# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 28 02:11:17 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: 2-amino-5-[(1-methoxy-2-methylindolizin-3-yl)carbonyl]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1c(C)c(n2ccccc12)C(=O)c3ccc(N)c(c3)C(O)=O
#
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
 SSF  SSF  '2-amino-5-[(1-methoxy-2-methylindolizin-3-yl)carbonyl]benzoic acid'  ligand  40  24  .  2022-07-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_SSF
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
 SSF  C1    C  CR16  0  -0.381   3.8075  -3.1199  -0.3045
 SSF  C2    C  CR16  0   0.017   2.5613  -2.5977  -0.1743
 SSF  C3    C  CR56  0   0.345   3.4992  -0.4187   0.0926
 SSF  C4    C  CR16  0  -0.380   4.7958  -0.9498  -0.0324
 SSF  C5    C  CR16  0  -0.158   4.9529  -2.2893  -0.2290
 SSF  C10   C  CR5   0   0.198   3.0207   0.8764   0.2864
 SSF  C11   C  CR5   0   0.204   1.2420  -0.4978   0.1359
 SSF  C12   C  CR5   0  -0.068   1.6301   0.8425   0.3093
 SSF  C13   C  CH3   0  -0.757   0.7779   2.0351   0.5939
 SSF  C17   C  C     0   0.298  -0.0727  -1.1037   0.2038
 SSF  C18   C  CR6   0  -0.048  -1.2322  -0.2968  -0.2296
 SSF  C19   C  CR16  0  -0.254  -1.1678   0.5807  -1.3232
 SSF  C20   C  CR16  0  -0.301  -2.4568  -0.4719   0.3903
 SSF  C21   C  CR16  0  -0.334  -2.2764   1.2554  -1.7568
 SSF  C23   C  CR6   0  -0.165  -3.6012   0.2228  -0.0043
 SSF  C25   C  CR6   0   0.377  -3.5267   1.1146  -1.1110
 SSF  O27   O  O     0  -0.446  -0.2390  -2.2554   0.5988
 SSF  C28   C  C     0   0.563  -4.8675   0.0258   0.7149
 SSF  O29   O  OH1   0  -0.597  -4.7764  -0.8321   1.7246
 SSF  O30   O  O     0  -0.468  -5.9149   0.5786   0.4421
 SSF  N31   N  NH2   0  -0.856  -4.5706   1.8191  -1.5659
 SSF  N34   N  N     0  -0.603   2.4001  -1.2546   0.0282
 SSF  O35   O  O2    0  -0.480   3.8156   1.9595   0.4613
 SSF  C36   C  CH3   0  -0.405   3.9736   2.7584  -0.7047
 SSF  H1    H  HCR6  0   0.277   3.9067  -4.1843  -0.4598
 SSF  H2    H  HCR6  0   0.311   1.6706  -3.1998  -0.2193
 SSF  H4    H  HCR6  0   0.273   5.6408  -0.2776   0.0274
 SSF  H5    H  HCR6  0   0.271   5.9397  -2.7193  -0.3299
 SSF  H13   H  HCH3  0   0.252   0.4506   2.5353  -0.3188
 SSF  H13A  H  HCH3  0   0.257  -0.1144   1.7743   1.1593
 SSF  H13B  H  HCH3  0   0.259   1.3441   2.7639   1.1734
 SSF  H19   H  HCR6  0   0.276  -0.2331   0.7116  -1.8545
 SSF  H20   H  HCR6  0   0.269  -2.5193  -1.1598   1.2224
 SSF  H21   H  HCR6  0   0.271  -2.2056   1.9136  -2.6139
 SSF  HO29  H  HOH1  0   0.487  -5.6380  -0.9145   2.1589
 SSF  HN31  H  HNH2  0   0.403  -4.4668   2.4118  -2.3703
 SSF  HN3A  H  HNH2  0   0.411  -5.4803   1.7220  -1.1503
 SSF  H36   H  HCH3  0   0.221   4.4283   2.1896  -1.5197
 SSF  H36A  H  HCH3  0   0.222   3.0184   3.1616  -1.0506
 SSF  H36B  H  HCH3  0   0.239   4.6294   3.5868  -0.4432

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
 SSF  C1   C2    aromatic  1.357  0.020  1.357
 SSF  C1   C5    aromatic  1.417  0.020  1.417
 SSF  C2   N34   aromatic  1.368  0.020  1.368
 SSF  C3   C4    aromatic  1.407  0.020  1.407
 SSF  C3   C10   aromatic  1.394  0.020  1.394
 SSF  C3   N34   aromatic  1.382  0.020  1.382
 SSF  C4   C5    aromatic  1.363  0.020  1.363
 SSF  C10  C12   aromatic  1.391  0.020  1.391
 SSF  C10  O35   single    1.355  0.020  1.355
 SSF  C11  C12   aromatic  1.406  0.020  1.406
 SSF  C11  C17   single    1.449  0.020  1.449
 SSF  C11  N34   aromatic  1.388  0.020  1.388
 SSF  C12  C13   single    1.493  0.020  1.493
 SSF  C17  C18   single    1.478  0.020  1.478
 SSF  C17  O27   double    1.229  0.020  1.229
 SSF  C18  C19   aromatic  1.404  0.020  1.404
 SSF  C18  C20   aromatic  1.384  0.020  1.384
 SSF  C19  C21   aromatic  1.368  0.020  1.368
 SSF  C20  C23   aromatic  1.396  0.020  1.396
 SSF  C21  C25   aromatic  1.414  0.020  1.414
 SSF  C23  C25   aromatic  1.423  0.020  1.423
 SSF  C23  C28   single    1.470  0.020  1.470
 SSF  C25  N31   single    1.339  0.020  1.339
 SSF  C28  O29   single    1.328  0.020  1.328
 SSF  C28  O30   double    1.215  0.020  1.215
 SSF  O35  C36   single    1.422  0.020  1.422
 SSF  C1   H1    single    0.930  0.020  1.080
 SSF  C2   H2    single    0.930  0.020  1.080
 SSF  C4   H4    single    0.930  0.020  1.080
 SSF  C5   H5    single    0.930  0.020  1.080
 SSF  C13  H13   single    0.970  0.020  1.090
 SSF  C13  H13A  single    0.970  0.020  1.090
 SSF  C13  H13B  single    0.970  0.020  1.090
 SSF  C19  H19   single    0.930  0.020  1.080
 SSF  C20  H20   single    0.930  0.020  1.080
 SSF  C21  H21   single    0.930  0.020  1.080
 SSF  O29  HO29  single    0.850  0.020  0.980
 SSF  N31  HN31  single    0.860  0.020  1.020
 SSF  N31  HN3A  single    0.860  0.020  1.020
 SSF  C36  H36   single    0.970  0.020  1.090
 SSF  C36  H36A  single    0.970  0.020  1.090
 SSF  C36  H36B  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
 SSF  H1    C1   C5    120.74  3.000
 SSF  H1    C1   C2    118.50  3.000
 SSF  C5    C1   C2    120.77  3.000
 SSF  H2    C2   N34   117.26  3.000
 SSF  H2    C2   C1    122.73  3.000
 SSF  N34   C2   C1    120.01  3.000
 SSF  N34   C3   C10   107.18  3.000
 SSF  N34   C3   C4    120.03  3.000
 SSF  C10   C3   C4    132.79  3.000
 SSF  H4    C4   C5    121.93  3.000
 SSF  H4    C4   C3    118.73  3.000
 SSF  C5    C4   C3    119.34  3.000
 SSF  H5    C5   C4    120.63  3.000
 SSF  H5    C5   C1    119.98  3.000
 SSF  C4    C5   C1    119.39  3.000
 SSF  O35   C10  C12   127.15  3.000
 SSF  O35   C10  C3    124.00  3.000
 SSF  C12   C10  C3    108.82  3.000
 SSF  N34   C11  C17   122.19  3.000
 SSF  N34   C11  C12   107.41  3.000
 SSF  C17   C11  C12   130.03  3.000
 SSF  C13   C12  C11   128.85  3.000
 SSF  C13   C12  C10   123.65  3.000
 SSF  C11   C12  C10   107.28  3.000
 SSF  H13B  C13  H13A  108.07  3.000
 SSF  H13B  C13  H13   107.10  3.000
 SSF  H13A  C13  H13   107.37  3.000
 SSF  H13B  C13  C12   109.82  3.000
 SSF  H13A  C13  C12   112.07  3.000
 SSF  H13   C13  C12   112.20  3.000
 SSF  O27   C17  C18   119.99  3.000
 SSF  O27   C17  C11   121.98  3.000
 SSF  C18   C17  C11   118.02  3.000
 SSF  C20   C18  C19   117.96  3.000
 SSF  C20   C18  C17   119.60  3.000
 SSF  C19   C18  C17   122.27  3.000
 SSF  H19   C19  C21   118.95  3.000
 SSF  H19   C19  C18   119.83  3.000
 SSF  C21   C19  C18   121.20  3.000
 SSF  H20   C20  C23   119.13  3.000
 SSF  H20   C20  C18   118.45  3.000
 SSF  C23   C20  C18   122.41  3.000
 SSF  H21   C21  C25   118.66  3.000
 SSF  H21   C21  C19   119.84  3.000
 SSF  C25   C21  C19   121.50  3.000
 SSF  C28   C23  C25   120.64  3.000
 SSF  C28   C23  C20   120.10  3.000
 SSF  C25   C23  C20   119.26  3.000
 SSF  N31   C25  C23   123.57  3.000
 SSF  N31   C25  C21   118.80  3.000
 SSF  C23   C25  C21   117.63  3.000
 SSF  O30   C28  O29   121.57  3.000
 SSF  O30   C28  C23   124.87  3.000
 SSF  O29   C28  C23   113.55  3.000
 SSF  HO29  O29  C28   109.57  3.000
 SSF  HN3A  N31  HN31  118.80  3.000
 SSF  HN3A  N31  C25   120.96  3.000
 SSF  HN31  N31  C25   120.12  3.000
 SSF  C11   N34  C3    109.27  3.000
 SSF  C11   N34  C2    130.20  3.000
 SSF  C3    N34  C2    120.46  3.000
 SSF  C36   O35  C10   114.10  3.000
 SSF  H36B  C36  H36A  108.77  3.000
 SSF  H36B  C36  H36   108.94  3.000
 SSF  H36A  C36  H36   108.64  3.000
 SSF  H36B  C36  O35   107.31  3.000
 SSF  H36A  C36  O35   111.69  3.000
 SSF  H36   C36  O35   111.42  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
 SSF  CONST_01  C3    N34  C2   C1     0.00   0.0  0
 SSF  CONST_02  C11   N34  C2   C1   180.00   0.0  0
 SSF  CONST_03  C3    C4   C5   C1     0.00   0.0  0
 SSF  CONST_04  C4    C5   C1   C2     0.00   0.0  0
 SSF  CONST_05  C4    C3   N34  C2     0.00   0.0  0
 SSF  CONST_06  C10   C3   N34  C2   180.00   0.0  0
 SSF  CONST_07  C12   C11  N34  C2   180.00   0.0  0
 SSF  CONST_08  C11   C12  C10  C3     0.00   0.0  0
 SSF  CONST_09  C12   C11  N34  C3     0.00   0.0  0
 SSF  CONST_10  C12   C10  C3   C4   180.00   0.0  0
 SSF  CONST_11  C11   N34  C3   C4   180.00   0.0  0
 SSF  CONST_12  N34   C2   C1   C5     0.00   0.0  0
 SSF  CONST_13  C10   C3   C4   C5   180.00   0.0  0
 SSF  CONST_14  N34   C3   C4   C5     0.00   0.0  0
 SSF  CONST_15  C11   N34  C3   C10    0.00   0.0  0
 SSF  CONST_16  N34   C11  C12  C10    0.00   0.0  0
 SSF  CONST_17  N34   C3   C10  C12    0.00   0.0  0
 SSF  CONST_18  C25   C21  C19  C18    0.00   0.0  0
 SSF  CONST_19  C25   C23  C20  C18    0.00   0.0  0
 SSF  CONST_20  C23   C20  C18  C19    0.00   0.0  0
 SSF  CONST_21  C23   C25  C21  C19    0.00   0.0  0
 SSF  CONST_22  C21   C19  C18  C20    0.00   0.0  0
 SSF  CONST_23  C21   C25  C23  C20    0.00   0.0  0
 SSF  CONST_24  C17   C11  N34  C2     0.00   0.0  0
 SSF  CONST_25  C13   C12  C10  C3   180.00   0.0  0
 SSF  CONST_26  C17   C11  N34  C3   180.00   0.0  0
 SSF  CONST_27  O35   C10  C3   C4     0.00   0.0  0
 SSF  CONST_28  C17   C11  C12  C10  180.00   0.0  0
 SSF  CONST_29  O35   C10  C12  C11  180.00   0.0  0
 SSF  CONST_30  N34   C11  C12  C13  180.00   0.0  0
 SSF  CONST_31  C21   C19  C18  C17  180.00   0.0  0
 SSF  CONST_32  C23   C20  C18  C17  180.00   0.0  0
 SSF  CONST_33  C28   C23  C20  C18  180.00   0.0  0
 SSF  CONST_34  N31   C25  C21  C19  180.00   0.0  0
 SSF  CONST_35  N31   C25  C23  C20  180.00   0.0  0
 SSF  CONST_36  C28   C23  C25  C21  180.00   0.0  0
 SSF  CONST_37  O35   C10  C3   N34  180.00   0.0  0
 SSF  CONST_38  H4    C4   C5   C1   180.00   0.0  0
 SSF  CONST_39  H5    C5   C1   C2   180.00   0.0  0
 SSF  CONST_40  H2    C2   N34  C3   180.00   0.0  0
 SSF  CONST_41  H1    C1   C5   C4   180.00   0.0  0
 SSF  CONST_42  H21   C21  C19  C18  180.00   0.0  0
 SSF  CONST_43  H20   C20  C18  C19  180.00   0.0  0
 SSF  CONST_44  H19   C19  C18  C20  180.00   0.0  0
 SSF  CONST_45  HN31  N31  C25  C21    0.00   0.0  0
 SSF  CONST_46  HN3A  N31  C25  C21  180.00   0.0  0
 SSF  CONST_47  HO29  O29  C28  C23  180.00   0.0  0
 SSF  Var_01    C19   C18  C17  C11   37.72  30.0  2
 SSF  Var_02    C18   C17  C11  C12   32.53  30.0  2
 SSF  Var_03    O29   C28  C23  C20    0.51  30.0  2
 SSF  Var_04    H13   C13  C12  C10   94.88  30.0  2
 SSF  Var_05    H36   C36  O35  C10  -60.59  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
 SSF  plan-1  C17   0.020
 SSF  plan-1  C18   0.020
 SSF  plan-1  C19   0.020
 SSF  plan-1  C20   0.020
 SSF  plan-1  C21   0.020
 SSF  plan-1  C23   0.020
 SSF  plan-1  C25   0.020
 SSF  plan-1  C28   0.020
 SSF  plan-1  N31   0.020
 SSF  plan-1  H19   0.020
 SSF  plan-1  H20   0.020
 SSF  plan-1  H21   0.020
 SSF  plan-2  C1    0.020
 SSF  plan-2  C2    0.020
 SSF  plan-2  C3    0.020
 SSF  plan-2  C4    0.020
 SSF  plan-2  C5    0.020
 SSF  plan-2  C10   0.020
 SSF  plan-2  C11   0.020
 SSF  plan-2  C12   0.020
 SSF  plan-2  C13   0.020
 SSF  plan-2  C17   0.020
 SSF  plan-2  N34   0.020
 SSF  plan-2  O35   0.020
 SSF  plan-2  H1    0.020
 SSF  plan-2  H2    0.020
 SSF  plan-2  H4    0.020
 SSF  plan-2  H5    0.020
 SSF  plan-3  C25   0.020
 SSF  plan-3  N31   0.020
 SSF  plan-3  HN31  0.020
 SSF  plan-3  HN3A  0.020
 SSF  plan-4  C11   0.020
 SSF  plan-4  C17   0.020
 SSF  plan-4  C18   0.020
 SSF  plan-4  O27   0.020
 SSF  plan-5  C23   0.020
 SSF  plan-5  C28   0.020
 SSF  plan-5  O29   0.020
 SSF  plan-5  O30   0.020
 SSF  plan-5  HO29  0.020

