# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 09:29:36 2022
#   Inital geometry file: a 109 line input string
#   Ligand name: 3-(3-chlorophenyl)-N-{2-[2-(1H-imidazol-1-yl)pyrimidin-4-yl]ethyl}propan-1-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cccc(CCCNCCc2ccnc(n2)n3ccnc3)c1
#
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
 HLW  HLW  3-(3-chlorophenyl)-N-{2-[2-(1H-imidazol-1-yl)pyrimidin-4-yl]ethyl}propan-1-amine  ligand  44  24  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HLW
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
 HLW  N01   N   N     0  -0.443   6.4912  -2.9420   0.2716
 HLW  C02   C   CR15  0   0.115   5.6001  -2.0064   0.4087
 HLW  N03   N   NR5   0  -0.528   6.0809  -0.7947   0.0058
 HLW  C04   C   CR15  0  -0.094   7.3759  -0.9963  -0.4156
 HLW  C05   C   CR15  0  -0.209   7.6049  -2.3237  -0.2423
 HLW  C1'   C   CR6   0   0.135  -4.8604  -0.8695  -0.2374
 HLW  N11   N   N     0  -0.440   6.0308   1.4716  -0.4372
 HLW  C12   C   CR6   0   0.635   5.3830   0.4170   0.0177
 HLW  N13   N   N     0  -0.452   4.1522   0.3726   0.4854
 HLW  C14   C   CR6   0   0.315   3.4702   1.5152   0.5048
 HLW  C15   C   CR16  0  -0.384   4.0519   2.6929   0.0485
 HLW  C16   C   CR16  0   0.004   5.3513   2.6121  -0.4156
 HLW  C17   C   CH2   0  -0.522   2.0625   1.4566   1.0035
 HLW  C18   C   CH2   0  -0.254   1.1402   0.8055  -0.0281
 HLW  N19   N   NH1   0  -0.603  -0.2052   0.6942   0.4944
 HLW  C2'   C   CR16  0  -0.276  -5.8446   0.0912  -0.4510
 HLW  C20   C   CH2   0  -0.253  -1.1266   0.1010  -0.4568
 HLW  C21   C   CH2   0  -0.440  -2.5177  -0.0418   0.1392
 HLW  C22   C   CH2   0  -0.511  -3.4923  -0.7047  -0.8356
 HLW  C3'   C   CR6   0  -0.019  -7.0893  -0.0527   0.1419
 HLW  C4'   C   CR16  0  -0.235  -7.3879  -1.1362   0.9520
 HLW  C5'   C   CR16  0  -0.244  -6.4039  -2.0926   1.1634
 HLW  C6'   C   CR16  0  -0.301  -5.1543  -1.9618   0.5764
 HLW  CL7'  CL  CL    0  -0.136  -8.3039   1.1551  -0.1429
 HLW  H02   H   HCR5  0   0.294   4.5980  -2.1274   0.7866
 HLW  H04   H   HCR5  0   0.300   7.9927  -0.1974  -0.7867
 HLW  H05   H   HCR5  0   0.261   8.5095  -2.8695  -0.4603
 HLW  H15   H   HCR6  0   0.284   3.5165   3.6311   0.0606
 HLW  H16   H   HCR6  0   0.287   5.8676   3.4915  -0.7814
 HLW  H17   H   HCH2  0   0.260   2.0450   0.8705   1.9263
 HLW  H17A  H   HCH2  0   0.257   1.7021   2.4592   1.2372
 HLW  H18   H   HCH2  0   0.230   1.1124   1.4282  -0.9272
 HLW  H18A  H   HCH2  0   0.206   1.5639  -0.1637  -0.3329
 HLW  HN19  H   HNH1  0   0.340  -0.1817   0.1118   1.3245
 HLW  H2'   H   HCR6  0   0.269  -5.6390   0.9459  -1.0835
 HLW  H20   H   HCH2  0   0.220  -1.1736   0.7483  -1.3384
 HLW  H20A  H   HCH2  0   0.190  -0.7834  -0.8832  -0.8164
 HLW  H21   H   HCH2  0   0.227  -2.4632  -0.6407   1.0543
 HLW  H21A  H   HCH2  0   0.232  -2.8963   0.9418   0.4305
 HLW  H22   H   HCH2  0   0.246  -3.1000  -1.6826  -1.1272
 HLW  H22A  H   HCH2  0   0.245  -3.5547  -0.1070  -1.7487
 HLW  H4'   H   HCR6  0   0.277  -8.3644  -1.2355   1.4064
 HLW  H5'   H   HCR6  0   0.265  -6.6210  -2.9473   1.7907
 HLW  H6'   H   HCR6  0   0.253  -4.3981  -2.7182   0.7495

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
 HLW  N01  C02   aromatic  1.299  0.020  1.299
 HLW  N01  C05   aromatic  1.374  0.020  1.374
 HLW  C02  N03   aromatic  1.365  0.020  1.365
 HLW  N03  C04   aromatic  1.377  0.020  1.377
 HLW  N03  C12   single    1.398  0.020  1.398
 HLW  C04  C05   aromatic  1.358  0.020  1.358
 HLW  C1'  C2'   aromatic  1.392  0.020  1.392
 HLW  C1'  C22   single    1.502  0.020  1.502
 HLW  C1'  C6'   aromatic  1.393  0.020  1.393
 HLW  N11  C12   aromatic  1.319  0.020  1.319
 HLW  N11  C16   aromatic  1.328  0.020  1.328
 HLW  C12  N13   aromatic  1.317  0.020  1.317
 HLW  N13  C14   aromatic  1.331  0.020  1.331
 HLW  C14  C15   aromatic  1.391  0.020  1.391
 HLW  C14  C17   single    1.495  0.020  1.495
 HLW  C15  C16   aromatic  1.382  0.020  1.382
 HLW  C17  C18   single    1.529  0.020  1.529
 HLW  C18  N19   single    1.448  0.020  1.448
 HLW  N19  C20   single    1.451  0.020  1.451
 HLW  C2'  C3'   aromatic  1.386  0.020  1.386
 HLW  C20  C21   single    1.520  0.020  1.520
 HLW  C21  C22   single    1.529  0.020  1.529
 HLW  C3'  C4'   aromatic  1.385  0.020  1.385
 HLW  C3'  CL7'  single    1.736  0.020  1.736
 HLW  C4'  C5'   aromatic  1.388  0.020  1.388
 HLW  C5'  C6'   aromatic  1.387  0.020  1.387
 HLW  C02  H02   single    0.930  0.020  1.080
 HLW  C04  H04   single    0.930  0.020  1.080
 HLW  C05  H05   single    0.930  0.020  1.080
 HLW  C15  H15   single    0.930  0.020  1.080
 HLW  C16  H16   single    0.930  0.020  1.080
 HLW  C17  H17   single    0.970  0.020  1.090
 HLW  C17  H17A  single    0.970  0.020  1.090
 HLW  C18  H18   single    0.970  0.020  1.090
 HLW  C18  H18A  single    0.970  0.020  1.090
 HLW  N19  HN19  single    0.890  0.020  1.040
 HLW  C2'  H2'   single    0.930  0.020  1.080
 HLW  C20  H20   single    0.970  0.020  1.090
 HLW  C20  H20A  single    0.970  0.020  1.090
 HLW  C21  H21   single    0.970  0.020  1.090
 HLW  C21  H21A  single    0.970  0.020  1.090
 HLW  C22  H22   single    0.970  0.020  1.090
 HLW  C22  H22A  single    0.970  0.020  1.090
 HLW  C4'  H4'   single    0.930  0.020  1.080
 HLW  C5'  H5'   single    0.930  0.020  1.080
 HLW  C6'  H6'   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
 HLW  C05   N01  C02  105.75  3.000
 HLW  H02   C02  N03  122.06  3.000
 HLW  H02   C02  N01  126.43  3.000
 HLW  N03   C02  N01  111.51  3.000
 HLW  C12   N03  C04  126.80  3.000
 HLW  C12   N03  C02  126.23  3.000
 HLW  C04   N03  C02  106.96  3.000
 HLW  H04   C04  C05  132.34  3.000
 HLW  H04   C04  N03  122.43  3.000
 HLW  C05   C04  N03  105.23  3.000
 HLW  H05   C05  C04  127.60  3.000
 HLW  H05   C05  N01  121.85  3.000
 HLW  C04   C05  N01  110.55  3.000
 HLW  C6'   C1'  C22  120.71  3.000
 HLW  C6'   C1'  C2'  118.79  3.000
 HLW  C22   C1'  C2'  120.47  3.000
 HLW  C16   N11  C12  115.46  3.000
 HLW  N13   C12  N11  127.47  3.000
 HLW  N13   C12  N03  116.12  3.000
 HLW  N11   C12  N03  116.41  3.000
 HLW  C14   N13  C12  117.07  3.000
 HLW  C17   C14  C15  122.46  3.000
 HLW  C17   C14  N13  116.99  3.000
 HLW  C15   C14  N13  120.53  3.000
 HLW  H15   C15  C16  121.37  3.000
 HLW  H15   C15  C14  121.64  3.000
 HLW  C16   C15  C14  117.00  3.000
 HLW  H16   C16  C15  120.93  3.000
 HLW  H16   C16  N11  116.60  3.000
 HLW  C15   C16  N11  122.47  3.000
 HLW  H17A  C17  H17  107.86  3.000
 HLW  H17A  C17  C18  109.67  3.000
 HLW  H17   C17  C18  109.36  3.000
 HLW  H17A  C17  C14  110.28  3.000
 HLW  H17   C17  C14  108.52  3.000
 HLW  C18   C17  C14  111.08  3.000
 HLW  H18A  C18  H18  106.46  3.000
 HLW  H18A  C18  N19  112.95  3.000
 HLW  H18   C18  N19  108.47  3.000
 HLW  H18A  C18  C17  109.24  3.000
 HLW  H18   C18  C17  109.11  3.000
 HLW  N19   C18  C17  110.47  3.000
 HLW  HN19  N19  C20  108.45  3.000
 HLW  HN19  N19  C18  108.54  3.000
 HLW  C20   N19  C18  112.64  3.000
 HLW  H2'   C2'  C3'  120.15  3.000
 HLW  H2'   C2'  C1'  120.01  3.000
 HLW  C3'   C2'  C1'  119.84  3.000
 HLW  H20A  C20  H20  106.17  3.000
 HLW  H20A  C20  C21  109.20  3.000
 HLW  H20   C20  C21  109.39  3.000
 HLW  H20A  C20  N19  112.40  3.000
 HLW  H20   C20  N19  108.27  3.000
 HLW  C21   C20  N19  111.25  3.000
 HLW  H21A  C21  H21  106.65  3.000
 HLW  H21A  C21  C22  109.82  3.000
 HLW  H21   C21  C22  109.11  3.000
 HLW  H21A  C21  C20  109.69  3.000
 HLW  H21   C21  C20  109.48  3.000
 HLW  C22   C21  C20  111.96  3.000
 HLW  H22A  C22  H22  106.67  3.000
 HLW  H22A  C22  C21  109.37  3.000
 HLW  H22   C22  C21  109.21  3.000
 HLW  H22A  C22  C1'  109.92  3.000
 HLW  H22   C22  C1'  109.56  3.000
 HLW  C21   C22  C1'  111.97  3.000
 HLW  CL7'  C3'  C4'  119.28  3.000
 HLW  CL7'  C3'  C2'  119.06  3.000
 HLW  C4'   C3'  C2'  121.66  3.000
 HLW  H4'   C4'  C5'  120.84  3.000
 HLW  H4'   C4'  C3'  120.80  3.000
 HLW  C5'   C4'  C3'  118.36  3.000
 HLW  H5'   C5'  C6'  120.04  3.000
 HLW  H5'   C5'  C4'  119.35  3.000
 HLW  C6'   C5'  C4'  120.61  3.000
 HLW  H6'   C6'  C5'  119.70  3.000
 HLW  H6'   C6'  C1'  119.56  3.000
 HLW  C5'   C6'  C1'  120.74  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
 HLW  CONST_01  C04   N03  C02  N01     0.00   0.0  0
 HLW  CONST_02  C12   N03  C02  N01   180.00   0.0  0
 HLW  CONST_03  N03   C04  C05  N01     0.00   0.0  0
 HLW  CONST_04  C04   C05  N01  C02     0.00   0.0  0
 HLW  CONST_05  C05   C04  N03  C02     0.00   0.0  0
 HLW  CONST_06  N11   C12  N03  C02   180.00   0.0  0
 HLW  CONST_07  N13   C12  N03  C02     0.00   0.0  0
 HLW  CONST_08  C05   N01  C02  N03     0.00   0.0  0
 HLW  CONST_09  C16   N11  C12  N03   180.00   0.0  0
 HLW  CONST_10  C14   N13  C12  N03   180.00   0.0  0
 HLW  CONST_11  N11   C12  N03  C04     0.00   0.0  0
 HLW  CONST_12  N13   C12  N03  C04   180.00   0.0  0
 HLW  CONST_13  C12   N03  C04  C05   180.00   0.0  0
 HLW  CONST_14  C4'   C3'  C2'  C1'     0.00   0.0  0
 HLW  CONST_15  C4'   C5'  C6'  C1'     0.00   0.0  0
 HLW  CONST_16  C14   N13  C12  N11     0.00   0.0  0
 HLW  CONST_17  C14   C15  C16  N11     0.00   0.0  0
 HLW  CONST_18  C15   C16  N11  C12     0.00   0.0  0
 HLW  CONST_19  C15   C14  N13  C12     0.00   0.0  0
 HLW  CONST_20  C16   N11  C12  N13     0.00   0.0  0
 HLW  CONST_21  C16   C15  C14  N13     0.00   0.0  0
 HLW  CONST_22  C5'   C6'  C1'  C2'     0.00   0.0  0
 HLW  CONST_23  C5'   C4'  C3'  C2'     0.00   0.0  0
 HLW  CONST_24  C6'   C1'  C2'  C3'     0.00   0.0  0
 HLW  CONST_25  C6'   C5'  C4'  C3'     0.00   0.0  0
 HLW  CONST_26  CL7'  C3'  C2'  C1'   180.00   0.0  0
 HLW  CONST_27  C17   C14  N13  C12   180.00   0.0  0
 HLW  CONST_28  C17   C14  C15  C16   180.00   0.0  0
 HLW  CONST_29  C3'   C2'  C1'  C22   180.00   0.0  0
 HLW  CONST_30  C5'   C6'  C1'  C22   180.00   0.0  0
 HLW  CONST_31  CL7'  C3'  C4'  C5'   180.00   0.0  0
 HLW  CONST_32  H04   C04  C05  N01   180.00   0.0  0
 HLW  CONST_33  H05   C05  N01  C02   180.00   0.0  0
 HLW  CONST_34  H02   C02  N03  C04   180.00   0.0  0
 HLW  CONST_35  H5'   C5'  C6'  C1'   180.00   0.0  0
 HLW  CONST_36  H15   C15  C16  N11   180.00   0.0  0
 HLW  CONST_37  H16   C16  N11  C12   180.00   0.0  0
 HLW  CONST_38  H6'   C6'  C1'  C2'   180.00   0.0  0
 HLW  CONST_39  H4'   C4'  C3'  C2'   180.00   0.0  0
 HLW  CONST_40  H2'   C2'  C3'  C4'   180.00   0.0  0
 HLW  Var_01    C18   C17  C14  N13   -73.97  30.0  2
 HLW  Var_02    C21   C22  C1'  C2'    94.27  30.0  2
 HLW  Var_03    C20   C21  C22  C1'   178.92  30.0  1
 HLW  Var_04    N19   C18  C17  C14   177.12  30.0  3
 HLW  Var_05    C20   N19  C18  C17   179.06  30.0  3
 HLW  Var_06    C21   C20  N19  C18   178.18  30.0  3
 HLW  Var_07    C22   C21  C20  N19  -178.27  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
 HLW  plan-1  N01   0.020
 HLW  plan-1  C02   0.020
 HLW  plan-1  N03   0.020
 HLW  plan-1  C04   0.020
 HLW  plan-1  C05   0.020
 HLW  plan-1  C12   0.020
 HLW  plan-1  H02   0.020
 HLW  plan-1  H04   0.020
 HLW  plan-1  H05   0.020
 HLW  plan-2  C1'   0.020
 HLW  plan-2  C2'   0.020
 HLW  plan-2  C22   0.020
 HLW  plan-2  C3'   0.020
 HLW  plan-2  C4'   0.020
 HLW  plan-2  C5'   0.020
 HLW  plan-2  C6'   0.020
 HLW  plan-2  CL7'  0.020
 HLW  plan-2  H2'   0.020
 HLW  plan-2  H4'   0.020
 HLW  plan-2  H5'   0.020
 HLW  plan-2  H6'   0.020
 HLW  plan-3  N03   0.020
 HLW  plan-3  N11   0.020
 HLW  plan-3  C12   0.020
 HLW  plan-3  N13   0.020
 HLW  plan-3  C14   0.020
 HLW  plan-3  C15   0.020
 HLW  plan-3  C16   0.020
 HLW  plan-3  C17   0.020
 HLW  plan-3  H15   0.020
 HLW  plan-3  H16   0.020

