3      0.00   0.0  0
 I2H  CONST_07  C15  C12  C11  C10     0.00   0.0  0
 I2H  CONST_08  C15  C18  C21  C10     0.00   0.0  0
 I2H  CONST_09  C12  C11  C10  C21     0.00   0.0  0
 I2H  CONST_10  C12  C15  C18  C21     0.00   0.0  0
 I2H  CONST_11  C11  C10  C21  C18     0.00   0.0  0
 I2H  CONST_12  C11  C12  C15  C18     0.00   0.0  0
 I2H  CONST_13  C3   N5   C6   N7    180.00   0.0  0
 I2H  CONST_14  C1   C8   C6   N7    180.00   0.0  0
 I2H  CONST_15  N4   C3   N5   C6    180.00   0.0  0
 I2H  CONST_16  C9   C8   C6   N5    180.00   0.0  0
 I2H  CONST_17  C1   N2   C3   N4    180.00   0.0  0
 I2H  CONST_18  C9   C8   C1   N2    180.00   0.0  0
 I2H  CONST_19  C27  C11  C10  C9      0.00   0.0  0
 I2H  CONST_20  C12  C11  C10  C9    180.00   0.0  0
 I2H  CONST_21  C18  C21  C10  C9    180.00   0.0  0
 I2H  CONST_22  O19  C18  C21  C10   180.00   0.0  0
 I2H  CONST_23  O16  C15  C18  C21   180.00   0.0  0
 I2H  CONST_24  C12  C15  C18  O19   180.00   0.0  0
 I2H  CONST_25  O16  C15  C12  C11   180.00   0.0  0
 I2H  CONST_26  O16  C15  C12  O13     0.00   0.0  0
 I2H  CONST_27  H5   C1   C8   C6    180.00   0.0  0
 I2H  CONST_28  H8   C21  C10  C11   180.00   0.0  0
 I2H  CONST_30  H2   N7   C6   N5      0.00   0.0  0
 I2H  Var_01    C28  C27  C11  C10  -167.94  30.0  1
 I2H  Var_02    C14  C28  C27  C11     2.83  30.0  1
 I2H  Var_03    C26  C25  C24  C14  -111.32  30.0  1
 I2H  Var_04    C10  C9   C8   C6     55.37  30.0  2
 I2H  Var_05    C11  C10  C9   C8     57.60  30.0  2
 I2H  Var_06    C15  C18  O19  C20  -177.38  30.0  3
 I2H  Var_07    H9   C20  O19  C18  -180.00  30.0  3
 I2H  Var_08    H12  C17  O16  C15    59.30  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
 I2H  chir_01  C14  C28  C24  O13  positiv
 I2H  chir_02  C24  C25  C26  C14  both

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
 I2H  plan-1  N7   0.020
 I2H  plan-1  C6   0.020
 I2H  plan-1  N5   0.020
 I2H  plan-1  C3   0.020
 I2H  plan-1  N4   0.020
 I2H  plan-1  N2   0.020
 I2H  plan-1  C1   0.020
 I2H  plan-1  C8   0.020
 I2H  plan-1  C9   0.020
 I2H  plan-1  H5   0.020
 I2H  plan-2  C9   0.020
 I2H  plan-2  C10  0.020
 I2H  plan-2  C21  0.020
 I2H  plan-2  C18  0.020
 I2H  plan-2  O19  0.020
 I2H  plan-2  C11  0.020
 I2H  plan-2  C12  0.020
 I2H  plan-2  O13  0.020
 I2H  plan-2  C15  0.020
 I2H  plan-2  O16  0.020
 I2H  plan-2  C27  0.020
 I2H  plan-2  H8   0.020
 I2H  plan-3  N7   0.020
 I2H  plan-3  C6   0.020
 I2H  plan-3  H1   0.020
 I2H  plan-3  H2   0.020
 I2H  plan-4  C3   0.020
 I2H  plan-4  N4   0.020
 I2H  plan-4  H3   0.020
 I2H  plan-4  H4   0.020

