# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 02:51:43 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: N-{4-[(1S)-1-aminoethyl]phenyl}cyclopropanecarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](N)c1ccc(NC(=O)C2CC2)cc1
#
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
 NY4  NY4  N-{4-[(1S)-1-aminoethyl]phenyl}cyclopropanecarboxamide  ligand  31  15  .  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_NY4
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
 NY4  N1   N  NH2   0  -0.783   4.5497  -0.6567   1.1866
 NY4  C4   C  CR16  0  -0.319   1.9729   1.4989   0.2349
 NY4  C5   C  CR16  0  -0.335   0.5931   1.6131   0.2387
 NY4  C6   C  CR6   0   0.354  -0.2172   0.4886   0.0750
 NY4  C7   C  C     0   0.590  -2.6121  -0.1992  -0.0090
 NY4  C8   C  CH1   0  -0.435  -3.9652   0.4163   0.0100
 NY4  C10  C  CH2   0  -0.464  -5.0434  -0.2445  -0.8105
 NY4  C1   C  CH3   0  -0.660   4.6086  -0.3460  -1.3044
 NY4  C11  C  CR16  0  -0.303   0.3952  -0.7554  -0.0932
 NY4  C12  C  CR16  0  -0.301   1.7797  -0.8459  -0.0992
 NY4  C2   C  CH1   0  -0.203   4.1039   0.1499   0.0520
 NY4  C3   C  CR6   0   0.168   2.5971   0.2680   0.0644
 NY4  C9   C  CH2   0  -0.464  -5.0803  -0.3544   0.6685
 NY4  O1   O  O     0  -0.480  -2.4453  -1.4048  -0.1014
 NY4  H1   H  HNH2  0   0.338   4.2546  -1.6185   1.0589
 NY4  H2   H  HNH2  0   0.347   5.5629  -0.6878   1.1838
 NY4  H4   H  HCR6  0   0.251   2.5732   2.3914   0.3681
 NY4  H5   H  HCR6  0   0.266   0.1399   2.5887   0.3738
 NY4  H6   H  HCH1  0   0.284  -4.0112   1.4962   0.0898
 NY4  H7   H  HCH2  0   0.265  -5.7498   0.4107  -1.3022
 NY4  H8   H  HCH2  0   0.260  -4.7622  -1.1207  -1.3796
 NY4  H9   H  HCH3  0   0.220   4.2441  -1.3525  -1.5196
 NY4  H10  H  HCH3  0   0.225   4.2821   0.3078  -2.1150
 NY4  H11  H  HCH3  0   0.230   5.6997  -0.3763  -1.3189
 NY4  H12  H  HCR6  0   0.278  -0.1926  -1.6488  -0.2244
 NY4  H13  H  HCR6  0   0.248   2.2197  -1.8264  -0.2436
 NY4  H14  H  HCH1  0   0.240   4.5070   1.1545   0.2105
 NY4  H15  H  HCH2  0   0.259  -4.8259  -1.3061   1.1166
 NY4  H16  H  HCH2  0   0.265  -5.8122   0.2250   1.2148
 NY4  H17  H  HNH1  0   0.415  -1.8747   1.6671   0.1740
 NY4  N2   N  NH1   0  -0.757  -1.5996   0.7010   0.0816

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
 NY4  C9   C8   single    1.507  0.020  1.507
 NY4  C9   C10  single    1.484  0.020  1.484
 NY4  C8   C10  single    1.507  0.020  1.507
 NY4  C8   C7   single    1.487  0.020  1.487
 NY4  C7   N2   single    1.358  0.020  1.358
 NY4  C7   O1   double    1.221  0.020  1.221
 NY4  N2   C6   single    1.399  0.020  1.399
 NY4  C6   C11  aromatic  1.397  0.020  1.397
 NY4  C6   C5   aromatic  1.396  0.020  1.396
 NY4  C11  C12  aromatic  1.388  0.020  1.388
 NY4  C5   C4   aromatic  1.385  0.020  1.385
 NY4  C12  C3   aromatic  1.391  0.020  1.391
 NY4  C4   C3   aromatic  1.391  0.020  1.391
 NY4  C3   C2   single    1.511  0.020  1.511
 NY4  C2   N1   single    1.462  0.020  1.462
 NY4  C2   C1   single    1.530  0.020  1.530
 NY4  N1   H1   single    0.890  0.020  1.040
 NY4  N1   H2   single    0.890  0.020  1.040
 NY4  C4   H4   single    0.930  0.020  1.080
 NY4  C5   H5   single    0.930  0.020  1.080
 NY4  C8   H6   single    0.970  0.020  1.090
 NY4  C10  H7   single    0.970  0.020  1.090
 NY4  C10  H8   single    0.970  0.020  1.090
 NY4  C1   H9   single    0.970  0.020  1.090
 NY4  C1   H10  single    0.970  0.020  1.090
 NY4  C1   H11  single    0.970  0.020  1.090
 NY4  C11  H12  single    0.930  0.020  1.080
 NY4  C12  H13  single    0.930  0.020  1.080
 NY4  C2   H14  single    0.970  0.020  1.090
 NY4  C9   H15  single    0.970  0.020  1.090
 NY4  C9   H16  single    0.970  0.020  1.090
 NY4  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
 NY4  H2   N1   H1   105.16  3.000
 NY4  H2   N1   C2   108.64  3.000
 NY4  H1   N1   C2   109.68  3.000
 NY4  H4   C4   C3   119.69  3.000
 NY4  H4   C4   C5   118.93  3.000
 NY4  C3   C4   C5   121.38  3.000
 NY4  H5   C5   C6   119.80  3.000
 NY4  H5   C5   C4   119.42  3.000
 NY4  C6   C5   C4   120.79  3.000
 NY4  N2   C6   C11  124.69  3.000
 NY4  C11  C6   C5   118.50  3.000
 NY4  N2   C6   C5   116.80  3.000
 NY4  O1   C7   N2   123.92  3.000
 NY4  O1   C7   C8   122.29  3.000
 NY4  N2   C7   C8   113.79  3.000
 NY4  H6   C8   C9   116.49  3.000
 NY4  H6   C8   C10  116.52  3.000
 NY4  C9   C8   C10   58.96  3.000
 NY4  H6   C8   C7   116.87  3.000
 NY4  C10  C8   C7   117.55  3.000
 NY4  C9   C8   C7   117.86  3.000
 NY4  H8   C10  H7   114.91  3.000
 NY4  H8   C10  C9   118.09  3.000
 NY4  H7   C10  C9   118.80  3.000
 NY4  H8   C10  C8   117.09  3.000
 NY4  H7   C10  C8   116.68  3.000
 NY4  C9   C10  C8    60.50  3.000
 NY4  H11  C1   H10  107.80  3.000
 NY4  H11  C1   H9   107.78  3.000
 NY4  H10  C1   H9   107.82  3.000
 NY4  H11  C1   C2   110.52  3.000
 NY4  H10  C1   C2   111.45  3.000
 NY4  H9   C1   C2   111.31  3.000
 NY4  H12  C11  C12  119.32  3.000
 NY4  H12  C11  C6   120.93  3.000
 NY4  C12  C11  C6   119.74  3.000
 NY4  H13  C12  C3   120.08  3.000
 NY4  H13  C12  C11  117.68  3.000
 NY4  C3   C12  C11  122.25  3.000
 NY4  H14  C2   C3   107.12  3.000
 NY4  H14  C2   C1   107.73  3.000
 NY4  C3   C2   C1   111.19  3.000
 NY4  H14  C2   N1   106.37  3.000
 NY4  C1   C2   N1   114.12  3.000
 NY4  C3   C2   N1   109.93  3.000
 NY4  C2   C3   C12  121.48  3.000
 NY4  C2   C3   C4   121.17  3.000
 NY4  C12  C3   C4   117.35  3.000
 NY4  H16  C9   H15  114.90  3.000
 NY4  H16  C9   C10  118.73  3.000
 NY4  H15  C9   C10  118.17  3.000
 NY4  H16  C9   C8   116.58  3.000
 NY4  H15  C9   C8   117.18  3.000
 NY4  C10  C9   C8    60.53  3.000
 NY4  H17  N2   C7   115.96  3.000
 NY4  H17  N2   C6   114.54  3.000
 NY4  C7   N2   C6   129.50  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
 NY4  CONST_01  C11  C6   C5   C4      0.00   0.0  0
 NY4  CONST_02  C11  C12  C3   C4      0.00   0.0  0
 NY4  CONST_03  C12  C11  C6   C5      0.00   0.0  0
 NY4  CONST_04  C12  C3   C4   C5      0.00   0.0  0
 NY4  CONST_05  C3   C12  C11  C6      0.00   0.0  0
 NY4  CONST_06  C3   C4   C5   C6      0.00   0.0  0
 NY4  CONST_07  N2   C6   C5   C4    180.00   0.0  0
 NY4  CONST_08  C2   C3   C4   C5    180.00   0.0  0
 NY4  CONST_09  C2   C3   C12  C11   180.00   0.0  0
 NY4  CONST_10  N2   C6   C11  C12   180.00   0.0  0
 NY4  CONST_11  H13  C12  C3   C4    180.00   0.0  0
 NY4  CONST_12  H12  C11  C6   C5    180.00   0.0  0
 NY4  CONST_13  H4   C4   C5   C6    180.00   0.0  0
 NY4  CONST_14  H5   C5   C6   C11   180.00   0.0  0
 NY4  CONST_15  C8   C7   N2   C6    180.00   0.0  0
 NY4  CONST_16  C7   N2   C6   C5    180.00   0.0  0
 NY4  CONST_17  C11  C6   N2   C7      0.00   0.0  0
 NY4  CONST_18  H17  N2   C6   C5      0.00   0.0  0
 NY4  CONST_19  O1   C7   N2   C6      0.00   0.0  0
 NY4  Var_01    C10  C9   C8   C7   -107.01  30.0  1
 NY4  Var_02    H7   C10  C9   C8   -106.12  30.0  1
 NY4  Var_03    N2   C7   C8   C10   146.14  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
 NY4  chir_02  C2  C3  N1   C1  negativ
 NY4  chir_03  C8  C9  C10  C7  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
 NY4  plan-1  C4   0.020
 NY4  plan-1  C5   0.020
 NY4  plan-1  C6   0.020
 NY4  plan-1  C11  0.020
 NY4  plan-1  C12  0.020
 NY4  plan-1  C2   0.020
 NY4  plan-1  C3   0.020
 NY4  plan-1  H4   0.020
 NY4  plan-1  H5   0.020
 NY4  plan-1  H12  0.020
 NY4  plan-1  H13  0.020
 NY4  plan-1  N2   0.020
 NY4  plan-2  C6   0.020
 NY4  plan-2  C7   0.020
 NY4  plan-2  C8   0.020
 NY4  plan-2  O1   0.020
 NY4  plan-2  H17  0.020
 NY4  plan-2  N2   0.020

