FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

tag_button

FMODB ID: JQ9K9

Calculation Name: 2HPW-A-Xray372

Preferred Name:

Target Type:

Ligand Name: [(4z)-2-(1-amino-2-hydroxyethyl)-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1h-imidazol-1-yl]acetic acid

ligand 3-letter code: GYS

PDB ID: 2HPW

Chain ID: A

ChEMBL ID:

UniProt ID: D7PM05

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 229
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2951244.844782
FMO2-HF: Nuclear repulsion 2860365.612048
FMO2-HF: Total energy -90879.232734
FMO2-MP2: Total energy -91145.632451


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:5:THR)


Summations of interaction energy for fragment #1(A:5:THR)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-14.278-9.8340.185-1.798-2.830.009
Interaction energy analysis for fragmet #1(A:5:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.007 / q_NPA : -0.010
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A7GLY00.0660.0443.746-1.4000.4860.003-0.820-1.0680.003
4A8ALA0-0.026-0.0313.190-1.425-0.9040.044-0.129-0.4370.000
5A9LYS10.9640.9843.010-7.090-5.5620.136-0.692-0.9720.005
6A10LEU0-0.058-0.0146.516-0.408-0.4080.0000.0000.0000.000
7A11PHE0-0.021-0.0228.119-0.235-0.2350.0000.0000.0000.000
8A12GLU-1-0.964-0.9787.1472.1362.1360.0000.0000.0000.000
9A13LYS10.8870.93810.636-0.653-0.6530.0000.0000.0000.000
10A14GLU-1-0.916-0.95214.0650.4300.4300.0000.0000.0000.000
11A15ILE0-0.037-0.00613.382-0.022-0.0220.0000.0000.0000.000
12A16PRO00.0240.00517.072-0.013-0.0130.0000.0000.0000.000
13A17TYR0-0.0160.00118.3480.0440.0440.0000.0000.0000.000
14A18ILE00.0190.02120.186-0.032-0.0320.0000.0000.0000.000
15A19THR0-0.051-0.02522.0650.0220.0220.0000.0000.0000.000
16A20GLU-1-0.954-0.97924.4240.1660.1660.0000.0000.0000.000
17A21LEU00.0290.01526.2650.0070.0070.0000.0000.0000.000
18A22GLU-1-0.909-0.95328.5550.1360.1360.0000.0000.0000.000
19A23GLY00.010-0.00631.2830.0020.0020.0000.0000.0000.000
20A24ASP-1-0.912-0.95833.4830.0690.0690.0000.0000.0000.000
21A25VAL00.0260.01535.7960.0000.0000.0000.0000.0000.000
22A26GLU-1-0.827-0.92038.1110.0630.0630.0000.0000.0000.000
23A27GLY0-0.047-0.01340.376-0.004-0.0040.0000.0000.0000.000
24A28MET0-0.053-0.01940.632-0.001-0.0010.0000.0000.0000.000
25A29LYS10.8910.94037.952-0.069-0.0690.0000.0000.0000.000
26A30PHE00.006-0.00132.981-0.001-0.0010.0000.0000.0000.000
27A31ILE00.0060.00332.0590.0020.0020.0000.0000.0000.000
28A32ILE0-0.0200.00029.884-0.001-0.0010.0000.0000.0000.000
29A33LYS10.9210.96829.055-0.141-0.1410.0000.0000.0000.000
30A34GLY00.012-0.00426.660-0.006-0.0060.0000.0000.0000.000
31A35GLU-1-0.940-0.96425.3980.2110.2110.0000.0000.0000.000
32A36GLY00.0330.00023.901-0.013-0.0130.0000.0000.0000.000
33A37THR0-0.034-0.01020.2440.0030.0030.0000.0000.0000.000
34A38GLY00.0380.00517.163-0.022-0.0220.0000.0000.0000.000
35A39ASP-1-0.785-0.88215.6610.6260.6260.0000.0000.0000.000
36A40ALA00.0090.00011.193-0.025-0.0250.0000.0000.0000.000
37A41THR0-0.077-0.03512.341-0.001-0.0010.0000.0000.0000.000
38A42THR0-0.080-0.05613.662-0.049-0.0490.0000.0000.0000.000
39A43GLY0-0.045-0.01515.745-0.045-0.0450.0000.0000.0000.000
40A44THR0-0.047-0.02116.669-0.063-0.0630.0000.0000.0000.000
41A45ILE00.0380.02518.2080.0310.0310.0000.0000.0000.000
42A46LYS10.9110.95620.714-0.315-0.3150.0000.0000.0000.000
43A47ALA00.0390.02223.7100.0120.0120.0000.0000.0000.000
44A48LYS10.8000.88125.871-0.157-0.1570.0000.0000.0000.000
45A49TYR0-0.034-0.05123.8280.0030.0030.0000.0000.0000.000
46A50ILE00.0610.02430.174-0.008-0.0080.0000.0000.0000.000
47A51CYS0-0.052-0.01533.1380.0040.0040.0000.0000.0000.000
48A52THR00.015-0.00533.850-0.004-0.0040.0000.0000.0000.000
49A53THR0-0.046-0.02336.590-0.003-0.0030.0000.0000.0000.000
50A54GLY00.0070.01039.071-0.007-0.0070.0000.0000.0000.000
51A55ASP-1-0.879-0.93439.5150.0910.0910.0000.0000.0000.000
52A56LEU0-0.086-0.04934.7630.0000.0000.0000.0000.0000.000
53A57PRO0-0.026-0.01537.714-0.003-0.0030.0000.0000.0000.000
54A58VAL00.006-0.00735.368-0.004-0.0040.0000.0000.0000.000
55A59PRO00.0160.00936.8520.0040.0040.0000.0000.0000.000
56A60TRP00.0670.01831.6450.0100.0100.0000.0000.0000.000
57A61ALA0-0.0040.00032.2730.0100.0100.0000.0000.0000.000
58A62THR0-0.093-0.05231.4040.0070.0070.0000.0000.0000.000
59A63ILE00.0460.02730.0090.0020.0020.0000.0000.0000.000
60A64LEU00.0490.02926.1930.0090.0090.0000.0000.0000.000
61A65SER0-0.085-0.05524.9240.0170.0170.0000.0000.0000.000
62A66SER00.0130.00823.9650.0190.0190.0000.0000.0000.000
63A67LEU00.0430.02824.2980.0160.0160.0000.0000.0000.000
64A68GYS10.1570.14819.068-0.279-0.2790.0000.0000.0000.000
65A71VAL-1-0.129-0.14416.9890.3960.3960.0000.0000.0000.000
66A72PHE00.0210.01514.9850.0240.0240.0000.0000.0000.000
67A73CYS0-0.022-0.00211.5880.0210.0210.0000.0000.0000.000
68A74PHE00.0170.00711.4990.1420.1420.0000.0000.0000.000
69A75ALA0-0.0110.00613.234-0.039-0.0390.0000.0000.0000.000
70A76LYS10.9730.98412.210-0.364-0.3640.0000.0000.0000.000
71A77TYR0-0.017-0.0549.247-0.091-0.0910.0000.0000.0000.000
72A78PRO0-0.068-0.01410.2630.1100.1100.0000.0000.0000.000
73A79ARG10.9800.9547.750-0.648-0.6480.0000.0000.0000.000
74A80HIS0-0.059-0.0537.885-0.014-0.0140.0000.0000.0000.000
75A81ILE0-0.0470.00110.135-0.145-0.1450.0000.0000.0000.000
76A82ALA00.0660.0466.6150.1720.1720.0000.0000.0000.000
77A83ASP-1-0.778-0.9105.9611.3931.3930.0000.0000.0000.000
78A84PHE00.026-0.0036.4360.5280.5280.0000.0000.0000.000
79A85PHE00.0080.0048.6990.1290.1290.0000.0000.0000.000
80A86LYS10.8500.9316.383-1.377-1.3770.0000.0000.0000.000
81A87SER0-0.051-0.0153.719-0.453-0.1210.004-0.138-0.1980.001
82A88THR00.002-0.0035.084-0.336-0.330-0.001-0.0050.0000.000
83A89GLN0-0.0680.0037.563-0.510-0.5100.0000.0000.0000.000
84A90PRO0-0.007-0.0287.3560.3370.3370.0000.0000.0000.000
85A91ASP-1-0.822-0.90810.7040.1070.1070.0000.0000.0000.000
86A92GLY00.0350.00711.503-0.073-0.0730.0000.0000.0000.000
87A93TYR0-0.047-0.03111.890-0.016-0.0160.0000.0000.0000.000
88A94SER0-0.020-0.00214.451-0.025-0.0250.0000.0000.0000.000
89A95GLN00.003-0.01517.3040.0530.0530.0000.0000.0000.000
90A96ASP-1-0.835-0.90919.3970.1480.1480.0000.0000.0000.000
91A97ARG10.7960.88121.954-0.222-0.2220.0000.0000.0000.000
92A98ILE00.0080.03525.152-0.004-0.0040.0000.0000.0000.000
93A99ILE0-0.027-0.01227.3040.0020.0020.0000.0000.0000.000
94A100SER0-0.001-0.01030.091-0.009-0.0090.0000.0000.0000.000
95A101PHE0-0.0120.00032.7020.0040.0040.0000.0000.0000.000
96A102ASP-1-0.775-0.86135.7740.0720.0720.0000.0000.0000.000
97A103ASN0-0.076-0.04938.146-0.003-0.0030.0000.0000.0000.000
98A104ASP-1-0.801-0.91939.0790.0700.0700.0000.0000.0000.000
99A105GLY00.0350.04438.552-0.002-0.0020.0000.0000.0000.000
100A106GLN0-0.035-0.02833.4330.0050.0050.0000.0000.0000.000
101A107TYR0-0.008-0.02730.945-0.005-0.0050.0000.0000.0000.000
102A108ASP-1-0.863-0.92329.3760.1010.1010.0000.0000.0000.000
103A109VAL0-0.013-0.01925.2700.0010.0010.0000.0000.0000.000
104A110LYS10.8840.94224.478-0.099-0.0990.0000.0000.0000.000
105A111ALA00.0380.01821.137-0.002-0.0020.0000.0000.0000.000
106A112LYS10.9340.98218.924-0.190-0.1900.0000.0000.0000.000
107A113VAL00.0060.00215.018-0.009-0.0090.0000.0000.0000.000
108A114THR0-0.006-0.02714.6960.0610.0610.0000.0000.0000.000
109A115TYR00.0350.03912.687-0.004-0.0040.0000.0000.0000.000
110A116GLU-1-0.781-0.85714.5800.2230.2230.0000.0000.0000.000
111A117ASN0-0.037-0.03417.057-0.013-0.0130.0000.0000.0000.000
112A118GLY00.0200.00715.924-0.027-0.0270.0000.0000.0000.000
113A119THR0-0.0140.01216.8370.0240.0240.0000.0000.0000.000
114A120LEU0-0.021-0.01413.7000.0170.0170.0000.0000.0000.000
115A121TYR00.0050.00616.955-0.047-0.0470.0000.0000.0000.000
116A122ASN0-0.017-0.01618.4610.0270.0270.0000.0000.0000.000
117A123ARG10.7870.88020.688-0.259-0.2590.0000.0000.0000.000
118A124VAL0-0.004-0.01923.0770.0020.0020.0000.0000.0000.000
119A125THR0-0.0300.00325.307-0.015-0.0150.0000.0000.0000.000
120A126VAL00.025-0.00628.2250.0050.0050.0000.0000.0000.000
121A127LYS10.9210.97330.738-0.079-0.0790.0000.0000.0000.000
122A128GLY0-0.016-0.01533.7200.0010.0010.0000.0000.0000.000
123A129THR0-0.041-0.02235.893-0.006-0.0060.0000.0000.0000.000
124A130GLY00.0410.01438.3020.0020.0020.0000.0000.0000.000
125A131PHE0-0.043-0.02035.7550.0000.0000.0000.0000.0000.000
126A132LYS10.9030.95441.562-0.058-0.0580.0000.0000.0000.000
127A133SER00.0350.00544.7490.0030.0030.0000.0000.0000.000
128A134ASN0-0.039-0.00947.2730.0020.0020.0000.0000.0000.000
129A135GLY00.0550.05043.5770.0000.0000.0000.0000.0000.000
130A136ASN0-0.007-0.03540.639-0.002-0.0020.0000.0000.0000.000
131A137ILE00.0150.02437.0190.0030.0030.0000.0000.0000.000
132A138LEU00.0540.01440.0920.0020.0020.0000.0000.0000.000
133A139GLY0-0.027-0.00142.883-0.001-0.0010.0000.0000.0000.000
134A140MET0-0.040-0.00740.3330.0000.0000.0000.0000.0000.000
135A141ARG10.8630.91742.358-0.069-0.0690.0000.0000.0000.000
136A142VAL0-0.028-0.01036.0630.0000.0000.0000.0000.0000.000
137A143LEU00.007-0.00738.9640.0010.0010.0000.0000.0000.000
138A144TYR0-0.037-0.02734.8190.0050.0050.0000.0000.0000.000
139A145HIS0-0.034-0.05733.4910.0040.0040.0000.0000.0000.000
140A146SER00.0390.00828.795-0.004-0.0040.0000.0000.0000.000
141A147PRO0-0.0180.00330.0300.0100.0100.0000.0000.0000.000
142A148PRO0-0.008-0.00627.2930.0100.0100.0000.0000.0000.000
143A149HIS00.0190.01625.798-0.026-0.0260.0000.0000.0000.000
144A150ALA0-0.001-0.00323.5180.0170.0170.0000.0000.0000.000
145A151VAL0-0.041-0.02319.776-0.019-0.0190.0000.0000.0000.000
146A152TYR0-0.013-0.00720.3340.0070.0070.0000.0000.0000.000
147A153ILE00.0560.02314.2200.0010.0010.0000.0000.0000.000
148A154LEU00.004-0.01117.238-0.022-0.0220.0000.0000.0000.000
149A155PRO00.0120.01814.8480.0140.0140.0000.0000.0000.000
150A156ASP-1-0.852-0.94616.3170.0100.0100.0000.0000.0000.000
151A157ARG11.0060.99813.4040.3100.3100.0000.0000.0000.000
152A158LYS10.8890.94717.5120.0360.0360.0000.0000.0000.000
153A159ASN0-0.039-0.01420.129-0.008-0.0080.0000.0000.0000.000
154A160GLY0-0.0150.00316.7180.0160.0160.0000.0000.0000.000
155A161GLY00.0290.00014.5720.0270.0270.0000.0000.0000.000
156A162MET0-0.056-0.00413.180-0.050-0.0500.0000.0000.0000.000
157A163LYS10.9230.97016.133-0.068-0.0680.0000.0000.0000.000
158A164ILE0-0.027-0.01916.1390.0050.0050.0000.0000.0000.000
159A165GLU-1-0.877-0.93420.3740.0860.0860.0000.0000.0000.000
160A166TYR0-0.013-0.01322.5350.0140.0140.0000.0000.0000.000
161A167ASN00.0240.01925.591-0.010-0.0100.0000.0000.0000.000
162A168LYS10.8430.94726.936-0.173-0.1730.0000.0000.0000.000
163A169ALA00.005-0.01530.018-0.011-0.0110.0000.0000.0000.000
164A170PHE00.005-0.00430.7210.0040.0040.0000.0000.0000.000
165A171ASP-1-0.799-0.86935.2500.1010.1010.0000.0000.0000.000
166A172VAL0-0.013-0.01538.5480.0030.0030.0000.0000.0000.000
167A173MET0-0.026-0.01841.554-0.001-0.0010.0000.0000.0000.000
168A174GLY0-0.029-0.00644.787-0.002-0.0020.0000.0000.0000.000
169A175GLY0-0.0120.00944.261-0.003-0.0030.0000.0000.0000.000
170A176GLY00.0010.00243.134-0.002-0.0020.0000.0000.0000.000
171A177HIS0-0.005-0.01437.8360.0000.0000.0000.0000.0000.000
172A178GLN0-0.036-0.00736.539-0.008-0.0080.0000.0000.0000.000
173A179MET0-0.044-0.00633.1480.0070.0070.0000.0000.0000.000
174A180ALA00.0230.00731.265-0.004-0.0040.0000.0000.0000.000
175A181ARG10.7980.85830.155-0.077-0.0770.0000.0000.0000.000
176A182HIS00.0040.02525.2350.0060.0060.0000.0000.0000.000
177A183ALA00.0560.04125.4660.0030.0030.0000.0000.0000.000
178A184GLN0-0.009-0.03319.2740.0260.0260.0000.0000.0000.000
179A185PHE0-0.048-0.02018.813-0.006-0.0060.0000.0000.0000.000
180A186ASN00.016-0.00215.080-0.028-0.0280.0000.0000.0000.000
181A187LYS10.9640.98215.391-0.083-0.0830.0000.0000.0000.000
182A188PRO00.0170.01911.5430.0540.0540.0000.0000.0000.000
183A189LEU0-0.090-0.03513.474-0.078-0.0780.0000.0000.0000.000
184A190GLY0-0.010-0.00313.097-0.053-0.0530.0000.0000.0000.000
185A191ALA0-0.066-0.0219.248-0.061-0.0610.0000.0000.0000.000
186A192TRP00.005-0.0216.7850.0660.0660.0000.0000.0000.000
187A193GLU-1-0.949-0.9724.558-4.365-4.194-0.001-0.014-0.1550.000
188A194GLU-1-1.013-1.0047.462-0.409-0.4090.0000.0000.0000.000
189A195ASP-1-0.925-0.9506.001-1.116-1.1160.0000.0000.0000.000
190A196TYR0-0.067-0.0488.1880.2720.2720.0000.0000.0000.000
191A197PRO00.0060.0149.592-0.055-0.0550.0000.0000.0000.000
192A198LEU00.0290.01111.431-0.015-0.0150.0000.0000.0000.000
193A199TYR0-0.036-0.01514.7570.0490.0490.0000.0000.0000.000
194A200HIS00.0040.03512.6900.0630.0630.0000.0000.0000.000
195A201HIS00.0150.01517.3160.0010.0010.0000.0000.0000.000
196A202LEU00.0300.03214.7130.0330.0330.0000.0000.0000.000
197A203THR0-0.062-0.02718.678-0.038-0.0380.0000.0000.0000.000
198A204VAL00.0360.01020.4680.0340.0340.0000.0000.0000.000
199A205TRP0-0.018-0.00522.857-0.026-0.0260.0000.0000.0000.000
200A206THR00.000-0.03824.7170.0190.0190.0000.0000.0000.000
201A207SER0-0.051-0.00427.172-0.019-0.0190.0000.0000.0000.000
202A208PHE00.009-0.00629.3880.0100.0100.0000.0000.0000.000
203A209GLY00.0220.00732.100-0.007-0.0070.0000.0000.0000.000
204A210LYS10.8700.94834.143-0.124-0.1240.0000.0000.0000.000
205A211ASP-1-0.775-0.89134.5550.1440.1440.0000.0000.0000.000
206A212PRO0-0.087-0.03636.108-0.005-0.0050.0000.0000.0000.000
207A213ASP-1-0.888-0.93938.1010.1140.1140.0000.0000.0000.000
208A214ASP-1-0.853-0.88037.3560.1170.1170.0000.0000.0000.000
209A215ASP-1-0.921-0.96239.6740.0950.0950.0000.0000.0000.000
210A216GLU-1-1.012-1.00841.4900.0870.0870.0000.0000.0000.000
211A217THR0-0.080-0.06437.4980.0000.0000.0000.0000.0000.000
212A218ASP-1-0.771-0.85838.6650.1110.1110.0000.0000.0000.000
213A219HIS0-0.008-0.01234.0560.0110.0110.0000.0000.0000.000
214A220LEU0-0.051-0.01129.828-0.004-0.0040.0000.0000.0000.000
215A221THR00.0110.01130.0960.0080.0080.0000.0000.0000.000
216A222ILE0-0.006-0.01324.172-0.009-0.0090.0000.0000.0000.000
217A223VAL0-0.009-0.00325.1850.0120.0120.0000.0000.0000.000
218A224GLU-1-0.816-0.88322.1360.2680.2680.0000.0000.0000.000
219A225VAL0-0.013-0.00120.1540.0240.0240.0000.0000.0000.000
220A226ILE00.0110.00817.073-0.025-0.0250.0000.0000.0000.000
221A227LYS10.9100.95316.282-0.253-0.2530.0000.0000.0000.000
222A228ALA00.0400.03413.594-0.044-0.0440.0000.0000.0000.000
223A229VAL0-0.064-0.03715.578-0.001-0.0010.0000.0000.0000.000
224A230ASP-1-0.736-0.85016.5580.1340.1340.0000.0000.0000.000
225A231LEU00.0210.01517.838-0.008-0.0080.0000.0000.0000.000
226A232GLU-1-0.887-0.93219.7540.0210.0210.0000.0000.0000.000
227A233THR0-0.131-0.08220.708-0.006-0.0060.0000.0000.0000.000
228A234TYR0-0.061-0.04823.3600.0010.0010.0000.0000.0000.000
229A235ARG10.8470.93823.611-0.047-0.0470.0000.0000.0000.000