# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 22 15:07:32 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: (1S,2S)-2-[(2R)-2-azanyl-4-phenyl-butyl]cyclopropan-1-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](CCc1ccccc1)C[C@@H]2C[C@@H]2N
#
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
 1K7  1K7  (1S,2S)-2-[(2R)-2-azanyl-4-phenyl-butyl]cyclopropan-1-amine  ligand  35  15  .  2022-09-22  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_1K7
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
 1K7  N29  N  NH2   0  -0.793   4.6598   1.7295  -0.9823
 1K7  C28  C  CH1   0  -0.115   4.8818   0.4629  -0.3485
 1K7  C27  C  CH2   0  -0.494   4.3751   0.2832   1.0514
 1K7  C26  C  CH1   0  -0.226   3.7085  -0.4348  -0.0865
 1K7  C25  C  CH2   0  -0.427   2.3129  -0.0541  -0.5039
 1K7  C9   C  CH1   0  -0.085   1.2273  -0.7245   0.3366
 1K7  C8   C  CH2   0  -0.411  -0.1526  -0.1914  -0.0668
 1K7  C7   C  CH2   0  -0.520  -1.3002  -0.7499   0.7765
 1K7  C6   C  CR6   0   0.144  -2.6314  -0.1943   0.3552
 1K7  C1   C  CR16  0  -0.315  -3.4086  -0.8477  -0.5988
 1K7  C2   C  CR16  0  -0.240  -4.6213  -0.3164  -1.0185
 1K7  C3   C  CR16  0  -0.276  -5.0784   0.8831  -0.4882
 1K7  C4   C  CR16  0  -0.239  -4.3129   1.5453   0.4634
 1K7  C5   C  CR16  0  -0.313  -3.1011   1.0094   0.8785
 1K7  N10  N  NH2   0  -0.793   1.3584  -2.1740   0.2480
 1K7  H22  H  HNH2  0   0.346   5.3984   2.3730  -0.7276
 1K7  H23  H  HCH1  0   0.225   5.8138  -0.0557  -0.5760
 1K7  H24  H  HCH2  0   0.240   4.9737  -0.2795   1.7566
 1K7  H25  H  HCH2  0   0.234   3.8368   1.1188   1.4849
 1K7  H26  H  HCH1  0   0.241   3.9203  -1.4958  -0.1581
 1K7  H27  H  HCH2  0   0.223   2.1935   1.0294  -0.4394
 1K7  H28  H  HCH2  0   0.210   2.1573  -0.3156  -1.5584
 1K7  H29  H  HCH1  0   0.215   1.4004  -0.4532   1.3851
 1K7  H30  H  HCH2  0   0.221  -0.1533   0.9006   0.0129
 1K7  H31  H  HCH2  0   0.231  -1.3231  -1.8396   0.6938
 1K7  H32  H  HCR6  0   0.243  -3.0643  -1.7874  -1.0159
 1K7  H33  H  HCR6  0   0.252  -5.2118  -0.8425  -1.7580
 1K7  H34  H  HCR6  0   0.252  -6.0254   1.2965  -0.8110
 1K7  H35  H  HCR6  0   0.252  -4.6602   2.4798   0.8856
 1K7  H36  H  HCR6  0   0.244  -2.5103   1.5315   1.6227
 1K7  H37  H  HNH2  0   0.348   0.7100  -2.6239   0.8820
 1K7  H2   H  HNH2  0   0.331   1.0928  -2.4808  -0.6823
 1K7  H1   H  HNH2  0   0.344   4.7099   1.6239  -1.9877
 1K7  H3   H  HCH2  0   0.216  -0.3298  -0.4237  -1.1232
 1K7  H4   H  HCH2  0   0.238  -1.1191  -0.5176   1.8304

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
 1K7  C5   C4   aromatic  1.388  0.020  1.388
 1K7  C5   C6   aromatic  1.394  0.020  1.394
 1K7  C4   C3   aromatic  1.389  0.020  1.389
 1K7  C7   C6   single    1.503  0.020  1.503
 1K7  C7   C8   single    1.530  0.020  1.530
 1K7  C6   C1   aromatic  1.393  0.020  1.393
 1K7  C3   C2   aromatic  1.389  0.020  1.389
 1K7  C9   C8   single    1.533  0.020  1.533
 1K7  C9   C25  single    1.528  0.020  1.528
 1K7  C9   N10  single    1.458  0.020  1.458
 1K7  C1   C2   aromatic  1.389  0.020  1.389
 1K7  C25  C26  single    1.506  0.020  1.506
 1K7  C27  C26  single    1.502  0.020  1.502
 1K7  C27  C28  single    1.500  0.020  1.500
 1K7  N29  C28  single    1.434  0.020  1.434
 1K7  C26  C28  single    1.500  0.020  1.500
 1K7  N29  H22  single    0.890  0.020  1.040
 1K7  C28  H23  single    0.970  0.020  1.090
 1K7  C27  H24  single    0.970  0.020  1.090
 1K7  C27  H25  single    0.970  0.020  1.090
 1K7  C26  H26  single    0.970  0.020  1.090
 1K7  C25  H27  single    0.970  0.020  1.090
 1K7  C25  H28  single    0.970  0.020  1.090
 1K7  C9   H29  single    0.970  0.020  1.090
 1K7  C8   H30  single    0.970  0.020  1.090
 1K7  C7   H31  single    0.970  0.020  1.090
 1K7  C1   H32  single    0.930  0.020  1.080
 1K7  C2   H33  single    0.930  0.020  1.080
 1K7  C3   H34  single    0.930  0.020  1.080
 1K7  C4   H35  single    0.930  0.020  1.080
 1K7  C5   H36  single    0.930  0.020  1.080
 1K7  N10  H37  single    0.890  0.020  1.040
 1K7  N10  H2   single    0.890  0.020  1.040
 1K7  N29  H1   single    0.890  0.020  1.040
 1K7  C8   H3   single    0.970  0.020  1.090
 1K7  C7   H4   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
 1K7  H1   N29  H22  106.28  3.000
 1K7  H1   N29  C28  109.83  3.000
 1K7  H22  N29  C28  109.72  3.000
 1K7  H23  C28  C26  114.84  3.000
 1K7  H23  C28  C27  115.24  3.000
 1K7  C26  C28  C27   60.07  3.000
 1K7  H23  C28  N29  117.41  3.000
 1K7  C26  C28  N29  119.00  3.000
 1K7  C27  C28  N29  117.79  3.000
 1K7  H25  C27  H24  114.49  3.000
 1K7  H25  C27  C26  116.81  3.000
 1K7  H24  C27  C26  119.37  3.000
 1K7  H25  C27  C28  116.66  3.000
 1K7  H24  C27  C28  118.92  3.000
 1K7  C26  C27  C28   59.99  3.000
 1K7  H26  C26  C25  114.22  3.000
 1K7  H26  C26  C27  115.55  3.000
 1K7  C25  C26  C27  120.04  3.000
 1K7  H26  C26  C28  114.91  3.000
 1K7  C27  C26  C28   59.94  3.000
 1K7  C25  C26  C28  121.68  3.000
 1K7  H28  C25  H27  106.12  3.000
 1K7  H28  C25  C9   108.86  3.000
 1K7  H27  C25  C9   108.98  3.000
 1K7  H28  C25  C26  109.73  3.000
 1K7  H27  C25  C26  109.63  3.000
 1K7  C9   C25  C26  113.27  3.000
 1K7  H29  C9   N10  106.85  3.000
 1K7  H29  C9   C8   107.91  3.000
 1K7  N10  C9   C8   114.24  3.000
 1K7  H29  C9   C25  107.77  3.000
 1K7  N10  C9   C25  109.81  3.000
 1K7  C8   C9   C25  110.01  3.000
 1K7  H3   C8   H30  106.34  3.000
 1K7  H3   C8   C7   109.43  3.000
 1K7  H30  C8   C7   108.88  3.000
 1K7  H3   C8   C9   108.99  3.000
 1K7  H30  C8   C9   109.16  3.000
 1K7  C7   C8   C9   113.78  3.000
 1K7  H4   C7   H31  106.74  3.000
 1K7  H4   C7   C6   109.77  3.000
 1K7  H31  C7   C6   109.19  3.000
 1K7  H4   C7   C8   109.23  3.000
 1K7  H31  C7   C8   109.76  3.000
 1K7  C6   C7   C8   112.03  3.000
 1K7  C5   C6   C1   118.30  3.000
 1K7  C1   C6   C7   120.85  3.000
 1K7  C5   C6   C7   120.82  3.000
 1K7  H32  C1   C2   119.51  3.000
 1K7  H32  C1   C6   119.52  3.000
 1K7  C2   C1   C6   120.97  3.000
 1K7  H33  C2   C3   120.06  3.000
 1K7  H33  C2   C1   119.78  3.000
 1K7  C3   C2   C1   120.16  3.000
 1K7  H34  C3   C4   120.28  3.000
 1K7  H34  C3   C2   120.26  3.000
 1K7  C4   C3   C2   119.46  3.000
 1K7  H35  C4   C5   119.77  3.000
 1K7  H35  C4   C3   120.12  3.000
 1K7  C5   C4   C3   120.12  3.000
 1K7  H36  C5   C4   119.67  3.000
 1K7  H36  C5   C6   119.33  3.000
 1K7  C4   C5   C6   121.00  3.000
 1K7  H2   N10  H37  105.79  3.000
 1K7  H2   N10  C9   109.43  3.000
 1K7  H37  N10  C9   110.25  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
 1K7  CONST_01  C3   C4   C5   C6      0.00   0.0  0
 1K7  CONST_02  C3   C2   C1   C6      0.00   0.0  0
 1K7  CONST_03  C4   C5   C6   C1      0.00   0.0  0
 1K7  CONST_04  C4   C3   C2   C1      0.00   0.0  0
 1K7  CONST_05  C5   C4   C3   C2      0.00   0.0  0
 1K7  CONST_06  C5   C6   C1   C2      0.00   0.0  0
 1K7  CONST_07  C4   C5   C6   C7    180.00   0.0  0
 1K7  CONST_08  C2   C1   C6   C7    180.00   0.0  0
 1K7  CONST_09  H35  C4   C5   C6    180.00   0.0  0
 1K7  CONST_10  H33  C2   C1   C6    180.00   0.0  0
 1K7  CONST_11  H36  C5   C6   C1    180.00   0.0  0
 1K7  CONST_12  H34  C3   C2   C1    180.00   0.0  0
 1K7  CONST_13  H32  C1   C2   C3    180.00   0.0  0
 1K7  Var_01    C26  C27  C28  N29   109.20  30.0  1
 1K7  Var_02    C25  C26  C27  C28  -111.48  30.0  1
 1K7  Var_03    C9   C25  C26  C28  -154.69  30.0  1
 1K7  Var_04    C5   C6   C7   C8    -86.57  30.0  2
 1K7  Var_05    H22  N29  C28  C27    85.21  30.0  3
 1K7  Var_06    C6   C7   C8   C9    179.57  30.0  1

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
 1K7  chir_03  C9   C8   C25  N10  positiv
 1K7  chir_04  C28  C27  N29  C26  both
 1K7  chir_05  C26  C25  C27  C28  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
 1K7  plan-1  C7   0.020
 1K7  plan-1  C6   0.020
 1K7  plan-1  C1   0.020
 1K7  plan-1  C2   0.020
 1K7  plan-1  C3   0.020
 1K7  plan-1  C4   0.020
 1K7  plan-1  C5   0.020
 1K7  plan-1  H32  0.020
 1K7  plan-1  H33  0.020
 1K7  plan-1  H34  0.020
 1K7  plan-1  H35  0.020
 1K7  plan-1  H36  0.020

