# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 16:26:53 2022
#   Inital geometry file: a 85 line input string
#   Ligand name: 1-[(1S,2S,4S,5R)-4-hydroxy-5-(hydroxymethyl)bicyclo[3.1.0]hex-2-yl]-5-methylpyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CN([C@H]2C[C@H](O)[C@]3(CO)C[C@H]23)C(=O)NC1=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
 TMC  TMC  1-[(1S,2S,4S,5R)-4-hydroxy-5-(hydroxymethyl)bicyclo[3.1.0]hex-2-yl]-5-methylpyrimidine-2,4(1H,3H)-dione  ligand  34  18  .  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_TMC
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
 TMC  O16   O  OH1   0  -0.663   1.5797  -0.2600  -4.2196
 TMC  O18   O  OH1   0  -0.661  -0.4550   1.8876  -3.2166
 TMC  O9    O  OC    0  -0.488  -2.6056   0.3691   1.9537
 TMC  O7    O  OC    0  -0.458   1.1930   0.2468   4.4059
 TMC  N8    N  NR6   0  -0.549  -0.6759  -0.1909   0.8748
 TMC  N5    N  NR16  0  -0.737  -0.6806   0.2750   3.1395
 TMC  C1    C  CT    0  -0.064   0.0423  -0.3287  -2.4076
 TMC  C10   C  CH1   0   0.098  -0.2452   1.1178  -2.0596
 TMC  C14   C  CH2   0  -0.542  -1.4685   1.0695  -1.1259
 TMC  C17   C  CH1   0  -0.040  -1.3964  -0.2847  -0.4090
 TMC  C13   C  CH1   0  -0.331  -0.6717  -1.1780  -1.3886
 TMC  C15   C  CH2   0  -0.478  -1.1513  -1.1371  -2.8063
 TMC  C12   C  CH2   0  -0.157   1.4023  -0.7194  -2.9002
 TMC  C11   C  CR6   0   0.732  -1.4077   0.1652   1.9826
 TMC  C6    C  CR6   0   0.555   0.6818   0.1094   3.3085
 TMC  C4    C  CR6   0  -0.182   1.3928  -0.2272   2.0939
 TMC  C2    C  CR16  0   0.075   0.6786  -0.3538   0.9603
 TMC  C3    C  CH3   0  -0.708   2.8722  -0.4209   2.1490
 TMC  H16   H  HOH1  0   0.453   2.4563  -0.5300  -4.5091
 TMC  H5    H  HNR6  0   0.424  -1.2159   0.5209   3.9633
 TMC  H10   H  HCH1  0   0.203   0.6203   1.5048  -1.5000
 TMC  H142  H  HCH2  0   0.258  -2.3829   1.1152  -1.7208
 TMC  H141  H  HCH2  0   0.270  -1.5015   1.9095  -0.4317
 TMC  H17   H  HCH1  0   0.286  -2.3871  -0.6697  -0.1771
 TMC  H13   H  HCH1  0   0.286  -0.2445  -2.1086  -1.0306
 TMC  H152  H  HCH2  0   0.259  -2.0843  -0.6441  -3.0509
 TMC  H151  H  HCH2  0   0.270  -0.9631  -2.0257  -3.3957
 TMC  H122  H  HCH2  0   0.191   2.1634  -0.2974  -2.2268
 TMC  H121  H  HCH2  0   0.201   1.4996  -1.8119  -2.8384
 TMC  H2    H  HCR6  0   0.307   1.1729  -0.6139   0.0358
 TMC  H33   H  HCH3  0   0.247   3.3824   0.4889   2.4690
 TMC  H32   H  HCH3  0   0.247   3.1447  -1.2082   2.8529
 TMC  H31   H  HCH3  0   0.244   3.2654  -0.6972   1.1718
 TMC  H18   H  HOH1  0   0.450  -0.5590   2.8061  -2.9490

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
 TMC  O16  C12   single    1.408  0.020  1.408
 TMC  O16  H16   single    0.850  0.020  0.980
 TMC  O18  C10   single    1.405  0.020  1.405
 TMC  O18  H18   single    0.850  0.020  0.980
 TMC  O9   C11   double    1.215  0.020  1.215
 TMC  O7   C6    double    1.218  0.020  1.218
 TMC  N8   C17   single    1.475  0.020  1.475
 TMC  N8   C11   aromatic  1.375  0.020  1.375
 TMC  N8   C2    aromatic  1.367  0.020  1.367
 TMC  N5   C11   aromatic  1.371  0.020  1.371
 TMC  N5   C6    aromatic  1.383  0.020  1.383
 TMC  N5   H5    single    0.860  0.020  1.020
 TMC  C1   C10   single    1.515  0.020  1.515
 TMC  C1   C13   single    1.507  0.020  1.507
 TMC  C1   C15   single    1.496  0.020  1.496
 TMC  C1   C12   single    1.498  0.020  1.498
 TMC  C10  C14   single    1.540  0.020  1.540
 TMC  C10  H10   single    0.970  0.020  1.090
 TMC  C14  C17   single    1.534  0.020  1.534
 TMC  C14  H142  single    0.970  0.020  1.090
 TMC  C14  H141  single    0.970  0.020  1.090
 TMC  C17  C13   single    1.511  0.020  1.511
 TMC  C17  H17   single    0.970  0.020  1.090
 TMC  C13  C15   single    1.497  0.020  1.497
 TMC  C13  H13   single    0.970  0.020  1.090
 TMC  C15  H152  single    0.970  0.020  1.090
 TMC  C15  H151  single    0.970  0.020  1.090
 TMC  C12  H122  single    0.970  0.020  1.090
 TMC  C12  H121  single    0.970  0.020  1.090
 TMC  C6   C4    aromatic  1.447  0.020  1.447
 TMC  C4   C2    aromatic  1.346  0.020  1.346
 TMC  C4   C3    single    1.493  0.020  1.493
 TMC  C2   H2    single    0.930  0.020  1.080
 TMC  C3   H33   single    0.970  0.020  1.090
 TMC  C3   H32   single    0.970  0.020  1.090
 TMC  C3   H31   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
 TMC  H16   O16  C12   107.77  3.000
 TMC  H18   O18  C10   108.06  3.000
 TMC  C2    N8   C11   120.53  3.000
 TMC  C2    N8   C17   122.07  3.000
 TMC  C11   N8   C17   117.25  3.000
 TMC  H5    N5   C6    116.78  3.000
 TMC  H5    N5   C11   115.19  3.000
 TMC  C6    N5   C11   128.03  3.000
 TMC  C12   C1   C15   119.72  3.000
 TMC  C12   C1   C13   120.37  3.000
 TMC  C15   C1   C13    59.83  3.000
 TMC  C12   C1   C10   119.78  3.000
 TMC  C15   C1   C10   115.20  3.000
 TMC  C13   C1   C10   107.03  3.000
 TMC  H10   C10  C14   109.11  3.000
 TMC  H10   C10  C1    107.64  3.000
 TMC  C14   C10  C1    105.07  3.000
 TMC  H10   C10  O18   110.08  3.000
 TMC  C14   C10  O18   113.45  3.000
 TMC  C1    C10  O18   111.23  3.000
 TMC  H141  C14  H142  106.81  3.000
 TMC  H141  C14  C17   112.58  3.000
 TMC  H142  C14  C17   109.33  3.000
 TMC  H141  C14  C10   112.71  3.000
 TMC  H142  C14  C10   109.49  3.000
 TMC  C17   C14  C10   105.89  3.000
 TMC  H17   C17  C13   111.46  3.000
 TMC  H17   C17  C14   111.67  3.000
 TMC  C13   C17  C14   103.98  3.000
 TMC  H17   C17  N8    106.37  3.000
 TMC  C13   C17  N8    111.56  3.000
 TMC  C14   C17  N8    111.94  3.000
 TMC  H13   C13  C15   117.52  3.000
 TMC  H13   C13  C17   118.83  3.000
 TMC  C15   C13  C17   116.37  3.000
 TMC  H13   C13  C1    121.35  3.000
 TMC  C15   C13  C1     59.73  3.000
 TMC  C17   C13  C1    109.42  3.000
 TMC  H151  C15  H152  113.60  3.000
 TMC  H151  C15  C13   115.93  3.000
 TMC  H152  C15  C13   120.14  3.000
 TMC  H151  C15  C1    116.74  3.000
 TMC  H152  C15  C1    120.10  3.000
 TMC  C13   C15  C1     60.44  3.000
 TMC  H121  C12  H122  106.60  3.000
 TMC  H121  C12  C1    108.73  3.000
 TMC  H122  C12  C1    109.06  3.000
 TMC  H121  C12  O16   111.47  3.000
 TMC  H122  C12  O16   111.17  3.000
 TMC  C1    C12  O16   109.71  3.000
 TMC  N5    C11  N8    114.74  3.000
 TMC  N5    C11  O9    121.96  3.000
 TMC  N8    C11  O9    123.30  3.000
 TMC  C4    C6   N5    114.16  3.000
 TMC  C4    C6   O7    125.18  3.000
 TMC  N5    C6   O7    120.66  3.000
 TMC  C3    C4   C2    123.00  3.000
 TMC  C3    C4   C6    119.08  3.000
 TMC  C2    C4   C6    117.92  3.000
 TMC  H2    C2   C4    120.05  3.000
 TMC  H2    C2   N8    115.38  3.000
 TMC  C4    C2   N8    124.57  3.000
 TMC  H31   C3   H32   107.80  3.000
 TMC  H31   C3   H33   107.82  3.000
 TMC  H32   C3   H33   107.21  3.000
 TMC  H31   C3   C4    110.95  3.000
 TMC  H32   C3   C4    111.41  3.000
 TMC  H33   C3   C4    111.47  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
 TMC  CONST_01  C6   N5   C11  N8     0.00   0.0  0
 TMC  CONST_02  C6   C4   C2   N8     0.00   0.0  0
 TMC  CONST_03  C2   N8   C11  N5     0.00   0.0  0
 TMC  CONST_04  C2   C4   C6   N5     0.00   0.0  0
 TMC  CONST_05  C4   C2   N8   C11    0.00   0.0  0
 TMC  CONST_06  C4   C6   N5   C11    0.00   0.0  0
 TMC  CONST_07  C17  N8   C11  N5   180.00   0.0  0
 TMC  CONST_08  C4   C2   N8   C17  180.00   0.0  0
 TMC  CONST_09  C17  N8   C11  O9     0.00   0.0  0
 TMC  CONST_10  C2   N8   C11  O9   180.00   0.0  0
 TMC  CONST_11  C6   N5   C11  O9   180.00   0.0  0
 TMC  CONST_12  C11  N5   C6   O7   180.00   0.0  0
 TMC  CONST_13  C2   C4   C6   O7   180.00   0.0  0
 TMC  CONST_14  C3   C4   C2   N8   180.00   0.0  0
 TMC  CONST_15  C3   C4   C6   N5   180.00   0.0  0
 TMC  CONST_16  H5   N5   C11  N8   180.00   0.0  0
 TMC  CONST_17  H2   C2   N8   C17    0.00   0.0  0
 TMC  Var_01    C17  C13  C15  C1    98.07  30.0  1
 TMC  Var_02    C10  C1   C12  O16  -72.92  30.0  3
 TMC  Var_03    H33  C3   C4   C6   -61.48  30.0  2

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
 TMC  chir_02  C10  O18  C1   C14  positiv
 TMC  chir_03  C17  N8   C13  C14  positiv
 TMC  chir_04  C1   C13  C15  C12  both
 TMC  chir_05  C13  C1   C17  C15  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
 TMC  plan-1  O9   0.020
 TMC  plan-1  O7   0.020
 TMC  plan-1  N8   0.020
 TMC  plan-1  N5   0.020
 TMC  plan-1  C17  0.020
 TMC  plan-1  C11  0.020
 TMC  plan-1  C6   0.020
 TMC  plan-1  C4   0.020
 TMC  plan-1  C2   0.020
 TMC  plan-1  C3   0.020
 TMC  plan-1  H5   0.020
 TMC  plan-1  H2   0.020

