# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 15:24:58 2022
#   Inital geometry file: a 75 line input string
#   Ligand name: 5-chloro-6-{[(2Z)-2-iminopyrrolidin-1-yl]methyl}pyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ClC1=C(CN2CCCC2=N)NC(=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
 CMU  CMU  5-chloro-6-{[(2Z)-2-iminopyrrolidin-1-yl]methyl}pyrimidine-2,4(1H,3H)-dione  ligand  27  16  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_CMU
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
 CMU  CL1   CL  CL    0  -0.077   3.9607   4.1342  -0.3579
 CMU  C2    C   CR6   0  -0.312   2.7397   5.1631   0.2637
 CMU  C3    C   CR6   0   0.507   1.4384   5.0130  -0.0586
 CMU  C4    C   CH2   0  -0.405   0.9074   3.9255  -0.9578
 CMU  N5    N   NT    0  -0.465   1.1659   2.6244  -0.4282
 CMU  C6    C   CH2   0  -0.260   0.5113   2.2017   0.7968
 CMU  C7    C   CH2   0  -0.477   1.1940   0.8731   1.1008
 CMU  C8    C   CH2   0  -0.531   1.5551   0.3482  -0.2846
 CMU  C9    C   C     0   0.441   1.7489   1.5930  -1.1152
 CMU  N10   N   N     0  -0.680   2.3406   1.5896  -2.2419
 CMU  N11   N   NR16  0  -0.727   0.5163   5.8787   0.4477
 CMU  C12   C   CR6   0   0.678   0.8063   6.9298   1.2791
 CMU  O13   O   O     0  -0.465  -0.0384   7.6872   1.7035
 CMU  N14   N   NR16  0  -0.719   2.1376   7.0374   1.5848
 CMU  C15   C   CR6   0   0.620   3.1718   6.2335   1.1420
 CMU  O16   O   O     0  -0.436   4.3186   6.4402   1.4770
 CMU  H4C1  H   HCH2  0   0.300   1.3684   4.0377  -1.9405
 CMU  H4C2  H   HCH2  0   0.293  -0.1675   4.0758  -1.1063
 CMU  H6C1  H   HCH2  0   0.239  -0.5676   2.0836   0.6422
 CMU  H6C2  H   HCH2  0   0.248   0.6537   2.9363   1.5920
 CMU  H7C1  H   HCH2  0   0.256   0.5517   0.2001   1.6650
 CMU  H7C2  H   HCH2  0   0.248   2.0968   1.0472   1.6876
 CMU  H8C1  H   HCH2  0   0.264   0.7307  -0.2264  -0.7162
 CMU  H8C2  H   HCH2  0   0.266   2.4404  -0.2848  -0.3048
 CMU  H10   H   H     0   0.319   2.3698   2.5070  -2.6761
 CMU  HN1   H   HNR6  0   0.440  -0.4562   5.7635   0.1956
 CMU  HN2   H   HNR6  0   0.435   2.3909   7.8055   2.1947

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
 CMU  CL1  C2    single  1.713  0.020  1.713
 CMU  C2   C3    double  1.349  0.020  1.349
 CMU  C2   C15   single  1.451  0.020  1.451
 CMU  C3   C4    single  1.508  0.020  1.508
 CMU  C3   N11   single  1.362  0.020  1.362
 CMU  C4   N5    single  1.428  0.020  1.428
 CMU  C4   H4C1  single  0.970  0.020  1.090
 CMU  C4   H4C2  single  0.970  0.020  1.090
 CMU  N5   C6    single  1.452  0.020  1.452
 CMU  N5   C9    single  1.370  0.020  1.370
 CMU  C6   C7    single  1.524  0.020  1.524
 CMU  C6   H6C1  single  0.970  0.020  1.090
 CMU  C6   H6C2  single  0.970  0.020  1.090
 CMU  C7   C8    single  1.525  0.020  1.525
 CMU  C7   H7C1  single  0.970  0.020  1.090
 CMU  C7   H7C2  single  0.970  0.020  1.090
 CMU  C8   C9    single  1.509  0.020  1.509
 CMU  C8   H8C1  single  0.970  0.020  1.090
 CMU  C8   H8C2  single  0.970  0.020  1.090
 CMU  C9   N10   double  1.273  0.020  1.273
 CMU  N10  H10   single  0.890  0.020  1.040
 CMU  N11  C12   single  1.371  0.020  1.371
 CMU  C12  O13   double  1.211  0.020  1.211
 CMU  C12  N14   single  1.370  0.020  1.370
 CMU  N14  C15   single  1.383  0.020  1.383
 CMU  C15  O16   double  1.213  0.020  1.213
 CMU  HN1  N11   single  0.860  0.020  1.020
 CMU  HN2  N14   single  0.860  0.020  1.020

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
 CMU  C15   C2   C3    120.94  3.000
 CMU  C15   C2   CL1   116.77  3.000
 CMU  C3    C2   CL1   122.27  3.000
 CMU  N11   C3   C4    116.21  3.000
 CMU  N11   C3   C2    119.57  3.000
 CMU  C4    C3   C2    124.23  3.000
 CMU  H4C2  C4   H4C1  106.16  3.000
 CMU  H4C2  C4   N5    110.66  3.000
 CMU  H4C1  C4   N5    110.55  3.000
 CMU  H4C2  C4   C3    109.12  3.000
 CMU  H4C1  C4   C3    108.30  3.000
 CMU  N5    C4   C3    111.85  3.000
 CMU  C9    N5   C6    113.32  3.000
 CMU  C9    N5   C4    125.25  3.000
 CMU  C6    N5   C4    119.76  3.000
 CMU  H6C2  C6   H6C1  107.67  3.000
 CMU  H6C2  C6   C7    112.50  3.000
 CMU  H6C1  C6   C7    112.02  3.000
 CMU  H6C2  C6   N5    111.09  3.000
 CMU  H6C1  C6   N5    110.86  3.000
 CMU  C7    C6   N5    102.72  3.000
 CMU  H7C2  C7   H7C1  107.96  3.000
 CMU  H7C2  C7   C8    110.35  3.000
 CMU  H7C1  C7   C8    113.45  3.000
 CMU  H7C2  C7   C6    109.81  3.000
 CMU  H7C1  C7   C6    112.22  3.000
 CMU  C8    C7   C6    103.00  3.000
 CMU  H8C2  C8   H8C1  107.48  3.000
 CMU  H8C2  C8   C9    111.41  3.000
 CMU  H8C1  C8   C9    108.24  3.000
 CMU  H8C2  C8   C7    114.18  3.000
 CMU  H8C1  C8   C7    111.16  3.000
 CMU  C9    C8   C7    104.27  3.000
 CMU  N10   C9   C8    123.01  3.000
 CMU  N10   C9   N5    130.09  3.000
 CMU  C8    C9   N5    106.89  3.000
 CMU  H10   N10  C9    112.92  3.000
 CMU  HN1   N11  C12   116.22  3.000
 CMU  HN1   N11  C3    119.07  3.000
 CMU  C12   N11  C3    124.70  3.000
 CMU  N14   C12  O13   123.38  3.000
 CMU  N14   C12  N11   113.64  3.000
 CMU  O13   C12  N11   122.98  3.000
 CMU  HN2   N14  C15   116.53  3.000
 CMU  HN2   N14  C12   115.90  3.000
 CMU  C15   N14  C12   127.56  3.000
 CMU  O16   C15  N14   121.32  3.000
 CMU  O16   C15  C2    125.09  3.000
 CMU  N14   C15  C2    113.59  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
 CMU  CONST_01  C12  N14  C15  C2     0.00   0.0  0
 CMU  CONST_02  N14  C12  N11  C3     0.00   0.0  0
 CMU  CONST_03  C8   C9   N5   C6     0.00   0.0  0
 CMU  CONST_04  C15  N14  C12  N11    0.00   0.0  0
 CMU  CONST_05  O13  C12  N11  C3   180.00   0.0  0
 CMU  CONST_06  C8   C9   N5   C4   180.00   0.0  0
 CMU  CONST_07  N10  C9   N5   C6   180.00   0.0  0
 CMU  CONST_08  O16  C15  N14  C12  180.00   0.0  0
 CMU  CONST_09  C15  N14  C12  O13  180.00   0.0  0
 CMU  CONST_10  HN2  N14  C15  C2   180.00   0.0  0
 CMU  CONST_11  HN1  N11  C12  N14  180.00   0.0  0
 CMU  CONST_12  N10  C9   N5   C4     0.00   0.0  0
 CMU  CONST_13  H10  N10  C9   N5     0.00   0.0  0
 CMU  Var_01    C8   C7   C6   N5   -30.06  30.0  1
 CMU  Var_02    C7   C8   C9   N5   -16.88  30.0  1
 CMU  Var_03    C9   C8   C7   C6    28.90  30.0  1
 CMU  Var_04    C9   N5   C6   C7    21.37  30.0  1
 CMU  Var_05    N5   C4   C3   C2    61.07  30.0  3
 CMU  Var_06    C6   N5   C4   C3    66.66  30.0  3

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
 CMU  plan-1  CL1  0.020
 CMU  plan-1  C2   0.020
 CMU  plan-1  C3   0.020
 CMU  plan-1  C4   0.020
 CMU  plan-1  N11  0.020
 CMU  plan-1  C12  0.020
 CMU  plan-1  O13  0.020
 CMU  plan-1  N14  0.020
 CMU  plan-1  C15  0.020
 CMU  plan-1  O16  0.020
 CMU  plan-1  HN1  0.020
 CMU  plan-1  HN2  0.020
 CMU  plan-2  C4   0.020
 CMU  plan-2  N5   0.020
 CMU  plan-2  C6   0.020
 CMU  plan-2  C8   0.020
 CMU  plan-2  C9   0.020
 CMU  plan-2  N10  0.020
 CMU  plan-2  H10  0.020

