# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 08:16:31 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: N-(4-chlorobenzyl)-N',N'-dimethyl-N-pyridin-2-ylethane-1,2-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)CCN(Cc1ccc(Cl)cc1)c2ccccn2
#
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
 C4C  C4C  N-(4-chlorobenzyl)-N',N'-dimethyl-N-pyridin-2-ylethane-1,2-diamine  ligand  40  20  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C4C
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
 C4C  C1    C   CH3   0  -0.518   0.7799   3.6734  -1.9918
 C4C  N3    N   NT    0  -0.408   1.0495   3.2980  -0.6203
 C4C  C2    C   CH3   0  -0.528   0.2233   4.0676   0.2867
 C4C  C3    C   CH2   0  -0.271   0.8988   1.8695  -0.4242
 C4C  C4    C   CH2   0  -0.336   1.5763   1.3951   0.8632
 C4C  N1    N   NT    0  -0.485   1.5382  -0.0408   1.0399
 C4C  C12   C   CR6   0   0.549   2.3459  -0.8681   0.3123
 C4C  C13   C   CR16  0  -0.398   3.3727  -0.3635  -0.5164
 C4C  C14   C   CR16  0  -0.154   4.1731  -1.2547  -1.1968
 C4C  C15   C   CR16  0  -0.370   3.9635  -2.6253  -1.0664
 C4C  C16   C   CR16  0  -0.063   2.9305  -3.0211  -0.2394
 C4C  N2    N   N     0  -0.487   2.1441  -2.1825   0.4241
 C4C  C5    C   CH2   0  -0.413   0.5133  -0.5662   1.9205
 C4C  C6    C   CR6   0   0.134  -0.8726  -0.4774   1.3323
 C4C  C11   C   CR16  0  -0.294  -1.2268  -1.2390   0.2201
 C4C  C10   C   CR16  0  -0.198  -2.4848  -1.1295  -0.3487
 C4C  C7    C   CR16  0  -0.311  -1.8125   0.3953   1.8659
 C4C  C8    C   CR16  0  -0.198  -3.0794   0.5198   1.3098
 C4C  C9    C   CR6   0  -0.054  -3.4019  -0.2456   0.2031
 C4C  CL1   CL  CL    0  -0.134  -4.9791  -0.1025  -0.5060
 C4C  H11A  H   HCH3  0   0.192  -0.2549   3.4652  -2.3063
 C4C  H12   H   HCH3  0   0.232   0.9567   4.7416  -2.1266
 C4C  H13A  H   HCH3  0   0.233   1.4480   3.1379  -2.6677
 C4C  H21   H   HCH3  0   0.193  -0.8540   3.8835   0.1468
 C4C  H22   H   HCH3  0   0.235   0.4633   3.8452   1.3263
 C4C  H23   H   HCH3  0   0.236   0.4012   5.1332   0.1363
 C4C  H31   H   HCH2  0   0.208  -0.1593   1.5595  -0.4203
 C4C  H32   H   HCH2  0   0.236   1.3647   1.3592  -1.2712
 C4C  H41   H   HCH2  0   0.249   2.6075   1.7567   0.8829
 C4C  H42   H   HCH2  0   0.258   1.0902   1.8351   1.7346
 C4C  H13   H   HCR6  0   0.268   3.5477   0.6967  -0.6255
 C4C  H14   H   HCR6  0   0.266   4.9658  -0.8775  -1.8306
 C4C  H15   H   HCR6  0   0.257   4.5711  -3.3502  -1.5886
 C4C  H16   H   HCR6  0   0.254   2.7135  -4.0755  -0.1032
 C4C  H51   H   HCH2  0   0.278   0.7572  -1.5990   2.1586
 C4C  H52   H   HCH2  0   0.265   0.5418  -0.0010   2.8556
 C4C  H11   H   HCR6  0   0.262  -0.5138  -1.9298  -0.2122
 C4C  H10   H   HCR6  0   0.277  -2.7475  -1.7265  -1.2117
 C4C  H7    H   HCR6  0   0.261  -1.5584   0.9957   2.7314
 C4C  H8    H   HCR6  0   0.278  -3.7981   1.2064   1.7362

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
 C4C  CL1  C9    single    1.735  0.020  1.735
 C4C  C8   C9    aromatic  1.384  0.020  1.384
 C4C  C8   C7    aromatic  1.389  0.020  1.389
 C4C  C9   C10   aromatic  1.388  0.020  1.388
 C4C  C7   C6    aromatic  1.389  0.020  1.389
 C4C  C10  C11   aromatic  1.385  0.020  1.385
 C4C  C6   C11   aromatic  1.394  0.020  1.394
 C4C  C6   C5    single    1.508  0.020  1.508
 C4C  C2   N3    single    1.448  0.020  1.448
 C4C  C5   N1    single    1.450  0.020  1.450
 C4C  N1   C4    single    1.447  0.020  1.447
 C4C  N1   C12   single    1.366  0.020  1.366
 C4C  N3   C1    single    1.447  0.020  1.447
 C4C  N3   C3    single    1.450  0.020  1.450
 C4C  C4   C3    single    1.530  0.020  1.530
 C4C  C12  C13   aromatic  1.413  0.020  1.413
 C4C  C12  N2    aromatic  1.334  0.020  1.334
 C4C  C13  C14   aromatic  1.378  0.020  1.378
 C4C  N2   C16   aromatic  1.327  0.020  1.327
 C4C  C14  C15   aromatic  1.393  0.020  1.393
 C4C  C16  C15   aromatic  1.381  0.020  1.381
 C4C  C1   H11A  single    0.970  0.020  1.090
 C4C  C1   H12   single    0.970  0.020  1.090
 C4C  C1   H13A  single    0.970  0.020  1.090
 C4C  C2   H21   single    0.970  0.020  1.090
 C4C  C2   H22   single    0.970  0.020  1.090
 C4C  C2   H23   single    0.970  0.020  1.090
 C4C  C3   H31   single    0.970  0.020  1.090
 C4C  C3   H32   single    0.970  0.020  1.090
 C4C  C4   H41   single    0.970  0.020  1.090
 C4C  C4   H42   single    0.970  0.020  1.090
 C4C  C13  H13   single    0.930  0.020  1.080
 C4C  C14  H14   single    0.930  0.020  1.080
 C4C  C15  H15   single    0.930  0.020  1.080
 C4C  C16  H16   single    0.930  0.020  1.080
 C4C  C5   H51   single    0.970  0.020  1.090
 C4C  C5   H52   single    0.970  0.020  1.090
 C4C  C11  H11   single    0.930  0.020  1.080
 C4C  C10  H10   single    0.930  0.020  1.080
 C4C  C7   H7    single    0.930  0.020  1.080
 C4C  C8   H8    single    0.930  0.020  1.080

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
 C4C  H13A  C1   H12   107.75  3.000
 C4C  H13A  C1   H11A  107.80  3.000
 C4C  H12   C1   H11A  107.58  3.000
 C4C  H13A  C1   N3    110.23  3.000
 C4C  H12   C1   N3    109.93  3.000
 C4C  H11A  C1   N3    113.36  3.000
 C4C  C3    N3   C2    112.31  3.000
 C4C  C3    N3   C1    111.37  3.000
 C4C  C2    N3   C1    110.45  3.000
 C4C  H23   C2   H22   107.16  3.000
 C4C  H23   C2   H21   107.77  3.000
 C4C  H22   C2   H21   107.60  3.000
 C4C  H23   C2   N3    109.86  3.000
 C4C  H22   C2   N3    111.30  3.000
 C4C  H21   C2   N3    112.92  3.000
 C4C  H32   C3   H31   106.29  3.000
 C4C  H32   C3   C4    108.57  3.000
 C4C  H31   C3   C4    109.55  3.000
 C4C  H32   C3   N3    108.12  3.000
 C4C  H31   C3   N3    112.16  3.000
 C4C  C4    C3   N3    111.92  3.000
 C4C  H42   C4   H41   105.82  3.000
 C4C  H42   C4   N1    106.92  3.000
 C4C  H41   C4   N1    110.54  3.000
 C4C  H42   C4   C3    110.48  3.000
 C4C  H41   C4   C3    109.29  3.000
 C4C  N1    C4   C3    113.49  3.000
 C4C  C5    N1   C12   121.47  3.000
 C4C  C12   N1   C4    121.35  3.000
 C4C  C5    N1   C4    116.89  3.000
 C4C  N2    C12  C13   120.72  3.000
 C4C  N2    C12  N1    117.55  3.000
 C4C  C13   C12  N1    121.72  3.000
 C4C  H13   C13  C14   119.41  3.000
 C4C  H13   C13  C12   121.84  3.000
 C4C  C14   C13  C12   118.75  3.000
 C4C  H14   C14  C15   120.52  3.000
 C4C  H14   C14  C13   119.28  3.000
 C4C  C15   C14  C13   120.20  3.000
 C4C  H15   C15  C16   121.18  3.000
 C4C  H15   C15  C14   122.03  3.000
 C4C  C16   C15  C14   116.78  3.000
 C4C  H16   C16  N2    115.64  3.000
 C4C  H16   C16  C15   120.21  3.000
 C4C  N2    C16  C15   124.15  3.000
 C4C  C16   N2   C12   119.39  3.000
 C4C  H52   C5   H51   107.33  3.000
 C4C  H52   C5   C6    109.10  3.000
 C4C  H51   C5   C6    110.33  3.000
 C4C  H52   C5   N1    108.29  3.000
 C4C  H51   C5   N1    108.58  3.000
 C4C  C6    C5   N1    113.04  3.000
 C4C  C7    C6   C11   118.55  3.000
 C4C  C11   C6   C5    120.83  3.000
 C4C  C7    C6   C5    120.59  3.000
 C4C  H11   C11  C10   118.98  3.000
 C4C  H11   C11  C6    119.99  3.000
 C4C  C10   C11  C6    121.02  3.000
 C4C  H10   C10  C9    120.54  3.000
 C4C  H10   C10  C11   120.31  3.000
 C4C  C9    C10  C11   119.16  3.000
 C4C  H7    C7   C8    118.94  3.000
 C4C  H7    C7   C6    119.76  3.000
 C4C  C8    C7   C6    121.30  3.000
 C4C  H8    C8   C9    120.77  3.000
 C4C  H8    C8   C7    120.34  3.000
 C4C  C9    C8   C7    118.89  3.000
 C4C  CL1   C9   C8    119.54  3.000
 C4C  C8    C9   C10   121.08  3.000
 C4C  CL1   C9   C10   119.38  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
 C4C  CONST_01  C15   C14  C13  C12     0.00   0.0  0
 C4C  CONST_02  C15   C16  N2   C12     0.00   0.0  0
 C4C  CONST_03  C16   N2   C12  C13     0.00   0.0  0
 C4C  CONST_04  C16   C15  C14  C13     0.00   0.0  0
 C4C  CONST_05  N2    C12  C13  C14     0.00   0.0  0
 C4C  CONST_06  N2    C16  C15  C14     0.00   0.0  0
 C4C  CONST_07  C9    C8   C7   C6      0.00   0.0  0
 C4C  CONST_08  C9    C10  C11  C6      0.00   0.0  0
 C4C  CONST_09  C8    C9   C10  C11     0.00   0.0  0
 C4C  CONST_10  C8    C7   C6   C11     0.00   0.0  0
 C4C  CONST_11  C7    C8   C9   C10     0.00   0.0  0
 C4C  CONST_12  C7    C6   C11  C10     0.00   0.0  0
 C4C  CONST_13  C14   C13  C12  N1    180.00   0.0  0
 C4C  CONST_14  C16   N2   C12  N1    180.00   0.0  0
 C4C  CONST_15  C8    C7   C6   C5    180.00   0.0  0
 C4C  CONST_16  C10   C11  C6   C5    180.00   0.0  0
 C4C  CONST_17  CL1   C9   C10  C11   180.00   0.0  0
 C4C  CONST_18  CL1   C9   C8   C7    180.00   0.0  0
 C4C  CONST_19  H14   C14  C13  C12   180.00   0.0  0
 C4C  CONST_20  H16   C16  N2   C12   180.00   0.0  0
 C4C  CONST_21  H15   C15  C14  C13   180.00   0.0  0
 C4C  CONST_22  H13   C13  C14  C15   180.00   0.0  0
 C4C  CONST_23  H8    C8   C7   C6    180.00   0.0  0
 C4C  CONST_24  H10   C10  C11  C6    180.00   0.0  0
 C4C  CONST_25  H7    C7   C6   C11   180.00   0.0  0
 C4C  CONST_26  H11   C11  C6   C7    180.00   0.0  0
 C4C  CONST_27  C13   C12  N1   C4      0.00   0.0  0
 C4C  CONST_28  N2    C12  N1   C4    180.00   0.0  0
 C4C  CONST_29  C5    N1   C12  C13   180.00   0.0  0
 C4C  CONST_30  C5    N1   C12  N2      0.00   0.0  0
 C4C  Var_01    C7    C6   C5   N1   -111.07  30.0  2
 C4C  Var_02    C6    C5   N1   C12  -102.28  30.0  2
 C4C  Var_03    C12   N1   C4   C3     74.75  30.0  2
 C4C  Var_04    C4    C3   N3   C1    162.54  30.0  3
 C4C  Var_05    N1    C4   C3   N3   -175.40  30.0  1
 C4C  Var_06    H21   C2   N3   C1     62.75  30.0  3
 C4C  Var_07    H11A  C1   N3   C2    -62.65  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
 C4C  plan-1  N1   0.020
 C4C  plan-1  C12  0.020
 C4C  plan-1  C13  0.020
 C4C  plan-1  C14  0.020
 C4C  plan-1  C15  0.020
 C4C  plan-1  C16  0.020
 C4C  plan-1  N2   0.020
 C4C  plan-1  H13  0.020
 C4C  plan-1  H14  0.020
 C4C  plan-1  H15  0.020
 C4C  plan-1  H16  0.020
 C4C  plan-2  C5   0.020
 C4C  plan-2  C6   0.020
 C4C  plan-2  C11  0.020
 C4C  plan-2  C10  0.020
 C4C  plan-2  C7   0.020
 C4C  plan-2  C8   0.020
 C4C  plan-2  C9   0.020
 C4C  plan-2  CL1  0.020
 C4C  plan-2  H11  0.020
 C4C  plan-2  H10  0.020
 C4C  plan-2  H7   0.020
 C4C  plan-2  H8   0.020
 C4C  plan-3  C4   0.020
 C4C  plan-3  N1   0.020
 C4C  plan-3  C12  0.020
 C4C  plan-3  C5   0.020

