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: 531JZ

Calculation Name: 3PLT-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3PLT

Chain ID: A

ChEMBL ID:

UniProt ID: Q12230

Base Structure: X-ray

Registration Date: 2023-06-20

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 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2035433.232791
FMO2-HF: Nuclear repulsion 1951669.003107
FMO2-HF: Total energy -83764.229684
FMO2-MP2: Total energy -84011.710677


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:51:GLY)


Summations of interaction energy for fragment #1(A:51:GLY)
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.
-14.857-19.56512.031-3.871-3.4530.031
Interaction energy analysis for fragmet #1(A:51:GLY)
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 : 0.011
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].
3A53GLU-1-0.756-0.8523.8892.1192.896-0.001-0.271-0.5050.000
4A54LEU0-0.029-0.0056.2970.5290.5290.0000.0000.0000.000
5A55ALA00.0580.0425.0250.2280.2280.0000.0000.0000.000
6A56ARG10.7570.8571.948-15.108-20.59312.032-3.600-2.9480.031
7A57LYS11.0020.9916.009-0.627-0.6270.0000.0000.0000.000
8A58LEU00.0880.0569.7020.0020.0020.0000.0000.0000.000
9A59SER0-0.030-0.0316.413-0.077-0.0770.0000.0000.0000.000
10A60GLN0-0.047-0.0258.362-0.033-0.0330.0000.0000.0000.000
11A61LEU00.0500.05510.298-0.072-0.0720.0000.0000.0000.000
12A62VAL00.0430.01411.252-0.036-0.0360.0000.0000.0000.000
13A63LYS10.8830.93710.488-0.672-0.6720.0000.0000.0000.000
14A64THR0-0.015-0.02712.708-0.046-0.0460.0000.0000.0000.000
15A65GLU-1-0.727-0.82615.6700.1760.1760.0000.0000.0000.000
16A66LYS10.8900.95514.663-0.281-0.2810.0000.0000.0000.000
17A67GLY0-0.028-0.00817.686-0.021-0.0210.0000.0000.0000.000
18A68VAL00.0100.00919.492-0.017-0.0170.0000.0000.0000.000
19A69LEU0-0.0240.00020.956-0.013-0.0130.0000.0000.0000.000
20A70ARG10.9780.98220.386-0.160-0.1600.0000.0000.0000.000
21A71ALA0-0.029-0.00623.526-0.010-0.0100.0000.0000.0000.000
22A72MET0-0.030-0.01124.581-0.012-0.0120.0000.0000.0000.000
23A73GLU-1-0.863-0.94223.7520.1150.1150.0000.0000.0000.000
24A74VAL0-0.020-0.00527.345-0.008-0.0080.0000.0000.0000.000
25A75VAL0-0.043-0.02329.629-0.007-0.0070.0000.0000.0000.000
26A76ALA00.0210.01431.073-0.006-0.0060.0000.0000.0000.000
27A77SER0-0.056-0.02632.153-0.008-0.0080.0000.0000.0000.000
28A78GLU-1-0.890-0.94833.2980.0720.0720.0000.0000.0000.000
29A79ARG10.8170.90934.355-0.079-0.0790.0000.0000.0000.000
30A80ARG10.7980.86633.138-0.064-0.0640.0000.0000.0000.000
31A81GLU-1-0.840-0.90438.3490.0460.0460.0000.0000.0000.000
32A82ALA0-0.007-0.00639.819-0.003-0.0030.0000.0000.0000.000
33A83ALA0-0.0160.00241.522-0.002-0.0020.0000.0000.0000.000
34A84LYS10.8370.89540.359-0.050-0.0500.0000.0000.0000.000
35A85GLN0-0.038-0.02941.404-0.001-0.0010.0000.0000.0000.000
36A86LEU0-0.0220.00845.721-0.001-0.0010.0000.0000.0000.000
37A87SER0-0.008-0.01347.596-0.002-0.0020.0000.0000.0000.000
38A88LEU0-0.053-0.04147.235-0.002-0.0020.0000.0000.0000.000
39A89TRP0-0.034-0.00850.029-0.001-0.0010.0000.0000.0000.000
40A90GLY00.0470.01851.786-0.001-0.0010.0000.0000.0000.000
41A91ALA0-0.0310.00253.608-0.002-0.0020.0000.0000.0000.000
42A92ASP-1-0.994-0.99055.5120.0300.0300.0000.0000.0000.000
43A93ASN0-0.070-0.04656.7800.0010.0010.0000.0000.0000.000
44A94ASP-1-0.875-0.92958.8890.0270.0270.0000.0000.0000.000
45A95ASP-1-0.914-0.96159.8430.0250.0250.0000.0000.0000.000
46A96ASP-1-0.821-0.90560.0560.0280.0280.0000.0000.0000.000
47A97VAL0-0.014-0.01455.5500.0010.0010.0000.0000.0000.000
48A98SER0-0.058-0.01555.5490.0010.0010.0000.0000.0000.000
49A99ASP-1-0.736-0.82255.1220.0280.0280.0000.0000.0000.000
50A100VAL00.0170.00553.3690.0010.0010.0000.0000.0000.000
51A101THR0-0.057-0.05050.7150.0020.0020.0000.0000.0000.000
52A102ASP-1-0.861-0.92650.2560.0330.0330.0000.0000.0000.000
53A103LYS10.7970.89849.875-0.027-0.0270.0000.0000.0000.000
54A104LEU0-0.0060.00048.0010.0020.0020.0000.0000.0000.000
55A105GLY00.0230.01646.1040.0030.0030.0000.0000.0000.000
56A106VAL0-0.014-0.01445.1120.0020.0020.0000.0000.0000.000
57A107LEU00.0120.00544.7250.0010.0010.0000.0000.0000.000
58A108ILE0-0.035-0.03041.2380.0030.0030.0000.0000.0000.000
59A109TYR0-0.051-0.04039.9420.0040.0040.0000.0000.0000.000
60A110GLU-1-0.827-0.90839.7300.0440.0440.0000.0000.0000.000
61A111LEU0-0.068-0.02738.2980.0030.0030.0000.0000.0000.000
62A112GLY0-0.019-0.01235.6510.0060.0060.0000.0000.0000.000
63A113GLU-1-0.754-0.86034.8760.0500.0500.0000.0000.0000.000
64A114LEU0-0.018-0.01135.3130.0010.0010.0000.0000.0000.000
65A115GLN00.0020.01330.3800.0030.0030.0000.0000.0000.000
66A116ASP-1-0.785-0.87430.2760.0770.0770.0000.0000.0000.000
67A117GLN00.0000.00630.0870.0000.0000.0000.0000.0000.000
68A118PHE0-0.031-0.01727.1570.0000.0000.0000.0000.0000.000
69A119ILE0-0.002-0.01125.3390.0080.0080.0000.0000.0000.000
70A120ASP-1-0.886-0.94125.3930.0620.0620.0000.0000.0000.000
71A121LYS10.8280.90425.746-0.051-0.0510.0000.0000.0000.000
72A122TYR0-0.027-0.05221.098-0.002-0.0020.0000.0000.0000.000
73A123ASP-1-0.811-0.90719.9220.1290.1290.0000.0000.0000.000
74A124GLN00.0270.02820.6350.0020.0020.0000.0000.0000.000
75A125TYR0-0.024-0.01519.910-0.011-0.0110.0000.0000.0000.000
76A126ARG10.8630.92514.523-0.192-0.1920.0000.0000.0000.000
77A127VAL0-0.086-0.06916.4110.0130.0130.0000.0000.0000.000
78A128THR00.0010.00716.920-0.024-0.0240.0000.0000.0000.000
79A129LEU00.0360.03015.117-0.017-0.0170.0000.0000.0000.000
80A130LYS10.8850.94612.368-0.076-0.0760.0000.0000.0000.000
81A131SER0-0.079-0.05412.486-0.042-0.0420.0000.0000.0000.000
82A132ILE00.0360.02513.760-0.044-0.0440.0000.0000.0000.000
83A133ARG10.9100.9566.922-0.350-0.3500.0000.0000.0000.000
84A134ASN0-0.033-0.0299.129-0.083-0.0830.0000.0000.0000.000
85A135ILE00.0190.02310.660-0.106-0.1060.0000.0000.0000.000
86A136GLU-1-0.862-0.9389.735-0.022-0.0220.0000.0000.0000.000
87A137ALA0-0.054-0.0386.839-0.168-0.1680.0000.0000.0000.000
88A138SER0-0.090-0.0598.173-0.135-0.1350.0000.0000.0000.000
89A139VAL00.0650.03711.506-0.004-0.0040.0000.0000.0000.000
90A140GLN0-0.049-0.0087.4550.2120.2120.0000.0000.0000.000
91A141PRO00.0510.0209.6480.0760.0760.0000.0000.0000.000
92A142SER0-0.066-0.03412.2090.0890.0890.0000.0000.0000.000
93A143ARG10.8400.88411.2260.4140.4140.0000.0000.0000.000
94A144ASP-1-0.805-0.91010.047-1.022-1.0220.0000.0000.0000.000
95A145ARG10.7880.89113.4770.3740.3740.0000.0000.0000.000
96A146LYS10.9010.93216.6610.2420.2420.0000.0000.0000.000
97A147GLU-1-0.930-0.94514.221-0.286-0.2860.0000.0000.0000.000
98A148LYS10.9150.94716.5370.3410.3410.0000.0000.0000.000
99A149ILE0-0.036-0.01518.1700.0290.0290.0000.0000.0000.000
100A150THR0-0.016-0.02120.7300.0330.0330.0000.0000.0000.000
101A151ASP-1-0.864-0.93118.930-0.176-0.1760.0000.0000.0000.000
102A152GLU-1-0.889-0.93721.560-0.202-0.2020.0000.0000.0000.000
103A153ILE0-0.031-0.01423.7320.0190.0190.0000.0000.0000.000
104A154ALA0-0.0060.00424.1650.0150.0150.0000.0000.0000.000
105A155HIS0-0.041-0.02423.6060.0180.0180.0000.0000.0000.000
106A156LEU00.0110.00126.2870.0110.0110.0000.0000.0000.000
107A157LYS10.8330.89729.0660.0980.0980.0000.0000.0000.000
108A158TYR0-0.047-0.01028.0690.0090.0090.0000.0000.0000.000
109A159LYS10.8850.93128.2080.0900.0900.0000.0000.0000.000
110A160ASP-1-0.826-0.89531.891-0.084-0.0840.0000.0000.0000.000
111A161PRO0-0.005-0.00333.684-0.004-0.0040.0000.0000.0000.000
112A162GLN0-0.023-0.00435.1780.0030.0030.0000.0000.0000.000
113A163SER0-0.027-0.02732.769-0.002-0.0020.0000.0000.0000.000
114A164THR0-0.001-0.00934.540-0.004-0.0040.0000.0000.0000.000
115A165LYS10.8980.94826.0730.1630.1630.0000.0000.0000.000
116A166ILE00.0200.02030.588-0.009-0.0090.0000.0000.0000.000
117A167PRO00.0230.00730.913-0.005-0.0050.0000.0000.0000.000
118A168VAL0-0.018-0.00529.507-0.002-0.0020.0000.0000.0000.000
119A169LEU00.0350.01625.035-0.006-0.0060.0000.0000.0000.000
120A170GLU-1-0.816-0.89926.911-0.102-0.1020.0000.0000.0000.000
121A171GLN0-0.036-0.01828.800-0.002-0.0020.0000.0000.0000.000
122A172GLU-1-0.936-0.97823.054-0.215-0.2150.0000.0000.0000.000
123A173LEU00.0060.00622.783-0.012-0.0120.0000.0000.0000.000
124A174VAL00.006-0.00224.513-0.004-0.0040.0000.0000.0000.000
125A175ARG10.9040.96625.6110.1570.1570.0000.0000.0000.000
126A176ALA00.0280.01320.538-0.006-0.0060.0000.0000.0000.000
127A177GLU-1-0.824-0.91020.913-0.176-0.1760.0000.0000.0000.000
128A178ALA0-0.0240.00322.5600.0000.0000.0000.0000.0000.000
129A179GLU-1-0.850-0.93220.587-0.230-0.2300.0000.0000.0000.000
130A180SER0-0.0030.01217.618-0.003-0.0030.0000.0000.0000.000
131A181LEU00.011-0.00419.2710.0030.0030.0000.0000.0000.000
132A182VAL00.0130.00421.7960.0120.0120.0000.0000.0000.000
133A183ALA0-0.0230.00116.9710.0090.0090.0000.0000.0000.000
134A184GLU-1-0.804-0.88215.687-0.249-0.2490.0000.0000.0000.000
135A185ALA0-0.0040.01118.1790.0280.0280.0000.0000.0000.000
136A186GLN0-0.048-0.03420.0060.0250.0250.0000.0000.0000.000
137A187LEU00.0190.01513.6930.0160.0160.0000.0000.0000.000
138A188SER0-0.030-0.02617.6540.0340.0340.0000.0000.0000.000
139A189ASN00.000-0.00119.7800.0300.0300.0000.0000.0000.000
140A190ILE00.0160.01717.6950.0140.0140.0000.0000.0000.000
141A191THR00.0480.00016.0640.0070.0070.0000.0000.0000.000
142A192ARG10.8780.94318.6410.0350.0350.0000.0000.0000.000
143A193GLU-1-0.901-0.95322.214-0.029-0.0290.0000.0000.0000.000
144A194LYS10.8920.95719.0500.0520.0520.0000.0000.0000.000
145A195LEU00.0310.02118.2190.0130.0130.0000.0000.0000.000
146A196LYS10.9610.98520.701-0.018-0.0180.0000.0000.0000.000
147A197ALA0-0.021-0.01623.6490.0040.0040.0000.0000.0000.000
148A198ALA00.0140.00720.7790.0030.0030.0000.0000.0000.000
149A199TYR00.003-0.01519.5320.0080.0080.0000.0000.0000.000
150A200SER0-0.039-0.01024.329-0.001-0.0010.0000.0000.0000.000
151A201TYR0-0.014-0.01025.779-0.002-0.0020.0000.0000.0000.000
152A202MET0-0.0140.01923.531-0.001-0.0010.0000.0000.0000.000
153A203PHE00.021-0.01425.6250.0030.0030.0000.0000.0000.000
154A204ASP-1-0.792-0.89329.0590.0460.0460.0000.0000.0000.000
155A205SER0-0.013-0.01328.870-0.003-0.0030.0000.0000.0000.000
156A206LEU0-0.021-0.01428.1100.0010.0010.0000.0000.0000.000
157A207ARG10.6880.82930.904-0.045-0.0450.0000.0000.0000.000
158A208GLU-1-0.756-0.85234.0780.0450.0450.0000.0000.0000.000
159A209LEU0-0.052-0.01331.486-0.001-0.0010.0000.0000.0000.000
160A210SER0-0.035-0.03833.7600.0000.0000.0000.0000.0000.000
161A211GLU-1-0.873-0.93536.2540.0450.0450.0000.0000.0000.000
162A212LYS10.9060.94537.558-0.044-0.0440.0000.0000.0000.000
163A213PHE00.001-0.01035.5880.0000.0000.0000.0000.0000.000
164A214ALA0-0.048-0.01539.650-0.001-0.0010.0000.0000.0000.000
165A215LEU0-0.0080.00342.125-0.002-0.0020.0000.0000.0000.000
166A216ILE00.0290.01840.879-0.001-0.0010.0000.0000.0000.000
167A217ALA0-0.019-0.00842.746-0.001-0.0010.0000.0000.0000.000
168A218GLY0-0.039-0.01044.700-0.001-0.0010.0000.0000.0000.000
169A219TYR00.0350.00947.351-0.001-0.0010.0000.0000.0000.000
170A220GLY00.0410.01547.299-0.001-0.0010.0000.0000.0000.000
171A221LYS10.9170.94548.318-0.041-0.0410.0000.0000.0000.000
172A222ALA00.0110.00750.267-0.001-0.0010.0000.0000.0000.000
173A223LEU00.0110.00450.104-0.001-0.0010.0000.0000.0000.000
174A224LEU0-0.031-0.01649.9600.0000.0000.0000.0000.0000.000
175A225GLU-1-0.986-0.98554.1580.0310.0310.0000.0000.0000.000
176A226LEU0-0.065-0.02256.707-0.001-0.0010.0000.0000.0000.000
177A227LEU0-0.048-0.01755.241-0.001-0.0010.0000.0000.0000.000
178A228ASP-1-0.798-0.86458.5150.0280.0280.0000.0000.0000.000
179A229ASP-1-0.925-0.95959.0320.0320.0320.0000.0000.0000.000
180A230SER0-0.074-0.06261.0500.0000.0000.0000.0000.0000.000
181A231PRO0-0.076-0.04764.3730.0000.0000.0000.0000.0000.000
182A232VAL00.0340.02466.000-0.001-0.0010.0000.0000.0000.000
183A233THR0-0.010-0.00568.6100.0010.0010.0000.0000.0000.000
184A234PRO0-0.039-0.03669.7860.0000.0000.0000.0000.0000.000
185A235GLY0-0.018-0.00471.577-0.001-0.0010.0000.0000.0000.000
186A236GLU-1-0.999-0.98572.9250.0200.0200.0000.0000.0000.000
187A237ALA0-0.016-0.01170.1350.0010.0010.0000.0000.0000.000
188A238ARG10.8410.90562.810-0.027-0.0270.0000.0000.0000.000
189A239PRO0-0.029-0.01867.239-0.001-0.0010.0000.0000.0000.000
190A240ALA0-0.017-0.00367.6800.0000.0000.0000.0000.0000.000
191A241TYR0-0.014-0.02358.9900.0000.0000.0000.0000.0000.000
192A242ASP-1-0.927-0.98064.8270.0200.0200.0000.0000.0000.000
193A243GLY00.0280.02061.0280.0000.0000.0000.0000.0000.000
194A244TYR00.0020.01059.8020.0000.0000.0000.0000.0000.000
195A245GLU-1-0.819-0.87559.5520.0200.0200.0000.0000.0000.000
196A246ALA00.0080.00559.3280.0000.0000.0000.0000.0000.000
197A247SER0-0.006-0.03355.5640.0010.0010.0000.0000.0000.000
198A248ARG10.7900.86254.702-0.020-0.0200.0000.0000.0000.000
199A249GLN0-0.088-0.05655.058-0.001-0.0010.0000.0000.0000.000
200A250ILE00.0440.01951.8000.0000.0000.0000.0000.0000.000
201A251ILE0-0.012-0.00349.8180.0010.0010.0000.0000.0000.000
202A252MET0-0.009-0.00150.5210.0000.0000.0000.0000.0000.000
203A253ASP-1-0.876-0.92651.9730.0260.0260.0000.0000.0000.000
204A254ALA0-0.033-0.02547.2850.0010.0010.0000.0000.0000.000
205A255GLU-1-0.962-0.98047.0980.0270.0270.0000.0000.0000.000
206A256SER00.021-0.00447.3410.0000.0000.0000.0000.0000.000
207A257ALA0-0.0380.00147.3430.0000.0000.0000.0000.0000.000
208A258LEU0-0.067-0.04541.6990.0020.0020.0000.0000.0000.000
209A259GLU-1-0.959-0.95943.5120.0230.0230.0000.0000.0000.000
210A260SER0-0.095-0.06745.366-0.001-0.0010.0000.0000.0000.000
211A261TRP0-0.022-0.02037.0880.0000.0000.0000.0000.0000.000
212A262THR0-0.028-0.02541.356-0.002-0.0020.0000.0000.0000.000
213A263LEU0-0.035-0.00435.3070.0010.0010.0000.0000.0000.000
214A264ASP-1-0.886-0.90239.0340.0330.0330.0000.0000.0000.000