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: NN74Q

Calculation Name: 2F20-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2F20

Chain ID: A

ChEMBL ID:

UniProt ID: Q8A8E9

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 233
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3179314.404792
FMO2-HF: Nuclear repulsion 3083695.049741
FMO2-HF: Total energy -95619.355051
FMO2-MP2: Total energy -95898.727414


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:2:CYS)


Summations of interaction energy for fragment #1(A:2:CYS)
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.
-33.448-18.4346.242-8.586-12.67-0.038
Interaction energy analysis for fragmet #1(A:2:CYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / q_NPA : 0.022
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].
3A4HIS00.0190.0133.356-5.187-1.4880.007-2.130-1.5760.010
4A5ASN00.0850.0464.4801.6441.9730.001-0.033-0.2970.000
5A6SER0-0.003-0.0045.685-0.464-0.4640.0000.0000.0000.000
6A7MET00.010-0.0108.928-0.046-0.0460.0000.0000.0000.000
7A8SER0-0.002-0.00411.821-0.061-0.0610.0000.0000.0000.000
8A9ALA00.0190.02714.794-0.047-0.0470.0000.0000.0000.000
9A10LYS10.8900.94117.125-0.145-0.1450.0000.0000.0000.000
10A11ALA00.0940.02418.5280.0080.0080.0000.0000.0000.000
11A12ILE00.010-0.00419.5790.0040.0040.0000.0000.0000.000
12A13LYS10.8970.95219.492-0.148-0.1480.0000.0000.0000.000
13A14VAL00.0390.02415.5600.0020.0020.0000.0000.0000.000
14A15ALA00.003-0.00418.1090.0000.0000.0000.0000.0000.000
15A16ALA0-0.030-0.01420.957-0.005-0.0050.0000.0000.0000.000
16A17ARG10.7470.87315.543-0.236-0.2360.0000.0000.0000.000
17A18TYR0-0.046-0.07913.8340.0080.0080.0000.0000.0000.000
18A19GLY0-0.0150.00320.240-0.007-0.0070.0000.0000.0000.000
19A20ARG10.7850.89520.571-0.163-0.1630.0000.0000.0000.000
20A21GLN0-0.004-0.01523.8930.0010.0010.0000.0000.0000.000
21A22SER00.045-0.00623.4920.0080.0080.0000.0000.0000.000
22A23ASP-1-0.844-0.87124.5370.0980.0980.0000.0000.0000.000
23A24VAL00.0180.00822.221-0.002-0.0020.0000.0000.0000.000
24A25VAL0-0.016-0.02418.7550.0010.0010.0000.0000.0000.000
25A26GLU-1-0.906-0.96121.5920.1190.1190.0000.0000.0000.000
26A27ILE0-0.0040.02224.460-0.003-0.0030.0000.0000.0000.000
27A28TYR0-0.055-0.03420.972-0.009-0.0090.0000.0000.0000.000
28A29GLN00.0520.02320.9430.0070.0070.0000.0000.0000.000
29A30SER0-0.033-0.01421.0980.0090.0090.0000.0000.0000.000
30A31ILE0-0.083-0.03318.1310.0000.0000.0000.0000.0000.000
31A32LEU0-0.030-0.02416.3750.0250.0250.0000.0000.0000.000
32A33ASP-1-0.837-0.91016.2770.2090.2090.0000.0000.0000.000
33A34GLU-1-0.960-0.98616.5140.1790.1790.0000.0000.0000.000
34A35GLN00.0050.01613.250-0.001-0.0010.0000.0000.0000.000
35A36TYR00.0160.00912.2460.0980.0980.0000.0000.0000.000
36A37HIS0-0.039-0.0168.8080.0010.0010.0000.0000.0000.000
37A38VAL0-0.0130.0068.453-0.161-0.1610.0000.0000.0000.000
38A39ASN00.027-0.0028.0290.3180.3180.0000.0000.0000.000
39A40ALA00.0980.0436.295-0.155-0.1550.0000.0000.0000.000
40A41PHE0-0.027-0.0137.130-0.077-0.0770.0000.0000.0000.000
41A42THR0-0.064-0.02211.072-0.005-0.0050.0000.0000.0000.000
42A43PHE0-0.055-0.03511.6930.0000.0000.0000.0000.0000.000
43A44PRO0-0.0050.01011.104-0.003-0.0030.0000.0000.0000.000
44A45ARG10.9460.97613.462-0.124-0.1240.0000.0000.0000.000
45A46TYR0-0.069-0.0569.4210.0720.0720.0000.0000.0000.000
46A47PRO00.0370.01813.115-0.033-0.0330.0000.0000.0000.000
47A48ILE0-0.006-0.00111.6360.0380.0380.0000.0000.0000.000
48A49ILE00.0000.01614.901-0.031-0.0310.0000.0000.0000.000
49A50THR00.0350.00516.4350.0140.0140.0000.0000.0000.000
50A51SER0-0.010-0.01719.055-0.001-0.0010.0000.0000.0000.000
51A52SER0-0.017-0.00122.219-0.009-0.0090.0000.0000.0000.000
52A53ASP-1-0.806-0.90223.1910.1120.1120.0000.0000.0000.000
53A54GLH0-0.096-0.08824.2010.0060.0060.0000.0000.0000.000
54A55VAL0-0.0190.00618.0290.0070.0070.0000.0000.0000.000
55A56GLN0-0.058-0.02818.451-0.016-0.0160.0000.0000.0000.000
56A57VAL0-0.008-0.00817.3970.0200.0200.0000.0000.0000.000
57A58PHE00.0080.02214.759-0.014-0.0140.0000.0000.0000.000
58A59ASN0-0.023-0.02514.5820.0240.0240.0000.0000.0000.000
59A60TRP0-0.045-0.0274.261-0.1910.060-0.001-0.080-0.1700.000
60A61GLY00.023-0.01810.769-0.044-0.0440.0000.0000.0000.000
61A62LEU0-0.046-0.01811.4900.0240.0240.0000.0000.0000.000
62A63ILE00.0300.03713.509-0.027-0.0270.0000.0000.0000.000
63A64PRO0-0.029-0.01416.5370.0120.0120.0000.0000.0000.000
64A65PHE0-0.002-0.00318.964-0.010-0.0100.0000.0000.0000.000
65A66TRP0-0.088-0.04319.326-0.009-0.0090.0000.0000.0000.000
66A67VAL0-0.017-0.00520.009-0.007-0.0070.0000.0000.0000.000
67A68ARG10.9050.95023.313-0.010-0.0100.0000.0000.0000.000
68A69SER00.0420.02525.1060.0010.0010.0000.0000.0000.000
69A70GLU-1-0.852-0.93223.5620.0070.0070.0000.0000.0000.000
70A71GLU-1-0.949-0.96622.453-0.031-0.0310.0000.0000.0000.000
71A72ASP-1-0.864-0.93921.701-0.037-0.0370.0000.0000.0000.000
72A73ALA0-0.047-0.02419.425-0.010-0.0100.0000.0000.0000.000
73A74THR0-0.056-0.02417.752-0.007-0.0070.0000.0000.0000.000
74A75GLU-1-0.857-0.93916.729-0.122-0.1220.0000.0000.0000.000
75A76ILE0-0.021-0.01915.130-0.029-0.0290.0000.0000.0000.000
76A77ARG10.9491.00513.675-0.001-0.0010.0000.0000.0000.000
77A78LYS10.8390.91411.3060.0930.0930.0000.0000.0000.000
78A79MET0-0.081-0.0309.997-0.107-0.1070.0000.0000.0000.000
79A80THR0-0.070-0.05410.1760.0200.0200.0000.0000.0000.000
80A81LEU00.0520.0546.6800.0670.0670.0000.0000.0000.000
81A82ASN0-0.077-0.0352.569-3.334-1.0751.028-1.432-1.855-0.016
82A83ALA00.0330.0156.195-0.070-0.0700.0000.0000.0000.000
83A84ARG10.8770.9438.4930.1510.1510.0000.0000.0000.000
84A85ALA00.0720.0269.355-0.151-0.1510.0000.0000.0000.000
85A86ASP-1-0.908-0.96111.3750.1270.1270.0000.0000.0000.000
86A87THR00.0340.03013.430-0.046-0.0460.0000.0000.0000.000
87A88ILE0-0.0100.00011.666-0.043-0.0430.0000.0000.0000.000
88A89PHE0-0.028-0.03414.875-0.025-0.0250.0000.0000.0000.000
89A90GLU-1-0.948-0.97017.9500.0610.0610.0000.0000.0000.000
90A91LYS10.9460.96912.076-0.092-0.0920.0000.0000.0000.000
91A92PRO00.017-0.00417.8260.0130.0130.0000.0000.0000.000
92A93SER00.0160.01315.2420.0020.0020.0000.0000.0000.000
93A94PHE00.0250.00011.1300.0190.0190.0000.0000.0000.000
94A95ARG10.9560.99416.076-0.040-0.0400.0000.0000.0000.000
95A96GLU-1-0.899-0.95819.1920.0680.0680.0000.0000.0000.000
96A97PRO00.0050.00116.1560.0050.0050.0000.0000.0000.000
97A98ILE00.0090.02314.6730.0110.0110.0000.0000.0000.000
98A99MET0-0.041-0.01617.1450.0050.0050.0000.0000.0000.000
99A100LYS10.8780.93020.419-0.097-0.0970.0000.0000.0000.000
100A101LYS10.8330.94718.266-0.109-0.1090.0000.0000.0000.000
101A102ARG10.9350.98015.503-0.180-0.1800.0000.0000.0000.000
102A103CYS0-0.062-0.02413.295-0.015-0.0150.0000.0000.0000.000
103A104ILE00.0230.02112.4490.0380.0380.0000.0000.0000.000
104A105VAL0-0.003-0.0047.860-0.036-0.0360.0000.0000.0000.000
105A106PRO00.0230.0209.3640.0510.0510.0000.0000.0000.000
106A107SER00.0230.0096.6330.0140.0140.0000.0000.0000.000
107A108THR00.0260.0329.264-0.102-0.1020.0000.0000.0000.000
108A109GLY0-0.006-0.0038.026-0.122-0.1220.0000.0000.0000.000
109A110TYR0-0.045-0.0272.536-2.089-0.5680.938-0.832-1.627-0.003
110A111PHE0-0.036-0.0254.948-1.113-0.998-0.001-0.009-0.1030.000
111A112GLU-1-0.862-0.9252.436-15.333-11.4771.393-2.676-2.573-0.031
112A113TRP0-0.050-0.0336.0900.4390.4390.0000.0000.0000.000
113A114ARG10.9541.0138.9900.1780.1780.0000.0000.0000.000
114A115HIS0-0.078-0.0609.8990.2200.2200.0000.0000.0000.000
115A116GLU-1-0.844-0.92013.678-0.297-0.2970.0000.0000.0000.000
116A117GLY00.0030.01317.2900.0400.0400.0000.0000.0000.000
117A118ALA0-0.021-0.02318.440-0.024-0.0240.0000.0000.0000.000
118A119ASN0-0.058-0.02517.7930.0140.0140.0000.0000.0000.000
119A120LYS10.9420.97411.6720.3980.3980.0000.0000.0000.000
120A121ILE00.0120.01613.3240.0730.0730.0000.0000.0000.000
121A122PRO0-0.0180.00110.834-0.122-0.1220.0000.0000.0000.000
122A123TYR00.0550.0059.3520.0280.0280.0000.0000.0000.000
123A124TYR0-0.029-0.0118.6060.0980.0980.0000.0000.0000.000
124A125ILE00.009-0.0105.820-0.161-0.1610.0000.0000.0000.000
125A126TYR0-0.002-0.0068.1890.2070.2070.0000.0000.0000.000
126A127VAL0-0.018-0.00310.343-0.073-0.0730.0000.0000.0000.000
127A128LYS10.8780.93812.6980.0070.0070.0000.0000.0000.000
128A129ASP-1-0.940-0.97016.3880.0880.0880.0000.0000.0000.000
129A130GLU-1-0.864-0.94514.5230.2280.2280.0000.0000.0000.000
130A131PRO0-0.076-0.03414.3580.0270.0270.0000.0000.0000.000
131A132ILE0-0.026-0.01013.1510.0330.0330.0000.0000.0000.000
132A133PHE00.0720.0407.044-0.029-0.0290.0000.0000.0000.000
133A134SER00.0530.04011.0890.0360.0360.0000.0000.0000.000
134A135MET0-0.0390.0084.502-0.0600.053-0.001-0.013-0.1000.000
135A136ALA00.0380.0228.849-0.085-0.0850.0000.0000.0000.000
136A137GLY00.0280.0028.8060.1310.1310.0000.0000.0000.000
137A138ILE0-0.046-0.01810.556-0.039-0.0390.0000.0000.0000.000
138A139TYR00.0670.01012.454-0.010-0.0100.0000.0000.0000.000
139A140ASP-1-0.828-0.93415.0880.0790.0790.0000.0000.0000.000
140A141ARG10.9390.97018.073-0.070-0.0700.0000.0000.0000.000
141A142TRP0-0.060-0.04220.908-0.003-0.0030.0000.0000.0000.000
142A143LEU00.0420.04222.5010.0010.0010.0000.0000.0000.000
143A144ASP-1-0.817-0.91025.3210.0120.0120.0000.0000.0000.000
144A145LYS10.8910.92526.671-0.016-0.0160.0000.0000.0000.000
145A146ASP-1-0.932-0.96229.6460.0080.0080.0000.0000.0000.000
146A147THR0-0.0210.01027.6080.0000.0000.0000.0000.0000.000
147A148GLY0-0.078-0.04129.8710.0020.0020.0000.0000.0000.000
148A149GLU-1-0.947-0.98224.2550.0480.0480.0000.0000.0000.000
149A150GLU-1-0.899-0.95824.2770.0530.0530.0000.0000.0000.000
150A151HIS10.8640.93319.756-0.040-0.0400.0000.0000.0000.000
151A152GLU-1-0.878-0.94318.7970.1080.1080.0000.0000.0000.000
152A153THR0-0.051-0.00614.2230.0010.0010.0000.0000.0000.000
153A154PHE00.0230.0018.3660.0000.0000.0000.0000.0000.000
154A155SER0-0.023-0.0258.636-0.016-0.0160.0000.0000.0000.000
155A156ILE00.0130.0164.051-0.1720.0600.001-0.034-0.1980.000
156A157ILE0-0.013-0.0076.0810.0630.0630.0000.0000.0000.000
157A158THR00.0000.0073.467-0.586-0.1800.556-0.184-0.7780.001
158A159THR0-0.019-0.0305.891-0.682-0.692-0.001-0.0050.0160.000
159A160ASP-1-0.942-0.9726.7380.1800.1800.0000.0000.0000.000
160A161THR0-0.012-0.0166.2940.1460.1460.0000.0000.0000.000
161A162ASN00.0000.0198.540-0.002-0.0020.0000.0000.0000.000
162A163SER00.036-0.01011.151-0.098-0.0980.0000.0000.0000.000
163A164LEU00.0150.02610.865-0.060-0.0600.0000.0000.0000.000
164A165THR00.016-0.0406.350-0.034-0.0340.0000.0000.0000.000
165A166ASP-1-0.834-0.8917.675-0.977-0.9770.0000.0000.0000.000
166A167TYR0-0.047-0.0109.8760.0040.0040.0000.0000.0000.000
167A168ILE0-0.035-0.0277.6060.0440.0440.0000.0000.0000.000
168A169ASP-1-0.715-0.8674.217-3.855-3.6820.000-0.016-0.1570.000
169A170ASN0-0.021-0.0187.0120.0720.0720.0000.0000.0000.000
170A171THR0-0.079-0.0418.7260.1460.1460.0000.0000.0000.000
171A172LYS10.8470.9195.6391.4251.4250.0000.0000.0000.000
172A173HIS0-0.050-0.0107.1580.3660.3660.0000.0000.0000.000
173A174ARG10.8210.9123.4820.0310.4800.250-0.176-0.5240.001
174A175MET00.0290.0373.074-3.977-3.0070.435-0.558-0.847-0.003
175A176PRO00.008-0.0102.9850.9171.5511.630-0.393-1.8710.003
176A177ALA0-0.016-0.0154.788-0.998-0.9810.007-0.015-0.0100.000
177A178ILE0-0.025-0.0087.405-0.075-0.0750.0000.0000.0000.000
178A179LEU0-0.017-0.0029.902-0.058-0.0580.0000.0000.0000.000
179A180THR0-0.048-0.04913.416-0.017-0.0170.0000.0000.0000.000
180A181GLN00.0780.02316.068-0.001-0.0010.0000.0000.0000.000
181A182GLU-1-0.949-0.97018.0700.1280.1280.0000.0000.0000.000
182A183GLU-1-0.933-0.94316.7590.2060.2060.0000.0000.0000.000
183A184GLU-1-0.775-0.86615.8790.2440.2440.0000.0000.0000.000
184A185GLU-1-0.782-0.90918.1350.1640.1640.0000.0000.0000.000
185A186LYS10.9130.96921.113-0.143-0.1430.0000.0000.0000.000
186A187TRP0-0.016-0.02013.353-0.002-0.0020.0000.0000.0000.000
187A188LEU0-0.033-0.01916.9520.0030.0030.0000.0000.0000.000
188A189ASN00.0310.02720.024-0.018-0.0180.0000.0000.0000.000
189A190PRO0-0.016-0.02323.0680.0040.0040.0000.0000.0000.000
190A191SER0-0.028-0.01524.500-0.006-0.0060.0000.0000.0000.000
191A192LEU0-0.0530.00020.261-0.004-0.0040.0000.0000.0000.000
192A193SER0-0.011-0.00423.970-0.001-0.0010.0000.0000.0000.000
193A194LYS11.0010.98021.182-0.099-0.0990.0000.0000.0000.000
194A195ALA0-0.022-0.01320.8350.0150.0150.0000.0000.0000.000
195A196GLU-1-0.839-0.91821.1070.1160.1160.0000.0000.0000.000
196A197ILE00.0030.01016.9050.0140.0140.0000.0000.0000.000
197A198ALA0-0.001-0.01116.6100.0320.0320.0000.0000.0000.000
198A199SER0-0.079-0.04316.4410.0130.0130.0000.0000.0000.000
199A200LEU0-0.031-0.00516.413-0.013-0.0130.0000.0000.0000.000
200A201LEU0-0.041-0.00211.4500.0490.0490.0000.0000.0000.000
201A202LYS10.9400.96312.723-0.182-0.1820.0000.0000.0000.000
202A203PRO00.0040.01010.2850.0790.0790.0000.0000.0000.000
203A204PHE00.0360.01310.632-0.039-0.0390.0000.0000.0000.000
204A205ASP-1-0.826-0.92712.566-0.046-0.0460.0000.0000.0000.000
205A206THR00.020-0.00713.577-0.022-0.0220.0000.0000.0000.000
206A207GLU-1-0.925-0.95214.581-0.063-0.0630.0000.0000.0000.000
207A208LYS10.8890.94915.408-0.102-0.1020.0000.0000.0000.000
208A209MET0-0.0420.0018.2220.0140.0140.0000.0000.0000.000
209A210ASP-1-0.841-0.92812.532-0.067-0.0670.0000.0000.0000.000
210A211ALA0-0.047-0.03310.7450.0080.0080.0000.0000.0000.000
211A212TYR0-0.076-0.02812.572-0.011-0.0110.0000.0000.0000.000
212A213VAL00.0230.02013.0080.0190.0190.0000.0000.0000.000
213A214ILE00.0130.00611.3030.0310.0310.0000.0000.0000.000
214A215ARG10.9230.96115.122-0.093-0.0930.0000.0000.0000.000
215A216ASN00.0460.00415.0740.0200.0200.0000.0000.0000.000
216A217ASP-1-0.967-0.98815.8500.0770.0770.0000.0000.0000.000
217A218PHE00.0410.0239.660-0.031-0.0310.0000.0000.0000.000
218A219LEU00.0080.00510.8500.0260.0260.0000.0000.0000.000
219A220LYS10.8660.93114.433-0.037-0.0370.0000.0000.0000.000
220A221LYS10.8730.95316.977-0.145-0.1450.0000.0000.0000.000
221A222SER00.0300.01617.0740.0160.0160.0000.0000.0000.000
222A223PRO00.0640.02614.6380.0070.0070.0000.0000.0000.000
223A224ASN00.0090.00115.3730.0400.0400.0000.0000.0000.000
224A225ASP-1-0.850-0.89917.8380.1280.1280.0000.0000.0000.000
225A226PRO00.0930.02217.2810.0280.0280.0000.0000.0000.000
226A227THR0-0.125-0.06517.7260.0040.0040.0000.0000.0000.000
227A228ILE0-0.044-0.01412.754-0.025-0.0250.0000.0000.0000.000
228A229VAL00.0410.02212.5280.0110.0110.0000.0000.0000.000
229A230GLN0-0.091-0.02514.964-0.054-0.0540.0000.0000.0000.000
230A231ARG11.0021.00517.226-0.049-0.0490.0000.0000.0000.000
231A232ALA00.0330.00018.0860.0080.0080.0000.0000.0000.000
232A233LEU0-0.128-0.04619.4280.0040.0040.0000.0000.0000.000
233A234GLU-1-0.902-0.96023.050-0.047-0.0470.0000.0000.0000.000