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: N1Q8Q

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 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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1665549.14974
FMO2-HF: Nuclear repulsion 1589524.406171
FMO2-HF: Total energy -76024.743569
FMO2-MP2: Total energy -76245.638515


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.
-2.4180.609-0.023-1.727-1.2770.005
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 : 0.034 / q_NPA : 0.017
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].
3A146ALA0-0.030-0.0243.869-1.6211.406-0.023-1.727-1.2770.005
4A147LEU0-0.0180.0156.7540.3460.3460.0000.0000.0000.000
5A148GLN00.0640.02210.317-0.093-0.0930.0000.0000.0000.000
6A149HIS0-0.026-0.01013.3690.0680.0680.0000.0000.0000.000
7A150SER00.1280.09615.7790.0010.0010.0000.0000.0000.000
8A151ILE0-0.056-0.06217.4880.0150.0150.0000.0000.0000.000
9A152ARG10.8200.87318.5930.1390.1390.0000.0000.0000.000
10A153GLU-1-0.888-0.93211.158-0.293-0.2930.0000.0000.0000.000
11A154ILE0-0.044-0.02815.3610.0220.0220.0000.0000.0000.000
12A155GLY00.015-0.00316.2780.0220.0220.0000.0000.0000.000
13A156LEU00.1150.06912.5500.0310.0310.0000.0000.0000.000
14A157ARG10.8590.91211.672-0.427-0.4270.0000.0000.0000.000
15A158LEU0-0.009-0.00614.3070.0230.0230.0000.0000.0000.000
16A159MET0-0.028-0.02317.678-0.002-0.0020.0000.0000.0000.000
17A160ARG10.9540.9839.552-0.115-0.1150.0000.0000.0000.000
18A161MET0-0.029-0.02915.7260.0170.0170.0000.0000.0000.000
19A162LYS10.8820.92918.210-0.058-0.0580.0000.0000.0000.000
20A163ASN0-0.050-0.02319.644-0.019-0.0190.0000.0000.0000.000
21A164ASP-1-0.945-0.95318.0370.1070.1070.0000.0000.0000.000
22A165GLY0-0.0100.00221.5420.0070.0070.0000.0000.0000.000
23A166MET0-0.038-0.00618.9170.0280.0280.0000.0000.0000.000
24A167SER00.0250.01524.246-0.012-0.0120.0000.0000.0000.000
25A168GLN00.0940.04624.3490.0050.0050.0000.0000.0000.000
26A169LYS10.8840.95025.183-0.099-0.0990.0000.0000.0000.000
27A170ASP-1-0.799-0.91024.6270.1430.1430.0000.0000.0000.000
28A171ILE00.0290.02419.9500.0240.0240.0000.0000.0000.000
29A172ALA0-0.128-0.07521.8000.0210.0210.0000.0000.0000.000
30A173ALA0-0.0150.00123.6780.0060.0060.0000.0000.0000.000
31A174LYS10.9120.95617.958-0.253-0.2530.0000.0000.0000.000
32A175GLU-1-0.786-0.90015.5900.4980.4980.0000.0000.0000.000
33A176GLY0-0.0180.02418.7350.0210.0210.0000.0000.0000.000
34A177LEU0-0.070-0.04219.057-0.013-0.0130.0000.0000.0000.000
35A178SER00.0620.01423.149-0.016-0.0160.0000.0000.0000.000
36A179GLN00.0940.02526.604-0.008-0.0080.0000.0000.0000.000
37A180ALA00.0280.02927.788-0.008-0.0080.0000.0000.0000.000
38A181LYS11.0221.01821.455-0.174-0.1740.0000.0000.0000.000
39A182VAL00.0370.02022.401-0.010-0.0100.0000.0000.0000.000
40A183THR0-0.006-0.01524.011-0.010-0.0100.0000.0000.0000.000
41A184ARG10.9450.96626.003-0.079-0.0790.0000.0000.0000.000
42A185ALA0-0.0010.00820.813-0.009-0.0090.0000.0000.0000.000
43A186LEU00.006-0.00821.062-0.017-0.0170.0000.0000.0000.000
44A187GLN0-0.026-0.00322.971-0.013-0.0130.0000.0000.0000.000
45A188ALA00.0250.01722.855-0.009-0.0090.0000.0000.0000.000
46A189ALA0-0.076-0.00819.510-0.015-0.0150.0000.0000.0000.000
47A190SER0-0.049-0.03121.102-0.013-0.0130.0000.0000.0000.000
48A191ALA0-0.051-0.02023.908-0.002-0.0020.0000.0000.0000.000
49A192PRO00.0650.05423.835-0.012-0.0120.0000.0000.0000.000
50A193GLU-1-0.784-0.87619.403-0.166-0.1660.0000.0000.0000.000
51A194GLU-1-0.855-0.92822.976-0.109-0.1090.0000.0000.0000.000
52A195LEU0-0.014-0.01425.463-0.004-0.0040.0000.0000.0000.000
53A196VAL0-0.071-0.03520.9690.0040.0040.0000.0000.0000.000
54A197ALA0-0.036-0.02422.840-0.005-0.0050.0000.0000.0000.000
55A198LEU0-0.015-0.00523.8010.0000.0000.0000.0000.0000.000
56A199PHE0-0.091-0.01724.8360.0120.0120.0000.0000.0000.000
57A200PRO00.0670.03524.061-0.016-0.0160.0000.0000.0000.000
58A201VAL00.0500.02621.761-0.024-0.0240.0000.0000.0000.000
59A202GLN0-0.0080.02018.6210.0200.0200.0000.0000.0000.000
60A203SER0-0.024-0.04719.5190.0080.0080.0000.0000.0000.000
61A204GLU-1-0.911-0.95021.8130.0040.0040.0000.0000.0000.000
62A205LEU0-0.0320.01623.8390.0110.0110.0000.0000.0000.000
63A206THR00.0250.01425.1900.0140.0140.0000.0000.0000.000
64A207PHE0-0.014-0.02026.126-0.001-0.0010.0000.0000.0000.000
65A208SER0-0.024-0.03327.614-0.003-0.0030.0000.0000.0000.000
66A209ASP-1-0.817-0.92629.183-0.013-0.0130.0000.0000.0000.000
67A210TYR00.0880.01322.105-0.004-0.0040.0000.0000.0000.000
68A211LYS10.9120.97727.784-0.017-0.0170.0000.0000.0000.000
69A212THR0-0.068-0.03430.326-0.003-0.0030.0000.0000.0000.000
70A213LEU0-0.0050.02426.765-0.002-0.0020.0000.0000.0000.000
71A214CYS00.051-0.00327.717-0.002-0.0020.0000.0000.0000.000
72A215ALA0-0.126-0.02829.6200.0010.0010.0000.0000.0000.000
73A216VAL00.058-0.00832.9000.0000.0000.0000.0000.0000.000
74A217GLY0-0.034-0.03430.484-0.004-0.0040.0000.0000.0000.000
75A218ASP-1-0.971-1.01731.333-0.020-0.0200.0000.0000.0000.000
76A219GLU-1-0.909-0.94833.607-0.011-0.0110.0000.0000.0000.000
77A220MET0-0.0270.01734.2950.0010.0010.0000.0000.0000.000
78A221GLY0-0.075-0.05537.056-0.002-0.0020.0000.0000.0000.000
79A222ASN0-0.0510.01529.461-0.005-0.0050.0000.0000.0000.000
80A223LYS10.8750.95032.5980.0380.0380.0000.0000.0000.000
81A224ASN00.0380.01231.9280.0000.0000.0000.0000.0000.000
82A225LEU0-0.043-0.01333.0240.0060.0060.0000.0000.0000.000
83A226GLU-1-0.840-0.93534.801-0.041-0.0410.0000.0000.0000.000
84A227PHE00.0140.00529.4070.0010.0010.0000.0000.0000.000
85A228ASP-1-0.890-0.94530.848-0.087-0.0870.0000.0000.0000.000
86A229GLN00.041-0.00232.669-0.001-0.0010.0000.0000.0000.000
87A230LEU00.0370.03033.1460.0000.0000.0000.0000.0000.000
88A231ILE0-0.032-0.02628.728-0.001-0.0010.0000.0000.0000.000
89A232GLN0-0.092-0.05032.248-0.004-0.0040.0000.0000.0000.000
90A233ASN0-0.048-0.03735.555-0.002-0.0020.0000.0000.0000.000
91A234ILE00.0320.03132.9630.0030.0030.0000.0000.0000.000
92A235SER0-0.023-0.00333.286-0.001-0.0010.0000.0000.0000.000
93A236PRO0-0.0060.00334.403-0.003-0.0030.0000.0000.0000.000
94A237GLU-1-0.827-0.93236.480-0.054-0.0540.0000.0000.0000.000
95A238ILE0-0.066-0.02630.5680.0020.0020.0000.0000.0000.000
96A239ASN00.0240.00632.464-0.007-0.0070.0000.0000.0000.000
97A240ASP-1-1.067-1.01833.552-0.055-0.0550.0000.0000.0000.000
98A241ILE0-0.036-0.04333.9320.0050.0050.0000.0000.0000.000
99A242LEU0-0.089-0.03328.530-0.001-0.0010.0000.0000.0000.000
100A243SER0-0.062-0.02432.670-0.002-0.0020.0000.0000.0000.000
101A244ILE0-0.015-0.01135.4330.0010.0010.0000.0000.0000.000
102A245GLU-1-0.923-0.96835.996-0.053-0.0530.0000.0000.0000.000
103A246GLU-1-1.020-0.98935.220-0.040-0.0400.0000.0000.0000.000
104A247MET00.019-0.00334.5990.0040.0040.0000.0000.0000.000
105A248ALA00.0400.03729.519-0.007-0.0070.0000.0000.0000.000
106A249GLU-1-0.878-0.97525.879-0.086-0.0860.0000.0000.0000.000
107A250ASP-1-0.980-0.99329.227-0.010-0.0100.0000.0000.0000.000
108A251GLU-1-0.827-0.91632.491-0.022-0.0220.0000.0000.0000.000
109A252VAL00.0720.06129.2440.0000.0000.0000.0000.0000.000
110A253LYS10.9050.95129.0920.0210.0210.0000.0000.0000.000
111A254ASN0-0.034-0.02331.638-0.001-0.0010.0000.0000.0000.000
112A255LYS10.7760.89434.6880.0340.0340.0000.0000.0000.000
113A256ILE00.1010.03530.1540.0010.0010.0000.0000.0000.000
114A257LEU0-0.002-0.01031.4270.0010.0010.0000.0000.0000.000
115A258ARG10.8810.93033.7130.0170.0170.0000.0000.0000.000
116A259LEU0-0.0300.01235.9900.0030.0030.0000.0000.0000.000
117A260ILE00.0470.03630.4200.0020.0020.0000.0000.0000.000
118A261THR00.023-0.00134.5740.0020.0020.0000.0000.0000.000
119A262LYS10.9040.95836.5580.0360.0360.0000.0000.0000.000
120A263GLU-1-0.854-0.94238.102-0.036-0.0360.0000.0000.0000.000
121A264ALA00.0100.00835.747-0.003-0.0030.0000.0000.0000.000
122A265SER0-0.059-0.01837.8590.0030.0030.0000.0000.0000.000
123A266LEU0-0.153-0.06940.8600.0030.0030.0000.0000.0000.000
124A267LEU00.0500.03038.1270.0000.0000.0000.0000.0000.000
125A268THR00.0600.01339.8260.0000.0000.0000.0000.0000.000
126A269ASP-1-0.836-0.89042.085-0.021-0.0210.0000.0000.0000.000
127A270LYS10.7900.88145.2740.0270.0270.0000.0000.0000.000
128A271GLY00.0760.02845.8950.0000.0000.0000.0000.0000.000
129A272SER0-0.025-0.00247.4370.0000.0000.0000.0000.0000.000
130A273LYS10.7660.87747.3780.0220.0220.0000.0000.0000.000
131A274ASP-1-0.840-0.91752.516-0.018-0.0180.0000.0000.0000.000
132A275LYS10.9170.94755.3360.0120.0120.0000.0000.0000.000
133A276SER0-0.064-0.04857.7200.0000.0000.0000.0000.0000.000
134A277VAL00.0580.04158.2430.0000.0000.0000.0000.0000.000
135A278VAL0-0.0050.01061.1230.0000.0000.0000.0000.0000.000
136A279THR0-0.008-0.00463.3590.0000.0000.0000.0000.0000.000
137A280GLU-1-0.783-0.88165.630-0.004-0.0040.0000.0000.0000.000
138A281LEU0-0.0110.00868.658-0.001-0.0010.0000.0000.0000.000
139A282TRP00.0170.00071.3400.0000.0000.0000.0000.0000.000
140A283LYS10.8700.93171.0850.0030.0030.0000.0000.0000.000
141A284PHE00.0120.01373.7920.0000.0000.0000.0000.0000.000
142A285GLH00.007-0.02476.6150.0000.0000.0000.0000.0000.000
143A286ASP-1-0.839-0.87779.201-0.002-0.0020.0000.0000.0000.000
144A287LYS10.9340.97178.4570.0010.0010.0000.0000.0000.000
145A288ASP-1-0.830-0.91676.897-0.002-0.0020.0000.0000.0000.000
146A289ARG10.8440.92977.6290.0020.0020.0000.0000.0000.000
147A290PHE0-0.012-0.02173.7250.0000.0000.0000.0000.0000.000
148A291ALA00.0520.01674.0000.0000.0000.0000.0000.0000.000
149A292ARG10.8430.92368.9070.0050.0050.0000.0000.0000.000
150A293LYS10.9771.00264.2860.0120.0120.0000.0000.0000.000
151A294ARG10.8380.87664.6890.0090.0090.0000.0000.0000.000
152A295VAL0-0.039-0.04861.0080.0000.0000.0000.0000.0000.000
153A296LYS10.9190.96960.4560.0140.0140.0000.0000.0000.000
154A297GLY00.0980.09358.6260.0000.0000.0000.0000.0000.000
155A298ARG10.9550.96958.2060.0230.0230.0000.0000.0000.000
156A299ALA00.005-0.01160.6990.0000.0000.0000.0000.0000.000
157A300PHE0-0.0150.00263.9660.0000.0000.0000.0000.0000.000
158A301SER00.0140.00366.0010.0000.0000.0000.0000.0000.000
159A302TYR0-0.011-0.01769.0010.0000.0000.0000.0000.0000.000
160A303GLU-1-0.803-0.86469.280-0.008-0.0080.0000.0000.0000.000
161A304PHE00.020-0.01073.2040.0000.0000.0000.0000.0000.000
162A305ASN0-0.050-0.02676.4560.0000.0000.0000.0000.0000.000
163A306ARG10.9050.94478.6920.0030.0030.0000.0000.0000.000
164A307LEU00.0430.01078.9220.0000.0000.0000.0000.0000.000
165A308SER00.0530.03683.4040.0000.0000.0000.0000.0000.000
166A309LYS10.9020.96085.5380.0060.0060.0000.0000.0000.000
167A310GLU-1-0.915-0.95086.931-0.005-0.0050.0000.0000.0000.000
168A311LEU00.021-0.00781.8020.0000.0000.0000.0000.0000.000
169A312GLN0-0.069-0.05082.0370.0000.0000.0000.0000.0000.000
170A313GLU-1-0.768-0.86782.887-0.008-0.0080.0000.0000.0000.000
171A314GLU-1-0.848-0.91182.892-0.008-0.0080.0000.0000.0000.000
172A315LEU0-0.0280.00077.695-0.001-0.0010.0000.0000.0000.000
173A316ASP-1-0.841-0.92880.514-0.008-0.0080.0000.0000.0000.000
174A317ARG10.8380.90181.5330.0070.0070.0000.0000.0000.000
175A318MET00.005-0.01180.158-0.001-0.0010.0000.0000.0000.000
176A319ILE0-0.057-0.01975.197-0.001-0.0010.0000.0000.0000.000
177A320GLY0-0.010-0.01477.691-0.001-0.0010.0000.0000.0000.000
178A321HIS0-0.042-0.01880.184-0.001-0.0010.0000.0000.0000.000
179A322ILE00.004-0.01274.050-0.001-0.0010.0000.0000.0000.000
180A323LEU0-0.0060.00373.840-0.001-0.0010.0000.0000.0000.000
181A324ARG10.9531.00076.1310.0100.0100.0000.0000.0000.000
182A325LYS10.9280.96975.7370.0130.0130.0000.0000.0000.000
183A326SER0-0.090-0.05773.6600.0000.0000.0000.0000.0000.000
184A327LEU0-0.028-0.01073.728-0.001-0.0010.0000.0000.0000.000
185A328ASP-1-0.840-0.91176.994-0.013-0.0130.0000.0000.0000.000
186A329LYS10.9540.99378.5250.0160.0160.0000.0000.0000.000
187A330LYS10.9180.95480.5010.0140.0140.0000.0000.0000.000
188A331PRO0-0.068-0.04982.6270.0000.0000.0000.0000.0000.000
189A332LYS11.0441.02985.3330.0150.0150.0000.0000.0000.000