# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 19:19:32 2022
#   Inital geometry file: a 56 line input string
#   Ligand name: N-(4-aminobutyl)acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)NCCCCN
#
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
 X5A  X5A  N-(4-aminobutyl)acetamide  ligand  23  9  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_X5A
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
 X5A  C01  C  CH3   0  -0.775  18.8670  41.7340  34.9913
 X5A  C02  C  C     0   0.517  20.0421  41.1964  34.2104
 X5A  C05  C  CH2   0  -0.231  22.4236  40.6177  34.2925
 X5A  C06  C  CH2   0  -0.476  23.5797  40.7321  35.2728
 X5A  C07  C  CH2   0  -0.426  24.8765  40.1900  34.6896
 X5A  C08  C  CH2   0  -0.270  26.0438  40.3031  35.6579
 X5A  N04  N  NH1   0  -0.633  21.2011  41.1217  34.8819
 X5A  N09  N  NH2   0  -0.797  27.2629  39.7693  35.0671
 X5A  O03  O  O     0  -0.505  19.9382  40.8540  33.0391
 X5A  H1   H  HCH3  0   0.262  18.4784  42.6237  34.4960
 X5A  H2   H  HCH3  0   0.261  18.0677  40.9929  34.9977
 X5A  H3   H  HCH3  0   0.246  19.1054  41.9910  36.0219
 X5A  H4   H  HCH2  0   0.227  22.2950  39.5722  33.9955
 X5A  H5   H  HCH2  0   0.229  22.6555  41.1779  33.3826
 X5A  H6   H  HCH2  0   0.229  23.7130  41.7809  35.5567
 X5A  H7   H  HCH2  0   0.228  23.3326  40.1884  36.1905
 X5A  H8   H  HCH2  0   0.216  24.7382  39.1393  34.4119
 X5A  H9   H  HCH2  0   0.218  25.1246  40.7247  33.7679
 X5A  H10  H  HCH2  0   0.212  26.2112  41.3580  35.8920
 X5A  H11  H  HCH2  0   0.188  25.7662  39.8191  36.6058
 X5A  H12  H  HNH1  0   0.399  21.2231  41.4009  35.8491
 X5A  H13  H  HNH2  0   0.344  28.0321  39.8918  35.7133
 X5A  H14  H  HNH2  0   0.336  27.1644  38.7678  34.9519

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
 X5A  O03  C02  double  1.225  0.020  1.225
 X5A  C02  C01  single  1.510  0.020  1.510
 X5A  C02  N04  single  1.342  0.020  1.342
 X5A  C05  N04  single  1.448  0.020  1.448
 X5A  C05  C06  single  1.520  0.020  1.520
 X5A  C07  C06  single  1.522  0.020  1.522
 X5A  C07  C08  single  1.521  0.020  1.521
 X5A  N09  C08  single  1.456  0.020  1.456
 X5A  C01  H1   single  0.970  0.020  1.090
 X5A  C01  H2   single  0.970  0.020  1.090
 X5A  C01  H3   single  0.970  0.020  1.090
 X5A  C05  H4   single  0.970  0.020  1.090
 X5A  C05  H5   single  0.970  0.020  1.090
 X5A  C06  H6   single  0.970  0.020  1.090
 X5A  C06  H7   single  0.970  0.020  1.090
 X5A  C07  H8   single  0.970  0.020  1.090
 X5A  C07  H9   single  0.970  0.020  1.090
 X5A  C08  H10  single  0.970  0.020  1.090
 X5A  C08  H11  single  0.970  0.020  1.090
 X5A  N04  H12  single  0.860  0.020  1.020
 X5A  N09  H13  single  0.890  0.020  1.040
 X5A  N09  H14  single  0.890  0.020  1.040

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
 X5A  H3   C01  H2   108.40  3.000
 X5A  H3   C01  H1   108.40  3.000
 X5A  H2   C01  H1   107.23  3.000
 X5A  H3   C01  C02  113.78  3.000
 X5A  H2   C01  C02  109.37  3.000
 X5A  H1   C01  C02  109.45  3.000
 X5A  O03  C02  N04  122.44  3.000
 X5A  N04  C02  C01  115.68  3.000
 X5A  O03  C02  C01  121.88  3.000
 X5A  H5   C05  H4   106.77  3.000
 X5A  H5   C05  N04  109.85  3.000
 X5A  H4   C05  N04  110.11  3.000
 X5A  H5   C05  C06  109.69  3.000
 X5A  H4   C05  C06  109.65  3.000
 X5A  N04  C05  C06  110.70  3.000
 X5A  H7   C06  H6   106.61  3.000
 X5A  H7   C06  C07  109.68  3.000
 X5A  H6   C06  C07  109.69  3.000
 X5A  H7   C06  C05  109.36  3.000
 X5A  H6   C06  C05  109.39  3.000
 X5A  C07  C06  C05  111.97  3.000
 X5A  H9   C07  H8   106.49  3.000
 X5A  H9   C07  C08  109.03  3.000
 X5A  H8   C07  C08  109.25  3.000
 X5A  H9   C07  C06  110.00  3.000
 X5A  H8   C07  C06  109.34  3.000
 X5A  C08  C07  C06  112.55  3.000
 X5A  H11  C08  H10  106.18  3.000
 X5A  H11  C08  N09  113.56  3.000
 X5A  H10  C08  N09  108.20  3.000
 X5A  H11  C08  C07  108.80  3.000
 X5A  H10  C08  C07  109.00  3.000
 X5A  N09  C08  C07  110.91  3.000
 X5A  H12  N04  C05  117.97  3.000
 X5A  H12  N04  C02  118.97  3.000
 X5A  C05  N04  C02  123.04  3.000
 X5A  H14  N09  H13  105.43  3.000
 X5A  H14  N09  C08  109.10  3.000
 X5A  H13  N09  C08  109.44  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
 X5A  CONST_01  C05  N04  C02  C01  180.00   0.0  0
 X5A  CONST_02  O03  C02  N04  C05    0.00   0.0  0
 X5A  CONST_03  H12  N04  C02  C01    0.00   0.0  0
 X5A  Var_01    C06  C05  N04  C02  176.76  30.0  1
 X5A  Var_02    C08  C07  C06  C05  179.77  30.0  1
 X5A  Var_03    N09  C08  C07  C06  179.73  30.0  3
 X5A  Var_04    N04  C05  C06  C07  179.13  30.0  1
 X5A  Var_05    H13  N09  C08  C07  177.58  30.0  3
 X5A  Var_06    H1   C01  C02  N04  120.91  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
 X5A  plan-1  C01  0.020
 X5A  plan-1  C02  0.020
 X5A  plan-1  C05  0.020
 X5A  plan-1  N04  0.020
 X5A  plan-1  O03  0.020
 X5A  plan-1  H12  0.020

