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: KG7Q3

Calculation Name: 2FD5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2FD5

Chain ID: A

ChEMBL ID:

UniProt ID: Q9HZ91

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 180
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1694932.745864
FMO2-HF: Nuclear repulsion 1627573.174015
FMO2-HF: Total energy -67359.571849
FMO2-MP2: Total energy -67555.665242


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.
-3.355-1.154-0.035-1.065-1.1010.004
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 : -0.013 / q_NPA : -0.013
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].
3A3ASP-1-0.757-0.8483.753-2.593-0.392-0.035-1.065-1.1010.004
4A4LYS10.9480.9626.619-0.582-0.5820.0000.0000.0000.000
5A5LYS10.9811.0199.8180.3700.3700.0000.0000.0000.000
6A6THR00.011-0.0318.2100.1360.1360.0000.0000.0000.000
7A7GLN00.004-0.0016.804-0.152-0.1520.0000.0000.0000.000
8A8THR0-0.033-0.0409.6590.0590.0590.0000.0000.0000.000
9A9ARG10.7930.86313.2510.1370.1370.0000.0000.0000.000
10A10ALA00.0220.01411.3090.0030.0030.0000.0000.0000.000
11A11ARG10.8530.92212.616-0.408-0.4080.0000.0000.0000.000
12A12ILE0-0.021-0.00214.906-0.020-0.0200.0000.0000.0000.000
13A13LEU00.0260.00916.180-0.007-0.0070.0000.0000.0000.000
14A14GLY00.0190.02116.563-0.014-0.0140.0000.0000.0000.000
15A15ALA00.0080.00417.500-0.010-0.0100.0000.0000.0000.000
16A16ALA0-0.009-0.01220.507-0.017-0.0170.0000.0000.0000.000
17A17THR0-0.017-0.01819.231-0.006-0.0060.0000.0000.0000.000
18A18GLN0-0.027-0.01120.696-0.007-0.0070.0000.0000.0000.000
19A19ALA00.0310.01523.157-0.011-0.0110.0000.0000.0000.000
20A20LEU0-0.0330.00224.752-0.010-0.0100.0000.0000.0000.000
21A21LEU0-0.050-0.03022.988-0.011-0.0110.0000.0000.0000.000
22A22GLU-1-0.979-0.98125.8160.1180.1180.0000.0000.0000.000
23A23ARG10.7550.84128.617-0.084-0.0840.0000.0000.0000.000
24A24GLY00.0270.04130.150-0.006-0.0060.0000.0000.0000.000
25A25ALA0-0.015-0.04829.6020.0060.0060.0000.0000.0000.000
26A26VAL0-0.061-0.02830.613-0.002-0.0020.0000.0000.0000.000
27A27GLU-1-0.890-0.93333.2450.0560.0560.0000.0000.0000.000
28A28PRO00.0130.03128.3120.0030.0030.0000.0000.0000.000
29A29SER00.016-0.02030.213-0.008-0.0080.0000.0000.0000.000
30A30VAL00.025-0.00825.6200.0090.0090.0000.0000.0000.000
31A31GLY0-0.008-0.00725.9660.0120.0120.0000.0000.0000.000
32A32GLU-1-0.744-0.83126.8160.0880.0880.0000.0000.0000.000
33A33VAL00.0230.02722.1140.0160.0160.0000.0000.0000.000
34A34MET0-0.046-0.02220.2880.0200.0200.0000.0000.0000.000
35A35GLY00.0250.00922.0050.0250.0250.0000.0000.0000.000
36A36ALA0-0.0070.00022.9620.0200.0200.0000.0000.0000.000
37A37ALA0-0.0060.01318.0590.0300.0300.0000.0000.0000.000
38A38GLY00.0070.01118.0250.0540.0540.0000.0000.0000.000
39A39LEU0-0.112-0.05016.0810.0230.0230.0000.0000.0000.000
40A40THR00.0320.00020.113-0.016-0.0160.0000.0000.0000.000
41A41VAL00.0620.01822.196-0.004-0.0040.0000.0000.0000.000
42A42GLY00.0090.00424.877-0.013-0.0130.0000.0000.0000.000
43A43GLY0-0.014-0.00620.956-0.013-0.0130.0000.0000.0000.000
44A44PHE00.0190.00621.121-0.016-0.0160.0000.0000.0000.000
45A45TYR00.0500.00622.201-0.012-0.0120.0000.0000.0000.000
46A46ALA0-0.052-0.00320.161-0.017-0.0170.0000.0000.0000.000
47A47HIS0-0.094-0.04314.922-0.053-0.0530.0000.0000.0000.000
48A48PHE00.0250.00218.338-0.025-0.0250.0000.0000.0000.000
49A49GLN00.0260.01122.8230.0050.0050.0000.0000.0000.000
50A50SER00.025-0.00226.4060.0080.0080.0000.0000.0000.000
51A51LYS10.8610.92326.503-0.027-0.0270.0000.0000.0000.000
52A52ASP-1-0.841-0.92427.319-0.008-0.0080.0000.0000.0000.000
53A53ALA0-0.028-0.00525.656-0.004-0.0040.0000.0000.0000.000
54A54LEU0-0.033-0.00521.322-0.007-0.0070.0000.0000.0000.000
55A55MET0-0.022-0.01323.3920.0030.0030.0000.0000.0000.000
56A56LEU00.0020.01525.6060.0020.0020.0000.0000.0000.000
57A57GLU-1-0.718-0.81818.351-0.123-0.1230.0000.0000.0000.000
58A58ALA0-0.015-0.02021.117-0.002-0.0020.0000.0000.0000.000
59A59PHE0-0.003-0.01322.1830.0040.0040.0000.0000.0000.000
60A60GLU-1-0.920-0.97323.225-0.109-0.1090.0000.0000.0000.000
61A61GLN0-0.045-0.01615.8670.0270.0270.0000.0000.0000.000
62A62LEU0-0.001-0.00120.565-0.001-0.0010.0000.0000.0000.000
63A63LEU0-0.028-0.01722.2100.0000.0000.0000.0000.0000.000
64A64GLY0-0.006-0.01121.840-0.005-0.0050.0000.0000.0000.000
65A65LYS10.8880.94216.2310.0410.0410.0000.0000.0000.000
66A66ARG10.8450.90720.863-0.012-0.0120.0000.0000.0000.000
67A67ARG10.9180.94624.4140.0960.0960.0000.0000.0000.000
68A68GLU-1-0.873-0.91917.645-0.124-0.1240.0000.0000.0000.000
69A69LEU0-0.006-0.00420.9700.0020.0020.0000.0000.0000.000
70A70LEU0-0.041-0.02123.3790.0020.0020.0000.0000.0000.000
71A71GLY0-0.010-0.00224.9990.0000.0000.0000.0000.0000.000
72A72GLU-1-0.961-0.98120.536-0.066-0.0660.0000.0000.0000.000
73A73LEU0-0.099-0.04124.6940.0090.0090.0000.0000.0000.000
74A74ASP-1-0.855-0.93428.366-0.066-0.0660.0000.0000.0000.000
75A75PRO0-0.012-0.02128.7760.0030.0030.0000.0000.0000.000
76A76GLY0-0.037-0.00931.6210.0000.0000.0000.0000.0000.000
77A77LEU0-0.063-0.01532.3980.0060.0060.0000.0000.0000.000
78A78SER00.006-0.04035.793-0.003-0.0030.0000.0000.0000.000
79A79GLY00.0860.03237.3320.0010.0010.0000.0000.0000.000
80A80LYS10.8840.93637.9350.0180.0180.0000.0000.0000.000
81A81GLU-1-0.846-0.88336.880-0.027-0.0270.0000.0000.0000.000
82A82ARG10.8140.88731.9440.0620.0620.0000.0000.0000.000
83A83ARG10.7370.83334.0150.0350.0350.0000.0000.0000.000
84A84ALA0-0.020-0.00435.9610.0050.0050.0000.0000.0000.000
85A85LEU00.0160.00131.3280.0060.0060.0000.0000.0000.000
86A86ALA00.0150.01731.1040.0060.0060.0000.0000.0000.000
87A87ALA00.015-0.00332.0620.0070.0070.0000.0000.0000.000
88A88ALA0-0.049-0.03333.7340.0070.0070.0000.0000.0000.000
89A89PHE0-0.008-0.00427.7530.0090.0090.0000.0000.0000.000
90A90TYR0-0.021-0.01529.7490.0110.0110.0000.0000.0000.000
91A91LEU0-0.0010.01631.2770.0080.0080.0000.0000.0000.000
92A92SER00.0280.01830.2260.0040.0040.0000.0000.0000.000
93A93ARG10.9110.92932.721-0.051-0.0510.0000.0000.0000.000
94A94LYS10.9030.95326.204-0.119-0.1190.0000.0000.0000.000
95A95HIS00.0020.00927.5470.0090.0090.0000.0000.0000.000
96A96ARG10.7700.83729.328-0.054-0.0540.0000.0000.0000.000
97A97ASP-1-0.822-0.88631.0810.0710.0710.0000.0000.0000.000
98A98ALA0-0.0010.00826.9990.0090.0090.0000.0000.0000.000
99A99GLN0-0.0030.00825.4250.0170.0170.0000.0000.0000.000
100A100VAL0-0.034-0.02723.869-0.002-0.0020.0000.0000.0000.000
101A101ASP-1-0.854-0.92018.4020.1880.1880.0000.0000.0000.000
102A102ALA0-0.0020.00319.6050.0040.0040.0000.0000.0000.000
103A103GLY00.0130.02021.332-0.018-0.0180.0000.0000.0000.000
104A104CYS0-0.015-0.00824.502-0.013-0.0130.0000.0000.0000.000
105A105PRO00.0670.03225.7490.0070.0070.0000.0000.0000.000
106A106LEU0-0.0020.01728.1370.0000.0000.0000.0000.0000.000
107A107PRO0-0.025-0.01530.923-0.001-0.0010.0000.0000.0000.000
108A108ALA0-0.0050.01230.600-0.001-0.0010.0000.0000.0000.000
109A109THR00.033-0.00929.635-0.003-0.0030.0000.0000.0000.000
110A110LEU0-0.0090.00232.984-0.005-0.0050.0000.0000.0000.000
111A111ALA0-0.001-0.00135.686-0.004-0.0040.0000.0000.0000.000
112A112GLU-1-0.786-0.91133.2760.0160.0160.0000.0000.0000.000
113A113VAL00.0170.01633.600-0.003-0.0030.0000.0000.0000.000
114A114ALA0-0.043-0.02335.985-0.004-0.0040.0000.0000.0000.000
115A115ARG10.8550.93338.343-0.003-0.0030.0000.0000.0000.000
116A116LEU0-0.0160.01832.2440.0020.0020.0000.0000.0000.000
117A117PRO00.0180.00232.332-0.004-0.0040.0000.0000.0000.000
118A118GLU-1-0.760-0.87733.850-0.043-0.0430.0000.0000.0000.000
119A119GLY00.0180.01730.819-0.002-0.0020.0000.0000.0000.000
120A120PHE00.0280.00328.798-0.003-0.0030.0000.0000.0000.000
121A121ARG10.9250.94231.6560.0340.0340.0000.0000.0000.000
122A122GLU-1-0.888-0.91932.182-0.087-0.0870.0000.0000.0000.000
123A123VAL0-0.042-0.01427.203-0.003-0.0030.0000.0000.0000.000
124A124LEU0-0.020-0.01530.1720.0000.0000.0000.0000.0000.000
125A125SER0-0.024-0.02532.2420.0020.0020.0000.0000.0000.000
126A126ARG10.9500.97828.9700.0970.0970.0000.0000.0000.000
127A127HIS0-0.0020.01327.285-0.010-0.0100.0000.0000.0000.000
128A128VAL0-0.013-0.01830.5500.0010.0010.0000.0000.0000.000
129A129GLU-1-0.885-0.93833.947-0.069-0.0690.0000.0000.0000.000
130A130ILE0-0.025-0.00928.526-0.002-0.0020.0000.0000.0000.000
131A131MET0-0.034-0.01128.4090.0030.0030.0000.0000.0000.000
132A132VAL00.0310.02032.1200.0020.0020.0000.0000.0000.000
133A133THR0-0.042-0.03134.3250.0010.0010.0000.0000.0000.000
134A134SER0-0.070-0.03531.3810.0000.0000.0000.0000.0000.000
135A135LEU0-0.015-0.00732.9520.0020.0020.0000.0000.0000.000
136A136ALA0-0.0270.00635.4380.0050.0050.0000.0000.0000.000
137A137GLU-1-0.818-0.89737.148-0.063-0.0630.0000.0000.0000.000
138A138SER0-0.067-0.05240.097-0.002-0.0020.0000.0000.0000.000
139A139PRO00.0330.01643.0780.0010.0010.0000.0000.0000.000
140A140GLU-1-0.848-0.90644.781-0.038-0.0380.0000.0000.0000.000
141A141GLU-1-0.784-0.86541.212-0.034-0.0340.0000.0000.0000.000
142A142THR0-0.020-0.01540.7520.0000.0000.0000.0000.0000.000
143A143ASP-1-0.888-0.95241.453-0.030-0.0300.0000.0000.0000.000
144A144VAL0-0.054-0.02042.2770.0030.0030.0000.0000.0000.000
145A145ALA00.0360.01537.6990.0030.0030.0000.0000.0000.000
146A146LEU0-0.0090.00238.4320.0020.0020.0000.0000.0000.000
147A147ALA00.0120.00039.8070.0030.0030.0000.0000.0000.000
148A148ASP-1-0.690-0.84838.261-0.013-0.0130.0000.0000.0000.000
149A149LEU0-0.015-0.00933.4470.0040.0040.0000.0000.0000.000
150A150VAL0-0.029-0.00436.6170.0040.0040.0000.0000.0000.000
151A151LEU0-0.018-0.00439.1720.0050.0050.0000.0000.0000.000
152A152MET0-0.025-0.01234.0110.0060.0060.0000.0000.0000.000
153A153ILE0-0.001-0.00133.3350.0060.0060.0000.0000.0000.000
154A154GLY00.0220.00735.4360.0050.0050.0000.0000.0000.000
155A155GLY00.0230.01338.5280.0030.0030.0000.0000.0000.000
156A156LEU0-0.046-0.03231.2770.0050.0050.0000.0000.0000.000
157A157ALA0-0.0120.00435.7750.0060.0060.0000.0000.0000.000
158A158LEU0-0.0010.00337.0430.0030.0030.0000.0000.0000.000
159A159ALA00.011-0.00637.3830.0030.0030.0000.0000.0000.000
160A160ARG10.8790.94129.595-0.052-0.0520.0000.0000.0000.000
161A161ALA0-0.034-0.00536.7400.0040.0040.0000.0000.0000.000
162A162LEU0-0.058-0.02839.6450.0010.0010.0000.0000.0000.000
163A163GLY00.0320.04338.2810.0020.0020.0000.0000.0000.000
164A164PRO0-0.044-0.03836.159-0.003-0.0030.0000.0000.0000.000
165A165GLY00.0720.03138.917-0.001-0.0010.0000.0000.0000.000
166A166GLU-1-0.932-0.97241.9520.0340.0340.0000.0000.0000.000
167A167LEU0-0.012-0.00144.447-0.002-0.0020.0000.0000.0000.000
168A168SER00.0410.01939.176-0.003-0.0030.0000.0000.0000.000
169A169ASP-1-0.777-0.88939.1170.0450.0450.0000.0000.0000.000
170A170ARG10.8850.94340.895-0.022-0.0220.0000.0000.0000.000
171A171VAL00.0140.01740.665-0.003-0.0030.0000.0000.0000.000
172A172LEU00.0050.01136.000-0.003-0.0030.0000.0000.0000.000
173A173ARG10.9180.95139.406-0.030-0.0300.0000.0000.0000.000
174A174ALA0-0.0150.00041.522-0.003-0.0030.0000.0000.0000.000
175A175ALA00.0290.01739.983-0.003-0.0030.0000.0000.0000.000
176A176LYS10.8830.92836.034-0.028-0.0280.0000.0000.0000.000
177A177GLN0-0.076-0.04839.8940.0000.0000.0000.0000.0000.000
178A178ALA0-0.0290.00543.243-0.002-0.0020.0000.0000.0000.000
179A179VAL0-0.0400.00138.455-0.002-0.0020.0000.0000.0000.000
180A180ASN0-0.058-0.03341.119-0.003-0.0030.0000.0000.0000.000