FMODB

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

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: XNNGQ

Calculation Name: 3B79-A-Xray21

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3B79

Chain ID: A

ChEMBL ID:

UniProt ID: Q87FE3

Base Structure: X-ray

Registration Date: 2018-06-07

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 231
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1318094.754172
FMO2-HF: Nuclear repulsion 1262210.779404
FMO2-HF: Total energy -55883.974768
FMO2-MP2: Total energy -56044.428315


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:-1:ACE)


Summations of interaction energy for fragment #1(A:-1: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.
1.0011.614-0.01-0.255-0.3480
Interaction energy analysis for fragmet #1(A:-1:ACE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.004 / q_NPA : -0.009
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].
3A1MET0-0.0240.0163.8431.4072.020-0.010-0.255-0.3480.000
4A2LYS11.0261.0006.1400.3020.3020.0000.0000.0000.000
5A3ASP-1-0.727-0.8279.747-0.062-0.0620.0000.0000.0000.000
6A4PRO00.0840.04512.302-0.014-0.0140.0000.0000.0000.000
7A5LEU00.0000.00814.3610.0180.0180.0000.0000.0000.000
8A6LEU0-0.042-0.01510.6770.0240.0240.0000.0000.0000.000
9A7ASN00.0370.00810.333-0.089-0.0890.0000.0000.0000.000
10A8SER00.0350.01512.2730.0210.0210.0000.0000.0000.000
11A9LEU0-0.036-0.01215.8570.0230.0230.0000.0000.0000.000
12A10ILE0-0.023-0.01210.8430.0340.0340.0000.0000.0000.000
13A11TYR00.0710.03514.0660.0360.0360.0000.0000.0000.000
14A12VAL00.0320.00815.4220.0250.0250.0000.0000.0000.000
15A13SER0-0.014-0.01016.4370.0230.0230.0000.0000.0000.000
16A14ARG10.8050.90712.6300.0050.0050.0000.0000.0000.000
17A15TYR00.0180.01617.1880.0100.0100.0000.0000.0000.000
18A16TYR0-0.044-0.01520.1120.0120.0120.0000.0000.0000.000
19A17GLY00.0050.01020.1690.0100.0100.0000.0000.0000.000
20A18LEU0-0.070-0.01819.7300.0140.0140.0000.0000.0000.000
21A19ALA00.0210.02116.295-0.011-0.0110.0000.0000.0000.000
22A20ASN0-0.048-0.05114.9890.0170.0170.0000.0000.0000.000
23A21SER00.0930.03811.478-0.030-0.0300.0000.0000.0000.000
24A22PRO00.0730.0058.186-0.026-0.0260.0000.0000.0000.000
25A23GLU-1-0.896-0.94411.2340.3870.3870.0000.0000.0000.000
26A24ALA00.0210.02612.857-0.032-0.0320.0000.0000.0000.000
27A25LEU0-0.0120.00314.436-0.023-0.0230.0000.0000.0000.000
28A26VAL00.009-0.00313.800-0.024-0.0240.0000.0000.0000.000
29A27ASN00.0240.03016.5410.0070.0070.0000.0000.0000.000
30A28GLY00.0330.01318.430-0.015-0.0150.0000.0000.0000.000
31A29LEU0-0.090-0.03119.118-0.015-0.0150.0000.0000.0000.000
32A30PRO00.0090.00420.1500.0060.0060.0000.0000.0000.000
33A31LEU00.0140.00715.114-0.013-0.0130.0000.0000.0000.000
34A32SER0-0.024-0.03119.2570.0110.0110.0000.0000.0000.000
35A33ASP-1-0.930-0.96117.386-0.112-0.1120.0000.0000.0000.000
36A34GLY00.0160.01614.448-0.020-0.0200.0000.0000.0000.000
37A35LYS10.9260.98113.5890.2360.2360.0000.0000.0000.000
38A36LEU00.014-0.00315.6540.0260.0260.0000.0000.0000.000
39A37THR00.0240.01617.704-0.019-0.0190.0000.0000.0000.000
40A38PRO00.0770.01621.0150.0080.0080.0000.0000.0000.000
41A39PHE00.0320.02023.5510.0070.0070.0000.0000.0000.000
42A40LEU0-0.020-0.01720.2270.0090.0090.0000.0000.0000.000
43A41LEU00.0250.03519.1640.0090.0090.0000.0000.0000.000
44A42PRO0-0.0230.00021.6790.0060.0060.0000.0000.0000.000
45A43ARG10.9350.95323.5750.0080.0080.0000.0000.0000.000
46A44ALA00.0410.02518.0870.0090.0090.0000.0000.0000.000
47A45ALA00.001-0.01219.7960.0060.0060.0000.0000.0000.000
48A46GLU-1-0.808-0.82321.4690.0330.0330.0000.0000.0000.000
49A47ARG10.8620.93919.571-0.039-0.0390.0000.0000.0000.000
50A48ALA00.0220.02418.6400.0130.0130.0000.0000.0000.000
51A49GLY0-0.0060.02619.9730.0020.0020.0000.0000.0000.000
52A50LEU0-0.024-0.01620.233-0.005-0.0050.0000.0000.0000.000
53A51VAL0-0.007-0.00924.1080.0050.0050.0000.0000.0000.000
54A52ALA00.0160.01123.541-0.006-0.0060.0000.0000.0000.000
55A53LYS10.9470.97725.6850.0370.0370.0000.0000.0000.000
56A54GLU-1-0.874-0.92227.492-0.068-0.0680.0000.0000.0000.000
57A55ASN0-0.040-0.02028.7490.0100.0100.0000.0000.0000.000
58A56ARG10.9310.94630.6230.0450.0450.0000.0000.0000.000
59A57ALA00.0250.02232.5110.0050.0050.0000.0000.0000.000
60A58GLU-1-0.847-0.91432.497-0.061-0.0610.0000.0000.0000.000
61A59LEU00.0700.03428.1590.0030.0030.0000.0000.0000.000
62A60GLU-1-0.772-0.85131.802-0.070-0.0700.0000.0000.0000.000
63A61LYS10.8680.94534.4930.0560.0560.0000.0000.0000.000
64A62ILE0-0.0330.01328.9720.0050.0050.0000.0000.0000.000
65A63SER00.0600.03932.671-0.002-0.0020.0000.0000.0000.000
66A64SER00.1350.04230.910-0.002-0.0020.0000.0000.0000.000
67A65LEU0-0.059-0.01930.486-0.002-0.0020.0000.0000.0000.000
68A66ILE0-0.067-0.02129.0730.0030.0030.0000.0000.0000.000
69A67LEU0-0.0770.00926.283-0.002-0.0020.0000.0000.0000.000
70A68PRO00.0230.02021.9560.0060.0060.0000.0000.0000.000
71A69ALA0-0.0200.00924.1270.0110.0110.0000.0000.0000.000
72A70ILE0-0.0090.00019.198-0.013-0.0130.0000.0000.0000.000
73A71LEU00.0040.00222.1420.0170.0170.0000.0000.0000.000
74A72VAL0-0.010-0.01022.035-0.016-0.0160.0000.0000.0000.000
75A73LEU00.0180.01820.5400.0140.0140.0000.0000.0000.000
76A74LYS10.8840.94623.7330.1090.1090.0000.0000.0000.000
77A75GLY00.0120.00423.111-0.014-0.0140.0000.0000.0000.000
78A76GLY0-0.057-0.02121.118-0.010-0.0100.0000.0000.0000.000
79A77ASP-1-0.696-0.82817.499-0.295-0.2950.0000.0000.0000.000
80A78SER0-0.056-0.03917.3570.0300.0300.0000.0000.0000.000
81A79CYS00.0280.04317.844-0.030-0.0300.0000.0000.0000.000
82A80VAL0-0.028-0.00217.4060.0290.0290.0000.0000.0000.000
83A81LEU00.0170.02120.058-0.009-0.0090.0000.0000.0000.000
84A82ASN00.028-0.01819.997-0.001-0.0010.0000.0000.0000.000
85A83SER00.005-0.00723.9390.0150.0150.0000.0000.0000.000
86A84ILE00.0240.01327.170-0.009-0.0090.0000.0000.0000.000
87A85ASN00.0640.05929.9740.0120.0120.0000.0000.0000.000
88A86MET00.003-0.02032.581-0.005-0.0050.0000.0000.0000.000
89A87GLU-1-0.990-0.96935.549-0.054-0.0540.0000.0000.0000.000
90A88THR00.0340.00332.3340.0010.0010.0000.0000.0000.000
91A89ARG10.9080.97133.5220.0710.0710.0000.0000.0000.000
92A90GLU-1-0.777-0.82428.209-0.127-0.1270.0000.0000.0000.000
93A91ALA0-0.019-0.00726.3600.0090.0090.0000.0000.0000.000
94A92GLU-1-0.780-0.85922.540-0.158-0.1580.0000.0000.0000.000
95A93VAL00.0340.00620.3090.0110.0110.0000.0000.0000.000
96A94THR0-0.014-0.01015.074-0.009-0.0090.0000.0000.0000.000
97A95THR00.0500.02115.9660.0150.0150.0000.0000.0000.000
98A96LEU0-0.026-0.01310.341-0.047-0.0470.0000.0000.0000.000
99A97GLU-1-0.819-0.90111.069-0.588-0.5880.0000.0000.0000.000
100A98SER0-0.0070.00612.177-0.079-0.0790.0000.0000.0000.000
101A99GLY0-0.0120.01510.552-0.016-0.0160.0000.0000.0000.000
102A100MET0-0.051-0.04210.6440.1330.1330.0000.0000.0000.000
103A101VAL00.0000.00813.0550.0690.0690.0000.0000.0000.000
104A102PRO0-0.0320.00915.839-0.025-0.0250.0000.0000.0000.000
105A103ILE00.0300.02518.0730.0000.0000.0000.0000.0000.000
106A104SER0-0.016-0.01420.7300.0110.0110.0000.0000.0000.000
107A105ILE0-0.032-0.00622.356-0.013-0.0130.0000.0000.0000.000
108A106PRO00.0780.05025.3160.0120.0120.0000.0000.0000.000
109A107LEU0-0.026-0.02528.161-0.005-0.0050.0000.0000.0000.000
110A108GLU-1-0.873-0.91230.058-0.099-0.0990.0000.0000.0000.000
111A109ASP-1-0.750-0.84726.143-0.138-0.1380.0000.0000.0000.000
112A110LEU00.0030.00324.214-0.005-0.0050.0000.0000.0000.000
113A111LEU0-0.047-0.03026.9950.0020.0020.0000.0000.0000.000
114A112GLU-1-0.864-0.92829.068-0.095-0.0950.0000.0000.0000.000
115A113GLN00.0360.02124.2570.0000.0000.0000.0000.0000.000
116A114TYR0-0.032-0.00526.224-0.001-0.0010.0000.0000.0000.000
117A115THR0-0.043-0.04026.4310.0120.0120.0000.0000.0000.000
118A116GLY0-0.024-0.00429.0080.0080.0080.0000.0000.0000.000
119A117ARG10.8290.90127.2880.0870.0870.0000.0000.0000.000
120A118TYR00.036-0.00326.011-0.009-0.0090.0000.0000.0000.000
121A119PHE00.001-0.00523.8350.0110.0110.0000.0000.0000.000
122A120LEU00.0160.01725.538-0.006-0.0060.0000.0000.0000.000
123A121VAL0-0.020-0.02322.1380.0070.0070.0000.0000.0000.000
124A122LYS10.9771.00425.4490.0210.0210.0000.0000.0000.000
125A123LYS10.9500.97725.467-0.002-0.0020.0000.0000.0000.000
126A124GLN0-0.049-0.03026.073-0.001-0.0010.0000.0000.0000.000
127A125NME00.0240.02228.5740.0020.0020.0000.0000.0000.000
128A127HOH00.003-0.01325.6410.0010.0010.0000.0000.0000.000
129A128HOH0-0.037-0.04234.8780.0010.0010.0000.0000.0000.000
130A129HOH0-0.027-0.02420.127-0.005-0.0050.0000.0000.0000.000
131A130HOH0-0.004-0.00515.385-0.022-0.0220.0000.0000.0000.000
132A131HOH00.0010.00237.238-0.001-0.0010.0000.0000.0000.000
133A132HOH00.0180.01725.4940.0030.0030.0000.0000.0000.000
134A134HOH0-0.027-0.02118.6510.0050.0050.0000.0000.0000.000
135A135HOH00.0290.01828.7790.0000.0000.0000.0000.0000.000
136A136HOH0-0.015-0.01724.9710.0010.0010.0000.0000.0000.000
137A137HOH0-0.040-0.03932.115-0.001-0.0010.0000.0000.0000.000
138A138HOH0-0.007-0.01924.7300.0010.0010.0000.0000.0000.000
139A139HOH0-0.002-0.00225.478-0.002-0.0020.0000.0000.0000.000
140A140HOH00.0080.00132.7850.0000.0000.0000.0000.0000.000
141A141HOH0-0.016-0.01915.888-0.007-0.0070.0000.0000.0000.000
142A142HOH0-0.057-0.04320.6430.0010.0010.0000.0000.0000.000
143A143HOH0-0.047-0.03728.0620.0020.0020.0000.0000.0000.000
144A144HOH0-0.036-0.02133.3420.0020.0020.0000.0000.0000.000
145A145HOH00.0310.02535.724-0.001-0.0010.0000.0000.0000.000
146A146HOH00.000-0.00232.0260.0020.0020.0000.0000.0000.000
147A147HOH0-0.040-0.02715.8360.0130.0130.0000.0000.0000.000
148A148HOH00.0030.00035.7220.0010.0010.0000.0000.0000.000
149A149HOH0-0.029-0.02123.9520.0040.0040.0000.0000.0000.000
150A150HOH0-0.061-0.05127.315-0.002-0.0020.0000.0000.0000.000
151A151HOH00.0330.0209.6990.0480.0480.0000.0000.0000.000
152A153HOH0-0.013-0.01422.813-0.003-0.0030.0000.0000.0000.000
153A154HOH00.0320.02533.213-0.001-0.0010.0000.0000.0000.000
154A155HOH0-0.024-0.02031.5690.0010.0010.0000.0000.0000.000
155A157HOH00.0290.04216.283-0.011-0.0110.0000.0000.0000.000
156A158HOH0-0.043-0.03915.101-0.016-0.0160.0000.0000.0000.000
157A159HOH0-0.043-0.0328.4690.0180.0180.0000.0000.0000.000
158A160HOH0-0.071-0.06112.6190.0100.0100.0000.0000.0000.000
159A161HOH0-0.074-0.06817.7470.0060.0060.0000.0000.0000.000
160A163HOH00.0280.01830.769-0.002-0.0020.0000.0000.0000.000
161A164HOH0-0.006-0.00126.732-0.002-0.0020.0000.0000.0000.000
162A170HOH0-0.042-0.03136.5110.0010.0010.0000.0000.0000.000
163A171HOH0-0.088-0.09327.268-0.005-0.0050.0000.0000.0000.000
164A172HOH0-0.036-0.02928.3950.0000.0000.0000.0000.0000.000
165A173HOH00.0090.02421.896-0.005-0.0050.0000.0000.0000.000
166A175HOH0-0.0070.00425.150-0.003-0.0030.0000.0000.0000.000
167A177HOH00.0310.03134.376-0.002-0.0020.0000.0000.0000.000
168A178HOH0-0.003-0.01324.4440.0010.0010.0000.0000.0000.000
169A180HOH00.0100.01531.9380.0000.0000.0000.0000.0000.000
170A181HOH0-0.035-0.02032.1540.0030.0030.0000.0000.0000.000
171A182HOH0-0.049-0.02916.338-0.010-0.0100.0000.0000.0000.000
172A183HOH0-0.013-0.00228.584-0.004-0.0040.0000.0000.0000.000
173A184HOH0-0.025-0.01828.1190.0030.0030.0000.0000.0000.000
174A185HOH0-0.020-0.00935.5750.0000.0000.0000.0000.0000.000
175A186HOH0-0.034-0.01912.6390.0080.0080.0000.0000.0000.000
176A188HOH0-0.041-0.03427.8480.0000.0000.0000.0000.0000.000
177A191HOH0-0.027-0.01230.8010.0020.0020.0000.0000.0000.000
178A192HOH0-0.022-0.01625.4900.0000.0000.0000.0000.0000.000
179A193HOH00.0570.03932.7080.0010.0010.0000.0000.0000.000
180A194HOH0-0.041-0.0279.352-0.047-0.0470.0000.0000.0000.000
181A197HOH00.0100.00421.6620.0020.0020.0000.0000.0000.000
182A199HOH0-0.041-0.03337.3170.0010.0010.0000.0000.0000.000
183A201HOH0-0.021-0.01830.0500.0010.0010.0000.0000.0000.000
184A202HOH00.0320.03827.455-0.003-0.0030.0000.0000.0000.000
185A204HOH0-0.045-0.04717.9180.0050.0050.0000.0000.0000.000
186A205HOH00.0210.01935.350-0.001-0.0010.0000.0000.0000.000
187A206HOH0-0.007-0.01320.4810.0060.0060.0000.0000.0000.000
188A207HOH0-0.003-0.00722.546-0.006-0.0060.0000.0000.0000.000
189A208HOH0-0.041-0.03835.8720.0000.0000.0000.0000.0000.000
190A209HOH0-0.0020.00118.5010.0010.0010.0000.0000.0000.000
191A211HOH0-0.007-0.01438.9090.0000.0000.0000.0000.0000.000
192A212HOH0-0.036-0.02232.8530.0020.0020.0000.0000.0000.000
193A214HOH00.0040.00118.983-0.002-0.0020.0000.0000.0000.000
194A215HOH0-0.020-0.0169.018-0.109-0.1090.0000.0000.0000.000
195A216HOH0-0.044-0.02625.6890.0000.0000.0000.0000.0000.000
196A217HOH0-0.055-0.04119.1530.0030.0030.0000.0000.0000.000
197A218HOH0-0.025-0.02133.0240.0020.0020.0000.0000.0000.000
198A219HOH0-0.045-0.03016.5860.0000.0000.0000.0000.0000.000
199A222HOH0-0.021-0.01818.906-0.007-0.0070.0000.0000.0000.000
200A224HOH0-0.038-0.02622.0150.0030.0030.0000.0000.0000.000
201A228HOH0-0.021-0.01629.715-0.001-0.0010.0000.0000.0000.000
202A229HOH0-0.014-0.0149.0860.0500.0500.0000.0000.0000.000
203A232HOH0-0.071-0.07427.7460.0000.0000.0000.0000.0000.000
204A233HOH0-0.062-0.04318.176-0.008-0.0080.0000.0000.0000.000
205A237HOH0-0.039-0.02524.1950.0040.0040.0000.0000.0000.000
206A238HOH00.0280.01926.952-0.003-0.0030.0000.0000.0000.000
207A240HOH0-0.023-0.00831.4140.0010.0010.0000.0000.0000.000
208A244HOH0-0.008-0.01120.686-0.002-0.0020.0000.0000.0000.000
209A246HOH0-0.021-0.02115.486-0.006-0.0060.0000.0000.0000.000
210A255HOH0-0.013-0.01111.1070.0290.0290.0000.0000.0000.000
211A257HOH0-0.044-0.04732.4420.0000.0000.0000.0000.0000.000
212A259HOH0-0.020-0.02826.4780.0040.0040.0000.0000.0000.000
213A261HOH0-0.005-0.00619.6670.0000.0000.0000.0000.0000.000
214A262HOH0-0.041-0.06036.189-0.001-0.0010.0000.0000.0000.000
215A263HOH00.0410.02430.3030.0000.0000.0000.0000.0000.000
216A265HOH00.0200.01329.436-0.001-0.0010.0000.0000.0000.000
217A266HOH0-0.033-0.02813.0220.0230.0230.0000.0000.0000.000
218A267HOH0-0.008-0.00318.495-0.005-0.0050.0000.0000.0000.000
219A268HOH0-0.031-0.01523.8430.0020.0020.0000.0000.0000.000
220A269HOH00.0100.01017.3310.0080.0080.0000.0000.0000.000
221A272HOH00.005-0.00338.555-0.001-0.0010.0000.0000.0000.000
222A282HOH0-0.026-0.01819.3080.0020.0020.0000.0000.0000.000
223A283HOH00.0280.01715.8910.0030.0030.0000.0000.0000.000
224A284HOH0-0.040-0.02126.4990.0030.0030.0000.0000.0000.000
225A285HOH00.0350.02221.059-0.002-0.0020.0000.0000.0000.000
226A286HOH0-0.011-0.00936.2800.0010.0010.0000.0000.0000.000
227A289HOH0-0.017-0.01227.111-0.003-0.0030.0000.0000.0000.000
228A291HOH0-0.026-0.03824.9920.0000.0000.0000.0000.0000.000
229A296HOH0-0.027-0.02535.7050.0010.0010.0000.0000.0000.000
230A297HOH0-0.019-0.00723.096-0.001-0.0010.0000.0000.0000.000
231A299HOH0-0.060-0.05030.1660.0020.0020.0000.0000.0000.000