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: QYVRY

Calculation Name: 2F6I-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2F6I

Chain ID: A

ChEMBL ID:

UniProt ID: O97252

Base Structure: X-ray

Registration Date: 2023-06-22

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 182
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2046214.530503
FMO2-HF: Nuclear repulsion 1972749.805133
FMO2-HF: Total energy -73464.72537
FMO2-MP2: Total energy -73680.04368


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:177:HIS)


Summations of interaction energy for fragment #1(A:177:HIS)
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.
-27.162-24.97610.994-5.773-7.406-0.042
Interaction energy analysis for fragmet #1(A:177:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.006 / q_NPA : -0.020
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].
3A179ASP-1-0.810-0.8741.900-31.067-29.27810.970-5.692-7.066-0.043
4A180ILE0-0.072-0.0394.119-1.286-0.8890.024-0.081-0.3400.001
5A181LYS10.8010.8875.2293.6593.6590.0000.0000.0000.000
6A182ASP-1-0.814-0.91710.122-0.013-0.0130.0000.0000.0000.000
7A183MET0-0.023-0.00812.9900.0320.0320.0000.0000.0000.000
8A184LYS10.9510.97614.5140.0320.0320.0000.0000.0000.000
9A185LYS10.9250.94913.5400.8300.8300.0000.0000.0000.000
10A186ASP-1-0.742-0.87010.195-1.138-1.1380.0000.0000.0000.000
11A187VAL00.0130.01811.594-0.075-0.0750.0000.0000.0000.000
12A188LYS10.9460.97612.9800.0590.0590.0000.0000.0000.000
13A189LEU00.0320.02211.545-0.054-0.0540.0000.0000.0000.000
14A190PHE00.003-0.0065.640-0.127-0.1270.0000.0000.0000.000
15A191PHE0-0.028-0.02010.587-0.007-0.0070.0000.0000.0000.000
16A192PHE00.0510.04013.330-0.042-0.0420.0000.0000.0000.000
17A193LYS10.9330.9558.6022.2852.2850.0000.0000.0000.000
18A194LYS10.8480.9386.8960.5460.5460.0000.0000.0000.000
19A195ARG10.8110.89813.3420.5250.5250.0000.0000.0000.000
20A196ILE0-0.046-0.01213.8990.0950.0950.0000.0000.0000.000
21A197ILE00.0310.00717.341-0.042-0.0420.0000.0000.0000.000
22A198TYR0-0.043-0.04215.3500.0660.0660.0000.0000.0000.000
23A199LEU00.0460.04121.832-0.016-0.0160.0000.0000.0000.000
24A200THR0-0.074-0.05822.8250.0230.0230.0000.0000.0000.000
25A201ASP-1-0.825-0.90425.867-0.065-0.0650.0000.0000.0000.000
26A202GLU-1-0.842-0.89428.910-0.057-0.0570.0000.0000.0000.000
27A203ILE0-0.0320.01331.813-0.018-0.0180.0000.0000.0000.000
28A204ASN00.005-0.02532.402-0.010-0.0100.0000.0000.0000.000
29A205LYS10.8530.90033.3990.1350.1350.0000.0000.0000.000
30A206LYS10.8330.91926.3010.1790.1790.0000.0000.0000.000
31A207THR0-0.003-0.03128.463-0.023-0.0230.0000.0000.0000.000
32A208ALA00.0160.00728.528-0.012-0.0120.0000.0000.0000.000
33A209ASP-1-0.903-0.93829.729-0.265-0.2650.0000.0000.0000.000
34A210GLU-1-0.791-0.88525.103-0.256-0.2560.0000.0000.0000.000
35A211LEU0-0.028-0.00224.889-0.034-0.0340.0000.0000.0000.000
36A212ILE00.0340.01025.776-0.019-0.0190.0000.0000.0000.000
37A213SER0-0.001-0.00225.100-0.022-0.0220.0000.0000.0000.000
38A214GLN0-0.106-0.07220.687-0.042-0.0420.0000.0000.0000.000
39A215LEU00.000-0.00322.167-0.033-0.0330.0000.0000.0000.000
40A216LEU00.0220.00924.399-0.014-0.0140.0000.0000.0000.000
41A217TYR0-0.023-0.00417.165-0.048-0.0480.0000.0000.0000.000
42A218LEU0-0.010-0.01617.594-0.034-0.0340.0000.0000.0000.000
43A219ASP-1-0.749-0.83520.930-0.307-0.3070.0000.0000.0000.000
44A220ASN0-0.067-0.02123.313-0.026-0.0260.0000.0000.0000.000
45A221ILE0-0.028-0.00216.892-0.028-0.0280.0000.0000.0000.000
46A222ASN0-0.034-0.02917.7730.0230.0230.0000.0000.0000.000
47A223HIS00.0130.00021.9030.0110.0110.0000.0000.0000.000
48A224ASN00.0040.01118.6740.0530.0530.0000.0000.0000.000
49A225ASP-1-0.795-0.87321.251-0.131-0.1310.0000.0000.0000.000
50A226ILE00.0040.02220.394-0.047-0.0470.0000.0000.0000.000
51A227LYS10.8900.96817.0300.0090.0090.0000.0000.0000.000
52A228ILE00.0210.01120.643-0.024-0.0240.0000.0000.0000.000
53A229TYR0-0.009-0.00716.8040.0320.0320.0000.0000.0000.000
54A230ILE0-0.022-0.01222.783-0.023-0.0230.0000.0000.0000.000
55A231ASN00.008-0.00225.9850.0300.0300.0000.0000.0000.000
56A232SER00.005-0.01227.714-0.007-0.0070.0000.0000.0000.000
57A233PRO00.0390.01730.6220.0040.0040.0000.0000.0000.000
58A234GLY00.0370.02033.528-0.001-0.0010.0000.0000.0000.000
59A235GLY00.0430.01435.004-0.003-0.0030.0000.0000.0000.000
60A236SER00.010-0.00237.4700.0060.0060.0000.0000.0000.000
61A237ILE00.0190.00538.007-0.005-0.0050.0000.0000.0000.000
62A238ASN00.0290.00939.292-0.007-0.0070.0000.0000.0000.000
63A239GLU-1-0.812-0.89235.127-0.139-0.1390.0000.0000.0000.000
64A240GLY00.0170.00234.720-0.009-0.0090.0000.0000.0000.000
65A241LEU0-0.001-0.00635.304-0.002-0.0020.0000.0000.0000.000
66A242ALA00.0270.02835.303-0.006-0.0060.0000.0000.0000.000
67A243ILE0-0.030-0.01830.056-0.013-0.0130.0000.0000.0000.000
68A244LEU0-0.020-0.00432.043-0.007-0.0070.0000.0000.0000.000
69A245ASP-1-0.851-0.92634.275-0.119-0.1190.0000.0000.0000.000
70A246ILE0-0.039-0.02829.299-0.010-0.0100.0000.0000.0000.000
71A247PHE0-0.026-0.04527.862-0.014-0.0140.0000.0000.0000.000
72A248ASN0-0.055-0.03130.8150.0040.0040.0000.0000.0000.000
73A249TYR0-0.0210.02131.1370.0030.0030.0000.0000.0000.000
74A250ILE0-0.059-0.02425.928-0.013-0.0130.0000.0000.0000.000
75A251LYS10.8730.92328.2640.2390.2390.0000.0000.0000.000
76A252SER0-0.057-0.06024.094-0.004-0.0040.0000.0000.0000.000
77A253ASP-1-0.760-0.83725.857-0.098-0.0980.0000.0000.0000.000
78A254ILE00.0250.01424.874-0.014-0.0140.0000.0000.0000.000
79A255GLN0-0.079-0.05520.9960.0490.0490.0000.0000.0000.000
80A256THR0-0.030-0.01724.466-0.011-0.0110.0000.0000.0000.000
81A257ILE0-0.022-0.01621.0820.0220.0220.0000.0000.0000.000
82A258SER00.0450.02124.543-0.001-0.0010.0000.0000.0000.000
83A259PHE0-0.044-0.03821.4920.0270.0270.0000.0000.0000.000
84A260GLY00.0250.01426.791-0.012-0.0120.0000.0000.0000.000
85A261LEU00.0190.01228.8970.0010.0010.0000.0000.0000.000
86A262VAL0-0.031-0.01929.758-0.009-0.0090.0000.0000.0000.000
87A263ALA00.0380.02732.5600.0050.0050.0000.0000.0000.000
88A264SER00.0490.02935.562-0.014-0.0140.0000.0000.0000.000
89A265MET00.0240.01035.9520.0040.0040.0000.0000.0000.000
90A266ALA00.0060.01831.452-0.007-0.0070.0000.0000.0000.000
91A267SER0-0.006-0.02632.1900.0030.0030.0000.0000.0000.000
92A268VAL0-0.0050.00134.5220.0020.0020.0000.0000.0000.000
93A269ILE00.0080.01029.877-0.003-0.0030.0000.0000.0000.000
94A270LEU0-0.0070.00128.909-0.006-0.0060.0000.0000.0000.000
95A271ALA00.0090.01131.0160.0010.0010.0000.0000.0000.000
96A272SER0-0.063-0.04932.029-0.004-0.0040.0000.0000.0000.000
97A273GLY00.0040.01629.469-0.011-0.0110.0000.0000.0000.000
98A274LYS10.8300.89728.5820.1120.1120.0000.0000.0000.000
99A275LYS10.8750.93930.0070.0470.0470.0000.0000.0000.000
100A276GLY0-0.008-0.00330.425-0.005-0.0050.0000.0000.0000.000
101A277LYS10.7320.82825.0310.1100.1100.0000.0000.0000.000
102A278ARG10.8030.92526.3700.0050.0050.0000.0000.0000.000
103A279LYS10.8150.89124.209-0.064-0.0640.0000.0000.0000.000
104A280SER00.022-0.00226.876-0.012-0.0120.0000.0000.0000.000
105A281LEU00.0100.00922.3200.0130.0130.0000.0000.0000.000
106A282PRO00.0470.01626.486-0.016-0.0160.0000.0000.0000.000
107A283ASN0-0.025-0.02628.781-0.021-0.0210.0000.0000.0000.000
108A284CYS0-0.109-0.00329.012-0.008-0.0080.0000.0000.0000.000
109A285ARG10.8700.93630.727-0.079-0.0790.0000.0000.0000.000
110A286ILE00.0300.00231.562-0.005-0.0050.0000.0000.0000.000
111A287MET0-0.0050.01835.1640.0050.0050.0000.0000.0000.000
112A288ILE00.0330.01937.846-0.007-0.0070.0000.0000.0000.000
113A289HIS00.0140.01940.552-0.011-0.0110.0000.0000.0000.000
114A290GLN0-0.015-0.02439.9460.0020.0020.0000.0000.0000.000
115A291PRO00.0010.01037.3150.0000.0000.0000.0000.0000.000
116A292LEU0-0.016-0.00936.1650.0040.0040.0000.0000.0000.000
117A293GLY00.0230.02340.547-0.003-0.0030.0000.0000.0000.000
118A294ASN0-0.003-0.02142.864-0.001-0.0010.0000.0000.0000.000
119A295ALA0-0.041-0.00645.226-0.006-0.0060.0000.0000.0000.000
120A296PHE0-0.014-0.00240.759-0.008-0.0080.0000.0000.0000.000
121A305GLN00.0740.04550.5850.0020.0020.0000.0000.0000.000
122A306THR00.036-0.01351.340-0.002-0.0020.0000.0000.0000.000
123A307LYS10.9730.98052.4970.0430.0430.0000.0000.0000.000
124A308GLU-1-0.820-0.90946.549-0.070-0.0700.0000.0000.0000.000
125A309ILE0-0.017-0.00647.6160.0000.0000.0000.0000.0000.000
126A310LEU00.006-0.00348.0600.0020.0020.0000.0000.0000.000
127A311TYR0-0.027-0.00146.9140.0040.0040.0000.0000.0000.000
128A312LEU00.0130.00443.2710.0000.0000.0000.0000.0000.000
129A313LYS10.7730.86444.8070.0170.0170.0000.0000.0000.000
130A314LYS10.9910.99445.7620.0370.0370.0000.0000.0000.000
131A315LEU0-0.0030.00643.5600.0020.0020.0000.0000.0000.000
132A316LEU0-0.0060.00040.125-0.001-0.0010.0000.0000.0000.000
133A317TYR0-0.008-0.02741.8910.0010.0010.0000.0000.0000.000
134A318HIS0-0.036-0.01844.3420.0030.0030.0000.0000.0000.000
135A319TYR00.0100.01539.5420.0030.0030.0000.0000.0000.000
136A320LEU00.0320.01837.9240.0020.0020.0000.0000.0000.000
137A321SER0-0.045-0.01740.4840.0030.0030.0000.0000.0000.000
138A322SER0-0.032-0.02941.1480.0010.0010.0000.0000.0000.000
139A323PHE0-0.045-0.02736.785-0.002-0.0020.0000.0000.0000.000
140A324THR0-0.042-0.04537.7040.0050.0050.0000.0000.0000.000
141A325ASN0-0.055-0.02640.0290.0020.0020.0000.0000.0000.000
142A326GLN00.0060.01642.1470.0020.0020.0000.0000.0000.000
143A327THR00.0110.00345.181-0.004-0.0040.0000.0000.0000.000
144A328VAL00.0450.01847.2450.0020.0020.0000.0000.0000.000
145A329GLU-1-0.807-0.89548.405-0.011-0.0110.0000.0000.0000.000
146A330THR0-0.072-0.03846.5700.0050.0050.0000.0000.0000.000
147A331ILE00.0080.01542.5680.0040.0040.0000.0000.0000.000
148A332GLU-1-0.855-0.93045.824-0.017-0.0170.0000.0000.0000.000
149A333LYS10.8270.91448.254-0.010-0.0100.0000.0000.0000.000
150A334ASP-1-0.783-0.86644.8040.0210.0210.0000.0000.0000.000
151A335SER0-0.038-0.01844.4190.0030.0030.0000.0000.0000.000
152A336ASP-1-0.827-0.88145.437-0.006-0.0060.0000.0000.0000.000
153A337ARG10.8110.90445.748-0.025-0.0250.0000.0000.0000.000
154A338ASP-1-0.820-0.89843.9610.0260.0260.0000.0000.0000.000
155A339TYR0-0.066-0.06342.3600.0050.0050.0000.0000.0000.000
156A340TYR0-0.059-0.05138.4170.0010.0010.0000.0000.0000.000
157A341MET0-0.0190.02037.8480.0040.0040.0000.0000.0000.000
158A342ASN0-0.019-0.01335.2860.0070.0070.0000.0000.0000.000
159A343ALA00.0670.02831.220-0.008-0.0080.0000.0000.0000.000
160A344LEU00.0230.01333.175-0.007-0.0070.0000.0000.0000.000
161A345GLU-1-0.774-0.87635.6440.0590.0590.0000.0000.0000.000
162A346ALA00.0360.01334.452-0.008-0.0080.0000.0000.0000.000
163A347LYS10.8630.93333.407-0.073-0.0730.0000.0000.0000.000
164A348GLN0-0.055-0.03235.722-0.006-0.0060.0000.0000.0000.000
165A349TYR0-0.015-0.03639.236-0.007-0.0070.0000.0000.0000.000
166A350GLY00.0520.03937.709-0.008-0.0080.0000.0000.0000.000
167A351ILE0-0.021-0.01134.088-0.009-0.0090.0000.0000.0000.000
168A352ILE0-0.039-0.02130.624-0.008-0.0080.0000.0000.0000.000
169A353ASP-1-0.735-0.84830.6260.0010.0010.0000.0000.0000.000
170A354GLU-1-0.895-0.95626.8530.1020.1020.0000.0000.0000.000
171A355VAL00.0140.00929.345-0.004-0.0040.0000.0000.0000.000
172A356ILE0-0.030-0.01522.6430.0040.0040.0000.0000.0000.000
173A357GLU-1-0.820-0.90526.2140.2160.2160.0000.0000.0000.000
174A358THR0-0.062-0.05023.7680.0310.0310.0000.0000.0000.000
175A359LYS10.9220.94719.779-0.566-0.5660.0000.0000.0000.000
176A360LEU0-0.020-0.00625.0680.0070.0070.0000.0000.0000.000
177A361PRO00.0480.04527.942-0.009-0.0090.0000.0000.0000.000
178A362HIS00.0330.00830.8540.0010.0010.0000.0000.0000.000
179A363PRO0-0.014-0.01933.019-0.006-0.0060.0000.0000.0000.000
180A364TYR0-0.026-0.00836.460-0.006-0.0060.0000.0000.0000.000
181A365PHE0-0.038-0.00632.149-0.009-0.0090.0000.0000.0000.000
182A366ASN00.0090.01135.0600.0000.0000.0000.0000.0000.000