# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 19:27:53 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: [4-amino-2-(prop-2-en-1-ylamino)-1,3-thiazol-5-yl](naphthalen-2-yl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(NCC=C)sc1C(=O)c2ccc3ccccc3c2
#
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
 Z31  Z31  '[4-amino-2-(prop-2-en-1-ylamino)-1,3-thiazol-5-yl](naphthalen-2-yl)methanone'  ligand  37  22  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Z31
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
 Z31  C1    C  C2    0  -0.520  -6.4983   2.3005   0.2736
 Z31  C2    C  C1    0  -0.170  -5.6272   1.3040   0.1826
 Z31  C3    C  CH2   0  -0.365  -5.0660   0.8057  -1.1154
 Z31  N4    N  NH1   0  -0.634  -3.6216   0.9488  -1.1851
 Z31  C5    C  CR5   0   0.365  -2.7850   0.0800  -0.6277
 Z31  S6    S  S2    0   0.159  -1.0668   0.3519  -0.6601
 Z31  C7    C  CR5   0  -0.471  -0.8530  -1.1654   0.2115
 Z31  C8    C  CR5   0   0.583  -2.1238  -1.7304   0.4220
 Z31  N9    N  N     0  -0.479  -3.1792  -1.0210  -0.0379
 Z31  N10   N  NH2   0  -0.824  -2.3471  -2.8871   1.0407
 Z31  C11   C  C     0   0.363   0.3886  -1.7616   0.5397
 Z31  C12   C  CR6   0  -0.029   1.6473  -1.0146   0.2391
 Z31  C13   C  CR16  0  -0.361   1.8180   0.2945   0.6112
 Z31  C14   C  CR66  0   0.140   3.0317   0.9735   0.3557
 Z31  C15   C  CR66  0   0.109   4.0818   0.2850  -0.3032
 Z31  C16   C  CR16  0  -0.303   3.8875  -1.0702  -0.6640
 Z31  C17   C  CR16  0  -0.286   2.7117  -1.7070  -0.3882
 Z31  C18   C  CR16  0  -0.312   3.2230   2.3227   0.7345
 Z31  C19   C  CR16  0  -0.257   4.4017   2.9614   0.4600
 Z31  C20   C  CR16  0  -0.255   5.4439   2.2786  -0.2021
 Z31  C21   C  CR16  0  -0.309   5.2884   0.9703  -0.5734
 Z31  O22   O  O     0  -0.482   0.4745  -2.8906   1.0409
 Z31  H1    H  H     0   0.240  -6.8574   2.8261  -0.6038
 Z31  H1A   H  H     0   0.245  -6.8886   2.6260   1.2292
 Z31  H2    H  H     0   0.255  -5.2844   0.7974   1.0796
 Z31  H3    H  HCH2  0   0.267  -5.3140  -0.2463  -1.2612
 Z31  H3A   H  HCH2  0   0.276  -5.4881   1.3593  -1.9532
 Z31  HN4   H  HNH1  0   0.417  -3.2591   1.8230  -1.5300
 Z31  HN10  H  HNH2  0   0.413  -1.5691  -3.4609   1.3203
 Z31  HN1A  H  HNH2  0   0.402  -3.2815  -3.2534   1.0963
 Z31  H13   H  HCR6  0   0.269   1.0333   0.8270   1.1367
 Z31  H16   H  HCR6  0   0.259   4.6891  -1.6006  -1.1638
 Z31  H17   H  HCR6  0   0.260   2.5803  -2.7446  -0.6658
 Z31  H18   H  HCR6  0   0.258   2.4214   2.8448   1.2431
 Z31  H19   H  HCR6  0   0.261   4.5405   3.9945   0.7501
 Z31  H20   H  HCR6  0   0.261   6.3707   2.7954  -0.4149
 Z31  H21   H  HCR6  0   0.258   6.0896   0.4451  -1.0788

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
 Z31  C2   C1    double    1.327  0.020  1.327
 Z31  C1   H1    single    0.930  0.020  1.080
 Z31  C1   H1A   single    0.930  0.020  1.080
 Z31  C3   C2    single    1.499  0.020  1.499
 Z31  C2   H2    single    0.930  0.020  1.080
 Z31  N4   C3    single    1.453  0.020  1.453
 Z31  C3   H3    single    0.970  0.020  1.090
 Z31  C3   H3A   single    0.970  0.020  1.090
 Z31  C5   N4    single    1.329  0.020  1.329
 Z31  N4   HN4   single    0.860  0.020  1.020
 Z31  N9   C5    aromatic  1.310  0.020  1.310
 Z31  C5   S6    aromatic  1.740  0.020  1.740
 Z31  C7   S6    aromatic  1.763  0.020  1.763
 Z31  C8   C7    aromatic  1.407  0.020  1.407
 Z31  C7   C11   single    1.416  0.020  1.416
 Z31  N10  C8    single    1.331  0.020  1.331
 Z31  C8   N9    aromatic  1.352  0.020  1.352
 Z31  N10  HN10  single    0.860  0.020  1.020
 Z31  N10  HN1A  single    0.860  0.020  1.020
 Z31  O22  C11   double    1.238  0.020  1.238
 Z31  C11  C12   single    1.494  0.020  1.494
 Z31  C12  C17   aromatic  1.416  0.020  1.416
 Z31  C12  C13   aromatic  1.372  0.020  1.372
 Z31  C13  C14   aromatic  1.414  0.020  1.414
 Z31  C13  H13   single    0.930  0.020  1.080
 Z31  C14  C15   aromatic  1.418  0.020  1.418
 Z31  C14  C18   aromatic  1.414  0.020  1.414
 Z31  C16  C15   aromatic  1.416  0.020  1.416
 Z31  C15  C21   aromatic  1.414  0.020  1.414
 Z31  C17  C16   aromatic  1.365  0.020  1.365
 Z31  C16  H16   single    0.930  0.020  1.080
 Z31  C17  H17   single    0.930  0.020  1.080
 Z31  C18  C19   aromatic  1.368  0.020  1.368
 Z31  C18  H18   single    0.930  0.020  1.080
 Z31  C19  C20   aromatic  1.411  0.020  1.411
 Z31  C19  H19   single    0.930  0.020  1.080
 Z31  C21  C20   aromatic  1.369  0.020  1.369
 Z31  C20  H20   single    0.930  0.020  1.080
 Z31  C21  H21   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
 Z31  H1A   C1   H1    116.70  3.000
 Z31  H1A   C1   C2    121.55  3.000
 Z31  H1    C1   C2    121.74  3.000
 Z31  H2    C2   C3    116.23  3.000
 Z31  H2    C2   C1    120.07  3.000
 Z31  C3    C2   C1    123.70  3.000
 Z31  H3A   C3   H3    107.41  3.000
 Z31  H3A   C3   N4    107.35  3.000
 Z31  H3    C3   N4    108.33  3.000
 Z31  H3A   C3   C2    110.60  3.000
 Z31  H3    C3   C2    110.56  3.000
 Z31  N4    C3   C2    112.39  3.000
 Z31  HN4   N4   C5    118.98  3.000
 Z31  HN4   N4   C3    117.36  3.000
 Z31  C5    N4   C3    122.78  3.000
 Z31  N9    C5   S6    115.91  3.000
 Z31  S6    C5   N4    120.78  3.000
 Z31  N9    C5   N4    123.30  3.000
 Z31  C7    S6   C5     88.63  3.000
 Z31  C11   C7   C8    126.04  3.000
 Z31  C11   C7   S6    125.69  3.000
 Z31  C8    C7   S6    108.07  3.000
 Z31  N10   C8   N9    118.90  3.000
 Z31  N9    C8   C7    116.33  3.000
 Z31  N10   C8   C7    124.78  3.000
 Z31  C8    N9   C5    111.05  3.000
 Z31  HN1A  N10  HN10  119.71  3.000
 Z31  HN1A  N10  C8    119.90  3.000
 Z31  HN10  N10  C8    119.67  3.000
 Z31  O22   C11  C12   118.60  3.000
 Z31  C12   C11  C7    118.79  3.000
 Z31  O22   C11  C7    122.59  3.000
 Z31  C17   C12  C13   119.55  3.000
 Z31  C13   C12  C11   121.83  3.000
 Z31  C17   C12  C11   118.54  3.000
 Z31  H13   C13  C14   118.23  3.000
 Z31  H13   C13  C12   120.67  3.000
 Z31  C14   C13  C12   121.07  3.000
 Z31  C18   C14  C15   119.17  3.000
 Z31  C18   C14  C13   121.72  3.000
 Z31  C15   C14  C13   119.11  3.000
 Z31  C21   C15  C16   122.17  3.000
 Z31  C21   C15  C14   119.04  3.000
 Z31  C16   C15  C14   118.78  3.000
 Z31  H16   C16  C17   120.14  3.000
 Z31  H16   C16  C15   118.99  3.000
 Z31  C17   C16  C15   120.88  3.000
 Z31  H17   C17  C16   120.00  3.000
 Z31  H17   C17  C12   119.41  3.000
 Z31  C16   C17  C12   120.57  3.000
 Z31  H18   C18  C19   120.44  3.000
 Z31  H18   C18  C14   119.04  3.000
 Z31  C19   C18  C14   120.53  3.000
 Z31  H19   C19  C20   119.54  3.000
 Z31  H19   C19  C18   120.15  3.000
 Z31  C20   C19  C18   120.31  3.000
 Z31  H20   C20  C21   120.02  3.000
 Z31  H20   C20  C19   119.59  3.000
 Z31  C21   C20  C19   120.39  3.000
 Z31  H21   C21  C20   120.40  3.000
 Z31  H21   C21  C15   119.04  3.000
 Z31  C20   C21  C15   120.56  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
 Z31  CONST_01  C7    C8   N9   C5      0.00   0.0  0
 Z31  CONST_02  C8    C7   S6   C5      0.00   0.0  0
 Z31  CONST_03  C8    N9   C5   S6      0.00   0.0  0
 Z31  CONST_04  N9    C8   C7   S6      0.00   0.0  0
 Z31  CONST_05  N9    C5   S6   C7      0.00   0.0  0
 Z31  CONST_06  C15   C16  C17  C12     0.00   0.0  0
 Z31  CONST_07  C15   C14  C13  C12     0.00   0.0  0
 Z31  CONST_08  C18   C14  C13  C12   180.00   0.0  0
 Z31  CONST_09  C16   C17  C12  C13     0.00   0.0  0
 Z31  CONST_10  C16   C15  C14  C13     0.00   0.0  0
 Z31  CONST_11  C21   C15  C14  C13   180.00   0.0  0
 Z31  CONST_12  C19   C18  C14  C13   180.00   0.0  0
 Z31  CONST_13  C17   C12  C13  C14     0.00   0.0  0
 Z31  CONST_14  C17   C16  C15  C14     0.00   0.0  0
 Z31  CONST_15  C20   C21  C15  C14     0.00   0.0  0
 Z31  CONST_16  C20   C19  C18  C14     0.00   0.0  0
 Z31  CONST_17  C19   C18  C14  C15     0.00   0.0  0
 Z31  CONST_18  C19   C20  C21  C15     0.00   0.0  0
 Z31  CONST_19  C18   C14  C15  C16   180.00   0.0  0
 Z31  CONST_20  C20   C21  C15  C16   180.00   0.0  0
 Z31  CONST_21  C21   C15  C16  C17   180.00   0.0  0
 Z31  CONST_22  C21   C15  C14  C18     0.00   0.0  0
 Z31  CONST_23  C21   C20  C19  C18     0.00   0.0  0
 Z31  CONST_24  C8    N9   C5   N4    180.00   0.0  0
 Z31  CONST_25  C7    S6   C5   N4    180.00   0.0  0
 Z31  CONST_26  N10   C8   N9   C5    180.00   0.0  0
 Z31  CONST_27  C11   C7   S6   C5    180.00   0.0  0
 Z31  CONST_28  N10   C8   C7   S6    180.00   0.0  0
 Z31  CONST_29  C11   C7   C8   N9    180.00   0.0  0
 Z31  CONST_30  C16   C17  C12  C11   180.00   0.0  0
 Z31  CONST_31  C14   C13  C12  C11   180.00   0.0  0
 Z31  CONST_32  H16   C16  C17  C12   180.00   0.0  0
 Z31  CONST_33  H17   C17  C12  C13   180.00   0.0  0
 Z31  CONST_34  H18   C18  C14  C13     0.00   0.0  0
 Z31  CONST_35  H21   C21  C15  C14   180.00   0.0  0
 Z31  CONST_36  H19   C19  C18  C14   180.00   0.0  0
 Z31  CONST_37  H13   C13  C14  C15   180.00   0.0  0
 Z31  CONST_38  H20   C20  C21  C15   180.00   0.0  0
 Z31  CONST_39  N9    C5   N4   C3      0.00   0.0  0
 Z31  CONST_40  S6    C5   N4   C3    180.00   0.0  0
 Z31  CONST_41  HN4   N4   C5   S6      0.00   0.0  0
 Z31  CONST_42  HN10  N10  C8   C7      0.00   0.0  0
 Z31  CONST_43  HN1A  N10  C8   C7    180.00   0.0  0
 Z31  Var_01    C12   C11  C7   S6      5.53  30.0  2
 Z31  Var_02    C17   C12  C11  C7   -133.73  30.0  2
 Z31  Var_03    C5    N4   C3   C2     81.39  30.0  1
 Z31  Var_04    N4    C3   C2   C1    118.80  30.0  1
 Z31  Var_05    H1    C1   C2   C3     -0.34   0.0  2

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
 Z31  plan-1  N4    0.020
 Z31  plan-1  C5    0.020
 Z31  plan-1  S6    0.020
 Z31  plan-1  C7    0.020
 Z31  plan-1  C8    0.020
 Z31  plan-1  N9    0.020
 Z31  plan-1  N10   0.020
 Z31  plan-1  C11   0.020
 Z31  plan-2  C11   0.020
 Z31  plan-2  C12   0.020
 Z31  plan-2  C13   0.020
 Z31  plan-2  C14   0.020
 Z31  plan-2  C15   0.020
 Z31  plan-2  C16   0.020
 Z31  plan-2  C17   0.020
 Z31  plan-2  C18   0.020
 Z31  plan-2  C19   0.020
 Z31  plan-2  C20   0.020
 Z31  plan-2  C21   0.020
 Z31  plan-2  H13   0.020
 Z31  plan-2  H16   0.020
 Z31  plan-2  H17   0.020
 Z31  plan-2  H18   0.020
 Z31  plan-2  H19   0.020
 Z31  plan-2  H20   0.020
 Z31  plan-2  H21   0.020
 Z31  plan-3  C3    0.020
 Z31  plan-3  N4    0.020
 Z31  plan-3  C5    0.020
 Z31  plan-3  HN4   0.020
 Z31  plan-4  C8    0.020
 Z31  plan-4  N10   0.020
 Z31  plan-4  HN10  0.020
 Z31  plan-4  HN1A  0.020
 Z31  plan-5  C7    0.020
 Z31  plan-5  C11   0.020
 Z31  plan-5  C12   0.020
 Z31  plan-5  O22   0.020
 Z31  plan-6  C1    0.020
 Z31  plan-6  C2    0.020
 Z31  plan-6  C3    0.020
 Z31  plan-6  H1    0.020
 Z31  plan-6  H1A   0.020
 Z31  plan-6  H2    0.020

