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: LNY99

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 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 178
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1822573.144123
FMO2-HF: Nuclear repulsion 1755156.816994
FMO2-HF: Total energy -67416.327129
FMO2-MP2: Total energy -67616.935633


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.
0.3836.1162.908-2.927-5.7130
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 : 0.079 / q_NPA : 0.036
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].
3A3ILE00.1010.0462.591-2.7740.3351.074-1.358-2.8260.002
4A4ALA00.0030.0072.067-0.3841.1211.827-1.277-2.054-0.002
5A5SER0-0.067-0.0363.3191.2051.9540.010-0.266-0.4930.000
6A6TYR00.0210.0025.1760.5340.679-0.001-0.009-0.1340.000
7A7ALA00.0570.0327.4370.2790.2790.0000.0000.0000.000
8A8GLN0-0.061-0.0345.6790.3580.3580.0000.0000.0000.000
9A9GLU-1-0.824-0.8969.116-0.624-0.6240.0000.0000.0000.000
10A10LEU0-0.013-0.00911.2290.1290.1290.0000.0000.0000.000
11A11LYS10.9690.98212.2870.1650.1650.0000.0000.0000.000
12A12LEU0-0.052-0.02412.7190.0530.0530.0000.0000.0000.000
13A13ALA0-0.035-0.00415.5420.0260.0260.0000.0000.0000.000
14A14LEU0-0.041-0.00216.8020.0220.0220.0000.0000.0000.000
15A15HIS0-0.024-0.00319.4150.0010.0010.0000.0000.0000.000
16A16GLN0-0.019-0.01721.2010.0110.0110.0000.0000.0000.000
17A17TYR0-0.075-0.04424.5530.0010.0010.0000.0000.0000.000
18A18PRO00.015-0.00628.1610.0040.0040.0000.0000.0000.000
19A19ASN0-0.0300.00630.1290.0010.0010.0000.0000.0000.000
20A20PHE00.0300.04329.353-0.001-0.0010.0000.0000.0000.000
21A21PRO0-0.025-0.02229.6690.0000.0000.0000.0000.0000.000
22A22SER00.027-0.00532.6310.0000.0000.0000.0000.0000.000
23A23GLU-1-0.951-0.98633.371-0.005-0.0050.0000.0000.0000.000
24A24GLY0-0.011-0.01033.0540.0020.0020.0000.0000.0000.000
25A25ILE0-0.051-0.00428.2290.0030.0030.0000.0000.0000.000
26A26LEU0-0.022-0.00624.518-0.003-0.0030.0000.0000.0000.000
27A27PHE0-0.016-0.00925.3640.0020.0020.0000.0000.0000.000
28A28GLU-1-0.801-0.90820.402-0.064-0.0640.0000.0000.0000.000
29A29ASP-1-0.870-0.94922.908-0.080-0.0800.0000.0000.0000.000
30A30PHE00.0680.01619.336-0.013-0.0130.0000.0000.0000.000
31A31LEU0-0.016-0.02121.139-0.017-0.0170.0000.0000.0000.000
32A32PRO0-0.076-0.04121.066-0.005-0.0050.0000.0000.0000.000
33A33ILE00.0170.01416.517-0.014-0.0140.0000.0000.0000.000
34A34PHE0-0.008-0.00819.690-0.015-0.0150.0000.0000.0000.000
35A35ARG10.8820.96622.3220.1100.1100.0000.0000.0000.000
36A36ASN00.0010.00919.783-0.007-0.0070.0000.0000.0000.000
37A37PRO00.0610.02220.036-0.019-0.0190.0000.0000.0000.000
38A38GLY00.0200.01817.893-0.013-0.0130.0000.0000.0000.000
39A39LEU0-0.014-0.00914.920-0.052-0.0520.0000.0000.0000.000
40A40PHE00.0180.00015.618-0.018-0.0180.0000.0000.0000.000
41A41GLN0-0.025-0.02514.4150.0440.0440.0000.0000.0000.000
42A42LYS10.8440.90611.0020.7690.7690.0000.0000.0000.000
43A43LEU0-0.0030.00411.409-0.038-0.0380.0000.0000.0000.000
44A44ILE0-0.035-0.02212.9840.0500.0500.0000.0000.0000.000
45A45ASP-1-0.834-0.91910.139-0.342-0.3420.0000.0000.0000.000
46A46ALA0-0.052-0.0238.2570.0200.0200.0000.0000.0000.000
47A47PHE0-0.001-0.0139.1400.1680.1680.0000.0000.0000.000
48A48LYS10.8750.95011.7810.1750.1750.0000.0000.0000.000
49A49LEU00.0060.0094.085-0.166-0.037-0.001-0.016-0.1120.000
50A50HIS10.7930.8878.349-0.224-0.2240.0000.0000.0000.000
51A51LEU00.019-0.0059.266-0.001-0.0010.0000.0000.0000.000
52A52GLU-1-0.951-0.97510.454-0.042-0.0420.0000.0000.0000.000
53A53GLU-1-0.947-0.9665.9061.0631.159-0.001-0.001-0.0940.000
54A54ALA0-0.046-0.0279.809-0.067-0.0670.0000.0000.0000.000
55A55PHE0-0.051-0.03712.204-0.040-0.0400.0000.0000.0000.000
56A56PRO00.0020.01412.807-0.019-0.0190.0000.0000.0000.000
57A57GLU-1-0.955-0.97615.4440.0060.0060.0000.0000.0000.000
58A58VAL0-0.047-0.02618.528-0.005-0.0050.0000.0000.0000.000
59A59LYS10.8800.94319.4130.0070.0070.0000.0000.0000.000
60A60ILE00.0510.02216.9630.0010.0010.0000.0000.0000.000
61A61ASP-1-0.844-0.91221.577-0.005-0.0050.0000.0000.0000.000
62A62TYR0-0.002-0.01624.315-0.008-0.0080.0000.0000.0000.000
63A63ILE00.0120.02819.2440.0060.0060.0000.0000.0000.000
64A64VAL00.011-0.00722.909-0.006-0.0060.0000.0000.0000.000
65A65GLY00.0240.01224.2310.0030.0030.0000.0000.0000.000
66A66LEU0-0.014-0.00525.2210.0000.0000.0000.0000.0000.000
67A67GLU-1-0.835-0.85327.076-0.027-0.0270.0000.0000.0000.000
68A68SER0-0.006-0.03829.2290.0040.0040.0000.0000.0000.000
69A69ARG10.9430.96724.5660.0320.0320.0000.0000.0000.000
70A70GLY00.1170.06923.128-0.008-0.0080.0000.0000.0000.000
71A71PHE0-0.096-0.06023.748-0.002-0.0020.0000.0000.0000.000
72A72LEU0-0.038-0.00823.594-0.003-0.0030.0000.0000.0000.000
73A73PHE00.0270.00617.684-0.015-0.0150.0000.0000.0000.000
74A74GLY00.0460.03920.260-0.002-0.0020.0000.0000.0000.000
75A75PRO0-0.019-0.01221.7560.0020.0020.0000.0000.0000.000
76A76THR0-0.012-0.00319.9020.0050.0050.0000.0000.0000.000
77A77LEU00.0200.01615.259-0.009-0.0090.0000.0000.0000.000
78A78ALA00.0070.00018.7560.0040.0040.0000.0000.0000.000
79A79LEU00.0090.00521.4250.0020.0020.0000.0000.0000.000
80A80ALA0-0.027-0.01217.467-0.002-0.0020.0000.0000.0000.000
81A81LEU0-0.024-0.01315.243-0.005-0.0050.0000.0000.0000.000
82A82GLY0-0.0300.00918.8180.0070.0070.0000.0000.0000.000
83A83VAL0-0.061-0.02321.1890.0070.0070.0000.0000.0000.000
84A84GLY00.0090.01523.708-0.006-0.0060.0000.0000.0000.000
85A85PHE00.002-0.01424.0310.0020.0020.0000.0000.0000.000
86A86VAL00.0080.00526.462-0.001-0.0010.0000.0000.0000.000
87A87PRO0-0.034-0.00327.9300.0020.0020.0000.0000.0000.000
88A88VAL00.0640.04529.3370.0020.0020.0000.0000.0000.000
89A89ARG10.8140.86331.0050.0200.0200.0000.0000.0000.000
90A90LYS10.9440.96532.9680.0210.0210.0000.0000.0000.000
91A91ALA00.014-0.01236.051-0.001-0.0010.0000.0000.0000.000
92A92GLY0-0.046-0.02839.239-0.001-0.0010.0000.0000.0000.000
93A93LYS10.8170.92637.1650.0140.0140.0000.0000.0000.000
94A94LEU0-0.0040.00734.628-0.002-0.0020.0000.0000.0000.000
95A95PRO00.0130.02638.6250.0010.0010.0000.0000.0000.000
96A96GLY00.0370.00640.3460.0000.0000.0000.0000.0000.000
97A97GLU-1-0.844-0.90442.332-0.006-0.0060.0000.0000.0000.000
98A98CYS0-0.033-0.01638.609-0.001-0.0010.0000.0000.0000.000
99A99PHE00.0370.03536.0900.0000.0000.0000.0000.0000.000
100A100LYS10.8510.88137.5730.0040.0040.0000.0000.0000.000
101A101ALA00.0810.06234.5100.0010.0010.0000.0000.0000.000
102A102THR0-0.008-0.01836.481-0.002-0.0020.0000.0000.0000.000
103A103TYR00.0350.05932.7840.0030.0030.0000.0000.0000.000
104A104GLU-1-0.933-0.97135.3980.0060.0060.0000.0000.0000.000
105A105LYS10.7740.87935.5170.0030.0030.0000.0000.0000.000
106A106GLU-1-0.796-0.87937.5990.0080.0080.0000.0000.0000.000
107A107TYR0-0.051-0.04539.8310.0000.0000.0000.0000.0000.000
108A108GLY00.0150.01241.226-0.001-0.0010.0000.0000.0000.000
109A109SER0-0.018-0.01338.8610.0020.0020.0000.0000.0000.000
110A110ASP-1-0.875-0.90535.443-0.005-0.0050.0000.0000.0000.000
111A111LEU00.0000.00536.7360.0010.0010.0000.0000.0000.000
112A112PHE00.002-0.01532.387-0.002-0.0020.0000.0000.0000.000
113A113GLU-1-0.783-0.88135.237-0.007-0.0070.0000.0000.0000.000
114A114ILE00.0550.02430.338-0.002-0.0020.0000.0000.0000.000
115A115GLN0-0.031-0.03434.5670.0000.0000.0000.0000.0000.000
116A116LYS10.8370.91535.5970.0040.0040.0000.0000.0000.000
117A117ASN0-0.028-0.02336.9960.0010.0010.0000.0000.0000.000
118A118ALA0-0.042-0.01132.730-0.001-0.0010.0000.0000.0000.000
119A119ILE00.0040.00528.410-0.001-0.0010.0000.0000.0000.000
120A120PRO0-0.0200.00531.5860.0010.0010.0000.0000.0000.000
121A121ALA00.0810.06231.9860.0010.0010.0000.0000.0000.000
122A122GLY0-0.039-0.02730.795-0.001-0.0010.0000.0000.0000.000
123A123SER0-0.064-0.04427.9930.0000.0000.0000.0000.0000.000
124A124ASN0-0.021-0.00422.9430.0030.0030.0000.0000.0000.000
125A125VAL0-0.013-0.02123.576-0.004-0.0040.0000.0000.0000.000
126A126ILE00.0280.03317.3810.0060.0060.0000.0000.0000.000
127A127ILE0-0.0060.00820.934-0.012-0.0120.0000.0000.0000.000
128A128VAL0-0.002-0.00718.9080.0090.0090.0000.0000.0000.000
129A129ASP-1-0.832-0.95320.503-0.024-0.0240.0000.0000.0000.000
130A130ASP-1-0.870-0.96920.206-0.050-0.0500.0000.0000.0000.000
131A131ILE0-0.011-0.00820.0780.0050.0050.0000.0000.0000.000
132A132ILE0-0.0210.02519.4970.0010.0010.0000.0000.0000.000
133A133ALA00.0600.00422.5370.0020.0020.0000.0000.0000.000
134A134THR00.003-0.00825.2710.0040.0040.0000.0000.0000.000
135A135GLY00.0430.02226.1200.0030.0030.0000.0000.0000.000
136A136GLY00.008-0.00826.8810.0010.0010.0000.0000.0000.000
137A137SER00.007-0.00128.0140.0020.0020.0000.0000.0000.000
138A138ALA00.0370.01924.673-0.001-0.0010.0000.0000.0000.000
139A139ALA00.0160.01426.6470.0020.0020.0000.0000.0000.000
140A140ALA00.0150.01728.7860.0000.0000.0000.0000.0000.000
141A141ALA0-0.001-0.01427.376-0.001-0.0010.0000.0000.0000.000
142A142GLY00.0260.01327.6760.0000.0000.0000.0000.0000.000
143A143GLU-1-0.884-0.94528.3570.0100.0100.0000.0000.0000.000
144A144LEU0-0.102-0.05331.449-0.002-0.0020.0000.0000.0000.000
145A145VAL0-0.019-0.01726.909-0.002-0.0020.0000.0000.0000.000
146A146GLU-1-0.923-0.95330.1880.0150.0150.0000.0000.0000.000
147A147GLN0-0.027-0.02432.004-0.002-0.0020.0000.0000.0000.000
148A148LEU0-0.108-0.04331.643-0.002-0.0020.0000.0000.0000.000
149A149GLU-1-0.942-0.96733.3700.0070.0070.0000.0000.0000.000
150A150ALA0-0.057-0.01528.7040.0000.0000.0000.0000.0000.000
151A151ASN0-0.020-0.01525.7520.0020.0020.0000.0000.0000.000
152A152LEU0-0.022-0.01522.8610.0000.0000.0000.0000.0000.000
153A153LEU0-0.028-0.00519.3120.0020.0020.0000.0000.0000.000
154A154GLU-1-0.804-0.89314.2310.1890.1890.0000.0000.0000.000
155A155TYR0-0.035-0.02518.683-0.013-0.0130.0000.0000.0000.000
156A156ASN0-0.075-0.06314.5490.0270.0270.0000.0000.0000.000
157A157PHE00.018-0.00616.248-0.022-0.0220.0000.0000.0000.000
158A158VAL00.0000.01115.5860.0140.0140.0000.0000.0000.000
159A159MET0-0.027-0.01615.4390.0020.0020.0000.0000.0000.000
160A160GLU-1-0.848-0.91517.7060.0770.0770.0000.0000.0000.000
161A161LEU0-0.042-0.02019.855-0.005-0.0050.0000.0000.0000.000
162A162ASP-1-0.817-0.91523.0090.0270.0270.0000.0000.0000.000
163A163PHE0-0.044-0.04625.982-0.005-0.0050.0000.0000.0000.000
164A164LEU0-0.023-0.00629.193-0.002-0.0020.0000.0000.0000.000
165A165LYS10.8150.89130.796-0.008-0.0080.0000.0000.0000.000
166A166GLY0-0.0090.01429.4020.0000.0000.0000.0000.0000.000
167A167ARG10.8870.93419.672-0.063-0.0630.0000.0000.0000.000
168A168SER0-0.041-0.02527.7560.0030.0030.0000.0000.0000.000
169A169LYS10.9020.94126.890-0.031-0.0310.0000.0000.0000.000
170A170LEU00.0240.02222.589-0.003-0.0030.0000.0000.0000.000
171A171ASN0-0.005-0.00524.7690.0050.0050.0000.0000.0000.000
172A172ALA00.0440.02321.759-0.002-0.0020.0000.0000.0000.000
173A173PRO00.0020.01216.8070.0010.0010.0000.0000.0000.000
174A174VAL0-0.017-0.02217.344-0.009-0.0090.0000.0000.0000.000
175A175PHE00.0110.0278.9270.0130.0130.0000.0000.0000.000
176A176THR0-0.024-0.01713.465-0.040-0.0400.0000.0000.0000.000
177A177LEU0-0.0160.0049.3570.0410.0410.0000.0000.0000.000
178A178LEU0-0.060-0.02210.6830.0190.0190.0000.0000.0000.000