# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 11:58:27 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: 3-(2-chlorophenyl)-7-[(trans-4-hydroxycyclohexyl)amino]-3,4-dihydropyrimido[4,5-d]pyrimidin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1CC[C@H](CC1)Nc2ncc3CN(C(=O)Nc3n2)c4ccccc4Cl
#
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
 RO6  RO6  3-(2-chlorophenyl)-7-[(trans-4-hydroxycyclohexyl)amino]-3,4-dihydropyrimido[4,5-d]pyrimidin-2(1H)-one  ligand  46  26  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RO6
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
 RO6  C1    C   CR6   0   0.611  -2.0027  -0.4371   0.1989
 RO6  N11   N   N     0  -0.502  -1.0192  -1.0102   0.9109
 RO6  C12   C   CR66  0   0.529   0.2066  -0.6315   0.6228
 RO6  N15   N   NR16  0  -0.740   1.2363  -1.2136   1.3159
 RO6  C16   C   CR6   0   0.678   2.5550  -1.1716   0.9160
 RO6  O19   O   O     0  -0.487   3.3907  -1.8879   1.4325
 RO6  N17   N   NR6   0  -0.602   2.8380  -0.3109  -0.1004
 RO6  C20   C   CR6   0   0.397   4.1912  -0.1914  -0.4958
 RO6  C21   C   CR16  0  -0.277   4.6264  -0.8030  -1.6628
 RO6  C22   C   CR16  0  -0.251   5.9387  -0.6600  -2.0882
 RO6  C23   C   CR16  0  -0.256   6.8273   0.0991  -1.3402
 RO6  C24   C   CR16  0  -0.226   6.4083   0.7189  -0.1716
 RO6  C25   C   CR6   0  -0.075   5.0939   0.5710   0.2412
 RO6  CL26  CL  CL    0  -0.108   4.5651   1.3416   1.6952
 RO6  C18   C   C     0  -0.294   1.9291   0.7410  -0.5521
 RO6  C14   C   CR66  0  -0.152   0.5132   0.3155  -0.3539
 RO6  N10   N   N     0  -0.482  -1.8291   0.4624  -0.7735
 RO6  C13   C   CR16  0  -0.043  -0.5762   0.8158  -1.0312
 RO6  N2    N   NH1   0  -0.668  -3.2519  -0.8349   0.4894
 RO6  C3    C   CH1   0  -0.039  -4.4542  -0.3106  -0.1211
 RO6  C4    C   CH2   0  -0.443  -4.9063   1.0027   0.5190
 RO6  C5    C   CH2   0  -0.466  -6.1981   1.5128  -0.1108
 RO6  C6    C   CH1   0   0.085  -7.2990   0.4686  -0.0183
 RO6  O9    O   OH1   0  -0.679  -8.4584   0.9958  -0.6312
 RO6  C7    C   CH2   0  -0.480  -6.8505  -0.8375  -0.6665
 RO6  C8    C   CH2   0  -0.459  -5.5607  -1.3573  -0.0422
 RO6  HN15  H   HNR6  0   0.414   1.0029  -1.9126   2.0070
 RO6  H21   H   HCR6  0   0.273   3.9238  -1.3961  -2.2336
 RO6  H22   H   HCR6  0   0.269   6.2658  -1.1429  -2.9988
 RO6  H23   H   HCR6  0   0.273   7.8534   0.2142  -1.6626
 RO6  H24   H   HCR6  0   0.286   7.0972   1.3134   0.4124
 RO6  H18   H   H     0   0.261   2.1444   1.6716  -0.0145
 RO6  H18A  H   H     0   0.277   2.1260   0.9299  -1.6079
 RO6  H13   H   HCR6  0   0.267  -0.4365   1.5480  -1.8210
 RO6  HN2   H   HNH1  0   0.388  -3.3485  -1.4689   1.2667
 RO6  H3    H   HCH1  0   0.236  -4.2355  -0.1218  -1.1759
 RO6  H4    H   HCH2  0   0.217  -5.0547   0.8409   1.5922
 RO6  H4A   H   HCH2  0   0.243  -4.1175   1.7511   0.4182
 RO6  H5    H   HCH2  0   0.240  -6.5131   2.4355   0.3825
 RO6  H5A   H   HCH2  0   0.219  -6.0235   1.7578  -1.1646
 RO6  H6    H   HCH1  0   0.186  -7.4894   0.2690   1.0483
 RO6  HO9   H   HOH1  0   0.446  -9.1668   0.3515  -0.5358
 RO6  H7    H   HCH2  0   0.239  -7.6360  -1.5927  -0.5702
 RO6  H7A   H   HCH2  0   0.221  -6.7008  -0.6704  -1.7387
 RO6  H8    H   HCH2  0   0.248  -5.2424  -2.2729  -0.5453
 RO6  H8A   H   HCH2  0   0.224  -5.7395  -1.6185   1.0074

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
 RO6  N10  C1    aromatic  1.336  0.020  1.336
 RO6  C1   N2    single    1.343  0.020  1.343
 RO6  C1   N11   aromatic  1.343  0.020  1.343
 RO6  C12  N11   aromatic  1.315  0.020  1.315
 RO6  C14  C12   aromatic  1.395  0.020  1.395
 RO6  C12  N15   single    1.371  0.020  1.371
 RO6  C16  N15   single    1.379  0.020  1.379
 RO6  N15  HN15  single    0.860  0.020  1.020
 RO6  N17  C16   single    1.362  0.020  1.362
 RO6  C16  O19   double    1.216  0.020  1.216
 RO6  C18  N17   single    1.462  0.020  1.462
 RO6  C20  N17   single    1.415  0.020  1.415
 RO6  C21  C20   aromatic  1.388  0.020  1.388
 RO6  C20  C25   aromatic  1.393  0.020  1.393
 RO6  C22  C21   aromatic  1.387  0.020  1.387
 RO6  C21  H21   single    0.930  0.020  1.080
 RO6  C22  C23   aromatic  1.388  0.020  1.388
 RO6  C22  H22   single    0.930  0.020  1.080
 RO6  C23  C24   aromatic  1.388  0.020  1.388
 RO6  C23  H23   single    0.930  0.020  1.080
 RO6  C24  C25   aromatic  1.386  0.020  1.386
 RO6  C24  H24   single    0.930  0.020  1.080
 RO6  C25  CL26  single    1.729  0.020  1.729
 RO6  C18  C14   single    1.492  0.020  1.492
 RO6  C18  H18   single    0.970  0.020  1.090
 RO6  C18  H18A  single    0.970  0.020  1.090
 RO6  C13  C14   aromatic  1.377  0.020  1.377
 RO6  C13  N10   aromatic  1.327  0.020  1.327
 RO6  C13  H13   single    0.930  0.020  1.080
 RO6  N2   C3    single    1.447  0.020  1.447
 RO6  N2   HN2   single    0.860  0.020  1.020
 RO6  C4   C3    single    1.529  0.020  1.529
 RO6  C3   C8    single    1.525  0.020  1.525
 RO6  C3   H3    single    0.970  0.020  1.090
 RO6  C4   C5    single    1.525  0.020  1.525
 RO6  C4   H4    single    0.970  0.020  1.090
 RO6  C4   H4A   single    0.970  0.020  1.090
 RO6  C5   C6    single    1.520  0.020  1.520
 RO6  C5   H5    single    0.970  0.020  1.090
 RO6  C5   H5A   single    0.970  0.020  1.090
 RO6  C6   O9    single    1.413  0.020  1.413
 RO6  C6   C7    single    1.526  0.020  1.526
 RO6  C6   H6    single    0.970  0.020  1.090
 RO6  O9   HO9   single    0.850  0.020  0.980
 RO6  C8   C7    single    1.524  0.020  1.524
 RO6  C7   H7    single    0.970  0.020  1.090
 RO6  C7   H7A   single    0.970  0.020  1.090
 RO6  C8   H8    single    0.970  0.020  1.090
 RO6  C8   H8A   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
 RO6  N2    C1   N10  118.54  3.000
 RO6  N2    C1   N11  116.12  3.000
 RO6  N10   C1   N11  125.33  3.000
 RO6  C12   N11  C1   116.34  3.000
 RO6  C14   C12  N15  118.51  3.000
 RO6  N15   C12  N11  117.85  3.000
 RO6  C14   C12  N11  123.64  3.000
 RO6  HN15  N15  C16  116.14  3.000
 RO6  HN15  N15  C12  117.78  3.000
 RO6  C16   N15  C12  123.98  3.000
 RO6  N17   C16  O19  123.14  3.000
 RO6  O19   C16  N15  121.09  3.000
 RO6  N17   C16  N15  115.76  3.000
 RO6  C18   N17  C20  116.59  3.000
 RO6  C20   N17  C16  117.44  3.000
 RO6  C18   N17  C16  123.80  3.000
 RO6  C25   C20  C21  118.89  3.000
 RO6  C25   C20  N17  121.22  3.000
 RO6  C21   C20  N17  119.85  3.000
 RO6  H21   C21  C22  120.60  3.000
 RO6  H21   C21  C20  118.78  3.000
 RO6  C22   C21  C20  120.62  3.000
 RO6  H22   C22  C23  120.30  3.000
 RO6  H22   C22  C21  119.90  3.000
 RO6  C23   C22  C21  119.80  3.000
 RO6  H23   C23  C24  119.34  3.000
 RO6  H23   C23  C22  120.33  3.000
 RO6  C24   C23  C22  120.33  3.000
 RO6  H24   C24  C25  120.14  3.000
 RO6  H24   C24  C23  120.54  3.000
 RO6  C25   C24  C23  119.32  3.000
 RO6  CL26  C25  C24  119.56  3.000
 RO6  CL26  C25  C20  119.40  3.000
 RO6  C24   C25  C20  121.04  3.000
 RO6  H18A  C18  H18  106.99  3.000
 RO6  H18A  C18  C14  110.45  3.000
 RO6  H18   C18  C14  111.31  3.000
 RO6  H18A  C18  N17  108.15  3.000
 RO6  H18   C18  N17  109.72  3.000
 RO6  C14   C18  N17  110.11  3.000
 RO6  C13   C14  C18  125.59  3.000
 RO6  C13   C14  C12  114.66  3.000
 RO6  C18   C14  C12  119.70  3.000
 RO6  C13   N10  C1   116.31  3.000
 RO6  H13   C13  N10  116.24  3.000
 RO6  H13   C13  C14  120.06  3.000
 RO6  N10   C13  C14  123.69  3.000
 RO6  HN2   N2   C3   118.29  3.000
 RO6  HN2   N2   C1   116.26  3.000
 RO6  C3    N2   C1   125.06  3.000
 RO6  H3    C3   C8   108.27  3.000
 RO6  H3    C3   C4   108.33  3.000
 RO6  C8    C3   C4   110.68  3.000
 RO6  H3    C3   N2   107.66  3.000
 RO6  C8    C3   N2   109.41  3.000
 RO6  C4    C3   N2   112.35  3.000
 RO6  H4A   C4   H4   106.83  3.000
 RO6  H4A   C4   C5   110.16  3.000
 RO6  H4    C4   C5   109.83  3.000
 RO6  H4A   C4   C3   109.65  3.000
 RO6  H4    C4   C3   108.86  3.000
 RO6  C5    C4   C3   111.39  3.000
 RO6  H5A   C5   H5   106.94  3.000
 RO6  H5A   C5   C6   109.12  3.000
 RO6  H5    C5   C6   110.11  3.000
 RO6  H5A   C5   C4   109.69  3.000
 RO6  H5    C5   C4   109.89  3.000
 RO6  C6    C5   C4   111.01  3.000
 RO6  H6    C6   C7   107.88  3.000
 RO6  H6    C6   O9   110.22  3.000
 RO6  C7    C6   O9   112.10  3.000
 RO6  H6    C6   C5   107.97  3.000
 RO6  C7    C6   C5   110.45  3.000
 RO6  O9    C6   C5   108.14  3.000
 RO6  HO9   O9   C6   108.12  3.000
 RO6  H7A   C7   H7   106.83  3.000
 RO6  H7A   C7   C8   109.71  3.000
 RO6  H7    C7   C8   109.65  3.000
 RO6  H7A   C7   C6   108.99  3.000
 RO6  H7    C7   C6   110.03  3.000
 RO6  C8    C7   C6   111.51  3.000
 RO6  H8A   C8   H8   106.79  3.000
 RO6  H8A   C8   C7   109.59  3.000
 RO6  H8    C8   C7   110.11  3.000
 RO6  H8A   C8   C3   109.35  3.000
 RO6  H8    C8   C3   109.88  3.000
 RO6  C7    C8   C3   111.02  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
 RO6  CONST_01  C14   C13  N10  C1     0.00   0.0  0
 RO6  CONST_02  C14   C12  N11  C1     0.00   0.0  0
 RO6  CONST_03  C13   N10  C1   N11    0.00   0.0  0
 RO6  CONST_04  C13   C14  C12  N11    0.00   0.0  0
 RO6  CONST_05  N10   C1   N11  C12    0.00   0.0  0
 RO6  CONST_06  N10   C13  C14  C12    0.00   0.0  0
 RO6  CONST_07  C23   C22  C21  C20    0.00   0.0  0
 RO6  CONST_08  C23   C24  C25  C20    0.00   0.0  0
 RO6  CONST_09  C24   C25  C20  C21    0.00   0.0  0
 RO6  CONST_10  C24   C23  C22  C21    0.00   0.0  0
 RO6  CONST_11  C25   C20  C21  C22    0.00   0.0  0
 RO6  CONST_12  C25   C24  C23  C22    0.00   0.0  0
 RO6  CONST_13  C22   C21  C20  N17  180.00   0.0  0
 RO6  CONST_14  C24   C25  C20  N17  180.00   0.0  0
 RO6  CONST_15  N17   C16  N15  C12    0.00   0.0  0
 RO6  CONST_16  C18   N17  C16  N15    0.00   0.0  0
 RO6  CONST_17  C20   N17  C16  N15  180.00   0.0  0
 RO6  CONST_18  N2    C1   N11  C12  180.00   0.0  0
 RO6  CONST_19  CL26  C25  C20  N17    0.00   0.0  0
 RO6  CONST_20  CL26  C25  C20  C21  180.00   0.0  0
 RO6  CONST_21  CL26  C25  C24  C23  180.00   0.0  0
 RO6  CONST_22  N2    C1   N10  C13  180.00   0.0  0
 RO6  CONST_23  C3    N2   C1   N11  180.00   0.0  0
 RO6  CONST_24  C3    N2   C1   N10    0.00   0.0  0
 RO6  CONST_25  O19   C16  N15  C12  180.00   0.0  0
 RO6  CONST_26  C18   N17  C16  O19  180.00   0.0  0
 RO6  CONST_27  C20   N17  C16  O19    0.00   0.0  0
 RO6  CONST_28  H13   C13  N10  C1   180.00   0.0  0
 RO6  CONST_29  H21   C21  C20  N17    0.00   0.0  0
 RO6  CONST_30  H22   C22  C21  C20  180.00   0.0  0
 RO6  CONST_31  H24   C24  C25  C20  180.00   0.0  0
 RO6  CONST_32  H23   C23  C22  C21  180.00   0.0  0
 RO6  CONST_33  HN15  N15  C16  N17  180.00   0.0  0
 RO6  CONST_34  HN2   N2   C1   N11    0.00   0.0  0
 RO6  Var_01    C21   C20  N17  C16  103.91  30.0  2
 RO6  Var_02    C6    C5   C4   C3    56.39  30.0  1
 RO6  Var_03    C6    C7   C8   C3   -56.14  30.0  1
 RO6  Var_04    H18   C18  C14  C12  -96.83  30.0  1

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
 RO6  chir_01  C3  N2  C4  C8  positiv
 RO6  chir_02  C6  O9  C5  C7  positiv

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
 RO6  plan-1  N17   0.020
 RO6  plan-1  C20   0.020
 RO6  plan-1  C21   0.020
 RO6  plan-1  C22   0.020
 RO6  plan-1  C23   0.020
 RO6  plan-1  C24   0.020
 RO6  plan-1  C25   0.020
 RO6  plan-1  CL26  0.020
 RO6  plan-1  H21   0.020
 RO6  plan-1  H22   0.020
 RO6  plan-1  H23   0.020
 RO6  plan-1  H24   0.020
 RO6  plan-2  C1    0.020
 RO6  plan-2  N2    0.020
 RO6  plan-2  C3    0.020
 RO6  plan-2  HN2   0.020
 RO6  plan-3  C1    0.020
 RO6  plan-3  N11   0.020
 RO6  plan-3  C12   0.020
 RO6  plan-3  N15   0.020
 RO6  plan-3  C16   0.020
 RO6  plan-3  O19   0.020
 RO6  plan-3  N17   0.020
 RO6  plan-3  C20   0.020
 RO6  plan-3  C18   0.020
 RO6  plan-3  C14   0.020
 RO6  plan-3  N10   0.020
 RO6  plan-3  C13   0.020
 RO6  plan-3  N2    0.020
 RO6  plan-3  HN15  0.020
 RO6  plan-3  H13   0.020

