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: XYQ82

Calculation Name: 2NR7-A-Xray13

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2NR7

Chain ID: A

ChEMBL ID:

UniProt ID: Q7MXB3

Base Structure: X-ray

Registration Date: 2018-03-01

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water No
Procedure Auto-FMO protocol ver. 1.20181228
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 195
LigandCharge
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -2183551.964909
FMO2-HF: Nuclear repulsion 2107518.436893
FMO2-HF: Total energy -76033.528015
FMO2-MP2: Total energy -76261.64832


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:-2:ACE)


Summations of interaction energy for fragment #1(A:-2:ACE)
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.
-0.990.352-0.01-0.642-0.691-0.001
Interaction energy analysis for fragmet #1(A:-2:ACE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.017 / q_NPA : -0.021
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].
3A0ALA0-0.033-0.0063.7250.4381.780-0.010-0.642-0.691-0.001
4A1MET00.0020.0285.771-0.079-0.0790.0000.0000.0000.000
5A2ALA0-0.0190.0029.1060.1600.1600.0000.0000.0000.000
6A3ASN00.013-0.01011.867-0.026-0.0260.0000.0000.0000.000
7A4VAL00.0650.02714.5280.0300.0300.0000.0000.0000.000
8A5LYS10.9140.94417.8310.0690.0690.0000.0000.0000.000
9A6LEU0-0.0040.00013.9550.0150.0150.0000.0000.0000.000
10A7LEU00.0150.02718.0790.0090.0090.0000.0000.0000.000
11A8LEU0-0.006-0.00820.2360.0050.0050.0000.0000.0000.000
12A9PRO00.0410.01721.6470.0010.0010.0000.0000.0000.000
13A10TYR0-0.007-0.01623.1410.0000.0000.0000.0000.0000.000
14A11ILE0-0.008-0.00524.3270.0000.0000.0000.0000.0000.000
15A12LEU00.0230.00826.7450.0010.0010.0000.0000.0000.000
16A13LYS10.9290.97927.647-0.014-0.0140.0000.0000.0000.000
17A14TRP0-0.083-0.05127.5410.0020.0020.0000.0000.0000.000
18A15GLU-1-0.744-0.86930.366-0.027-0.0270.0000.0000.0000.000
19A16GLY00.0010.00232.5620.0000.0000.0000.0000.0000.000
20A17GLY0-0.027-0.01933.5980.0010.0010.0000.0000.0000.000
21A18PHE0-0.017-0.01534.2700.0010.0010.0000.0000.0000.000
22A19VAL0-0.019-0.00632.9050.0010.0010.0000.0000.0000.000
23A20HIS00.0360.01632.393-0.002-0.0020.0000.0000.0000.000
24A21ASP-1-0.876-0.92035.0000.0210.0210.0000.0000.0000.000
25A22PRO00.002-0.01734.9140.0000.0000.0000.0000.0000.000
26A23ALA00.032-0.00836.010-0.002-0.0020.0000.0000.0000.000
27A24ASP-1-0.968-0.97637.9500.0270.0270.0000.0000.0000.000
28A25ALA0-0.0010.01140.103-0.001-0.0010.0000.0000.0000.000
29A26GLY0-0.035-0.02241.562-0.002-0.0020.0000.0000.0000.000
30A27GLY0-0.064-0.02338.334-0.002-0.0020.0000.0000.0000.000
31A28ALA00.0050.02038.824-0.002-0.0020.0000.0000.0000.000
32A29THR0-0.005-0.00337.0420.0010.0010.0000.0000.0000.000
33A30ASN0-0.031-0.01338.250-0.003-0.0030.0000.0000.0000.000
34A31LYS10.8910.95438.0820.0050.0050.0000.0000.0000.000
35A32GLY00.0140.00538.1270.0010.0010.0000.0000.0000.000
36A33VAL0-0.048-0.03035.728-0.002-0.0020.0000.0000.0000.000
37A34THR0-0.001-0.00235.4360.0000.0000.0000.0000.0000.000
38A35ILE0-0.114-0.04032.6850.0000.0000.0000.0000.0000.000
39A36ALA00.0510.03432.813-0.002-0.0020.0000.0000.0000.000
40A37THR0-0.075-0.06330.651-0.001-0.0010.0000.0000.0000.000
41A38TRP00.0160.01630.9980.0000.0000.0000.0000.0000.000
42A39LYS10.9090.92832.5010.0490.0490.0000.0000.0000.000
43A40ARG10.8550.93534.2830.0270.0270.0000.0000.0000.000
44A41VAL0-0.042-0.01132.6380.0030.0030.0000.0000.0000.000
45A42GLY0-0.008-0.00633.904-0.003-0.0030.0000.0000.0000.000
46A43TYR0-0.096-0.05131.368-0.003-0.0030.0000.0000.0000.000
47A44ASP-1-0.885-0.92833.882-0.054-0.0540.0000.0000.0000.000
48A45LYS10.9990.97033.6430.0390.0390.0000.0000.0000.000
49A46ASP-1-0.895-0.93534.872-0.069-0.0690.0000.0000.0000.000
50A47GLY00.004-0.01232.388-0.004-0.0040.0000.0000.0000.000
51A48ASP-1-0.867-0.90530.985-0.064-0.0640.0000.0000.0000.000
52A49GLY0-0.004-0.00631.712-0.002-0.0020.0000.0000.0000.000
53A50ASP-1-0.977-0.97733.354-0.050-0.0500.0000.0000.0000.000
54A51ILE0-0.0270.00731.0590.0030.0030.0000.0000.0000.000
55A52ASP-1-0.911-0.97334.433-0.034-0.0340.0000.0000.0000.000
56A53VAL0-0.064-0.02934.9130.0000.0000.0000.0000.0000.000
57A54GLU-1-0.913-0.94237.686-0.020-0.0200.0000.0000.0000.000
58A55ASP-1-0.810-0.92138.680-0.016-0.0160.0000.0000.0000.000
59A56LEU0-0.012-0.00531.9350.0010.0010.0000.0000.0000.000
60A57LYS10.7790.88134.7520.0160.0160.0000.0000.0000.000
61A58LEU0-0.0230.00036.5150.0020.0020.0000.0000.0000.000
62A59LEU0-0.0240.00733.525-0.001-0.0010.0000.0000.0000.000
63A60THR00.0450.02032.4030.0010.0010.0000.0000.0000.000
64A61ASP-1-0.830-0.93027.812-0.011-0.0110.0000.0000.0000.000
65A62ASP-1-0.929-0.96927.104-0.027-0.0270.0000.0000.0000.000
66A63ASP-1-0.894-0.94328.255-0.041-0.0410.0000.0000.0000.000
67A64VAL0-0.0060.00228.016-0.006-0.0060.0000.0000.0000.000
68A65LEU0-0.008-0.01321.952-0.008-0.0080.0000.0000.0000.000
69A66ASN0-0.033-0.03725.287-0.016-0.0160.0000.0000.0000.000
70A67ARG10.8820.93826.8070.0360.0360.0000.0000.0000.000
71A68VAL00.0150.02428.724-0.001-0.0010.0000.0000.0000.000
72A69LEU00.004-0.00422.987-0.007-0.0070.0000.0000.0000.000
73A70LYS10.7690.85119.0530.1560.1560.0000.0000.0000.000
74A71PRO00.0080.02823.499-0.012-0.0120.0000.0000.0000.000
75A72PHE00.001-0.00425.738-0.006-0.0060.0000.0000.0000.000
76A73TYR0-0.056-0.02525.1120.0020.0020.0000.0000.0000.000
77A74TRP0-0.015-0.03615.1380.0110.0110.0000.0000.0000.000
78A75ASP-1-0.793-0.90120.362-0.178-0.1780.0000.0000.0000.000
79A76ARG10.8850.97021.7350.0790.0790.0000.0000.0000.000
80A77TRP0-0.028-0.03119.295-0.008-0.0080.0000.0000.0000.000
81A78LYS10.8600.91418.3920.1650.1650.0000.0000.0000.000
82A79ALA00.0670.02716.191-0.043-0.0430.0000.0000.0000.000
83A80ASP-1-0.822-0.87814.398-0.241-0.2410.0000.0000.0000.000
84A81LEU0-0.039-0.02812.599-0.058-0.0580.0000.0000.0000.000
85A82ILE0-0.057-0.00812.180-0.064-0.0640.0000.0000.0000.000
86A83GLU-1-0.869-0.9546.917-1.522-1.5220.0000.0000.0000.000
87A84SER0-0.0040.0218.1150.1020.1020.0000.0000.0000.000
88A85GLN00.0520.00110.4360.0010.0010.0000.0000.0000.000
89A86LYS10.8860.93712.600-0.041-0.0410.0000.0000.0000.000
90A87VAL00.0260.01213.9550.0060.0060.0000.0000.0000.000
91A88ALA00.0350.01714.5800.0070.0070.0000.0000.0000.000
92A89ASN00.0280.00916.271-0.001-0.0010.0000.0000.0000.000
93A90ILE0-0.0150.00118.5480.0060.0060.0000.0000.0000.000
94A91LEU00.0330.01517.8690.0080.0080.0000.0000.0000.000
95A92VAL00.0010.00719.5380.0070.0070.0000.0000.0000.000
96A93ASP-1-0.778-0.88422.021-0.032-0.0320.0000.0000.0000.000
97A94TRP0-0.0070.00224.0100.0050.0050.0000.0000.0000.000
98A95VAL0-0.014-0.00124.7020.0050.0050.0000.0000.0000.000
99A96TRP0-0.043-0.01726.2910.0030.0030.0000.0000.0000.000
100A97GLY00.0440.01728.0780.0050.0050.0000.0000.0000.000
101A98SER0-0.038-0.05729.7030.0040.0040.0000.0000.0000.000
102A99GLY00.0170.02130.1070.0000.0000.0000.0000.0000.000
103A100LYS10.9230.96029.0510.0660.0660.0000.0000.0000.000
104A101TYR00.000-0.00329.462-0.005-0.0050.0000.0000.0000.000
105A102GLY00.0080.00626.644-0.001-0.0010.0000.0000.0000.000
106A103ILE0-0.0080.00024.600-0.009-0.0090.0000.0000.0000.000
107A104VAL00.002-0.00825.800-0.005-0.0050.0000.0000.0000.000
108A105ILE0-0.033-0.00527.4610.0000.0000.0000.0000.0000.000
109A106PRO00.0350.01022.3670.0000.0000.0000.0000.0000.000
110A107GLN00.0110.00623.6150.0030.0030.0000.0000.0000.000
111A108ARG10.9610.99325.0720.0610.0610.0000.0000.0000.000
112A109ILE0-0.077-0.04122.3890.0020.0020.0000.0000.0000.000
113A110LEU0-0.009-0.00118.9890.0000.0000.0000.0000.0000.000
114A111GLY0-0.0060.02322.575-0.007-0.0070.0000.0000.0000.000
115A112VAL0-0.089-0.04422.457-0.005-0.0050.0000.0000.0000.000
116A113GLN0-0.027-0.02725.6460.0110.0110.0000.0000.0000.000
117A114ALA00.0070.00427.682-0.006-0.0060.0000.0000.0000.000
118A115ASP-1-0.854-0.93828.147-0.110-0.1100.0000.0000.0000.000
119A116GLY0-0.040-0.02928.4610.0040.0040.0000.0000.0000.000
120A117ILE0-0.034-0.00726.287-0.002-0.0020.0000.0000.0000.000
121A118VAL00.0420.03120.371-0.006-0.0060.0000.0000.0000.000
122A119GLY00.0240.01522.659-0.009-0.0090.0000.0000.0000.000
123A120ASN00.035-0.00118.490-0.039-0.0390.0000.0000.0000.000
124A121LYS10.9680.98319.1940.1450.1450.0000.0000.0000.000
125A122THR00.0590.03420.2460.0010.0010.0000.0000.0000.000
126A123LEU00.0410.01515.8640.0030.0030.0000.0000.0000.000
127A124GLN0-0.048-0.01715.493-0.026-0.0260.0000.0000.0000.000
128A125ALA0-0.0010.00315.636-0.018-0.0180.0000.0000.0000.000
129A126VAL0-0.032-0.02514.2620.0120.0120.0000.0000.0000.000
130A127ASN00.016-0.01411.0390.0360.0360.0000.0000.0000.000
131A128SER0-0.051-0.00911.596-0.034-0.0340.0000.0000.0000.000
132A129ALA0-0.039-0.00313.9660.0310.0310.0000.0000.0000.000
133A130ASP-1-0.769-0.88313.018-0.057-0.0570.0000.0000.0000.000
134A131PRO0-0.025-0.0269.9330.0090.0090.0000.0000.0000.000
135A132ASP-1-0.841-0.90713.1530.0770.0770.0000.0000.0000.000
136A133GLU-1-0.932-0.96315.580-0.045-0.0450.0000.0000.0000.000
137A134LEU0-0.004-0.00215.8210.0000.0000.0000.0000.0000.000
138A135PHE0-0.041-0.03416.5720.0040.0040.0000.0000.0000.000
139A136GLU-1-0.811-0.90818.3980.0110.0110.0000.0000.0000.000
140A137SER00.0090.02021.0670.0010.0010.0000.0000.0000.000
141A138ILE0-0.054-0.03519.0400.0000.0000.0000.0000.0000.000
142A139PHE00.000-0.01722.5400.0050.0050.0000.0000.0000.000
143A140ASP-1-0.929-0.95624.273-0.018-0.0180.0000.0000.0000.000
144A141ALA00.0240.00826.2210.0010.0010.0000.0000.0000.000
145A142ARG10.7840.89124.0860.0500.0500.0000.0000.0000.000
146A143ARG10.9450.97128.0880.0070.0070.0000.0000.0000.000
147A144GLU-1-0.917-0.95530.460-0.034-0.0340.0000.0000.0000.000
148A145PHE0-0.022-0.00730.8620.0010.0010.0000.0000.0000.000
149A146LEU0-0.017-0.01130.5850.0020.0020.0000.0000.0000.000
150A147GLU-1-0.873-0.94733.999-0.010-0.0100.0000.0000.0000.000
151A148ASP-1-0.867-0.91435.710-0.029-0.0290.0000.0000.0000.000
152A149ILE0-0.028-0.02135.2780.0020.0020.0000.0000.0000.000
153A150THR0-0.050-0.03937.8010.0020.0020.0000.0000.0000.000
154A151ALA00.0250.01440.1050.0010.0010.0000.0000.0000.000
155A152ARG10.8920.93239.5930.0310.0310.0000.0000.0000.000
156A153SER0-0.059-0.00642.4670.0010.0010.0000.0000.0000.000
157A154ILE00.008-0.01443.8440.0010.0010.0000.0000.0000.000
158A155LYS10.9140.95845.9030.0200.0200.0000.0000.0000.000
159A156LYS10.9410.97343.3940.0260.0260.0000.0000.0000.000
160A157TYR00.0090.00048.5320.0010.0010.0000.0000.0000.000
161A158GLU-1-0.812-0.92850.309-0.010-0.0100.0000.0000.0000.000
162A159ASP-1-0.845-0.91751.021-0.016-0.0160.0000.0000.0000.000
163A160SER0-0.089-0.03752.8860.0000.0000.0000.0000.0000.000
164A161ILE0-0.070-0.03154.4200.0010.0010.0000.0000.0000.000
165A162GLY00.0120.02256.2630.0010.0010.0000.0000.0000.000
166A163ARG10.7780.85956.3480.0090.0090.0000.0000.0000.000
167A164LYS10.9030.95950.6740.0070.0070.0000.0000.0000.000
168A165ALA00.0080.01351.3570.0000.0000.0000.0000.0000.000
169A166THR0-0.021-0.01452.9240.0010.0010.0000.0000.0000.000
170A167GLU-1-0.895-0.96148.352-0.003-0.0030.0000.0000.0000.000
171A168ARG10.9970.99149.6770.0040.0040.0000.0000.0000.000
172A169GLU-1-0.801-0.87450.992-0.008-0.0080.0000.0000.0000.000
173A170LEU00.0380.01647.071-0.001-0.0010.0000.0000.0000.000
174A171LEU00.0040.01744.817-0.001-0.0010.0000.0000.0000.000
175A172ARG10.8620.92546.8230.0070.0070.0000.0000.0000.000
176A173HIS0-0.0020.00448.642-0.001-0.0010.0000.0000.0000.000
177A174THR0-0.017-0.00345.252-0.001-0.0010.0000.0000.0000.000
178A175ASN00.0520.00539.9130.0010.0010.0000.0000.0000.000
179A176LYS10.9620.99040.6700.0070.0070.0000.0000.0000.000
180A177ARG10.8470.93642.0140.0120.0120.0000.0000.0000.000
181A178PHE00.000-0.00837.9060.0020.0020.0000.0000.0000.000
182A179LEU00.0210.03835.6820.0000.0000.0000.0000.0000.000
183A180ARG10.9810.98735.817-0.002-0.0020.0000.0000.0000.000
184A181GLY00.0020.00535.1370.0020.0020.0000.0000.0000.000
185A182TRP00.0750.01532.7940.0000.0000.0000.0000.0000.000
186A183LEU00.0140.01431.126-0.001-0.0010.0000.0000.0000.000
187A184ASN0-0.020-0.01630.4490.0020.0020.0000.0000.0000.000
188A185ARG10.8270.91027.3530.0280.0280.0000.0000.0000.000
189A186LEU0-0.0040.01625.4560.0010.0010.0000.0000.0000.000
190A187GLU-1-0.885-0.95625.5820.0160.0160.0000.0000.0000.000
191A188ASP-1-0.910-0.96625.3740.0220.0220.0000.0000.0000.000
192A189ILE0-0.0120.00421.1010.0040.0040.0000.0000.0000.000
193A190ARG10.7600.87420.619-0.010-0.0100.0000.0000.0000.000
194A191LYS10.8530.92820.061-0.021-0.0210.0000.0000.0000.000
195A192LEU-1-0.937-0.93417.7160.0760.0760.0000.0000.0000.000