Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: QY32Y

Calculation Name: 3NUM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NUM

Chain ID: A

ChEMBL ID:

UniProt ID: Q92743

Base Structure: X-ray

Registration Date: 2023-09-20

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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2040764.662561
FMO2-HF: Nuclear repulsion 1968610.25456
FMO2-HF: Total energy -72154.408
FMO2-MP2: Total energy -72371.619177


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:161:ASP)


Summations of interaction energy for fragment #1(A:161:ASP)
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.
-140.839-137.90421.861-11.448-13.3470.123
Interaction energy analysis for fragmet #1(A:161:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.793 / q_NPA : -0.913
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].
3A163ASN00.0090.0031.851-39.770-38.52012.940-7.364-6.8260.070
4A164SER0-0.026-0.0152.097-28.792-28.5118.773-3.445-5.6080.044
5A165LEU00.0410.0013.466-9.583-8.9360.139-0.338-0.4480.008
6A166ARG10.9290.9766.390-31.648-31.6480.0000.0000.0000.000
7A167HIS0-0.018-0.0233.330-9.472-8.7150.009-0.301-0.4650.001
8A168LYS10.8880.9656.471-45.972-45.9720.0000.0000.0000.000
9A169TYR00.027-0.0048.481-1.455-1.4550.0000.0000.0000.000
10A170ASN0-0.052-0.02910.183-3.394-3.3940.0000.0000.0000.000
11A171PHE00.0620.03712.995-1.133-1.1330.0000.0000.0000.000
12A172ILE00.0060.00615.889-0.953-0.9530.0000.0000.0000.000
13A173ALA0-0.027-0.01414.180-0.936-0.9360.0000.0000.0000.000
14A174ASP-1-0.837-0.92913.89621.16221.1620.0000.0000.0000.000
15A175VAL0-0.033-0.00416.598-0.972-0.9720.0000.0000.0000.000
16A176VAL0-0.013-0.01018.952-0.807-0.8070.0000.0000.0000.000
17A177GLU-1-0.970-0.98715.83116.82116.8210.0000.0000.0000.000
18A178LYS10.8490.91519.630-14.286-14.2860.0000.0000.0000.000
19A179ILE0-0.013-0.00521.646-0.659-0.6590.0000.0000.0000.000
20A180ALA00.0260.00823.263-0.594-0.5940.0000.0000.0000.000
21A181PRO0-0.048-0.03223.534-0.520-0.5200.0000.0000.0000.000
22A182ALA0-0.0180.00026.621-0.408-0.4080.0000.0000.0000.000
23A183VAL0-0.0190.00128.209-0.369-0.3690.0000.0000.0000.000
24A184VAL0-0.059-0.03029.8530.1150.1150.0000.0000.0000.000
25A185HIS00.006-0.00132.6610.0090.0090.0000.0000.0000.000
26A186ILE0-0.039-0.02434.593-0.166-0.1660.0000.0000.0000.000
27A187GLU-1-0.844-0.90038.3187.6327.6320.0000.0000.0000.000
28A188LEU00.0120.02141.245-0.149-0.1490.0000.0000.0000.000
29A189PHE00.039-0.00943.012-0.105-0.1050.0000.0000.0000.000
30A190ARG10.9290.95547.652-6.031-6.0310.0000.0000.0000.000
31A191LYS10.9120.96951.344-5.745-5.7450.0000.0000.0000.000
32A192LEU00.0010.00253.226-0.014-0.0140.0000.0000.0000.000
33A193PRO00.007-0.00756.164-0.046-0.0460.0000.0000.0000.000
34A194PHE00.0670.04759.501-0.053-0.0530.0000.0000.0000.000
35A195SER0-0.057-0.03858.088-0.032-0.0320.0000.0000.0000.000
36A196LYS10.9960.99757.298-5.257-5.2570.0000.0000.0000.000
37A197ARG10.9560.98553.347-5.514-5.5140.0000.0000.0000.000
38A198GLU-1-0.827-0.91950.1555.9965.9960.0000.0000.0000.000
39A199VAL0-0.021-0.00648.3270.0340.0340.0000.0000.0000.000
40A200PRO00.0390.03243.920-0.088-0.0880.0000.0000.0000.000
41A201VAL0-0.073-0.04245.962-0.110-0.1100.0000.0000.0000.000
42A202ALA00.0250.01343.4110.0170.0170.0000.0000.0000.000
43A203SER0-0.025-0.05038.8980.0500.0500.0000.0000.0000.000
44A204GLY00.0300.02436.617-0.019-0.0190.0000.0000.0000.000
45A205SER00.0160.03032.8010.2090.2090.0000.0000.0000.000
46A206GLY00.0560.03234.103-0.273-0.2730.0000.0000.0000.000
47A207PHE00.000-0.00132.1070.3150.3150.0000.0000.0000.000
48A208ILE0-0.0070.00832.218-0.334-0.3340.0000.0000.0000.000
49A209VAL0-0.002-0.01533.6700.2530.2530.0000.0000.0000.000
50A210SER0-0.004-0.03436.257-0.053-0.0530.0000.0000.0000.000
51A211GLU-1-0.797-0.88634.6698.7438.7430.0000.0000.0000.000
52A212ASP-1-0.802-0.87236.4557.6337.6330.0000.0000.0000.000
53A213GLY00.0000.00138.187-0.183-0.1830.0000.0000.0000.000
54A214LEU0-0.006-0.00139.204-0.133-0.1330.0000.0000.0000.000
55A215ILE0-0.010-0.01236.3910.2740.2740.0000.0000.0000.000
56A216VAL00.0080.00837.349-0.272-0.2720.0000.0000.0000.000
57A217THR00.005-0.01537.1420.1900.1900.0000.0000.0000.000
58A218ASN0-0.012-0.01338.901-0.089-0.0890.0000.0000.0000.000
59A219ALA0-0.0040.00441.156-0.061-0.0610.0000.0000.0000.000
60A220HIS0-0.095-0.04642.526-0.249-0.2490.0000.0000.0000.000
61A221VAL0-0.0250.00638.472-0.065-0.0650.0000.0000.0000.000
62A222VAL0-0.026-0.01941.850-0.085-0.0850.0000.0000.0000.000
63A223THR00.015-0.00844.383-0.056-0.0560.0000.0000.0000.000
64A224ASN0-0.029-0.03148.069-0.001-0.0010.0000.0000.0000.000
65A225LYS10.8160.91251.069-6.183-6.1830.0000.0000.0000.000
66A226HIS0-0.060-0.03648.743-0.094-0.0940.0000.0000.0000.000
67A227ARG10.7550.84347.744-6.353-6.3530.0000.0000.0000.000
68A228VAL00.0340.01742.7320.0690.0690.0000.0000.0000.000
69A229LYS10.8430.94641.916-7.011-7.0110.0000.0000.0000.000
70A230VAL00.0380.01636.7310.0720.0720.0000.0000.0000.000
71A231GLU-1-0.802-0.90133.7978.6338.6330.0000.0000.0000.000
72A232LEU00.0110.01332.2190.2040.2040.0000.0000.0000.000
73A233LYS10.9550.98523.368-12.168-12.1680.0000.0000.0000.000
74A234ASN0-0.016-0.03228.7770.1160.1160.0000.0000.0000.000
75A235GLY00.0430.03329.791-0.032-0.0320.0000.0000.0000.000
76A236ALA0-0.068-0.01632.772-0.279-0.2790.0000.0000.0000.000
77A237THR0-0.011-0.01135.588-0.009-0.0090.0000.0000.0000.000
78A238TYR0-0.036-0.04936.279-0.034-0.0340.0000.0000.0000.000
79A239GLU-1-0.789-0.86140.9026.6446.6440.0000.0000.0000.000
80A240ALA0-0.019-0.01342.0830.0750.0750.0000.0000.0000.000
81A241LYS10.7910.87944.126-6.815-6.8150.0000.0000.0000.000
82A242ILE00.0410.01245.9940.1350.1350.0000.0000.0000.000
83A243LYS10.8490.92245.878-6.545-6.5450.0000.0000.0000.000
84A244ASP-1-0.770-0.85846.9556.4106.4100.0000.0000.0000.000
85A245VAL0-0.030-0.02346.5500.1630.1630.0000.0000.0000.000
86A246ASP-1-0.757-0.83947.1096.3806.3800.0000.0000.0000.000
87A247GLU-1-0.780-0.90547.5966.2896.2890.0000.0000.0000.000
88A248LYS10.7940.88749.173-6.355-6.3550.0000.0000.0000.000
89A249ALA0-0.028-0.01645.9060.0040.0040.0000.0000.0000.000
90A250ASP-1-0.782-0.87642.5657.7047.7040.0000.0000.0000.000
91A251ILE0-0.012-0.00341.0120.2410.2410.0000.0000.0000.000
92A252ALA00.0020.00242.277-0.234-0.2340.0000.0000.0000.000
93A253LEU00.0070.00841.7640.2470.2470.0000.0000.0000.000
94A254ILE00.0080.00140.069-0.235-0.2350.0000.0000.0000.000
95A255LYS10.8510.91642.035-7.106-7.1060.0000.0000.0000.000
96A256ILE0-0.0210.00737.225-0.152-0.1520.0000.0000.0000.000
97A257ASP-1-0.806-0.88541.6136.8696.8690.0000.0000.0000.000
98A258HIS10.8670.92835.008-8.559-8.5590.0000.0000.0000.000
99A259GLN00.0660.03938.3560.0670.0670.0000.0000.0000.000
100A260GLY00.0060.01137.3370.2140.2140.0000.0000.0000.000
101A261LYS10.8100.89434.423-8.521-8.5210.0000.0000.0000.000
102A262LEU0-0.0080.00532.8060.0610.0610.0000.0000.0000.000
103A263PRO00.0120.01528.439-0.026-0.0260.0000.0000.0000.000
104A264VAL0-0.016-0.01230.291-0.247-0.2470.0000.0000.0000.000
105A265LEU0-0.0100.01127.6130.3470.3470.0000.0000.0000.000
106A266LEU00.0090.00529.893-0.361-0.3610.0000.0000.0000.000
107A267LEU00.0080.00431.9240.1740.1740.0000.0000.0000.000
108A268GLY00.1330.08032.319-0.189-0.1890.0000.0000.0000.000
109A269ARG10.7680.85933.228-8.818-8.8180.0000.0000.0000.000
110A270SER00.008-0.00335.0970.0930.0930.0000.0000.0000.000
111A271SER0-0.076-0.06336.159-0.054-0.0540.0000.0000.0000.000
112A272GLU-1-0.832-0.87433.2348.9008.9000.0000.0000.0000.000
113A273LEU0-0.062-0.01331.1900.2720.2720.0000.0000.0000.000
114A274ARG10.8460.89926.319-11.949-11.9490.0000.0000.0000.000
115A275PRO0-0.014-0.02030.7360.2910.2910.0000.0000.0000.000
116A276GLY0-0.0120.00128.6140.1100.1100.0000.0000.0000.000
117A277GLU-1-0.819-0.88526.28011.99611.9960.0000.0000.0000.000
118A278PHE0-0.004-0.01021.144-0.197-0.1970.0000.0000.0000.000
119A279VAL00.0020.00724.871-0.063-0.0630.0000.0000.0000.000
120A280VAL0-0.017-0.00222.4730.3460.3460.0000.0000.0000.000
121A281ALA00.0200.02725.741-0.373-0.3730.0000.0000.0000.000
122A282ILE0-0.008-0.00124.6490.1390.1390.0000.0000.0000.000
123A283GLY00.021-0.01227.804-0.415-0.4150.0000.0000.0000.000
124A284SER0-0.013-0.01628.4600.5590.5590.0000.0000.0000.000
125A285PRO00.0000.02829.405-0.332-0.3320.0000.0000.0000.000
126A286PHE00.0150.01130.8650.2440.2440.0000.0000.0000.000
127A287SER0-0.048-0.04230.6920.2200.2200.0000.0000.0000.000
128A288LEU0-0.048-0.01324.1860.2370.2370.0000.0000.0000.000
129A289GLN0-0.065-0.02625.2920.5910.5910.0000.0000.0000.000
130A290ASN0-0.025-0.02425.0460.6030.6030.0000.0000.0000.000
131A291THR0-0.029-0.01225.974-0.049-0.0490.0000.0000.0000.000
132A292VAL00.020-0.00121.840-0.083-0.0830.0000.0000.0000.000
133A293THR0-0.045-0.02725.1450.1600.1600.0000.0000.0000.000
134A294THR0-0.014-0.03121.7690.2590.2590.0000.0000.0000.000
135A295GLY00.0410.01725.153-0.227-0.2270.0000.0000.0000.000
136A296ILE00.0130.01625.8230.4350.4350.0000.0000.0000.000
137A297VAL00.0250.02728.016-0.401-0.4010.0000.0000.0000.000
138A298SER00.028-0.01331.260-0.019-0.0190.0000.0000.0000.000
139A299THR0-0.083-0.04833.341-0.350-0.3500.0000.0000.0000.000
140A300THR00.0390.04135.8470.0270.0270.0000.0000.0000.000
141A315ASP-1-0.841-0.90843.2247.4167.4160.0000.0000.0000.000
142A316TYR0-0.060-0.04840.243-0.057-0.0570.0000.0000.0000.000
143A317ILE00.0160.02933.946-0.017-0.0170.0000.0000.0000.000
144A318GLN0-0.029-0.03236.333-0.261-0.2610.0000.0000.0000.000
145A319THR0-0.012-0.02630.4760.2960.2960.0000.0000.0000.000
146A320ASP-1-0.853-0.90429.01310.43410.4340.0000.0000.0000.000
147A321ALA0-0.0260.01428.4770.1360.1360.0000.0000.0000.000
148A322ILE00.0410.02829.613-0.423-0.4230.0000.0000.0000.000
149A323ILE00.0050.02930.7590.2260.2260.0000.0000.0000.000
150A324ASN0-0.011-0.01231.241-0.305-0.3050.0000.0000.0000.000
151A325TYR00.0440.00433.6550.0260.0260.0000.0000.0000.000
152A326GLY00.0000.01531.663-0.085-0.0850.0000.0000.0000.000
153A327ASN00.004-0.02029.303-0.135-0.1350.0000.0000.0000.000
154A328ALA00.0390.02331.964-0.004-0.0040.0000.0000.0000.000
155A329GLY0-0.007-0.00835.585-0.045-0.0450.0000.0000.0000.000
156A330GLY00.0110.00432.469-0.032-0.0320.0000.0000.0000.000
157A331PRO0-0.033-0.00429.521-0.174-0.1740.0000.0000.0000.000
158A332LEU00.0380.02029.6360.2930.2930.0000.0000.0000.000
159A333VAL0-0.014-0.01925.506-0.230-0.2300.0000.0000.0000.000
160A334ASN00.0460.00427.0120.4480.4480.0000.0000.0000.000
161A335LEU00.016-0.00820.4540.2060.2060.0000.0000.0000.000
162A336ASP-1-0.886-0.92222.18514.02714.0270.0000.0000.0000.000
163A337GLY0-0.045-0.01824.4290.0010.0010.0000.0000.0000.000
164A338GLU-1-0.889-0.92925.34010.35210.3520.0000.0000.0000.000
165A339VAL0-0.028-0.02329.0830.1000.1000.0000.0000.0000.000
166A340ILE0-0.024-0.03030.499-0.268-0.2680.0000.0000.0000.000
167A341GLY00.0360.00033.107-0.293-0.2930.0000.0000.0000.000
168A342ILE0-0.0260.00534.0510.2390.2390.0000.0000.0000.000
169A343ASN0-0.014-0.01330.954-0.071-0.0710.0000.0000.0000.000
170A344THR0-0.017-0.02435.159-0.216-0.2160.0000.0000.0000.000
171A345LEU00.0230.00537.3810.1360.1360.0000.0000.0000.000
172A346LYS10.8280.95139.301-7.586-7.5860.0000.0000.0000.000
173A347VAL00.0620.02637.0690.1970.1970.0000.0000.0000.000
174A348THR0-0.080-0.06239.379-0.338-0.3380.0000.0000.0000.000
175A349ALA0-0.016-0.00539.4190.1470.1470.0000.0000.0000.000
176A350GLY00.0140.01636.3880.1220.1220.0000.0000.0000.000
177A351ILE00.0000.01834.7490.2440.2440.0000.0000.0000.000
178A352SER00.009-0.02133.369-0.434-0.4340.0000.0000.0000.000
179A353PHE00.0410.00436.100-0.025-0.0250.0000.0000.0000.000
180A354ALA00.0350.01735.0310.0680.0680.0000.0000.0000.000
181A355ILE0-0.0160.00237.161-0.086-0.0860.0000.0000.0000.000
182A356PRO00.0330.02037.6290.1950.1950.0000.0000.0000.000
183A357SER00.0470.00735.395-0.278-0.2780.0000.0000.0000.000
184A358ASP-1-0.756-0.86437.5428.4498.4490.0000.0000.0000.000
185A359LYS10.8160.89340.519-7.689-7.6890.0000.0000.0000.000
186A360ILE00.0100.01836.839-0.156-0.1560.0000.0000.0000.000
187A361LYS10.7730.87936.701-8.860-8.8600.0000.0000.0000.000
188A362LYS10.8250.90341.757-6.717-6.7170.0000.0000.0000.000
189A363PHE00.010-0.00142.851-0.126-0.1260.0000.0000.0000.000
190A364LEU00.0180.00439.810-0.112-0.1120.0000.0000.0000.000
191A365THR0-0.049-0.03944.370-0.073-0.0730.0000.0000.0000.000
192A366GLU-1-0.851-0.90546.5626.3986.3980.0000.0000.0000.000
193A367SER0-0.029-0.03746.817-0.108-0.1080.0000.0000.0000.000
194A368HIS0-0.154-0.07045.5380.0690.0690.0000.0000.0000.000
195A369ASP-1-0.970-0.96648.9365.8315.8310.0000.0000.0000.000