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: K97G3

Calculation Name: 3NB6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NB6

Chain ID: A

ChEMBL ID:

UniProt ID: O66874

Base Structure: X-ray

Registration Date: 2023-06-21

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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2062844.30257
FMO2-HF: Nuclear repulsion 1990591.855896
FMO2-HF: Total energy -72252.446674
FMO2-MP2: Total energy -72468.916191


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:61:GLN)


Summations of interaction energy for fragment #1(A:61: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.
-31.185-23.12811.01-6.653-12.4120.007
Interaction energy analysis for fragmet #1(A:61:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.007 / q_NPA : -0.010
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].
3A63ARG10.9290.9642.266-17.833-14.6404.711-3.457-4.4460.029
4A64PHE00.0700.0395.3870.1950.346-0.001-0.007-0.1420.000
5A65TYR0-0.049-0.0467.718-0.993-0.9930.0000.0000.0000.000
6A66VAL0-0.046-0.01910.2630.4060.4060.0000.0000.0000.000
7A67SER0-0.012-0.02213.285-0.175-0.1750.0000.0000.0000.000
8A68ILE00.016-0.01915.6990.0500.0500.0000.0000.0000.000
9A69ASP-1-0.872-0.90917.183-0.636-0.6360.0000.0000.0000.000
10A70LYS10.9070.96517.0730.6820.6820.0000.0000.0000.000
11A71ILE0-0.037-0.01413.741-0.043-0.0430.0000.0000.0000.000
12A72PRO00.0370.02117.8720.0440.0440.0000.0000.0000.000
13A73GLU-1-0.878-0.94820.257-0.461-0.4610.0000.0000.0000.000
14A74HIS00.0450.02222.233-0.027-0.0270.0000.0000.0000.000
15A75VAL00.0090.00515.856-0.007-0.0070.0000.0000.0000.000
16A76ILE0-0.010-0.00917.735-0.044-0.0440.0000.0000.0000.000
17A77ASN00.0320.00418.781-0.019-0.0190.0000.0000.0000.000
18A78ALA00.0560.03519.4600.0370.0370.0000.0000.0000.000
19A79PHE0-0.019-0.00912.1350.0010.0010.0000.0000.0000.000
20A80VAL0-0.031-0.00617.4840.0350.0350.0000.0000.0000.000
21A81ALA00.0180.00819.8610.0430.0430.0000.0000.0000.000
22A82THR0-0.082-0.04718.6040.0680.0680.0000.0000.0000.000
23A83GLU-1-0.854-0.93115.475-0.408-0.4080.0000.0000.0000.000
24A84ASP-1-0.800-0.89818.511-0.431-0.4310.0000.0000.0000.000
25A85ARG10.9170.95520.2260.2280.2280.0000.0000.0000.000
26A86ASN0-0.037-0.02923.3690.0020.0020.0000.0000.0000.000
27A87PHE0-0.028-0.00317.327-0.001-0.0010.0000.0000.0000.000
28A88TRP00.025-0.01320.199-0.027-0.0270.0000.0000.0000.000
29A89HIS00.0240.01923.4810.0090.0090.0000.0000.0000.000
30A90HIS0-0.074-0.02219.5120.0510.0510.0000.0000.0000.000
31A91PHE00.0350.01223.829-0.018-0.0180.0000.0000.0000.000
32A92GLY00.0450.02019.5450.0040.0040.0000.0000.0000.000
33A93ILE0-0.054-0.02419.521-0.007-0.0070.0000.0000.0000.000
34A94ASP-1-0.712-0.85622.220-0.244-0.2440.0000.0000.0000.000
35A95PRO00.008-0.00824.5780.0130.0130.0000.0000.0000.000
36A96VAL00.0340.02927.5700.0180.0180.0000.0000.0000.000
37A97ALA00.0160.01523.8610.0120.0120.0000.0000.0000.000
38A98ILE0-0.012-0.00323.6580.0140.0140.0000.0000.0000.000
39A99VAL00.0220.01026.3170.0170.0170.0000.0000.0000.000
40A100ARG10.9420.96228.0760.1560.1560.0000.0000.0000.000
41A101ALA0-0.004-0.00925.3010.0060.0060.0000.0000.0000.000
42A102ALA0-0.0020.00127.3410.0140.0140.0000.0000.0000.000
43A103ILE0-0.025-0.03330.3290.0090.0090.0000.0000.0000.000
44A104VAL0-0.015-0.00729.6070.0050.0050.0000.0000.0000.000
45A105ASN0-0.026-0.00327.9500.0110.0110.0000.0000.0000.000
46A106TYR00.0430.01230.3650.0040.0040.0000.0000.0000.000
47A107ARG10.8870.94833.9690.0820.0820.0000.0000.0000.000
48A108ALA00.0120.01631.116-0.002-0.0020.0000.0000.0000.000
49A109GLY00.0320.02131.9410.0030.0030.0000.0000.0000.000
50A110ARG10.9230.96728.9950.0090.0090.0000.0000.0000.000
51A111ILE0-0.045-0.02924.0890.0070.0070.0000.0000.0000.000
52A112ALA00.0280.01926.411-0.001-0.0010.0000.0000.0000.000
53A113GLN0-0.0170.00324.0060.0010.0010.0000.0000.0000.000
54A114GLY00.0280.00920.1430.0200.0200.0000.0000.0000.000
55A115GLY0-0.026-0.01220.6150.0090.0090.0000.0000.0000.000
56A116SER0-0.078-0.03116.9870.0230.0230.0000.0000.0000.000
57A117THR00.0150.00317.794-0.052-0.0520.0000.0000.0000.000
58A118ILE00.008-0.00113.523-0.024-0.0240.0000.0000.0000.000
59A119THR0-0.038-0.03513.273-0.137-0.1370.0000.0000.0000.000
60A120GLN00.0430.01713.931-0.022-0.0220.0000.0000.0000.000
61A121GLN0-0.074-0.03511.5100.0000.0000.0000.0000.0000.000
62A122LEU00.0250.0128.262-0.094-0.0940.0000.0000.0000.000
63A123ALA00.0140.0049.2900.0050.0050.0000.0000.0000.000
64A124LYS10.8310.9229.9290.5560.5560.0000.0000.0000.000
65A125ASN0-0.042-0.0305.2591.0381.0380.0000.0000.0000.000
66A126LEU0-0.0030.0126.1380.0470.0470.0000.0000.0000.000
67A127PHE0-0.072-0.0278.5970.1070.1070.0000.0000.0000.000
68A128LEU00.0340.0207.7990.3630.3630.0000.0000.0000.000
69A129THR00.006-0.0068.7570.3960.3960.0000.0000.0000.000
70A130ARG10.9910.9929.040-1.356-1.3560.0000.0000.0000.000
71A131GLU-1-0.794-0.86411.0790.3830.3830.0000.0000.0000.000
72A132ARG10.8100.83714.407-0.211-0.2110.0000.0000.0000.000
73A133THR00.0770.04016.948-0.057-0.0570.0000.0000.0000.000
74A134LEU00.0340.01619.960-0.016-0.0160.0000.0000.0000.000
75A135GLU-1-0.805-0.90820.7900.1260.1260.0000.0000.0000.000
76A136ARG10.7530.88712.643-0.478-0.4780.0000.0000.0000.000
77A137LYS10.9340.96817.451-0.119-0.1190.0000.0000.0000.000
78A138ILE00.0210.02218.873-0.045-0.0450.0000.0000.0000.000
79A139LYS10.9060.94217.706-0.175-0.1750.0000.0000.0000.000
80A140GLU-1-0.784-0.86713.7690.0050.0050.0000.0000.0000.000
81A141ALA00.0190.00816.212-0.074-0.0740.0000.0000.0000.000
82A142LEU0-0.010-0.00619.273-0.032-0.0320.0000.0000.0000.000
83A143LEU0-0.0060.00712.895-0.023-0.0230.0000.0000.0000.000
84A144ALA00.0230.00016.225-0.061-0.0610.0000.0000.0000.000
85A145ILE00.0090.00117.120-0.028-0.0280.0000.0000.0000.000
86A146LYS10.8660.93419.0720.3040.3040.0000.0000.0000.000
87A147ILE0-0.0020.00413.405-0.010-0.0100.0000.0000.0000.000
88A148GLU-1-0.707-0.84417.680-0.518-0.5180.0000.0000.0000.000
89A149ARG10.8740.95720.2780.2380.2380.0000.0000.0000.000
90A150THR0-0.057-0.03319.0900.0510.0510.0000.0000.0000.000
91A151PHE0-0.019-0.00916.044-0.028-0.0280.0000.0000.0000.000
92A152ASP-1-0.754-0.86819.469-0.590-0.5900.0000.0000.0000.000
93A153LYS10.8160.90218.6870.3720.3720.0000.0000.0000.000
94A154LYS10.9890.98218.0790.4750.4750.0000.0000.0000.000
95A155LYS10.8730.92115.0360.8530.8530.0000.0000.0000.000
96A156ILE0-0.008-0.00114.277-0.203-0.2030.0000.0000.0000.000
97A157MET0-0.0130.00513.165-0.228-0.2280.0000.0000.0000.000
98A158GLU-1-0.761-0.84312.659-1.337-1.3370.0000.0000.0000.000
99A159LEU00.0180.01510.152-0.364-0.3640.0000.0000.0000.000
100A160TYR0-0.031-0.0208.546-0.777-0.7770.0000.0000.0000.000
101A161LEU00.0520.0078.505-0.527-0.5270.0000.0000.0000.000
102A162ASN0-0.046-0.0227.882-0.078-0.0780.0000.0000.0000.000
103A163GLN0-0.035-0.0123.739-1.639-1.4990.000-0.024-0.1160.000
104A164ILE0-0.044-0.0053.901-1.793-1.5400.000-0.080-0.1730.000
105A165TYR0-0.0120.0015.074-0.006-0.0060.0000.0000.0000.000
106A166LEU0-0.011-0.0126.5830.5520.5520.0000.0000.0000.000
107A167GLY00.0420.0208.6490.2620.2620.0000.0000.0000.000
108A168SER00.0060.0029.393-0.157-0.1570.0000.0000.0000.000
109A169GLY00.0170.0206.3600.1310.1310.0000.0000.0000.000
110A170ALA0-0.0070.0045.012-0.547-0.420-0.001-0.005-0.1210.000
111A171TYR0-0.046-0.0432.635-8.148-3.9596.302-3.071-7.420-0.022
112A172GLY00.0410.0334.881-0.121-0.117-0.001-0.0090.0060.000
113A173VAL00.001-0.0277.6370.5220.5220.0000.0000.0000.000
114A174GLU-1-0.770-0.86510.097-0.581-0.5810.0000.0000.0000.000
115A175ALA00.0120.0046.4940.3150.3150.0000.0000.0000.000
116A176ALA0-0.004-0.0088.4370.3310.3310.0000.0000.0000.000
117A177ALA00.0150.01110.6970.2050.2050.0000.0000.0000.000
118A178GLN0-0.046-0.02411.0360.2730.2730.0000.0000.0000.000
119A179VAL0-0.066-0.0388.9370.1240.1240.0000.0000.0000.000
120A180TYR0-0.067-0.05311.9530.0680.0680.0000.0000.0000.000
121A181PHE0-0.001-0.00515.1880.0380.0380.0000.0000.0000.000
122A182GLY0-0.0020.02115.9540.0380.0380.0000.0000.0000.000
123A183LYS10.7750.88016.2400.3740.3740.0000.0000.0000.000
124A184HIS10.8550.88714.5760.3460.3460.0000.0000.0000.000
125A185VAL00.006-0.02714.1920.0360.0360.0000.0000.0000.000
126A186TRP0-0.032-0.02715.323-0.002-0.0020.0000.0000.0000.000
127A187GLU-1-0.816-0.87019.032-0.326-0.3260.0000.0000.0000.000
128A188LEU0-0.062-0.01316.1780.0260.0260.0000.0000.0000.000
129A189SER0-0.002-0.02620.685-0.002-0.0020.0000.0000.0000.000
130A190LEU00.013-0.00322.494-0.045-0.0450.0000.0000.0000.000
131A191ASP-1-0.769-0.87523.506-0.318-0.3180.0000.0000.0000.000
132A192GLU-1-0.778-0.85519.552-0.381-0.3810.0000.0000.0000.000
133A193ALA0-0.004-0.00418.750-0.070-0.0700.0000.0000.0000.000
134A194ALA00.017-0.00318.746-0.064-0.0640.0000.0000.0000.000
135A195LEU0-0.025-0.00917.9890.0020.0020.0000.0000.0000.000
136A196LEU0-0.014-0.01113.628-0.047-0.0470.0000.0000.0000.000
137A197ALA00.0090.00314.884-0.084-0.0840.0000.0000.0000.000
138A198ALA00.0020.01016.8050.0350.0350.0000.0000.0000.000
139A199LEU0-0.0130.01613.2280.0740.0740.0000.0000.0000.000
140A200PRO00.0210.00211.6360.0880.0880.0000.0000.0000.000
141A201LYS10.9100.96612.3990.2840.2840.0000.0000.0000.000
142A202ALA0-0.055-0.04114.6890.1080.1080.0000.0000.0000.000
143A203PRO00.0450.03910.6850.0680.0680.0000.0000.0000.000
144A204ALA00.0260.01213.6680.0080.0080.0000.0000.0000.000
145A205LYS10.8890.95115.3010.0920.0920.0000.0000.0000.000
146A206TYR00.0320.00217.2680.0320.0320.0000.0000.0000.000
147A207ASN00.0550.03613.766-0.088-0.0880.0000.0000.0000.000
148A208PRO00.0620.01616.1370.0570.0570.0000.0000.0000.000
149A209PHE0-0.002-0.00413.7130.0240.0240.0000.0000.0000.000
150A210TYR0-0.010-0.00614.6530.0120.0120.0000.0000.0000.000
151A211HIS0-0.064-0.01619.1260.0430.0430.0000.0000.0000.000
152A212PRO00.0710.03421.720-0.028-0.0280.0000.0000.0000.000
153A213GLU-1-0.784-0.87823.053-0.092-0.0920.0000.0000.0000.000
154A214ARG10.7900.86921.9800.0480.0480.0000.0000.0000.000
155A215ALA0-0.0170.00320.106-0.022-0.0220.0000.0000.0000.000
156A216LEU00.0380.02921.446-0.032-0.0320.0000.0000.0000.000
157A217GLN0-0.013-0.00124.649-0.011-0.0110.0000.0000.0000.000
158A218ARG10.7530.85417.1650.3860.3860.0000.0000.0000.000
159A219ARG10.8410.91522.1070.2300.2300.0000.0000.0000.000
160A220ASN00.0620.02223.101-0.027-0.0270.0000.0000.0000.000
161A221LEU0-0.027-0.00524.4750.0060.0060.0000.0000.0000.000
162A222VAL0-0.014-0.00820.2850.0030.0030.0000.0000.0000.000
163A223LEU00.0340.01523.632-0.008-0.0080.0000.0000.0000.000
164A224LYS10.8890.93226.4030.1820.1820.0000.0000.0000.000
165A225ARG10.6610.79624.3130.2940.2940.0000.0000.0000.000
166A226MET0-0.018-0.00323.542-0.008-0.0080.0000.0000.0000.000
167A227LEU00.0060.01626.4570.0050.0050.0000.0000.0000.000
168A228GLU-1-0.869-0.90829.111-0.193-0.1930.0000.0000.0000.000
169A229GLU-1-0.841-0.90125.623-0.265-0.2650.0000.0000.0000.000
170A230GLY00.0140.01828.903-0.006-0.0060.0000.0000.0000.000
171A231TYR0-0.042-0.02824.674-0.012-0.0120.0000.0000.0000.000
172A232ILE0-0.041-0.01427.501-0.013-0.0130.0000.0000.0000.000
173A233THR0-0.007-0.02830.3110.0060.0060.0000.0000.0000.000
174A234PRO00.0310.00033.231-0.007-0.0070.0000.0000.0000.000
175A235GLU-1-0.795-0.87935.155-0.174-0.1740.0000.0000.0000.000
176A236GLN00.0100.00730.813-0.009-0.0090.0000.0000.0000.000
177A237TYR0-0.023-0.00829.947-0.016-0.0160.0000.0000.0000.000
178A238GLU-1-0.884-0.95531.367-0.152-0.1520.0000.0000.0000.000
179A239GLU-1-0.816-0.88131.076-0.184-0.1840.0000.0000.0000.000
180A240ALA0-0.022-0.01027.425-0.004-0.0040.0000.0000.0000.000
181A241VAL0-0.038-0.02728.402-0.005-0.0050.0000.0000.0000.000
182A242ASN0-0.025-0.01029.7780.0150.0150.0000.0000.0000.000
183A243LYS10.7230.87727.2990.1930.1930.0000.0000.0000.000