# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 14 03:22:20 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: N-cycloheptylpyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CCCC(CC1)Nc2ncccn2
#
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
 LD4  LD4  N-cycloheptylpyrimidin-2-amine  ligand  31  14  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_LD4
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
 LD4  N1   N  N     0  -0.462   2.7402  -1.1791  -0.4111
 LD4  C4   C  CH1   0  -0.033  -0.8021  -0.4142   0.1075
 LD4  C5   C  CH2   0  -0.452  -1.8340  -1.5224   0.3281
 LD4  C6   C  CH2   0  -0.432  -3.1864  -1.0757   0.8691
 LD4  C7   C  CH2   0  -0.436  -3.9129   0.0160   0.0857
 LD4  C8   C  CH2   0  -0.443  -3.2705   1.3946   0.2336
 LD4  C10  C  CH2   0  -0.444  -1.1882   0.5082  -1.0579
 LD4  N    N  N     0  -0.460   1.7113   0.7959   0.4350
 LD4  C    C  CR16  0  -0.395   4.0792   0.6929   0.1972
 LD4  C1   C  CR16  0  -0.013   2.9098   1.3463   0.5469
 LD4  C2   C  CR6   0   0.590   1.6713  -0.4562  -0.0360
 LD4  C3   C  CR16  0  -0.023   3.9184  -0.5976  -0.2886
 LD4  C9   C  CH2   0  -0.431  -2.0893   1.6875  -0.6979
 LD4  N2   N  NH1   0  -0.662   0.4756  -1.0617  -0.1331
 LD4  H1   H  HCH1  0   0.231  -0.7020   0.1777   1.0225
 LD4  H2   H  HCH2  0   0.220  -1.9791  -2.0469  -0.6237
 LD4  H3   H  HCH2  0   0.236  -1.4150  -2.2557   1.0231
 LD4  H4   H  HCH2  0   0.230  -3.8247  -1.9614   0.9237
 LD4  H5   H  HCH2  0   0.213  -3.0644  -0.7312   1.9017
 LD4  H6   H  HCH2  0   0.215  -4.0010  -0.2624  -0.9699
 LD4  H7   H  HCH2  0   0.229  -4.9373   0.0705   0.4628
 LD4  H8   H  HCH2  0   0.229  -4.0260   2.1677   0.0735
 LD4  H9   H  HCH2  0   0.213  -2.9565   1.5109   1.2756
 LD4  H10  H  HCH2  0   0.237  -0.2796   0.9158  -1.5054
 LD4  H11  H  HCH2  0   0.216  -1.6570  -0.1011  -1.8377
 LD4  H12  H  HCR6  0   0.267   5.0492   1.1563   0.2931
 LD4  H13  H  HCR6  0   0.265   2.9381   2.3597   0.9342
 LD4  H14  H  HCR6  0   0.268   4.7795  -1.1852  -0.5905
 LD4  H15  H  HCH2  0   0.221  -2.4668   2.1090  -1.6334
 LD4  H16  H  HCH2  0   0.220  -1.4782   2.4717  -0.2434
 LD4  H17  H  HNH1  0   0.386   0.4753  -1.9706  -0.5687

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
 LD4  C    C1   aromatic  1.384  0.020  1.384
 LD4  C    C3   aromatic  1.388  0.020  1.388
 LD4  C1   N    aromatic  1.324  0.020  1.324
 LD4  C3   N1   aromatic  1.320  0.020  1.320
 LD4  N    C2   aromatic  1.338  0.020  1.338
 LD4  N1   C2   aromatic  1.344  0.020  1.344
 LD4  C2   N2   single    1.344  0.020  1.344
 LD4  N2   C4   single    1.452  0.020  1.452
 LD4  C10  C9   single    1.527  0.020  1.527
 LD4  C10  C4   single    1.536  0.020  1.536
 LD4  C9   C8   single    1.533  0.020  1.533
 LD4  C4   C5   single    1.530  0.020  1.530
 LD4  C8   C7   single    1.528  0.020  1.528
 LD4  C5   C6   single    1.524  0.020  1.524
 LD4  C7   C6   single    1.527  0.020  1.527
 LD4  C4   H1   single    0.970  0.020  1.090
 LD4  C5   H2   single    0.970  0.020  1.090
 LD4  C5   H3   single    0.970  0.020  1.090
 LD4  C6   H4   single    0.970  0.020  1.090
 LD4  C6   H5   single    0.970  0.020  1.090
 LD4  C7   H6   single    0.970  0.020  1.090
 LD4  C7   H7   single    0.970  0.020  1.090
 LD4  C8   H8   single    0.970  0.020  1.090
 LD4  C8   H9   single    0.970  0.020  1.090
 LD4  C10  H10  single    0.970  0.020  1.090
 LD4  C10  H11  single    0.970  0.020  1.090
 LD4  C    H12  single    0.930  0.020  1.080
 LD4  C1   H13  single    0.930  0.020  1.080
 LD4  C3   H14  single    0.930  0.020  1.080
 LD4  C9   H15  single    0.970  0.020  1.090
 LD4  C9   H16  single    0.970  0.020  1.090
 LD4  N2   H17  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
 LD4  C3   N1   C2   116.57  3.000
 LD4  H1   C4   N2   107.41  3.000
 LD4  H1   C4   C10  109.44  3.000
 LD4  N2   C4   C10  111.30  3.000
 LD4  H1   C4   C5   109.43  3.000
 LD4  C10  C4   C5   112.01  3.000
 LD4  N2   C4   C5   107.11  3.000
 LD4  H3   C5   H2   106.35  3.000
 LD4  H3   C5   C6   108.12  3.000
 LD4  H2   C5   C6   109.33  3.000
 LD4  H3   C5   C4   108.60  3.000
 LD4  H2   C5   C4   108.09  3.000
 LD4  C6   C5   C4   115.94  3.000
 LD4  H5   C6   H4   105.83  3.000
 LD4  H5   C6   C7   108.16  3.000
 LD4  H4   C6   C7   109.09  3.000
 LD4  H5   C6   C5   109.15  3.000
 LD4  H4   C6   C5   107.36  3.000
 LD4  C7   C6   C5   116.72  3.000
 LD4  H7   C7   H6   105.65  3.000
 LD4  H7   C7   C8   108.40  3.000
 LD4  H6   C7   C8   110.88  3.000
 LD4  H7   C7   C6   107.73  3.000
 LD4  H6   C7   C6   110.55  3.000
 LD4  C8   C7   C6   113.27  3.000
 LD4  H9   C8   H8   105.23  3.000
 LD4  H9   C8   C9   109.71  3.000
 LD4  H8   C8   C9   107.98  3.000
 LD4  H9   C8   C7   107.98  3.000
 LD4  H8   C8   C7   109.47  3.000
 LD4  C9   C8   C7   115.95  3.000
 LD4  H11  C10  H10  105.80  3.000
 LD4  H11  C10  C9   110.18  3.000
 LD4  H10  C10  C9   107.42  3.000
 LD4  H11  C10  C4   108.29  3.000
 LD4  H10  C10  C4   109.03  3.000
 LD4  C9   C10  C4   115.68  3.000
 LD4  C2   N    C1   116.48  3.000
 LD4  H12  C    C3   122.30  3.000
 LD4  H12  C    C1   122.28  3.000
 LD4  C3   C    C1   115.42  3.000
 LD4  H13  C1   C    120.58  3.000
 LD4  H13  C1   N    116.24  3.000
 LD4  C    C1   N    123.18  3.000
 LD4  N2   C2   N    118.27  3.000
 LD4  N2   C2   N1   116.44  3.000
 LD4  N    C2   N1   125.29  3.000
 LD4  H14  C3   C    120.58  3.000
 LD4  H14  C3   N1   116.36  3.000
 LD4  C    C3   N1   123.06  3.000
 LD4  H16  C9   H15  105.79  3.000
 LD4  H16  C9   C10  108.80  3.000
 LD4  H15  C9   C10  107.44  3.000
 LD4  H16  C9   C8   108.37  3.000
 LD4  H15  C9   C8   109.12  3.000
 LD4  C10  C9   C8   116.77  3.000
 LD4  H17  N2   C2   115.97  3.000
 LD4  H17  N2   C4   118.25  3.000
 LD4  C2   N2   C4   124.74  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
 LD4  CONST_01  C1   C   C3  N1    0.00  0.0  0
 LD4  CONST_02  C1   N   C2  N1    0.00  0.0  0
 LD4  CONST_03  C3   C   C1  N     0.00  0.0  0
 LD4  CONST_04  C3   N1  C2  N     0.00  0.0  0
 LD4  CONST_05  C2   N   C1  C     0.00  0.0  0
 LD4  CONST_06  C2   N1  C3  C     0.00  0.0  0
 LD4  CONST_07  N2   C2  N   C1  180.00  0.0  0
 LD4  CONST_08  N2   C2  N1  C3  180.00  0.0  0
 LD4  CONST_09  C4   N2  C2  N1  180.00  0.0  0
 LD4  CONST_10  N    C2  N2  C4    0.00  0.0  0
 LD4  CONST_11  H12  C   C3  N1  180.00  0.0  0
 LD4  CONST_12  H14  C3  C   C1  180.00  0.0  0
 LD4  CONST_13  H13  C1  N   C2  180.00  0.0  0
 LD4  CONST_14  H17  N2  C2  N1    0.00  0.0  0

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
 LD4  chir_01  C4  N2  C10  C5  negativ

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
 LD4  plan-1  N1   0.020
 LD4  plan-1  N    0.020
 LD4  plan-1  C    0.020
 LD4  plan-1  C1   0.020
 LD4  plan-1  C2   0.020
 LD4  plan-1  C3   0.020
 LD4  plan-1  N2   0.020
 LD4  plan-1  H12  0.020
 LD4  plan-1  H13  0.020
 LD4  plan-1  H14  0.020
 LD4  plan-2  C4   0.020
 LD4  plan-2  C2   0.020
 LD4  plan-2  N2   0.020
 LD4  plan-2  H17  0.020

