# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 20:34:03 2020
#   Inital geometry file: a 67 line input string
#   Ligand name: 7-methyl-3,4-dihydro-2~{H}-pyrido[1,2-a]pyrimidin-3-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CN2C[C@@H](O)CN=C2C=C1
#
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
 5GQ  5GQ  7-methyl-3,4-dihydro-2~{H}-pyrido[1,2-a]pyrimidin-3-ol  ligand  24  12  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5GQ
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
 5GQ  C4   C  CH1   0  -0.030   2.3624   0.7595  -0.1206
 5GQ  C6   C  CR6   0   0.518   0.2049  -0.9363  -0.1159
 5GQ  N1   N  N     0  -0.505   1.3551  -1.5106  -0.1743
 5GQ  C7   C  CR16  0  -0.394  -0.9778  -1.6987   0.2136
 5GQ  C8   C  CR16  0  -0.155  -2.1982  -1.1279   0.2990
 5GQ  O    O  OH1   0  -0.669   2.2287   0.9822   1.2661
 5GQ  C3   C  CH2   0  -0.302   1.0880   1.2485  -0.7717
 5GQ  N    N  NR6   0  -0.535  -0.0301   0.4111  -0.3558
 5GQ  C2   C  CR16  0   0.003  -1.2682   0.9745  -0.2501
 5GQ  C1   C  CR6   0  -0.059  -2.3792   0.2718   0.0688
 5GQ  C    C  CH3   0  -0.722  -3.7283   0.9119   0.1811
 5GQ  H1   H  HCH1  0   0.233   3.2052   1.3242  -0.5400
 5GQ  H5   H  HCR6  0   0.258  -0.8356  -2.7558   0.3927
 5GQ  H6   H  HCR6  0   0.258  -3.0585  -1.7376   0.5506
 5GQ  H7   H  HOH1  0   0.452   2.9707   0.5636   1.7134
 5GQ  H8   H  HCH2  0   0.271   0.8763   2.2806  -0.4918
 5GQ  H9   H  HCH2  0   0.265   1.1966   1.2156  -1.8579
 5GQ  H10  H  HCR6  0   0.284  -1.3040   2.0392  -0.4436
 5GQ  H11  H  HCH3  0   0.240  -4.4392   0.4703  -0.5202
 5GQ  H12  H  HCH3  0   0.240  -4.1466   0.7868   1.1816
 5GQ  H13  H  HCH3  0   0.242  -3.6802   1.9804  -0.0260
 5GQ  C5   C  CH2   0  -0.343   2.5236  -0.7162  -0.4551
 5GQ  H2   H  HCH2  0   0.221   2.8064  -0.8022  -1.5121
 5GQ  H3   H  HCH2  0   0.228   3.3739  -1.1253   0.1028

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
 5GQ  N1  C6   double  1.287  0.020  1.287
 5GQ  O   C4   single  1.411  0.020  1.411
 5GQ  C6  C7   single  1.445  0.020  1.445
 5GQ  C6  N    single  1.389  0.020  1.389
 5GQ  C4  C3   single  1.512  0.020  1.512
 5GQ  C7  C8   double  1.350  0.020  1.350
 5GQ  N   C3   single  1.458  0.020  1.458
 5GQ  N   C2   single  1.364  0.020  1.364
 5GQ  C8  C1   single  1.430  0.020  1.430
 5GQ  C2  C1   double  1.353  0.020  1.353
 5GQ  C1  C    single  1.497  0.020  1.497
 5GQ  C4  H1   single  0.970  0.020  1.090
 5GQ  C7  H5   single  0.930  0.020  1.080
 5GQ  C8  H6   single  0.930  0.020  1.080
 5GQ  O   H7   single  0.850  0.020  0.980
 5GQ  C3  H8   single  0.970  0.020  1.090
 5GQ  C3  H9   single  0.970  0.020  1.090
 5GQ  C2  H10  single  0.930  0.020  1.080
 5GQ  C   H11  single  0.970  0.020  1.090
 5GQ  C   H12  single  0.970  0.020  1.090
 5GQ  C   H13  single  0.970  0.020  1.090
 5GQ  N1  C5   single  1.441  0.020  1.441
 5GQ  C4  C5   single  1.522  0.020  1.522
 5GQ  C5  H2   single  0.970  0.020  1.090
 5GQ  C5  H3   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
 5GQ  C5   C4  H1   109.49  3.000
 5GQ  C5   C4  C3   107.95  3.000
 5GQ  H1   C4  C3   108.43  3.000
 5GQ  C5   C4  O    112.28  3.000
 5GQ  H1   C4  O    111.54  3.000
 5GQ  C3   C4  O    106.99  3.000
 5GQ  N    C6  C7   114.38  3.000
 5GQ  N    C6  N1   125.20  3.000
 5GQ  C7   C6  N1   120.42  3.000
 5GQ  C5   N1  C6   119.19  3.000
 5GQ  H5   C7  C8   121.44  3.000
 5GQ  H5   C7  C6   116.47  3.000
 5GQ  C8   C7  C6   122.08  3.000
 5GQ  H6   C8  C1   119.18  3.000
 5GQ  H6   C8  C7   119.62  3.000
 5GQ  C1   C8  C7   121.20  3.000
 5GQ  H7   O   C4   108.37  3.000
 5GQ  H9   C3  H8   107.65  3.000
 5GQ  H9   C3  N    110.04  3.000
 5GQ  H8   C3  N    108.77  3.000
 5GQ  H9   C3  C4   109.55  3.000
 5GQ  H8   C3  C4   111.05  3.000
 5GQ  N    C3  C4   109.74  3.000
 5GQ  C2   N   C3   118.74  3.000
 5GQ  C2   N   C6   122.75  3.000
 5GQ  C3   N   C6   118.49  3.000
 5GQ  H10  C2  C1   121.73  3.000
 5GQ  H10  C2  N    114.98  3.000
 5GQ  C1   C2  N    123.30  3.000
 5GQ  C    C1  C2   122.38  3.000
 5GQ  C    C1  C8   121.36  3.000
 5GQ  C2   C1  C8   116.27  3.000
 5GQ  H13  C   H12  107.67  3.000
 5GQ  H13  C   H11  107.66  3.000
 5GQ  H12  C   H11  107.02  3.000
 5GQ  H13  C   C1   111.42  3.000
 5GQ  H12  C   C1   111.41  3.000
 5GQ  H11  C   C1   111.45  3.000
 5GQ  H3   C5  H2   105.13  3.000
 5GQ  H3   C5  N1   108.91  3.000
 5GQ  H2   C5  N1   110.70  3.000
 5GQ  H3   C5  C4   109.40  3.000
 5GQ  H2   C5  C4   108.36  3.000
 5GQ  N1   C5  C4   113.96  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
 5GQ  CONST_01  C3   N   C6  N1    0.00   0.0  0
 5GQ  CONST_02  C2   N   C6  N1  180.00   0.0  0
 5GQ  CONST_03  C5   N1  C6  C7  180.00   0.0  0
 5GQ  CONST_04  C3   N   C6  C7  180.00   0.0  0
 5GQ  CONST_05  C2   N   C6  C7    0.00   0.0  0
 5GQ  CONST_06  C5   N1  C6  N     0.00   0.0  0
 5GQ  Var_01    C6   N   C3  C4  -33.24  30.0  1
 5GQ  Var_02    H2   C5  N1  C6  -99.63  30.0  1
 5GQ  Var_03    H11  C   C1  C8  -59.76  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
 5GQ  chir_01  C4  O  C3  C5  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
 5GQ  plan-1  C6   0.020
 5GQ  plan-1  N1   0.020
 5GQ  plan-1  C7   0.020
 5GQ  plan-1  C8   0.020
 5GQ  plan-1  C3   0.020
 5GQ  plan-1  N    0.020
 5GQ  plan-1  C2   0.020
 5GQ  plan-1  C1   0.020
 5GQ  plan-1  C    0.020
 5GQ  plan-1  H5   0.020
 5GQ  plan-1  H6   0.020
 5GQ  plan-1  H10  0.020
 5GQ  plan-1  C5   0.020

