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: 6641Z

Calculation Name: 3SNP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3SNP

Chain ID: A

ChEMBL ID:

UniProt ID: Q01059

Base Structure: X-ray

Registration Date: 2023-03-14

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 850
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -22419616.217558
FMO2-HF: Nuclear repulsion 22090273.126982
FMO2-HF: Total energy -329343.090576
FMO2-MP2: Total energy -330310.84227


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:SER)


Summations of interaction energy for fragment #1(A:2:SER)
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.
-13.726-13.7926.016-2.613-3.3380.022
Interaction energy analysis for fragmet #1(A:2:SER)
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 : 0.000
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].
3A4PRO0-0.032-0.0143.8740.2741.516-0.006-0.483-0.7540.001
4A5PHE00.0420.0015.701-0.114-0.1140.0000.0000.0000.000
5A6ALA00.0100.0054.939-0.168-0.077-0.001-0.005-0.0850.000
6A7TYR0-0.017-0.0026.884-0.134-0.1340.0000.0000.0000.000
7A8LEU0-0.0110.0029.363-0.036-0.0360.0000.0000.0000.000
8A9ALA0-0.061-0.0119.890-0.017-0.0170.0000.0000.0000.000
9A10GLU-1-0.793-0.87411.7450.0010.0010.0000.0000.0000.000
10A11PRO0-0.009-0.01814.8390.0140.0140.0000.0000.0000.000
11A12LEU0-0.0340.00417.765-0.006-0.0060.0000.0000.0000.000
12A13ASP-1-0.812-0.91120.6330.0080.0080.0000.0000.0000.000
13A14PRO00.0320.01721.5370.0020.0020.0000.0000.0000.000
14A15ALA00.0200.02722.590-0.005-0.0050.0000.0000.0000.000
15A16GLN0-0.087-0.05621.8370.0040.0040.0000.0000.0000.000
16A17PRO00.0600.02117.8710.0130.0130.0000.0000.0000.000
17A18GLY00.0060.00416.4200.0150.0150.0000.0000.0000.000
18A19LYS10.7690.87216.413-0.028-0.0280.0000.0000.0000.000
19A20LYS10.8680.94312.494-0.195-0.1950.0000.0000.0000.000
20A21PHE00.0280.00215.4070.0040.0040.0000.0000.0000.000
21A22PHE00.0510.0288.633-0.005-0.0050.0000.0000.0000.000
22A23ASN00.018-0.00213.988-0.017-0.0170.0000.0000.0000.000
23A24LEU00.0450.00815.234-0.007-0.0070.0000.0000.0000.000
24A25ASN0-0.015-0.00617.380-0.007-0.0070.0000.0000.0000.000
25A26LYS10.8290.89316.280-0.024-0.0240.0000.0000.0000.000
26A27LEU0-0.062-0.01013.778-0.008-0.0080.0000.0000.0000.000
27A28ASP-1-0.740-0.85916.5530.0410.0410.0000.0000.0000.000
28A29TYR00.0020.00320.2140.0030.0030.0000.0000.0000.000
29A30SER0-0.094-0.04723.0800.0000.0000.0000.0000.0000.000
30A31ARG10.8020.85219.795-0.072-0.0720.0000.0000.0000.000
31A32TYR0-0.032-0.03820.8290.0030.0030.0000.0000.0000.000
32A33GLY0-0.006-0.00323.2540.0000.0000.0000.0000.0000.000
33A34ARG10.8470.90126.483-0.034-0.0340.0000.0000.0000.000
34A35LEU00.0050.02221.9300.0000.0000.0000.0000.0000.000
35A36PRO00.0020.01326.388-0.003-0.0030.0000.0000.0000.000
36A37PHE00.016-0.00825.8820.0050.0050.0000.0000.0000.000
37A38SER0-0.037-0.03924.9090.0050.0050.0000.0000.0000.000
38A39ILE00.0440.00922.5650.0060.0060.0000.0000.0000.000
39A40ARG10.8140.91021.462-0.042-0.0420.0000.0000.0000.000
40A41VAL00.0170.00020.0440.0090.0090.0000.0000.0000.000
41A42LEU0-0.042-0.01219.1880.0070.0070.0000.0000.0000.000
42A43LEU00.0200.01816.4210.0110.0110.0000.0000.0000.000
43A44GLU-1-0.795-0.88415.2400.1550.1550.0000.0000.0000.000
44A45ALA00.0020.00914.2460.0190.0190.0000.0000.0000.000
45A46ALA00.0220.01813.2760.0050.0050.0000.0000.0000.000
46A47VAL00.015-0.01011.3970.0120.0120.0000.0000.0000.000
47A48ARG10.8290.9019.676-0.095-0.0950.0000.0000.0000.000
48A49ASN0-0.084-0.0648.9650.0160.0160.0000.0000.0000.000
49A50CYS0-0.0710.0047.701-0.016-0.0160.0000.0000.0000.000
50A51ASP-1-0.775-0.8883.976-0.208-0.118-0.001-0.023-0.0660.000
51A52LYS10.7730.8662.254-13.294-14.7836.024-2.102-2.4330.021
52A53PHE0-0.038-0.0196.636-0.043-0.0430.0000.0000.0000.000
53A54LEU0-0.008-0.0068.529-0.072-0.0720.0000.0000.0000.000
54A55VAL0-0.011-0.0048.955-0.036-0.0360.0000.0000.0000.000
55A56LYS10.8340.9108.459-0.353-0.3530.0000.0000.0000.000
56A57LYS10.9720.9679.259-0.244-0.2440.0000.0000.0000.000
57A58GLU-1-0.837-0.94011.1610.3710.3710.0000.0000.0000.000
58A59ASP-1-0.822-0.90013.0580.2060.2060.0000.0000.0000.000
59A60ILE0-0.043-0.01711.395-0.026-0.0260.0000.0000.0000.000
60A61GLU-1-0.785-0.86214.8270.0750.0750.0000.0000.0000.000
61A62ASN0-0.007-0.01917.174-0.031-0.0310.0000.0000.0000.000
62A63ILE0-0.0110.00716.513-0.014-0.0140.0000.0000.0000.000
63A64LEU0-0.017-0.00917.879-0.011-0.0110.0000.0000.0000.000
64A65ASN0-0.002-0.00420.244-0.017-0.0170.0000.0000.0000.000
65A66TRP00.000-0.00522.888-0.006-0.0060.0000.0000.0000.000
66A67ASN0-0.066-0.03324.747-0.003-0.0030.0000.0000.0000.000
67A68VAL00.0350.02326.717-0.004-0.0040.0000.0000.0000.000
68A69THR00.037-0.02322.717-0.004-0.0040.0000.0000.0000.000
69A70GLN0-0.0030.02125.9140.0010.0010.0000.0000.0000.000
70A71HIS0-0.037-0.02328.069-0.003-0.0030.0000.0000.0000.000
71A72MET0-0.060-0.01825.032-0.002-0.0020.0000.0000.0000.000
72A73ASN0-0.058-0.02427.6880.0000.0000.0000.0000.0000.000
73A74ILE00.0330.03121.2690.0010.0010.0000.0000.0000.000
74A75GLU-1-0.784-0.84821.0770.0870.0870.0000.0000.0000.000
75A76VAL0-0.009-0.00418.3770.0110.0110.0000.0000.0000.000
76A77PRO0-0.0170.00314.025-0.012-0.0120.0000.0000.0000.000
77A78PHE00.0270.00616.818-0.002-0.0020.0000.0000.0000.000
78A79LYS10.8700.92810.370-0.057-0.0570.0000.0000.0000.000
79A80PRO0-0.0210.00316.2140.0030.0030.0000.0000.0000.000
80A81ALA0-0.0180.01017.6260.0010.0010.0000.0000.0000.000
81A82ARG10.8000.86718.881-0.049-0.0490.0000.0000.0000.000
82A83VAL00.001-0.00121.3320.0020.0020.0000.0000.0000.000
83A84ILE0-0.0130.00223.914-0.003-0.0030.0000.0000.0000.000
84A85LEU0-0.034-0.02826.1430.0010.0010.0000.0000.0000.000
85A86GLN00.0410.01829.703-0.001-0.0010.0000.0000.0000.000
86A87ASP-1-0.789-0.88433.4380.0230.0230.0000.0000.0000.000
87A88PHE00.033-0.00734.9320.0000.0000.0000.0000.0000.000
88A89THR0-0.057-0.03331.8790.0010.0010.0000.0000.0000.000
89A90GLY00.0670.03829.3320.0020.0020.0000.0000.0000.000
90A91VAL0-0.020-0.00529.5040.0000.0000.0000.0000.0000.000
91A92PRO00.011-0.00629.997-0.001-0.0010.0000.0000.0000.000
92A93SER00.0150.01324.8060.0010.0010.0000.0000.0000.000
93A94VAL00.010-0.00826.137-0.001-0.0010.0000.0000.0000.000
94A95VAL0-0.031-0.01227.977-0.002-0.0020.0000.0000.0000.000
95A96ASP-1-0.710-0.80624.8210.0330.0330.0000.0000.0000.000
96A97PHE00.030-0.01219.479-0.002-0.0020.0000.0000.0000.000
97A98ALA0-0.038-0.01424.566-0.003-0.0030.0000.0000.0000.000
98A99ALA00.0360.01727.526-0.002-0.0020.0000.0000.0000.000
99A100MET0-0.020-0.00220.1480.0000.0000.0000.0000.0000.000
100A101ARG10.7590.87622.661-0.012-0.0120.0000.0000.0000.000
101A102ASP-1-0.856-0.92225.0530.0070.0070.0000.0000.0000.000
102A103ALA0-0.013-0.00524.568-0.002-0.0020.0000.0000.0000.000
103A104VAL00.005-0.00420.422-0.001-0.0010.0000.0000.0000.000
104A105LYS10.9200.97423.443-0.002-0.0020.0000.0000.0000.000
105A106LYS10.9110.95626.615-0.013-0.0130.0000.0000.0000.000
106A107LEU0-0.039-0.01522.7760.0000.0000.0000.0000.0000.000
107A108GLY0-0.0090.00924.196-0.003-0.0030.0000.0000.0000.000
108A109GLY00.0100.01221.807-0.005-0.0050.0000.0000.0000.000
109A110ASP-1-0.792-0.89720.854-0.010-0.0100.0000.0000.0000.000
110A111PRO00.011-0.00821.3270.0010.0010.0000.0000.0000.000
111A112GLU-1-0.801-0.89122.2190.0090.0090.0000.0000.0000.000
112A113LYS10.8590.91616.4020.0280.0280.0000.0000.0000.000
113A114ILE0-0.0040.01717.6510.0010.0010.0000.0000.0000.000
114A115ASN00.001-0.01818.678-0.001-0.0010.0000.0000.0000.000
115A116PRO00.0010.01018.237-0.001-0.0010.0000.0000.0000.000
116A117ILE0-0.013-0.00113.409-0.003-0.0030.0000.0000.0000.000
117A118CYS0-0.0410.00215.7420.0060.0060.0000.0000.0000.000
118A119PRO0-0.020-0.02118.219-0.005-0.0050.0000.0000.0000.000
119A120VAL00.0150.00621.6320.0020.0020.0000.0000.0000.000
120A121ASP-1-0.716-0.82524.6300.0350.0350.0000.0000.0000.000
121A122LEU0-0.003-0.00728.2960.0010.0010.0000.0000.0000.000
122A123VAL00.010-0.00430.864-0.001-0.0010.0000.0000.0000.000
123A124ILE0-0.038-0.01633.8920.0000.0000.0000.0000.0000.000
124A125ASP-1-0.741-0.83337.1790.0230.0230.0000.0000.0000.000
125A126HIS0-0.036-0.02539.599-0.001-0.0010.0000.0000.0000.000
126A127SER0-0.061-0.02142.042-0.001-0.0010.0000.0000.0000.000
127A146GLU-1-0.836-0.92346.7910.0160.0160.0000.0000.0000.000
128A147PHE00.0130.00744.4350.0010.0010.0000.0000.0000.000
129A148GLU-1-0.746-0.88445.6860.0120.0120.0000.0000.0000.000
130A149ARG10.8060.90546.387-0.015-0.0150.0000.0000.0000.000
131A150ASN00.0130.01641.9610.0010.0010.0000.0000.0000.000
132A151ARG10.8660.94541.447-0.011-0.0110.0000.0000.0000.000
133A152GLU-1-0.773-0.87540.1770.0140.0140.0000.0000.0000.000
134A153ARG10.8450.92237.557-0.019-0.0190.0000.0000.0000.000
135A154PHE00.0140.01336.7050.0010.0010.0000.0000.0000.000
136A155GLU-1-0.803-0.90137.2410.0120.0120.0000.0000.0000.000
137A156PHE0-0.0040.00731.0570.0000.0000.0000.0000.0000.000
138A157LEU00.0270.00231.5980.0000.0000.0000.0000.0000.000
139A158LYS10.8290.92932.472-0.012-0.0120.0000.0000.0000.000
140A159TRP0-0.0220.00428.7410.0000.0000.0000.0000.0000.000
141A160GLY00.0530.01629.567-0.001-0.0010.0000.0000.0000.000
142A161SER0-0.059-0.05228.7260.0000.0000.0000.0000.0000.000
143A162LYS10.8920.95429.932-0.011-0.0110.0000.0000.0000.000
144A163ALA0-0.046-0.00528.477-0.001-0.0010.0000.0000.0000.000
145A164PHE0-0.010-0.00523.256-0.002-0.0020.0000.0000.0000.000
146A165ARG10.8580.92118.724-0.010-0.0100.0000.0000.0000.000
147A166ASN00.007-0.00119.550-0.001-0.0010.0000.0000.0000.000
148A167MET00.0080.02923.5140.0020.0020.0000.0000.0000.000
149A168ARG10.8810.94826.237-0.033-0.0330.0000.0000.0000.000
150A169ILE0-0.012-0.01529.0290.0010.0010.0000.0000.0000.000
151A170ILE00.0130.01632.484-0.001-0.0010.0000.0000.0000.000
152A171PRO00.0020.01135.4480.0010.0010.0000.0000.0000.000
153A172PRO00.0280.01638.3460.0000.0000.0000.0000.0000.000
154A173GLY0-0.037-0.01141.655-0.001-0.0010.0000.0000.0000.000
155A174SER00.009-0.00439.9770.0000.0000.0000.0000.0000.000
156A175GLY00.0410.03440.183-0.001-0.0010.0000.0000.0000.000
157A176ILE00.000-0.00140.4170.0010.0010.0000.0000.0000.000
158A177ILE0-0.020-0.00241.9660.0000.0000.0000.0000.0000.000
159A178HIS10.8090.86035.172-0.027-0.0270.0000.0000.0000.000
160A179GLN0-0.004-0.01137.1700.0000.0000.0000.0000.0000.000
161A180VAL00.0200.00636.7400.0010.0010.0000.0000.0000.000
162A181ASN0-0.059-0.04835.6670.0000.0000.0000.0000.0000.000
163A182LEU00.001-0.00832.0330.0010.0010.0000.0000.0000.000
164A183GLU-1-0.822-0.89631.9390.0270.0270.0000.0000.0000.000
165A184TYR0-0.0110.00432.6560.0010.0010.0000.0000.0000.000
166A185LEU0-0.091-0.04329.4630.0010.0010.0000.0000.0000.000
167A186ALA0-0.0020.01428.2240.0030.0030.0000.0000.0000.000
168A187ARG10.7680.86423.750-0.044-0.0440.0000.0000.0000.000
169A188VAL00.0110.01026.446-0.001-0.0010.0000.0000.0000.000
170A189VAL0-0.030-0.01821.9880.0040.0040.0000.0000.0000.000
171A190PHE0-0.015-0.00319.549-0.006-0.0060.0000.0000.0000.000
172A191ASP-1-0.800-0.90320.0820.0580.0580.0000.0000.0000.000
173A192GLN0-0.050-0.03416.858-0.015-0.0150.0000.0000.0000.000
174A193ASP-1-0.843-0.91314.1820.0910.0910.0000.0000.0000.000
175A194GLY00.0050.01214.0230.0270.0270.0000.0000.0000.000
176A195TYR0-0.068-0.0379.9190.0160.0160.0000.0000.0000.000
177A196TYR00.0240.01415.707-0.021-0.0210.0000.0000.0000.000
178A197TYR0-0.031-0.00915.9690.0160.0160.0000.0000.0000.000
179A198PRO00.0540.02818.376-0.011-0.0110.0000.0000.0000.000
180A199ASP-1-0.788-0.87320.3440.0540.0540.0000.0000.0000.000
181A200SER00.0150.00520.3820.0010.0010.0000.0000.0000.000
182A201LEU0-0.046-0.02821.9850.0010.0010.0000.0000.0000.000
183A202VAL00.0490.03422.5750.0010.0010.0000.0000.0000.000
184A203GLY00.0690.01825.077-0.002-0.0020.0000.0000.0000.000
185A204THR0-0.072-0.03427.7600.0010.0010.0000.0000.0000.000
186A205ASP-1-0.745-0.86130.6160.0290.0290.0000.0000.0000.000
187A206SER00.0070.01732.4350.0020.0020.0000.0000.0000.000
188A207HIS0-0.076-0.05234.9630.0000.0000.0000.0000.0000.000
189A208THR0-0.026-0.03028.2420.0000.0000.0000.0000.0000.000
190A209THR00.0260.01531.0080.0010.0010.0000.0000.0000.000
191A210MET0-0.063-0.01132.168-0.001-0.0010.0000.0000.0000.000
192A211ILE0-0.009-0.00629.145-0.001-0.0010.0000.0000.0000.000
193A212ASP-1-0.742-0.86929.0290.0480.0480.0000.0000.0000.000
194A213GLY0-0.003-0.01630.9650.0000.0000.0000.0000.0000.000
195A214LEU0-0.073-0.04931.454-0.002-0.0020.0000.0000.0000.000
196A215GLY00.0090.01629.4830.0010.0010.0000.0000.0000.000
197A216VAL0-0.075-0.04325.6810.0040.0040.0000.0000.0000.000
198A217LEU0-0.0090.00622.950-0.002-0.0020.0000.0000.0000.000
199A218GLY00.039-0.00124.7840.0040.0040.0000.0000.0000.000
200A219TRP00.0290.00323.574-0.002-0.0020.0000.0000.0000.000
201A220GLY00.0010.01027.7410.0010.0010.0000.0000.0000.000
202A221VAL0-0.051-0.03125.1140.0020.0020.0000.0000.0000.000
203A222GLY00.0560.02227.984-0.003-0.0030.0000.0000.0000.000
204A223GLY00.009-0.00727.1770.0010.0010.0000.0000.0000.000
205A224ILE0-0.023-0.00524.349-0.001-0.0010.0000.0000.0000.000
206A225GLU-1-0.808-0.91122.9190.0590.0590.0000.0000.0000.000
207A226ALA00.0140.00922.1920.0020.0020.0000.0000.0000.000
208A227GLH0-0.043-0.08122.370-0.001-0.0010.0000.0000.0000.000
209A228ALA0-0.009-0.00519.380-0.001-0.0010.0000.0000.0000.000
210A229VAL00.0560.02917.7210.0010.0010.0000.0000.0000.000
211A230MET0-0.0370.01217.372-0.003-0.0030.0000.0000.0000.000
212A231LEU0-0.013-0.00317.194-0.006-0.0060.0000.0000.0000.000
213A232GLY0-0.015-0.00213.471-0.004-0.0040.0000.0000.0000.000
214A233GLN00.0030.01113.1760.0130.0130.0000.0000.0000.000
215A234PRO0-0.029-0.01513.318-0.008-0.0080.0000.0000.0000.000
216A235ILE00.0130.01516.2320.0000.0000.0000.0000.0000.000
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