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

tag_button

FMODB ID: VQ7M1

Calculation Name: 4YO2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4YO2

Chain ID: A

ChEMBL ID:

UniProt ID: A0AVK6

Base Structure: X-ray

Registration Date: 2023-09-24

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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2063895.09252
FMO2-HF: Nuclear repulsion 1988110.512687
FMO2-HF: Total energy -75784.579833
FMO2-MP2: Total energy -76005.892619


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:110:GLN)


Summations of interaction energy for fragment #1(A:110: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.
-13.72-8.7870.479-2.612-2.799-0.019
Interaction energy analysis for fragmet #1(A:110:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.026 / q_NPA : 0.009
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].
3A112SER0-0.0020.0063.276-0.5091.483-0.006-0.913-1.0730.002
4A113ARG11.0300.9995.092-0.739-0.700-0.001-0.007-0.0310.000
5A114LYS10.9150.9367.6051.0031.0030.0000.0000.0000.000
6A115GLU-1-0.868-0.9282.632-13.012-10.1100.486-1.692-1.695-0.021
7A116LYS10.9720.9885.232-0.690-0.6900.0000.0000.0000.000
8A117SER0-0.046-0.0188.9330.3720.3720.0000.0000.0000.000
9A118LEU00.0340.00811.995-0.034-0.0340.0000.0000.0000.000
10A119GLY00.0660.02115.2890.0150.0150.0000.0000.0000.000
11A120LEU00.0020.0389.7770.0180.0180.0000.0000.0000.000
12A121LEU00.0320.01413.3530.0440.0440.0000.0000.0000.000
13A122CYS0-0.041-0.00415.4530.0650.0650.0000.0000.0000.000
14A123HIS00.000-0.01616.5730.0580.0580.0000.0000.0000.000
15A124LYS10.8100.90515.6340.3920.3920.0000.0000.0000.000
16A125PHE0-0.014-0.00818.2700.0370.0370.0000.0000.0000.000
17A126LEU0-0.038-0.03421.0500.0270.0270.0000.0000.0000.000
18A127ALA0-0.038-0.01020.4680.0130.0130.0000.0000.0000.000
19A128ARG10.7450.87121.1960.2040.2040.0000.0000.0000.000
20A129TYR00.0220.01123.7450.0150.0150.0000.0000.0000.000
21A130PRO00.0270.03127.101-0.008-0.0080.0000.0000.0000.000
22A131ASN00.021-0.00227.5420.0030.0030.0000.0000.0000.000
23A132TYR0-0.048-0.04230.6490.0100.0100.0000.0000.0000.000
24A133PRO00.0140.02832.833-0.001-0.0010.0000.0000.0000.000
25A134ASN0-0.011-0.01335.0190.0100.0100.0000.0000.0000.000
26A135PRO0-0.011-0.02437.635-0.003-0.0030.0000.0000.0000.000
27A136ALA00.0800.05836.5720.0020.0020.0000.0000.0000.000
28A137VAL0-0.022-0.00434.8280.0070.0070.0000.0000.0000.000
29A138ASN0-0.031-0.01432.173-0.011-0.0110.0000.0000.0000.000
30A139ASN0-0.053-0.04131.8620.0060.0060.0000.0000.0000.000
31A140ASP-1-0.821-0.89627.320-0.104-0.1040.0000.0000.0000.000
32A141ILE0-0.008-0.00726.6240.0210.0210.0000.0000.0000.000
33A142CYS0-0.053-0.01623.5140.0030.0030.0000.0000.0000.000
34A143LEU0-0.010-0.03622.2980.0060.0060.0000.0000.0000.000
35A144ASP-1-0.795-0.90922.277-0.013-0.0130.0000.0000.0000.000
36A145GLU-1-0.853-0.90220.587-0.183-0.1830.0000.0000.0000.000
37A146VAL0-0.135-0.06717.346-0.013-0.0130.0000.0000.0000.000
38A147ALA0-0.030-0.01117.6730.0070.0070.0000.0000.0000.000
39A148GLU-1-0.879-0.91519.299-0.197-0.1970.0000.0000.0000.000
40A149GLU-1-0.843-0.90814.620-0.388-0.3880.0000.0000.0000.000
41A150LEU0-0.0130.0029.2810.0510.0510.0000.0000.0000.000
42A151ASN0-0.088-0.04511.4590.1360.1360.0000.0000.0000.000
43A152VAL00.1070.02411.831-0.015-0.0150.0000.0000.0000.000
44A153GLU-1-0.903-0.94114.4810.5300.5300.0000.0000.0000.000
45A154ARG10.9910.97216.416-0.205-0.2050.0000.0000.0000.000
46A155ARG10.8580.92519.042-0.154-0.1540.0000.0000.0000.000
47A156ARG10.9590.98215.011-0.138-0.1380.0000.0000.0000.000
48A157ILE00.1020.06318.465-0.023-0.0230.0000.0000.0000.000
49A158TYR0-0.034-0.01320.762-0.005-0.0050.0000.0000.0000.000
50A159ASP-1-0.885-0.95820.275-0.010-0.0100.0000.0000.0000.000
51A160ILE00.0820.04018.188-0.007-0.0070.0000.0000.0000.000
52A161VAL00.0390.02822.660-0.007-0.0070.0000.0000.0000.000
53A162ASN0-0.115-0.07225.7220.0170.0170.0000.0000.0000.000
54A163VAL00.0170.00024.1490.0040.0040.0000.0000.0000.000
55A164LEU00.0440.05024.697-0.003-0.0030.0000.0000.0000.000
56A165GLU-1-0.777-0.88327.947-0.003-0.0030.0000.0000.0000.000
57A166SER0-0.116-0.07229.8590.0050.0050.0000.0000.0000.000
58A167LEU00.010-0.00429.6600.0030.0030.0000.0000.0000.000
59A168HIS0-0.088-0.04433.362-0.002-0.0020.0000.0000.0000.000
60A169MET0-0.028-0.00527.658-0.007-0.0070.0000.0000.0000.000
61A170VAL00.0120.02728.656-0.004-0.0040.0000.0000.0000.000
62A171SER0-0.032-0.01831.9950.0100.0100.0000.0000.0000.000
63A172ARG10.8360.90930.909-0.018-0.0180.0000.0000.0000.000
64A173LEU00.0030.01833.960-0.001-0.0010.0000.0000.0000.000
65A174ALA00.0340.00334.2750.0060.0060.0000.0000.0000.000
66A175LYS10.9740.98430.859-0.076-0.0760.0000.0000.0000.000
67A176ASN0-0.051-0.05026.360-0.011-0.0110.0000.0000.0000.000
68A177ARG10.9871.01429.7730.0070.0070.0000.0000.0000.000
69A178TYR00.012-0.00429.0690.0130.0130.0000.0000.0000.000
70A179THR00.0580.02431.210-0.003-0.0030.0000.0000.0000.000
71A180TRP00.0610.01627.5010.0030.0030.0000.0000.0000.000
72A181HIS0-0.104-0.04730.964-0.005-0.0050.0000.0000.0000.000
73A182GLY00.0770.04032.050-0.009-0.0090.0000.0000.0000.000
74A183ARG10.8790.94229.2670.1500.1500.0000.0000.0000.000
75A184HIS00.0310.01734.1660.0020.0020.0000.0000.0000.000
76A185ASN00.0290.00837.4910.0070.0070.0000.0000.0000.000
77A186LEU00.0590.04032.8060.0020.0020.0000.0000.0000.000
78A187ASN0-0.023-0.02936.2420.0020.0020.0000.0000.0000.000
79A188LYS11.0281.01639.0370.0450.0450.0000.0000.0000.000
80A189THR0-0.0240.00036.1670.0060.0060.0000.0000.0000.000
81A190LEU00.0260.01535.7530.0040.0040.0000.0000.0000.000
82A191GLY0-0.0010.00538.6380.0040.0040.0000.0000.0000.000
83A192THR0-0.028-0.04241.5230.0040.0040.0000.0000.0000.000
84A193LEU0-0.002-0.00736.4610.0050.0050.0000.0000.0000.000
85A194LYS10.9590.96240.8950.0500.0500.0000.0000.0000.000
86A195SER0-0.053-0.01643.1100.0020.0020.0000.0000.0000.000
87A196ILE0-0.068-0.03042.0790.0030.0030.0000.0000.0000.000
88A197GLY00.0170.00242.4190.0030.0030.0000.0000.0000.000
89A198GLU-1-0.881-0.93342.930-0.003-0.0030.0000.0000.0000.000
90A199GLU-1-0.885-0.96142.872-0.020-0.0200.0000.0000.0000.000
91A200ASN00.007-0.00743.925-0.002-0.0020.0000.0000.0000.000
92A201LYS10.9480.98144.5050.0000.0000.0000.0000.0000.000
93A202TYR0-0.039-0.01840.0790.0050.0050.0000.0000.0000.000
94A203ALA00.0530.01941.7350.0010.0010.0000.0000.0000.000
95A204GLU-1-0.895-0.95043.2760.0020.0020.0000.0000.0000.000
96A205GLN0-0.002-0.01340.2650.0040.0040.0000.0000.0000.000
97A206ILE0-0.022-0.01539.4880.0020.0020.0000.0000.0000.000
98A207MET0-0.084-0.03841.3040.0000.0000.0000.0000.0000.000
99A208MET0-0.0390.00443.6500.0030.0030.0000.0000.0000.000
100A209ILE00.0080.00437.7690.0020.0020.0000.0000.0000.000
101A210LYS10.9070.97740.6840.0110.0110.0000.0000.0000.000
102A211LYS10.8690.90541.7350.0000.0000.0000.0000.0000.000
103A212LYS11.0441.04944.110-0.008-0.0080.0000.0000.0000.000
104A259ASN00.0420.00842.424-0.002-0.0020.0000.0000.0000.000
105A260SER00.0190.01240.6780.0020.0020.0000.0000.0000.000
106A261ARG11.0221.01341.114-0.061-0.0610.0000.0000.0000.000
107A262LYS10.8770.92435.647-0.097-0.0970.0000.0000.0000.000
108A263ASP-1-0.879-0.90536.3790.0340.0340.0000.0000.0000.000
109A264LYS10.9620.96233.408-0.089-0.0890.0000.0000.0000.000
110A265SER00.009-0.01931.389-0.001-0.0010.0000.0000.0000.000
111A266LEU0-0.0260.00025.994-0.004-0.0040.0000.0000.0000.000
112A267ARG11.0141.00929.806-0.028-0.0280.0000.0000.0000.000
113A268VAL00.1040.07531.565-0.009-0.0090.0000.0000.0000.000
114A269MET0-0.057-0.02628.638-0.002-0.0020.0000.0000.0000.000
115A270SER0-0.021-0.02328.974-0.006-0.0060.0000.0000.0000.000
116A271GLN00.0210.00730.820-0.004-0.0040.0000.0000.0000.000
117A272LYS10.9550.97134.340-0.012-0.0120.0000.0000.0000.000
118A273PHE0-0.053-0.00427.972-0.001-0.0010.0000.0000.0000.000
119A274VAL00.0560.01131.587-0.005-0.0050.0000.0000.0000.000
120A275MET0-0.0940.00033.766-0.002-0.0020.0000.0000.0000.000
121A276LEU0-0.012-0.01733.2160.0010.0010.0000.0000.0000.000
122A277PHE00.0160.01629.283-0.006-0.0060.0000.0000.0000.000
123A278LEU0-0.106-0.04035.237-0.005-0.0050.0000.0000.0000.000
124A279VAL00.0360.02238.3590.0060.0060.0000.0000.0000.000
125A280SER00.012-0.00340.281-0.005-0.0050.0000.0000.0000.000
126A281THR0-0.042-0.02540.363-0.002-0.0020.0000.0000.0000.000
127A282PRO0-0.006-0.00935.4660.0040.0040.0000.0000.0000.000
128A283GLN0-0.002-0.00435.6810.0010.0010.0000.0000.0000.000
129A284ILE00.0250.06931.4170.0040.0040.0000.0000.0000.000
130A285VAL00.021-0.01028.2390.0030.0030.0000.0000.0000.000
131A286SER0-0.007-0.02729.6440.0040.0040.0000.0000.0000.000
132A287LEU00.0690.04331.7070.0110.0110.0000.0000.0000.000
133A288GLU-1-0.752-0.89532.945-0.033-0.0330.0000.0000.0000.000
134A289VAL0-0.075-0.03229.7230.0060.0060.0000.0000.0000.000
135A290ALA00.0390.01932.8770.0090.0090.0000.0000.0000.000
136A291ALA00.0730.03936.1610.0040.0040.0000.0000.0000.000
137A292LYS10.8060.89332.4730.0060.0060.0000.0000.0000.000
138A293ILE0-0.061-0.03833.2370.0080.0080.0000.0000.0000.000
139A294LEU00.0950.05036.7710.0030.0030.0000.0000.0000.000
140A295ILE0-0.057-0.02136.518-0.001-0.0010.0000.0000.0000.000
141A296GLY0-0.139-0.07337.3840.0020.0020.0000.0000.0000.000
142A297GLU-1-0.971-0.97938.3920.0790.0790.0000.0000.0000.000
143A298ASP-1-0.970-0.98540.5940.0330.0330.0000.0000.0000.000
144A299HIS00.0300.00643.528-0.001-0.0010.0000.0000.0000.000
145A300VAL0-0.040-0.00244.253-0.001-0.0010.0000.0000.0000.000
146A301GLU-1-0.922-0.94741.5340.0730.0730.0000.0000.0000.000
147A302ASP-1-0.914-0.97339.3720.0690.0690.0000.0000.0000.000
148A303LEU0-0.053-0.03436.5060.0060.0060.0000.0000.0000.000
149A304ASP-1-0.786-0.85636.3100.0700.0700.0000.0000.0000.000
150A305LYS10.9140.98033.187-0.100-0.1000.0000.0000.0000.000
151A306SER0-0.116-0.10430.5970.0090.0090.0000.0000.0000.000
152A307LYS10.9941.01530.373-0.138-0.1380.0000.0000.0000.000
153A308PHE00.1150.02729.9330.0000.0000.0000.0000.0000.000
154A309LYS11.0091.00026.093-0.165-0.1650.0000.0000.0000.000
155A310THR0-0.069-0.05524.9280.0020.0020.0000.0000.0000.000
156A311LYS10.9160.96626.049-0.058-0.0580.0000.0000.0000.000
157A312ILE00.0660.04324.732-0.011-0.0110.0000.0000.0000.000
158A313ARG10.8880.95921.317-0.185-0.1850.0000.0000.0000.000
159A314ARG10.9220.95520.712-0.144-0.1440.0000.0000.0000.000
160A315LEU00.0350.03124.499-0.014-0.0140.0000.0000.0000.000
161A316TYR0-0.006-0.01120.814-0.013-0.0130.0000.0000.0000.000
162A317ASP-1-0.939-0.96620.066-0.027-0.0270.0000.0000.0000.000
163A318ILE0-0.008-0.02221.339-0.022-0.0220.0000.0000.0000.000
164A319ALA00.0060.01722.783-0.013-0.0130.0000.0000.0000.000
165A320ASN00.001-0.01616.7780.0090.0090.0000.0000.0000.000
166A321VAL0-0.043-0.01720.129-0.036-0.0360.0000.0000.0000.000
167A322LEU00.000-0.00821.452-0.004-0.0040.0000.0000.0000.000
168A323SER0-0.076-0.03320.2820.0020.0020.0000.0000.0000.000
169A324SER0-0.027-0.01019.508-0.051-0.0510.0000.0000.0000.000
170A325LEU0-0.0080.00721.4240.0240.0240.0000.0000.0000.000
171A326ASP-1-0.799-0.91624.219-0.183-0.1830.0000.0000.0000.000
172A327LEU0-0.180-0.09426.928-0.003-0.0030.0000.0000.0000.000
173A328ILE00.0980.05424.7970.0150.0150.0000.0000.0000.000
174A329LYS10.8610.93226.2330.1170.1170.0000.0000.0000.000
175A330LYS10.9840.99919.4810.2170.2170.0000.0000.0000.000
176A331VAL0-0.066-0.02824.047-0.003-0.0030.0000.0000.0000.000
177A332HIS00.0540.02725.3790.0020.0020.0000.0000.0000.000
178A333VAL00.0120.00524.295-0.009-0.0090.0000.0000.0000.000
179A334THR0-0.092-0.06026.4020.0100.0100.0000.0000.0000.000
180A335GLU-1-0.804-0.91124.336-0.170-0.1700.0000.0000.0000.000
181A336GLU-1-0.796-0.90028.705-0.064-0.0640.0000.0000.0000.000
182A337ARG10.8050.90228.6810.1500.1500.0000.0000.0000.000
183A338GLY00.1570.07431.159-0.001-0.0010.0000.0000.0000.000
184A339ARG10.8670.94330.4770.1550.1550.0000.0000.0000.000
185A340LYS10.9680.98033.4350.1190.1190.0000.0000.0000.000
186A341PRO00.0810.06735.8130.0040.0040.0000.0000.0000.000