# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 06:28:34 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 6-(3-aminopropyl)-4,9-dimethylpyrrolo[3,4-c]carbazole-1,3(2H,6H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc2n(CCCN)c3cc(C)c4C(=O)NC(=O)c4c3c2c1
#
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
 BD4  BD4  6-(3-aminopropyl)-4,9-dimethylpyrrolo[3,4-c]carbazole-1,3(2H,6H)-dione  ligand  43  24  .  2022-07-24  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_BD4
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
 BD4  O23   O  O     0  -0.408  -4.6870  -2.0047   0.2281
 BD4  C20   C  CR5   0   0.568  -3.8676  -1.1180   0.2084
 BD4  N21   N  NR15  0  -0.743  -4.1447   0.2203   0.4383
 BD4  C22   C  CR5   0   0.522  -3.0289   1.0213   0.3508
 BD4  O24   O  O     0  -0.400  -3.0108   2.2182   0.5073
 BD4  C13   C  CR56  0  -0.136  -1.9062   0.1032   0.0320
 BD4  C12   C  CR56  0  -0.133  -2.4155  -1.1870  -0.0516
 BD4  C11   C  CR6   0   0.054  -1.6218  -2.3026  -0.3329
 BD4  C15   C  CH3   0  -0.726  -2.1797  -3.6907  -0.4074
 BD4  C10   C  CR16  0  -0.390  -0.2662  -2.0747  -0.5390
 BD4  C8    C  CR56  0   0.373   0.2446  -0.7802  -0.4660
 BD4  C9    C  CR56  0   0.143  -0.5604   0.3533  -0.1676
 BD4  C5    C  CR56  0   0.052   0.3222   1.4901  -0.1569
 BD4  C6    C  CR16  0  -0.458   0.1552   2.8567   0.0773
 BD4  C1    C  CR6   0   0.097   1.2491   3.7047   0.0230
 BD4  C14   C  CH3   0  -0.725   1.1012   5.1788   0.2714
 BD4  C2    C  CR16  0  -0.300   2.5153   3.1694  -0.2699
 BD4  C3    C  CR16  0  -0.306   2.7139   1.8228  -0.5079
 BD4  C4    C  CR56  0   0.333   1.6032   0.9867  -0.4508
 BD4  N7    N  NR5   0  -0.631   1.5328  -0.3746  -0.6513
 BD4  C16   C  CH2   0  -0.338   2.6642  -1.2452  -0.8821
 BD4  C17   C  CH2   0  -0.445   3.2768  -1.7672   0.4110
 BD4  C18   C  CH2   0  -0.275   4.4854  -2.6503   0.1419
 BD4  N19   N  NH2   0  -0.798   5.0466  -3.1446   1.3897
 BD4  H21   H  HNR5  0   0.424  -5.0697   0.5720   0.6414
 BD4  H151  H  HCH3  0   0.253  -2.6403  -3.9849   0.5355
 BD4  H152  H  HCH3  0   0.253  -2.9472  -3.7725  -1.1770
 BD4  H153  H  HCH3  0   0.249  -1.3938  -4.4082  -0.6368
 BD4  H10   H  HCR6  0   0.273   0.3866  -2.9131  -0.7484
 BD4  H6    H  HCR6  0   0.255  -0.8254   3.2508   0.3060
 BD4  H141  H  HCH3  0   0.244   1.3806   5.7606  -0.6087
 BD4  H142  H  HCH3  0   0.244   0.0751   5.4379   0.5284
 BD4  H143  H  HCH3  0   0.243   1.7422   5.5115   1.0895
 BD4  H2    H  HCR6  0   0.253   3.3687   3.8362  -0.3073
 BD4  H3    H  HCR6  0   0.267   3.7040   1.4463  -0.7296
 BD4  H161  H  HCH2  0   0.270   2.3376  -2.0727  -1.5146
 BD4  H162  H  HCH2  0   0.271   3.4036  -0.6926  -1.4632
 BD4  H171  H  HCH2  0   0.233   3.5741  -0.9190   1.0358
 BD4  H172  H  HCH2  0   0.236   2.5299  -2.3325   0.9751
 BD4  H181  H  HCH2  0   0.219   4.1735  -3.5098  -0.4580
 BD4  H182  H  HCH2  0   0.196   5.2046  -2.0911  -0.4740
 BD4  H191  H  HNH2  0   0.348   5.8339  -3.7469   1.1867
 BD4  H192  H  HNH2  0   0.339   5.4301  -2.3670   1.9134

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
 BD4  O23  C20   double    1.207  0.020  1.207
 BD4  C20  N21   single    1.386  0.020  1.386
 BD4  C20  C12   single    1.477  0.020  1.477
 BD4  N21  C22   single    1.376  0.020  1.376
 BD4  N21  H21   single    0.860  0.020  1.020
 BD4  C22  O24   double    1.207  0.020  1.207
 BD4  C22  C13   single    1.485  0.020  1.485
 BD4  C13  C12   aromatic  1.390  0.020  1.390
 BD4  C13  C9    aromatic  1.383  0.020  1.383
 BD4  C12  C11   aromatic  1.398  0.020  1.398
 BD4  C11  C15   single    1.498  0.020  1.498
 BD4  C11  C10   aromatic  1.390  0.020  1.390
 BD4  C15  H151  single    0.970  0.020  1.090
 BD4  C15  H152  single    0.970  0.020  1.090
 BD4  C15  H153  single    0.970  0.020  1.090
 BD4  C10  C8    aromatic  1.394  0.020  1.394
 BD4  C10  H10   single    0.930  0.020  1.080
 BD4  C8   C9    aromatic  1.422  0.020  1.422
 BD4  C8   N7    aromatic  1.363  0.020  1.363
 BD4  C9   C5    aromatic  1.439  0.020  1.439
 BD4  C5   C6    aromatic  1.397  0.020  1.397
 BD4  C5   C4    aromatic  1.407  0.020  1.407
 BD4  C6   C1    aromatic  1.385  0.020  1.385
 BD4  C6   H6    single    0.930  0.020  1.080
 BD4  C1   C14   single    1.502  0.020  1.502
 BD4  C1   C2    aromatic  1.406  0.020  1.406
 BD4  C14  H141  single    0.970  0.020  1.090
 BD4  C14  H142  single    0.970  0.020  1.090
 BD4  C14  H143  single    0.970  0.020  1.090
 BD4  C2   C3    aromatic  1.382  0.020  1.382
 BD4  C2   H2    single    0.930  0.020  1.080
 BD4  C3   C4    aromatic  1.391  0.020  1.391
 BD4  C3   H3    single    0.930  0.020  1.080
 BD4  C4   N7    aromatic  1.378  0.020  1.378
 BD4  N7   C16   single    1.446  0.020  1.446
 BD4  C16  C17   single    1.523  0.020  1.523
 BD4  C16  H161  single    0.970  0.020  1.090
 BD4  C16  H162  single    0.970  0.020  1.090
 BD4  C17  C18   single    1.521  0.020  1.521
 BD4  C17  H171  single    0.970  0.020  1.090
 BD4  C17  H172  single    0.970  0.020  1.090
 BD4  C18  N19   single    1.455  0.020  1.455
 BD4  C18  H181  single    0.970  0.020  1.090
 BD4  C18  H182  single    0.970  0.020  1.090
 BD4  N19  H191  single    0.890  0.020  1.040
 BD4  N19  H192  single    0.890  0.020  1.040

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
 BD4  C12   C20  N21   105.72  3.000
 BD4  C12   C20  O23   129.48  3.000
 BD4  N21   C20  O23   124.80  3.000
 BD4  H21   N21  C22   123.54  3.000
 BD4  H21   N21  C20   123.55  3.000
 BD4  C22   N21  C20   112.91  3.000
 BD4  C13   C22  O24   129.01  3.000
 BD4  C13   C22  N21   105.47  3.000
 BD4  O24   C22  N21   125.51  3.000
 BD4  C9    C13  C12   121.05  3.000
 BD4  C9    C13  C22   130.90  3.000
 BD4  C12   C13  C22   108.05  3.000
 BD4  C11   C12  C13   123.02  3.000
 BD4  C11   C12  C20   129.13  3.000
 BD4  C13   C12  C20   107.85  3.000
 BD4  C10   C11  C15   120.52  3.000
 BD4  C10   C11  C12   116.92  3.000
 BD4  C15   C11  C12   122.56  3.000
 BD4  H153  C15  H152  108.07  3.000
 BD4  H153  C15  H151  108.03  3.000
 BD4  H152  C15  H151  107.04  3.000
 BD4  H153  C15  C11   110.63  3.000
 BD4  H152  C15  C11   111.53  3.000
 BD4  H151  C15  C11   111.38  3.000
 BD4  H10   C10  C8    120.56  3.000
 BD4  H10   C10  C11   119.31  3.000
 BD4  C8    C10  C11   120.13  3.000
 BD4  N7    C8   C9    109.05  3.000
 BD4  N7    C8   C10   128.00  3.000
 BD4  C9    C8   C10   122.95  3.000
 BD4  C5    C9   C8    106.50  3.000
 BD4  C5    C9   C13   137.59  3.000
 BD4  C8    C9   C13   115.91  3.000
 BD4  C4    C5   C6    119.59  3.000
 BD4  C4    C5   C9    105.91  3.000
 BD4  C6    C5   C9    134.49  3.000
 BD4  H6    C6   C1    120.09  3.000
 BD4  H6    C6   C5    120.04  3.000
 BD4  C1    C6   C5    119.87  3.000
 BD4  C2    C1   C14   119.80  3.000
 BD4  C2    C1   C6    119.11  3.000
 BD4  C14   C1   C6    121.09  3.000
 BD4  H143  C14  H142  107.70  3.000
 BD4  H143  C14  H141  106.95  3.000
 BD4  H142  C14  H141  107.74  3.000
 BD4  H143  C14  C1    111.43  3.000
 BD4  H142  C14  C1    111.42  3.000
 BD4  H141  C14  C1    111.38  3.000
 BD4  H2    C2   C3    118.72  3.000
 BD4  H2    C2   C1    118.84  3.000
 BD4  C3    C2   C1    122.45  3.000
 BD4  H3    C3   C4    121.98  3.000
 BD4  H3    C3   C2    120.38  3.000
 BD4  C4    C3   C2    117.63  3.000
 BD4  N7    C4   C3    128.94  3.000
 BD4  N7    C4   C5    109.71  3.000
 BD4  C3    C4   C5    121.35  3.000
 BD4  C16   N7   C4    125.31  3.000
 BD4  C16   N7   C8    125.58  3.000
 BD4  C4    N7   C8    108.81  3.000
 BD4  H162  C16  H161  106.15  3.000
 BD4  H162  C16  C17   110.68  3.000
 BD4  H161  C16  C17   110.63  3.000
 BD4  H162  C16  N7    108.09  3.000
 BD4  H161  C16  N7    108.35  3.000
 BD4  C17   C16  N7    112.68  3.000
 BD4  H172  C17  H171  106.95  3.000
 BD4  H172  C17  C18   109.51  3.000
 BD4  H171  C17  C18   109.58  3.000
 BD4  H172  C17  C16   109.90  3.000
 BD4  H171  C17  C16   109.16  3.000
 BD4  C18   C17  C16   111.62  3.000
 BD4  H182  C18  H181  106.20  3.000
 BD4  H182  C18  N19   113.63  3.000
 BD4  H181  C18  N19   108.27  3.000
 BD4  H182  C18  C17   108.88  3.000
 BD4  H181  C18  C17   109.08  3.000
 BD4  N19   C18  C17   110.62  3.000
 BD4  H192  N19  H191  105.43  3.000
 BD4  H192  N19  C18   109.19  3.000
 BD4  H191  N19  C18   109.29  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
 BD4  CONST_01  C10   C11  C12  C13     0.00   0.0  0
 BD4  CONST_02  C10   C8   C9   C13     0.00   0.0  0
 BD4  CONST_03  N7    C8   C9   C13   180.00   0.0  0
 BD4  CONST_04  C6    C5   C9   C13     0.00   0.0  0
 BD4  CONST_05  C4    C5   C9   C13   180.00   0.0  0
 BD4  CONST_06  C8    C9   C13  C12     0.00   0.0  0
 BD4  CONST_07  C5    C9   C13  C12   180.00   0.0  0
 BD4  CONST_08  C8    C10  C11  C12     0.00   0.0  0
 BD4  CONST_09  C9    C13  C12  C11     0.00   0.0  0
 BD4  CONST_10  C9    C8   C10  C11     0.00   0.0  0
 BD4  CONST_11  N7    C8   C10  C11   180.00   0.0  0
 BD4  CONST_12  C5    C9   C8   C10   180.00   0.0  0
 BD4  CONST_13  C4    N7   C8   C10   180.00   0.0  0
 BD4  CONST_14  C6    C5   C9   C8    180.00   0.0  0
 BD4  CONST_15  C4    C5   C9   C8      0.00   0.0  0
 BD4  CONST_16  C5    C4   N7   C8      0.00   0.0  0
 BD4  CONST_17  C3    C4   N7   C8    180.00   0.0  0
 BD4  CONST_18  C4    N7   C8   C9      0.00   0.0  0
 BD4  CONST_19  C1    C6   C5   C9    180.00   0.0  0
 BD4  CONST_20  C3    C4   C5   C9    180.00   0.0  0
 BD4  CONST_21  N7    C4   C5   C9      0.00   0.0  0
 BD4  CONST_22  N7    C8   C9   C5      0.00   0.0  0
 BD4  CONST_23  C2    C1   C6   C5      0.00   0.0  0
 BD4  CONST_24  C2    C3   C4   C5      0.00   0.0  0
 BD4  CONST_25  C3    C4   C5   C6      0.00   0.0  0
 BD4  CONST_26  N7    C4   C5   C6    180.00   0.0  0
 BD4  CONST_27  C3    C2   C1   C6      0.00   0.0  0
 BD4  CONST_28  C4    C5   C6   C1      0.00   0.0  0
 BD4  CONST_29  C4    C3   C2   C1      0.00   0.0  0
 BD4  CONST_30  N7    C4   C3   C2    180.00   0.0  0
 BD4  CONST_31  C12   C20  N21  C22     0.00   0.0  0
 BD4  CONST_32  C15   C11  C12  C20     0.00   0.0  0
 BD4  CONST_33  C15   C11  C12  C13   180.00   0.0  0
 BD4  CONST_34  C8    C10  C11  C15   180.00   0.0  0
 BD4  CONST_35  C16   N7   C8   C10     0.00   0.0  0
 BD4  CONST_36  C16   N7   C8   C9    180.00   0.0  0
 BD4  CONST_37  C14   C1   C6   C5    180.00   0.0  0
 BD4  CONST_38  C16   N7   C4   C5    180.00   0.0  0
 BD4  CONST_39  C3    C2   C1   C14   180.00   0.0  0
 BD4  CONST_40  C16   N7   C4   C3      0.00   0.0  0
 BD4  CONST_41  C22   N21  C20  O23   180.00   0.0  0
 BD4  CONST_42  H10   C10  C11  C12   180.00   0.0  0
 BD4  CONST_43  H6    C6   C5   C9      0.00   0.0  0
 BD4  CONST_44  H3    C3   C4   C5    180.00   0.0  0
 BD4  CONST_45  H2    C2   C1   C6    180.00   0.0  0
 BD4  CONST_46  H21   N21  C20  C12   180.00   0.0  0
 BD4  Var_01    C17   C16  N7   C8    -85.29  30.0  2
 BD4  Var_02    H151  C15  C11  C12   -59.80  30.0  2
 BD4  Var_03    H141  C14  C1   C6   -117.80  30.0  2
 BD4  Var_04    C18   C17  C16  N7   -178.53  30.0  3
 BD4  Var_05    N19   C18  C17  C16  -179.57  30.0  3
 BD4  Var_06    H191  N19  C18  C17   178.62  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
 BD4  plan-1  O23  0.020
 BD4  plan-1  C20  0.020
 BD4  plan-1  N21  0.020
 BD4  plan-1  C22  0.020
 BD4  plan-1  O24  0.020
 BD4  plan-1  C13  0.020
 BD4  plan-1  C12  0.020
 BD4  plan-1  C11  0.020
 BD4  plan-1  C15  0.020
 BD4  plan-1  C10  0.020
 BD4  plan-1  C8   0.020
 BD4  plan-1  C9   0.020
 BD4  plan-1  C5   0.020
 BD4  plan-1  C6   0.020
 BD4  plan-1  C1   0.020
 BD4  plan-1  C14  0.020
 BD4  plan-1  C2   0.020
 BD4  plan-1  C3   0.020
 BD4  plan-1  C4   0.020
 BD4  plan-1  N7   0.020
 BD4  plan-1  C16  0.020
 BD4  plan-1  H21  0.020
 BD4  plan-1  H10  0.020
 BD4  plan-1  H6   0.020
 BD4  plan-1  H2   0.020
 BD4  plan-1  H3   0.020

