# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 16:00:21 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: 11-bromo-5,6,7,8-tetrahydropyrimido[4',5':3,4]cyclohepta[1,2-b]indol-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncc2CCCc3[nH]c4ccc(Br)cc4c3c2n1
#
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
 T28  T28  11-bromo-5,6,7,8-tetrahydropyrimido[4',5':3,4]cyclohepta[1,2-b]indol-2-amine  ligand  33  20  .  2021-08-23  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_T28
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
 T28  BR1   BR  BR    0  -0.069  -3.9301  -1.2179  -0.0082
 T28  C12   C   CR6   0  -0.115  -2.5833   0.1075  -0.1574
 T28  C6    C   CR16  0  -0.362  -1.2594  -0.2745  -0.0795
 T28  C2    C   CR56  0   0.093  -0.2878   0.7231  -0.1969
 T28  C5    C   CR56  0   0.334  -0.6878   2.0621  -0.3899
 T28  C11   C   CR16  0  -0.295  -2.0252   2.4324  -0.4653
 T28  C17   C   CR16  0  -0.260  -2.9786   1.4387  -0.3478
 T28  C1    C   CR5   0  -0.071   1.1429   0.7306  -0.1420
 T28  C4    C   CR5   0   0.348   1.5450   2.0372  -0.3299
 T28  N9    N   NR15  0  -0.739   0.4476   2.8220  -0.4732
 T28  C3    C   CR6   0   0.197   2.0667  -0.3751   0.0208
 T28  N8    N   N     0  -0.483   1.7279  -1.5525  -0.4964
 T28  C15   C   CR6   0   0.522   2.6056  -2.5491  -0.3817
 T28  N20   N   NH2   0  -0.830   2.2705  -3.7358  -0.9413
 T28  N19   N   N     0  -0.458   3.8034  -2.4650   0.2031
 T28  C13   C   CR16  0  -0.076   4.1001  -1.2956   0.7510
 T28  C7    C   CR6   0  -0.012   3.2737  -0.1856   0.7159
 T28  C14   C   CH2   0  -0.547   3.5606   1.0598   1.5043
 T28  C16   C   CH2   0  -0.403   3.8508   2.3323   0.7073
 T28  C10   C   CH2   0  -0.553   2.9383   2.5318  -0.5104
 T28  H6    H   HCR6  0   0.264  -0.9704  -1.3075   0.0580
 T28  H11   H   HCR6  0   0.273  -2.3207   3.4628  -0.6135
 T28  H17   H   HCR6  0   0.274  -4.0270   1.6970  -0.4076
 T28  H1    H   HNR5  0   0.415   0.4716   3.8152  -0.6411
 T28  H201  H   HNH2  0   0.389   1.3052  -3.8884  -1.1769
 T28  H202  H   HNH2  0   0.390   2.7936  -4.5491  -0.6659
 T28  H13   H   HCR6  0   0.258   5.0536  -1.2401   1.2698
 T28  H142  H   HCH2  0   0.245   2.6996   1.2478   2.1538
 T28  H141  H   HCH2  0   0.256   4.4017   0.8717   2.1754
 T28  H162  H   HCH2  0   0.239   3.7578   3.1835   1.3843
 T28  H161  H   HCH2  0   0.238   4.8828   2.3260   0.3519
 T28  H102  H   HCH2  0   0.266   3.3627   1.9859  -1.3575
 T28  H101  H   HCH2  0   0.272   2.9304   3.5838  -0.7983

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
 T28  N20  C15   single    1.354  0.020  1.354
 T28  N19  C15   aromatic  1.336  0.020  1.336
 T28  N19  C13   aromatic  1.325  0.020  1.325
 T28  C15  N8    aromatic  1.333  0.020  1.333
 T28  C13  C7    aromatic  1.384  0.020  1.384
 T28  BR1  C12   single    1.895  0.020  1.895
 T28  N8   C3    aromatic  1.330  0.020  1.330
 T28  C7   C3    aromatic  1.406  0.020  1.406
 T28  C7   C14   single    1.502  0.020  1.502
 T28  C3   C1    aromatic  1.450  0.020  1.450
 T28  C6   C12   aromatic  1.380  0.020  1.380
 T28  C6   C2    aromatic  1.398  0.020  1.398
 T28  C12  C17   aromatic  1.402  0.020  1.402
 T28  C14  C16   single    1.529  0.020  1.529
 T28  C2   C1    aromatic  1.432  0.020  1.432
 T28  C2   C5    aromatic  1.411  0.020  1.411
 T28  C1   C4    aromatic  1.380  0.020  1.380
 T28  C17  C11   aromatic  1.382  0.020  1.382
 T28  C16  C10   single    1.535  0.020  1.535
 T28  C5   C11   aromatic  1.390  0.020  1.390
 T28  C5   N9    aromatic  1.369  0.020  1.369
 T28  C4   C10   single    1.490  0.020  1.490
 T28  C4   N9    aromatic  1.357  0.020  1.357
 T28  C6   H6    single    0.930  0.020  1.080
 T28  C11  H11   single    0.930  0.020  1.080
 T28  C17  H17   single    0.930  0.020  1.080
 T28  N9   H1    single    0.860  0.020  1.020
 T28  N20  H201  single    0.890  0.020  1.040
 T28  N20  H202  single    0.890  0.020  1.040
 T28  C13  H13   single    0.930  0.020  1.080
 T28  C14  H142  single    0.970  0.020  1.090
 T28  C14  H141  single    0.970  0.020  1.090
 T28  C16  H162  single    0.970  0.020  1.090
 T28  C16  H161  single    0.970  0.020  1.090
 T28  C10  H102  single    0.970  0.020  1.090
 T28  C10  H101  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
 T28  C17   C12  C6    122.76  3.000
 T28  C17   C12  BR1   118.32  3.000
 T28  C6    C12  BR1   118.92  3.000
 T28  H6    C6   C2    120.45  3.000
 T28  H6    C6   C12   121.87  3.000
 T28  C2    C6   C12   117.69  3.000
 T28  C1    C2   C5    106.48  3.000
 T28  C5    C2   C6    119.47  3.000
 T28  C1    C2   C6    134.04  3.000
 T28  N9    C5   C11   130.31  3.000
 T28  N9    C5   C2    107.47  3.000
 T28  C11   C5   C2    122.22  3.000
 T28  H11   C11  C17   120.52  3.000
 T28  H11   C11  C5    121.60  3.000
 T28  C17   C11  C5    117.88  3.000
 T28  H17   C17  C11   119.49  3.000
 T28  H17   C17  C12   120.52  3.000
 T28  C11   C17  C12   119.99  3.000
 T28  C3    C1   C4    123.48  3.000
 T28  C4    C1   C2    106.91  3.000
 T28  C3    C1   C2    129.57  3.000
 T28  C10   C4   N9    123.49  3.000
 T28  N9    C4   C1    109.05  3.000
 T28  C10   C4   C1    127.12  3.000
 T28  H1    N9   C4    124.65  3.000
 T28  H1    N9   C5    125.26  3.000
 T28  C4    N9   C5    110.08  3.000
 T28  C7    C3   N8    122.03  3.000
 T28  C7    C3   C1    119.99  3.000
 T28  N8    C3   C1    117.98  3.000
 T28  C15   N8   C3    117.44  3.000
 T28  N19   C15  N20   117.26  3.000
 T28  N19   C15  N8    125.53  3.000
 T28  N20   C15  N8    117.18  3.000
 T28  H202  N20  H201  116.17  3.000
 T28  H202  N20  C15   117.84  3.000
 T28  H201  N20  C15   117.87  3.000
 T28  C13   N19  C15   115.94  3.000
 T28  H13   C13  C7    119.66  3.000
 T28  H13   C13  N19   116.03  3.000
 T28  C7    C13  N19   124.30  3.000
 T28  C14   C7   C13   122.52  3.000
 T28  C14   C7   C3    122.37  3.000
 T28  C13   C7   C3    114.65  3.000
 T28  H141  C14  H142  105.71  3.000
 T28  H141  C14  C16   108.50  3.000
 T28  H142  C14  C16   108.40  3.000
 T28  H141  C14  C7    109.08  3.000
 T28  H142  C14  C7    107.68  3.000
 T28  C16   C14  C7    116.92  3.000
 T28  H161  C16  H162  106.68  3.000
 T28  H161  C16  C10   107.73  3.000
 T28  H162  C16  C10   109.88  3.000
 T28  H161  C16  C14   110.14  3.000
 T28  H162  C16  C14   108.02  3.000
 T28  C10   C16  C14   114.14  3.000
 T28  H101  C10  H102  106.26  3.000
 T28  H101  C10  C16   109.83  3.000
 T28  H102  C10  C16   108.61  3.000
 T28  H101  C10  C4    110.21  3.000
 T28  H102  C10  C4    106.93  3.000
 T28  C16   C10  C4    114.63  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
 T28  CONST_01  C1   C2   C6   C12  180.00   0.0  0
 T28  CONST_02  C5   C2   C6   C12    0.00   0.0  0
 T28  CONST_03  C5   C11  C17  C12    0.00   0.0  0
 T28  CONST_04  C11  C17  C12  C6     0.00   0.0  0
 T28  CONST_05  C3   C1   C2   C6     0.00   0.0  0
 T28  CONST_06  C4   C1   C2   C6   180.00   0.0  0
 T28  CONST_07  C11  C5   C2   C6     0.00   0.0  0
 T28  CONST_08  N9   C5   C2   C6   180.00   0.0  0
 T28  CONST_09  C17  C12  C6   C2     0.00   0.0  0
 T28  CONST_12  N9   C4   C1   C2     0.00   0.0  0
 T28  CONST_13  C17  C11  C5   C2     0.00   0.0  0
 T28  CONST_14  C4   N9   C5   C2     0.00   0.0  0
 T28  CONST_15  C3   C1   C2   C5   180.00   0.0  0
 T28  CONST_16  C4   C1   C2   C5     0.00   0.0  0
 T28  CONST_17  C1   C4   N9   C5     0.00   0.0  0
 T28  CONST_18  C1   C2   C5   C11  180.00   0.0  0
 T28  CONST_19  C4   N9   C5   C11  180.00   0.0  0
 T28  CONST_20  N9   C5   C11  C17  180.00   0.0  0
 T28  CONST_21  C15  N8   C3   C1   180.00   0.0  0
 T28  CONST_22  C13  C7   C3   C1   180.00   0.0  0
 T28  CONST_23  N9   C5   C2   C1     0.00   0.0  0
 T28  CONST_26  C3   C1   C4   N9   180.00   0.0  0
 T28  CONST_27  N19  C15  N8   C3     0.00   0.0  0
 T28  CONST_28  N19  C13  C7   C3     0.00   0.0  0
 T28  CONST_29  C13  N19  C15  N8     0.00   0.0  0
 T28  CONST_30  C13  C7   C3   N8     0.00   0.0  0
 T28  CONST_31  C7   C13  N19  C15    0.00   0.0  0
 T28  CONST_32  C7   C3   N8   C15    0.00   0.0  0
 T28  CONST_33  C2   C6   C12  BR1  180.00   0.0  0
 T28  CONST_34  C11  C17  C12  BR1  180.00   0.0  0
 T28  CONST_35  N20  C15  N8   C3   180.00   0.0  0
 T28  CONST_36  C13  N19  C15  N20  180.00   0.0  0
 T28  CONST_37  H11  C11  C17  C12  180.00   0.0  0
 T28  CONST_38  H17  C17  C12  C6   180.00   0.0  0
 T28  CONST_39  H1   N9   C5   C2   180.00   0.0  0
 T28  CONST_40  H6   C6   C2   C5   180.00   0.0  0
 T28  CONST_41  H13  C13  C7   C3   180.00   0.0  0
 T28  Var_01    C16  C10  C4   C1   -64.73  30.0  1
 T28  Var_02    C14  C16  C10  C4    34.03  30.0  1
 T28  Var_03    C16  C14  C7   C3   -72.61  30.0  1
 T28  Var_04    C10  C16  C14  C7    41.71  30.0  1

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
 T28  plan-1  BR1   0.020
 T28  plan-1  C12   0.020
 T28  plan-1  C6    0.020
 T28  plan-1  C2    0.020
 T28  plan-1  C5    0.020
 T28  plan-1  C11   0.020
 T28  plan-1  C17   0.020
 T28  plan-1  C1    0.020
 T28  plan-1  C4    0.020
 T28  plan-1  N9    0.020
 T28  plan-1  C3    0.020
 T28  plan-1  C10   0.020
 T28  plan-1  H6    0.020
 T28  plan-1  H11   0.020
 T28  plan-1  H17   0.020
 T28  plan-1  H1    0.020
 T28  plan-2  C15   0.020
 T28  plan-2  N20   0.020
 T28  plan-2  H201  0.020
 T28  plan-2  H202  0.020
 T28  plan-3  C1    0.020
 T28  plan-3  C3    0.020
 T28  plan-3  N8    0.020
 T28  plan-3  C15   0.020
 T28  plan-3  N20   0.020
 T28  plan-3  N19   0.020
 T28  plan-3  C13   0.020
 T28  plan-3  C7    0.020
 T28  plan-3  C14   0.020
 T28  plan-3  H13   0.020

