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: G5V31

Calculation Name: 3F56-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3F56

Chain ID: A

ChEMBL ID:

UniProt ID: Q7V2D3

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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2288503.788002
FMO2-HF: Nuclear repulsion 2209224.62226
FMO2-HF: Total energy -79279.165742
FMO2-MP2: Total energy -79507.763652


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:50:GLN)


Summations of interaction energy for fragment #1(A:50:GLN)
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.
-28.99-20.381.63-4.473-5.767-0.004
Interaction energy analysis for fragmet #1(A:50:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.031 / q_NPA : -0.038
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].
3A52GLU-1-0.851-0.9072.478-14.689-9.4981.158-2.663-3.686-0.024
4A53GLN0-0.088-0.0413.9211.2591.8400.000-0.127-0.4540.000
5A54ILE0-0.060-0.0355.5211.0061.0060.0000.0000.0000.000
6A55GLU-1-0.783-0.8577.801-0.199-0.1990.0000.0000.0000.000
7A56LEU0-0.009-0.02011.4690.1340.1340.0000.0000.0000.000
8A57ARG10.8470.92713.680-0.050-0.0500.0000.0000.0000.000
9A58THR00.007-0.02216.573-0.009-0.0090.0000.0000.0000.000
10A59TYR00.0100.00717.3730.0130.0130.0000.0000.0000.000
11A60VAL00.003-0.00519.560-0.010-0.0100.0000.0000.0000.000
12A61PHE00.0340.01923.0600.0090.0090.0000.0000.0000.000
13A62LEU0-0.010-0.00824.981-0.004-0.0040.0000.0000.0000.000
14A63ASP-1-0.804-0.88728.371-0.057-0.0570.0000.0000.0000.000
15A64SER0-0.025-0.01730.4880.0040.0040.0000.0000.0000.000
16A65LEU0-0.0160.01229.5580.0010.0010.0000.0000.0000.000
17A66GLN00.0080.01033.1030.0010.0010.0000.0000.0000.000
18A67PRO00.0530.01035.9620.0060.0060.0000.0000.0000.000
19A68GLN0-0.023-0.01637.8140.0100.0100.0000.0000.0000.000
20A69LEU00.0010.00430.9160.0080.0080.0000.0000.0000.000
21A70ALA0-0.0100.00433.1120.0080.0080.0000.0000.0000.000
22A71ALA00.0140.00734.0040.0080.0080.0000.0000.0000.000
23A72TYR0-0.061-0.04030.6910.0090.0090.0000.0000.0000.000
24A73MET0-0.014-0.01526.3030.0050.0050.0000.0000.0000.000
25A74GLY0-0.0050.00730.0460.0120.0120.0000.0000.0000.000
26A75THR0-0.075-0.03132.2780.0080.0080.0000.0000.0000.000
27A76VAL0-0.016-0.00828.7080.0090.0090.0000.0000.0000.000
28A77SER0-0.116-0.05626.4440.0170.0170.0000.0000.0000.000
29A78ARG10.8910.92524.849-0.166-0.1660.0000.0000.0000.000
30A79GLY00.0000.02225.4930.0140.0140.0000.0000.0000.000
31A80PHE0-0.060-0.05025.476-0.011-0.0110.0000.0000.0000.000
32A81LEU00.0250.00828.478-0.003-0.0030.0000.0000.0000.000
33A82PRO00.0010.01529.908-0.003-0.0030.0000.0000.0000.000
34A83ILE0-0.037-0.02731.5000.0030.0030.0000.0000.0000.000
35A84PRO00.010-0.01533.921-0.004-0.0040.0000.0000.0000.000
36A85GLY0-0.0150.00035.227-0.002-0.0020.0000.0000.0000.000
37A86ASP-1-0.843-0.91930.223-0.003-0.0030.0000.0000.0000.000
38A87SER0-0.034-0.02627.921-0.004-0.0040.0000.0000.0000.000
39A88CYS0-0.037-0.03125.7680.0160.0160.0000.0000.0000.000
40A89LEU0-0.0290.00818.730-0.017-0.0170.0000.0000.0000.000
41A90TRP00.0340.00821.0640.0360.0360.0000.0000.0000.000
42A91MET0-0.020-0.01515.859-0.059-0.0590.0000.0000.0000.000
43A92GLU-1-0.803-0.88816.5220.1170.1170.0000.0000.0000.000
44A93VAL0-0.006-0.00910.963-0.071-0.0710.0000.0000.0000.000
45A94SER00.0240.03011.4210.1370.1370.0000.0000.0000.000
46A95PRO00.0820.0366.916-0.161-0.1610.0000.0000.0000.000
47A96GLY00.0600.0259.9260.0730.0730.0000.0000.0000.000
48A97MET00.003-0.0189.901-0.016-0.0160.0000.0000.0000.000
49A98ALA00.0010.0067.2690.2570.2570.0000.0000.0000.000
50A99VAL00.0230.0118.707-0.053-0.0530.0000.0000.0000.000
51A100HIS00.0210.02211.088-0.141-0.1410.0000.0000.0000.000
52A101ARG10.9170.9752.777-14.438-11.6000.472-1.683-1.6270.020
53A102VAL00.0350.01710.037-0.209-0.2090.0000.0000.0000.000
54A103THR00.007-0.01811.862-0.142-0.1420.0000.0000.0000.000
55A104ASP-1-0.862-0.91412.6930.3100.3100.0000.0000.0000.000
56A105ILE0-0.007-0.0138.927-0.076-0.0760.0000.0000.0000.000
57A106ALA0-0.001-0.00113.547-0.079-0.0790.0000.0000.0000.000
58A107LEU0-0.037-0.02616.547-0.030-0.0300.0000.0000.0000.000
59A108LYS10.7860.88215.340-0.292-0.2920.0000.0000.0000.000
60A109ALA0-0.0090.01617.096-0.035-0.0350.0000.0000.0000.000
61A110SER0-0.018-0.03019.041-0.023-0.0230.0000.0000.0000.000
62A111ASN0-0.016-0.00322.4540.0250.0250.0000.0000.0000.000
63A112VAL0-0.0180.01321.0060.0100.0100.0000.0000.0000.000
64A113ARG10.8900.95523.808-0.046-0.0460.0000.0000.0000.000
65A114LEU00.0340.01319.417-0.008-0.0080.0000.0000.0000.000
66A115GLY00.0490.01722.9960.0050.0050.0000.0000.0000.000
67A116GLN00.0320.00822.1870.0140.0140.0000.0000.0000.000
68A117MET0-0.006-0.00217.0200.0150.0150.0000.0000.0000.000
69A118ILE0-0.051-0.01218.7430.0060.0060.0000.0000.0000.000
70A119VAL0-0.004-0.00414.6810.0130.0130.0000.0000.0000.000
71A120GLU-1-0.837-0.91517.3180.2310.2310.0000.0000.0000.000
72A121ARG10.9160.95417.785-0.234-0.2340.0000.0000.0000.000
73A122ALA0-0.039-0.02315.9460.0440.0440.0000.0000.0000.000
74A123PHE00.0160.00114.4190.0270.0270.0000.0000.0000.000
75A124GLY00.0200.02214.3260.0300.0300.0000.0000.0000.000
76A125SER0-0.020-0.00115.238-0.052-0.0520.0000.0000.0000.000
77A126LEU0-0.039-0.02015.9930.0410.0410.0000.0000.0000.000
78A127ALA00.0300.01919.189-0.038-0.0380.0000.0000.0000.000
79A128LEU0-0.034-0.00818.2130.0200.0200.0000.0000.0000.000
80A129TYR00.0520.02722.705-0.019-0.0190.0000.0000.0000.000
81A130HIS00.023-0.00626.291-0.002-0.0020.0000.0000.0000.000
82A131LYS10.9310.97228.3080.0310.0310.0000.0000.0000.000
83A132ASP-1-0.887-0.92529.952-0.054-0.0540.0000.0000.0000.000
84A133GLN00.0800.02528.480-0.013-0.0130.0000.0000.0000.000
85A134SER00.0180.00526.828-0.004-0.0040.0000.0000.0000.000
86A135THR0-0.026-0.00725.064-0.021-0.0210.0000.0000.0000.000
87A136VAL00.0020.00223.363-0.004-0.0040.0000.0000.0000.000
88A137LEU0-0.003-0.00721.929-0.005-0.0050.0000.0000.0000.000
89A138HIS00.0400.03720.972-0.037-0.0370.0000.0000.0000.000
90A139SER0-0.011-0.00318.904-0.018-0.0180.0000.0000.0000.000
91A140GLY0-0.017-0.01817.104-0.002-0.0020.0000.0000.0000.000
92A141ASP-1-0.908-0.94616.401-0.344-0.3440.0000.0000.0000.000
93A142VAL00.0110.00514.585-0.077-0.0770.0000.0000.0000.000
94A143VAL0-0.051-0.02712.184-0.068-0.0680.0000.0000.0000.000
95A144LEU0-0.047-0.02811.574-0.093-0.0930.0000.0000.0000.000
96A145ASP-1-0.862-0.91912.016-0.883-0.8830.0000.0000.0000.000
97A146ALA0-0.076-0.0319.621-0.272-0.2720.0000.0000.0000.000
98A147ILE0-0.105-0.0657.142-0.242-0.2420.0000.0000.0000.000
99A148GLY00.0230.0288.174-0.347-0.3470.0000.0000.0000.000
100A149SER0-0.054-0.04910.0570.0550.0550.0000.0000.0000.000
101A150GLU-1-0.800-0.90812.497-0.599-0.5990.0000.0000.0000.000
102A151VAL00.0530.02616.2750.0280.0280.0000.0000.0000.000
103A152ARG10.8620.90619.1110.3160.3160.0000.0000.0000.000
104A153LYS10.8260.91912.7630.9500.9500.0000.0000.0000.000
105A154ARG10.7870.93616.1590.1870.1870.0000.0000.0000.000
106A155THR0-0.017-0.03016.834-0.012-0.0120.0000.0000.0000.000
107A156LYS10.8640.92918.8210.1990.1990.0000.0000.0000.000
108A157PRO0-0.0190.00422.5780.0140.0140.0000.0000.0000.000
109A158SER00.0060.00524.981-0.008-0.0080.0000.0000.0000.000
110A159THR00.005-0.02626.9850.0100.0100.0000.0000.0000.000
111A160SER0-0.035-0.03429.120-0.003-0.0030.0000.0000.0000.000
112A161TRP0-0.063-0.04630.9430.0020.0020.0000.0000.0000.000
113A162THR0-0.024-0.01133.849-0.003-0.0030.0000.0000.0000.000
114A163GLU-1-0.856-0.91336.4620.0210.0210.0000.0000.0000.000
115A164VAL00.008-0.00340.1370.0010.0010.0000.0000.0000.000
116A165ILE0-0.0170.01042.1170.0000.0000.0000.0000.0000.000
117A166CYS0-0.037-0.04445.1450.0010.0010.0000.0000.0000.000
118A167ALA0-0.0140.00548.4580.0020.0020.0000.0000.0000.000
119A168ILE0-0.0020.01044.7000.0020.0020.0000.0000.0000.000
120A169THR00.0620.01648.3960.0000.0000.0000.0000.0000.000
121A170PRO00.047-0.01049.0950.0020.0020.0000.0000.0000.000
122A171ASP-1-0.913-0.95049.3850.0400.0400.0000.0000.0000.000
123A172HIS00.0290.00742.0370.0050.0050.0000.0000.0000.000
124A173ALA00.0390.02144.6130.0030.0030.0000.0000.0000.000
125A174VAL0-0.028-0.02044.8500.0030.0030.0000.0000.0000.000
126A175LEU0-0.005-0.00842.3320.0050.0050.0000.0000.0000.000
127A176ILE00.0220.01839.6740.0050.0050.0000.0000.0000.000
128A177ASN0-0.066-0.04140.1520.0040.0040.0000.0000.0000.000
129A178ARG10.9450.97141.586-0.062-0.0620.0000.0000.0000.000
130A179GLN0-0.0190.00737.1260.0100.0100.0000.0000.0000.000
131A180ASN0-0.039-0.01631.505-0.001-0.0010.0000.0000.0000.000
132A181ARG10.8780.96334.613-0.054-0.0540.0000.0000.0000.000
133A182SER0-0.059-0.03233.5880.0050.0050.0000.0000.0000.000
134A183GLY00.0330.02235.723-0.002-0.0020.0000.0000.0000.000
135A184SER0-0.031-0.01337.5340.0030.0030.0000.0000.0000.000
136A185MET0-0.045-0.03241.1380.0020.0020.0000.0000.0000.000
137A186ILE00.0370.03042.860-0.004-0.0040.0000.0000.0000.000
138A187GLN0-0.038-0.04144.7230.0010.0010.0000.0000.0000.000
139A188SER00.0300.01148.501-0.001-0.0010.0000.0000.0000.000
140A189GLY0-0.048-0.01750.128-0.001-0.0010.0000.0000.0000.000
141A190MET0-0.0450.00946.816-0.002-0.0020.0000.0000.0000.000
142A191SER00.0320.01546.3660.0020.0020.0000.0000.0000.000
143A192MET0-0.022-0.01640.6950.0030.0030.0000.0000.0000.000
144A193PHE00.0470.01535.765-0.002-0.0020.0000.0000.0000.000
145A194ILE0-0.041-0.01736.2540.0040.0040.0000.0000.0000.000
146A195LEU00.021-0.00331.281-0.006-0.0060.0000.0000.0000.000
147A196GLU-1-0.798-0.84729.2650.0640.0640.0000.0000.0000.000
148A197THR0-0.023-0.01925.742-0.008-0.0080.0000.0000.0000.000
149A198GLU-1-0.905-0.94522.9140.0660.0660.0000.0000.0000.000
150A199PRO0-0.006-0.00919.563-0.013-0.0130.0000.0000.0000.000
151A200ALA00.0290.02921.645-0.012-0.0120.0000.0000.0000.000
152A201GLY00.0470.00021.757-0.004-0.0040.0000.0000.0000.000
153A202TYR00.021-0.01520.496-0.011-0.0110.0000.0000.0000.000
154A203VAL0-0.0190.01125.366-0.008-0.0080.0000.0000.0000.000
155A204LEU00.0140.00125.465-0.001-0.0010.0000.0000.0000.000
156A205LYS10.8490.92227.1180.0740.0740.0000.0000.0000.000
157A206ALA00.0260.01128.937-0.003-0.0030.0000.0000.0000.000
158A207ALA00.0150.01131.4100.0000.0000.0000.0000.0000.000
159A208ASN0-0.021-0.01931.4530.0070.0070.0000.0000.0000.000
160A209GLU-1-0.797-0.89532.194-0.053-0.0530.0000.0000.0000.000
161A210ALA00.0230.01534.9440.0000.0000.0000.0000.0000.000
162A211GLU-1-0.807-0.91936.6770.0070.0070.0000.0000.0000.000
163A212LYS10.7430.84833.3920.0510.0510.0000.0000.0000.000
164A213SER0-0.058-0.02538.864-0.003-0.0030.0000.0000.0000.000
165A214ALA0-0.0060.01041.3220.0000.0000.0000.0000.0000.000
166A215ASN0-0.041-0.00542.7440.0030.0030.0000.0000.0000.000
167A216ILE0-0.010-0.00239.4380.0020.0020.0000.0000.0000.000
168A217THR0-0.024-0.00642.0370.0010.0010.0000.0000.0000.000
169A218ILE00.0110.00535.4440.0010.0010.0000.0000.0000.000
170A219ILE0-0.028-0.00738.0740.0040.0040.0000.0000.0000.000
171A220ASP-1-0.709-0.85333.4260.0790.0790.0000.0000.0000.000
172A221VAL00.0100.00729.254-0.008-0.0080.0000.0000.0000.000
173A222LYS10.7900.89328.499-0.078-0.0780.0000.0000.0000.000
174A223ALA00.0390.01724.842-0.003-0.0030.0000.0000.0000.000
175A224VAL0-0.003-0.00921.0000.0010.0010.0000.0000.0000.000
176A225GLY00.0170.01321.662-0.001-0.0010.0000.0000.0000.000
177A226ALA0-0.029-0.01921.646-0.004-0.0040.0000.0000.0000.000
178A227PHE00.0080.01022.750-0.010-0.0100.0000.0000.0000.000
179A228GLY0-0.0080.00925.6360.0120.0120.0000.0000.0000.000
180A229ARG10.7720.86126.782-0.086-0.0860.0000.0000.0000.000
181A230LEU0-0.0060.01130.5060.0040.0040.0000.0000.0000.000
182A231THR0-0.034-0.02532.9760.0000.0000.0000.0000.0000.000
183A232LEU00.0500.01936.3220.0020.0020.0000.0000.0000.000
184A233ALA00.0040.01239.2450.0000.0000.0000.0000.0000.000
185A234GLY00.0590.01943.000-0.001-0.0010.0000.0000.0000.000
186A235LYS10.9420.97046.375-0.003-0.0030.0000.0000.0000.000
187A236GLU-1-0.829-0.90147.6520.0020.0020.0000.0000.0000.000
188A237GLY00.0700.03447.414-0.001-0.0010.0000.0000.0000.000
189A238ASP-1-0.891-0.95246.007-0.006-0.0060.0000.0000.0000.000
190A239VAL0-0.041-0.02842.627-0.001-0.0010.0000.0000.0000.000
191A240GLU-1-0.927-0.96042.685-0.007-0.0070.0000.0000.0000.000
192A241GLU-1-0.786-0.88442.841-0.033-0.0330.0000.0000.0000.000
193A242ALA0-0.020-0.01139.972-0.003-0.0030.0000.0000.0000.000
194A243ALA0-0.004-0.00638.734-0.002-0.0020.0000.0000.0000.000
195A244ALA0-0.0030.00138.321-0.004-0.0040.0000.0000.0000.000
196A245ALA0-0.023-0.02637.851-0.006-0.0060.0000.0000.0000.000
197A246ALA0-0.0240.00134.609-0.005-0.0050.0000.0000.0000.000
198A247ILE00.0230.00633.498-0.004-0.0040.0000.0000.0000.000
199A248ARG10.8330.91733.8080.0320.0320.0000.0000.0000.000
200A249ALA0-0.0180.00031.380-0.011-0.0110.0000.0000.0000.000
201A250ILE00.011-0.00628.645-0.011-0.0110.0000.0000.0000.000
202A251ASP-1-0.862-0.93429.217-0.073-0.0730.0000.0000.0000.000
203A252GLN0-0.057-0.03830.126-0.011-0.0110.0000.0000.0000.000
204A253ILE0-0.075-0.03124.495-0.020-0.0200.0000.0000.0000.000
205A254SER00.0280.01725.663-0.025-0.0250.0000.0000.0000.000
206A255ASN0-0.069-0.02826.475-0.022-0.0220.0000.0000.0000.000
207A256TYR00.0090.03023.115-0.035-0.0350.0000.0000.0000.000