FMODB

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

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: 3JVGL

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 OptAll
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 -2950618.301889
FMO2-HF: Nuclear repulsion 2859737.468952
FMO2-HF: Total energy -90880.832937
FMO2-MP2: Total energy -91147.049202


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.
-27.33-17.5714.203-6.633-7.331-0.033
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 : -0.025
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].
3A7GLY00.0770.0433.866-0.5211.606-0.006-1.004-1.1190.003
4A8ALA0-0.030-0.0283.263-1.071-0.5070.050-0.162-0.4520.000
5A9LYS10.8530.9072.137-3.366-1.3141.056-1.524-1.5850.011
6A10LEU0-0.074-0.0186.978-0.240-0.2400.0000.0000.0000.000
7A11PHE00.010-0.0038.457-0.170-0.1700.0000.0000.0000.000
8A12GLU-1-0.946-0.9727.5381.7361.7360.0000.0000.0000.000
9A13LYS10.8930.93510.872-0.582-0.5820.0000.0000.0000.000
10A14GLU-1-0.814-0.86614.4140.4070.4070.0000.0000.0000.000
11A15ILE0-0.041-0.00213.620-0.036-0.0360.0000.0000.0000.000
12A16PRO00.0330.00217.4200.0040.0040.0000.0000.0000.000
13A17TYR0-0.029-0.00918.6520.0320.0320.0000.0000.0000.000
14A18ILE00.0170.01420.518-0.025-0.0250.0000.0000.0000.000
15A19THR0-0.029-0.01421.7700.0250.0250.0000.0000.0000.000
16A20GLU-1-0.869-0.90624.2020.0770.0770.0000.0000.0000.000
17A21LEU00.0450.01525.9240.0050.0050.0000.0000.0000.000
18A22GLU-1-0.838-0.90128.4320.0720.0720.0000.0000.0000.000
19A23GLY00.022-0.00130.9020.0020.0020.0000.0000.0000.000
20A24ASP-1-0.834-0.89833.3330.0320.0320.0000.0000.0000.000
21A25VAL00.0370.02435.7620.0020.0020.0000.0000.0000.000
22A26GLU-1-0.809-0.90638.0790.0420.0420.0000.0000.0000.000
23A27GLY0-0.039-0.01040.209-0.003-0.0030.0000.0000.0000.000
24A28MET0-0.026-0.01540.558-0.002-0.0020.0000.0000.0000.000
25A29LYS10.8480.90837.737-0.030-0.0300.0000.0000.0000.000
26A30PHE00.0110.00332.9260.0000.0000.0000.0000.0000.000
27A31ILE00.004-0.00332.020-0.001-0.0010.0000.0000.0000.000
28A32ILE0-0.0330.00230.4010.0010.0010.0000.0000.0000.000
29A33LYS10.7990.88728.960-0.081-0.0810.0000.0000.0000.000
30A34GLY00.025-0.00127.515-0.002-0.0020.0000.0000.0000.000
31A35GLU-1-0.935-0.95325.5960.1470.1470.0000.0000.0000.000
32A36GLY00.0470.01824.442-0.003-0.0030.0000.0000.0000.000
33A37THR0-0.068-0.05820.623-0.011-0.0110.0000.0000.0000.000
34A38GLY00.0400.01517.909-0.015-0.0150.0000.0000.0000.000
35A39ASP-1-0.741-0.82715.6650.6600.6600.0000.0000.0000.000
36A40ALA00.0150.01611.421-0.015-0.0150.0000.0000.0000.000
37A41THR0-0.094-0.06612.6400.0460.0460.0000.0000.0000.000
38A42THR0-0.068-0.06014.207-0.036-0.0360.0000.0000.0000.000
39A43GLY0-0.033-0.01015.944-0.023-0.0230.0000.0000.0000.000
40A44THR0-0.054-0.03016.866-0.059-0.0590.0000.0000.0000.000
41A45ILE00.0080.00218.5580.0320.0320.0000.0000.0000.000
42A46LYS10.8270.89721.080-0.374-0.3740.0000.0000.0000.000
43A47ALA00.0130.01224.1720.0050.0050.0000.0000.0000.000
44A48LYS10.8070.87826.166-0.127-0.1270.0000.0000.0000.000
45A49TYR0-0.008-0.02424.0120.0040.0040.0000.0000.0000.000
46A50ILE00.0710.02530.387-0.004-0.0040.0000.0000.0000.000
47A51CYS0-0.073-0.02633.333-0.001-0.0010.0000.0000.0000.000
48A52THR0-0.032-0.02933.950-0.006-0.0060.0000.0000.0000.000
49A53THR0-0.009-0.00736.419-0.004-0.0040.0000.0000.0000.000
50A54GLY00.0050.00539.063-0.006-0.0060.0000.0000.0000.000
51A55ASP-1-0.871-0.93139.5100.0700.0700.0000.0000.0000.000
52A56LEU0-0.037-0.01434.441-0.002-0.0020.0000.0000.0000.000
53A57PRO0-0.047-0.02137.8710.0000.0000.0000.0000.0000.000
54A58VAL00.004-0.02335.107-0.003-0.0030.0000.0000.0000.000
55A59PRO00.000-0.00136.5210.0040.0040.0000.0000.0000.000
56A60TRP00.045-0.00431.7020.0110.0110.0000.0000.0000.000
57A61ALA0-0.0170.00132.1330.0100.0100.0000.0000.0000.000
58A62THR0-0.043-0.02831.3680.0100.0100.0000.0000.0000.000
59A63ILE00.0440.03230.0840.0030.0030.0000.0000.0000.000
60A64LEU00.0430.03426.5800.0080.0080.0000.0000.0000.000
61A65SER0-0.095-0.06724.8880.0160.0160.0000.0000.0000.000
62A66SER0-0.0090.00524.1620.0070.0070.0000.0000.0000.000
63A67LEU00.0210.01824.1180.0100.0100.0000.0000.0000.000
64A68GYS1-0.045-0.02920.677-0.226-0.2260.0000.0000.0000.000
65A71VAL-10.0780.03816.9750.3080.3080.0000.0000.0000.000
66A72PHE0-0.050-0.02515.1810.0410.0410.0000.0000.0000.000
67A73CYS0-0.0100.00711.5940.0490.0490.0000.0000.0000.000
68A74PHE00.0350.01711.7150.1760.1760.0000.0000.0000.000
69A75ALA0-0.0130.00213.276-0.027-0.0270.0000.0000.0000.000
70A76LYS10.9100.94612.237-0.528-0.5280.0000.0000.0000.000
71A77TYR0-0.046-0.0509.552-0.104-0.1040.0000.0000.0000.000
72A78PRO0-0.061-0.01110.9380.0810.0810.0000.0000.0000.000
73A79ARG10.9760.9568.150-1.038-1.0380.0000.0000.0000.000
74A80HIS0-0.046-0.0278.3050.1770.1770.0000.0000.0000.000
75A81ILE0-0.032-0.00410.172-0.196-0.1960.0000.0000.0000.000
76A82ALA00.0610.0416.6270.2760.2760.0000.0000.0000.000
77A83ASP-1-0.771-0.8846.1741.5591.5590.0000.0000.0000.000
78A84PHE00.0230.0016.4850.6610.6610.0000.0000.0000.000
79A85PHE00.0070.0168.4550.0060.0060.0000.0000.0000.000
80A86LYS10.8190.8936.647-1.747-1.7470.0000.0000.0000.000
81A87SER0-0.026-0.0123.307-1.150-0.4550.026-0.330-0.3900.002
82A88THR0-0.013-0.0144.788-1.233-1.196-0.001-0.013-0.0230.000
83A89GLN0-0.0820.0007.169-0.578-0.5780.0000.0000.0000.000
84A90PRO00.001-0.0217.1770.0320.0320.0000.0000.0000.000
85A91ASP-1-0.841-0.92010.611-0.359-0.3590.0000.0000.0000.000
86A92GLY00.0390.01711.058-0.014-0.0140.0000.0000.0000.000
87A93TYR0-0.029-0.02011.708-0.026-0.0260.0000.0000.0000.000
88A94SER0-0.0020.00614.170-0.004-0.0040.0000.0000.0000.000
89A95GLN00.015-0.01016.9930.0700.0700.0000.0000.0000.000
90A96ASP-1-0.805-0.89819.3120.0630.0630.0000.0000.0000.000
91A97ARG10.7930.86822.250-0.171-0.1710.0000.0000.0000.000
92A98ILE00.0010.02425.042-0.006-0.0060.0000.0000.0000.000
93A99ILE0-0.015-0.01126.8300.0090.0090.0000.0000.0000.000
94A100SER00.0100.00330.043-0.010-0.0100.0000.0000.0000.000
95A101PHE0-0.023-0.01232.3050.0080.0080.0000.0000.0000.000
96A102ASP-1-0.778-0.85835.8240.0720.0720.0000.0000.0000.000
97A103ASN0-0.033-0.02238.185-0.003-0.0030.0000.0000.0000.000
98A104ASP-1-0.779-0.90239.2630.0570.0570.0000.0000.0000.000
99A105GLY00.0400.03738.696-0.003-0.0030.0000.0000.0000.000
100A106GLN0-0.045-0.02833.4890.0040.0040.0000.0000.0000.000
101A107TYR00.012-0.01130.861-0.008-0.0080.0000.0000.0000.000
102A108ASP-1-0.808-0.88328.8870.0540.0540.0000.0000.0000.000
103A109VAL0-0.014-0.01525.3330.0010.0010.0000.0000.0000.000
104A110LYS10.8360.91824.357-0.037-0.0370.0000.0000.0000.000
105A111ALA00.0190.00621.2030.0000.0000.0000.0000.0000.000
106A112LYS10.8260.92318.616-0.100-0.1000.0000.0000.0000.000
107A113VAL00.0120.01215.359-0.005-0.0050.0000.0000.0000.000
108A114THR00.0480.01314.2550.0400.0400.0000.0000.0000.000
109A115TYR00.0110.02612.400-0.035-0.0350.0000.0000.0000.000
110A116GLU-1-0.784-0.87414.3400.0250.0250.0000.0000.0000.000
111A117ASN0-0.040-0.03817.2560.0000.0000.0000.0000.0000.000
112A118GLY00.0310.02516.323-0.011-0.0110.0000.0000.0000.000
113A119THR0-0.042-0.00817.2640.0360.0360.0000.0000.0000.000
114A120LEU0-0.0040.00213.859-0.007-0.0070.0000.0000.0000.000
115A121TYR00.017-0.00217.030-0.032-0.0320.0000.0000.0000.000
116A122ASN00.0010.00018.5630.0000.0000.0000.0000.0000.000
117A123ARG10.7920.86420.398-0.129-0.1290.0000.0000.0000.000
118A124VAL0-0.014-0.01522.606-0.004-0.0040.0000.0000.0000.000
119A125THR0-0.037-0.00924.853-0.014-0.0140.0000.0000.0000.000
120A126VAL00.023-0.00527.9300.0060.0060.0000.0000.0000.000
121A127LYS10.8420.91830.597-0.044-0.0440.0000.0000.0000.000
122A128GLY0-0.018-0.01633.6010.0010.0010.0000.0000.0000.000
123A129THR0-0.052-0.03335.778-0.007-0.0070.0000.0000.0000.000
124A130GLY00.0200.01438.1700.0020.0020.0000.0000.0000.000
125A131PHE0-0.049-0.02035.4470.0010.0010.0000.0000.0000.000
126A132LYS10.8510.92541.359-0.049-0.0490.0000.0000.0000.000
127A133SER00.0390.00944.8600.0020.0020.0000.0000.0000.000
128A134ASN0-0.0080.00247.4820.0010.0010.0000.0000.0000.000
129A135GLY00.0320.02443.5840.0010.0010.0000.0000.0000.000
130A136ASN0-0.007-0.02140.746-0.002-0.0020.0000.0000.0000.000
131A137ILE0-0.0060.00936.9670.0030.0030.0000.0000.0000.000
132A138LEU00.0360.00940.0500.0010.0010.0000.0000.0000.000
133A139GLY0-0.034-0.00242.907-0.002-0.0020.0000.0000.0000.000
134A140MET0-0.030-0.00639.9660.0010.0010.0000.0000.0000.000
135A141ARG10.8440.91242.690-0.059-0.0590.0000.0000.0000.000
136A142VAL0-0.046-0.01936.2940.0010.0010.0000.0000.0000.000
137A143LEU00.0090.00039.0510.0000.0000.0000.0000.0000.000
138A144TYR0-0.016-0.02235.3410.0030.0030.0000.0000.0000.000
139A145HIS0-0.029-0.03433.7990.0050.0050.0000.0000.0000.000
140A146SER00.0430.01428.775-0.004-0.0040.0000.0000.0000.000
141A147PRO00.0100.01930.3700.0110.0110.0000.0000.0000.000
142A148PRO00.0010.00027.5580.0110.0110.0000.0000.0000.000
143A149HIS0-0.0150.00225.980-0.029-0.0290.0000.0000.0000.000
144A150ALA00.0020.00123.3170.0230.0230.0000.0000.0000.000
145A151VAL0-0.030-0.01519.852-0.025-0.0250.0000.0000.0000.000
146A152TYR0-0.0070.00420.2130.0230.0230.0000.0000.0000.000
147A153ILE00.0430.01614.000-0.012-0.0120.0000.0000.0000.000
148A154LEU00.014-0.00516.900-0.010-0.0100.0000.0000.0000.000
149A155PRO00.0180.01814.3620.0000.0000.0000.0000.0000.000
150A156ASP-1-0.808-0.91415.963-0.051-0.0510.0000.0000.0000.000
151A157ARG10.8960.91713.2010.4750.4750.0000.0000.0000.000
152A158LYS10.8680.95017.2260.0480.0480.0000.0000.0000.000
153A159ASN0-0.038-0.03020.414-0.017-0.0170.0000.0000.0000.000
154A160GLY0-0.0170.01316.7520.0030.0030.0000.0000.0000.000
155A161GLY00.018-0.01114.289-0.009-0.0090.0000.0000.0000.000
156A162MET0-0.0400.00812.763-0.036-0.0360.0000.0000.0000.000
157A163LYS10.9100.95115.781-0.052-0.0520.0000.0000.0000.000
158A164ILE0-0.024-0.01416.0690.0250.0250.0000.0000.0000.000
159A165GLU-1-0.840-0.90720.1580.0710.0710.0000.0000.0000.000
160A166TYR0-0.019-0.02022.4050.0220.0220.0000.0000.0000.000
161A167ASN00.0070.00825.523-0.025-0.0250.0000.0000.0000.000
162A168LYS10.8440.93426.876-0.172-0.1720.0000.0000.0000.000
163A169ALA00.0270.00730.221-0.013-0.0130.0000.0000.0000.000
164A170PHE00.0120.00630.4120.0090.0090.0000.0000.0000.000
165A171ASP-1-0.791-0.87735.3670.1070.1070.0000.0000.0000.000
166A172VAL0-0.008-0.00938.9230.0010.0010.0000.0000.0000.000
167A173MET0-0.010-0.00341.981-0.001-0.0010.0000.0000.0000.000
168A174GLY0-0.020-0.00345.283-0.003-0.0030.0000.0000.0000.000
169A175GLY0-0.014-0.00344.835-0.002-0.0020.0000.0000.0000.000
170A176GLY0-0.0100.00142.818-0.002-0.0020.0000.0000.0000.000
171A177HIS0-0.044-0.04837.7450.0000.0000.0000.0000.0000.000
172A178GLN0-0.056-0.01836.551-0.009-0.0090.0000.0000.0000.000
173A179MET0-0.027-0.00533.0310.0090.0090.0000.0000.0000.000
174A180ALA00.0440.01931.605-0.007-0.0070.0000.0000.0000.000
175A181ARG10.8020.86330.303-0.075-0.0750.0000.0000.0000.000
176A182HIS0-0.0140.00525.4910.0010.0010.0000.0000.0000.000
177A183ALA00.0360.02825.3930.0080.0080.0000.0000.0000.000
178A184GLN00.010-0.01919.6910.0210.0210.0000.0000.0000.000
179A185PHE0-0.045-0.01718.144-0.005-0.0050.0000.0000.0000.000
180A186ASN00.0350.02215.246-0.025-0.0250.0000.0000.0000.000
181A187LYS10.8570.91714.9010.0770.0770.0000.0000.0000.000
182A188PRO00.0390.01910.9910.0660.0660.0000.0000.0000.000
183A189LEU0-0.079-0.02712.883-0.042-0.0420.0000.0000.0000.000
184A190GLY0-0.006-0.00612.787-0.020-0.0200.0000.0000.0000.000
185A191ALA0-0.067-0.0298.684-0.036-0.0360.0000.0000.0000.000
186A192TRP0-0.006-0.0176.1420.0420.0420.0000.0000.0000.000
187A193GLU-1-0.909-0.9592.238-20.259-15.9753.078-3.600-3.762-0.049
188A194GLU-1-0.827-0.8816.674-0.414-0.4140.0000.0000.0000.000
189A195ASP-1-0.891-0.9375.426-0.714-0.7140.0000.0000.0000.000
190A196TYR0-0.095-0.0767.6310.4380.4380.0000.0000.0000.000
191A197PRO0-0.0210.0029.584-0.016-0.0160.0000.0000.0000.000
192A198LEU00.0350.01011.375-0.044-0.0440.0000.0000.0000.000
193A199TYR0-0.049-0.01814.7420.0530.0530.0000.0000.0000.000
194A200HIS00.0130.01912.5850.0860.0860.0000.0000.0000.000
195A201HIS00.0200.01617.356-0.013-0.0130.0000.0000.0000.000
196A202LEU00.0120.02714.7010.0570.0570.0000.0000.0000.000
197A203THR0-0.036-0.02418.646-0.052-0.0520.0000.0000.0000.000
198A204VAL0-0.004-0.00920.5250.0400.0400.0000.0000.0000.000
199A205TRP0-0.018-0.00622.911-0.026-0.0260.0000.0000.0000.000
200A206THR0-0.002-0.03624.8410.0190.0190.0000.0000.0000.000
201A207SER0-0.0170.00627.350-0.017-0.0170.0000.0000.0000.000
202A208PHE0-0.012-0.02229.5160.0070.0070.0000.0000.0000.000
203A209GLY00.0190.01832.220-0.002-0.0020.0000.0000.0000.000
204A210LYS10.8470.94034.495-0.106-0.1060.0000.0000.0000.000
205A211ASP-1-0.792-0.89834.9390.1290.1290.0000.0000.0000.000
206A212PRO0-0.087-0.04136.383-0.005-0.0050.0000.0000.0000.000
207A213ASP-1-0.897-0.94238.1990.0980.0980.0000.0000.0000.000
208A214ASP-1-0.839-0.89137.6300.0920.0920.0000.0000.0000.000
209A215ASP-1-0.925-0.96240.1900.0790.0790.0000.0000.0000.000
210A216GLU-1-1.010-0.99641.9340.0620.0620.0000.0000.0000.000
211A217THR0-0.056-0.04637.921-0.001-0.0010.0000.0000.0000.000
212A218ASP-1-0.775-0.87338.8480.0970.0970.0000.0000.0000.000
213A219HIS0-0.023-0.02034.5050.0090.0090.0000.0000.0000.000
214A220LEU0-0.0350.01030.196-0.002-0.0020.0000.0000.0000.000
215A221THR00.0160.00930.4920.0050.0050.0000.0000.0000.000
216A222ILE0-0.037-0.02924.672-0.004-0.0040.0000.0000.0000.000
217A223VAL00.0180.01925.4040.0100.0100.0000.0000.0000.000
218A224GLU-1-0.824-0.89122.2380.2640.2640.0000.0000.0000.000
219A225VAL0-0.005-0.00420.3530.0250.0250.0000.0000.0000.000
220A226ILE00.0070.00817.138-0.030-0.0300.0000.0000.0000.000
221A227LYS10.9520.96816.580-0.298-0.2980.0000.0000.0000.000
222A228ALA00.0450.03013.882-0.056-0.0560.0000.0000.0000.000
223A229VAL0-0.055-0.03215.8570.0070.0070.0000.0000.0000.000
224A230ASP-1-0.775-0.88016.9630.3130.3130.0000.0000.0000.000
225A231LEU00.0190.02618.114-0.019-0.0190.0000.0000.0000.000
226A232GLU-1-0.777-0.84220.0740.1430.1430.0000.0000.0000.000
227A233THR0-0.126-0.08020.650-0.011-0.0110.0000.0000.0000.000
228A234TYR0-0.056-0.03922.874-0.002-0.0020.0000.0000.0000.000
229A235ARG10.7560.85123.867-0.169-0.1690.0000.0000.0000.000