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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: 1NZRZ

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 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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2062129.626339
FMO2-HF: Nuclear repulsion 1986343.120121
FMO2-HF: Total energy -75786.506218
FMO2-MP2: Total energy -76007.556038


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.
-16.382-11.783.454-3.878-4.177-0.04
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 : 0.011 / q_NPA : 0.000
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].
3A112SER0-0.0110.0113.172-0.1281.832-0.004-0.831-1.1250.003
4A113ARG11.0120.9865.004-0.330-0.302-0.001-0.008-0.0190.000
5A114LYS10.9300.9487.5571.1291.1290.0000.0000.0000.000
6A115GLU-1-0.847-0.9192.134-16.828-14.3793.460-3.027-2.881-0.043
7A116LYS10.9700.9844.032-0.653-0.488-0.001-0.012-0.1520.000
8A117SER0-0.041-0.0128.9020.3120.3120.0000.0000.0000.000
9A118LEU00.0270.00811.9550.0030.0030.0000.0000.0000.000
10A119GLY00.0790.03415.2720.0270.0270.0000.0000.0000.000
11A120LEU0-0.0090.0199.8390.0120.0120.0000.0000.0000.000
12A121LEU00.0440.01713.5260.0520.0520.0000.0000.0000.000
13A122CYS0-0.045-0.00815.4180.0620.0620.0000.0000.0000.000
14A123HIS0-0.009-0.01616.6360.0420.0420.0000.0000.0000.000
15A124LYS10.7340.86316.2660.1450.1450.0000.0000.0000.000
16A125PHE00.005-0.00818.3220.0370.0370.0000.0000.0000.000
17A126LEU0-0.049-0.03821.0160.0220.0220.0000.0000.0000.000
18A127ALA0-0.039-0.00920.4960.0100.0100.0000.0000.0000.000
19A128ARG10.7280.84721.1860.0680.0680.0000.0000.0000.000
20A129TYR0-0.025-0.02223.7820.0190.0190.0000.0000.0000.000
21A130PRO00.0350.03227.152-0.011-0.0110.0000.0000.0000.000
22A131ASN00.008-0.00927.4520.0010.0010.0000.0000.0000.000
23A132TYR0-0.041-0.03830.6890.0040.0040.0000.0000.0000.000
24A133PRO00.0190.03132.9220.0000.0000.0000.0000.0000.000
25A134ASN0-0.021-0.02035.0720.0050.0050.0000.0000.0000.000
26A135PRO00.001-0.01837.6110.0000.0000.0000.0000.0000.000
27A136ALA00.0760.05436.5970.0010.0010.0000.0000.0000.000
28A137VAL0-0.0130.00334.9740.0040.0040.0000.0000.0000.000
29A138ASN0-0.030-0.01232.210-0.004-0.0040.0000.0000.0000.000
30A139ASN0-0.060-0.05130.7470.0110.0110.0000.0000.0000.000
31A140ASP-1-0.809-0.89227.295-0.027-0.0270.0000.0000.0000.000
32A141ILE00.0170.00526.6480.0100.0100.0000.0000.0000.000
33A142CYS0-0.045-0.01123.4290.0090.0090.0000.0000.0000.000
34A143LEU0-0.009-0.03122.2940.0110.0110.0000.0000.0000.000
35A144ASP-1-0.799-0.90922.3030.0980.0980.0000.0000.0000.000
36A145GLU-1-0.824-0.87620.454-0.064-0.0640.0000.0000.0000.000
37A146VAL0-0.122-0.06317.499-0.005-0.0050.0000.0000.0000.000
38A147ALA0-0.029-0.00917.6780.0330.0330.0000.0000.0000.000
39A148GLU-1-0.846-0.88419.304-0.018-0.0180.0000.0000.0000.000
40A149GLU-1-0.830-0.88814.578-0.164-0.1640.0000.0000.0000.000
41A150LEU0-0.004-0.0019.3440.0540.0540.0000.0000.0000.000
42A151ASN0-0.087-0.04111.4400.1050.1050.0000.0000.0000.000
43A152VAL00.1020.02711.931-0.037-0.0370.0000.0000.0000.000
44A153GLU-1-0.840-0.90414.3520.3830.3830.0000.0000.0000.000
45A154ARG10.9850.96516.494-0.262-0.2620.0000.0000.0000.000
46A155ARG10.8590.92318.948-0.147-0.1470.0000.0000.0000.000
47A156ARG10.8620.92214.976-0.166-0.1660.0000.0000.0000.000
48A157ILE00.1060.05818.453-0.031-0.0310.0000.0000.0000.000
49A158TYR0-0.023-0.00620.747-0.004-0.0040.0000.0000.0000.000
50A159ASP-1-0.860-0.93020.3420.0100.0100.0000.0000.0000.000
51A160ILE00.0630.03318.124-0.011-0.0110.0000.0000.0000.000
52A161VAL00.0470.02822.634-0.009-0.0090.0000.0000.0000.000
53A162ASN0-0.115-0.07025.6990.0080.0080.0000.0000.0000.000
54A163VAL00.006-0.00824.0800.0000.0000.0000.0000.0000.000
55A164LEU00.0430.03924.673-0.005-0.0050.0000.0000.0000.000
56A165GLU-1-0.747-0.84327.9150.0160.0160.0000.0000.0000.000
57A166SER0-0.121-0.06229.9190.0020.0020.0000.0000.0000.000
58A167LEU00.0210.00629.7300.0010.0010.0000.0000.0000.000
59A168HIS0-0.096-0.05333.325-0.001-0.0010.0000.0000.0000.000
60A169MET0-0.0160.00027.914-0.004-0.0040.0000.0000.0000.000
61A170VAL00.0290.03628.5140.0000.0000.0000.0000.0000.000
62A171SER0-0.016-0.01631.9660.0020.0020.0000.0000.0000.000
63A172ARG10.8410.92231.045-0.029-0.0290.0000.0000.0000.000
64A173LEU0-0.0150.00933.936-0.002-0.0020.0000.0000.0000.000
65A174ALA00.0390.00534.2660.0030.0030.0000.0000.0000.000
66A175LYS10.9670.98131.322-0.105-0.1050.0000.0000.0000.000
67A176ASN0-0.035-0.04426.341-0.007-0.0070.0000.0000.0000.000
68A177ARG11.0031.02129.771-0.037-0.0370.0000.0000.0000.000
69A178TYR0-0.044-0.04729.0470.0050.0050.0000.0000.0000.000
70A179THR00.0300.02031.1940.0010.0010.0000.0000.0000.000
71A180TRP00.0480.00626.809-0.004-0.0040.0000.0000.0000.000
72A181HIS0-0.087-0.04330.936-0.009-0.0090.0000.0000.0000.000
73A182GLY00.0700.03632.080-0.006-0.0060.0000.0000.0000.000
74A183ARG10.8340.92128.1290.1140.1140.0000.0000.0000.000
75A184HIS00.0270.02034.196-0.002-0.0020.0000.0000.0000.000
76A185ASN00.0520.02337.4810.0020.0020.0000.0000.0000.000
77A186LEU00.0570.04332.9400.0000.0000.0000.0000.0000.000
78A187ASN0-0.017-0.02036.2590.0010.0010.0000.0000.0000.000
79A188LYS11.0100.99939.0460.0270.0270.0000.0000.0000.000
80A189THR0-0.034-0.00936.2160.0040.0040.0000.0000.0000.000
81A190LEU00.0170.01535.6290.0020.0020.0000.0000.0000.000
82A191GLY00.0060.00838.6380.0020.0020.0000.0000.0000.000
83A192THR0-0.026-0.04041.6920.0030.0030.0000.0000.0000.000
84A193LEU0-0.006-0.00836.3600.0030.0030.0000.0000.0000.000
85A194LYS10.9460.96640.8560.0450.0450.0000.0000.0000.000
86A195SER0-0.041-0.01443.1010.0020.0020.0000.0000.0000.000
87A196ILE0-0.052-0.02341.8660.0020.0020.0000.0000.0000.000
88A197GLY0-0.003-0.02742.3930.0020.0020.0000.0000.0000.000
89A198GLU-1-0.804-0.87342.888-0.011-0.0110.0000.0000.0000.000
90A199GLU-1-0.855-0.93042.864-0.028-0.0280.0000.0000.0000.000
91A200ASN0-0.038-0.04043.896-0.002-0.0020.0000.0000.0000.000
92A201LYS10.9000.93944.5120.0110.0110.0000.0000.0000.000
93A202TYR0-0.037-0.02439.8970.0020.0020.0000.0000.0000.000
94A203ALA00.0340.01441.692-0.002-0.0020.0000.0000.0000.000
95A204GLU-1-0.894-0.94843.232-0.017-0.0170.0000.0000.0000.000
96A205GLN00.013-0.00940.3560.0010.0010.0000.0000.0000.000
97A206ILE0-0.034-0.02038.9970.0000.0000.0000.0000.0000.000
98A207MET0-0.064-0.03941.251-0.002-0.0020.0000.0000.0000.000
99A208MET0-0.0060.02243.6720.0010.0010.0000.0000.0000.000
100A209ILE0-0.004-0.00537.6680.0000.0000.0000.0000.0000.000
101A210LYS10.8610.95640.6200.0350.0350.0000.0000.0000.000
102A211LYS10.9270.94441.6680.0310.0310.0000.0000.0000.000
103A212LYS11.0021.02144.0390.0250.0250.0000.0000.0000.000
104A259ASN00.0610.03841.819-0.003-0.0030.0000.0000.0000.000
105A260SER0-0.007-0.02240.6180.0010.0010.0000.0000.0000.000
106A261ARG11.0221.01541.099-0.037-0.0370.0000.0000.0000.000
107A262LYS10.9060.93135.351-0.070-0.0700.0000.0000.0000.000
108A263ASP-1-0.815-0.86436.2300.0270.0270.0000.0000.0000.000
109A264LYS10.9440.96633.588-0.042-0.0420.0000.0000.0000.000
110A265SER00.023-0.02431.436-0.002-0.0020.0000.0000.0000.000
111A266LEU0-0.0160.00725.993-0.005-0.0050.0000.0000.0000.000
112A267ARG10.9460.96829.785-0.033-0.0330.0000.0000.0000.000
113A268VAL00.0820.05431.540-0.008-0.0080.0000.0000.0000.000
114A269MET0-0.044-0.01828.450-0.004-0.0040.0000.0000.0000.000
115A270SER00.002-0.00728.815-0.006-0.0060.0000.0000.0000.000
116A271GLN00.0150.00930.786-0.003-0.0030.0000.0000.0000.000
117A272LYS10.9580.97034.3050.0070.0070.0000.0000.0000.000
118A273PHE0-0.061-0.01027.913-0.002-0.0020.0000.0000.0000.000
119A274VAL00.0380.00331.485-0.004-0.0040.0000.0000.0000.000
120A275MET0-0.0700.02133.753-0.001-0.0010.0000.0000.0000.000
121A276LEU0-0.021-0.02733.5180.0000.0000.0000.0000.0000.000
122A277PHE0-0.0060.00429.400-0.006-0.0060.0000.0000.0000.000
123A278LEU0-0.090-0.02535.211-0.003-0.0030.0000.0000.0000.000
124A279VAL00.0250.00938.3750.0050.0050.0000.0000.0000.000
125A280SER00.0150.00140.246-0.004-0.0040.0000.0000.0000.000
126A281THR0-0.036-0.01740.313-0.001-0.0010.0000.0000.0000.000
127A282PRO0-0.005-0.00535.4880.0020.0020.0000.0000.0000.000
128A283GLN0-0.0040.00135.614-0.001-0.0010.0000.0000.0000.000
129A284ILE0-0.0080.02831.4430.0040.0040.0000.0000.0000.000
130A285VAL00.0420.00628.0350.0000.0000.0000.0000.0000.000
131A286SER00.004-0.01829.6730.0040.0040.0000.0000.0000.000
132A287LEU00.0580.03731.6520.0090.0090.0000.0000.0000.000
133A288GLU-1-0.667-0.84332.307-0.055-0.0550.0000.0000.0000.000
134A289VAL0-0.098-0.05229.5620.0060.0060.0000.0000.0000.000
135A290ALA00.0220.01432.8450.0080.0080.0000.0000.0000.000
136A291ALA00.0700.03836.1300.0050.0050.0000.0000.0000.000
137A292LYS10.7920.88532.2510.0430.0430.0000.0000.0000.000
138A293ILE0-0.038-0.02433.5640.0080.0080.0000.0000.0000.000
139A294LEU00.0740.04636.7470.0040.0040.0000.0000.0000.000
140A295ILE0-0.036-0.01736.7380.0020.0020.0000.0000.0000.000
141A296GLY0-0.139-0.06937.3500.0030.0030.0000.0000.0000.000
142A297GLU-1-0.999-0.99737.9610.0380.0380.0000.0000.0000.000
143A298ASP-1-0.947-0.96640.5510.0080.0080.0000.0000.0000.000
144A299HIS00.005-0.00643.5800.0010.0010.0000.0000.0000.000
145A300VAL0-0.0150.00944.333-0.002-0.0020.0000.0000.0000.000
146A301GLU-1-0.914-0.94741.6900.0300.0300.0000.0000.0000.000
147A302ASP-1-0.955-1.00139.4940.0200.0200.0000.0000.0000.000
148A303LEU0-0.011-0.01736.4300.0040.0040.0000.0000.0000.000
149A304ASP-1-0.762-0.84136.4930.0110.0110.0000.0000.0000.000
150A305LYS10.9050.97033.288-0.025-0.0250.0000.0000.0000.000
151A306SER0-0.061-0.05530.807-0.001-0.0010.0000.0000.0000.000
152A307LYS11.0031.02030.469-0.066-0.0660.0000.0000.0000.000
153A308PHE00.0850.02029.991-0.001-0.0010.0000.0000.0000.000
154A309LYS10.9360.94126.215-0.047-0.0470.0000.0000.0000.000
155A310THR0-0.045-0.03124.975-0.006-0.0060.0000.0000.0000.000
156A311LYS10.8870.94926.013-0.016-0.0160.0000.0000.0000.000
157A312ILE00.0580.03724.854-0.007-0.0070.0000.0000.0000.000
158A313ARG10.8870.95721.557-0.063-0.0630.0000.0000.0000.000
159A314ARG10.8590.90820.331-0.055-0.0550.0000.0000.0000.000
160A315LEU00.0140.02024.474-0.008-0.0080.0000.0000.0000.000
161A316TYR00.0150.00020.837-0.015-0.0150.0000.0000.0000.000
162A317ASP-1-0.856-0.91619.637-0.069-0.0690.0000.0000.0000.000
163A318ILE0-0.012-0.02021.305-0.013-0.0130.0000.0000.0000.000
164A319ALA00.0180.02322.850-0.007-0.0070.0000.0000.0000.000
165A320ASN0-0.036-0.03617.673-0.042-0.0420.0000.0000.0000.000
166A321VAL0-0.023-0.00520.120-0.022-0.0220.0000.0000.0000.000
167A322LEU0-0.008-0.00821.4400.0030.0030.0000.0000.0000.000
168A323SER0-0.064-0.03220.330-0.002-0.0020.0000.0000.0000.000
169A324SER0-0.024-0.00219.616-0.044-0.0440.0000.0000.0000.000
170A325LEU00.0030.01421.4300.0250.0250.0000.0000.0000.000
171A326ASP-1-0.771-0.91124.231-0.147-0.1470.0000.0000.0000.000
172A327LEU0-0.162-0.07326.934-0.004-0.0040.0000.0000.0000.000
173A328ILE00.1140.05724.7960.0100.0100.0000.0000.0000.000
174A329LYS10.8420.91226.2190.1180.1180.0000.0000.0000.000
175A330LYS10.8590.92320.3350.2160.2160.0000.0000.0000.000
176A331VAL0-0.051-0.03424.0040.0000.0000.0000.0000.0000.000
177A332HIS00.0530.03025.281-0.001-0.0010.0000.0000.0000.000
178A333VAL00.0120.00124.141-0.016-0.0160.0000.0000.0000.000
179A334THR0-0.065-0.03426.3370.0120.0120.0000.0000.0000.000
180A335GLU-1-0.741-0.85423.736-0.192-0.1920.0000.0000.0000.000
181A336GLU-1-0.763-0.88628.657-0.075-0.0750.0000.0000.0000.000
182A337ARG10.7580.87727.5100.1430.1430.0000.0000.0000.000
183A338GLY00.1630.07931.138-0.001-0.0010.0000.0000.0000.000
184A339ARG10.8870.95330.5360.1270.1270.0000.0000.0000.000
185A340LYS10.9750.98233.4240.0880.0880.0000.0000.0000.000
186A341PRO00.0750.05535.8110.0030.0030.0000.0000.0000.000