Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 3JL8L

Calculation Name: 1G2Q-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1G2Q

Chain ID: A

ChEMBL ID:

UniProt ID: P49435

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:


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 178
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1821094.237429
FMO2-HF: Nuclear repulsion 1753678.512931
FMO2-HF: Total energy -67415.724497
FMO2-MP2: Total energy -67616.318991


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.
-0.0349999999999994.8122.732-2.454-5.125-0.003
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 : 0.032 / q_NPA : 0.004
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].
3A3ILE00.1050.0422.546-2.1510.4090.610-0.868-2.302-0.001
4A4ALA0-0.0090.0042.081-0.0781.2192.115-1.326-2.086-0.002
5A5SER0-0.039-0.0213.2241.3262.0630.009-0.238-0.5090.000
6A6TYR00.003-0.0035.0270.3360.471-0.001-0.007-0.1260.000
7A7ALA00.0560.0317.3820.2150.2150.0000.0000.0000.000
8A8GLN0-0.068-0.0366.8460.3370.3370.0000.0000.0000.000
9A9GLU-1-0.896-0.9569.0590.1290.1290.0000.0000.0000.000
10A10LEU0-0.017-0.01111.1330.0530.0530.0000.0000.0000.000
11A11LYS10.9640.98212.0780.1420.1420.0000.0000.0000.000
12A12LEU0-0.056-0.02812.9100.0250.0250.0000.0000.0000.000
13A13ALA0-0.031-0.00215.4640.0170.0170.0000.0000.0000.000
14A14LEU0-0.042-0.00416.8460.0060.0060.0000.0000.0000.000
15A15HIS0-0.032-0.00619.3550.0090.0090.0000.0000.0000.000
16A16GLN0-0.013-0.00421.9070.0020.0020.0000.0000.0000.000
17A17TYR0-0.062-0.03524.5270.0050.0050.0000.0000.0000.000
18A18PRO00.014-0.00828.140-0.002-0.0020.0000.0000.0000.000
19A19ASN0-0.0330.00330.1310.0000.0000.0000.0000.0000.000
20A20PHE00.0310.04529.3000.0010.0010.0000.0000.0000.000
21A21PRO0-0.034-0.02629.607-0.001-0.0010.0000.0000.0000.000
22A22SER00.032-0.00232.5650.0010.0010.0000.0000.0000.000
23A23GLU-1-0.952-0.98833.316-0.008-0.0080.0000.0000.0000.000
24A24GLY0-0.007-0.00833.010-0.001-0.0010.0000.0000.0000.000
25A25ILE0-0.048-0.00228.134-0.001-0.0010.0000.0000.0000.000
26A26LEU0-0.025-0.00724.5330.0020.0020.0000.0000.0000.000
27A27PHE0-0.021-0.01425.310-0.003-0.0030.0000.0000.0000.000
28A28GLU-1-0.814-0.92120.631-0.026-0.0260.0000.0000.0000.000
29A29ASP-1-0.874-0.95122.835-0.015-0.0150.0000.0000.0000.000
30A30PHE00.0610.01319.3600.0010.0010.0000.0000.0000.000
31A31LEU0-0.018-0.02021.057-0.001-0.0010.0000.0000.0000.000
32A32PRO0-0.072-0.04120.9980.0030.0030.0000.0000.0000.000
33A33ILE00.0250.02116.6350.0050.0050.0000.0000.0000.000
34A34PHE0-0.007-0.00919.5760.0030.0030.0000.0000.0000.000
35A35ARG10.8920.96922.3120.0030.0030.0000.0000.0000.000
36A36ASN0-0.0040.00719.3710.0060.0060.0000.0000.0000.000
37A37PRO00.0550.02219.882-0.008-0.0080.0000.0000.0000.000
38A38GLY00.0230.01817.808-0.005-0.0050.0000.0000.0000.000
39A39LEU00.000-0.00414.645-0.014-0.0140.0000.0000.0000.000
40A40PHE00.0200.00115.635-0.025-0.0250.0000.0000.0000.000
41A41GLN0-0.012-0.01114.711-0.002-0.0020.0000.0000.0000.000
42A42LYS10.9260.96910.799-0.027-0.0270.0000.0000.0000.000
43A43LEU00.0050.01011.430-0.059-0.0590.0000.0000.0000.000
44A44ILE0-0.037-0.02112.959-0.002-0.0020.0000.0000.0000.000
45A45ASP-1-0.845-0.93410.123-0.074-0.0740.0000.0000.0000.000
46A46ALA0-0.037-0.0198.233-0.035-0.0350.0000.0000.0000.000
47A47PHE0-0.005-0.0149.0720.0650.0650.0000.0000.0000.000
48A48LYS10.9250.97111.6350.0790.0790.0000.0000.0000.000
49A49LEU00.0260.0184.082-0.193-0.075-0.001-0.015-0.1020.000
50A50HIS10.8210.9098.372-0.023-0.0230.0000.0000.0000.000
51A51LEU0-0.003-0.0139.298-0.007-0.0070.0000.0000.0000.000
52A52GLU-1-0.965-0.97510.294-0.094-0.0940.0000.0000.0000.000
53A53GLU-1-0.989-0.9885.9890.3370.3370.0000.0000.0000.000
54A54ALA0-0.053-0.02710.024-0.054-0.0540.0000.0000.0000.000
55A55PHE0-0.052-0.03912.407-0.020-0.0200.0000.0000.0000.000
56A56PRO0-0.0070.00712.6690.0040.0040.0000.0000.0000.000
57A57GLU-1-0.954-0.97415.343-0.108-0.1080.0000.0000.0000.000
58A58VAL0-0.044-0.01818.6670.0060.0060.0000.0000.0000.000
59A59LYS10.9350.98219.6550.0410.0410.0000.0000.0000.000
60A60ILE00.0520.02517.1110.0020.0020.0000.0000.0000.000
61A61ASP-1-0.860-0.92821.589-0.036-0.0360.0000.0000.0000.000
62A62TYR0-0.008-0.02124.2600.0020.0020.0000.0000.0000.000
63A63ILE00.0180.03219.001-0.001-0.0010.0000.0000.0000.000
64A64VAL00.001-0.01422.8220.0020.0020.0000.0000.0000.000
65A65GLY00.0230.01124.123-0.001-0.0010.0000.0000.0000.000
66A66LEU0-0.014-0.00625.1170.0020.0020.0000.0000.0000.000
67A67GLU-1-0.835-0.86626.982-0.013-0.0130.0000.0000.0000.000
68A68SER0-0.010-0.03929.1500.0000.0000.0000.0000.0000.000
69A69ARG10.9540.96724.4590.0190.0190.0000.0000.0000.000
70A70GLY00.1160.06823.043-0.002-0.0020.0000.0000.0000.000
71A71PHE0-0.098-0.06223.6770.0000.0000.0000.0000.0000.000
72A72LEU0-0.037-0.00923.6600.0010.0010.0000.0000.0000.000
73A73PHE00.0220.00817.7330.0000.0000.0000.0000.0000.000
74A74GLY00.0420.03620.221-0.002-0.0020.0000.0000.0000.000
75A75PRO0-0.018-0.01221.706-0.001-0.0010.0000.0000.0000.000
76A76THR00.0000.00119.7220.0020.0020.0000.0000.0000.000
77A77LEU00.0130.01415.307-0.001-0.0010.0000.0000.0000.000
78A78ALA00.0060.00118.728-0.001-0.0010.0000.0000.0000.000
79A79LEU00.0180.00621.3880.0000.0000.0000.0000.0000.000
80A80ALA0-0.051-0.02417.4710.0010.0010.0000.0000.0000.000
81A81LEU0-0.039-0.02315.206-0.002-0.0020.0000.0000.0000.000
82A82GLY0-0.0330.00818.806-0.001-0.0010.0000.0000.0000.000
83A83VAL0-0.058-0.01821.2160.0000.0000.0000.0000.0000.000
84A84GLY00.0010.00923.6700.0020.0020.0000.0000.0000.000
85A85PHE00.001-0.01324.095-0.001-0.0010.0000.0000.0000.000
86A86VAL00.0120.00726.4020.0020.0020.0000.0000.0000.000
87A87PRO0-0.042-0.01027.842-0.001-0.0010.0000.0000.0000.000
88A88VAL00.0700.05129.2940.0000.0000.0000.0000.0000.000
89A89ARG10.8090.87130.9040.0130.0130.0000.0000.0000.000
90A90LYS10.9670.98233.4840.0130.0130.0000.0000.0000.000
91A91ALA00.012-0.01135.9410.0010.0010.0000.0000.0000.000
92A92GLY0-0.045-0.01939.1740.0010.0010.0000.0000.0000.000
93A93LYS10.8010.90736.5340.0120.0120.0000.0000.0000.000
94A94LEU0-0.011-0.00234.6330.0010.0010.0000.0000.0000.000
95A95PRO00.0060.02438.5260.0000.0000.0000.0000.0000.000
96A96GLY00.032-0.00140.263-0.001-0.0010.0000.0000.0000.000
97A97GLU-1-0.917-0.95642.236-0.013-0.0130.0000.0000.0000.000
98A98CYS0-0.028-0.01138.623-0.001-0.0010.0000.0000.0000.000
99A99PHE00.0450.03336.1540.0010.0010.0000.0000.0000.000
100A100LYS10.8530.89537.7230.0150.0150.0000.0000.0000.000
101A101ALA00.0770.05734.725-0.001-0.0010.0000.0000.0000.000
102A102THR0-0.003-0.01436.7260.0010.0010.0000.0000.0000.000
103A103TYR00.0140.04632.990-0.001-0.0010.0000.0000.0000.000
104A104GLU-1-0.926-0.97135.615-0.018-0.0180.0000.0000.0000.000
105A105LYS10.8540.92935.7370.0140.0140.0000.0000.0000.000
106A106GLU-1-0.850-0.94037.688-0.017-0.0170.0000.0000.0000.000
107A107TYR0-0.012-0.01339.9940.0000.0000.0000.0000.0000.000
108A108GLY00.0080.00541.4370.0010.0010.0000.0000.0000.000
109A109SER0-0.032-0.02139.070-0.001-0.0010.0000.0000.0000.000
110A110ASP-1-0.923-0.93435.461-0.015-0.0150.0000.0000.0000.000
111A111LEU0-0.011-0.00436.976-0.001-0.0010.0000.0000.0000.000
112A112PHE0-0.002-0.02032.4970.0010.0010.0000.0000.0000.000
113A113GLU-1-0.778-0.89435.251-0.014-0.0140.0000.0000.0000.000
114A114ILE00.0520.02330.4890.0000.0000.0000.0000.0000.000
115A115GLN0-0.028-0.02034.5420.0000.0000.0000.0000.0000.000
116A116LYS10.9090.96335.5400.0160.0160.0000.0000.0000.000
117A117ASN0-0.009-0.01037.031-0.001-0.0010.0000.0000.0000.000
118A118ALA0-0.052-0.01732.5880.0000.0000.0000.0000.0000.000
119A119ILE0-0.0070.00028.6320.0000.0000.0000.0000.0000.000
120A120PRO0-0.0150.00831.5580.0000.0000.0000.0000.0000.000
121A121ALA00.0830.06332.177-0.001-0.0010.0000.0000.0000.000
122A122GLY0-0.048-0.03131.0310.0000.0000.0000.0000.0000.000
123A123SER0-0.059-0.04228.123-0.002-0.0020.0000.0000.0000.000
124A124ASN0-0.035-0.02223.1420.0000.0000.0000.0000.0000.000
125A125VAL0-0.012-0.02423.6680.0020.0020.0000.0000.0000.000
126A126ILE00.0170.03317.868-0.001-0.0010.0000.0000.0000.000
127A127ILE0-0.0070.00421.1210.0010.0010.0000.0000.0000.000
128A128VAL0-0.008-0.00918.6400.0010.0010.0000.0000.0000.000
129A129ASP-1-0.836-0.95520.406-0.023-0.0230.0000.0000.0000.000
130A130ASP-1-0.858-0.95720.094-0.034-0.0340.0000.0000.0000.000
131A131ILE00.008-0.00120.003-0.002-0.0020.0000.0000.0000.000
132A132ILE0-0.0420.01919.7170.0020.0020.0000.0000.0000.000
133A133ALA00.0670.00722.543-0.001-0.0010.0000.0000.0000.000
134A134THR0-0.001-0.00825.306-0.001-0.0010.0000.0000.0000.000
135A135GLY00.0400.02026.323-0.001-0.0010.0000.0000.0000.000
136A136GLY00.009-0.00527.0750.0000.0000.0000.0000.0000.000
137A137SER00.005-0.00228.2250.0000.0000.0000.0000.0000.000
138A138ALA00.0400.02224.9140.0000.0000.0000.0000.0000.000
139A139ALA00.0090.00126.882-0.001-0.0010.0000.0000.0000.000
140A140ALA00.0230.02028.9990.0000.0000.0000.0000.0000.000
141A141ALA0-0.007-0.01427.6100.0000.0000.0000.0000.0000.000
142A142GLY00.0210.00927.9140.0000.0000.0000.0000.0000.000
143A143GLU-1-0.892-0.95128.591-0.025-0.0250.0000.0000.0000.000
144A144LEU0-0.098-0.04931.7170.0000.0000.0000.0000.0000.000
145A145VAL0-0.020-0.01627.2310.0000.0000.0000.0000.0000.000
146A146GLU-1-0.930-0.95930.446-0.030-0.0300.0000.0000.0000.000
147A147GLN0-0.026-0.02132.2370.0010.0010.0000.0000.0000.000
148A148LEU0-0.105-0.04331.6300.0010.0010.0000.0000.0000.000
149A149GLU-1-0.935-0.96033.657-0.028-0.0280.0000.0000.0000.000
150A150ALA0-0.052-0.01428.820-0.001-0.0010.0000.0000.0000.000
151A151ASN0-0.025-0.01725.969-0.001-0.0010.0000.0000.0000.000
152A152LEU0-0.021-0.01323.2350.0000.0000.0000.0000.0000.000
153A153LEU0-0.024-0.00619.558-0.002-0.0020.0000.0000.0000.000
154A154GLU-1-0.814-0.91614.764-0.006-0.0060.0000.0000.0000.000
155A155TYR0-0.0260.00118.8930.0000.0000.0000.0000.0000.000
156A156ASN0-0.084-0.05515.0410.0060.0060.0000.0000.0000.000
157A157PHE00.025-0.00416.500-0.004-0.0040.0000.0000.0000.000
158A158VAL0-0.0060.01015.6010.0000.0000.0000.0000.0000.000
159A159MET0-0.027-0.01715.367-0.008-0.0080.0000.0000.0000.000
160A160GLU-1-0.940-0.96717.641-0.026-0.0260.0000.0000.0000.000
161A161LEU0-0.046-0.02019.803-0.001-0.0010.0000.0000.0000.000
162A162ASP-1-0.820-0.91122.959-0.023-0.0230.0000.0000.0000.000
163A163PHE0-0.041-0.04625.9400.0020.0020.0000.0000.0000.000
164A164LEU0-0.014-0.00629.1630.0010.0010.0000.0000.0000.000
165A165LYS10.8270.92630.7600.0170.0170.0000.0000.0000.000
166A166GLY0-0.0010.01629.5050.0000.0000.0000.0000.0000.000
167A167ARG10.9650.98020.0930.0300.0300.0000.0000.0000.000
168A168SER0-0.049-0.02327.889-0.001-0.0010.0000.0000.0000.000
169A169LYS10.9300.95127.0380.0330.0330.0000.0000.0000.000
170A170LEU00.0220.02022.5930.0010.0010.0000.0000.0000.000
171A171ASN00.0070.00125.006-0.003-0.0030.0000.0000.0000.000
172A172ALA00.0390.01921.919-0.002-0.0020.0000.0000.0000.000
173A173PRO00.0010.01517.0730.0020.0020.0000.0000.0000.000
174A174VAL00.009-0.01417.2730.0030.0030.0000.0000.0000.000
175A175PHE00.0020.0159.2670.0040.0040.0000.0000.0000.000
176A176THR0-0.015-0.01313.636-0.012-0.0120.0000.0000.0000.000
177A177LEU0-0.0240.0019.3190.0150.0150.0000.0000.0000.000
178A178LEU0-0.059-0.02410.619-0.017-0.0170.0000.0000.0000.000