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: XRY18

Calculation Name: 2FB6-A-Xray27

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2FB6

Chain ID: A

ChEMBL ID:

UniProt ID: Q8A7V2

Base Structure: X-ray

Registration Date: 2018-07-26

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 Apo structure with with a 3 angstrom solvent shell.
Procedure Auto-FMO protocol ver. 1.20180227
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 210
LigandCharge
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1184606.8029
FMO2-HF: Nuclear repulsion 1130659.117881
FMO2-HF: Total energy -53947.685019
FMO2-MP2: Total energy -54098.315748


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.
1.2252.15-0.011-0.427-0.487-0.001
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 : 0.024 / q_NPA : 0.003
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].
3A0ALA00.0490.0603.8480.7551.680-0.011-0.427-0.487-0.001
4A1MET00.0190.0126.3830.2200.2200.0000.0000.0000.000
5A2SER00.0100.0128.1690.1170.1170.0000.0000.0000.000
6A3ALA00.0110.0159.1160.0190.0190.0000.0000.0000.000
7A4ASN0-0.006-0.02810.870-0.002-0.0020.0000.0000.0000.000
8A5ASP-1-0.765-0.84713.0650.0030.0030.0000.0000.0000.000
9A6LYS10.8330.91815.3840.1700.1700.0000.0000.0000.000
10A7LEU0-0.0010.03317.896-0.005-0.0050.0000.0000.0000.000
11A8THR00.014-0.00321.0580.0000.0000.0000.0000.0000.000
12A9ILE0-0.0040.00623.4350.0050.0050.0000.0000.0000.000
13A10LEU0-0.017-0.00527.041-0.003-0.0030.0000.0000.0000.000
14A11TRP00.0300.00629.2990.0040.0040.0000.0000.0000.000
15A12THR0-0.066-0.05032.6160.0000.0000.0000.0000.0000.000
16A13THR00.0030.00035.5470.0030.0030.0000.0000.0000.000
17A14ASP-1-0.799-0.88737.965-0.030-0.0300.0000.0000.0000.000
18A15ASN00.0340.02240.2020.0030.0030.0000.0000.0000.000
19A16LYS10.9360.94140.2230.0190.0190.0000.0000.0000.000
20A17ASP-1-0.844-0.88840.937-0.014-0.0140.0000.0000.0000.000
21A18THR0-0.032-0.01736.0660.0010.0010.0000.0000.0000.000
22A19VAL0-0.0080.00136.428-0.001-0.0010.0000.0000.0000.000
23A20PHE00.0270.01236.332-0.001-0.0010.0000.0000.0000.000
24A21ASN00.0230.01537.0350.0020.0020.0000.0000.0000.000
25A22MET0-0.0550.00129.8140.0010.0010.0000.0000.0000.000
26A23LEU00.014-0.00431.4170.0000.0000.0000.0000.0000.000
27A24ALA00.0310.01031.487-0.001-0.0010.0000.0000.0000.000
28A25MET00.0340.03832.5600.0010.0010.0000.0000.0000.000
29A26TYR00.0050.00824.6480.0010.0010.0000.0000.0000.000
30A27ALA00.0370.02027.6600.0010.0010.0000.0000.0000.000
31A28LEU00.0540.02527.9080.0000.0000.0000.0000.0000.000
32A29ASN0-0.080-0.04429.4590.0060.0060.0000.0000.0000.000
33A30SER0-0.028-0.02424.4780.0060.0060.0000.0000.0000.000
34A31LYS10.7900.90322.4660.0530.0530.0000.0000.0000.000
35A32ASN00.0280.01425.5510.0020.0020.0000.0000.0000.000
36A33ARG10.9250.98526.631-0.004-0.0040.0000.0000.0000.000
37A34GLY00.0360.04022.6460.0100.0100.0000.0000.0000.000
38A35TRP0-0.041-0.02720.9960.0050.0050.0000.0000.0000.000
39A36TRP00.0040.00317.348-0.001-0.0010.0000.0000.0000.000
40A37LYS10.9070.96215.186-0.020-0.0200.0000.0000.0000.000
41A38HIS0-0.0040.00115.8930.0010.0010.0000.0000.0000.000
42A39ILE00.0380.01620.433-0.001-0.0010.0000.0000.0000.000
43A40ASN0-0.0100.00723.2960.0080.0080.0000.0000.0000.000
44A41ILE0-0.010-0.00224.8170.0010.0010.0000.0000.0000.000
45A42ILE0-0.012-0.00425.888-0.002-0.0020.0000.0000.0000.000
46A43LEU00.0180.01129.7580.0040.0040.0000.0000.0000.000
47A44TRP00.015-0.02830.301-0.003-0.0030.0000.0000.0000.000
48A45GLY00.0460.02634.9270.0000.0000.0000.0000.0000.000
49A46ALA00.0220.00738.1140.0010.0010.0000.0000.0000.000
50A47SER0-0.019-0.02535.6850.0020.0020.0000.0000.0000.000
51A48VAL0-0.0020.00437.1920.0010.0010.0000.0000.0000.000
52A49LYS10.8840.91539.3880.0340.0340.0000.0000.0000.000
53A50LEU00.0150.02239.9940.0020.0020.0000.0000.0000.000
54A51VAL00.0110.00437.3320.0020.0020.0000.0000.0000.000
55A52ALA0-0.023-0.01040.7760.0010.0010.0000.0000.0000.000
56A53ASN0-0.055-0.04643.2810.0020.0020.0000.0000.0000.000
57A54ASP-1-0.770-0.85243.819-0.019-0.0190.0000.0000.0000.000
58A55THR00.019-0.01343.855-0.001-0.0010.0000.0000.0000.000
59A56GLN00.0400.04144.1500.0000.0000.0000.0000.0000.000
60A57VAL00.009-0.00239.0780.0000.0000.0000.0000.0000.000
61A58GLN0-0.032-0.01939.4720.0000.0000.0000.0000.0000.000
62A59THR00.0130.01539.7280.0000.0000.0000.0000.0000.000
63A60GLU-1-0.750-0.84236.752-0.019-0.0190.0000.0000.0000.000
64A61ILE0-0.062-0.02335.200-0.002-0.0020.0000.0000.0000.000
65A62LEU0-0.0180.00034.900-0.002-0.0020.0000.0000.0000.000
66A63GLU-1-0.790-0.87534.747-0.015-0.0150.0000.0000.0000.000
67A64MET0-0.019-0.01931.448-0.001-0.0010.0000.0000.0000.000
68A65LEU0-0.0200.00230.751-0.002-0.0020.0000.0000.0000.000
69A66GLN0-0.013-0.00430.933-0.002-0.0020.0000.0000.0000.000
70A67SER0-0.056-0.02029.5950.0010.0010.0000.0000.0000.000
71A68GLY00.0220.01226.6990.0010.0010.0000.0000.0000.000
72A69ILE0-0.063-0.00625.756-0.009-0.0090.0000.0000.0000.000
73A70THR0-0.0040.00924.7990.0000.0000.0000.0000.0000.000
74A71ILE00.0210.00227.3260.0000.0000.0000.0000.0000.000
75A72GLU-1-0.679-0.79826.576-0.107-0.1070.0000.0000.0000.000
76A73ALA00.0230.00630.8160.0020.0020.0000.0000.0000.000
77A74CYS0-0.0450.03133.763-0.003-0.0030.0000.0000.0000.000
78A75GLN00.0820.04934.6690.0010.0010.0000.0000.0000.000
79A76ASP-1-0.780-0.89736.877-0.060-0.0600.0000.0000.0000.000
80A77CYS0-0.054-0.03637.9130.0030.0030.0000.0000.0000.000
81A78CYS0-0.016-0.00637.7000.0040.0040.0000.0000.0000.000
82A79GLU-1-0.710-0.78740.626-0.049-0.0490.0000.0000.0000.000
83A80ASN00.009-0.00341.9870.0040.0040.0000.0000.0000.000
84A81PHE0-0.080-0.04841.0450.0020.0020.0000.0000.0000.000
85A82GLY00.0360.03845.0550.0020.0020.0000.0000.0000.000
86A83VAL0-0.030-0.02841.7540.0020.0020.0000.0000.0000.000
87A84ALA00.0310.01940.7750.0000.0000.0000.0000.0000.000
88A85SER00.0580.03540.964-0.001-0.0010.0000.0000.0000.000
89A86ILE00.0270.02742.6240.0000.0000.0000.0000.0000.000
90A87ILE00.0390.00637.1660.0000.0000.0000.0000.0000.000
91A88THR00.0320.01537.617-0.002-0.0020.0000.0000.0000.000
92A89ASN0-0.039-0.03238.349-0.002-0.0020.0000.0000.0000.000
93A90LEU0-0.056-0.00738.4710.0020.0020.0000.0000.0000.000
94A91GLY00.0270.02735.7280.0010.0010.0000.0000.0000.000
95A92ILE00.0000.01533.259-0.004-0.0040.0000.0000.0000.000
96A93THR0-0.0040.00429.7850.0030.0030.0000.0000.0000.000
97A94VAL0-0.0010.01332.645-0.002-0.0020.0000.0000.0000.000
98A95ARG10.9060.94925.0840.1130.1130.0000.0000.0000.000
99A96TYR0-0.032-0.06133.1380.0000.0000.0000.0000.0000.000
100A97MET00.0190.01227.380-0.008-0.0080.0000.0000.0000.000
101A98GLY0-0.0010.01329.282-0.004-0.0040.0000.0000.0000.000
102A99ILE00.0230.01425.803-0.005-0.0050.0000.0000.0000.000
103A100PRO00.0130.00924.781-0.011-0.0110.0000.0000.0000.000
104A101LEU00.0310.02524.150-0.009-0.0090.0000.0000.0000.000
105A102THR0-0.028-0.02924.611-0.003-0.0030.0000.0000.0000.000
106A103GLU-1-0.859-0.91420.596-0.232-0.2320.0000.0000.0000.000
107A104TYR0-0.062-0.06020.092-0.020-0.0200.0000.0000.0000.000
108A105LEU00.0130.00319.998-0.008-0.0080.0000.0000.0000.000
109A106LYS10.8900.94420.0890.1550.1550.0000.0000.0000.000
110A107ASN0-0.026-0.00815.897-0.038-0.0380.0000.0000.0000.000
111A108GLY0-0.0120.00915.384-0.033-0.0330.0000.0000.0000.000
112A109GLU-1-0.744-0.81316.951-0.158-0.1580.0000.0000.0000.000
113A110LYS10.8470.92914.5810.1380.1380.0000.0000.0000.000
114A111ILE0-0.004-0.01820.0730.0010.0010.0000.0000.0000.000
115A112LEU0-0.0100.00723.6690.0060.0060.0000.0000.0000.000
116A113SER00.0280.03326.790-0.004-0.0040.0000.0000.0000.000
117A114ILE-1-0.733-0.80529.708-0.039-0.0390.0000.0000.0000.000
118A115HOH00.0330.01322.8080.0000.0000.0000.0000.0000.000
119A116HOH0-0.044-0.04022.601-0.001-0.0010.0000.0000.0000.000
120A117HOH0-0.011-0.02122.4010.0020.0020.0000.0000.0000.000
121A118HOH0-0.012-0.03634.918-0.001-0.0010.0000.0000.0000.000
122A119HOH00.0070.00622.634-0.006-0.0060.0000.0000.0000.000
123A120HOH0-0.063-0.04628.959-0.002-0.0020.0000.0000.0000.000
124A121HOH0-0.021-0.00918.806-0.009-0.0090.0000.0000.0000.000
125A122HOH0-0.007-0.00130.670-0.002-0.0020.0000.0000.0000.000
126A123HOH00.0240.01516.5060.0000.0000.0000.0000.0000.000
127A124HOH00.0240.00829.294-0.002-0.0020.0000.0000.0000.000
128A125HOH0-0.025-0.02345.6840.0000.0000.0000.0000.0000.000
129A126HOH0-0.045-0.03341.0070.0000.0000.0000.0000.0000.000
130A127HOH0-0.044-0.03933.6580.0000.0000.0000.0000.0000.000
131A128HOH0-0.036-0.03744.4620.0000.0000.0000.0000.0000.000
132A129HOH0-0.007-0.00733.896-0.001-0.0010.0000.0000.0000.000
133A130HOH0-0.028-0.02718.108-0.006-0.0060.0000.0000.0000.000
134A131HOH0-0.068-0.05043.0340.0000.0000.0000.0000.0000.000
135A132HOH0-0.023-0.0255.6640.0450.0450.0000.0000.0000.000
136A133HOH0-0.018-0.01243.8500.0010.0010.0000.0000.0000.000
137A134HOH00.0250.02045.0690.0000.0000.0000.0000.0000.000
138A135HOH0-0.026-0.02438.1490.0000.0000.0000.0000.0000.000
139A136HOH00.0170.00015.3890.0080.0080.0000.0000.0000.000
140A137HOH0-0.089-0.06640.5990.0010.0010.0000.0000.0000.000
141A138HOH0-0.036-0.03327.7860.0000.0000.0000.0000.0000.000
142A139HOH0-0.026-0.01722.449-0.006-0.0060.0000.0000.0000.000
143A140HOH00.0270.01821.8100.0020.0020.0000.0000.0000.000
144A141HOH0-0.040-0.03535.207-0.001-0.0010.0000.0000.0000.000
145A142HOH00.0370.02948.7350.0000.0000.0000.0000.0000.000
146A143HOH0-0.006-0.0127.2770.0510.0510.0000.0000.0000.000
147A144HOH0-0.028-0.02544.2610.0010.0010.0000.0000.0000.000
148A146HOH0-0.011-0.00431.268-0.001-0.0010.0000.0000.0000.000
149A147HOH00.0180.01635.600-0.002-0.0020.0000.0000.0000.000
150A148HOH0-0.087-0.07537.1570.0010.0010.0000.0000.0000.000
151A149HOH00.0120.00340.959-0.001-0.0010.0000.0000.0000.000
152A150HOH0-0.034-0.03111.7560.0000.0000.0000.0000.0000.000
153A151HOH00.000-0.00235.9030.0010.0010.0000.0000.0000.000
154A152HOH0-0.022-0.01439.1750.0010.0010.0000.0000.0000.000
155A154HOH0-0.036-0.01836.0610.0010.0010.0000.0000.0000.000
156A155HOH0-0.042-0.02844.6170.0000.0000.0000.0000.0000.000
157A157HOH00.0070.01236.3310.0000.0000.0000.0000.0000.000
158A158HOH0-0.023-0.02517.356-0.002-0.0020.0000.0000.0000.000
159A160HOH0-0.047-0.02735.8900.0010.0010.0000.0000.0000.000
160A161HOH0-0.008-0.00746.3670.0000.0000.0000.0000.0000.000
161A162HOH0-0.030-0.03038.6880.0010.0010.0000.0000.0000.000
162A163HOH0-0.0080.00126.5470.0030.0030.0000.0000.0000.000
163A164HOH0-0.0060.00519.712-0.001-0.0010.0000.0000.0000.000
164A165HOH00.0230.02322.047-0.002-0.0020.0000.0000.0000.000
165A166HOH0-0.002-0.00844.1650.0000.0000.0000.0000.0000.000
166A167HOH0-0.033-0.02025.866-0.001-0.0010.0000.0000.0000.000
167A169HOH00.0390.02847.0680.0000.0000.0000.0000.0000.000
168A171HOH0-0.059-0.04217.9620.0070.0070.0000.0000.0000.000
169A172HOH00.001-0.00242.8270.0010.0010.0000.0000.0000.000
170A173HOH00.0430.03222.4820.0060.0060.0000.0000.0000.000
171A174HOH0-0.037-0.02113.6380.0050.0050.0000.0000.0000.000
172A175HOH0-0.034-0.02646.3700.0000.0000.0000.0000.0000.000
173A176HOH0-0.006-0.00729.506-0.003-0.0030.0000.0000.0000.000
174A177HOH0-0.032-0.02231.9990.0020.0020.0000.0000.0000.000
175A178HOH0-0.010-0.01120.392-0.002-0.0020.0000.0000.0000.000
176A181HOH0-0.014-0.03542.5730.0010.0010.0000.0000.0000.000
177A183HOH0-0.039-0.02641.5950.0010.0010.0000.0000.0000.000
178A185HOH0-0.0020.00544.4190.0010.0010.0000.0000.0000.000
179A186HOH0-0.039-0.02443.8060.0010.0010.0000.0000.0000.000
180A187HOH0-0.039-0.02813.064-0.029-0.0290.0000.0000.0000.000
181A189HOH0-0.046-0.03031.0260.0000.0000.0000.0000.0000.000
182A190HOH00.0460.04148.974-0.001-0.0010.0000.0000.0000.000
183A191HOH0-0.014-0.01427.507-0.003-0.0030.0000.0000.0000.000
184A193HOH0-0.074-0.06618.4440.0010.0010.0000.0000.0000.000
185A195HOH00.0170.01732.5840.0000.0000.0000.0000.0000.000
186A198HOH00.0300.05420.4660.0040.0040.0000.0000.0000.000
187A199HOH00.0140.03141.078-0.002-0.0020.0000.0000.0000.000
188A201HOH0-0.045-0.04225.084-0.001-0.0010.0000.0000.0000.000
189A202HOH00.0030.00810.330-0.022-0.0220.0000.0000.0000.000
190A205HOH0-0.029-0.02832.996-0.002-0.0020.0000.0000.0000.000
191A207HOH00.0020.00844.9870.0000.0000.0000.0000.0000.000
192A208HOH0-0.042-0.02243.5100.0000.0000.0000.0000.0000.000
193A209HOH0-0.051-0.03122.0900.0040.0040.0000.0000.0000.000
194A211HOH0-0.031-0.02447.0020.0010.0010.0000.0000.0000.000
195A212HOH0-0.019-0.01239.6000.0010.0010.0000.0000.0000.000
196A213HOH0-0.019-0.02213.916-0.005-0.0050.0000.0000.0000.000
197A215HOH0-0.094-0.10721.0530.0030.0030.0000.0000.0000.000
198A216HOH0-0.035-0.04127.1470.0000.0000.0000.0000.0000.000
199A217HOH0-0.053-0.05832.6470.0010.0010.0000.0000.0000.000
200A220HOH0-0.030-0.02428.6440.0010.0010.0000.0000.0000.000
201A222HOH0-0.029-0.03244.021-0.001-0.0010.0000.0000.0000.000
202A223HOH0-0.035-0.02748.0550.0000.0000.0000.0000.0000.000
203A225HOH0-0.021-0.00714.5950.0150.0150.0000.0000.0000.000
204A226HOH0-0.048-0.03535.541-0.001-0.0010.0000.0000.0000.000
205A227HOH00.002-0.00220.7800.0010.0010.0000.0000.0000.000
206A230HOH0-0.021-0.01146.3230.0010.0010.0000.0000.0000.000
207A237HOH0-0.003-0.00140.5500.0000.0000.0000.0000.0000.000
208A238HOH0-0.034-0.0205.2180.2020.2020.0000.0000.0000.000
209A240HOH0-0.016-0.01112.8490.0190.0190.0000.0000.0000.000
210A246HOH00.0170.01447.4440.0000.0000.0000.0000.0000.000