Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 494NN

Calculation Name: 2QHT-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2QHT

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SLQ3

Base Structure: X-ray

Registration Date: 2023-09-20

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

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHSide
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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2470172.755832
FMO2-HF: Nuclear repulsion 2390094.919164
FMO2-HF: Total energy -80077.836668
FMO2-MP2: Total energy -80316.063759


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-12.849-9.9828.135-4.124-6.8770.014
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.023 / q_NPA : -0.002
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].
3A3PHE0-0.043-0.0203.817-1.1130.910-0.031-1.086-0.906-0.001
4A4LEU00.0190.0226.6320.1140.1140.0000.0000.0000.000
5A5VAL00.0040.00310.046-0.064-0.0640.0000.0000.0000.000
6A6GLU-1-0.756-0.84113.204-0.006-0.0060.0000.0000.0000.000
7A7ASP-1-0.791-0.88516.486-0.119-0.1190.0000.0000.0000.000
8A8LEU0-0.022-0.02219.4620.0170.0170.0000.0000.0000.000
9A9GLY00.0080.01622.2630.0100.0100.0000.0000.0000.000
10A10LEU0-0.029-0.01825.032-0.009-0.0090.0000.0000.0000.000
11A11VAL00.0410.01524.3500.0060.0060.0000.0000.0000.000
12A12PRO00.0640.02727.732-0.008-0.0080.0000.0000.0000.000
13A13TYR00.0140.01125.633-0.004-0.0040.0000.0000.0000.000
14A14GLY00.0390.01827.453-0.005-0.0050.0000.0000.0000.000
15A15GLU-1-0.886-0.95827.775-0.054-0.0540.0000.0000.0000.000
16A16ALA00.0440.02223.965-0.002-0.0020.0000.0000.0000.000
17A17TRP0-0.022-0.01023.060-0.009-0.0090.0000.0000.0000.000
18A18ALA00.009-0.00823.551-0.006-0.0060.0000.0000.0000.000
19A19TYR0-0.071-0.05918.2800.0050.0050.0000.0000.0000.000
20A20GLN00.0590.02419.143-0.019-0.0190.0000.0000.0000.000
21A21LYS10.8230.93118.8510.1130.1130.0000.0000.0000.000
22A22ARG10.9210.96120.1570.0410.0410.0000.0000.0000.000
23A23VAL00.0770.04114.6700.0060.0060.0000.0000.0000.000
24A24HIS0-0.055-0.03615.2800.0170.0170.0000.0000.0000.000
25A25ARG10.9330.96415.8890.0750.0750.0000.0000.0000.000
26A26GLU-1-0.871-0.92014.935-0.017-0.0170.0000.0000.0000.000
27A27VAL0-0.026-0.00610.1240.0140.0140.0000.0000.0000.000
28A28VAL0-0.056-0.02912.176-0.011-0.0110.0000.0000.0000.000
29A29ALA0-0.073-0.03114.702-0.006-0.0060.0000.0000.0000.000
30A30GLY0-0.0120.00511.1430.0060.0060.0000.0000.0000.000
31A31ASN0-0.066-0.03811.6940.0760.0760.0000.0000.0000.000
32A32ARG10.7940.86611.3050.0610.0610.0000.0000.0000.000
33A33PRO00.0100.0186.282-0.016-0.0160.0000.0000.0000.000
34A34PRO00.0330.0134.874-0.106-0.1060.0000.0000.0000.000
35A35THR00.0140.0107.9320.0170.0170.0000.0000.0000.000
36A36LEU0-0.058-0.02310.923-0.028-0.0280.0000.0000.0000.000
37A37LEU0-0.0090.00813.0520.0380.0380.0000.0000.0000.000
38A38LEU00.000-0.00416.531-0.019-0.0190.0000.0000.0000.000
39A39LEU0-0.0110.00219.0560.0190.0190.0000.0000.0000.000
40A40GLU-1-0.839-0.92322.726-0.087-0.0870.0000.0000.0000.000
41A41HIS0-0.0050.01325.105-0.008-0.0080.0000.0000.0000.000
42A42PRO00.0590.02528.7030.0010.0010.0000.0000.0000.000
43A43ARG10.7620.85132.0500.0490.0490.0000.0000.0000.000
44A44VAL0-0.028-0.00130.0160.0020.0020.0000.0000.0000.000
45A45ILE00.0100.01632.645-0.005-0.0050.0000.0000.0000.000
46A46THR0-0.030-0.00528.615-0.003-0.0030.0000.0000.0000.000
47A47LEU00.0170.00131.566-0.003-0.0030.0000.0000.0000.000
48A48GLY00.0130.01129.5680.0000.0000.0000.0000.0000.000
49A49ARG10.8870.91224.1190.1590.1590.0000.0000.0000.000
50A50LYS10.8640.92830.7650.1110.1110.0000.0000.0000.000
51A51ALA00.0030.01933.2840.0030.0030.0000.0000.0000.000
52A52THR0-0.017-0.03935.1260.0010.0010.0000.0000.0000.000
53A53GLY00.0390.00638.831-0.001-0.0010.0000.0000.0000.000
54A54GLU-1-0.875-0.90641.629-0.061-0.0610.0000.0000.0000.000
55A55ASN0-0.062-0.04536.733-0.001-0.0010.0000.0000.0000.000
56A56LEU0-0.037-0.00937.842-0.002-0.0020.0000.0000.0000.000
57A57LEU0-0.0030.01840.9670.0020.0020.0000.0000.0000.000
58A58PHE00.0050.00243.6900.0030.0030.0000.0000.0000.000
59A59PRO00.0620.01644.188-0.002-0.0020.0000.0000.0000.000
60A60GLU-1-0.737-0.87239.736-0.058-0.0580.0000.0000.0000.000
61A61SER0-0.040-0.02642.633-0.001-0.0010.0000.0000.0000.000
62A62TRP00.0820.04942.014-0.001-0.0010.0000.0000.0000.000
63A63TYR00.003-0.01639.7710.0010.0010.0000.0000.0000.000
64A64ARG10.8110.88638.2370.0540.0540.0000.0000.0000.000
65A65GLU-1-0.954-0.96241.957-0.035-0.0350.0000.0000.0000.000
66A66ASN0-0.053-0.02843.6380.0030.0030.0000.0000.0000.000
67A67GLY00.0150.01840.815-0.001-0.0010.0000.0000.0000.000
68A68PHE0-0.048-0.02736.379-0.003-0.0030.0000.0000.0000.000
69A69GLU-1-0.847-0.89933.276-0.060-0.0600.0000.0000.0000.000
70A70LEU0-0.024-0.02935.109-0.003-0.0030.0000.0000.0000.000
71A71TYR0-0.075-0.06431.4120.0020.0020.0000.0000.0000.000
72A72TRP0-0.0030.00532.717-0.006-0.0060.0000.0000.0000.000
73A73VAL0-0.038-0.02327.286-0.002-0.0020.0000.0000.0000.000
74A74GLU-1-0.857-0.93725.823-0.120-0.1200.0000.0000.0000.000
75A75ARG10.7730.89424.1050.1140.1140.0000.0000.0000.000
76A76GLY0-0.037-0.02024.4430.0110.0110.0000.0000.0000.000
77A77GLY00.0280.00926.244-0.003-0.0030.0000.0000.0000.000
78A78ASP-1-0.782-0.88929.047-0.095-0.0950.0000.0000.0000.000
79A79VAL00.0660.05531.360-0.004-0.0040.0000.0000.0000.000
80A80THR0-0.089-0.05127.925-0.003-0.0030.0000.0000.0000.000
81A81TYR00.046-0.01031.3160.0030.0030.0000.0000.0000.000
82A82HIS10.8050.90025.9190.1140.1140.0000.0000.0000.000
83A83GLY00.0820.04530.0400.0060.0060.0000.0000.0000.000
84A84PRO00.0250.01130.203-0.006-0.0060.0000.0000.0000.000
85A85GLY00.0310.02430.0050.0020.0020.0000.0000.0000.000
86A86GLN0-0.015-0.00726.572-0.009-0.0090.0000.0000.0000.000
87A87LEU00.0000.00120.7430.0010.0010.0000.0000.0000.000
88A88VAL0-0.026-0.01622.085-0.013-0.0130.0000.0000.0000.000
89A89GLY00.0380.01618.4430.0010.0010.0000.0000.0000.000
90A90TYR0-0.069-0.07317.500-0.001-0.0010.0000.0000.0000.000
91A91PRO00.0140.02012.8350.0020.0020.0000.0000.0000.000
92A92ILE0-0.0200.01713.0070.0060.0060.0000.0000.0000.000
93A93PHE00.040-0.0019.188-0.029-0.0290.0000.0000.0000.000
94A94PRO00.0350.0237.6920.0630.0630.0000.0000.0000.000
95A95VAL0-0.0060.0049.817-0.105-0.1050.0000.0000.0000.000
96A96GLY00.0020.00712.0820.0080.0080.0000.0000.0000.000
97A97ARG10.9640.94914.3660.2780.2780.0000.0000.0000.000
98A98GLU-1-0.856-0.90414.808-0.400-0.4000.0000.0000.0000.000
99A99VAL00.0440.01615.811-0.035-0.0350.0000.0000.0000.000
100A100ARG10.9670.97017.9290.1780.1780.0000.0000.0000.000
101A101ARG10.8700.93011.6330.6350.6350.0000.0000.0000.000
102A102PHE00.0640.03612.0130.0040.0040.0000.0000.0000.000
103A103LEU0-0.016-0.01515.113-0.004-0.0040.0000.0000.0000.000
104A104ARG10.9800.99918.2310.2960.2960.0000.0000.0000.000
105A105GLN0-0.0040.00810.5760.0550.0550.0000.0000.0000.000
106A106ILE0-0.0020.00615.4240.0030.0030.0000.0000.0000.000
107A107GLU-1-0.922-0.98316.685-0.214-0.2140.0000.0000.0000.000
108A108GLU-1-0.897-0.95016.560-0.242-0.2420.0000.0000.0000.000
109A109ALA00.0050.00814.8870.0210.0210.0000.0000.0000.000
110A110ILE00.001-0.02216.7800.0380.0380.0000.0000.0000.000
111A111VAL0-0.015-0.00720.3090.0280.0280.0000.0000.0000.000
112A112ARG10.8370.90815.7330.2760.2760.0000.0000.0000.000
113A113VAL0-0.0110.00318.8140.0240.0240.0000.0000.0000.000
114A114ALA0-0.038-0.02121.1010.0230.0230.0000.0000.0000.000
115A115ALA00.0460.02422.7190.0170.0170.0000.0000.0000.000
116A116GLY00.0120.01423.0210.0150.0150.0000.0000.0000.000
117A117TYR0-0.116-0.09123.8360.0090.0090.0000.0000.0000.000
118A118GLY0-0.0080.00626.9880.0080.0080.0000.0000.0000.000
119A119ILE0-0.056-0.02327.7440.0050.0050.0000.0000.0000.000
120A120SER00.0250.01327.175-0.010-0.0100.0000.0000.0000.000
121A121ALA0-0.024-0.01725.4690.0050.0050.0000.0000.0000.000
122A122TYR0-0.025-0.01925.774-0.005-0.0050.0000.0000.0000.000
123A123PRO00.0660.03023.1010.0070.0070.0000.0000.0000.000
124A124THR0-0.0290.00225.8110.0120.0120.0000.0000.0000.000
125A125PRO00.012-0.01728.080-0.009-0.0090.0000.0000.0000.000
126A126GLY0-0.014-0.00130.010-0.002-0.0020.0000.0000.0000.000
127A127TYR0-0.046-0.00730.3560.0050.0050.0000.0000.0000.000
128A128ALA00.0390.02426.596-0.007-0.0070.0000.0000.0000.000
129A129GLY0-0.031-0.01524.9640.0120.0120.0000.0000.0000.000
130A130VAL00.0130.00822.754-0.001-0.0010.0000.0000.0000.000
131A131TRP0-0.027-0.01326.0380.0140.0140.0000.0000.0000.000
132A132VAL00.0540.02028.966-0.005-0.0050.0000.0000.0000.000
133A133GLY00.0290.01931.2410.0060.0060.0000.0000.0000.000
134A134GLU-1-0.834-0.90433.692-0.069-0.0690.0000.0000.0000.000
135A135ASP-1-0.794-0.90034.188-0.074-0.0740.0000.0000.0000.000
136A136LYS10.8860.94028.5090.1190.1190.0000.0000.0000.000
137A137LEU0-0.0140.00426.6520.0050.0050.0000.0000.0000.000
138A138CYS0-0.0160.00522.323-0.002-0.0020.0000.0000.0000.000
139A139ALA0-0.0140.01325.962-0.002-0.0020.0000.0000.0000.000
140A140ILE00.032-0.00320.562-0.010-0.0100.0000.0000.0000.000
141A141GLY0-0.015-0.00522.4500.0130.0130.0000.0000.0000.000
142A142VAL00.0070.01718.2000.0020.0020.0000.0000.0000.000
143A143ALA0-0.011-0.02020.0740.0210.0210.0000.0000.0000.000
144A144VAL0-0.002-0.00316.769-0.021-0.0210.0000.0000.0000.000
145A145LYS10.8180.89918.3500.1470.1470.0000.0000.0000.000
146A146GLU-1-0.766-0.87417.922-0.144-0.1440.0000.0000.0000.000
147A147GLY0-0.0120.00715.581-0.007-0.0070.0000.0000.0000.000
148A148VAL00.0260.02012.578-0.062-0.0620.0000.0000.0000.000
149A149SER0-0.031-0.03313.8370.0260.0260.0000.0000.0000.000
150A150PHE00.0470.00015.6370.0180.0180.0000.0000.0000.000
151A151HIS0-0.0120.00017.957-0.006-0.0060.0000.0000.0000.000
152A152GLY00.007-0.00718.453-0.024-0.0240.0000.0000.0000.000
153A153PHE0-0.015-0.00316.3060.0090.0090.0000.0000.0000.000
154A154ALA00.0040.00121.3110.0060.0060.0000.0000.0000.000
155A155LEU00.0520.01722.3930.0050.0050.0000.0000.0000.000
156A156ASN00.0020.01524.8070.0090.0090.0000.0000.0000.000
157A157VAL00.0220.01525.623-0.001-0.0010.0000.0000.0000.000
158A158ASN0-0.009-0.03128.6250.0070.0070.0000.0000.0000.000
159A159THR0-0.045-0.02330.2830.0030.0030.0000.0000.0000.000
160A160ASP-1-0.811-0.88932.622-0.053-0.0530.0000.0000.0000.000
161A161LEU0-0.051-0.04533.027-0.002-0.0020.0000.0000.0000.000
162A162ASN00.0220.00736.297-0.001-0.0010.0000.0000.0000.000
163A163ASP-1-0.721-0.79536.507-0.057-0.0570.0000.0000.0000.000
164A164PHE0-0.056-0.03930.814-0.003-0.0030.0000.0000.0000.000
165A165THR0-0.045-0.02436.920-0.001-0.0010.0000.0000.0000.000
166A166VAL0-0.0130.00939.3730.0010.0010.0000.0000.0000.000
167A167ILE0-0.0380.00534.3090.0000.0000.0000.0000.0000.000
168A168VAL00.0200.00538.652-0.001-0.0010.0000.0000.0000.000
169A169PRO00.0260.03034.463-0.001-0.0010.0000.0000.0000.000
170A170CYS00.0000.00336.0030.0050.0050.0000.0000.0000.000
171A171GLY0-0.013-0.00535.460-0.006-0.0060.0000.0000.0000.000
172A172LEU0-0.026-0.02334.5310.0030.0030.0000.0000.0000.000
173A173LYS10.8410.91234.1110.0730.0730.0000.0000.0000.000
174A174GLY00.0180.01334.5930.0040.0040.0000.0000.0000.000
175A175LYS10.8060.87536.3170.0620.0620.0000.0000.0000.000
176A176GLY00.0660.04137.0040.0030.0030.0000.0000.0000.000
177A177VAL0-0.0350.00233.149-0.007-0.0070.0000.0000.0000.000
178A178THR00.014-0.00731.6150.0090.0090.0000.0000.0000.000
179A179SER00.0510.01630.505-0.006-0.0060.0000.0000.0000.000
180A180LEU00.0120.00125.5530.0040.0040.0000.0000.0000.000
181A181GLU-1-0.791-0.87230.261-0.053-0.0530.0000.0000.0000.000
182A182LYS10.8030.90133.3700.0750.0750.0000.0000.0000.000
183A183LEU0-0.075-0.04230.7160.0030.0030.0000.0000.0000.000
184A184LEU0-0.034-0.01629.7960.0040.0040.0000.0000.0000.000
185A185GLY00.0030.01734.4320.0050.0050.0000.0000.0000.000
186A186ARG10.9240.96331.4070.0550.0550.0000.0000.0000.000
187A187LYS10.8570.91433.4680.0500.0500.0000.0000.0000.000
188A188VAL0-0.0160.00227.4200.0040.0040.0000.0000.0000.000
189A189PRO00.0310.01727.743-0.003-0.0030.0000.0000.0000.000
190A190MET00.0280.01725.200-0.013-0.0130.0000.0000.0000.000
191A191GLU-1-0.920-0.95623.588-0.053-0.0530.0000.0000.0000.000
192A192GLU-1-0.777-0.86622.458-0.083-0.0830.0000.0000.0000.000
193A193ALA00.0140.00722.092-0.015-0.0150.0000.0000.0000.000
194A194LYS10.8360.89519.8200.0780.0780.0000.0000.0000.000
195A195ALA00.0280.02218.111-0.036-0.0360.0000.0000.0000.000
196A196ARG10.8020.88517.2910.0660.0660.0000.0000.0000.000
197A197VAL00.0060.00316.381-0.033-0.0330.0000.0000.0000.000
198A198VAL0-0.0070.00212.622-0.070-0.0700.0000.0000.0000.000
199A199ALA00.0060.00012.642-0.104-0.1040.0000.0000.0000.000
200A200ALA00.0020.01013.132-0.051-0.0510.0000.0000.0000.000
201A201PHE00.002-0.02211.229-0.034-0.0340.0000.0000.0000.000
202A202ALA0-0.015-0.0018.578-0.174-0.1740.0000.0000.0000.000
203A203GLU-1-0.845-0.9058.537-0.464-0.4640.0000.0000.0000.000
204A204VAL0-0.060-0.02610.619-0.039-0.0390.0000.0000.0000.000
205A205PHE0-0.076-0.0587.4910.0530.0530.0000.0000.0000.000
206A206GLY00.0150.0346.609-0.291-0.2910.0000.0000.0000.000
207A207LEU0-0.100-0.0392.425-1.882-1.3291.417-0.387-1.583-0.006
208A208ARG10.8510.8812.492-9.903-9.6126.749-2.651-4.3880.021
209A209PRO0-0.0110.0075.938-0.138-0.1380.0000.0000.0000.000
210A210VAL00.0190.0048.3430.1580.1580.0000.0000.0000.000