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: 431JN

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 OptHSide
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 -2029704.328197
FMO2-HF: Nuclear repulsion 1945940.855107
FMO2-HF: Total energy -83763.47309
FMO2-MP2: Total energy -84010.952756


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.
-14.227-19.74413.275-4.197-3.5610.032
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 : -0.003 / q_NPA : 0.007
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-1-0.774-0.8823.8161.6812.4690.003-0.297-0.4940.001
4A54LEU0-0.027-0.0086.3090.5540.5540.0000.0000.0000.000
5A55ALA00.0230.0294.2990.1820.245-0.001-0.006-0.0550.000
6A56ARG10.8300.8861.940-13.970-20.33813.273-3.894-3.0120.031
7A57LYS11.0040.9895.576-0.616-0.6160.0000.0000.0000.000
8A58LEU00.0980.0698.973-0.006-0.0060.0000.0000.0000.000
9A59SER0-0.037-0.0296.067-0.083-0.0830.0000.0000.0000.000
10A60GLN0-0.054-0.0307.960-0.056-0.0560.0000.0000.0000.000
11A61LEU00.0520.0449.906-0.064-0.0640.0000.0000.0000.000
12A62VAL00.0410.01510.759-0.046-0.0460.0000.0000.0000.000
13A63LYS10.8830.93910.444-0.633-0.6330.0000.0000.0000.000
14A64THR0-0.025-0.02312.567-0.047-0.0470.0000.0000.0000.000
15A65GLU-1-0.717-0.81915.4500.1630.1630.0000.0000.0000.000
16A66LYS10.8770.94614.464-0.256-0.2560.0000.0000.0000.000
17A67GLY0-0.036-0.01317.154-0.024-0.0240.0000.0000.0000.000
18A68VAL00.0320.02018.999-0.016-0.0160.0000.0000.0000.000
19A69LEU00.0090.01620.695-0.013-0.0130.0000.0000.0000.000
20A70ARG10.9460.96019.587-0.159-0.1590.0000.0000.0000.000
21A71ALA0-0.027-0.00322.940-0.011-0.0110.0000.0000.0000.000
22A72MET0-0.029-0.01424.211-0.012-0.0120.0000.0000.0000.000
23A73GLU-1-0.857-0.93523.8420.1040.1040.0000.0000.0000.000
24A74VAL0-0.0160.00327.177-0.007-0.0070.0000.0000.0000.000
25A75VAL0-0.032-0.00729.529-0.007-0.0070.0000.0000.0000.000
26A76ALA00.0130.02131.074-0.006-0.0060.0000.0000.0000.000
27A77SER0-0.002-0.00632.045-0.007-0.0070.0000.0000.0000.000
28A78GLU-1-0.921-0.96733.0880.0710.0710.0000.0000.0000.000
29A79ARG10.8520.92633.883-0.078-0.0780.0000.0000.0000.000
30A80ARG10.7950.86533.165-0.060-0.0600.0000.0000.0000.000
31A81GLU-1-0.841-0.90938.0940.0450.0450.0000.0000.0000.000
32A82ALA0-0.036-0.02139.621-0.003-0.0030.0000.0000.0000.000
33A83ALA0-0.0140.00641.432-0.002-0.0020.0000.0000.0000.000
34A84LYS10.8450.90340.209-0.048-0.0480.0000.0000.0000.000
35A85GLN0-0.026-0.01741.471-0.001-0.0010.0000.0000.0000.000
36A86LEU0-0.0170.00545.553-0.001-0.0010.0000.0000.0000.000
37A87SER00.0340.01047.411-0.002-0.0020.0000.0000.0000.000
38A88LEU0-0.036-0.03447.256-0.002-0.0020.0000.0000.0000.000
39A89TRP0-0.044-0.01649.767-0.001-0.0010.0000.0000.0000.000
40A90GLY00.0250.00251.444-0.001-0.0010.0000.0000.0000.000
41A91ALA0-0.026-0.01653.011-0.001-0.0010.0000.0000.0000.000
42A92ASP-1-1.012-0.99454.8980.0290.0290.0000.0000.0000.000
43A93ASN0-0.074-0.04456.5730.0010.0010.0000.0000.0000.000
44A94ASP-1-0.870-0.92458.7090.0260.0260.0000.0000.0000.000
45A95ASP-1-0.927-0.96959.5370.0240.0240.0000.0000.0000.000
46A96ASP-1-0.819-0.91759.7710.0280.0280.0000.0000.0000.000
47A97VAL0-0.015-0.00754.9900.0010.0010.0000.0000.0000.000
48A98SER00.0200.01955.0890.0010.0010.0000.0000.0000.000
49A99ASP-1-0.780-0.83755.0990.0260.0260.0000.0000.0000.000
50A100VAL00.0150.00052.7560.0010.0010.0000.0000.0000.000
51A101THR0-0.077-0.04150.0950.0020.0020.0000.0000.0000.000
52A102ASP-1-0.875-0.93049.9720.0310.0310.0000.0000.0000.000
53A103LYS10.8200.89549.757-0.026-0.0260.0000.0000.0000.000
54A104LEU0-0.034-0.01847.5130.0020.0020.0000.0000.0000.000
55A105GLY00.0120.01045.8490.0030.0030.0000.0000.0000.000
56A106VAL0-0.004-0.00544.9770.0010.0010.0000.0000.0000.000
57A107LEU0-0.0010.00044.2980.0020.0020.0000.0000.0000.000
58A108ILE0-0.028-0.02640.8020.0030.0030.0000.0000.0000.000
59A109TYR0-0.006-0.00439.7340.0040.0040.0000.0000.0000.000
60A110GLU-1-0.871-0.92539.5720.0400.0400.0000.0000.0000.000
61A111LEU0-0.049-0.01837.6230.0030.0030.0000.0000.0000.000
62A112GLY0-0.024-0.00335.6110.0050.0050.0000.0000.0000.000
63A113GLU-1-0.774-0.88434.6880.0470.0470.0000.0000.0000.000
64A114LEU0-0.018-0.02034.7770.0020.0020.0000.0000.0000.000
65A115GLN0-0.025-0.01730.0480.0040.0040.0000.0000.0000.000
66A116ASP-1-0.784-0.88430.3430.0720.0720.0000.0000.0000.000
67A117GLN00.0040.01230.148-0.001-0.0010.0000.0000.0000.000
68A118PHE0-0.034-0.02326.9080.0010.0010.0000.0000.0000.000
69A119ILE00.000-0.00825.3290.0080.0080.0000.0000.0000.000
70A120ASP-1-0.893-0.92925.5280.0530.0530.0000.0000.0000.000
71A121LYS10.8690.93425.747-0.045-0.0450.0000.0000.0000.000
72A122TYR0-0.030-0.05220.887-0.003-0.0030.0000.0000.0000.000
73A123ASP-1-0.854-0.92220.3980.1010.1010.0000.0000.0000.000
74A124GLN00.0140.01220.5410.0030.0030.0000.0000.0000.000
75A125TYR0-0.019-0.01819.646-0.012-0.0120.0000.0000.0000.000
76A126ARG10.9120.95214.800-0.156-0.1560.0000.0000.0000.000
77A127VAL0-0.079-0.05016.2240.0070.0070.0000.0000.0000.000
78A128THR00.0290.02416.404-0.025-0.0250.0000.0000.0000.000
79A129LEU00.0550.04314.781-0.021-0.0210.0000.0000.0000.000
80A130LYS10.8800.94312.030-0.067-0.0670.0000.0000.0000.000
81A131SER0-0.115-0.08212.232-0.048-0.0480.0000.0000.0000.000
82A132ILE00.0440.01713.585-0.049-0.0490.0000.0000.0000.000
83A133ARG10.9210.9666.896-0.218-0.2180.0000.0000.0000.000
84A134ASN0-0.052-0.0419.324-0.117-0.1170.0000.0000.0000.000
85A135ILE00.0100.01810.688-0.107-0.1070.0000.0000.0000.000
86A136GLU-1-0.849-0.9269.761-0.121-0.1210.0000.0000.0000.000
87A137ALA0-0.078-0.0427.199-0.190-0.1900.0000.0000.0000.000
88A138SER0-0.090-0.0568.435-0.131-0.1310.0000.0000.0000.000
89A139VAL00.0650.03011.6070.0080.0080.0000.0000.0000.000
90A140GLN0-0.0300.0017.3080.1950.1950.0000.0000.0000.000
91A141PRO00.0400.0359.6870.0810.0810.0000.0000.0000.000
92A142SER0-0.083-0.04512.1570.0820.0820.0000.0000.0000.000
93A143ARG10.8550.89311.2200.4900.4900.0000.0000.0000.000
94A144ASP-1-0.806-0.91910.118-1.071-1.0710.0000.0000.0000.000
95A145ARG10.8120.91013.4900.4050.4050.0000.0000.0000.000
96A146LYS10.8900.93516.6570.2640.2640.0000.0000.0000.000
97A147GLU-1-0.923-0.95314.151-0.305-0.3050.0000.0000.0000.000
98A148LYS10.9100.95116.6110.3450.3450.0000.0000.0000.000
99A149ILE0-0.016-0.01418.2770.0310.0310.0000.0000.0000.000
100A150THR0-0.022-0.02020.6990.0340.0340.0000.0000.0000.000
101A151ASP-1-0.876-0.94318.716-0.181-0.1810.0000.0000.0000.000
102A152GLU-1-0.914-0.96221.545-0.205-0.2050.0000.0000.0000.000
103A153ILE0-0.019-0.00323.6570.0190.0190.0000.0000.0000.000
104A154ALA0-0.0160.00924.1690.0150.0150.0000.0000.0000.000
105A155HIS0-0.044-0.02324.1450.0160.0160.0000.0000.0000.000
106A156LEU0-0.002-0.00226.4350.0100.0100.0000.0000.0000.000
107A157LYS10.8400.89929.2950.0990.0990.0000.0000.0000.000
108A158TYR0-0.056-0.01528.3810.0090.0090.0000.0000.0000.000
109A159LYS10.8960.93528.3840.0870.0870.0000.0000.0000.000
110A160ASP-1-0.835-0.90731.887-0.086-0.0860.0000.0000.0000.000
111A161PRO00.0040.00733.848-0.003-0.0030.0000.0000.0000.000
112A162GLN0-0.024-0.01035.3280.0000.0000.0000.0000.0000.000
113A163SER0-0.021-0.01333.425-0.001-0.0010.0000.0000.0000.000
114A164THR00.001-0.00635.506-0.002-0.0020.0000.0000.0000.000
115A165LYS10.9100.95626.3920.1600.1600.0000.0000.0000.000
116A166ILE00.0370.01930.792-0.010-0.0100.0000.0000.0000.000
117A167PRO00.0230.01931.516-0.004-0.0040.0000.0000.0000.000
118A168VAL0-0.0010.00430.071-0.002-0.0020.0000.0000.0000.000
119A169LEU00.0260.01425.472-0.005-0.0050.0000.0000.0000.000
120A170GLU-1-0.838-0.92027.493-0.101-0.1010.0000.0000.0000.000
121A171GLN0-0.034-0.01629.147-0.002-0.0020.0000.0000.0000.000
122A172GLU-1-0.959-1.00223.580-0.214-0.2140.0000.0000.0000.000
123A173LEU00.0310.01822.990-0.015-0.0150.0000.0000.0000.000
124A174VAL0-0.0060.00524.862-0.005-0.0050.0000.0000.0000.000
125A175ARG10.9360.96726.1020.1490.1490.0000.0000.0000.000
126A176ALA00.0380.02221.019-0.006-0.0060.0000.0000.0000.000
127A177GLU-1-0.811-0.91021.381-0.191-0.1910.0000.0000.0000.000
128A178ALA0-0.042-0.01222.8330.0020.0020.0000.0000.0000.000
129A179GLU-1-0.907-0.95420.769-0.248-0.2480.0000.0000.0000.000
130A180SER00.0010.01017.833-0.003-0.0030.0000.0000.0000.000
131A181LEU00.0180.00819.5310.0020.0020.0000.0000.0000.000
132A182VAL00.0060.01021.7860.0080.0080.0000.0000.0000.000
133A183ALA0-0.005-0.00117.4170.0070.0070.0000.0000.0000.000
134A184GLU-1-0.815-0.89015.836-0.282-0.2820.0000.0000.0000.000
135A185ALA0-0.018-0.00918.5710.0250.0250.0000.0000.0000.000
136A186GLN0-0.047-0.03419.9930.0280.0280.0000.0000.0000.000
137A187LEU00.0310.02413.8950.0130.0130.0000.0000.0000.000
138A188SER0-0.021-0.01117.6720.0320.0320.0000.0000.0000.000
139A189ASN0-0.008-0.01519.8200.0290.0290.0000.0000.0000.000
140A190ILE00.0260.03517.8160.0100.0100.0000.0000.0000.000
141A191THR00.002-0.01115.9190.0100.0100.0000.0000.0000.000
142A192ARG10.9180.96018.4360.0500.0500.0000.0000.0000.000
143A193GLU-1-0.930-0.95421.879-0.035-0.0350.0000.0000.0000.000
144A194LYS10.9570.97618.3350.0740.0740.0000.0000.0000.000
145A195LEU00.0030.00218.4460.0140.0140.0000.0000.0000.000
146A196LYS10.9410.96920.651-0.005-0.0050.0000.0000.0000.000
147A197ALA0-0.009-0.02323.6600.0060.0060.0000.0000.0000.000
148A198ALA0-0.0020.00320.4600.0050.0050.0000.0000.0000.000
149A199TYR0-0.005-0.01519.2280.0040.0040.0000.0000.0000.000
150A200SER0-0.040-0.00524.086-0.001-0.0010.0000.0000.0000.000
151A201TYR0-0.016-0.00725.480-0.001-0.0010.0000.0000.0000.000
152A202MET0-0.0030.00623.2030.0000.0000.0000.0000.0000.000
153A203PHE00.021-0.01525.5960.0040.0040.0000.0000.0000.000
154A204ASP-1-0.815-0.90228.8980.0380.0380.0000.0000.0000.000
155A205SER0-0.027-0.00928.819-0.002-0.0020.0000.0000.0000.000
156A206LEU0-0.029-0.02027.9760.0010.0010.0000.0000.0000.000
157A207ARG10.7420.85430.740-0.038-0.0380.0000.0000.0000.000
158A208GLU-1-0.786-0.87033.7540.0380.0380.0000.0000.0000.000
159A209LEU0-0.046-0.01331.1850.0000.0000.0000.0000.0000.000
160A210SER0-0.044-0.04333.3580.0000.0000.0000.0000.0000.000
161A211GLU-1-0.888-0.94535.8560.0410.0410.0000.0000.0000.000
162A212LYS10.9060.94637.788-0.039-0.0390.0000.0000.0000.000
163A213PHE0-0.017-0.01635.3310.0010.0010.0000.0000.0000.000
164A214ALA0-0.049-0.01939.377-0.001-0.0010.0000.0000.0000.000
165A215LEU0-0.0060.00841.761-0.001-0.0010.0000.0000.0000.000
166A216ILE00.0550.03240.784-0.001-0.0010.0000.0000.0000.000
167A217ALA0-0.0290.00042.587-0.001-0.0010.0000.0000.0000.000
168A218GLY0-0.023-0.01044.499-0.001-0.0010.0000.0000.0000.000
169A219TYR00.0440.01047.141-0.001-0.0010.0000.0000.0000.000
170A220GLY00.023-0.00347.166-0.001-0.0010.0000.0000.0000.000
171A221LYS10.8830.92548.154-0.040-0.0400.0000.0000.0000.000
172A222ALA00.0290.01250.144-0.001-0.0010.0000.0000.0000.000
173A223LEU00.0130.00850.015-0.001-0.0010.0000.0000.0000.000
174A224LEU0-0.046-0.02549.5300.0000.0000.0000.0000.0000.000
175A225GLU-1-0.985-0.98053.7770.0300.0300.0000.0000.0000.000
176A226LEU0-0.083-0.03456.508-0.001-0.0010.0000.0000.0000.000
177A227LEU0-0.038-0.00555.072-0.001-0.0010.0000.0000.0000.000
178A228ASP-1-0.795-0.85658.2080.0270.0270.0000.0000.0000.000
179A229ASP-1-0.935-0.96758.6050.0320.0320.0000.0000.0000.000
180A230SER0-0.060-0.05460.7020.0000.0000.0000.0000.0000.000
181A231PRO0-0.085-0.04863.8320.0000.0000.0000.0000.0000.000
182A232VAL00.0500.03465.504-0.001-0.0010.0000.0000.0000.000
183A233THR0-0.042-0.01867.9960.0010.0010.0000.0000.0000.000
184A234PRO0-0.025-0.02969.4040.0000.0000.0000.0000.0000.000
185A235GLY0-0.021-0.01071.169-0.001-0.0010.0000.0000.0000.000
186A236GLU-1-0.995-0.98773.1540.0190.0190.0000.0000.0000.000
187A237ALA0-0.014-0.00470.2850.0010.0010.0000.0000.0000.000
188A238ARG10.8350.89862.184-0.027-0.0270.0000.0000.0000.000
189A239PRO0-0.024-0.02067.148-0.001-0.0010.0000.0000.0000.000
190A240ALA0-0.022-0.00367.7120.0000.0000.0000.0000.0000.000
191A241TYR00.010-0.00958.7960.0000.0000.0000.0000.0000.000
192A242ASP-1-0.939-0.98364.7880.0190.0190.0000.0000.0000.000
193A243GLY00.0180.01661.0640.0000.0000.0000.0000.0000.000
194A244TYR00.0160.01159.5610.0000.0000.0000.0000.0000.000
195A245GLU-1-0.861-0.91659.4330.0180.0180.0000.0000.0000.000
196A246ALA0-0.001-0.00559.5550.0000.0000.0000.0000.0000.000
197A247SER00.022-0.01355.5060.0000.0000.0000.0000.0000.000
198A248ARG10.8110.88654.868-0.019-0.0190.0000.0000.0000.000
199A249GLN0-0.078-0.05255.128-0.001-0.0010.0000.0000.0000.000
200A250ILE00.0440.02851.4140.0000.0000.0000.0000.0000.000
201A251ILE0-0.023-0.00949.6220.0010.0010.0000.0000.0000.000
202A252MET00.0050.00450.4330.0000.0000.0000.0000.0000.000
203A253ASP-1-0.865-0.91451.9970.0240.0240.0000.0000.0000.000
204A254ALA0-0.036-0.02347.1580.0000.0000.0000.0000.0000.000
205A255GLU-1-0.976-0.99346.9480.0240.0240.0000.0000.0000.000
206A256SER00.0120.01747.551-0.001-0.0010.0000.0000.0000.000
207A257ALA0-0.019-0.01247.1280.0000.0000.0000.0000.0000.000
208A258LEU0-0.055-0.04441.5650.0010.0010.0000.0000.0000.000
209A259GLU-1-0.978-0.97243.2150.0200.0200.0000.0000.0000.000
210A260SER0-0.091-0.05744.900-0.001-0.0010.0000.0000.0000.000
211A261TRP0-0.027-0.01736.903-0.001-0.0010.0000.0000.0000.000
212A262THR0-0.023-0.02241.348-0.002-0.0020.0000.0000.0000.000
213A263LEU0-0.037-0.01135.2560.0010.0010.0000.0000.0000.000
214A264ASP-1-0.877-0.89938.7860.0280.0280.0000.0000.0000.000