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: KGV33

Calculation Name: 2FM9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2FM9

Chain ID: A

ChEMBL ID:

UniProt ID: P0CL52

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 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 201
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2195851.515212
FMO2-HF: Nuclear repulsion 2117625.050371
FMO2-HF: Total energy -78226.464841
FMO2-MP2: Total energy -78451.175125


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:49:PRO)


Summations of interaction energy for fragment #1(A:49:PRO)
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.
-2.1071.721.292-2.089-3.031-0.005
Interaction energy analysis for fragmet #1(A:49:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.021 / 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].
3A51LEU00.018-0.0063.8790.1701.769-0.013-0.802-0.7850.003
4A52GLU-1-0.809-0.8996.668-0.804-0.8040.0000.0000.0000.000
5A53ASP-1-0.830-0.8982.917-1.944-0.3060.279-0.922-0.995-0.008
6A54PHE0-0.052-0.0312.430-0.5340.0561.026-0.365-1.2510.000
7A55PRO00.027-0.0077.692-0.063-0.0630.0000.0000.0000.000
8A56ALA0-0.023-0.00811.3030.0010.0010.0000.0000.0000.000
9A57LEU00.0550.0306.7200.0070.0070.0000.0000.0000.000
10A58ILE00.0260.02510.3540.0040.0040.0000.0000.0000.000
11A59LYS10.9200.96711.6550.2290.2290.0000.0000.0000.000
12A60GLN00.0120.00213.307-0.013-0.0130.0000.0000.0000.000
13A61ALA00.0350.01712.3680.0260.0260.0000.0000.0000.000
14A62SER0-0.044-0.04214.4340.0230.0230.0000.0000.0000.000
15A63LEU0-0.040-0.01516.9430.0350.0350.0000.0000.0000.000
16A64ASP-1-0.800-0.87817.643-0.270-0.2700.0000.0000.0000.000
17A65ALA0-0.068-0.02917.8040.0180.0180.0000.0000.0000.000
18A66LEU0-0.015-0.00719.7160.0230.0230.0000.0000.0000.000
19A67PHE00.033-0.01122.5510.0190.0190.0000.0000.0000.000
20A68LYS10.9440.98221.5390.2990.2990.0000.0000.0000.000
21A69CYS0-0.0370.00524.3650.0070.0070.0000.0000.0000.000
22A70GLY00.0060.02126.9400.0140.0140.0000.0000.0000.000
23A71LYS10.8590.91029.1920.1060.1060.0000.0000.0000.000
24A72ASP-1-0.810-0.90130.223-0.130-0.1300.0000.0000.0000.000
25A73ALA0-0.007-0.00324.8470.0010.0010.0000.0000.0000.000
26A74GLU-1-0.866-0.93825.390-0.180-0.1800.0000.0000.0000.000
27A75ALA00.0350.01627.4950.0040.0040.0000.0000.0000.000
28A76LEU0-0.058-0.02426.8340.0060.0060.0000.0000.0000.000
29A77LYS10.8520.92119.6700.2500.2500.0000.0000.0000.000
30A78GLU-1-0.919-0.93425.752-0.104-0.1040.0000.0000.0000.000
31A79VAL0-0.025-0.00428.8240.0070.0070.0000.0000.0000.000
32A80PHE0-0.013-0.01521.6730.0040.0040.0000.0000.0000.000
33A81THR0-0.067-0.05823.7400.0070.0070.0000.0000.0000.000
34A82ASN0-0.012-0.01826.2020.0110.0110.0000.0000.0000.000
35A83SER0-0.032-0.01029.3270.0090.0090.0000.0000.0000.000
36A84ASN00.006-0.01129.103-0.001-0.0010.0000.0000.0000.000
37A85ASN0-0.0150.00731.0770.0050.0050.0000.0000.0000.000
38A86VAL00.0360.00726.170-0.008-0.0080.0000.0000.0000.000
39A87ALA00.0300.02527.127-0.007-0.0070.0000.0000.0000.000
40A88GLY00.0830.02428.522-0.005-0.0050.0000.0000.0000.000
41A89LYS10.8470.91024.9660.0990.0990.0000.0000.0000.000
42A90LYS10.8350.92222.9680.0830.0830.0000.0000.0000.000
43A91ALA00.0250.00624.347-0.007-0.0070.0000.0000.0000.000
44A92ILE0-0.0060.00223.950-0.010-0.0100.0000.0000.0000.000
45A93MET00.0080.00120.121-0.019-0.0190.0000.0000.0000.000
46A94GLU-1-0.846-0.88820.587-0.119-0.1190.0000.0000.0000.000
47A95PHE00.0180.01222.232-0.012-0.0120.0000.0000.0000.000
48A96ALA00.0350.01519.989-0.011-0.0110.0000.0000.0000.000
49A97GLY00.0140.01117.849-0.029-0.0290.0000.0000.0000.000
50A98LEU00.0100.00618.657-0.021-0.0210.0000.0000.0000.000
51A99PHE00.0250.01421.373-0.002-0.0020.0000.0000.0000.000
52A100ARG10.8510.91111.0520.7630.7630.0000.0000.0000.000
53A101SER0-0.041-0.03117.763-0.023-0.0230.0000.0000.0000.000
54A102ALA00.0550.01818.6680.0040.0040.0000.0000.0000.000
55A103LEU0-0.057-0.01219.6870.0080.0080.0000.0000.0000.000
56A104ASN0-0.032-0.02714.707-0.004-0.0040.0000.0000.0000.000
57A105ALA0-0.0120.00618.7580.0120.0120.0000.0000.0000.000
58A106THR00.027-0.01321.5440.0200.0200.0000.0000.0000.000
59A107SER0-0.094-0.07320.5940.0040.0040.0000.0000.0000.000
60A108ASP-1-0.871-0.90422.617-0.206-0.2060.0000.0000.0000.000
61A109SER0-0.027-0.01625.4470.0190.0190.0000.0000.0000.000
62A110PRO00.0280.00728.242-0.004-0.0040.0000.0000.0000.000
63A111GLU-1-0.790-0.86730.359-0.103-0.1030.0000.0000.0000.000
64A112ALA00.0830.03928.6920.0000.0000.0000.0000.0000.000
65A113LYS10.8380.92922.6250.2330.2330.0000.0000.0000.000
66A114THR0-0.050-0.03928.076-0.004-0.0040.0000.0000.0000.000
67A115LEU0-0.021-0.01331.4220.0010.0010.0000.0000.0000.000
68A116LEU00.0160.00923.8410.0030.0030.0000.0000.0000.000
69A117MET0-0.019-0.01524.510-0.003-0.0030.0000.0000.0000.000
70A118LYS10.8820.94228.9790.0950.0950.0000.0000.0000.000
71A119VAL00.0160.00729.2870.0050.0050.0000.0000.0000.000
72A120GLY00.0440.00627.6100.0020.0020.0000.0000.0000.000
73A121ALA0-0.0200.00928.3800.0020.0020.0000.0000.0000.000
74A122GLU-1-0.844-0.90231.239-0.087-0.0870.0000.0000.0000.000
75A123TYR00.0140.01726.9760.0090.0090.0000.0000.0000.000
76A124THR0-0.010-0.04127.3340.0060.0060.0000.0000.0000.000
77A125ALA00.002-0.00130.1950.0050.0050.0000.0000.0000.000
78A126GLN0-0.059-0.04733.6490.0110.0110.0000.0000.0000.000
79A127ILE0-0.0010.00527.7330.0040.0040.0000.0000.0000.000
80A128ILE0-0.018-0.01031.2890.0050.0050.0000.0000.0000.000
81A129LYS10.9200.95734.0550.0780.0780.0000.0000.0000.000
82A130ASP-1-0.799-0.86634.873-0.066-0.0660.0000.0000.0000.000
83A131GLY00.0460.02634.5330.0050.0050.0000.0000.0000.000
84A132LEU0-0.051-0.01328.475-0.001-0.0010.0000.0000.0000.000
85A133LYS10.8670.95533.0760.0660.0660.0000.0000.0000.000
86A134GLU-1-0.837-0.91435.327-0.045-0.0450.0000.0000.0000.000
87A135LYS10.8380.91736.8250.0470.0470.0000.0000.0000.000
88A136SER0-0.033-0.05134.430-0.004-0.0040.0000.0000.0000.000
89A137ALA00.0520.03336.0690.0030.0030.0000.0000.0000.000
90A138PHE0-0.038-0.01130.048-0.002-0.0020.0000.0000.0000.000
91A139GLY00.010-0.01030.7520.0010.0010.0000.0000.0000.000
92A140PRO0-0.012-0.01631.7950.0020.0020.0000.0000.0000.000
93A141TRP00.0600.03533.2070.0050.0050.0000.0000.0000.000
94A142LEU0-0.0110.00927.282-0.004-0.0040.0000.0000.0000.000
95A143PRO00.0260.02027.7630.0060.0060.0000.0000.0000.000
96A144GLU-1-0.917-0.95729.313-0.032-0.0320.0000.0000.0000.000
97A145THR0-0.008-0.01130.5890.0060.0060.0000.0000.0000.000
98A146LYS10.8640.89523.5530.0200.0200.0000.0000.0000.000
99A147LYS10.9720.99528.9870.0050.0050.0000.0000.0000.000
100A148ALA00.0200.01432.107-0.001-0.0010.0000.0000.0000.000
101A149GLU-1-0.796-0.88024.541-0.041-0.0410.0000.0000.0000.000
102A150ALA00.0320.01228.779-0.004-0.0040.0000.0000.0000.000
103A151LYS10.8640.91929.6500.0240.0240.0000.0000.0000.000
104A152LEU00.0070.01628.410-0.001-0.0010.0000.0000.0000.000
105A153GLU-1-0.808-0.91124.845-0.048-0.0480.0000.0000.0000.000
106A154ASN0-0.125-0.05328.7730.0010.0010.0000.0000.0000.000
107A155LEU00.0280.02131.952-0.001-0.0010.0000.0000.0000.000
108A156GLU-1-0.787-0.89427.495-0.088-0.0880.0000.0000.0000.000
109A157LYS10.8130.89825.7400.0380.0380.0000.0000.0000.000
110A158GLN0-0.028-0.02530.6600.0040.0040.0000.0000.0000.000
111A159LEU00.0120.01033.5910.0010.0010.0000.0000.0000.000
112A160LEU0-0.014-0.01228.335-0.002-0.0020.0000.0000.0000.000
113A161ASP-1-0.926-0.96332.456-0.036-0.0360.0000.0000.0000.000
114A162ILE00.0060.00034.6360.0010.0010.0000.0000.0000.000
115A163ILE00.023-0.00534.4300.0010.0010.0000.0000.0000.000
116A164LYS10.9140.96629.4150.0570.0570.0000.0000.0000.000
117A165ASN0-0.056-0.01835.6400.0000.0000.0000.0000.0000.000
118A166ASN0-0.088-0.04339.0010.0060.0060.0000.0000.0000.000
119A167THR00.017-0.01040.323-0.003-0.0030.0000.0000.0000.000
120A168GLY00.0130.00242.7190.0030.0030.0000.0000.0000.000
121A169GLY0-0.011-0.01445.2670.0000.0000.0000.0000.0000.000
122A170GLU-1-0.777-0.86946.059-0.027-0.0270.0000.0000.0000.000
123A171LEU00.0220.03039.1200.0010.0010.0000.0000.0000.000
124A172SER00.0210.02642.690-0.001-0.0010.0000.0000.0000.000
125A173LYS10.7800.89144.7460.0270.0270.0000.0000.0000.000
126A174LEU00.0280.01042.0790.0010.0010.0000.0000.0000.000
127A175SER0-0.019-0.03140.0080.0000.0000.0000.0000.0000.000
128A176THR00.014-0.00441.2150.0000.0000.0000.0000.0000.000
129A177ASN0-0.053-0.03843.9970.0000.0000.0000.0000.0000.000
130A178LEU00.0110.02036.2050.0010.0010.0000.0000.0000.000
131A179VAL00.010-0.01039.935-0.001-0.0010.0000.0000.0000.000
132A180MET0-0.020-0.01341.1810.0010.0010.0000.0000.0000.000
133A181GLN0-0.027-0.01142.6160.0010.0010.0000.0000.0000.000
134A182GLU-1-0.840-0.91136.897-0.030-0.0300.0000.0000.0000.000
135A183VAL00.0070.01036.4210.0000.0000.0000.0000.0000.000
136A184MET00.0270.02738.347-0.002-0.0020.0000.0000.0000.000
137A185PRO0-0.022-0.00840.3290.0010.0010.0000.0000.0000.000
138A186TYR0-0.039-0.01231.9560.0030.0030.0000.0000.0000.000
139A187ILE00.0350.01037.6130.0000.0000.0000.0000.0000.000
140A188ALA0-0.034-0.01638.9670.0000.0000.0000.0000.0000.000
141A189SER0-0.001-0.01938.2940.0020.0020.0000.0000.0000.000
142A190CYS0-0.059-0.01435.9460.0010.0010.0000.0000.0000.000
143A191ILE0-0.0040.00138.0680.0000.0000.0000.0000.0000.000
144A192GLU-1-0.828-0.90241.368-0.021-0.0210.0000.0000.0000.000
145A193HIS0-0.019-0.01736.6420.0040.0040.0000.0000.0000.000
146A194ASN0-0.090-0.03937.6780.0010.0010.0000.0000.0000.000
147A195PHE00.000-0.00840.7280.0000.0000.0000.0000.0000.000
148A196GLY00.0200.03543.4510.0020.0020.0000.0000.0000.000
149A197CYS0-0.087-0.04145.1890.0010.0010.0000.0000.0000.000
150A198THR0-0.009-0.01046.534-0.001-0.0010.0000.0000.0000.000
151A199LEU0-0.013-0.00844.6410.0000.0000.0000.0000.0000.000
152A200ASP-1-0.765-0.84947.938-0.025-0.0250.0000.0000.0000.000
153A201PRO00.027-0.01450.556-0.001-0.0010.0000.0000.0000.000
154A202LEU0-0.0030.02052.085-0.001-0.0010.0000.0000.0000.000
155A203THR0-0.012-0.05146.950-0.002-0.0020.0000.0000.0000.000
156A204ARG10.8370.91245.6140.0220.0220.0000.0000.0000.000
157A205SER00.0210.03047.578-0.001-0.0010.0000.0000.0000.000
158A206ASN0-0.027-0.02449.065-0.001-0.0010.0000.0000.0000.000
159A207LEU00.001-0.00142.825-0.002-0.0020.0000.0000.0000.000
160A208THR00.012-0.02144.230-0.002-0.0020.0000.0000.0000.000
161A209HIS0-0.017-0.00545.372-0.002-0.0020.0000.0000.0000.000
162A210LEU0-0.076-0.02641.286-0.001-0.0010.0000.0000.0000.000
163A211VAL00.025-0.00439.480-0.003-0.0030.0000.0000.0000.000
164A212ASP-1-0.875-0.93841.113-0.044-0.0440.0000.0000.0000.000
165A213LYS10.9760.99442.9080.0500.0500.0000.0000.0000.000
166A214ALA0-0.045-0.02139.352-0.002-0.0020.0000.0000.0000.000
167A215ALA00.0290.00538.200-0.004-0.0040.0000.0000.0000.000
168A216ALA00.0310.01539.092-0.002-0.0020.0000.0000.0000.000
169A217LYS10.7960.87140.2410.0570.0570.0000.0000.0000.000
170A218ALA00.0000.00635.278-0.003-0.0030.0000.0000.0000.000
171A219VAL00.0220.00136.489-0.004-0.0040.0000.0000.0000.000
172A220GLU-1-0.835-0.88238.283-0.060-0.0600.0000.0000.0000.000
173A221ALA0-0.025-0.01836.566-0.001-0.0010.0000.0000.0000.000
174A222LEU0-0.012-0.01131.803-0.004-0.0040.0000.0000.0000.000
175A223ASP-1-0.748-0.85535.598-0.056-0.0560.0000.0000.0000.000
176A224MET0-0.063-0.03738.4860.0000.0000.0000.0000.0000.000
177A225CYS0-0.077-0.03432.836-0.005-0.0050.0000.0000.0000.000
178A226HIS00.0000.00434.716-0.008-0.0080.0000.0000.0000.000
179A227GLN0-0.074-0.02935.7350.0020.0020.0000.0000.0000.000
180A228LYS10.8100.89234.2740.0810.0810.0000.0000.0000.000
181A243HIS00.006-0.00125.706-0.010-0.0100.0000.0000.0000.000
182A244LEU00.0030.00020.9480.0090.0090.0000.0000.0000.000
183A245GLU-1-0.803-0.88924.930-0.131-0.1310.0000.0000.0000.000
184A246MET00.0360.01226.721-0.002-0.0020.0000.0000.0000.000
185A247GLN0-0.027-0.01223.559-0.005-0.0050.0000.0000.0000.000
186A248THR0-0.026-0.01621.672-0.003-0.0030.0000.0000.0000.000
187A249LEU00.0080.00424.743-0.003-0.0030.0000.0000.0000.000
188A250ILE0-0.0090.01427.9420.0030.0030.0000.0000.0000.000
189A251PRO00.0200.01325.2920.0030.0030.0000.0000.0000.000
190A252LEU0-0.0360.00024.3030.0030.0030.0000.0000.0000.000
191A253LEU00.018-0.00528.0150.0050.0050.0000.0000.0000.000
192A254LEU0-0.0020.01030.9710.0050.0050.0000.0000.0000.000
193A255ARG10.7580.84126.3370.1030.1030.0000.0000.0000.000
194A256ASN0-0.017-0.02831.1030.0010.0010.0000.0000.0000.000
195A257VAL0-0.0230.01033.0420.0040.0040.0000.0000.0000.000
196A258PHE0-0.002-0.02031.7870.0040.0040.0000.0000.0000.000
197A259ALA0-0.026-0.00632.9590.0030.0030.0000.0000.0000.000
198A260GLN0-0.051-0.02535.0220.0050.0050.0000.0000.0000.000
199A261ILE0-0.045-0.00938.0670.0050.0050.0000.0000.0000.000
200A262PRO0-0.035-0.01239.352-0.002-0.0020.0000.0000.0000.000
201A263ALA0-0.0070.00139.2840.0020.0020.0000.0000.0000.000