# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 01:45:48 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: 7-[(4-fluoranylphenoxy)methyl]-3-[(1~{R},2~{R})-2-(hydroxymethyl)cyclopropyl]-2-methyl-[1,3]thiazolo[3,2-a]pyrimidin-5-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=C([C@@H]2C[C@H]2CO)N3C(=O)C=C(COc4ccc(F)cc4)N=C3S1
#
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
 6RM  6RM  7-[(4-fluoranylphenoxy)methyl]-3-[(1~{R},2~{R})-2-(hydroxymethyl)cyclopropyl]-2-methyl-[1,3]thiazolo[3,2-a]pyrimidin-5-one  ligand  42  25  .  2022-09-16  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_6RM
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
 6RM  C4   C  CR16  0  -0.495   0.0669   1.5599  -1.1527
 6RM  C14  C  CH1   0  -0.318  -4.2287   0.7761  -0.3146
 6RM  C5   C  CR6   0   0.264   0.8801   0.5005  -0.8910
 6RM  C6   C  CR56  0   0.308  -0.8702  -0.8079  -0.3945
 6RM  C11  C  CR6   0   0.500   7.0301  -0.1358   0.5736
 6RM  C7   C  CH2   0  -0.246   2.3667   0.6071  -1.0470
 6RM  C8   C  CR6   0   0.382   4.2973   0.1029   0.2363
 6RM  C9   C  CR16  0  -0.330   4.8213  -0.3694   1.4407
 6RM  C10  C  CR16  0  -0.392   6.1884  -0.4896   1.6132
 6RM  C12  C  CR16  0  -0.395   6.5376   0.3333  -0.6238
 6RM  C13  C  CR16  0  -0.364   5.1623   0.4551  -0.7952
 6RM  N1   N  N     0  -0.470   0.4136  -0.7145  -0.5302
 6RM  C3   C  CR6   0   0.589  -1.3586   1.4503  -1.0728
 6RM  O1   O  O2    0  -0.469   2.9509   0.1873   0.1666
 6RM  O    O  O     0  -0.454  -2.1600   2.3068  -1.3901
 6RM  S    S  S2    0   0.267  -1.6559  -2.2812   0.0273
 6RM  C1   C  CR5   0  -0.332  -3.2138  -1.5031  -0.0186
 6RM  C    C  CH3   0  -0.732  -4.4289  -2.3123   0.2751
 6RM  N    N  N     0  -0.626  -1.7821   0.1906  -0.5768
 6RM  C2   C  CR5   0   0.538  -3.1158  -0.1945  -0.3181
 6RM  C16  C  CH1   0  -0.298  -5.2726   0.7059   0.7658
 6RM  C15  C  CH2   0  -0.447  -4.2985   1.8350   0.7451
 6RM  C17  C  CH2   0  -0.141  -6.7049   0.9280   0.3846
 6RM  O2   O  OH1   0  -0.671  -7.3928   1.4496   1.4999
 6RM  H1   H  HCR6  0   0.283   0.4721   2.5125  -1.4644
 6RM  H3   H  HCH1  0   0.288  -4.5801   1.0801  -1.2953
 6RM  H4   H  HCH2  0   0.253   2.6817  -0.0366  -1.8775
 6RM  H5   H  HCH2  0   0.253   2.6507   1.6347  -1.2945
 6RM  H6   H  HCR6  0   0.275   4.1502  -0.6439   2.2445
 6RM  H7   H  HCR6  0   0.282   6.5917  -0.8575   2.5474
 6RM  H8   H  HCR6  0   0.283   7.2099   0.6066  -1.4266
 6RM  H9   H  HCR6  0   0.293   4.7968   0.8298  -1.7409
 6RM  H10  H  HCH3  0   0.271  -4.3483  -3.3034  -0.1706
 6RM  H11  H  HCH3  0   0.269  -4.5719  -2.4456   1.3484
 6RM  H12  H  HCH3  0   0.271  -5.3181  -1.8392  -0.1330
 6RM  H13  H  HCH1  0   0.268  -5.1192  -0.0350   1.5438
 6RM  H14  H  HCH2  0   0.257  -3.5263   1.8505   1.5038
 6RM  H15  H  HCH2  0   0.256  -4.6397   2.8141   0.4333
 6RM  H16  H  HCH2  0   0.193  -6.7473   1.6132  -0.4730
 6RM  H17  H  HCH2  0   0.205  -7.1434  -0.0221   0.0516
 6RM  H18  H  HOH1  0   0.454  -8.3276   1.4948   1.2795
 6RM  F    F  F     0  -0.321   8.3606  -0.2550   0.7387

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
 6RM  C14  C15  single    1.500  0.020  1.500
 6RM  C14  C2   single    1.477  0.020  1.477
 6RM  C14  C16  single    1.504  0.020  1.504
 6RM  O    C3   double    1.215  0.020  1.215
 6RM  C15  C16  single    1.491  0.020  1.491
 6RM  C17  C16  single    1.499  0.020  1.499
 6RM  C17  O2   single    1.410  0.020  1.410
 6RM  C2   N    single    1.412  0.020  1.412
 6RM  C2   C1   double    1.346  0.020  1.346
 6RM  C3   N    single    1.418  0.020  1.418
 6RM  C3   C4   single    1.432  0.020  1.432
 6RM  C    C1   single    1.489  0.020  1.489
 6RM  N    C6   single    1.365  0.020  1.365
 6RM  C1   S    single    1.742  0.020  1.742
 6RM  C4   C5   double    1.361  0.020  1.361
 6RM  C6   S    single    1.722  0.020  1.722
 6RM  C6   N1   double    1.294  0.020  1.294
 6RM  C5   N1   single    1.350  0.020  1.350
 6RM  C5   C7   single    1.499  0.020  1.499
 6RM  C7   O1   single    1.411  0.020  1.411
 6RM  O1   C8   single    1.351  0.020  1.351
 6RM  C8   C9   aromatic  1.396  0.020  1.396
 6RM  C8   C13  aromatic  1.391  0.020  1.391
 6RM  C9   C10  aromatic  1.383  0.020  1.383
 6RM  C13  C12  aromatic  1.391  0.020  1.391
 6RM  C10  C11  aromatic  1.384  0.020  1.384
 6RM  C12  C11  aromatic  1.377  0.020  1.377
 6RM  C11  F    single    1.346  0.020  1.346
 6RM  C4   H1   single    0.930  0.020  1.080
 6RM  C14  H3   single    0.970  0.020  1.090
 6RM  C7   H4   single    0.970  0.020  1.090
 6RM  C7   H5   single    0.970  0.020  1.090
 6RM  C9   H6   single    0.930  0.020  1.080
 6RM  C10  H7   single    0.930  0.020  1.080
 6RM  C12  H8   single    0.930  0.020  1.080
 6RM  C13  H9   single    0.930  0.020  1.080
 6RM  C    H10  single    0.970  0.020  1.090
 6RM  C    H11  single    0.970  0.020  1.090
 6RM  C    H12  single    0.970  0.020  1.090
 6RM  C16  H13  single    0.970  0.020  1.090
 6RM  C15  H14  single    0.970  0.020  1.090
 6RM  C15  H15  single    0.970  0.020  1.090
 6RM  C17  H16  single    0.970  0.020  1.090
 6RM  C17  H17  single    0.970  0.020  1.090
 6RM  O2   H18  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
 6RM  H1   C4   C3   117.17  3.000
 6RM  H1   C4   C5   121.16  3.000
 6RM  C3   C4   C5   121.63  3.000
 6RM  H3   C14  C15  115.19  3.000
 6RM  H3   C14  C16  115.94  3.000
 6RM  C15  C14  C16   59.54  3.000
 6RM  H3   C14  C2   115.22  3.000
 6RM  C16  C14  C2   119.61  3.000
 6RM  C15  C14  C2   120.06  3.000
 6RM  N1   C5   C7   115.75  3.000
 6RM  C7   C5   C4   121.15  3.000
 6RM  N1   C5   C4   123.05  3.000
 6RM  N    C6   S    110.72  3.000
 6RM  S    C6   N1   122.68  3.000
 6RM  N    C6   N1   126.59  3.000
 6RM  F    C11  C12  119.36  3.000
 6RM  F    C11  C10  119.11  3.000
 6RM  C12  C11  C10  121.53  3.000
 6RM  H5   C7   H4   107.78  3.000
 6RM  H5   C7   O1   111.49  3.000
 6RM  H4   C7   O1   110.96  3.000
 6RM  H5   C7   C5   110.35  3.000
 6RM  H4   C7   C5   108.78  3.000
 6RM  O1   C7   C5   107.46  3.000
 6RM  O1   C8   C13  124.44  3.000
 6RM  C13  C8   C9   119.47  3.000
 6RM  O1   C8   C9   116.10  3.000
 6RM  H6   C9   C10  119.88  3.000
 6RM  H6   C9   C8   119.59  3.000
 6RM  C10  C9   C8   120.53  3.000
 6RM  H7   C10  C9   120.37  3.000
 6RM  H7   C10  C11  120.59  3.000
 6RM  C9   C10  C11  119.03  3.000
 6RM  H8   C12  C13  120.04  3.000
 6RM  H8   C12  C11  120.59  3.000
 6RM  C13  C12  C11  119.37  3.000
 6RM  H9   C13  C12  118.19  3.000
 6RM  H9   C13  C8   121.74  3.000
 6RM  C12  C13  C8   120.07  3.000
 6RM  C6   N1   C5   115.82  3.000
 6RM  N    C3   O    121.36  3.000
 6RM  N    C3   C4   112.63  3.000
 6RM  O    C3   C4   126.02  3.000
 6RM  C8   O1   C7   118.41  3.000
 6RM  C1   S    C6    91.11  3.000
 6RM  C2   C1   C    129.17  3.000
 6RM  C    C1   S    118.80  3.000
 6RM  C2   C1   S    112.03  3.000
 6RM  H12  C    H11  108.39  3.000
 6RM  H12  C    H10  107.63  3.000
 6RM  H11  C    H10  107.51  3.000
 6RM  H12  C    C1   110.92  3.000
 6RM  H11  C    C1   111.56  3.000
 6RM  H10  C    C1   110.68  3.000
 6RM  C2   N    C3   126.03  3.000
 6RM  C3   N    C6   119.80  3.000
 6RM  C2   N    C6   114.03  3.000
 6RM  N    C2   C1   112.00  3.000
 6RM  C1   C2   C14  125.71  3.000
 6RM  N    C2   C14  122.21  3.000
 6RM  H13  C16  C17  114.74  3.000
 6RM  H13  C16  C15  115.76  3.000
 6RM  C17  C16  C15  120.56  3.000
 6RM  H13  C16  C14  116.66  3.000
 6RM  C17  C16  C14  118.28  3.000
 6RM  C15  C16  C14   60.09  3.000
 6RM  H15  C15  H14  114.43  3.000
 6RM  H15  C15  C16  118.87  3.000
 6RM  H14  C15  C16  117.84  3.000
 6RM  H15  C15  C14  116.72  3.000
 6RM  H14  C15  C14  118.17  3.000
 6RM  C16  C15  C14   60.38  3.000
 6RM  H17  C17  H16  106.71  3.000
 6RM  H17  C17  O2   111.41  3.000
 6RM  H16  C17  O2   111.58  3.000
 6RM  H17  C17  C16  109.30  3.000
 6RM  H16  C17  C16  109.14  3.000
 6RM  O2   C17  C16  108.65  3.000
 6RM  H18  O2   C17  108.08  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
 6RM  CONST_01  C8   C9   C10  C11     0.00   0.0  0
 6RM  CONST_02  C8   C13  C12  C11     0.00   0.0  0
 6RM  CONST_03  C12  C13  C8   C9      0.00   0.0  0
 6RM  CONST_04  C12  C11  C10  C9      0.00   0.0  0
 6RM  CONST_05  C13  C8   C9   C10     0.00   0.0  0
 6RM  CONST_06  C13  C12  C11  C10     0.00   0.0  0
 6RM  CONST_07  C2   N    C3   C4    180.00   0.0  0
 6RM  CONST_08  C6   N    C3   C4      0.00   0.0  0
 6RM  CONST_09  N    C6   N1   C5      0.00   0.0  0
 6RM  CONST_10  S    C6   N1   C5    180.00   0.0  0
 6RM  CONST_11  C2   N    C6   N1    180.00   0.0  0
 6RM  CONST_12  C3   N    C6   N1      0.00   0.0  0
 6RM  CONST_13  S    C6   N    C3    180.00   0.0  0
 6RM  CONST_14  C2   N    C6   S       0.00   0.0  0
 6RM  CONST_15  F    C11  C10  C9    180.00   0.0  0
 6RM  CONST_16  O1   C8   C9   C10   180.00   0.0  0
 6RM  CONST_17  O1   C8   C13  C12   180.00   0.0  0
 6RM  CONST_18  F    C11  C12  C13   180.00   0.0  0
 6RM  CONST_19  O    C3   N    C6    180.00   0.0  0
 6RM  CONST_20  C2   N    C3   O       0.00   0.0  0
 6RM  CONST_21  H6   C9   C10  C11   180.00   0.0  0
 6RM  CONST_22  H9   C13  C12  C11   180.00   0.0  0
 6RM  CONST_23  H7   C10  C9   C8    180.00   0.0  0
 6RM  CONST_24  H8   C12  C13  C8    180.00   0.0  0
 6RM  Var_01    C15  C14  C2   C1    109.40  30.0  2
 6RM  Var_02    C16  C15  C14  C2   -108.78  30.0  1
 6RM  Var_03    C17  C16  C15  C14  -107.16  30.0  1
 6RM  Var_04    O1   C7   C5   C4    126.82  30.0  3
 6RM  Var_05    O2   C17  C16  C14  -152.16  30.0  2
 6RM  Var_06    C9   C8   O1   C7   -177.47  30.0  2
 6RM  Var_07    H10  C    C1   S     -39.58  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
 6RM  chir_01  C14  C15  C2   C16  both
 6RM  chir_02  C16  C14  C15  C17  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
 6RM  plan-1  C11  0.020
 6RM  plan-1  C8   0.020
 6RM  plan-1  C9   0.020
 6RM  plan-1  C10  0.020
 6RM  plan-1  C12  0.020
 6RM  plan-1  C13  0.020
 6RM  plan-1  O1   0.020
 6RM  plan-1  H6   0.020
 6RM  plan-1  H7   0.020
 6RM  plan-1  H8   0.020
 6RM  plan-1  H9   0.020
 6RM  plan-1  F    0.020
 6RM  plan-2  C4   0.020
 6RM  plan-2  C14  0.020
 6RM  plan-2  C5   0.020
 6RM  plan-2  C6   0.020
 6RM  plan-2  C7   0.020
 6RM  plan-2  N1   0.020
 6RM  plan-2  C3   0.020
 6RM  plan-2  O    0.020
 6RM  plan-2  S    0.020
 6RM  plan-2  C1   0.020
 6RM  plan-2  C    0.020
 6RM  plan-2  N    0.020
 6RM  plan-2  C2   0.020
 6RM  plan-2  H1   0.020

