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: K34G3

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 OptH
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 -2027115.930931
FMO2-HF: Nuclear repulsion 1943354.06438
FMO2-HF: Total energy -83761.866551
FMO2-MP2: Total energy -84009.335044


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.
-5.176-4.12.884-1.409-2.5510.003
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 : -0.013 / q_NPA : -0.018
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-1-0.833-0.9323.8160.5761.4160.003-0.301-0.5420.001
4A54LEU0-0.050-0.0196.3090.6270.6270.0000.0000.0000.000
5A55ALA00.0170.0304.2200.2290.298-0.001-0.008-0.0600.000
6A56ARG10.9410.9702.421-3.375-3.2082.882-1.100-1.9490.002
7A57LYS10.9990.9915.583-0.341-0.3410.0000.0000.0000.000
8A58LEU00.0970.0818.9760.0150.0150.0000.0000.0000.000
9A59SER0-0.044-0.0396.032-0.008-0.0080.0000.0000.0000.000
10A60GLN0-0.043-0.0278.016-0.191-0.1910.0000.0000.0000.000
11A61LEU00.0430.0389.908-0.065-0.0650.0000.0000.0000.000
12A62VAL00.0350.01510.782-0.046-0.0460.0000.0000.0000.000
13A63LYS10.8680.93210.597-0.756-0.7560.0000.0000.0000.000
14A64THR00.021-0.00212.566-0.065-0.0650.0000.0000.0000.000
15A65GLU-1-0.681-0.77315.4570.1960.1960.0000.0000.0000.000
16A66LYS10.8410.93114.608-0.357-0.3570.0000.0000.0000.000
17A67GLY0-0.038-0.01317.160-0.028-0.0280.0000.0000.0000.000
18A68VAL00.0410.02718.997-0.019-0.0190.0000.0000.0000.000
19A69LEU00.0240.02320.692-0.014-0.0140.0000.0000.0000.000
20A70ARG10.9530.95818.164-0.246-0.2460.0000.0000.0000.000
21A71ALA0-0.0080.00422.937-0.013-0.0130.0000.0000.0000.000
22A72MET0-0.029-0.01124.356-0.016-0.0160.0000.0000.0000.000
23A73GLU-1-0.885-0.94124.3620.1420.1420.0000.0000.0000.000
24A74VAL0-0.027-0.00127.168-0.009-0.0090.0000.0000.0000.000
25A75VAL0-0.031-0.00529.528-0.009-0.0090.0000.0000.0000.000
26A76ALA00.0090.01331.079-0.008-0.0080.0000.0000.0000.000
27A77SER0-0.003-0.01232.042-0.009-0.0090.0000.0000.0000.000
28A78GLU-1-0.925-0.96733.2420.0940.0940.0000.0000.0000.000
29A79ARG10.8950.95234.222-0.097-0.0970.0000.0000.0000.000
30A80ARG10.9070.96933.064-0.086-0.0860.0000.0000.0000.000
31A81GLU-1-0.938-0.97138.0750.0660.0660.0000.0000.0000.000
32A82ALA0-0.043-0.02239.614-0.004-0.0040.0000.0000.0000.000
33A83ALA0-0.0220.00141.428-0.003-0.0030.0000.0000.0000.000
34A84LYS10.9670.98240.359-0.065-0.0650.0000.0000.0000.000
35A85GLN0-0.009-0.01141.793-0.001-0.0010.0000.0000.0000.000
36A86LEU0-0.0240.00945.548-0.002-0.0020.0000.0000.0000.000
37A87SER00.0500.00647.408-0.003-0.0030.0000.0000.0000.000
38A88LEU0-0.045-0.03947.319-0.002-0.0020.0000.0000.0000.000
39A89TRP0-0.047-0.01349.768-0.001-0.0010.0000.0000.0000.000
40A90GLY00.0180.00251.443-0.001-0.0010.0000.0000.0000.000
41A91ALA0-0.017-0.01153.006-0.002-0.0020.0000.0000.0000.000
42A92ASP-1-1.012-0.99754.8950.0380.0380.0000.0000.0000.000
43A93ASN0-0.055-0.03256.2450.0000.0000.0000.0000.0000.000
44A94ASP-1-0.885-0.93258.7070.0320.0320.0000.0000.0000.000
45A95ASP-1-0.924-0.97459.5350.0300.0300.0000.0000.0000.000
46A96ASP-1-0.832-0.91859.7690.0350.0350.0000.0000.0000.000
47A97VAL0-0.033-0.02254.9160.0010.0010.0000.0000.0000.000
48A98SER0-0.023-0.01055.0870.0020.0020.0000.0000.0000.000
49A99ASP-1-0.758-0.85655.0970.0350.0350.0000.0000.0000.000
50A100VAL0-0.012-0.01352.5810.0010.0010.0000.0000.0000.000
51A101THR0-0.062-0.02949.9780.0030.0030.0000.0000.0000.000
52A102ASP-1-0.888-0.92249.9700.0420.0420.0000.0000.0000.000
53A103LYS10.8640.91449.755-0.033-0.0330.0000.0000.0000.000
54A104LEU0-0.033-0.01747.4220.0020.0020.0000.0000.0000.000
55A105GLY00.0130.01045.8470.0030.0030.0000.0000.0000.000
56A106VAL00.000-0.00244.9750.0020.0020.0000.0000.0000.000
57A107LEU0-0.007-0.00444.2960.0020.0020.0000.0000.0000.000
58A108ILE0-0.028-0.02340.7070.0030.0030.0000.0000.0000.000
59A109TYR0-0.007-0.00540.3180.0060.0060.0000.0000.0000.000
60A110GLU-1-0.854-0.92139.5700.0560.0560.0000.0000.0000.000
61A111LEU0-0.066-0.02437.5450.0040.0040.0000.0000.0000.000
62A112GLY0-0.019-0.00435.6110.0060.0060.0000.0000.0000.000
63A113GLU-1-0.854-0.93434.6860.0690.0690.0000.0000.0000.000
64A114LEU0-0.019-0.02234.7750.0030.0030.0000.0000.0000.000
65A115GLN0-0.051-0.03929.9260.0080.0080.0000.0000.0000.000
66A116ASP-1-0.847-0.95330.3440.1030.1030.0000.0000.0000.000
67A117GLN00.0030.01230.1460.0020.0020.0000.0000.0000.000
68A118PHE0-0.044-0.02726.7420.0020.0020.0000.0000.0000.000
69A119ILE00.0120.00725.3260.0100.0100.0000.0000.0000.000
70A120ASP-1-0.903-0.93225.5270.0880.0880.0000.0000.0000.000
71A121LYS10.9230.95525.745-0.064-0.0640.0000.0000.0000.000
72A122TYR0-0.078-0.10921.0290.0030.0030.0000.0000.0000.000
73A123ASP-1-0.896-0.95020.8120.1590.1590.0000.0000.0000.000
74A124GLN0-0.011-0.01920.5400.0060.0060.0000.0000.0000.000
75A125TYR0-0.023-0.01919.547-0.012-0.0120.0000.0000.0000.000
76A126ARG10.9630.98214.406-0.257-0.2570.0000.0000.0000.000
77A127VAL0-0.082-0.04916.2240.0210.0210.0000.0000.0000.000
78A128THR00.0300.02516.404-0.021-0.0210.0000.0000.0000.000
79A129LEU00.0410.02114.720-0.018-0.0180.0000.0000.0000.000
80A130LYS10.8780.93712.067-0.204-0.2040.0000.0000.0000.000
81A131SER0-0.092-0.05412.233-0.041-0.0410.0000.0000.0000.000
82A132ILE00.0550.02713.368-0.049-0.0490.0000.0000.0000.000
83A133ARG10.9340.9517.264-0.409-0.4090.0000.0000.0000.000
84A134ASN0-0.055-0.0299.327-0.092-0.0920.0000.0000.0000.000
85A135ILE00.0090.02110.688-0.107-0.1070.0000.0000.0000.000
86A136GLU-1-0.867-0.9369.751-0.153-0.1530.0000.0000.0000.000
87A137ALA0-0.077-0.0347.241-0.211-0.2110.0000.0000.0000.000
88A138SER0-0.093-0.0588.438-0.150-0.1500.0000.0000.0000.000
89A139VAL00.0710.03011.605-0.002-0.0020.0000.0000.0000.000
90A140GLN0-0.014-0.0067.1620.0930.0930.0000.0000.0000.000
91A141PRO00.0120.0199.5440.0700.0700.0000.0000.0000.000
92A142SER0-0.066-0.03112.1510.0740.0740.0000.0000.0000.000
93A143ARG10.9180.95512.3650.5470.5470.0000.0000.0000.000
94A144ASP-1-0.827-0.92910.070-1.245-1.2450.0000.0000.0000.000
95A145ARG10.9020.95413.4830.4780.4780.0000.0000.0000.000
96A146LYS10.9801.00016.6500.3550.3550.0000.0000.0000.000
97A147GLU-1-0.943-0.96914.175-0.462-0.4620.0000.0000.0000.000
98A148LYS10.9720.99216.1090.4660.4660.0000.0000.0000.000
99A149ILE00.0160.00718.1930.0350.0350.0000.0000.0000.000
100A150THR0-0.027-0.01820.5610.0410.0410.0000.0000.0000.000
101A151ASP-1-0.886-0.95018.253-0.282-0.2820.0000.0000.0000.000
102A152GLU-1-1.006-1.00821.436-0.248-0.2480.0000.0000.0000.000
103A153ILE0-0.013-0.00223.5800.0250.0250.0000.0000.0000.000
104A154ALA0-0.0270.00024.0800.0180.0180.0000.0000.0000.000
105A155HIS0-0.044-0.02124.3980.0180.0180.0000.0000.0000.000
106A156LEU00.009-0.00126.3460.0130.0130.0000.0000.0000.000
107A157LYS10.8620.89729.2170.1330.1330.0000.0000.0000.000
108A158TYR0-0.073-0.01828.4980.0100.0100.0000.0000.0000.000
109A159LYS10.8970.93528.4710.1260.1260.0000.0000.0000.000
110A160ASP-1-0.901-0.94831.806-0.106-0.1060.0000.0000.0000.000
111A161PRO0-0.0040.00533.777-0.003-0.0030.0000.0000.0000.000
112A162GLN00.0010.00035.2390.0000.0000.0000.0000.0000.000
113A163SER0-0.0110.01232.7910.0020.0020.0000.0000.0000.000
114A164THR00.0450.01035.449-0.002-0.0020.0000.0000.0000.000
115A165LYS10.9460.96627.1390.1770.1770.0000.0000.0000.000
116A166ILE00.0420.02230.733-0.012-0.0120.0000.0000.0000.000
117A167PRO00.0230.03031.430-0.005-0.0050.0000.0000.0000.000
118A168VAL0-0.013-0.00830.276-0.002-0.0020.0000.0000.0000.000
119A169LEU00.0340.01825.710-0.005-0.0050.0000.0000.0000.000
120A170GLU-1-0.835-0.91527.486-0.128-0.1280.0000.0000.0000.000
121A171GLN0-0.039-0.01629.139-0.001-0.0010.0000.0000.0000.000
122A172GLU-1-0.958-1.01023.743-0.240-0.2400.0000.0000.0000.000
123A173LEU00.0230.01823.178-0.015-0.0150.0000.0000.0000.000
124A174VAL0-0.0110.00624.862-0.006-0.0060.0000.0000.0000.000
125A175ARG10.9340.96426.0420.1580.1580.0000.0000.0000.000
126A176ALA00.0450.02920.993-0.006-0.0060.0000.0000.0000.000
127A177GLU-1-0.901-0.96821.375-0.242-0.2420.0000.0000.0000.000
128A178ALA0-0.044-0.01322.8330.0030.0030.0000.0000.0000.000
129A179GLU-1-0.971-0.99620.742-0.247-0.2470.0000.0000.0000.000
130A180SER0-0.0170.00017.409-0.008-0.0080.0000.0000.0000.000
131A181LEU00.0150.00819.5310.0020.0020.0000.0000.0000.000
132A182VAL0-0.0020.01121.7920.0100.0100.0000.0000.0000.000
133A183ALA0-0.012-0.00317.4160.0090.0090.0000.0000.0000.000
134A184GLU-1-0.858-0.93015.964-0.341-0.3410.0000.0000.0000.000
135A185ALA0-0.018-0.01118.5770.0280.0280.0000.0000.0000.000
136A186GLN0-0.033-0.03420.0340.0270.0270.0000.0000.0000.000
137A187LEU00.0310.02513.8330.0190.0190.0000.0000.0000.000
138A188SER0-0.005-0.00717.6770.0380.0380.0000.0000.0000.000
139A189ASN0-0.027-0.01919.8260.0320.0320.0000.0000.0000.000
140A190ILE00.0150.02917.6830.0140.0140.0000.0000.0000.000
141A191THR0-0.023-0.01816.5380.0230.0230.0000.0000.0000.000
142A192ARG10.9520.97718.4410.0570.0570.0000.0000.0000.000
143A193GLU-1-0.925-0.95721.884-0.026-0.0260.0000.0000.0000.000
144A194LYS10.9490.97718.2810.0450.0450.0000.0000.0000.000
145A195LEU00.0000.00418.9370.0160.0160.0000.0000.0000.000
146A196LYS10.9490.97020.655-0.006-0.0060.0000.0000.0000.000
147A197ALA00.004-0.01823.6960.0060.0060.0000.0000.0000.000
148A198ALA0-0.012-0.00120.4530.0060.0060.0000.0000.0000.000
149A199TYR00.005-0.01419.0480.0040.0040.0000.0000.0000.000
150A200SER0-0.0300.00324.090-0.002-0.0020.0000.0000.0000.000
151A201TYR00.0110.02225.420-0.002-0.0020.0000.0000.0000.000
152A202MET00.0020.00423.233-0.002-0.0020.0000.0000.0000.000
153A203PHE00.011-0.01925.9450.0040.0040.0000.0000.0000.000
154A204ASP-1-0.873-0.91828.9000.0490.0490.0000.0000.0000.000
155A205SER0-0.039-0.02428.842-0.002-0.0020.0000.0000.0000.000
156A206LEU0-0.031-0.02028.2380.0010.0010.0000.0000.0000.000
157A207ARG10.8410.92530.741-0.050-0.0500.0000.0000.0000.000
158A208GLU-1-0.874-0.93233.7680.0520.0520.0000.0000.0000.000
159A209LEU0-0.051-0.01531.0650.0000.0000.0000.0000.0000.000
160A210SER0-0.035-0.03333.271-0.001-0.0010.0000.0000.0000.000
161A211GLU-1-0.880-0.94635.8570.0490.0490.0000.0000.0000.000
162A212LYS10.9750.99137.888-0.053-0.0530.0000.0000.0000.000
163A213PHE0-0.023-0.01535.1920.0010.0010.0000.0000.0000.000
164A214ALA0-0.047-0.02039.378-0.002-0.0020.0000.0000.0000.000
165A215LEU0-0.0090.00741.762-0.002-0.0020.0000.0000.0000.000
166A216ILE00.0540.03341.000-0.002-0.0020.0000.0000.0000.000
167A217ALA0-0.031-0.00242.669-0.001-0.0010.0000.0000.0000.000
168A218GLY0-0.026-0.01244.500-0.001-0.0010.0000.0000.0000.000
169A219TYR00.0380.00947.298-0.002-0.0020.0000.0000.0000.000
170A220GLY00.034-0.00147.166-0.001-0.0010.0000.0000.0000.000
171A221LYS10.8780.92748.154-0.047-0.0470.0000.0000.0000.000
172A222ALA00.0110.00750.145-0.001-0.0010.0000.0000.0000.000
173A223LEU00.0270.00550.191-0.002-0.0020.0000.0000.0000.000
174A224LEU0-0.047-0.02449.646-0.001-0.0010.0000.0000.0000.000
175A225GLU-1-0.988-0.98353.7770.0340.0340.0000.0000.0000.000
176A226LEU0-0.071-0.03256.207-0.001-0.0010.0000.0000.0000.000
177A227LEU0-0.049-0.00954.772-0.001-0.0010.0000.0000.0000.000
178A228ASP-1-0.823-0.89258.2080.0320.0320.0000.0000.0000.000
179A229ASP-1-0.950-0.97658.5980.0370.0370.0000.0000.0000.000
180A230SER0-0.069-0.05460.7020.0000.0000.0000.0000.0000.000
181A231PRO0-0.095-0.05263.7420.0000.0000.0000.0000.0000.000
182A232VAL00.0660.04265.504-0.001-0.0010.0000.0000.0000.000
183A233THR0-0.055-0.02567.9950.0010.0010.0000.0000.0000.000
184A234PRO0-0.030-0.03169.5580.0000.0000.0000.0000.0000.000
185A235GLY0-0.015-0.00771.167-0.001-0.0010.0000.0000.0000.000
186A236GLU-1-0.992-0.98573.1530.0230.0230.0000.0000.0000.000
187A237ALA0-0.014-0.00270.2840.0010.0010.0000.0000.0000.000
188A238ARG10.9020.94962.067-0.032-0.0320.0000.0000.0000.000
189A239PRO0-0.019-0.01667.078-0.001-0.0010.0000.0000.0000.000
190A240ALA0-0.0170.00067.7100.0000.0000.0000.0000.0000.000
191A241TYR0-0.009-0.02658.9530.0000.0000.0000.0000.0000.000
192A242ASP-1-0.948-0.98464.8700.0250.0250.0000.0000.0000.000
193A243GLY00.0290.02461.0630.0000.0000.0000.0000.0000.000
194A244TYR00.0210.01059.5860.0010.0010.0000.0000.0000.000
195A245GLU-1-0.976-0.98859.4320.0240.0240.0000.0000.0000.000
196A246ALA00.0120.00359.4990.0000.0000.0000.0000.0000.000
197A247SER00.0320.02255.6100.0010.0010.0000.0000.0000.000
198A248ARG10.9060.94054.867-0.026-0.0260.0000.0000.0000.000
199A249GLN0-0.073-0.04055.1270.0000.0000.0000.0000.0000.000
200A250ILE00.0510.03651.4710.0000.0000.0000.0000.0000.000
201A251ILE0-0.028-0.01049.8880.0010.0010.0000.0000.0000.000
202A252MET00.005-0.00250.4320.0000.0000.0000.0000.0000.000
203A253ASP-1-0.845-0.90551.9960.0310.0310.0000.0000.0000.000
204A254ALA0-0.044-0.02647.1580.0000.0000.0000.0000.0000.000
205A255GLU-1-0.986-0.99846.9470.0340.0340.0000.0000.0000.000
206A256SER00.0230.02147.550-0.001-0.0010.0000.0000.0000.000
207A257ALA0-0.038-0.03147.1050.0000.0000.0000.0000.0000.000
208A258LEU0-0.051-0.03841.5670.0010.0010.0000.0000.0000.000
209A259GLU-1-0.970-0.97143.2140.0320.0320.0000.0000.0000.000
210A260SER0-0.090-0.04644.900-0.001-0.0010.0000.0000.0000.000
211A261TRP0-0.036-0.00836.989-0.001-0.0010.0000.0000.0000.000
212A262THR0-0.026-0.02741.351-0.001-0.0010.0000.0000.0000.000
213A263LEU0-0.041-0.01535.3450.0010.0010.0000.0000.0000.000
214A264ASP-1-0.916-0.95139.2150.0330.0330.0000.0000.0000.000