# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 18:44:30 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: 4-{4-[bis(2-chloroethyl)amino]phenyl}butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCCc1ccc(cc1)N(CCCl)CCCl
#
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
 CBL  CBL  '4-{4-[bis(2-chloroethyl)amino]phenyl}butanoic acid'  ligand  38  19  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_CBL
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
 CBL  C1    C   CR6   0   0.390   0.0944  -0.3992  -1.0371
 CBL  C2    C   CR16  0  -0.336   1.3067  -0.2114  -0.3538
 CBL  C3    C   CR16  0  -0.296   1.4265  -0.5268   0.9896
 CBL  C4    C   CR6   0   0.106   0.3676  -1.0525   1.7231
 CBL  C5    C   CR16  0  -0.301  -0.8294  -1.2479   1.0426
 CBL  C6    C   CR16  0  -0.338  -0.9745  -0.9307  -0.2990
 CBL  C7    C   CH2   0  -0.507   0.5003  -1.3433   3.1908
 CBL  C8    C   CH2   0  -0.413   0.1850  -0.1211   4.0546
 CBL  C9    C   CH2   0  -0.584   0.3470  -0.4294   5.5334
 CBL  C10   C   C     0   0.548   0.0327   0.7323   6.4334
 CBL  N11   N   NT    0  -0.522  -0.0357  -0.0801  -2.3755
 CBL  C12   C   CH2   0  -0.338   0.9713   0.6803  -3.0752
 CBL  C13   C   CH2   0  -0.450   1.9897  -0.2358  -3.7368
 CBL  CL14  CL  CL    0  -0.171   3.2033   0.7449  -4.6312
 CBL  C15   C   CH2   0  -0.341  -1.2223  -0.4160  -3.1221
 CBL  C16   C   CH2   0  -0.453  -2.2781   0.6751  -3.0073
 CBL  CL17  CL  CL    0  -0.170  -3.7265   0.2271  -3.9733
 CBL  O18   O   O     0  -0.445  -0.3050   1.8294   6.0634
 CBL  O19   O   OH1   0  -0.598   0.1701   0.4138   7.7179
 CBL  H2    H   HCR6  0   0.257   2.1802   0.1714  -0.8640
 CBL  H3    H   HCR6  0   0.242   2.3835  -0.3646   1.4733
 CBL  H5    H   HCR6  0   0.243  -1.6847  -1.6561   1.5694
 CBL  H6    H   HCR6  0   0.257  -1.9405  -1.0981  -0.7564
 CBL  H71   H   HCH2  0   0.236   1.5163  -1.6855   3.4096
 CBL  H72   H   HCH2  0   0.237  -0.1677  -2.1633   3.4705
 CBL  H81   H   HCH2  0   0.234  -0.8353   0.2113   3.8494
 CBL  H82   H   HCH2  0   0.234   0.8445   0.7024   3.7696
 CBL  H91   H   HCH2  0   0.278   1.3696  -0.7577   5.7459
 CBL  H92   H   HCH2  0   0.277  -0.2932  -1.2683   5.8251
 CBL  H121  H   HCH2  0   0.278   0.4873   1.2923  -3.8389
 CBL  H122  H   HCH2  0   0.268   1.4689   1.3770  -2.3993
 CBL  H131  H   HCH2  0   0.286   2.5335  -0.8358  -3.0104
 CBL  H132  H   HCH2  0   0.289   1.5157  -0.9001  -4.4568
 CBL  H151  H   HCH2  0   0.279  -0.9539  -0.5457  -4.1722
 CBL  H152  H   HCH2  0   0.267  -1.6278  -1.3737  -2.7920
 CBL  H161  H   HCH2  0   0.288  -2.6073   0.8193  -1.9806
 CBL  H162  H   HCH2  0   0.289  -1.9108   1.6233  -3.3949
 CBL  HO9   H   HOH1  0   0.478  -0.0446   1.1778   8.2734

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
 CBL  C1   C2    aromatic  1.404  0.020  1.404
 CBL  C1   C6    aromatic  1.403  0.020  1.403
 CBL  C1   N11   single    1.382  0.020  1.382
 CBL  C2   C3    aromatic  1.385  0.020  1.385
 CBL  C2   H2    single    0.930  0.020  1.080
 CBL  C3   C4    aromatic  1.391  0.020  1.391
 CBL  C3   H3    single    0.930  0.020  1.080
 CBL  C4   C5    aromatic  1.391  0.020  1.391
 CBL  C4   C7    single    1.502  0.020  1.502
 CBL  C5   C6    aromatic  1.386  0.020  1.386
 CBL  C5   H5    single    0.930  0.020  1.080
 CBL  C6   H6    single    0.930  0.020  1.080
 CBL  C7   C8    single    1.529  0.020  1.529
 CBL  C7   H71   single    0.970  0.020  1.090
 CBL  C7   H72   single    0.970  0.020  1.090
 CBL  C8   C9    single    1.519  0.020  1.519
 CBL  C8   H81   single    0.970  0.020  1.090
 CBL  C8   H82   single    0.970  0.020  1.090
 CBL  C9   C10   single    1.503  0.020  1.503
 CBL  C9   H91   single    0.970  0.020  1.090
 CBL  C9   H92   single    0.970  0.020  1.090
 CBL  C10  O18   double    1.206  0.020  1.206
 CBL  C10  O19   single    1.330  0.020  1.330
 CBL  N11  C12   single    1.443  0.020  1.443
 CBL  N11  C15   single    1.442  0.020  1.442
 CBL  C12  C13   single    1.521  0.020  1.521
 CBL  C12  H121  single    0.970  0.020  1.090
 CBL  C12  H122  single    0.970  0.020  1.090
 CBL  C13  CL14  single    1.799  0.020  1.799
 CBL  C13  H131  single    0.970  0.020  1.090
 CBL  C13  H132  single    0.970  0.020  1.090
 CBL  C15  C16   single    1.523  0.020  1.523
 CBL  C15  H151  single    0.970  0.020  1.090
 CBL  C15  H152  single    0.970  0.020  1.090
 CBL  C16  CL17  single    1.798  0.020  1.798
 CBL  C16  H161  single    0.970  0.020  1.090
 CBL  C16  H162  single    0.970  0.020  1.090
 CBL  O19  HO9   single    0.850  0.020  0.980

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
 CBL  N11   C1   C6    121.67  3.000
 CBL  N11   C1   C2    121.44  3.000
 CBL  C6    C1   C2    116.89  3.000
 CBL  H2    C2   C3    117.92  3.000
 CBL  H2    C2   C1    121.00  3.000
 CBL  C3    C2   C1    121.07  3.000
 CBL  H3    C3   C4    119.54  3.000
 CBL  H3    C3   C2    118.35  3.000
 CBL  C4    C3   C2    122.11  3.000
 CBL  C7    C4   C5    121.80  3.000
 CBL  C7    C4   C3    121.40  3.000
 CBL  C5    C4   C3    116.76  3.000
 CBL  H5    C5   C6    118.28  3.000
 CBL  H5    C5   C4    119.61  3.000
 CBL  C6    C5   C4    122.11  3.000
 CBL  H6    C6   C5    117.85  3.000
 CBL  H6    C6   C1    121.09  3.000
 CBL  C5    C6   C1    121.06  3.000
 CBL  H72   C7   H71   106.35  3.000
 CBL  H72   C7   C8    109.19  3.000
 CBL  H71   C7   C8    109.17  3.000
 CBL  H72   C7   C4    109.93  3.000
 CBL  H71   C7   C4    109.75  3.000
 CBL  C8    C7   C4    112.26  3.000
 CBL  H82   C8   H81   106.58  3.000
 CBL  H82   C8   C9    110.02  3.000
 CBL  H81   C8   C9    110.13  3.000
 CBL  H82   C8   C7    109.30  3.000
 CBL  H81   C8   C7    109.24  3.000
 CBL  C9    C8   C7    111.44  3.000
 CBL  H92   C9   H91   105.35  3.000
 CBL  H92   C9   C10   108.09  3.000
 CBL  H91   C9   C10   108.11  3.000
 CBL  H92   C9   C8    110.64  3.000
 CBL  H91   C9   C8    110.45  3.000
 CBL  C10   C9   C8    113.81  3.000
 CBL  O19   C10  O18   122.88  3.000
 CBL  O19   C10  C9    111.81  3.000
 CBL  O18   C10  C9    125.31  3.000
 CBL  C15   N11  C12   116.49  3.000
 CBL  C15   N11  C1    121.68  3.000
 CBL  C12   N11  C1    121.71  3.000
 CBL  H122  C12  H121  106.12  3.000
 CBL  H122  C12  C13   110.41  3.000
 CBL  H121  C12  C13   109.28  3.000
 CBL  H122  C12  N11   110.76  3.000
 CBL  H121  C12  N11   108.98  3.000
 CBL  C13   C12  N11   111.14  3.000
 CBL  H132  C13  H131  108.84  3.000
 CBL  H132  C13  CL14  107.32  3.000
 CBL  H131  C13  CL14  107.19  3.000
 CBL  H132  C13  C12   111.33  3.000
 CBL  H131  C13  C12   112.11  3.000
 CBL  CL14  C13  C12   109.85  3.000
 CBL  H152  C15  H151  106.15  3.000
 CBL  H152  C15  C16   110.40  3.000
 CBL  H151  C15  C16   109.16  3.000
 CBL  H152  C15  N11   110.71  3.000
 CBL  H151  C15  N11   108.87  3.000
 CBL  C16   C15  N11   111.39  3.000
 CBL  H162  C16  H161  108.83  3.000
 CBL  H162  C16  CL17  107.32  3.000
 CBL  H161  C16  CL17  107.24  3.000
 CBL  H162  C16  C15   111.32  3.000
 CBL  H161  C16  C15   112.09  3.000
 CBL  CL17  C16  C15   109.85  3.000
 CBL  HO9   O19  C10   110.00  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
 CBL  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 CBL  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 CBL  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 CBL  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 CBL  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 CBL  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 CBL  CONST_07  C7    C4   C3   C2    180.00   0.0  0
 CBL  CONST_08  N11   C1   C2   C3    180.00   0.0  0
 CBL  CONST_09  N11   C1   C6   C5    180.00   0.0  0
 CBL  CONST_10  C7    C4   C5   C6    180.00   0.0  0
 CBL  CONST_11  H3    C3   C2   C1    180.00   0.0  0
 CBL  CONST_12  H5    C5   C6   C1    180.00   0.0  0
 CBL  CONST_13  H6    C6   C1   C2    180.00   0.0  0
 CBL  CONST_14  H2    C2   C3   C4    180.00   0.0  0
 CBL  CONST_15  C12   N11  C1   C2      0.00   0.0  0
 CBL  CONST_16  C15   N11  C1   C2    180.00   0.0  0
 CBL  CONST_17  C12   N11  C1   C6    180.00   0.0  0
 CBL  CONST_18  C15   N11  C1   C6      0.00   0.0  0
 CBL  CONST_19  HO9   O19  C10  C9    180.00   0.0  0
 CBL  Var_01    C8    C7   C4   C3     86.76  30.0  2
 CBL  Var_02    C13   C12  N11  C1     92.13  30.0  3
 CBL  Var_03    C16   C15  N11  C1     87.55  30.0  3
 CBL  Var_04    C9    C8   C7   C4   -179.07  30.0  3
 CBL  Var_05    C10   C9   C8   C7   -179.27  30.0  3
 CBL  Var_06    O18   C10  C9   C8     -0.83  30.0  3
 CBL  Var_07    CL14  C13  C12  N11   178.61  30.0  3
 CBL  Var_08    CL17  C16  C15  N11   179.09  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
 CBL  plan-1  C1   0.020
 CBL  plan-1  C2   0.020
 CBL  plan-1  C3   0.020
 CBL  plan-1  C4   0.020
 CBL  plan-1  C5   0.020
 CBL  plan-1  C6   0.020
 CBL  plan-1  C7   0.020
 CBL  plan-1  N11  0.020
 CBL  plan-1  H2   0.020
 CBL  plan-1  H3   0.020
 CBL  plan-1  H5   0.020
 CBL  plan-1  H6   0.020
 CBL  plan-2  C1   0.020
 CBL  plan-2  N11  0.020
 CBL  plan-2  C12  0.020
 CBL  plan-2  C15  0.020
 CBL  plan-3  C9   0.020
 CBL  plan-3  C10  0.020
 CBL  plan-3  O18  0.020
 CBL  plan-3  O19  0.020
 CBL  plan-3  HO9  0.020

