FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

tag_button

FMODB ID: 534YZ

Calculation Name: 3FFV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3FFV

Chain ID: A

ChEMBL ID:

UniProt ID: P0A8U0

Base Structure: X-ray

Registration Date: 2023-06-19

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 180
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2006736.391887
FMO2-HF: Nuclear repulsion 1934070.971865
FMO2-HF: Total energy -72665.420023
FMO2-MP2: Total energy -72877.741565


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.
-0.4691.059-0.021-0.568-0.939-0.001
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 : -0.070 / q_NPA : -0.050
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-1-0.817-0.9113.8231.7543.282-0.021-0.568-0.939-0.001
4A4LEU00.027-0.0176.075-0.523-0.5230.0000.0000.0000.000
5A5THR0-0.029-0.0079.237-0.013-0.0130.0000.0000.0000.000
6A6ALA00.0200.0027.531-0.044-0.0440.0000.0000.0000.000
7A7GLN0-0.060-0.0279.000-0.447-0.4470.0000.0000.0000.000
8A8ALA00.0410.02510.5650.0820.0820.0000.0000.0000.000
9A9LEU0-0.025-0.00212.5570.0500.0500.0000.0000.0000.000
10A10LYS10.9580.9849.5421.6491.6490.0000.0000.0000.000
11A11ASP-1-0.842-0.91614.074-0.689-0.6890.0000.0000.0000.000
12A12PHE0-0.055-0.03116.1570.0630.0630.0000.0000.0000.000
13A13THR00.026-0.01016.6160.0400.0400.0000.0000.0000.000
14A14ALA00.001-0.00117.5550.0320.0320.0000.0000.0000.000
15A15ARG10.8790.94218.8440.3520.3520.0000.0000.0000.000
16A16TYR0-0.018-0.01421.8400.0430.0430.0000.0000.0000.000
17A17CYS0-0.010-0.02021.5640.0220.0220.0000.0000.0000.000
18A18ASP-1-0.891-0.93523.226-0.376-0.3760.0000.0000.0000.000
19A19ALA0-0.048-0.02225.4630.0250.0250.0000.0000.0000.000
20A20TRP00.0390.01026.9920.0180.0180.0000.0000.0000.000
21A21HIS0-0.0190.00727.6050.0190.0190.0000.0000.0000.000
22A22GLU-1-0.975-0.98229.467-0.186-0.1860.0000.0000.0000.000
23A23GLU-1-0.945-0.97131.486-0.138-0.1380.0000.0000.0000.000
24A24HIS0-0.070-0.04232.2730.0150.0150.0000.0000.0000.000
25A25LYS10.8000.91232.3460.1820.1820.0000.0000.0000.000
26A26SER0-0.034-0.02830.6800.0030.0030.0000.0000.0000.000
27A27TRP00.0220.00921.708-0.022-0.0220.0000.0000.0000.000
28A28PRO00.005-0.00824.4400.0210.0210.0000.0000.0000.000
29A29LEU00.0050.00327.599-0.010-0.0100.0000.0000.0000.000
30A30SER0-0.042-0.02328.4230.0140.0140.0000.0000.0000.000
31A31GLU-1-0.845-0.94130.388-0.143-0.1430.0000.0000.0000.000
32A32GLU-1-0.986-0.98630.251-0.143-0.1430.0000.0000.0000.000
33A33LEU0-0.022-0.00825.3340.0010.0010.0000.0000.0000.000
34A34TYR0-0.0210.00829.319-0.007-0.0070.0000.0000.0000.000
35A35GLY0-0.008-0.00532.0200.0100.0100.0000.0000.0000.000
36A36VAL0-0.049-0.01826.5690.0060.0060.0000.0000.0000.000
37A37PRO0-0.011-0.01026.795-0.016-0.0160.0000.0000.0000.000
38A38SER00.019-0.01721.818-0.013-0.0130.0000.0000.0000.000
39A39PRO0-0.028-0.01119.5420.0100.0100.0000.0000.0000.000
40A40CYS0-0.034-0.00119.686-0.014-0.0140.0000.0000.0000.000
41A41ILE0-0.0090.01322.2910.0070.0070.0000.0000.0000.000
42A42ILE0-0.0320.00125.270-0.006-0.0060.0000.0000.0000.000
43A43SER0-0.052-0.04427.5920.0160.0160.0000.0000.0000.000
44A44THR0-0.009-0.01531.120-0.003-0.0030.0000.0000.0000.000
45A45THR0-0.033-0.00733.4220.0040.0040.0000.0000.0000.000
46A46GLU-1-0.920-0.97636.697-0.130-0.1300.0000.0000.0000.000
47A47ASP-1-0.971-0.97637.216-0.132-0.1320.0000.0000.0000.000
48A48ALA00.0590.03433.251-0.002-0.0020.0000.0000.0000.000
49A49VAL0-0.038-0.01128.288-0.004-0.0040.0000.0000.0000.000
50A50TYR0-0.0070.01029.1050.0010.0010.0000.0000.0000.000
51A51TRP0-0.019-0.00920.618-0.025-0.0250.0000.0000.0000.000
52A52GLN00.009-0.00521.4480.0130.0130.0000.0000.0000.000
53A53PRO0-0.0040.00116.6880.0040.0040.0000.0000.0000.000
54A54GLN0-0.020-0.00117.031-0.045-0.0450.0000.0000.0000.000
55A55PRO0-0.030-0.03012.669-0.046-0.0460.0000.0000.0000.000
56A56PHE00.0250.03611.1370.0930.0930.0000.0000.0000.000
57A57THR0-0.083-0.09712.110-0.103-0.1030.0000.0000.0000.000
58A58GLY00.0660.02813.5240.0690.0690.0000.0000.0000.000
59A59GLU-1-0.962-0.99811.668-0.242-0.2420.0000.0000.0000.000
60A60GLN0-0.053-0.0306.765-0.165-0.1650.0000.0000.0000.000
61A61ASN0-0.025-0.0158.7060.0490.0490.0000.0000.0000.000
62A62VAL00.0560.02611.315-0.021-0.0210.0000.0000.0000.000
63A63ASN00.0220.00212.1800.0830.0830.0000.0000.0000.000
64A64ALA0-0.055-0.01915.7800.0240.0240.0000.0000.0000.000
65A65VAL0-0.005-0.00518.2820.0130.0130.0000.0000.0000.000
66A66GLU-1-0.830-0.91315.5110.2370.2370.0000.0000.0000.000
67A67ARG10.8920.95216.8100.0350.0350.0000.0000.0000.000
68A68ALA0-0.058-0.01821.1320.0050.0050.0000.0000.0000.000
69A69PHE0-0.052-0.03322.757-0.002-0.0020.0000.0000.0000.000
70A70ASP-1-0.922-0.96022.4440.1770.1770.0000.0000.0000.000
71A71ILE0-0.076-0.03720.0900.0030.0030.0000.0000.0000.000
72A72VAL00.0120.01916.0700.0010.0010.0000.0000.0000.000
73A73ILE0-0.048-0.03615.2200.0100.0100.0000.0000.0000.000
74A74GLN0-0.009-0.02714.4770.0910.0910.0000.0000.0000.000
75A75PRO00.0290.0059.685-0.080-0.0800.0000.0000.0000.000
76A76THR00.0280.01010.670-0.111-0.1110.0000.0000.0000.000
77A77ILE00.0340.02712.431-0.126-0.1260.0000.0000.0000.000
78A78HIS00.0140.01210.178-0.154-0.1540.0000.0000.0000.000
79A79THR0-0.0120.0087.802-0.087-0.0870.0000.0000.0000.000
80A80PHE0-0.041-0.0099.796-0.165-0.1650.0000.0000.0000.000
81A81TYR0-0.020-0.02213.097-0.051-0.0510.0000.0000.0000.000
82A82THR0-0.024-0.0069.882-0.057-0.0570.0000.0000.0000.000
83A83THR0-0.024-0.0198.978-0.252-0.2520.0000.0000.0000.000
84A84GLN0-0.112-0.08110.029-0.251-0.2510.0000.0000.0000.000
85A85PHE0-0.0270.00513.1260.0700.0700.0000.0000.0000.000
86A86ALA00.004-0.03716.653-0.033-0.0330.0000.0000.0000.000
87A87GLY00.0560.02219.2090.0260.0260.0000.0000.0000.000
88A88ASP-1-0.882-0.94221.683-0.234-0.2340.0000.0000.0000.000
89A89MET0-0.102-0.04418.631-0.014-0.0140.0000.0000.0000.000
90A90HIS00.0660.05224.2450.0210.0210.0000.0000.0000.000
91A91ALA00.002-0.01524.590-0.017-0.0170.0000.0000.0000.000
92A92GLN0-0.040-0.02426.7140.0260.0260.0000.0000.0000.000
93A93PHE00.0240.01924.203-0.009-0.0090.0000.0000.0000.000
94A94GLY0-0.025-0.01427.7270.0140.0140.0000.0000.0000.000
95A95ASP-1-0.878-0.94930.859-0.055-0.0550.0000.0000.0000.000
96A96ILE0-0.110-0.05229.7660.0010.0010.0000.0000.0000.000
97A97LYS10.9700.98529.9870.0770.0770.0000.0000.0000.000
98A98LEU0-0.014-0.00424.5000.0120.0120.0000.0000.0000.000
99A99THR00.0490.03425.926-0.008-0.0080.0000.0000.0000.000
100A100LEU0-0.080-0.04318.7990.0150.0150.0000.0000.0000.000
101A101LEU00.0370.01821.698-0.017-0.0170.0000.0000.0000.000
102A102GLN0-0.015-0.01416.215-0.103-0.1030.0000.0000.0000.000
103A103THR0-0.011-0.00416.0650.0570.0570.0000.0000.0000.000
104A104TRP00.0560.03918.172-0.067-0.0670.0000.0000.0000.000
105A105SER00.0270.01119.748-0.015-0.0150.0000.0000.0000.000
106A106GLU-1-0.801-0.85417.784-0.380-0.3800.0000.0000.0000.000
107A107ASP-1-0.936-0.96819.757-0.176-0.1760.0000.0000.0000.000
108A108ASP-1-0.863-0.94321.984-0.187-0.1870.0000.0000.0000.000
109A109PHE00.0090.00814.6630.0170.0170.0000.0000.0000.000
110A110ARG10.8830.94619.5910.1600.1600.0000.0000.0000.000
111A111ARG10.9110.94821.9660.1860.1860.0000.0000.0000.000
112A112VAL00.0030.01218.9540.0240.0240.0000.0000.0000.000
113A113GLN00.027-0.00617.4210.0560.0560.0000.0000.0000.000
114A114GLU-1-0.891-0.94021.189-0.068-0.0680.0000.0000.0000.000
115A115ASN00.0090.00024.7030.0270.0270.0000.0000.0000.000
116A116LEU0-0.0080.00519.2120.0200.0200.0000.0000.0000.000
117A117ILE00.0110.01022.7160.0240.0240.0000.0000.0000.000
118A118GLY0-0.012-0.00324.9320.0140.0140.0000.0000.0000.000
119A119HIS0-0.037-0.01524.9310.0000.0000.0000.0000.0000.000
120A120LEU00.0440.01921.9230.0130.0130.0000.0000.0000.000
121A121VAL0-0.0030.00526.6020.0130.0130.0000.0000.0000.000
122A122THR0-0.057-0.02229.5540.0050.0050.0000.0000.0000.000
123A123GLN00.0400.00426.8210.0120.0120.0000.0000.0000.000
124A124LYS10.9851.01529.341-0.091-0.0910.0000.0000.0000.000
125A125ARG10.9140.95831.046-0.016-0.0160.0000.0000.0000.000
126A126LEU0-0.032-0.01233.9030.0000.0000.0000.0000.0000.000
127A127LYS10.8750.94132.937-0.070-0.0700.0000.0000.0000.000
128A128LEU0-0.035-0.01631.2010.0040.0040.0000.0000.0000.000
129A129PRO00.0080.00028.2910.0040.0040.0000.0000.0000.000
130A130PRO00.0260.02924.075-0.012-0.0120.0000.0000.0000.000
131A131THR0-0.059-0.06223.1570.0200.0200.0000.0000.0000.000
132A132LEU00.0300.01918.125-0.008-0.0080.0000.0000.0000.000
133A133PHE00.0390.01721.3660.0040.0040.0000.0000.0000.000
134A134ILE0-0.028-0.01318.607-0.011-0.0110.0000.0000.0000.000
135A135ALA00.0310.01121.263-0.030-0.0300.0000.0000.0000.000
136A136THR00.0320.03124.3680.0160.0160.0000.0000.0000.000
137A137LEU0-0.045-0.03928.060-0.006-0.0060.0000.0000.0000.000
138A138GLU-1-0.861-0.92331.158-0.085-0.0850.0000.0000.0000.000
139A139GLU-1-0.958-0.98534.708-0.035-0.0350.0000.0000.0000.000
140A140GLU-1-0.908-0.96034.374-0.037-0.0370.0000.0000.0000.000
141A141LEU0-0.030-0.02234.146-0.001-0.0010.0000.0000.0000.000
142A142GLU-1-0.847-0.90231.9700.0080.0080.0000.0000.0000.000
143A143VAL00.0150.01027.160-0.011-0.0110.0000.0000.0000.000
144A144ILE0-0.0090.00623.5190.0170.0170.0000.0000.0000.000
145A145SER00.010-0.04922.707-0.024-0.0240.0000.0000.0000.000
146A146VAL00.0080.03017.6540.0120.0120.0000.0000.0000.000
147A147CYS0-0.076-0.04820.905-0.001-0.0010.0000.0000.0000.000
148A148ASN00.0390.00218.9340.0270.0270.0000.0000.0000.000
149A149LEU0-0.056-0.00620.4870.0330.0330.0000.0000.0000.000
150A150SER0-0.027-0.02921.3310.0300.0300.0000.0000.0000.000
151A151GLY00.0310.02918.2410.0450.0450.0000.0000.0000.000
152A152GLU-1-0.891-0.92519.0490.1330.1330.0000.0000.0000.000
153A153VAL00.0080.00720.226-0.016-0.0160.0000.0000.0000.000
154A155LYS10.9460.99226.0720.0040.0040.0000.0000.0000.000
155A156GLU-1-0.858-0.89426.9620.0420.0420.0000.0000.0000.000
156A157THR0-0.0040.00130.606-0.007-0.0070.0000.0000.0000.000
157A158LEU00.0430.00729.4660.0110.0110.0000.0000.0000.000
158A159GLY0-0.011-0.01132.9750.0000.0000.0000.0000.0000.000
159A160THR0-0.039-0.01634.3800.0050.0050.0000.0000.0000.000
160A161ARG10.8530.89733.575-0.067-0.0670.0000.0000.0000.000
161A162LYS10.8890.96433.199-0.007-0.0070.0000.0000.0000.000
162A163ARG10.8880.93328.060-0.066-0.0660.0000.0000.0000.000
163A164THR0-0.014-0.00830.3030.0010.0010.0000.0000.0000.000
164A165HIS0-0.046-0.02724.308-0.015-0.0150.0000.0000.0000.000
165A166LEU0-0.059-0.02025.633-0.010-0.0100.0000.0000.0000.000
166A167ALA00.0420.01822.045-0.012-0.0120.0000.0000.0000.000
167A168SER0-0.017-0.02320.2510.0190.0190.0000.0000.0000.000
168A169ASN0-0.031-0.00716.4870.0050.0050.0000.0000.0000.000
169A170LEU00.0490.02214.100-0.028-0.0280.0000.0000.0000.000
170A171ALA00.0410.02313.544-0.062-0.0620.0000.0000.0000.000
171A172GLU-1-0.869-0.93015.5850.0520.0520.0000.0000.0000.000
172A173PHE00.0310.00418.760-0.032-0.0320.0000.0000.0000.000
173A174LEU00.0190.00615.091-0.020-0.0200.0000.0000.0000.000
174A175ASN0-0.015-0.02015.541-0.097-0.0970.0000.0000.0000.000
175A176GLN0-0.055-0.01719.431-0.016-0.0160.0000.0000.0000.000
176A177LEU0-0.0530.00220.9850.0060.0060.0000.0000.0000.000
177A178LYS10.9360.97923.5070.0910.0910.0000.0000.0000.000
178A179PRO00.0240.01024.2320.0110.0110.0000.0000.0000.000
179A180LEU0-0.046-0.01326.5450.0180.0180.0000.0000.0000.000
180A181LEU00.0290.02129.114-0.003-0.0030.0000.0000.0000.000