# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 08:24:46 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: (3Z)-3-(1-hydroxyethylidene)-1-(pyridin-2-yl)-3H-indolizinium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(/O)=C/1C=C(c2ccccn2)c3cccc[n+]/13
#
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
 P9I  P9I  (3Z)-3-(1-hydroxyethylidene)-1-(pyridin-2-yl)-3H-indolizinium  ligand  31  18  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_P9I
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
 P9I  O     O  OH1   0  -0.547   3.9387   1.0809  -0.0211
 P9I  C2    C  C     0   0.368   2.7632   1.6529  -0.0029
 P9I  C1    C  CH3   0  -0.776   2.7145   3.1354   0.0079
 P9I  C3    C  CR5   0   0.335   1.6361   0.8703   0.0025
 P9I  N2    N  N     1  -0.627   1.5786  -0.5382  -0.0092
 P9I  C15   C  CR16  0   0.044   2.5903  -1.4392  -0.0286
 P9I  C14   C  CR16  0  -0.358   2.3080  -2.7747  -0.0389
 P9I  C13   C  CR16  0  -0.103   0.9785  -3.2068  -0.0295
 P9I  C12   C  CR16  0  -0.389  -0.0429  -2.2871  -0.0087
 P9I  C11   C  CR56  0   0.485   0.2623  -0.9279   0.0019
 P9I  C5    C  CR5   0   0.050  -0.5571   0.2519   0.0207
 P9I  C4    C  CR15  0  -0.428   0.2913   1.3194   0.0209
 P9I  C6    C  CR6   0   0.223  -2.0210   0.2966   0.0398
 P9I  N1    N  N     0  -0.451  -2.6678  -0.8657   0.0946
 P9I  C10   C  CR16  0  -0.062  -3.9937  -0.8628   0.1173
 P9I  C9    C  CR16  0  -0.328  -4.7538   0.2947   0.0882
 P9I  C8    C  CR16  0  -0.149  -4.0845   1.5091   0.0294
 P9I  C7    C  CR16  0  -0.340  -2.7023   1.5153   0.0033
 P9I  H     H  HOH1  0   0.519   4.6625   1.7245  -0.0228
 P9I  H11C  H  HCH3  0   0.302   3.2009   3.5199  -0.8912
 P9I  H12C  H  HCH3  0   0.287   1.7072   3.5321   0.0489
 P9I  H13C  H  HCH3  0   0.301   3.2691   3.5106   0.8705
 P9I  H4    H  HCR5  0   0.296   0.0076   2.3589   0.0357
 P9I  H15   H  HCR6  0   0.346   3.5993  -1.0690  -0.0352
 P9I  H14   H  HCR6  0   0.303   3.1271  -3.4775  -0.0537
 P9I  H13   H  HCR6  0   0.299   0.7538  -4.2642  -0.0376
 P9I  H12   H  HCR6  0   0.305  -1.0787  -2.5841   0.0020
 P9I  H7    H  HCR6  0   0.274  -2.1682   2.4540  -0.0479
 P9I  H10   H  HCR6  0   0.266  -4.4740  -1.8337   0.1617
 P9I  H9    H  HCR6  0   0.276  -5.8332   0.2437   0.1096
 P9I  H8    H  HCR6  0   0.279  -4.6328   2.4413   0.0022

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
 P9I  O    C2    single    1.307  0.020  1.307
 P9I  C2   C1    single    1.483  0.020  1.483
 P9I  C2   C3    double    1.372  0.020  1.372
 P9I  C3   N2    single    1.410  0.020  1.410
 P9I  C3   C4    single    1.418  0.020  1.418
 P9I  N2   C15   aromatic  1.355  0.020  1.355
 P9I  N2   C11   aromatic  1.373  0.020  1.373
 P9I  C15  C14   aromatic  1.365  0.020  1.365
 P9I  C14  C13   aromatic  1.398  0.020  1.398
 P9I  C13  C12   aromatic  1.375  0.020  1.375
 P9I  C12  C11   aromatic  1.393  0.020  1.393
 P9I  C11  C5    single    1.437  0.020  1.437
 P9I  C5   C4    double    1.364  0.020  1.364
 P9I  C5   C6    single    1.465  0.020  1.465
 P9I  C6   N1    aromatic  1.331  0.020  1.331
 P9I  C6   C7    aromatic  1.397  0.020  1.397
 P9I  N1   C10   aromatic  1.326  0.020  1.326
 P9I  C10  C9    aromatic  1.385  0.020  1.385
 P9I  C9   C8    aromatic  1.388  0.020  1.388
 P9I  C8   C7    aromatic  1.382  0.020  1.382
 P9I  O    H     single    0.850  0.020  0.980
 P9I  C1   H11C  single    0.970  0.020  1.090
 P9I  C1   H12C  single    0.970  0.020  1.090
 P9I  C1   H13C  single    0.970  0.020  1.090
 P9I  C4   H4    single    0.930  0.020  1.080
 P9I  C15  H15   single    0.930  0.020  1.080
 P9I  C14  H14   single    0.930  0.020  1.080
 P9I  C13  H13   single    0.930  0.020  1.080
 P9I  C12  H12   single    0.930  0.020  1.080
 P9I  C7   H7    single    0.930  0.020  1.080
 P9I  C10  H10   single    0.930  0.020  1.080
 P9I  C9   H9    single    0.930  0.020  1.080
 P9I  C8   H8    single    0.930  0.020  1.080

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
 P9I  H     O    C2    112.40  3.000
 P9I  C3    C2   C1    122.89  3.000
 P9I  C3    C2   O     119.27  3.000
 P9I  C1    C2   O     117.84  3.000
 P9I  H13C  C1   H12C  108.45  3.000
 P9I  H13C  C1   H11C  107.65  3.000
 P9I  H12C  C1   H11C  108.44  3.000
 P9I  H13C  C1   C2    109.41  3.000
 P9I  H12C  C1   C2    113.38  3.000
 P9I  H11C  C1   C2    109.34  3.000
 P9I  C4    C3   N2    106.13  3.000
 P9I  C4    C3   C2    126.76  3.000
 P9I  N2    C3   C2    127.11  3.000
 P9I  C11   N2   C15   121.83  3.000
 P9I  C11   N2   C3    108.82  3.000
 P9I  C15   N2   C3    129.35  3.000
 P9I  H15   C15  C14   122.08  3.000
 P9I  H15   C15  N2    118.16  3.000
 P9I  C14   C15  N2    119.76  3.000
 P9I  H14   C14  C13   121.37  3.000
 P9I  H14   C14  C15   118.70  3.000
 P9I  C13   C14  C15   119.93  3.000
 P9I  H13   C13  C12   120.01  3.000
 P9I  H13   C13  C14   119.99  3.000
 P9I  C12   C13  C14   120.00  3.000
 P9I  H12   C12  C11   118.65  3.000
 P9I  H12   C12  C13   122.00  3.000
 P9I  C11   C12  C13   119.35  3.000
 P9I  C5    C11  C12   132.56  3.000
 P9I  C5    C11  N2    108.30  3.000
 P9I  C12   C11  N2    119.14  3.000
 P9I  C6    C5   C4    126.72  3.000
 P9I  C6    C5   C11   126.54  3.000
 P9I  C4    C5   C11   106.74  3.000
 P9I  H4    C4   C5    126.26  3.000
 P9I  H4    C4   C3    123.73  3.000
 P9I  C5    C4   C3    110.01  3.000
 P9I  C7    C6   N1    121.73  3.000
 P9I  C7    C6   C5    120.92  3.000
 P9I  N1    C6   C5    117.35  3.000
 P9I  C10   N1   C6    118.99  3.000
 P9I  H10   C10  C9    120.41  3.000
 P9I  H10   C10  N1    116.22  3.000
 P9I  C9    C10  N1    123.37  3.000
 P9I  H9    C9   C8    121.59  3.000
 P9I  H9    C9   C10   120.54  3.000
 P9I  C8    C9   C10   117.87  3.000
 P9I  H8    C8   C7    120.16  3.000
 P9I  H8    C8   C9    120.71  3.000
 P9I  C7    C8   C9    119.14  3.000
 P9I  H7    C7   C8    119.91  3.000
 P9I  H7    C7   C6    121.18  3.000
 P9I  C8    C7   C6    118.90  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
 P9I  CONST_01  C13   C14  C15  N2      0.00   0.0  0
 P9I  CONST_02  C13   C12  C11  N2      0.00   0.0  0
 P9I  CONST_03  C12   C11  N2   C15     0.00   0.0  0
 P9I  CONST_04  C12   C13  C14  C15     0.00   0.0  0
 P9I  CONST_05  C11   N2   C15  C14     0.00   0.0  0
 P9I  CONST_06  C11   C12  C13  C14     0.00   0.0  0
 P9I  CONST_07  C9    C10  N1   C6      0.00   0.0  0
 P9I  CONST_08  C9    C8   C7   C6      0.00   0.0  0
 P9I  CONST_09  C8    C7   C6   N1      0.00   0.0  0
 P9I  CONST_10  C8    C9   C10  N1      0.00   0.0  0
 P9I  CONST_11  C7    C6   N1   C10     0.00   0.0  0
 P9I  CONST_12  C7    C8   C9   C10     0.00   0.0  0
 P9I  CONST_13  C10   N1   C6   C5    180.00   0.0  0
 P9I  CONST_14  C8    C7   C6   C5    180.00   0.0  0
 P9I  CONST_15  H15   C15  N2   C3      0.00   0.0  0
 P9I  CONST_16  H14   C14  C15  N2    180.00   0.0  0
 P9I  CONST_17  H12   C12  C11  N2    180.00   0.0  0
 P9I  CONST_18  H13   C13  C14  C15   180.00   0.0  0
 P9I  CONST_19  H7    C7   C6   C5      0.00   0.0  0
 P9I  CONST_20  H10   C10  N1   C6    180.00   0.0  0
 P9I  CONST_21  H8    C8   C7   C6    180.00   0.0  0
 P9I  CONST_22  H9    C9   C10  N1    180.00   0.0  0
 P9I  Var_01    N1    C6   C5   C11     2.65  30.0  2
 P9I  Var_02    N2    C3   C2   O       0.02  30.0  2
 P9I  Var_03    H11C  C1   C2   C3   -119.49  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
 P9I  plan-1  C5   0.020
 P9I  plan-1  C6   0.020
 P9I  plan-1  N1   0.020
 P9I  plan-1  C10  0.020
 P9I  plan-1  C9   0.020
 P9I  plan-1  C8   0.020
 P9I  plan-1  C7   0.020
 P9I  plan-1  H7   0.020
 P9I  plan-1  H10  0.020
 P9I  plan-1  H9   0.020
 P9I  plan-1  H8   0.020
 P9I  plan-2  C2   0.020
 P9I  plan-2  C3   0.020
 P9I  plan-2  N2   0.020
 P9I  plan-2  C15  0.020
 P9I  plan-2  C14  0.020
 P9I  plan-2  C13  0.020
 P9I  plan-2  C12  0.020
 P9I  plan-2  C11  0.020
 P9I  plan-2  C5   0.020
 P9I  plan-2  C4   0.020
 P9I  plan-2  C6   0.020
 P9I  plan-2  H4   0.020
 P9I  plan-2  H15  0.020
 P9I  plan-2  H14  0.020
 P9I  plan-2  H13  0.020
 P9I  plan-2  H12  0.020

