# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Sep 21 00:39:04 2022
#   Inital geometry file: a 87 line input string
#   Ligand name: N-(cyclopent-3-ene-1-carbonyl)-L-histidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@H](Cc1c[nH]cn1)NC(=O)C2CC=CC2
#
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
 A1I  A1I  "N-(cyclopent-3-ene-1-carbonyl)-L-histidine"  ligand  33  18  .  2022-09-16  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A1I
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
 A1I  C10  C  CR15  0  -0.120  -14.3932  14.6551  3.5263
 A1I  C15  C  CH2   0  -0.468  -16.1709   9.3411  7.5885
 A1I  C17  C  CR15  0  -0.219  -18.3970   9.3429  8.3423
 A1I  C02  C  C     0   0.564  -16.9958  10.3908  5.4859
 A1I  N03  N  NH1   0  -0.643  -16.1001  10.3116  4.4798
 A1I  C04  C  CH1   0  -0.170  -15.7434  11.4398  3.6568
 A1I  C05  C  C     0   0.544  -15.4423  10.9388  2.2570
 A1I  O06  O  O     0  -0.431  -14.8160   9.9338  2.0350
 A1I  O07  O  OH1   0  -0.580  -15.9304  11.7329  1.3201
 A1I  C08  C  CH2   0  -0.522  -14.5183  12.1838  4.2303
 A1I  C09  C  CR5   0   0.132  -14.0708  13.3322  3.3951
 A1I  N11  N  NR15  0  -0.563  -13.7637  15.2863  2.4937
 A1I  C12  C  CR15  0   0.087  -13.0983  14.3514  1.7898
 A1I  N13  N  N     0  -0.452  -13.2611  13.1594  2.3049
 A1I  C14  C  CR15  0  -0.411  -17.0852   9.1454  6.3441
 A1I  C16  C  CR15  0  -0.219  -17.1407   9.5640  8.7098
 A1I  C18  C  CH2   0  -0.461  -18.5069   8.9313  6.9046
 A1I  H1   H  HCR5  0   0.283  -14.9974  15.1810  4.2464
 A1I  H3   H  HCH2  0   0.246  -15.4670  10.1695  7.4690
 A1I  H4   H  HCR5  0   0.240  -19.2580   9.4150  8.9947
 A1I  H6   H  HNH1  0   0.402  -15.5467   9.4734  4.3869
 A1I  H7   H  HCH1  0   0.288  -16.5901  12.1249  3.6252
 A1I  H8   H  HOH1  0   0.480  -15.6695  11.4136  0.4418
 A1I  H9   H  HCH2  0   0.268  -14.7925  12.5288  5.2285
 A1I  H10  H  HCH2  0   0.253  -13.7016  11.4674  4.3486
 A1I  H11  H  HNR5  0   0.419  -13.7823  16.2752  2.3003
 A1I  H12  H  HCR5  0   0.276  -12.5084  14.5928  0.9190
 A1I  H14  H  HCR5  0   0.274  -16.7556   8.2804  5.7664
 A1I  H15  H  HCR5  0   0.241  -16.8219   9.8437  9.7059
 A1I  H17  H  HCH2  0   0.246  -18.8050   7.8819  6.8238
 A1I  H18  H  HCH2  0   0.243  -19.2616   9.5047  6.3624
 A1I  H2   H  HCH2  0   0.252  -15.5587   8.4528  7.7675
 A1I  O01  O  O     0  -0.478  -17.6502  11.3973  5.7103

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
 A1I  C10  C09  aromatic  1.368  0.020  1.368
 A1I  C10  N11  aromatic  1.364  0.020  1.364
 A1I  C15  C14  single    1.557  0.020  1.557
 A1I  C15  C16  single    1.499  0.020  1.499
 A1I  C17  C16  double    1.327  0.020  1.327
 A1I  C17  C18  single    1.500  0.020  1.500
 A1I  O01  C02  double    1.221  0.020  1.221
 A1I  C02  N03  single    1.349  0.020  1.349
 A1I  N03  C04  single    1.441  0.020  1.441
 A1I  C04  C05  single    1.517  0.020  1.517
 A1I  C04  C08  single    1.544  0.020  1.544
 A1I  C05  O06  double    1.205  0.020  1.205
 A1I  C05  O07  single    1.322  0.020  1.322
 A1I  C08  C09  single    1.489  0.020  1.489
 A1I  C09  N13  aromatic  1.369  0.020  1.369
 A1I  N11  C12  aromatic  1.346  0.020  1.346
 A1I  C12  N13  aromatic  1.309  0.020  1.309
 A1I  C14  C18  single    1.543  0.020  1.543
 A1I  C02  C14  single    1.515  0.020  1.515
 A1I  C10  H1   single    0.930  0.020  1.080
 A1I  C15  H2   single    0.970  0.020  1.090
 A1I  C15  H3   single    0.970  0.020  1.090
 A1I  C17  H4   single    0.930  0.020  1.080
 A1I  N03  H6   single    0.860  0.020  1.020
 A1I  C04  H7   single    0.970  0.020  1.090
 A1I  O07  H8   single    0.850  0.020  0.980
 A1I  C08  H9   single    0.970  0.020  1.090
 A1I  C08  H10  single    0.970  0.020  1.090
 A1I  N11  H11  single    0.860  0.020  1.020
 A1I  C12  H12  single    0.930  0.020  1.080
 A1I  C14  H14  single    0.970  0.020  1.090
 A1I  C16  H15  single    0.930  0.020  1.080
 A1I  C18  H17  single    0.970  0.020  1.090
 A1I  C18  H18  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
 A1I  H1   C10  N11  122.61  3.000
 A1I  H1   C10  C09  131.96  3.000
 A1I  N11  C10  C09  105.43  3.000
 A1I  H3   C15  H2   105.83  3.000
 A1I  H3   C15  C16  112.67  3.000
 A1I  H2   C15  C16  111.13  3.000
 A1I  H3   C15  C14  112.70  3.000
 A1I  H2   C15  C14  110.95  3.000
 A1I  C16  C15  C14  103.69  3.000
 A1I  H4   C17  C18  122.53  3.000
 A1I  H4   C17  C16  125.08  3.000
 A1I  C18  C17  C16  112.36  3.000
 A1I  C14  C02  N03  114.41  3.000
 A1I  C14  C02  O01  122.80  3.000
 A1I  N03  C02  O01  122.75  3.000
 A1I  H6   N03  C04  117.52  3.000
 A1I  H6   N03  C02  118.79  3.000
 A1I  C04  N03  C02  122.97  3.000
 A1I  H7   C04  C08  108.93  3.000
 A1I  H7   C04  C05  109.58  3.000
 A1I  C08  C04  C05  110.15  3.000
 A1I  H7   C04  N03  108.45  3.000
 A1I  C08  C04  N03  111.19  3.000
 A1I  C05  C04  N03  108.52  3.000
 A1I  O07  C05  O06  124.23  3.000
 A1I  O07  C05  C04  112.49  3.000
 A1I  O06  C05  C04  123.28  3.000
 A1I  H8   O07  C05  110.17  3.000
 A1I  H10  C08  H9   107.22  3.000
 A1I  H10  C08  C09  109.98  3.000
 A1I  H9   C08  C09  110.17  3.000
 A1I  H10  C08  C04  108.50  3.000
 A1I  H9   C08  C04  107.03  3.000
 A1I  C09  C08  C04  113.69  3.000
 A1I  N13  C09  C08  121.81  3.000
 A1I  N13  C09  C10  109.75  3.000
 A1I  C08  C09  C10  128.41  3.000
 A1I  H11  N11  C12  126.17  3.000
 A1I  H11  N11  C10  126.22  3.000
 A1I  C12  N11  C10  107.61  3.000
 A1I  H12  C12  N13  126.11  3.000
 A1I  H12  C12  N11  122.46  3.000
 A1I  N13  C12  N11  111.42  3.000
 A1I  C12  N13  C09  105.79  3.000
 A1I  H14  C14  C18  111.14  3.000
 A1I  H14  C14  C02  109.51  3.000
 A1I  C18  C14  C02  111.97  3.000
 A1I  H14  C14  C15  110.21  3.000
 A1I  C02  C14  C15  108.35  3.000
 A1I  C18  C14  C15  105.56  3.000
 A1I  H15  C16  C17  125.20  3.000
 A1I  H15  C16  C15  122.41  3.000
 A1I  C17  C16  C15  112.36  3.000
 A1I  H18  C18  H17  106.18  3.000
 A1I  H18  C18  C14  112.55  3.000
 A1I  H17  C18  C14  110.94  3.000
 A1I  H18  C18  C17  112.50  3.000
 A1I  H17  C18  C17  110.74  3.000
 A1I  C14  C18  C17  104.04  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
 A1I  CONST_01  C12  N13  C09  C10     0.00   0.0  0
 A1I  CONST_02  N13  C12  N11  C10     0.00   0.0  0
 A1I  CONST_03  C12  N11  C10  C09     0.00   0.0  0
 A1I  CONST_04  N11  C12  N13  C09     0.00   0.0  0
 A1I  CONST_05  N13  C09  C10  N11     0.00   0.0  0
 A1I  CONST_06  N11  C10  C09  C08   180.00   0.0  0
 A1I  CONST_07  C12  N13  C09  C08   180.00   0.0  0
 A1I  CONST_08  H12  C12  N11  C10   180.00   0.0  0
 A1I  CONST_09  H11  N11  C10  C09   180.00   0.0  0
 A1I  CONST_10  H12  C12  N13  C09   180.00   0.0  0
 A1I  CONST_11  H1   C10  N11  C12   180.00   0.0  0
 A1I  CONST_12  H1   C10  C09  N13   180.00   0.0  0
 A1I  CONST_13  H11  N11  C12  N13   180.00   0.0  0
 A1I  CONST_14  C14  C02  N03  C04   180.00   0.0  0
 A1I  CONST_15  H6   N03  C02  C14     0.00   0.0  0
 A1I  CONST_16  C04  N03  C02  O01     0.00   0.0  0
 A1I  CONST_17  H6   N03  C02  O01   180.00   0.0  0
 A1I  CONST_18  H8   O07  C05  C04   180.00   0.0  0
 A1I  CONST_19  H8   O07  C05  O06     0.00   0.0  0
 A1I  Var_01    C18  C17  C16  C15    -0.06  30.0  1
 A1I  Var_02    C14  C15  C16  C17     8.71  30.0  1
 A1I  Var_03    C16  C17  C18  C14    -8.71  30.0  1
 A1I  Var_04    H4   C17  C16  C15   178.16  30.0  1
 A1I  Var_05    H2   C15  C16  C17  -110.54  30.0  1
 A1I  Var_06    H3   C15  C16  C17   130.88  30.0  1
 A1I  Var_07    H15  C16  C15  C14  -173.04  30.0  1
 A1I  Var_08    H4   C17  C18  C14   173.01  30.0  1
 A1I  Var_09    H17  C18  C17  C16   110.54  30.0  1
 A1I  Var_10    H18  C18  C17  C16  -130.82  30.0  1
 A1I  Var_11    H15  C16  C17  C18  -178.24  30.0  1
 A1I  Var_12    C04  C08  C09  C10    95.20  30.0  2
 A1I  Var_13    N13  C09  C08  C04   -82.68  30.0  2
 A1I  Var_14    H9   C08  C09  C10   -24.93  30.0  2
 A1I  Var_15    H10  C08  C09  C10  -142.91  30.0  2
 A1I  Var_16    H9   C08  C09  N13   157.20  30.0  2
 A1I  Var_17    H10  C08  C09  N13    39.21  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
 A1I  chir_01  C04  N03  C05  C08  positiv
 A1I  chir_02  C14  C02  C18  C15  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
 A1I  plan-1  C10  0.020
 A1I  plan-1  C08  0.020
 A1I  plan-1  C09  0.020
 A1I  plan-1  N11  0.020
 A1I  plan-1  C12  0.020
 A1I  plan-1  N13  0.020
 A1I  plan-1  H1   0.020
 A1I  plan-1  H11  0.020
 A1I  plan-1  H12  0.020
 A1I  plan-2  C02  0.020
 A1I  plan-2  N03  0.020
 A1I  plan-2  C04  0.020
 A1I  plan-2  C14  0.020
 A1I  plan-2  H6   0.020
 A1I  plan-2  O01  0.020
 A1I  plan-3  C04  0.020
 A1I  plan-3  C05  0.020
 A1I  plan-3  O06  0.020
 A1I  plan-3  O07  0.020
 A1I  plan-3  H8   0.020

