FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 94N82

Calculation Name: 3NWC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NWC

Chain ID: A

ChEMBL ID:

UniProt ID: Q8TZY2

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 OptH
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 182
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1763295.664554
FMO2-HF: Nuclear repulsion 1693859.01761
FMO2-HF: Total energy -69436.646944
FMO2-MP2: Total energy -69641.913761


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:487:MET)


Summations of interaction energy for fragment #1(A:487:MET)
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.
-25.642-16.1428.136-12.891-24.745-0.018
Interaction energy analysis for fragmet #1(A:487:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.006 / 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].
3A489LEU0-0.0130.0023.4320.0001.5080.001-0.611-0.8980.001
4A490GLU-1-0.762-0.8833.458-2.772-2.3680.028-0.192-0.239-0.001
5A491SER0-0.074-0.0525.4540.2180.2180.0000.0000.0000.000
6A492SER00.018-0.0382.2500.370-1.1176.596-2.051-3.0590.002
7A493GLU-1-0.888-0.9312.227-13.282-8.9443.666-2.982-5.022-0.025
8A494ARG10.7730.8663.3552.6832.7530.0340.190-0.2950.000
9A495GLU-1-0.756-0.8574.9610.0310.0310.0000.0000.0000.000
10A496LEU00.0480.0322.914-0.5280.4880.150-0.212-0.9540.000
11A497ILE00.0250.0215.1040.1000.166-0.001-0.002-0.0620.000
12A498ALA0-0.054-0.0288.0440.1520.1520.0000.0000.0000.000
13A499ALA00.000-0.0078.1450.0350.0350.0000.0000.0000.000
14A500GLU-1-0.905-0.9557.7941.2331.2330.0000.0000.0000.000
15A501ALA0-0.010-0.00510.862-0.065-0.0650.0000.0000.0000.000
16A502GLN0-0.075-0.05512.9700.0120.0120.0000.0000.0000.000
17A503ARG10.8200.89812.027-0.956-0.9560.0000.0000.0000.000
18A504GLU-1-0.970-0.96915.2310.2670.2670.0000.0000.0000.000
19A505VAL0-0.091-0.03917.218-0.037-0.0370.0000.0000.0000.000
20A506ARG10.8510.93716.397-0.229-0.2290.0000.0000.0000.000
21A507GLY00.0880.05120.1720.0130.0130.0000.0000.0000.000
22A508ASN0-0.015-0.02221.457-0.038-0.0380.0000.0000.0000.000
23A509ARG11.0011.00221.554-0.205-0.2050.0000.0000.0000.000
24A510ALA0-0.005-0.01324.620-0.004-0.0040.0000.0000.0000.000
25A511ALA0-0.001-0.00224.247-0.010-0.0100.0000.0000.0000.000
26A512GLU-1-0.887-0.94823.8490.3130.3130.0000.0000.0000.000
27A513GLU-1-0.888-0.95727.0150.1410.1410.0000.0000.0000.000
28A514LEU00.0130.01128.914-0.012-0.0120.0000.0000.0000.000
29A515LYS10.9431.01026.688-0.300-0.3000.0000.0000.0000.000
30A516ARG10.9070.94730.880-0.167-0.1670.0000.0000.0000.000
31A517SER0-0.010-0.01933.814-0.013-0.0130.0000.0000.0000.000
32A518GLY0-0.023-0.00735.537-0.010-0.0100.0000.0000.0000.000
33A519ILE0-0.077-0.03634.747-0.006-0.0060.0000.0000.0000.000
34A520GLY00.0120.01334.2880.0110.0110.0000.0000.0000.000
35A521GLY00.0420.00932.889-0.003-0.0030.0000.0000.0000.000
36A522ILE0-0.020-0.01428.1350.0100.0100.0000.0000.0000.000
37A523TYR0-0.055-0.03825.978-0.009-0.0090.0000.0000.0000.000
38A524GLY00.0550.04323.8010.0060.0060.0000.0000.0000.000
39A525THR0-0.030-0.02019.9390.0130.0130.0000.0000.0000.000
40A526LEU0-0.003-0.01317.4850.0140.0140.0000.0000.0000.000
41A527ALA00.0060.00415.3220.0840.0840.0000.0000.0000.000
42A528GLU-1-0.912-0.94415.7490.5160.5160.0000.0000.0000.000
43A529LEU0-0.091-0.04618.344-0.023-0.0230.0000.0000.0000.000
44A530ILE0-0.034-0.00613.183-0.031-0.0310.0000.0000.0000.000
45A531LYS10.9620.99413.184-1.022-1.0220.0000.0000.0000.000
46A532VAL00.0310.0046.854-0.212-0.2120.0000.0000.0000.000
47A533LYS10.8230.91110.297-1.072-1.0720.0000.0000.0000.000
48A534ASP-1-0.866-0.9376.9182.8432.8430.0000.0000.0000.000
49A535GLU-1-0.925-0.9562.6891.2922.0701.368-0.797-1.3490.006
50A536ALA00.0170.0123.0254.5996.2611.738-1.004-2.395-0.011
51A537TYR0-0.020-0.0302.850-3.922-2.6721.476-1.049-1.677-0.015
52A538ALA00.0050.0033.160-3.081-1.8000.761-0.626-1.4150.000
53A539LEU00.0220.0092.415-5.787-8.37610.896-3.400-4.9070.029
54A540ALA00.0160.0093.648-2.487-2.9730.0060.773-0.2930.004
55A541ILE0-0.012-0.0125.511-0.922-0.9220.0000.0000.0000.000
56A542GLU-1-0.802-0.8807.2240.6940.6940.0000.0000.0000.000
57A543VAL0-0.019-0.0097.284-0.595-0.5950.0000.0000.0000.000
58A544ALA0-0.048-0.0229.432-0.319-0.3190.0000.0000.0000.000
59A545LEU0-0.009-0.01011.439-0.248-0.2480.0000.0000.0000.000
60A546GLY00.0710.04412.764-0.193-0.1930.0000.0000.0000.000
61A547ASN00.012-0.02314.4300.0290.0290.0000.0000.0000.000
62A548ARG10.8050.91217.203-0.474-0.4740.0000.0000.0000.000
63A549ALA00.0610.04314.680-0.027-0.0270.0000.0000.0000.000
64A550ASP-1-0.842-0.92616.6990.4870.4870.0000.0000.0000.000
65A551ASN0-0.110-0.05819.949-0.072-0.0720.0000.0000.0000.000
66A552VAL00.0320.01521.9310.0300.0300.0000.0000.0000.000
67A553VAL00.0250.01422.741-0.028-0.0280.0000.0000.0000.000
68A554VAL0-0.053-0.03725.529-0.014-0.0140.0000.0000.0000.000
69A555GLU-1-0.884-0.95329.3110.2650.2650.0000.0000.0000.000
70A556ASP-1-0.824-0.92331.9560.2030.2030.0000.0000.0000.000
71A557GLU-1-0.847-0.96133.6130.1930.1930.0000.0000.0000.000
72A558LEU00.0010.01434.961-0.009-0.0090.0000.0000.0000.000
73A559VAL0-0.029-0.00932.604-0.007-0.0070.0000.0000.0000.000
74A560ALA00.0010.00632.0240.0000.0000.0000.0000.0000.000
75A561GLU-1-0.945-0.97333.3490.1480.1480.0000.0000.0000.000
76A562LYS10.9100.95136.674-0.170-0.1700.0000.0000.0000.000
77A563ALA00.0460.02132.326-0.008-0.0080.0000.0000.0000.000
78A564ILE00.000-0.00432.704-0.007-0.0070.0000.0000.0000.000
79A565LYS10.9090.95034.934-0.137-0.1370.0000.0000.0000.000
80A566TYR0-0.0100.00734.190-0.012-0.0120.0000.0000.0000.000
81A567LEU00.005-0.00630.648-0.008-0.0080.0000.0000.0000.000
82A568LYS10.9030.95434.547-0.142-0.1420.0000.0000.0000.000
83A569GLU-1-0.962-0.97037.4800.0950.0950.0000.0000.0000.000
84A570HIS10.8840.94136.191-0.133-0.1330.0000.0000.0000.000
85A571LYS10.9230.97236.215-0.094-0.0940.0000.0000.0000.000
86A572LEU00.0290.02731.335-0.002-0.0020.0000.0000.0000.000
87A573GLY00.0190.02430.2990.0140.0140.0000.0000.0000.000
88A574ARG10.9170.94128.977-0.173-0.1730.0000.0000.0000.000
89A575LEU00.0720.03625.3600.0090.0090.0000.0000.0000.000
90A576THR0-0.038-0.00924.556-0.022-0.0220.0000.0000.0000.000
91A577PHE00.0180.00425.6390.0220.0220.0000.0000.0000.000
92A578LEU0-0.020-0.01422.193-0.011-0.0110.0000.0000.0000.000
93A579PRO00.0120.01426.8160.0080.0080.0000.0000.0000.000
94A580LEU00.0530.03426.1030.0010.0010.0000.0000.0000.000
95A581ASN00.0100.01029.4560.0110.0110.0000.0000.0000.000
96A582LYS10.8640.93231.402-0.202-0.2020.0000.0000.0000.000
97A583ILE0-0.077-0.02525.199-0.009-0.0090.0000.0000.0000.000
98A584LYS10.9760.97327.354-0.226-0.2260.0000.0000.0000.000
99A585PRO0-0.0060.00423.8050.0180.0180.0000.0000.0000.000
100A586LYS10.8430.94620.397-0.433-0.4330.0000.0000.0000.000
101A587HIS00.020-0.00621.4960.0390.0390.0000.0000.0000.000
102A588VAL00.0140.01717.125-0.023-0.0230.0000.0000.0000.000
103A589ASP-1-0.947-0.97120.3610.2300.2300.0000.0000.0000.000
104A590SER0-0.034-0.02419.677-0.029-0.0290.0000.0000.0000.000
105A591SER00.002-0.00719.4900.0240.0240.0000.0000.0000.000
106A592VAL0-0.024-0.00915.269-0.014-0.0140.0000.0000.0000.000
107A593GLY00.0650.02213.683-0.039-0.0390.0000.0000.0000.000
108A594LEU0-0.0050.0159.715-0.016-0.0160.0000.0000.0000.000
109A595PRO00.0080.00712.1510.0740.0740.0000.0000.0000.000
110A596ALA00.0690.02811.2270.0900.0900.0000.0000.0000.000
111A597VAL0-0.052-0.04212.1550.1370.1370.0000.0000.0000.000
112A598ASP-1-0.886-0.94113.9120.6950.6950.0000.0000.0000.000
113A599VAL0-0.047-0.0218.770-0.006-0.0060.0000.0000.0000.000
114A600ILE0-0.0270.00111.0120.3310.3310.0000.0000.0000.000
115A601GLU-1-0.957-0.98213.3110.7580.7580.0000.0000.0000.000
116A602TYR00.011-0.01116.4700.0120.0120.0000.0000.0000.000
117A603ASP-1-0.856-0.92419.1410.3910.3910.0000.0000.0000.000
118A604GLN00.0640.02822.9050.0350.0350.0000.0000.0000.000
119A605LYS10.9070.96424.865-0.320-0.3200.0000.0000.0000.000
120A606ILE0-0.030-0.02120.633-0.029-0.0290.0000.0000.0000.000
121A607GLU-1-0.865-0.93822.5520.4230.4230.0000.0000.0000.000
122A608ASN0-0.043-0.02522.8790.0290.0290.0000.0000.0000.000
123A609ALA0-0.011-0.01022.920-0.005-0.0050.0000.0000.0000.000
124A610VAL00.0410.02317.4100.0140.0140.0000.0000.0000.000
125A611LYS10.9950.99318.638-0.480-0.4800.0000.0000.0000.000
126A612PHE0-0.038-0.01020.511-0.025-0.0250.0000.0000.0000.000
127A613ALA0-0.059-0.02917.388-0.024-0.0240.0000.0000.0000.000
128A614LEU00.0380.00912.7860.0070.0070.0000.0000.0000.000
129A615GLY0-0.021-0.00215.9320.0170.0170.0000.0000.0000.000
130A616ASP-1-0.917-0.97718.3580.3860.3860.0000.0000.0000.000
131A617THR0-0.0090.00511.949-0.033-0.0330.0000.0000.0000.000
132A618VAL0-0.0370.00113.2100.0630.0630.0000.0000.0000.000
133A619ILE00.0000.0066.933-0.008-0.0080.0000.0000.0000.000
134A620VAL0-0.004-0.0099.386-0.052-0.0520.0000.0000.0000.000
135A621ASN00.0500.0088.0980.0300.0300.0000.0000.0000.000
136A622SER00.0130.0118.370-0.176-0.1760.0000.0000.0000.000
137A623MET00.0550.02610.5790.0920.0920.0000.0000.0000.000
138A624GLU-1-0.940-0.97813.298-0.226-0.2260.0000.0000.0000.000
139A625GLU-1-0.944-0.97513.405-0.062-0.0620.0000.0000.0000.000
140A626ALA00.0380.02113.4900.0500.0500.0000.0000.0000.000
141A627ARG10.8790.93215.5860.1540.1540.0000.0000.0000.000
142A628PRO0-0.019-0.01518.6350.0120.0120.0000.0000.0000.000
143A629HIS00.031-0.00217.6870.0160.0160.0000.0000.0000.000
144A630ILE00.0060.02218.3310.0280.0280.0000.0000.0000.000
145A631GLY00.0090.00920.264-0.014-0.0140.0000.0000.0000.000
146A632LYS10.8690.94521.538-0.130-0.1300.0000.0000.0000.000
147A633VAL0-0.016-0.01216.8430.0090.0090.0000.0000.0000.000
148A634ARG10.8290.92614.286-0.623-0.6230.0000.0000.0000.000
149A635MET0-0.038-0.00312.8070.0210.0210.0000.0000.0000.000
150A636VAL0-0.0060.0057.432-0.008-0.0080.0000.0000.0000.000
151A637THR0-0.034-0.0467.8530.0310.0310.0000.0000.0000.000
152A638ILE00.003-0.0042.3040.0830.4690.776-0.218-0.9450.000
153A639GLU-1-0.803-0.8762.758-5.287-4.0300.642-0.708-1.191-0.008
154A640GLY0-0.0250.0054.7480.2450.293-0.001-0.002-0.0440.000
155A641GLU-1-0.884-0.9196.705-0.257-0.2570.0000.0000.0000.000
156A642LEU0-0.024-0.01810.0480.1110.1110.0000.0000.0000.000
157A643TYR0-0.002-0.00512.523-0.096-0.0960.0000.0000.0000.000
158A644GLU-1-0.913-0.96715.5040.3420.3420.0000.0000.0000.000
159A645ARG10.9170.95217.960-0.298-0.2980.0000.0000.0000.000
160A646SER0-0.039-0.02320.386-0.024-0.0240.0000.0000.0000.000
161A647GLY00.0360.01321.050-0.022-0.0220.0000.0000.0000.000
162A648ALA0-0.068-0.01220.150-0.026-0.0260.0000.0000.0000.000
163A649ILE00.003-0.00216.2010.0270.0270.0000.0000.0000.000
164A650THR0-0.018-0.00313.706-0.021-0.0210.0000.0000.0000.000
165A651GLY00.0480.01012.4600.0160.0160.0000.0000.0000.000
166A652GLY0-0.045-0.01612.1530.0110.0110.0000.0000.0000.000
167A653HIS0-0.042-0.01510.6510.0130.0130.0000.0000.0000.000
168A654PHE00.0300.0088.5170.0920.0920.0000.0000.0000.000
169A655ARG10.8170.9109.1570.8470.8470.0000.0000.0000.000
170A656ALA0-0.012-0.01111.6800.0160.0160.0000.0000.0000.000
171A657ARG10.9180.95515.2220.2230.2230.0000.0000.0000.000
172A658GLY00.0310.02017.767-0.038-0.0380.0000.0000.0000.000
173A659LEU0-0.019-0.02219.1250.0120.0120.0000.0000.0000.000
174A660ALA00.0110.00820.681-0.035-0.0350.0000.0000.0000.000
175A661VAL00.005-0.00519.7390.0200.0200.0000.0000.0000.000
176A662ASP-1-0.936-0.95722.022-0.290-0.2900.0000.0000.0000.000
177A663THR00.001-0.00721.630-0.027-0.0270.0000.0000.0000.000
178A664THR0-0.0020.00023.216-0.015-0.0150.0000.0000.0000.000
179A665LYS10.9880.98422.2830.4390.4390.0000.0000.0000.000
180A666LEU00.0310.01326.9100.0170.0170.0000.0000.0000.000
181A667ARG10.9200.97128.3070.2270.2270.0000.0000.0000.000
182A668LEU00.0020.01327.970-0.006-0.0060.0000.0000.0000.000