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: J3GY9

Calculation Name: 2NTZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2NTZ

Chain ID: A

ChEMBL ID:

UniProt ID: Q38420

Base Structure: X-ray

Registration Date: 2023-06-20

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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1665319.024075
FMO2-HF: Nuclear repulsion 1589291.163369
FMO2-HF: Total energy -76027.860706
FMO2-MP2: Total energy -76248.191944


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:144:GLN)


Summations of interaction energy for fragment #1(A:144: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.
-2.1490.091-0.018-1.193-1.0290.004
Interaction energy analysis for fragmet #1(A:144:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.036 / q_NPA : 0.018
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].
3A146ALA0-0.031-0.0183.887-0.7991.441-0.018-1.193-1.0290.004
4A147LEU0-0.0150.0086.6700.2040.2040.0000.0000.0000.000
5A148GLN00.0300.02810.077-0.118-0.1180.0000.0000.0000.000
6A149HIS0-0.012-0.02312.8450.0930.0930.0000.0000.0000.000
7A150SER00.0330.02015.3520.0240.0240.0000.0000.0000.000
8A151ILE00.012-0.00917.1470.0160.0160.0000.0000.0000.000
9A152ARG10.8420.88918.5700.1980.1980.0000.0000.0000.000
10A153GLU-1-0.834-0.90311.350-0.396-0.3960.0000.0000.0000.000
11A154ILE0-0.060-0.03514.5790.0420.0420.0000.0000.0000.000
12A155GLY00.0150.00516.1960.0370.0370.0000.0000.0000.000
13A156LEU00.0520.03612.6410.0310.0310.0000.0000.0000.000
14A157ARG10.8210.88311.129-0.535-0.5350.0000.0000.0000.000
15A158LEU0-0.023-0.03014.0960.0480.0480.0000.0000.0000.000
16A159MET00.0050.00717.6220.0060.0060.0000.0000.0000.000
17A160ARG10.9870.9929.533-0.179-0.1790.0000.0000.0000.000
18A161MET0-0.025-0.01515.8690.0270.0270.0000.0000.0000.000
19A162LYS10.9140.94518.271-0.085-0.0850.0000.0000.0000.000
20A163ASN0-0.072-0.03419.384-0.031-0.0310.0000.0000.0000.000
21A164ASP-1-0.921-0.95117.3970.2060.2060.0000.0000.0000.000
22A165GLY0-0.0060.00321.0170.0130.0130.0000.0000.0000.000
23A166MET0-0.080-0.00518.5380.0270.0270.0000.0000.0000.000
24A167SER00.0370.01023.846-0.020-0.0200.0000.0000.0000.000
25A168GLN00.0400.00224.3530.0120.0120.0000.0000.0000.000
26A169LYS10.8830.94425.262-0.141-0.1410.0000.0000.0000.000
27A170ASP-1-0.790-0.90024.4770.2000.2000.0000.0000.0000.000
28A171ILE0-0.0020.00019.6980.0320.0320.0000.0000.0000.000
29A172ALA0-0.050-0.02321.5640.0280.0280.0000.0000.0000.000
30A173ALA0-0.0080.00523.6040.0140.0140.0000.0000.0000.000
31A174LYS10.8930.93617.791-0.403-0.4030.0000.0000.0000.000
32A175GLU-1-0.775-0.86915.8770.6440.6440.0000.0000.0000.000
33A176GLY0-0.0060.02819.0510.0090.0090.0000.0000.0000.000
34A177LEU0-0.055-0.03819.225-0.029-0.0290.0000.0000.0000.000
35A178SER00.0290.00923.280-0.015-0.0150.0000.0000.0000.000
36A179GLN00.1060.03125.980-0.001-0.0010.0000.0000.0000.000
37A180ALA00.0050.02327.375-0.010-0.0100.0000.0000.0000.000
38A181LYS10.9770.98821.090-0.191-0.1910.0000.0000.0000.000
39A182VAL00.0410.02322.001-0.013-0.0130.0000.0000.0000.000
40A183THR00.008-0.00723.363-0.014-0.0140.0000.0000.0000.000
41A184ARG10.9130.96425.923-0.081-0.0810.0000.0000.0000.000
42A185ALA00.0200.01320.263-0.017-0.0170.0000.0000.0000.000
43A186LEU0-0.006-0.00420.708-0.022-0.0220.0000.0000.0000.000
44A187GLN0-0.0010.00122.715-0.016-0.0160.0000.0000.0000.000
45A188ALA00.0400.02722.292-0.012-0.0120.0000.0000.0000.000
46A189ALA0-0.040-0.02219.567-0.021-0.0210.0000.0000.0000.000
47A190SER0-0.081-0.04621.052-0.015-0.0150.0000.0000.0000.000
48A191ALA0-0.0110.00024.133-0.002-0.0020.0000.0000.0000.000
49A192PRO00.0630.03623.648-0.016-0.0160.0000.0000.0000.000
50A193GLU-1-0.808-0.88018.639-0.238-0.2380.0000.0000.0000.000
51A194GLU-1-0.876-0.94922.443-0.151-0.1510.0000.0000.0000.000
52A195LEU0-0.001-0.00725.049-0.001-0.0010.0000.0000.0000.000
53A196VAL0-0.049-0.03521.0460.0050.0050.0000.0000.0000.000
54A197ALA0-0.021-0.01322.253-0.008-0.0080.0000.0000.0000.000
55A198LEU0-0.0200.00223.265-0.006-0.0060.0000.0000.0000.000
56A199PHE0-0.044-0.01924.8550.0160.0160.0000.0000.0000.000
57A200PRO00.0210.01723.716-0.021-0.0210.0000.0000.0000.000
58A201VAL00.0100.01321.145-0.034-0.0340.0000.0000.0000.000
59A202GLN00.0650.02818.6640.0110.0110.0000.0000.0000.000
60A203SER0-0.063-0.04219.2080.0130.0130.0000.0000.0000.000
61A204GLU-1-0.872-0.93321.457-0.036-0.0360.0000.0000.0000.000
62A205LEU0-0.0550.00323.7510.0180.0180.0000.0000.0000.000
63A206THR00.0270.01324.8570.0150.0150.0000.0000.0000.000
64A207PHE0-0.023-0.03126.0470.0010.0010.0000.0000.0000.000
65A208SER0-0.021-0.02127.241-0.001-0.0010.0000.0000.0000.000
66A209ASP-1-0.698-0.84928.597-0.042-0.0420.0000.0000.0000.000
67A210TYR00.013-0.01221.691-0.004-0.0040.0000.0000.0000.000
68A211LYS10.8260.91727.2830.0050.0050.0000.0000.0000.000
69A212THR0-0.027-0.02829.8250.0030.0030.0000.0000.0000.000
70A213LEU00.0160.02826.2430.0000.0000.0000.0000.0000.000
71A214CYS0-0.033-0.02027.300-0.001-0.0010.0000.0000.0000.000
72A215ALA0-0.0220.00229.2110.0010.0010.0000.0000.0000.000
73A216VAL00.007-0.00532.8860.0010.0010.0000.0000.0000.000
74A217GLY00.0110.00830.410-0.005-0.0050.0000.0000.0000.000
75A218ASP-1-0.950-0.98231.358-0.023-0.0230.0000.0000.0000.000
76A219GLU-1-0.926-0.95733.680-0.019-0.0190.0000.0000.0000.000
77A220MET0-0.0520.00433.972-0.001-0.0010.0000.0000.0000.000
78A221GLY0-0.053-0.03336.449-0.002-0.0020.0000.0000.0000.000
79A222ASN0-0.081-0.03629.280-0.008-0.0080.0000.0000.0000.000
80A223LYS10.8740.95132.0290.0520.0520.0000.0000.0000.000
81A224ASN00.0350.01231.318-0.001-0.0010.0000.0000.0000.000
82A225LEU0-0.046-0.01432.4730.0080.0080.0000.0000.0000.000
83A226GLU-1-0.822-0.92234.751-0.060-0.0600.0000.0000.0000.000
84A227PHE00.0230.01029.4020.0000.0000.0000.0000.0000.000
85A228ASP-1-0.854-0.92230.679-0.119-0.1190.0000.0000.0000.000
86A229GLN00.012-0.00532.334-0.003-0.0030.0000.0000.0000.000
87A230LEU00.0120.01132.7010.0000.0000.0000.0000.0000.000
88A231ILE0-0.013-0.01528.448-0.001-0.0010.0000.0000.0000.000
89A232GLN0-0.084-0.05031.980-0.005-0.0050.0000.0000.0000.000
90A233ASN0-0.085-0.04935.314-0.002-0.0020.0000.0000.0000.000
91A234ILE00.0290.01632.3640.0030.0030.0000.0000.0000.000
92A235SER0-0.0360.00333.612-0.005-0.0050.0000.0000.0000.000
93A236PRO0-0.015-0.01334.609-0.005-0.0050.0000.0000.0000.000
94A237GLU-1-0.842-0.93636.742-0.083-0.0830.0000.0000.0000.000
95A238ILE0-0.047-0.02530.2000.0000.0000.0000.0000.0000.000
96A239ASN0-0.006-0.00332.534-0.014-0.0140.0000.0000.0000.000
97A240ASP-1-0.969-0.98333.629-0.088-0.0880.0000.0000.0000.000
98A241ILE0-0.018-0.03133.7910.0020.0020.0000.0000.0000.000
99A242LEU0-0.062-0.02028.457-0.001-0.0010.0000.0000.0000.000
100A243SER0-0.044-0.02832.643-0.006-0.0060.0000.0000.0000.000
101A244ILE0-0.070-0.01935.3650.0040.0040.0000.0000.0000.000
102A245GLU-1-0.935-0.96635.540-0.090-0.0900.0000.0000.0000.000
103A246GLU-1-1.031-1.01135.684-0.081-0.0810.0000.0000.0000.000
104A247MET0-0.006-0.00134.2140.0070.0070.0000.0000.0000.000
105A248ALA00.0430.02429.703-0.010-0.0100.0000.0000.0000.000
106A249GLU-1-0.876-0.97425.596-0.144-0.1440.0000.0000.0000.000
107A250ASP-1-0.845-0.92528.905-0.046-0.0460.0000.0000.0000.000
108A251GLU-1-0.885-0.93332.125-0.056-0.0560.0000.0000.0000.000
109A252VAL00.0600.04729.6380.0030.0030.0000.0000.0000.000
110A253LYS10.8170.92828.6650.0580.0580.0000.0000.0000.000
111A254ASN0-0.027-0.02731.3930.0030.0030.0000.0000.0000.000
112A255LYS10.7880.88634.9760.0640.0640.0000.0000.0000.000
113A256ILE00.0620.03430.2580.0040.0040.0000.0000.0000.000
114A257LEU00.0150.00831.1270.0020.0020.0000.0000.0000.000
115A258ARG10.9150.96233.5270.0420.0420.0000.0000.0000.000
116A259LEU00.0020.01935.6670.0050.0050.0000.0000.0000.000
117A260ILE00.0280.01930.4760.0040.0040.0000.0000.0000.000
118A261THR0-0.041-0.04634.5940.0050.0050.0000.0000.0000.000
119A262LYS10.8240.91636.4790.0620.0620.0000.0000.0000.000
120A263GLU-1-0.792-0.90137.483-0.058-0.0580.0000.0000.0000.000
121A264ALA00.0290.01735.4140.0010.0010.0000.0000.0000.000
122A265SER0-0.030-0.02837.5100.0050.0050.0000.0000.0000.000
123A266LEU0-0.089-0.02640.5440.0050.0050.0000.0000.0000.000
124A267LEU00.0390.03938.0740.0010.0010.0000.0000.0000.000
125A268THR00.039-0.00839.4750.0010.0010.0000.0000.0000.000
126A269ASP-1-0.824-0.87941.948-0.032-0.0320.0000.0000.0000.000
127A270LYS10.7450.84744.9330.0420.0420.0000.0000.0000.000
128A271GLY00.0740.02946.1450.0010.0010.0000.0000.0000.000
129A272SER0-0.030-0.00947.2580.0000.0000.0000.0000.0000.000
130A273LYS10.7810.88547.2810.0310.0310.0000.0000.0000.000
131A274ASP-1-0.811-0.92552.580-0.027-0.0270.0000.0000.0000.000
132A275LYS10.8700.92755.3480.0180.0180.0000.0000.0000.000
133A276SER0-0.030-0.01657.6060.0000.0000.0000.0000.0000.000
134A277VAL00.0570.05057.7690.0010.0010.0000.0000.0000.000
135A278VAL00.005-0.01460.5670.0000.0000.0000.0000.0000.000
136A279THR0-0.012-0.01163.1360.0000.0000.0000.0000.0000.000
137A280GLU-1-0.776-0.86265.444-0.010-0.0100.0000.0000.0000.000
138A281LEU0-0.025-0.01268.497-0.001-0.0010.0000.0000.0000.000
139A282TRP00.0170.00271.0890.0000.0000.0000.0000.0000.000
140A283LYS10.8640.93471.0900.0070.0070.0000.0000.0000.000
141A284PHE00.0180.00473.7630.0000.0000.0000.0000.0000.000
142A285GLH00.020-0.02576.4120.0000.0000.0000.0000.0000.000
143A286ASP-1-0.836-0.84578.817-0.005-0.0050.0000.0000.0000.000
144A287LYS10.9060.93977.8010.0030.0030.0000.0000.0000.000
145A288ASP-1-0.817-0.89576.503-0.005-0.0050.0000.0000.0000.000
146A289ARG10.8450.92177.6990.0060.0060.0000.0000.0000.000
147A290PHE0-0.012-0.01873.5630.0000.0000.0000.0000.0000.000
148A291ALA00.0560.01974.1060.0000.0000.0000.0000.0000.000
149A292ARG10.8270.91268.3670.0110.0110.0000.0000.0000.000
150A293LYS10.9550.99364.2990.0200.0200.0000.0000.0000.000
151A294ARG10.8250.88164.4930.0150.0150.0000.0000.0000.000
152A295VAL00.013-0.00860.532-0.001-0.0010.0000.0000.0000.000
153A296LYS10.8690.94060.0690.0230.0230.0000.0000.0000.000
154A297GLY00.1240.09357.4540.0000.0000.0000.0000.0000.000
155A298ARG10.9250.95958.2000.0340.0340.0000.0000.0000.000
156A299ALA00.0220.00760.1480.0000.0000.0000.0000.0000.000
157A300PHE0-0.034-0.02163.1550.0000.0000.0000.0000.0000.000
158A301SER0-0.008-0.00665.6090.0000.0000.0000.0000.0000.000
159A302TYR00.010-0.00968.5850.0000.0000.0000.0000.0000.000
160A303GLU-1-0.793-0.84769.139-0.014-0.0140.0000.0000.0000.000
161A304PHE00.036-0.00173.1380.0000.0000.0000.0000.0000.000
162A305ASN0-0.015-0.01176.2810.0000.0000.0000.0000.0000.000
163A306ARG10.8850.92078.7510.0060.0060.0000.0000.0000.000
164A307LEU00.0200.01978.4520.0000.0000.0000.0000.0000.000
165A308SER0-0.011-0.02882.7750.0000.0000.0000.0000.0000.000
166A309LYS10.8690.91384.9190.0110.0110.0000.0000.0000.000
167A310GLU-1-0.809-0.87886.632-0.010-0.0100.0000.0000.0000.000
168A311LEU00.0080.00481.726-0.001-0.0010.0000.0000.0000.000
169A312GLN0-0.045-0.03081.5970.0000.0000.0000.0000.0000.000
170A313GLU-1-0.811-0.87282.784-0.013-0.0130.0000.0000.0000.000
171A314GLU-1-0.871-0.93182.361-0.013-0.0130.0000.0000.0000.000
172A315LEU0-0.050-0.01577.086-0.001-0.0010.0000.0000.0000.000
173A316ASP-1-0.814-0.90179.826-0.013-0.0130.0000.0000.0000.000
174A317ARG10.7970.87181.5740.0120.0120.0000.0000.0000.000
175A318MET00.014-0.00179.760-0.001-0.0010.0000.0000.0000.000
176A319ILE0-0.010-0.00674.550-0.001-0.0010.0000.0000.0000.000
177A320GLY00.0290.01677.450-0.001-0.0010.0000.0000.0000.000
178A321HIS0-0.030-0.01280.065-0.001-0.0010.0000.0000.0000.000
179A322ILE00.009-0.00573.691-0.001-0.0010.0000.0000.0000.000
180A323LEU0-0.006-0.00473.473-0.001-0.0010.0000.0000.0000.000
181A324ARG10.8860.95176.0950.0170.0170.0000.0000.0000.000
182A325LYS10.9200.96875.3070.0210.0210.0000.0000.0000.000
183A326SER0-0.046-0.02273.632-0.001-0.0010.0000.0000.0000.000
184A327LEU0-0.008-0.00973.756-0.001-0.0010.0000.0000.0000.000
185A328ASP-1-0.813-0.88876.552-0.020-0.0200.0000.0000.0000.000
186A329LYS10.9120.95878.4400.0230.0230.0000.0000.0000.000
187A330LYS10.8810.94980.6350.0220.0220.0000.0000.0000.000
188A331PRO00.001-0.01681.873-0.001-0.0010.0000.0000.0000.000
189A332LYS11.0161.00985.0070.0220.0220.0000.0000.0000.000