# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 01:14:58 2022
#   Inital geometry file: a 77 line input string
#   Ligand name: 8-cyclopropyl-2-methyl-9~{H}-pyrido[2,3-b]indole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc2c([nH]c3c(cccc23)C4CC4)n1
#
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
 6I4  6I4  "8-cyclopropyl-2-methyl-9H-pyrido[2,3-b]indole"
  ligand  31  17  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6I4
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
 6I4  C1   C  CR16  0  -0.356  35.8323  39.1803  62.6995
 6I4  C2   C  CR16  0  -0.251  35.8833  38.4538  63.8963
 6I4  C3   C  CR16  0  -0.387  35.1553  37.2883  64.0517
 6I4  C4   C  CR6   0   0.080  35.0559  38.7779  61.6230
 6I4  C5   C  CR56  0   0.336  34.3278  37.5993  61.7964
 6I4  C6   C  CR56  0   0.034  34.3663  36.8512  62.9892
 6I4  C8   C  CH1   0  -0.313  34.9875  39.5142  60.3351
 6I4  C9   C  CH2   0  -0.489  35.0693  41.0063  60.2868
 6I4  C10  C  CH2   0  -0.473  33.7671  40.3271  59.9973
 6I4  C11  C  CR56  0   0.434  32.9717  35.8510  61.4812
 6I4  C12  C  CR56  0   0.008  33.4947  35.7261  62.7841
 6I4  C13  C  CR16  0  -0.238  33.0833  34.6262  63.5237
 6I4  C14  C  CR16  0  -0.344  32.1947  33.7464  62.9304
 6I4  C15  C  CR6   0   0.227  31.7364  33.9739  61.6233
 6I4  C17  C  CH3   0  -0.733  30.7721  33.0158  60.9913
 6I4  N16  N  N     0  -0.454  32.1226  35.0212  60.8993
 6I4  N7   N  NR15  0  -0.768  33.4856  36.9779  60.9053
 6I4  H1   H  HCR6  0   0.247  36.4192  40.0864  62.6101
 6I4  H2   H  HCR6  0   0.247  36.5035  38.8135  64.7068
 6I4  H3   H  HCR6  0   0.246  35.1952  36.7289  64.9780
 6I4  H4   H  HCH1  0   0.275  35.4360  38.9901  59.4953
 6I4  H5   H  HCH2  0   0.253  35.6092  41.4553  59.4635
 6I4  H6   H  HCH2  0   0.250  35.1592  41.5451  61.2216
 6I4  H7   H  HCH2  0   0.249  32.9866  40.3969  60.7450
 6I4  H8   H  HCH2  0   0.253  33.4084  40.3073  58.9764
 6I4  H9   H  HCR6  0   0.258  33.4410  34.4573  64.5319
 6I4  H10  H  HCR6  0   0.256  31.8451  32.8755  63.4692
 6I4  H11  H  HCH3  0   0.247  30.5025  33.3398  59.9884
 6I4  H12  H  HCH3  0   0.249  31.2007  32.0145  60.9242
 6I4  H13  H  HCH3  0   0.249  29.8590  32.9312  61.5824
 6I4  H14  H  HNR5  0   0.409  33.2525  37.3117  59.9838

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
 6I4  C9   C10  single    1.497  0.020  1.497
 6I4  C9   C8   single    1.495  0.020  1.495
 6I4  C10  C8   single    1.505  0.020  1.505
 6I4  C8   C4   single    1.485  0.020  1.485
 6I4  N16  C11  aromatic  1.322  0.020  1.322
 6I4  N16  C15  aromatic  1.330  0.020  1.330
 6I4  N7   C11  aromatic  1.366  0.020  1.366
 6I4  N7   C5   aromatic  1.375  0.020  1.375
 6I4  C17  C15  single    1.499  0.020  1.499
 6I4  C11  C12  aromatic  1.409  0.020  1.409
 6I4  C4   C5   aromatic  1.396  0.020  1.396
 6I4  C4   C1   aromatic  1.387  0.020  1.387
 6I4  C15  C14  aromatic  1.404  0.020  1.404
 6I4  C5   C6   aromatic  1.409  0.020  1.409
 6I4  C1   C2   aromatic  1.401  0.020  1.401
 6I4  C12  C6   aromatic  1.438  0.020  1.438
 6I4  C12  C13  aromatic  1.388  0.020  1.388
 6I4  C14  C13  aromatic  1.384  0.020  1.384
 6I4  C6   C3   aromatic  1.394  0.020  1.394
 6I4  C2   C3   aromatic  1.383  0.020  1.383
 6I4  C1   H1   single    0.930  0.020  1.080
 6I4  C2   H2   single    0.930  0.020  1.080
 6I4  C3   H3   single    0.930  0.020  1.080
 6I4  C8   H4   single    0.970  0.020  1.090
 6I4  C9   H5   single    0.970  0.020  1.090
 6I4  C9   H6   single    0.970  0.020  1.090
 6I4  C10  H7   single    0.970  0.020  1.090
 6I4  C10  H8   single    0.970  0.020  1.090
 6I4  C13  H9   single    0.930  0.020  1.080
 6I4  C14  H10  single    0.930  0.020  1.080
 6I4  C17  H11  single    0.970  0.020  1.090
 6I4  C17  H12  single    0.970  0.020  1.090
 6I4  C17  H13  single    0.970  0.020  1.090
 6I4  N7   H14  single    0.860  0.020  1.020

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
 6I4  H1   C1   C4   118.81  3.000
 6I4  H1   C1   C2   118.98  3.000
 6I4  C4   C1   C2   122.20  3.000
 6I4  H2   C2   C3   119.85  3.000
 6I4  H2   C2   C1   119.23  3.000
 6I4  C3   C2   C1   120.92  3.000
 6I4  H3   C3   C6   120.73  3.000
 6I4  H3   C3   C2   120.80  3.000
 6I4  C6   C3   C2   118.47  3.000
 6I4  C8   C4   C5   120.14  3.000
 6I4  C5   C4   C1   116.14  3.000
 6I4  C8   C4   C1   123.71  3.000
 6I4  N7   C5   C6   109.00  3.000
 6I4  C6   C5   C4   122.63  3.000
 6I4  N7   C5   C4   128.37  3.000
 6I4  C12  C6   C5   106.15  3.000
 6I4  C12  C6   C3   134.21  3.000
 6I4  C5   C6   C3   119.64  3.000
 6I4  H4   C8   C10  114.95  3.000
 6I4  H4   C8   C9   115.71  3.000
 6I4  C10  C8   C9    59.87  3.000
 6I4  H4   C8   C4   114.33  3.000
 6I4  C10  C8   C4   119.99  3.000
 6I4  C9   C8   C4   121.35  3.000
 6I4  H6   C9   H5   114.14  3.000
 6I4  H6   C9   C10  117.71  3.000
 6I4  H5   C9   C10  118.38  3.000
 6I4  H6   C9   C8   118.25  3.000
 6I4  H5   C9   C8   117.78  3.000
 6I4  C10  C9   C8    60.39  3.000
 6I4  H8   C10  H7   114.43  3.000
 6I4  H8   C10  C9   118.62  3.000
 6I4  H7   C10  C9   117.65  3.000
 6I4  H8   C10  C8   118.08  3.000
 6I4  H7   C10  C8   117.67  3.000
 6I4  C9   C10  C8    59.75  3.000
 6I4  N7   C11  N16  125.02  3.000
 6I4  N7   C11  C12  108.86  3.000
 6I4  N16  C11  C12  126.12  3.000
 6I4  C13  C12  C11  116.93  3.000
 6I4  C13  C12  C6   136.37  3.000
 6I4  C11  C12  C6   106.70  3.000
 6I4  H9   C13  C14  120.79  3.000
 6I4  H9   C13  C12  121.45  3.000
 6I4  C14  C13  C12  117.76  3.000
 6I4  H10  C14  C15  119.25  3.000
 6I4  H10  C14  C13  120.37  3.000
 6I4  C15  C14  C13  120.37  3.000
 6I4  N16  C15  C17  117.41  3.000
 6I4  C17  C15  C14  119.93  3.000
 6I4  N16  C15  C14  122.66  3.000
 6I4  H13  C17  H12  106.91  3.000
 6I4  H13  C17  H11  108.37  3.000
 6I4  H12  C17  H11  108.30  3.000
 6I4  H13  C17  C15  111.07  3.000
 6I4  H12  C17  C15  111.09  3.000
 6I4  H11  C17  C15  110.96  3.000
 6I4  C15  N16  C11  116.16  3.000
 6I4  H14  N7   C11  124.89  3.000
 6I4  H14  N7   C5   125.80  3.000
 6I4  C11  N7   C5   109.28  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
 6I4  CONST_01  N7   C5   C4   C1    180.00   0.0  0
 6I4  CONST_02  C6   C5   C4   C1      0.00   0.0  0
 6I4  CONST_03  C6   C3   C2   C1      0.00   0.0  0
 6I4  CONST_04  C5   C4   C1   C2      0.00   0.0  0
 6I4  CONST_05  C5   C6   C3   C2      0.00   0.0  0
 6I4  CONST_06  C12  C6   C3   C2    180.00   0.0  0
 6I4  CONST_07  N7   C5   C6   C3    180.00   0.0  0
 6I4  CONST_08  C4   C5   C6   C3      0.00   0.0  0
 6I4  CONST_09  C11  C12  C6   C3    180.00   0.0  0
 6I4  CONST_10  C13  C12  C6   C3      0.00   0.0  0
 6I4  CONST_11  C4   C1   C2   C3      0.00   0.0  0
 6I4  CONST_12  C11  N7   C5   C4    180.00   0.0  0
 6I4  CONST_13  C12  C6   C5   C4    180.00   0.0  0
 6I4  CONST_14  N16  C11  N7   C5    180.00   0.0  0
 6I4  CONST_15  C12  C11  N7   C5      0.00   0.0  0
 6I4  CONST_16  C11  C12  C6   C5      0.00   0.0  0
 6I4  CONST_17  C13  C12  C6   C5    180.00   0.0  0
 6I4  CONST_18  C11  N7   C5   C6      0.00   0.0  0
 6I4  CONST_19  N16  C11  C12  C6    180.00   0.0  0
 6I4  CONST_20  N7   C11  C12  C6      0.00   0.0  0
 6I4  CONST_21  C14  C13  C12  C6    180.00   0.0  0
 6I4  CONST_22  C14  C15  N16  C11     0.00   0.0  0
 6I4  CONST_23  C14  C13  C12  C11     0.00   0.0  0
 6I4  CONST_24  C15  N16  C11  C12     0.00   0.0  0
 6I4  CONST_25  N7   C5   C6   C12     0.00   0.0  0
 6I4  CONST_26  C15  C14  C13  C12     0.00   0.0  0
 6I4  CONST_27  N16  C11  C12  C13     0.00   0.0  0
 6I4  CONST_28  N7   C11  C12  C13   180.00   0.0  0
 6I4  CONST_29  N16  C15  C14  C13     0.00   0.0  0
 6I4  CONST_30  N7   C11  N16  C15   180.00   0.0  0
 6I4  CONST_31  C8   C4   C1   C2    180.00   0.0  0
 6I4  CONST_32  C8   C4   C5   C6    180.00   0.0  0
 6I4  CONST_33  N7   C5   C4   C8      0.00   0.0  0
 6I4  CONST_34  C17  C15  N16  C11   180.00   0.0  0
 6I4  CONST_35  C17  C15  C14  C13   180.00   0.0  0
 6I4  CONST_36  H3   C3   C2   C1    180.00   0.0  0
 6I4  CONST_37  H1   C1   C2   C3    180.00   0.0  0
 6I4  CONST_38  H14  N7   C5   C4      0.00   0.0  0
 6I4  CONST_39  H2   C2   C1   C4    180.00   0.0  0
 6I4  CONST_40  H1   C1   C4   C5    180.00   0.0  0
 6I4  CONST_41  H3   C3   C6   C5    180.00   0.0  0
 6I4  CONST_42  H14  N7   C5   C6    180.00   0.0  0
 6I4  CONST_43  H9   C13  C12  C6      0.00   0.0  0
 6I4  CONST_44  H2   C2   C3   C6    180.00   0.0  0
 6I4  CONST_45  H1   C1   C4   C8      0.00   0.0  0
 6I4  CONST_46  H9   C13  C12  C11   180.00   0.0  0
 6I4  CONST_47  H14  N7   C11  C12   180.00   0.0  0
 6I4  CONST_48  H3   C3   C6   C12     0.00   0.0  0
 6I4  CONST_49  H10  C14  C13  C12   180.00   0.0  0
 6I4  CONST_50  H9   C13  C14  C15   180.00   0.0  0
 6I4  CONST_51  H14  N7   C11  N16     0.00   0.0  0
 6I4  CONST_52  H10  C14  C15  N16   180.00   0.0  0
 6I4  Var_01    C9   C8   C4   C1    -34.73  30.0  2
 6I4  Var_02    C10  C8   C4   C1   -105.63  30.0  2
 6I4  Var_03    C10  C9   C8   C4   -108.85  30.0  1
 6I4  Var_04    C9   C8   C4   C5    146.20  30.0  2
 6I4  Var_05    C10  C8   C4   C5     75.30  30.0  2
 6I4  Var_06    H4   C8   C4   C1    111.68  30.0  2
 6I4  Var_07    H5   C9   C8   C4    142.58  30.0  1
 6I4  Var_08    H6   C9   C8   C4     -1.28  30.0  1
 6I4  Var_09    H7   C10  C8   C4      3.56  30.0  1
 6I4  Var_10    H8   C10  C8   C4   -140.43  30.0  1
 6I4  Var_11    H4   C8   C4   C5    -67.39  30.0  2
 6I4  Var_12    H7   C10  C9   C8    107.53  30.0  1
 6I4  Var_13    H8   C10  C9   C8   -107.60  30.0  1
 6I4  Var_14    H5   C9   C10  C8    107.59  30.0  1
 6I4  Var_15    H6   C9   C10  C8   -108.45  30.0  1
 6I4  Var_16    H4   C8   C10  C9   -106.45  30.0  1
 6I4  Var_17    H11  C17  C15  C14   179.05  30.0  2
 6I4  Var_18    H12  C17  C15  C14   -60.41  30.0  2
 6I4  Var_19    H13  C17  C15  C14    58.44  30.0  2
 6I4  Var_20    H11  C17  C15  N16    -0.92  30.0  2
 6I4  Var_21    H12  C17  C15  N16   119.61  30.0  2
 6I4  Var_22    H13  C17  C15  N16  -121.53  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
 6I4  chir_01  C8  C9  C10  C4  both

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
 6I4  plan-1  C1   0.020
 6I4  plan-1  C2   0.020
 6I4  plan-1  C3   0.020
 6I4  plan-1  C4   0.020
 6I4  plan-1  C5   0.020
 6I4  plan-1  C6   0.020
 6I4  plan-1  C8   0.020
 6I4  plan-1  C11  0.020
 6I4  plan-1  C12  0.020
 6I4  plan-1  C13  0.020
 6I4  plan-1  C14  0.020
 6I4  plan-1  C15  0.020
 6I4  plan-1  C17  0.020
 6I4  plan-1  N16  0.020
 6I4  plan-1  N7   0.020
 6I4  plan-1  H1   0.020
 6I4  plan-1  H2   0.020
 6I4  plan-1  H3   0.020
 6I4  plan-1  H9   0.020
 6I4  plan-1  H10  0.020
 6I4  plan-1  H14  0.020

