# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 12 17:57:05 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: (1S,7S)-7-amino-7-benzyl-8-oxohexahydro-1H-pyrazolo[1,2-a]pyridazine-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@]1(CCN2CC[C@H](N2C1=O)C(O)=O)Cc3ccccc3
#
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
 00U  00U  '(1S,7S)-7-amino-7-benzyl-8-oxohexahydro-1H-pyrazolo[1,2-a]pyridazine-1-carboxylic acid'  peptide  39  21  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_00U
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
 00U  C1    C  CH1    0  -0.149   2.3853   0.8745   0.4783
 00U  N1    N  NT     0  -0.288   2.2266  -1.4658   0.2390
 00U  O1    O  O      0  -0.519  -0.1043   1.0644  -0.6769
 00U  C2    C  CH2    0  -0.515   3.5928   0.1731   1.1297
 00U  N2    N  NT     0  -0.344   1.5239  -0.2366   0.1208
 00U  C3    C  CH2    0  -0.263   3.0817  -1.2347   1.3897
 00U  N3    N  NH2    0  -0.789  -1.2122  -1.1773  -2.0277
 00U  C4    C  CH2    0  -0.306   1.3279  -2.5889   0.3585
 00U  C5    C  CH2    0  -0.458   0.3540  -2.5605  -0.8003
 00U  C6    C  CT     0  -0.026  -0.5174  -1.3041  -0.7611
 00U  C7    C  C      0   0.578   0.3335  -0.0630  -0.4544
 00U  C8    C  C      0   0.406   2.8323   1.7393  -0.7191
 00U  C9    C  CH2    0  -0.508  -1.5728  -1.4603   0.3660
 00U  C10   C  CR6    0   0.152  -2.6112  -0.3779   0.4555
 00U  C11   C  CR16   0  -0.291  -2.4618   0.6889   1.3400
 00U  C12   C  CR16   0  -0.249  -3.4281   1.6797   1.4352
 00U  C13   C  CR16   0  -0.273  -4.5672   1.6216   0.6414
 00U  C14   C  CR16   0  -0.244  -4.7332   0.5605  -0.2382
 00U  C15   C  CR16   0  -0.317  -3.7646  -0.4317  -0.3251
 00U  H1    H  HCH1   0   0.242   1.8656   1.4978   1.2093
 00U  H2    H  HCH2   0   0.245   4.4388   0.1356   0.4413
 00U  H2A   H  HCH2   0   0.255   3.9196   0.6748   2.0379
 00U  H3    H  HCH2   0   0.211   2.5172  -1.2825   2.3330
 00U  H3A   H  HCH2   0   0.252   3.8716  -1.9846   1.4202
 00U  HN3   H  HNH2   0   0.352  -1.7031  -0.2913  -2.0558
 00U  HN3A  H  HNH2   0   0.345  -0.5410  -1.1471  -2.7866
 00U  H4    H  HCH2   0   0.261   1.9317  -3.4969   0.3297
 00U  H4A   H  HCH2   0   0.215   0.7955  -2.5869   1.3224
 00U  H5    H  HCH2   0   0.246   0.9218  -2.5830  -1.7358
 00U  H5A   H  HCH2   0   0.252  -0.2796  -3.4493  -0.7868
 00U  H9    H  HCH2   0   0.253  -2.0674  -2.4190   0.1890
 00U  H9A   H  HCH2   0   0.253  -1.0622  -1.5461   1.3271
 00U  H11   H  HCR6   0   0.239  -1.5806   0.7399   1.9685
 00U  H12   H  HCR6   0   0.250  -3.2933   2.4976   2.1316
 00U  H13   H  HCR6   0   0.251  -5.3236   2.3922   0.7160
 00U  H14   H  HCR6   0   0.250  -5.6224   0.4997  -0.8531
 00U  H15   H  HCR6   0   0.246  -3.9087  -1.2620  -1.0061
 00U  OXT   O  OC    -1  -0.617   3.1519   2.9087  -0.4267
 00U  O2    O  O      0  -0.597   2.8968   1.1877  -1.8287

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
 00U  C1   N2    single    1.451  0.020  1.451
 00U  C1   H1    single    0.970  0.020  1.090
 00U  N1   N2    single    1.421  0.020  1.421
 00U  N1   C4    single    1.443  0.020  1.443
 00U  C2   C1    single    1.541  0.020  1.541
 00U  C2   C3    single    1.520  0.020  1.520
 00U  C2   H2    single    0.970  0.020  1.090
 00U  C2   H2A   single    0.970  0.020  1.090
 00U  N2   C7    single    1.333  0.020  1.333
 00U  O2   C8    deloc     1.241  0.020  1.241
 00U  C3   N1    single    1.452  0.020  1.452
 00U  C3   H3    single    0.970  0.020  1.090
 00U  C3   H3A   single    0.970  0.020  1.090
 00U  N3   HN3   single    0.890  0.020  1.040
 00U  N3   HN3A  single    0.890  0.020  1.040
 00U  C4   C5    single    1.514  0.020  1.514
 00U  C4   H4    single    0.970  0.020  1.090
 00U  C4   H4A   single    0.970  0.020  1.090
 00U  C5   C6    single    1.530  0.020  1.530
 00U  C5   H5    single    0.970  0.020  1.090
 00U  C5   H5A   single    0.970  0.020  1.090
 00U  C6   N3    single    1.450  0.020  1.450
 00U  C6   C9    single    1.552  0.020  1.552
 00U  C7   O1    double    1.230  0.020  1.230
 00U  C7   C6    single    1.536  0.020  1.536
 00U  C8   C1    single    1.543  0.020  1.543
 00U  C9   C10   single    1.503  0.020  1.503
 00U  C9   H9    single    0.970  0.020  1.090
 00U  C9   H9A   single    0.970  0.020  1.090
 00U  C10  C15   aromatic  1.394  0.020  1.394
 00U  C10  C11   aromatic  1.394  0.020  1.394
 00U  C11  C12   aromatic  1.387  0.020  1.387
 00U  C11  H11   single    0.930  0.020  1.080
 00U  C12  C13   aromatic  1.390  0.020  1.390
 00U  C12  H12   single    0.930  0.020  1.080
 00U  C13  H13   single    0.930  0.020  1.080
 00U  C14  C13   aromatic  1.388  0.020  1.388
 00U  C14  H14   single    0.930  0.020  1.080
 00U  C15  C14   aromatic  1.389  0.020  1.389
 00U  C15  H15   single    0.930  0.020  1.080
 00U  C8   OXT   deloc     1.247  0.020  1.247

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
 00U  H1    C1   C8   109.72  3.000
 00U  C8    C1   N2   114.21  3.000
 00U  H1    C1   N2   108.64  3.000
 00U  C8    C1   C2   110.86  3.000
 00U  H1    C1   C2   110.46  3.000
 00U  N2    C1   C2   102.76  3.000
 00U  C4    N1   C3   115.14  3.000
 00U  C3    N1   N2   102.68  3.000
 00U  C4    N1   N2   111.85  3.000
 00U  H2A   C2   H2   108.04  3.000
 00U  H2A   C2   C3   112.67  3.000
 00U  H2    C2   C3   109.68  3.000
 00U  H2A   C2   C1   112.23  3.000
 00U  H2    C2   C1   110.88  3.000
 00U  C3    C2   C1   103.32  3.000
 00U  C7    N2   N1   126.16  3.000
 00U  C7    N2   C1   122.46  3.000
 00U  N1    N2   C1   110.39  3.000
 00U  H3A   C3   H3   108.54  3.000
 00U  H3A   C3   C2   113.48  3.000
 00U  H3    C3   C2   111.06  3.000
 00U  H3A   C3   N1   109.84  3.000
 00U  H3    C3   N1   111.73  3.000
 00U  C2    C3   N1   102.11  3.000
 00U  HN3A  N3   HN3  105.90  3.000
 00U  HN3A  N3   C6   109.83  3.000
 00U  HN3   N3   C6   109.43  3.000
 00U  H4A   C4   H4   106.99  3.000
 00U  H4A   C4   C5   111.04  3.000
 00U  H4    C4   C5   110.58  3.000
 00U  H4A   C4   N1   111.84  3.000
 00U  H4    C4   N1   107.51  3.000
 00U  C5    C4   N1   108.82  3.000
 00U  H5A   C5   H5   107.15  3.000
 00U  H5A   C5   C6   109.74  3.000
 00U  H5    C5   C6   109.53  3.000
 00U  H5A   C5   C4   110.41  3.000
 00U  H5    C5   C4   108.67  3.000
 00U  C6    C5   C4   111.24  3.000
 00U  C9    C6   C7   108.24  3.000
 00U  C7    C6   C5   110.69  3.000
 00U  C9    C6   C5   108.86  3.000
 00U  C7    C6   N3   111.67  3.000
 00U  C9    C6   N3   108.50  3.000
 00U  C5    C6   N3   108.81  3.000
 00U  C6    C7   N2   118.40  3.000
 00U  C6    C7   O1   120.50  3.000
 00U  N2    C7   O1   121.01  3.000
 00U  OXT   C8   O2   127.82  3.000
 00U  OXT   C8   C1   114.70  3.000
 00U  O2    C8   C1   117.38  3.000
 00U  H9A   C9   H9   106.57  3.000
 00U  H9A   C9   C10  109.11  3.000
 00U  H9    C9   C10  109.19  3.000
 00U  H9A   C9   C6   109.23  3.000
 00U  H9    C9   C6   106.17  3.000
 00U  C10   C9   C6   116.15  3.000
 00U  C15   C10  C11  118.27  3.000
 00U  C11   C10  C9   121.00  3.000
 00U  C15   C10  C9   120.71  3.000
 00U  H11   C11  C12  119.54  3.000
 00U  H11   C11  C10  119.42  3.000
 00U  C12   C11  C10  121.03  3.000
 00U  H12   C12  C13  120.07  3.000
 00U  H12   C12  C11  119.80  3.000
 00U  C13   C12  C11  120.13  3.000
 00U  H13   C13  C14  120.29  3.000
 00U  C14   C13  C12  119.47  3.000
 00U  H13   C13  C12  120.24  3.000
 00U  H14   C14  C15  119.79  3.000
 00U  C15   C14  C13  120.14  3.000
 00U  H14   C14  C13  120.06  3.000
 00U  H15   C15  C14  119.60  3.000
 00U  H15   C15  C10  119.45  3.000
 00U  C14   C15  C10  120.96  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
 00U  CONST_01  C13  C14  C15  C10    0.00   0.0  0
 00U  CONST_02  C13  C12  C11  C10    0.00   0.0  0
 00U  CONST_03  C14  C15  C10  C11    0.00   0.0  0
 00U  CONST_04  C14  C13  C12  C11    0.00   0.0  0
 00U  CONST_05  C15  C10  C11  C12    0.00   0.0  0
 00U  CONST_06  C15  C14  C13  C12    0.00   0.0  0
 00U  CONST_07  C6   C7   N2   C1   180.00   0.0  0
 00U  CONST_08  C6   C7   N2   N1     0.00   0.0  0
 00U  CONST_09  C14  C15  C10  C9   180.00   0.0  0
 00U  CONST_10  C12  C11  C10  C9   180.00   0.0  0
 00U  CONST_11  O1   C7   N2   C1     0.00   0.0  0
 00U  CONST_12  O1   C7   N2   N1   180.00   0.0  0
 00U  CONST_13  H14  C14  C15  C10  180.00   0.0  0
 00U  CONST_14  H12  C12  C11  C10  180.00   0.0  0
 00U  CONST_15  H15  C15  C10  C11  180.00   0.0  0
 00U  CONST_16  H13  C13  C12  C11  180.00   0.0  0
 00U  CONST_17  H11  C11  C12  C13  180.00   0.0  0
 00U  Var_01    C4   N1   N2   C1   159.64  30.0  1
 00U  Var_02    N1   C3   C2   C1    35.73  30.0  1
 00U  Var_03    C6   C5   C4   N1   -63.10  30.0  1
 00U  Var_04    N2   N1   C3   C2   -43.21  30.0  1
 00U  Var_05    C5   C4   N1   N2    53.87  30.0  1
 00U  Var_06    C15  C10  C9   C6    85.16  30.0  2

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
 00U  chir_01  C1  N2  C2  C8  negativ
 00U  chir_02  C6  C7  C9  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
 00U  plan-1  C9   0.020
 00U  plan-1  C10  0.020
 00U  plan-1  C11  0.020
 00U  plan-1  C12  0.020
 00U  plan-1  C13  0.020
 00U  plan-1  C14  0.020
 00U  plan-1  C15  0.020
 00U  plan-1  H11  0.020
 00U  plan-1  H12  0.020
 00U  plan-1  H13  0.020
 00U  plan-1  H14  0.020
 00U  plan-1  H15  0.020
 00U  plan-2  C1   0.020
 00U  plan-2  N1   0.020
 00U  plan-2  O1   0.020
 00U  plan-2  N2   0.020
 00U  plan-2  C6   0.020
 00U  plan-2  C7   0.020
 00U  plan-3  C1   0.020
 00U  plan-3  C8   0.020
 00U  plan-3  OXT  0.020
 00U  plan-3  O2   0.020

