# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 12:01:22 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: 1-(3-chloro-4-methylphenyl)-3-{2-[({5-[(dimethylamino)methyl]furan-2-yl}methyl)sulfanyl]ethyl}urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)Cc1oc(CSCCNC(=O)Nc2ccc(C)c(Cl)c2)cc1
#
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
 JPR  JPR  1-(3-chloro-4-methylphenyl)-3-{2-[({5-[(dimethylamino)methyl]furan-2-yl}methyl)sulfanyl]ethyl}urea  ligand  49  25  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_JPR
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
 JPR  CL1   CL  CL    0  -0.132   5.8768   2.7781   1.3724
 JPR  N1    N   NH1   0  -0.790   3.6594  -1.1485  -1.0894
 JPR  O1    O   O     0  -0.517   2.0398   0.4469  -0.8231
 JPR  S1    S   S2    0  -0.030  -2.3970  -1.0588  -1.4939
 JPR  C2    C   CR6   0   0.144   6.9279   0.2975   1.1732
 JPR  N2    N   NH1   0  -0.677   1.6028  -1.4052  -2.0481
 JPR  O2    O   O     0  -0.431  -4.9525  -0.0415   0.2183
 JPR  C3    C   CR16  0  -0.305   6.8437  -1.0135   0.7092
 JPR  N3    N   NT    0  -0.407  -8.2271   1.3764   0.8556
 JPR  C4    C   CR6   0  -0.092   5.8569   1.1211   0.8447
 JPR  C5    C   CR16  0  -0.329   5.7633  -1.4710  -0.0211
 JPR  C6    C   CR16  0  -0.263   4.7592   0.7021   0.1086
 JPR  C7    C   CR6   0   0.358   4.6997  -0.6201  -0.3312
 JPR  C8    C   C     0   0.744   2.4036  -0.6262  -1.2815
 JPR  C9    C   CH2   0  -0.284   0.2176  -1.0780  -2.2778
 JPR  C10   C   CH2   0  -0.551  -0.6785  -1.5079  -1.1199
 JPR  C11   C   CH2   0  -0.657  -3.2022  -1.7068   0.0135
 JPR  C12   C   CR5   0   0.371  -4.6340  -1.3441   0.0265
 JPR  C13   C   CR15  0  -0.359  -5.7677  -2.0691  -0.1285
 JPR  C14   C   CR15  0  -0.358  -6.8542  -1.1479  -0.0211
 JPR  C15   C   CR5   0   0.355  -6.2984   0.0701   0.1885
 JPR  C16   C   CH2   0  -0.376  -6.8770   1.4356   0.3388
 JPR  C17   C   CH3   0  -0.521  -8.2580   1.0349   2.2625
 JPR  C18   C   CH3   0  -0.522  -8.9476   2.6064   0.6037
 JPR  H11   H   HCH3  0   0.247   8.6169   1.6006   1.4799
 JPR  H12   H   HCH3  0   0.248   7.8032   1.1240   2.9598
 JPR  H13A  H   HCH3  0   0.249   8.8236  -0.0314   2.1084
 JPR  HN1   H   HNH1  0   0.410   3.8325  -2.0745  -1.4501
 JPR  HN2   H   HNH1  0   0.402   1.9151  -2.3169  -2.3393
 JPR  H3    H   HCR6  0   0.260   7.6502  -1.7008   0.9330
 JPR  H5    H   HCR6  0   0.271   5.7444  -2.5019  -0.3537
 JPR  H6    H   HCR6  0   0.293   3.9710   1.4009  -0.1167
 JPR  H91   H   HCH2  0   0.254   0.1209  -0.0062  -2.4513
 JPR  H92   H   HCH2  0   0.263  -0.0926  -1.5802  -3.1941
 JPR  H101  H   HCH2  0   0.270  -0.3686  -1.0128  -0.1980
 JPR  H102  H   HCH2  0   0.267  -0.6076  -2.5871  -0.9718
 JPR  H111  H   HCH2  0   0.292  -3.1097  -2.7926   0.0377
 JPR  H112  H   HCH2  0   0.288  -2.6823  -1.3022   0.8851
 JPR  H13   H   HCR5  0   0.261  -5.8236  -3.1334  -0.2930
 JPR  H14   H   HCR5  0   0.255  -7.9079  -1.3639  -0.0855
 JPR  H161  H   HCH2  0   0.261  -6.9082   1.9210  -0.6423
 JPR  H162  H   HCH2  0   0.222  -6.2087   2.0545   0.9615
 JPR  H171  H   HCH3  0   0.235  -9.2918   0.9285   2.5936
 JPR  H172  H   HCH3  0   0.237  -7.7562   0.0834   2.4387
 JPR  H173  H   HCH3  0   0.196  -7.7774   1.7945   2.8986
 JPR  H181  H   HCH3  0   0.195  -8.5153   3.4801   1.1150
 JPR  H182  H   HCH3  0   0.236  -8.9641   2.8208  -0.4658
 JPR  H183  H   HCH3  0   0.236  -9.9799   2.5040   0.9405
 JPR  C1    C   CH3   0  -0.719   8.1027   0.7729   1.9711

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
 JPR  C11  S1    single    1.828  0.020  1.828
 JPR  C11  C12   single    1.477  0.020  1.477
 JPR  S1   C10   single    1.815  0.020  1.815
 JPR  C12  C13   aromatic  1.355  0.020  1.355
 JPR  C12  O2    aromatic  1.355  0.020  1.355
 JPR  C13  C14   aromatic  1.429  0.020  1.429
 JPR  CL1  C4    single    1.739  0.020  1.739
 JPR  O2   C15   aromatic  1.351  0.020  1.351
 JPR  C14  C15   aromatic  1.355  0.020  1.355
 JPR  C15  C16   single    1.491  0.020  1.491
 JPR  C6   C4    aromatic  1.387  0.020  1.387
 JPR  C6   C7    aromatic  1.395  0.020  1.395
 JPR  C4   C2    aromatic  1.390  0.020  1.390
 JPR  C10  C9    single    1.526  0.020  1.526
 JPR  N2   C9    single    1.442  0.020  1.442
 JPR  N2   C8    single    1.355  0.020  1.355
 JPR  N1   C7    single    1.391  0.020  1.391
 JPR  N1   C8    single    1.374  0.020  1.374
 JPR  C16  N3    single    1.447  0.020  1.447
 JPR  C7   C5    aromatic  1.397  0.020  1.397
 JPR  C8   O1    double    1.222  0.020  1.222
 JPR  C2   C1    single    1.498  0.020  1.498
 JPR  C2   C3    aromatic  1.393  0.020  1.393
 JPR  C5   C3    aromatic  1.382  0.020  1.382
 JPR  N3   C17   single    1.448  0.020  1.448
 JPR  N3   C18   single    1.448  0.020  1.448
 JPR  C1   H11   single    0.970  0.020  1.090
 JPR  C1   H12   single    0.970  0.020  1.090
 JPR  C1   H13A  single    0.970  0.020  1.090
 JPR  N1   HN1   single    0.860  0.020  1.020
 JPR  N2   HN2   single    0.860  0.020  1.020
 JPR  C3   H3    single    0.930  0.020  1.080
 JPR  C5   H5    single    0.930  0.020  1.080
 JPR  C6   H6    single    0.930  0.020  1.080
 JPR  C9   H91   single    0.970  0.020  1.090
 JPR  C9   H92   single    0.970  0.020  1.090
 JPR  C10  H101  single    0.970  0.020  1.090
 JPR  C10  H102  single    0.970  0.020  1.090
 JPR  C11  H111  single    0.970  0.020  1.090
 JPR  C11  H112  single    0.970  0.020  1.090
 JPR  C13  H13   single    0.930  0.020  1.080
 JPR  C14  H14   single    0.930  0.020  1.080
 JPR  C16  H161  single    0.970  0.020  1.090
 JPR  C16  H162  single    0.970  0.020  1.090
 JPR  C17  H171  single    0.970  0.020  1.090
 JPR  C17  H172  single    0.970  0.020  1.090
 JPR  C17  H173  single    0.970  0.020  1.090
 JPR  C18  H181  single    0.970  0.020  1.090
 JPR  C18  H182  single    0.970  0.020  1.090
 JPR  C18  H183  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
 JPR  HN1   N1   C8    117.12  3.000
 JPR  HN1   N1   C7    114.53  3.000
 JPR  C8    N1   C7    127.97  3.000
 JPR  C11   S1   C10    99.18  3.000
 JPR  C4    C2   C3    115.60  3.000
 JPR  C3    C2   C1    121.57  3.000
 JPR  C4    C2   C1    122.83  3.000
 JPR  HN2   N2   C9    117.23  3.000
 JPR  HN2   N2   C8    120.07  3.000
 JPR  C9    N2   C8    121.83  3.000
 JPR  C15   O2   C12   108.10  3.000
 JPR  H3    C3   C5    118.77  3.000
 JPR  H3    C3   C2    118.90  3.000
 JPR  C5    C3   C2    122.33  3.000
 JPR  C18   N3   C17   111.03  3.000
 JPR  C18   N3   C16   111.56  3.000
 JPR  C17   N3   C16   112.12  3.000
 JPR  C6    C4   C2    123.80  3.000
 JPR  C2    C4   CL1   118.94  3.000
 JPR  C6    C4   CL1   117.26  3.000
 JPR  H5    C5   C7    119.88  3.000
 JPR  H5    C5   C3    119.40  3.000
 JPR  C7    C5   C3    120.72  3.000
 JPR  H6    C6   C7    121.19  3.000
 JPR  H6    C6   C4    119.62  3.000
 JPR  C7    C6   C4    119.19  3.000
 JPR  C6    C7   C5    118.36  3.000
 JPR  C5    C7   N1    117.31  3.000
 JPR  C6    C7   N1    124.31  3.000
 JPR  N2    C8   O1    122.75  3.000
 JPR  O1    C8   N1    123.61  3.000
 JPR  N2    C8   N1    113.63  3.000
 JPR  H92   C9   H91   107.10  3.000
 JPR  H92   C9   C10   109.94  3.000
 JPR  H91   C9   C10   110.22  3.000
 JPR  H92   C9   N2    107.63  3.000
 JPR  H91   C9   N2    109.50  3.000
 JPR  C10   C9   N2    112.30  3.000
 JPR  H102  C10  H101  108.39  3.000
 JPR  H102  C10  C9    110.08  3.000
 JPR  H101  C10  C9    110.27  3.000
 JPR  H102  C10  S1    109.51  3.000
 JPR  H101  C10  S1    109.31  3.000
 JPR  C9    C10  S1    109.26  3.000
 JPR  H112  C11  H111  108.10  3.000
 JPR  H112  C11  C12   111.30  3.000
 JPR  H111  C11  C12   109.07  3.000
 JPR  H112  C11  S1    108.48  3.000
 JPR  H111  C11  S1    109.52  3.000
 JPR  C12   C11  S1    110.32  3.000
 JPR  C13   C12  C11   132.75  3.000
 JPR  C13   C12  O2    109.51  3.000
 JPR  C11   C12  O2    117.73  3.000
 JPR  H13   C13  C14   127.48  3.000
 JPR  H13   C13  C12   126.09  3.000
 JPR  C14   C13  C12   106.43  3.000
 JPR  H14   C14  C15   126.20  3.000
 JPR  H14   C14  C13   127.59  3.000
 JPR  C15   C14  C13   106.22  3.000
 JPR  C16   C15  C14   132.82  3.000
 JPR  C16   C15  O2    117.40  3.000
 JPR  C14   C15  O2    109.75  3.000
 JPR  H162  C16  H161  105.92  3.000
 JPR  H162  C16  C15   109.61  3.000
 JPR  H161  C16  C15   109.07  3.000
 JPR  H162  C16  N3    112.75  3.000
 JPR  H161  C16  N3    108.15  3.000
 JPR  C15   C16  N3    111.15  3.000
 JPR  H173  C17  H172  107.93  3.000
 JPR  H173  C17  H171  107.79  3.000
 JPR  H172  C17  H171  107.58  3.000
 JPR  H173  C17  N3    112.91  3.000
 JPR  H172  C17  N3    110.68  3.000
 JPR  H171  C17  N3    109.76  3.000
 JPR  H183  C18  H182  107.87  3.000
 JPR  H183  C18  H181  107.62  3.000
 JPR  H182  C18  H181  107.78  3.000
 JPR  H183  C18  N3    109.73  3.000
 JPR  H182  C18  N3    110.19  3.000
 JPR  H181  C18  N3    113.46  3.000
 JPR  H13A  C1   H12   107.77  3.000
 JPR  H13A  C1   H11   107.76  3.000
 JPR  H12   C1   H11   107.05  3.000
 JPR  H13A  C1   C2    110.62  3.000
 JPR  H12   C1   C2    111.69  3.000
 JPR  H11   C1   C2    111.75  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
 JPR  CONST_01  C7    C6   C4   C2      0.00   0.0  0
 JPR  CONST_02  C7    C5   C3   C2      0.00   0.0  0
 JPR  CONST_03  C14   C13  C12  O2      0.00   0.0  0
 JPR  CONST_04  C13   C14  C15  O2      0.00   0.0  0
 JPR  CONST_05  C6    C4   C2   C3      0.00   0.0  0
 JPR  CONST_06  C6    C7   C5   C3      0.00   0.0  0
 JPR  CONST_07  C5    C7   C6   C4      0.00   0.0  0
 JPR  CONST_08  C5    C3   C2   C4      0.00   0.0  0
 JPR  CONST_09  C15   C14  C13  C12     0.00   0.0  0
 JPR  CONST_10  C14   C15  O2   C12     0.00   0.0  0
 JPR  CONST_11  C15   O2   C12  C13     0.00   0.0  0
 JPR  CONST_12  C7    C6   C4   CL1   180.00   0.0  0
 JPR  CONST_13  C3    C2   C4   CL1   180.00   0.0  0
 JPR  CONST_14  C6    C4   C2   C1    180.00   0.0  0
 JPR  CONST_15  C5    C3   C2   C1    180.00   0.0  0
 JPR  CONST_16  C4    C6   C7   N1    180.00   0.0  0
 JPR  CONST_17  C3    C5   C7   N1    180.00   0.0  0
 JPR  CONST_18  C14   C13  C12  C11   180.00   0.0  0
 JPR  CONST_19  C15   O2   C12  C11   180.00   0.0  0
 JPR  CONST_20  C16   C15  O2   C12   180.00   0.0  0
 JPR  CONST_21  C16   C15  C14  C13   180.00   0.0  0
 JPR  CONST_22  H6    C6   C4   C2    180.00   0.0  0
 JPR  CONST_23  H5    C5   C3   C2    180.00   0.0  0
 JPR  CONST_24  H13   C13  C12  O2    180.00   0.0  0
 JPR  CONST_25  H14   C14  C15  O2    180.00   0.0  0
 JPR  CONST_26  H3    C3   C2   C4    180.00   0.0  0
 JPR  CONST_29  HN1   N1   C7   C5      0.00   0.0  0
 JPR  CONST_30  C7    N1   C8   O1      0.00   0.0  0
 JPR  CONST_31  C7    N1   C8   N2    180.00   0.0  0
 JPR  CONST_32  C9    N2   C8   O1      0.00   0.0  0
 JPR  CONST_33  C9    N2   C8   N1    180.00   0.0  0
 JPR  CONST_34  HN2   N2   C8   O1    180.00   0.0  0
 JPR  Var_01    C13   C12  C11  S1    109.38  30.0  2
 JPR  Var_02    N3    C16  C15  O2   -155.33  30.0  2
 JPR  Var_03    H11   C1   C2   C3    120.22  30.0  2
 JPR  Var_04    C12   C11  S1   C10   174.36  30.0  1
 JPR  Var_05    C17   N3   C16  C15    73.48  30.0  3
 JPR  Var_06    N2    C9   C10  S1   -179.98  30.0  3
 JPR  Var_07    C10   C9   N2   C8    -81.19  30.0  3
 JPR  Var_08    H171  C17  N3   C16  -175.84  30.0  3
 JPR  Var_09    H181  C18  N3   C16   -63.60  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
 JPR  plan-1  O2   0.020
 JPR  plan-1  C11  0.020
 JPR  plan-1  C12  0.020
 JPR  plan-1  C13  0.020
 JPR  plan-1  C14  0.020
 JPR  plan-1  C15  0.020
 JPR  plan-1  C16  0.020
 JPR  plan-1  H13  0.020
 JPR  plan-1  H14  0.020
 JPR  plan-2  CL1  0.020
 JPR  plan-2  N1   0.020
 JPR  plan-2  C2   0.020
 JPR  plan-2  C3   0.020
 JPR  plan-2  C4   0.020
 JPR  plan-2  C5   0.020
 JPR  plan-2  C6   0.020
 JPR  plan-2  C7   0.020
 JPR  plan-2  H3   0.020
 JPR  plan-2  H5   0.020
 JPR  plan-2  H6   0.020
 JPR  plan-2  C1   0.020
 JPR  plan-3  N1   0.020
 JPR  plan-3  O1   0.020
 JPR  plan-3  N2   0.020
 JPR  plan-3  C7   0.020
 JPR  plan-3  C8   0.020
 JPR  plan-3  C9   0.020
 JPR  plan-3  HN1  0.020
 JPR  plan-3  HN2  0.020

