# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 05:46:53 2020
#   Inital geometry file: a 145 line input string
#   Ligand name: 3-[(3aS,4R,8aS,8bR)-4-(4-carbamimidoylphenyl)-1,3-dioxooctahydropyrrolo[3,4-a]pyrrolizin-2(3H)-yl]-N,N,N-trimethylpropan-1-aminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[N+](C)(C)CCCN1C(=O)[C@H]2[C@@H]3CCCN3[C@H]([C@H]2C1=O)c4ccc(cc4)C(N)=N
#
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
 784  784  3-[(3aS,4R,8aS,8bR)-4-(4-carbamimidoylphenyl)-1,3-dioxooctahydropyrrolo[3,4-a]pyrrolizin-2(3H)-yl]-N,N,N-trimethylpropan-1-aminium  ligand  61  29  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_784
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
 784  O18   O  O     0  -0.428   1.8231   2.7113  -1.2498
 784  C11   C  CR5   0   0.596   1.1380   2.1466  -0.4333
 784  N12   N  NR5   0  -0.532   1.2165   0.8013  -0.1496
 784  C19   C  CH2   0  -0.311   2.1880  -0.0889  -0.7448
 784  C21   C  CH2   0  -0.490   3.4393  -0.2187   0.1213
 784  C23   C  CH2   0  -0.315   4.4435  -1.0918  -0.6060
 784  N29   N  NT    1  -0.384   5.7133  -1.3692   0.1513
 784  C32   C  CH3   0  -0.552   5.4292  -2.0940   1.4212
 784  C31   C  CH3   0  -0.552   6.4432  -0.1061   0.4498
 784  C30   C  CH3   0  -0.549   6.5731  -2.2300  -0.7088
 784  C5    C  C     0  -0.400   0.0779   2.7649   0.4491
 784  C2    C  C     0  -0.427  -0.5646   1.5721   1.1625
 784  C6    C  CR5   0   0.603   0.3262   0.4022   0.8252
 784  O13   O  O     0  -0.418   0.2987  -0.7041   1.3016
 784  C7    C  C     0  -0.113  -1.0385   3.3965  -0.3659
 784  C14   C  CH2   0  -0.463  -1.9112   4.4306   0.3721
 784  C15   C  CH2   0  -0.478  -3.3414   4.1232  -0.1121
 784  C8    C  CH2   0  -0.333  -3.1867   2.8852  -1.0253
 784  N3    N  N     0  -0.411  -1.9147   2.2711  -0.6669
 784  C1    C  CR15  0  -0.104  -1.9943   1.4754   0.5539
 784  C4    C  CR6   0   0.125  -2.4806   0.0756   0.2941
 784  C10   C  CR16  0  -0.297  -3.1996  -0.6029   1.2724
 784  C17   C  CR16  0  -0.263  -3.6110  -1.9095   1.0745
 784  C20   C  CR6   0   0.035  -3.3077  -2.5763  -0.1105
 784  C22   C  C     0   0.332  -3.7622  -3.9813  -0.2983
 784  N25   N  N     0  -0.652  -4.7843  -4.3873   0.3525
 784  N24   N  NH2   0  -0.823  -3.0503  -4.7068  -1.2109
 784  C16   C  CR16  0  -0.277  -2.6011  -1.8912  -1.0972
 784  C9    C  CR16  0  -0.283  -2.1968  -0.5801  -0.8983
 784  H191  H  HCH2  0   0.281   2.4389   0.3021  -1.7304
 784  H192  H  HCH2  0   0.280   1.7184  -1.0620  -0.8898
 784  H211  H  HCH2  0   0.274   3.1617  -0.6531   1.0821
 784  H212  H  HCH2  0   0.273   3.8479   0.7758   0.3072
 784  H231  H  HCH2  0   0.308   4.7423  -0.6262  -1.5453
 784  H232  H  HCH2  0   0.307   4.0115  -2.0656  -0.8409
 784  H321  H  HCH3  0   0.296   4.8980  -1.4434   2.1085
 784  H322  H  HCH3  0   0.297   4.8309  -2.9746   1.2030
 784  H323  H  HCH3  0   0.299   6.3716  -2.3966   1.8694
 784  H311  H  HCH3  0   0.299   7.3850  -0.3523   0.9323
 784  H312  H  HCH3  0   0.296   6.6373   0.4214  -0.4805
 784  H313  H  HCH3  0   0.297   5.8508   0.5153   1.1141
 784  H301  H  HCH3  0   0.298   6.0486  -3.1577  -0.9196
 784  H302  H  HCH3  0   0.298   6.7858  -1.7077  -1.6375
 784  H303  H  HCH3  0   0.296   7.5009  -2.4420  -0.1849
 784  H5    H  H     0   0.327   0.5616   3.4741   1.1237
 784  H2    H  H     0   0.320  -0.6232   1.6730   2.2452
 784  H7    H  H     0   0.267  -0.6659   3.8341  -1.2963
 784  H141  H  HCH2  0   0.242  -1.8292   4.3120   1.4547
 784  H142  H  HCH2  0   0.252  -1.5964   5.4478   0.1407
 784  H151  H  HCH2  0   0.240  -4.0011   3.9132   0.7299
 784  H152  H  HCH2  0   0.247  -3.7823   4.9570  -0.6578
 784  H8C1  H  HCH2  0   0.248  -4.0043   2.1699  -0.9303
 784  H8C2  H  HCH2  0   0.245  -3.1443   3.1893  -2.0733
 784  H1    H  HCR5  0   0.261  -2.6678   1.9323   1.2942
 784  H10   H  HCR6  0   0.249  -3.4429  -0.1036   2.2034
 784  H17   H  HCR6  0   0.254  -4.1703  -2.4239   1.8441
 784  H25   H  H     0   0.323  -4.9729  -5.3686   0.1656
 784  H241  H  HNH2  0   0.394  -2.0820  -4.4735  -1.3569
 784  H242  H  HNH2  0   0.391  -3.2380  -5.6955  -1.2631
 784  H16   H  HCR6  0   0.255  -2.3764  -2.3658  -2.0442
 784  H9    H  HCR6  0   0.252  -1.6644  -0.0577  -1.6824

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
 784  O18  C11   double    1.206  0.020  1.206
 784  C11  N12   single    1.377  0.020  1.377
 784  C11  C5    single    1.512  0.020  1.512
 784  N12  C19   single    1.446  0.020  1.446
 784  N12  C6    single    1.379  0.020  1.379
 784  C19  C21   single    1.527  0.020  1.527
 784  C19  H191  single    0.970  0.020  1.090
 784  C19  H192  single    0.970  0.020  1.090
 784  C21  C23   single    1.517  0.020  1.517
 784  C21  H211  single    0.970  0.020  1.090
 784  C21  H212  single    0.970  0.020  1.090
 784  C23  N29   single    1.504  0.020  1.504
 784  C23  H231  single    0.970  0.020  1.090
 784  C23  H232  single    0.970  0.020  1.090
 784  N29  C32   single    1.490  0.020  1.490
 784  N29  C31   single    1.489  0.020  1.489
 784  N29  C30   single    1.490  0.020  1.490
 784  C32  H321  single    0.970  0.020  1.090
 784  C32  H322  single    0.970  0.020  1.090
 784  C32  H323  single    0.970  0.020  1.090
 784  C31  H311  single    0.970  0.020  1.090
 784  C31  H312  single    0.970  0.020  1.090
 784  C31  H313  single    0.970  0.020  1.090
 784  C30  H301  single    0.970  0.020  1.090
 784  C30  H302  single    0.970  0.020  1.090
 784  C30  H303  single    0.970  0.020  1.090
 784  C5   C2    single    1.531  0.020  1.531
 784  C5   C7    single    1.520  0.020  1.520
 784  C5   H5    single    0.970  0.020  1.090
 784  C2   C6    single    1.509  0.020  1.509
 784  C2   C1    single    1.557  0.020  1.557
 784  C2   H2    single    0.970  0.020  1.090
 784  C6   O13   double    1.205  0.020  1.205
 784  C7   C14   single    1.541  0.020  1.541
 784  C7   N3    single    1.458  0.020  1.458
 784  C7   H7    single    0.970  0.020  1.090
 784  C14  C15   single    1.541  0.020  1.541
 784  C14  H141  single    0.970  0.020  1.090
 784  C14  H142  single    0.970  0.020  1.090
 784  C15  C8    single    1.546  0.020  1.546
 784  C15  H151  single    0.970  0.020  1.090
 784  C15  H152  single    0.970  0.020  1.090
 784  C8   N3    single    1.457  0.020  1.457
 784  C8   H8C1  single    0.970  0.020  1.090
 784  C8   H8C2  single    0.970  0.020  1.090
 784  N3   C1    single    1.459  0.020  1.459
 784  C1   C4    single    1.504  0.020  1.504
 784  C1   H1    single    0.970  0.020  1.090
 784  C4   C10   aromatic  1.391  0.020  1.391
 784  C4   C9    aromatic  1.390  0.020  1.390
 784  C10  C17   aromatic  1.384  0.020  1.384
 784  C10  H10   single    0.930  0.020  1.080
 784  C17  C20   aromatic  1.393  0.020  1.393
 784  C17  H17   single    0.930  0.020  1.080
 784  C20  C22   single    1.489  0.020  1.489
 784  C20  C16   aromatic  1.394  0.020  1.394
 784  C22  N25   double    1.278  0.020  1.278
 784  C22  N24   single    1.366  0.020  1.366
 784  N25  H25   single    0.890  0.020  1.040
 784  N24  H241  single    0.890  0.020  1.040
 784  N24  H242  single    0.890  0.020  1.040
 784  C16  C9    aromatic  1.386  0.020  1.386
 784  C16  H16   single    0.930  0.020  1.080
 784  C9   H9    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
 784  C5    C11  N12   108.62  3.000
 784  C5    C11  O18   127.01  3.000
 784  N12   C11  O18   124.37  3.000
 784  C6    N12  C19   123.13  3.000
 784  C6    N12  C11   113.05  3.000
 784  C19   N12  C11   123.71  3.000
 784  H192  C19  H191  107.41  3.000
 784  H192  C19  C21   110.64  3.000
 784  H191  C19  C21   110.78  3.000
 784  H192  C19  N12   108.35  3.000
 784  H191  C19  N12   107.83  3.000
 784  C21   C19  N12   111.68  3.000
 784  H212  C21  H211  107.96  3.000
 784  H212  C21  C23   111.01  3.000
 784  H211  C21  C23   111.21  3.000
 784  H212  C21  C19   109.03  3.000
 784  H211  C21  C19   108.96  3.000
 784  C23   C21  C19   108.63  3.000
 784  H232  C23  H231  107.71  3.000
 784  H232  C23  N29   106.15  3.000
 784  H231  C23  N29   106.33  3.000
 784  H232  C23  C21   110.79  3.000
 784  H231  C23  C21   110.41  3.000
 784  N29   C23  C21   115.07  3.000
 784  C30   N29  C31   108.84  3.000
 784  C30   N29  C32   108.73  3.000
 784  C31   N29  C32   109.59  3.000
 784  C30   N29  C23   107.64  3.000
 784  C31   N29  C23   111.00  3.000
 784  C32   N29  C23   110.98  3.000
 784  H323  C32  H322  109.55  3.000
 784  H323  C32  H321  109.28  3.000
 784  H322  C32  H321  110.09  3.000
 784  H323  C32  N29   108.77  3.000
 784  H322  C32  N29   109.15  3.000
 784  H321  C32  N29   109.97  3.000
 784  H313  C31  H312  110.08  3.000
 784  H313  C31  H311  109.32  3.000
 784  H312  C31  H311  109.59  3.000
 784  H313  C31  N29   109.92  3.000
 784  H312  C31  N29   109.13  3.000
 784  H311  C31  N29   108.77  3.000
 784  H303  C30  H302  109.81  3.000
 784  H303  C30  H301  109.83  3.000
 784  H302  C30  H301  109.82  3.000
 784  H303  C30  N29   109.10  3.000
 784  H302  C30  N29   109.19  3.000
 784  H301  C30  N29   109.08  3.000
 784  H5    C5   C7    112.76  3.000
 784  H5    C5   C2    113.83  3.000
 784  C7    C5   C2    105.39  3.000
 784  H5    C5   C11   108.41  3.000
 784  C7    C5   C11   111.85  3.000
 784  C2    C5   C11   104.34  3.000
 784  H2    C2   C1    110.18  3.000
 784  H2    C2   C6    109.02  3.000
 784  C1    C2   C6    114.00  3.000
 784  H2    C2   C5    114.43  3.000
 784  C1    C2   C5    104.57  3.000
 784  C6    C2   C5    104.60  3.000
 784  O13   C6   C2    127.60  3.000
 784  O13   C6   N12   124.05  3.000
 784  C2    C6   N12   108.35  3.000
 784  H7    C7   N3    109.76  3.000
 784  H7    C7   C14   109.38  3.000
 784  N3    C7   C14   106.05  3.000
 784  H7    C7   C5    111.86  3.000
 784  N3    C7   C5    103.38  3.000
 784  C14   C7   C5    115.98  3.000
 784  H142  C14  H141  106.86  3.000
 784  H142  C14  C15   112.81  3.000
 784  H141  C14  C15   111.07  3.000
 784  H142  C14  C7    111.17  3.000
 784  H141  C14  C7    111.06  3.000
 784  C15   C14  C7    103.96  3.000
 784  H152  C15  H151  106.82  3.000
 784  H152  C15  C8    110.94  3.000
 784  H151  C15  C8    111.26  3.000
 784  H152  C15  C14   112.35  3.000
 784  H151  C15  C14   110.94  3.000
 784  C8    C15  C14   104.62  3.000
 784  H8C2  C8   H8C1  107.18  3.000
 784  H8C2  C8   N3    108.63  3.000
 784  H8C1  C8   N3    110.89  3.000
 784  H8C2  C8   C15   110.35  3.000
 784  H8C1  C8   C15   113.50  3.000
 784  N3    C8   C15   106.23  3.000
 784  C1    N3   C8    112.82  3.000
 784  C1    N3   C7    106.32  3.000
 784  C8    N3   C7    104.49  3.000
 784  H1    C1   C4    107.75  3.000
 784  H1    C1   N3    111.70  3.000
 784  C4    C1   N3    112.36  3.000
 784  H1    C1   C2    105.86  3.000
 784  C4    C1   C2    114.97  3.000
 784  N3    C1   C2    104.07  3.000
 784  C9    C4   C10   118.60  3.000
 784  C9    C4   C1    121.40  3.000
 784  C10   C4   C1    119.97  3.000
 784  H10   C10  C17   119.40  3.000
 784  H10   C10  C4    119.70  3.000
 784  C17   C10  C4    120.91  3.000
 784  H17   C17  C20   119.35  3.000
 784  H17   C17  C10   120.06  3.000
 784  C20   C17  C10   120.58  3.000
 784  C16   C20  C22   121.97  3.000
 784  C16   C20  C17   118.51  3.000
 784  C22   C20  C17   119.51  3.000
 784  N24   C22  N25   126.04  3.000
 784  N24   C22  C20   115.24  3.000
 784  N25   C22  C20   118.67  3.000
 784  H25   N25  C22   111.19  3.000
 784  H242  N24  H241  113.52  3.000
 784  H242  N24  C22   117.30  3.000
 784  H241  N24  C22   118.37  3.000
 784  H16   C16  C9    118.65  3.000
 784  H16   C16  C20   120.59  3.000
 784  C9    C16  C20   120.74  3.000
 784  H9    C9   C16   119.73  3.000
 784  H9    C9   C4    119.62  3.000
 784  C16   C9   C4    120.64  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
 784  CONST_01  C20   C17  C10  C4      0.00   0.0  0
 784  CONST_02  C20   C16  C9   C4      0.00   0.0  0
 784  CONST_03  C16   C9   C4   C10     0.00   0.0  0
 784  CONST_04  C16   C20  C17  C10     0.00   0.0  0
 784  CONST_05  C9    C4   C10  C17     0.00   0.0  0
 784  CONST_06  C9    C16  C20  C17     0.00   0.0  0
 784  CONST_07  C17   C10  C4   C1    180.00   0.0  0
 784  CONST_08  C16   C9   C4   C1    180.00   0.0  0
 784  CONST_09  C6    N12  C11  C5      0.00   0.0  0
 784  CONST_10  C22   C20  C17  C10   180.00   0.0  0
 784  CONST_11  C9    C16  C20  C22   180.00   0.0  0
 784  CONST_12  C6    N12  C11  O18   180.00   0.0  0
 784  CONST_13  C5    C11  N12  C19   180.00   0.0  0
 784  CONST_14  H10   C10  C4   C1      0.00   0.0  0
 784  CONST_15  H9    C9   C4   C1      0.00   0.0  0
 784  CONST_16  H17   C17  C10  C4    180.00   0.0  0
 784  CONST_17  H16   C16  C9   C4    180.00   0.0  0
 784  CONST_18  C19   N12  C11  O18     0.00   0.0  0
 784  CONST_19  H25   N25  C22  C20   180.00   0.0  0
 784  CONST_21  H242  N24  C22  C20   180.00   0.0  0
 784  Var_01    C2    C6   N12  C11     6.15  30.0  1
 784  Var_02    C8    C15  C14  C7      3.19  30.0  1
 784  Var_03    C15   C8   N3   C7    -36.23  30.0  1
 784  Var_04    N3    C8   C15  C14    19.83  30.0  1
 784  Var_05    C21   C19  N12  C11    93.08  30.0  3
 784  Var_06    N25   C22  C20  C17    25.06  30.0  2
 784  Var_07    C23   C21  C19  N12  -176.40  30.0  3
 784  Var_08    N29   C23  C21  C19  -177.27  30.0  3
 784  Var_09    C32   N29  C23  C21    61.26  30.0  3
 784  Var_10    H321  C32  N29  C23   -68.12  30.0  3
 784  Var_11    H311  C31  N29  C23  -176.00  30.0  3
 784  Var_12    H301  C30  N29  C23   -60.26  30.0  3

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
 784  chir_01  C5  C11  C2  C7   positiv
 784  chir_02  C2  C5   C6  C1   positiv
 784  chir_03  C7  N3   C5  C14  positiv
 784  chir_04  C1  N3   C2  C4   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
 784  plan-1  C1    0.020
 784  plan-1  C4    0.020
 784  plan-1  C10   0.020
 784  plan-1  C17   0.020
 784  plan-1  C20   0.020
 784  plan-1  C22   0.020
 784  plan-1  C16   0.020
 784  plan-1  C9    0.020
 784  plan-1  H10   0.020
 784  plan-1  H17   0.020
 784  plan-1  H16   0.020
 784  plan-1  H9    0.020
 784  plan-2  N12   0.020
 784  plan-2  C2    0.020
 784  plan-2  C6    0.020
 784  plan-2  O13   0.020
 784  plan-3  C20   0.020
 784  plan-3  C22   0.020
 784  plan-3  N25   0.020
 784  plan-3  N24   0.020
 784  plan-3  H25   0.020
 784  plan-3  H241  0.020
 784  plan-3  H242  0.020
 784  plan-4  O18   0.020
 784  plan-4  C11   0.020
 784  plan-4  N12   0.020
 784  plan-4  C19   0.020
 784  plan-4  C5    0.020
 784  plan-4  C6    0.020

