# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 03:55:45 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: 3-[4,5,6,7-tetrakis(bromanyl)benzimidazol-1-yl]propan-1-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCn1cnc2c(Br)c(Br)c(Br)c(Br)c12
#
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
 B0K  B0K  3-[4,5,6,7-tetrakis(bromanyl)benzimidazol-1-yl]propan-1-amine  ligand  26  17  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_B0K
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
 B0K  C2   C   CR56  0   0.206  -0.1168  -1.8230  -0.2795
 B0K  C3   C   CR56  0   0.438   1.0200  -0.9991  -0.3893
 B0K  C4   C   CR6   0  -0.144   0.9029   0.3889  -0.3067
 B0K  C5   C   CR6   0  -0.122  -0.3641   0.9256  -0.0939
 B0K  C6   C   CR6   0  -0.106  -1.5033   0.0993   0.0236
 B0K  N9   N   N     0  -0.434   0.2246  -3.1351  -0.4029
 B0K  C16  C   CH2   0  -0.277   5.6272  -1.1018   0.5177
 B0K  C1   C   CR6   0  -0.207  -1.3796  -1.2758  -0.0737
 B0K  C15  C   CH2   0  -0.442   4.1513  -1.4391   0.6711
 B0K  C8   C   CR15  0   0.132   1.5124  -3.1164  -0.5780
 B0K  N17  N   NH2   0  -0.799   6.2501  -0.9374   1.8215
 B0K  N7   N   NR5   0  -0.519   2.0597  -1.8764  -0.5880
 B0K  BR1  BR  BR    0   0.045   2.3911   1.5101  -0.4927
 B0K  BR2  BR  BR    0   0.042  -0.5661   2.7836   0.0333
 B0K  BR3  BR  BR    0   0.037  -3.1931   0.8540   0.3081
 B0K  BR4  BR  BR    0   0.032  -2.8264  -2.4458   0.0572
 B0K  H1   H   HCH2  0   0.272   3.6881  -0.8308  -1.3662
 B0K  H2   H   HCH2  0   0.281   3.9090  -2.5454  -1.1607
 B0K  H3   H   HCH2  0   0.198   6.1098  -1.8665  -0.1085
 B0K  H4   H   HCH2  0   0.221   5.7191  -0.1584  -0.0275
 B0K  H5   H   HCH2  0   0.236   3.6555  -0.6346   1.2192
 B0K  H6   H   HCH2  0   0.239   4.0369  -2.3472   1.2711
 B0K  H7   H   HCR5  0   0.307   2.1313  -3.9919  -0.7128
 B0K  H8   H   HNH2  0   0.340   6.3114  -1.8391   2.2784
 B0K  H9   H   HNH2  0   0.349   7.2065  -0.6303   1.6999
 B0K  C14  C   CH2   0  -0.325   3.4964  -1.6557  -0.6841

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
 B0K  BR3  C6   single    1.872  0.020  1.872
 B0K  BR4  C1   single    1.865  0.020  1.865
 B0K  C6   C1   aromatic  1.384  0.020  1.384
 B0K  C6   C5   aromatic  1.412  0.020  1.412
 B0K  C1   C2   aromatic  1.392  0.020  1.392
 B0K  BR2  C5   single    1.873  0.020  1.873
 B0K  C5   C4   aromatic  1.392  0.020  1.392
 B0K  C2   N9   aromatic  1.361  0.020  1.361
 B0K  C2   C3   aromatic  1.408  0.020  1.408
 B0K  N9   C8   aromatic  1.300  0.020  1.300
 B0K  C4   C3   aromatic  1.395  0.020  1.395
 B0K  C4   BR1  single    1.872  0.020  1.872
 B0K  C3   N7   aromatic  1.375  0.020  1.375
 B0K  C8   N7   aromatic  1.355  0.020  1.355
 B0K  N7   C14  single    1.457  0.020  1.457
 B0K  C14  C15  single    1.521  0.020  1.521
 B0K  C15  C16  single    1.522  0.020  1.522
 B0K  C16  N17  single    1.454  0.020  1.454
 B0K  C14  H1   single    0.970  0.020  1.090
 B0K  C14  H2   single    0.970  0.020  1.090
 B0K  C16  H3   single    0.970  0.020  1.090
 B0K  C16  H4   single    0.970  0.020  1.090
 B0K  C15  H5   single    0.970  0.020  1.090
 B0K  C15  H6   single    0.970  0.020  1.090
 B0K  C8   H7   single    0.930  0.020  1.080
 B0K  N17  H8   single    0.890  0.020  1.040
 B0K  N17  H9   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
 B0K  C1   C2   N9   128.31  3.000
 B0K  N9   C2   C3   110.75  3.000
 B0K  C1   C2   C3   120.94  3.000
 B0K  N7   C3   C4   134.97  3.000
 B0K  N7   C3   C2   104.39  3.000
 B0K  C4   C3   C2   120.64  3.000
 B0K  BR1  C4   C5   120.50  3.000
 B0K  BR1  C4   C3   121.54  3.000
 B0K  C5   C4   C3   117.96  3.000
 B0K  BR2  C5   C6   119.19  3.000
 B0K  BR2  C5   C4   119.40  3.000
 B0K  C6   C5   C4   121.41  3.000
 B0K  BR3  C6   C1   119.46  3.000
 B0K  C1   C6   C5   120.22  3.000
 B0K  BR3  C6   C5   120.32  3.000
 B0K  C8   N9   C2   104.29  3.000
 B0K  H4   C16  H3   106.21  3.000
 B0K  H4   C16  N17  108.27  3.000
 B0K  H3   C16  N17  113.65  3.000
 B0K  H4   C16  C15  108.84  3.000
 B0K  H3   C16  C15  109.20  3.000
 B0K  N17  C16  C15  110.49  3.000
 B0K  BR4  C1   C6   123.29  3.000
 B0K  C6   C1   C2   118.82  3.000
 B0K  BR4  C1   C2   117.88  3.000
 B0K  H6   C15  H5   106.78  3.000
 B0K  H6   C15  C16  109.91  3.000
 B0K  H5   C15  C16  109.12  3.000
 B0K  H6   C15  C14  108.99  3.000
 B0K  H5   C15  C14  110.89  3.000
 B0K  C16  C15  C14  111.06  3.000
 B0K  H7   C8   N7   120.60  3.000
 B0K  H7   C8   N9   124.93  3.000
 B0K  N7   C8   N9   114.47  3.000
 B0K  H9   N17  H8   105.50  3.000
 B0K  H9   N17  C16  109.36  3.000
 B0K  H8   N17  C16  109.25  3.000
 B0K  C8   N7   C14  122.50  3.000
 B0K  C14  N7   C3   131.20  3.000
 B0K  C8   N7   C3   106.10  3.000
 B0K  H2   C14  H1   106.15  3.000
 B0K  H2   C14  N7   106.16  3.000
 B0K  H1   C14  N7   109.28  3.000
 B0K  H2   C14  C15  110.05  3.000
 B0K  H1   C14  C15  112.03  3.000
 B0K  N7   C14  C15  112.80  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
 B0K  CONST_01  C5   C6   C1   C2      0.00   0.0  0
 B0K  CONST_02  N7   C8   N9   C2      0.00   0.0  0
 B0K  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 B0K  CONST_04  C8   N7   C3   C2      0.00   0.0  0
 B0K  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 B0K  CONST_06  C8   N9   C2   C3      0.00   0.0  0
 B0K  CONST_07  C6   C5   C4   C3      0.00   0.0  0
 B0K  CONST_08  N9   C8   N7   C3      0.00   0.0  0
 B0K  CONST_09  C1   C6   C5   C4      0.00   0.0  0
 B0K  CONST_10  C1   C2   C3   C4      0.00   0.0  0
 B0K  CONST_11  N9   C2   C3   C4    180.00   0.0  0
 B0K  CONST_12  C8   N7   C3   C4    180.00   0.0  0
 B0K  CONST_13  N7   C3   C4   C5    180.00   0.0  0
 B0K  CONST_14  N9   C2   C1   C6    180.00   0.0  0
 B0K  CONST_15  N7   C3   C2   N9      0.00   0.0  0
 B0K  CONST_16  C8   N9   C2   C1    180.00   0.0  0
 B0K  CONST_17  N7   C3   C2   C1    180.00   0.0  0
 B0K  CONST_18  BR3  C6   C1   C2    180.00   0.0  0
 B0K  CONST_19  BR1  C4   C3   C2    180.00   0.0  0
 B0K  CONST_20  C14  N7   C3   C2    180.00   0.0  0
 B0K  CONST_21  BR4  C1   C2   C3    180.00   0.0  0
 B0K  CONST_22  BR2  C5   C4   C3    180.00   0.0  0
 B0K  CONST_23  BR3  C6   C5   C4    180.00   0.0  0
 B0K  CONST_24  C14  N7   C3   C4      0.00   0.0  0
 B0K  CONST_25  BR4  C1   C6   C5    180.00   0.0  0
 B0K  CONST_26  BR1  C4   C5   C6    180.00   0.0  0
 B0K  CONST_27  BR4  C1   C2   N9      0.00   0.0  0
 B0K  CONST_28  C14  N7   C8   N9    180.00   0.0  0
 B0K  CONST_29  BR2  C5   C6   C1    180.00   0.0  0
 B0K  CONST_30  BR1  C4   C3   N7      0.00   0.0  0
 B0K  CONST_31  H7   C8   N9   C2    180.00   0.0  0
 B0K  Var_01    C15  C14  N7   C3     77.57  30.0  2
 B0K  Var_02    N7   C14  C15  C16  -175.43  30.0  1
 B0K  Var_03    N17  C16  C15  C14  -178.27  30.0  3
 B0K  Var_04    H8   N17  C16  C15    70.20  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
 B0K  plan-1  C2   0.020
 B0K  plan-1  C3   0.020
 B0K  plan-1  C4   0.020
 B0K  plan-1  C5   0.020
 B0K  plan-1  C6   0.020
 B0K  plan-1  N9   0.020
 B0K  plan-1  C1   0.020
 B0K  plan-1  C8   0.020
 B0K  plan-1  N7   0.020
 B0K  plan-1  BR1  0.020
 B0K  plan-1  BR2  0.020
 B0K  plan-1  BR3  0.020
 B0K  plan-1  BR4  0.020
 B0K  plan-1  H7   0.020
 B0K  plan-1  C14  0.020

