Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

tag_button

FMODB ID: 53KRZ

Calculation Name: 4TR4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4TR4

Chain ID: A

ChEMBL ID:

UniProt ID: Q91ZI8

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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2015603.664183
FMO2-HF: Nuclear repulsion 1941314.361135
FMO2-HF: Total energy -74289.303048
FMO2-MP2: Total energy -74505.129167


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:114:GLY)


Summations of interaction energy for fragment #1(A:114: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.
0.9193.0780.602-0.948-1.8110
Interaction energy analysis for fragmet #1(A:114:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.007 / q_NPA : -0.005
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].
3A116ASP-1-0.771-0.8763.797-0.8170.049-0.009-0.276-0.5810.001
4A117PRO0-0.030-0.0206.5290.3300.3300.0000.0000.0000.000
5A118PHE0-0.041-0.0289.0940.1960.1960.0000.0000.0000.000
6A119THR0-0.051-0.0199.7500.1490.1490.0000.0000.0000.000
7A120GLY0-0.022-0.0079.0160.1470.1470.0000.0000.0000.000
8A121GLN00.012-0.0118.3660.1250.1250.0000.0000.0000.000
9A122LYS10.8280.9113.7511.0921.2810.001-0.063-0.1280.000
10A123LEU00.0130.0002.5120.4581.3350.611-0.568-0.919-0.001
11A124ASP-1-0.854-0.9275.018-0.979-0.904-0.001-0.005-0.0680.000
12A125PHE0-0.029-0.0123.925-0.0450.1070.000-0.036-0.1150.000
13A126PHE0-0.0310.0008.9710.1980.1980.0000.0000.0000.000
14A127LYS10.8980.95412.0060.2370.2370.0000.0000.0000.000
15A128GLN00.0200.00415.3120.0390.0390.0000.0000.0000.000
16A129ALA00.0580.03218.2080.0180.0180.0000.0000.0000.000
17A130HIS0-0.015-0.01620.0070.0090.0090.0000.0000.0000.000
18A131GLU-1-0.796-0.88923.773-0.107-0.1070.0000.0000.0000.000
19A132GLY0-0.023-0.01126.349-0.003-0.0030.0000.0000.0000.000
20A133GLY00.0000.00922.3780.0020.0020.0000.0000.0000.000
21A134PRO0-0.023-0.01718.9310.0120.0120.0000.0000.0000.000
22A135ALA00.007-0.00221.225-0.019-0.0190.0000.0000.0000.000
23A136PRO0-0.0040.00818.4150.0070.0070.0000.0000.0000.000
24A137ASN00.0680.04319.2820.0120.0120.0000.0000.0000.000
25A138SER0-0.006-0.01818.9810.0030.0030.0000.0000.0000.000
26A139GLU-1-0.916-0.95219.689-0.079-0.0790.0000.0000.0000.000
27A140VAL00.0020.00821.479-0.014-0.0140.0000.0000.0000.000
28A141VAL00.0000.00425.0000.0080.0080.0000.0000.0000.000
29A142ARG10.9821.00727.7040.0270.0270.0000.0000.0000.000
30A143PRO00.0540.01231.2070.0020.0020.0000.0000.0000.000
31A144ASP-1-0.934-0.96933.771-0.032-0.0320.0000.0000.0000.000
32A145GLY0-0.033-0.02534.2790.0020.0020.0000.0000.0000.000
33A146PHE0-0.056-0.02329.4670.0020.0020.0000.0000.0000.000
34A147GLN00.0170.00928.760-0.004-0.0040.0000.0000.0000.000
35A148SER0-0.041-0.02322.981-0.005-0.0050.0000.0000.0000.000
36A149GLN00.0610.07225.3900.0040.0040.0000.0000.0000.000
37A150ARG10.8830.92717.9020.0830.0830.0000.0000.0000.000
38A151ILE00.0080.01223.6180.0090.0090.0000.0000.0000.000
39A152LEU0-0.017-0.02723.0450.0070.0070.0000.0000.0000.000
40A153ASP-1-0.869-0.91626.121-0.040-0.0400.0000.0000.0000.000
41A154TYR0-0.084-0.10128.1860.0070.0070.0000.0000.0000.000
42A155ALA0-0.0290.00529.3960.0000.0000.0000.0000.0000.000
43A156GLN0-0.032-0.01831.0940.0090.0090.0000.0000.0000.000
44A157GLY0-0.006-0.01233.2270.0010.0010.0000.0000.0000.000
45A158THR0-0.016-0.01632.574-0.004-0.0040.0000.0000.0000.000
46A159ARG10.7750.86634.5740.0380.0380.0000.0000.0000.000
47A160PRO0-0.025-0.00433.378-0.003-0.0030.0000.0000.0000.000
48A161LEU00.0080.01329.1780.0040.0040.0000.0000.0000.000
49A162VAL0-0.015-0.01631.574-0.007-0.0070.0000.0000.0000.000
50A163LEU0-0.018-0.00326.7340.0030.0030.0000.0000.0000.000
51A164ASN00.002-0.00730.964-0.007-0.0070.0000.0000.0000.000
52A165PHE00.0310.01725.0600.0030.0030.0000.0000.0000.000
53A166GLY00.048-0.00530.1940.0000.0000.0000.0000.0000.000
54A167SER0-0.0040.01632.0710.0030.0030.0000.0000.0000.000
55A168CYS00.048-0.01333.9980.0020.0020.0000.0000.0000.000
56A169THR0-0.057-0.03535.3260.0010.0010.0000.0000.0000.000
57A170CYS00.0110.03033.999-0.002-0.0020.0000.0000.0000.000
58A171PRO00.028-0.00136.1260.0030.0030.0000.0000.0000.000
59A172PRO00.0450.01936.3890.0040.0040.0000.0000.0000.000
60A173PHE00.0070.00534.1600.0030.0030.0000.0000.0000.000
61A174MET0-0.0190.01537.0510.0030.0030.0000.0000.0000.000
62A175ALA0-0.042-0.01240.2670.0040.0040.0000.0000.0000.000
63A176ARG10.7870.88833.4930.0970.0970.0000.0000.0000.000
64A177MET00.0630.04737.5170.0020.0020.0000.0000.0000.000
65A178SER00.006-0.00941.2270.0020.0020.0000.0000.0000.000
66A179ALA0-0.024-0.02142.8120.0020.0020.0000.0000.0000.000
67A180PHE00.0290.00935.9530.0010.0010.0000.0000.0000.000
68A181GLN00.0530.01439.7990.0030.0030.0000.0000.0000.000
69A182ARG10.9150.95242.9870.0490.0490.0000.0000.0000.000
70A183LEU0-0.046-0.01939.9210.0020.0020.0000.0000.0000.000
71A184VAL00.0630.04839.7030.0010.0010.0000.0000.0000.000
72A185THR0-0.022-0.01242.1100.0030.0030.0000.0000.0000.000
73A186LYS10.8640.94045.2360.0440.0440.0000.0000.0000.000
74A187TYR00.024-0.01241.6540.0010.0010.0000.0000.0000.000
75A188GLN00.0640.04841.5610.0000.0000.0000.0000.0000.000
76A189ARG10.8870.96142.3990.0310.0310.0000.0000.0000.000
77A190ASP-1-0.819-0.89041.300-0.034-0.0340.0000.0000.0000.000
78A191VAL0-0.025-0.00236.507-0.002-0.0020.0000.0000.0000.000
79A192ASP-1-0.772-0.84635.082-0.042-0.0420.0000.0000.0000.000
80A193PHE00.005-0.01235.194-0.005-0.0050.0000.0000.0000.000
81A194LEU0-0.023-0.00429.5310.0040.0040.0000.0000.0000.000
82A195ILE0-0.019-0.01632.666-0.005-0.0050.0000.0000.0000.000
83A196ILE0-0.014-0.00526.6340.0030.0030.0000.0000.0000.000
84A197TYR0-0.013-0.02930.105-0.003-0.0030.0000.0000.0000.000
85A198ILE0-0.049-0.02726.925-0.003-0.0030.0000.0000.0000.000
86A199GLU-1-0.925-0.96725.989-0.152-0.1520.0000.0000.0000.000
87A200GLU-1-0.709-0.82328.693-0.085-0.0850.0000.0000.0000.000
88A201ALA0-0.047-0.01931.050-0.008-0.0080.0000.0000.0000.000
89A202HIS0-0.039-0.02632.682-0.004-0.0040.0000.0000.0000.000
90A203PRO00.0290.02932.2310.0070.0070.0000.0000.0000.000
91A204SER00.005-0.02635.2080.0010.0010.0000.0000.0000.000
92A205ASP-1-0.929-0.96034.698-0.082-0.0820.0000.0000.0000.000
93A206GLY00.0210.02834.156-0.004-0.0040.0000.0000.0000.000
94A207TRP0-0.031-0.02231.8670.0060.0060.0000.0000.0000.000
95A208VAL0-0.039-0.02235.7470.0050.0050.0000.0000.0000.000
96A209THR0-0.0060.00037.8990.0010.0010.0000.0000.0000.000
97A210THR00.0050.00739.0260.0010.0010.0000.0000.0000.000
98A211ASP-1-0.924-0.96041.133-0.061-0.0610.0000.0000.0000.000
99A212SER0-0.007-0.00439.7900.0020.0020.0000.0000.0000.000
100A213PRO0-0.022-0.02042.4350.0020.0020.0000.0000.0000.000
101A214TYR0-0.041-0.01240.3100.0030.0030.0000.0000.0000.000
102A215VAL00.0350.00540.975-0.003-0.0030.0000.0000.0000.000
103A216ILE0-0.030-0.01535.6690.0030.0030.0000.0000.0000.000
104A217PRO0-0.0040.01235.930-0.004-0.0040.0000.0000.0000.000
105A218GLN00.0360.01427.5160.0040.0040.0000.0000.0000.000
106A219HIS0-0.080-0.04229.473-0.001-0.0010.0000.0000.0000.000
107A220ARG10.9620.97129.0770.0630.0630.0000.0000.0000.000
108A221SER0-0.017-0.00728.4630.0020.0020.0000.0000.0000.000
109A222LEU00.0570.00426.373-0.004-0.0040.0000.0000.0000.000
110A223GLU-1-0.870-0.93829.937-0.045-0.0450.0000.0000.0000.000
111A224ASP-1-0.845-0.90232.279-0.065-0.0650.0000.0000.0000.000
112A225ARG10.8070.89825.2140.1210.1210.0000.0000.0000.000
113A226VAL0-0.028-0.01832.2610.0010.0010.0000.0000.0000.000
114A227SER0-0.041-0.01134.3720.0030.0030.0000.0000.0000.000
115A228ALA00.0250.01534.6620.0020.0020.0000.0000.0000.000
116A229ALA00.009-0.00834.0720.0010.0010.0000.0000.0000.000
117A230ARG10.9200.95236.1480.0440.0440.0000.0000.0000.000
118A231VAL0-0.0030.02239.4870.0030.0030.0000.0000.0000.000
119A232LEU0-0.028-0.02036.3770.0010.0010.0000.0000.0000.000
120A233GLN0-0.083-0.04938.3640.0030.0030.0000.0000.0000.000
121A234GLN00.0060.03041.0320.0040.0040.0000.0000.0000.000
122A235GLY0-0.052-0.02043.5290.0020.0020.0000.0000.0000.000
123A236ALA0-0.048-0.04141.437-0.001-0.0010.0000.0000.0000.000
124A237PRO00.0180.01342.5310.0000.0000.0000.0000.0000.000
125A238GLY00.0170.00041.4700.0000.0000.0000.0000.0000.000
126A239CYS0-0.0330.01036.8100.0000.0000.0000.0000.0000.000
127A240ALA00.0150.01335.0640.0010.0010.0000.0000.0000.000
128A241LEU00.0040.00133.517-0.004-0.0040.0000.0000.0000.000
129A242VAL0-0.008-0.00128.6690.0050.0050.0000.0000.0000.000
130A243LEU0-0.028-0.01228.834-0.004-0.0040.0000.0000.0000.000
131A244ASP-1-0.686-0.81623.277-0.165-0.1650.0000.0000.0000.000
132A245THR00.000-0.00620.6000.0060.0060.0000.0000.0000.000
133A246MET00.0210.01523.607-0.010-0.0100.0000.0000.0000.000
134A247ALA0-0.0300.00418.059-0.006-0.0060.0000.0000.0000.000
135A248ASN00.0240.00519.400-0.011-0.0110.0000.0000.0000.000
136A249SER00.0190.00518.415-0.028-0.0280.0000.0000.0000.000
137A250SER00.016-0.02219.111-0.024-0.0240.0000.0000.0000.000
138A251SER0-0.025-0.02821.7970.0000.0000.0000.0000.0000.000
139A252SER0-0.0150.00617.420-0.011-0.0110.0000.0000.0000.000
140A253ALA0-0.046-0.01017.796-0.020-0.0200.0000.0000.0000.000
141A254TYR00.003-0.02918.7280.0010.0010.0000.0000.0000.000
142A255GLY00.0160.04021.1250.0120.0120.0000.0000.0000.000
143A256ALA0-0.070-0.05022.5180.0160.0160.0000.0000.0000.000
144A257TYR00.0710.01720.0920.0190.0190.0000.0000.0000.000
145A258PHE00.0020.00226.2850.0030.0030.0000.0000.0000.000
146A259GLU-1-0.768-0.88729.988-0.099-0.0990.0000.0000.0000.000
147A260ARG10.7850.90124.9120.1600.1600.0000.0000.0000.000
148A261LEU0-0.0230.00230.2880.0060.0060.0000.0000.0000.000
149A262TYR00.006-0.02124.409-0.010-0.0100.0000.0000.0000.000
150A263VAL0-0.0090.00530.1170.0080.0080.0000.0000.0000.000
151A264ILE00.0050.01126.388-0.008-0.0080.0000.0000.0000.000
152A265GLN00.012-0.01329.1270.0050.0050.0000.0000.0000.000
153A266SER00.0160.00129.383-0.002-0.0020.0000.0000.0000.000
154A267GLY00.0080.01225.4530.0010.0010.0000.0000.0000.000
155A268THR0-0.0110.01624.212-0.014-0.0140.0000.0000.0000.000
156A269ILE0-0.028-0.01923.0050.0070.0070.0000.0000.0000.000
157A270MET0-0.052-0.02526.8090.0000.0000.0000.0000.0000.000
158A271TYR0-0.039-0.03830.0830.0030.0030.0000.0000.0000.000
159A272GLN0-0.085-0.06624.0770.0010.0010.0000.0000.0000.000
160A273GLY00.0250.02529.1700.0030.0030.0000.0000.0000.000
161A274GLY00.0380.02629.748-0.013-0.0130.0000.0000.0000.000
162A275ARG10.8430.90726.8870.1560.1560.0000.0000.0000.000
163A276GLY00.0300.00631.6210.0020.0020.0000.0000.0000.000
164A277PRO0-0.026-0.00135.041-0.001-0.0010.0000.0000.0000.000
165A278ASP-1-0.846-0.92537.198-0.094-0.0940.0000.0000.0000.000
166A279GLY0-0.010-0.01938.8650.0040.0040.0000.0000.0000.000
167A280TYR00.0200.00238.2520.0040.0040.0000.0000.0000.000
168A281GLN00.0910.07032.101-0.002-0.0020.0000.0000.0000.000
169A282VAL00.0110.00836.5180.0020.0020.0000.0000.0000.000
170A283SER0-0.101-0.05539.0460.0040.0040.0000.0000.0000.000
171A284GLU-1-0.827-0.91735.311-0.091-0.0910.0000.0000.0000.000
172A285LEU00.0250.02135.0970.0020.0020.0000.0000.0000.000
173A286ARG10.9090.95437.5610.0600.0600.0000.0000.0000.000
174A287THR00.0260.01840.2880.0040.0040.0000.0000.0000.000
175A288TRP00.0220.01234.5660.0040.0040.0000.0000.0000.000
176A289LEU0-0.016-0.02337.8430.0030.0030.0000.0000.0000.000
177A290GLU-1-0.993-0.99540.293-0.046-0.0460.0000.0000.0000.000
178A291ARG10.9700.98740.7900.0560.0560.0000.0000.0000.000
179A292TYR00.0310.02738.5670.0030.0030.0000.0000.0000.000
180A293ASP-1-0.799-0.90741.009-0.035-0.0350.0000.0000.0000.000
181A294GLU-1-0.867-0.91644.144-0.039-0.0390.0000.0000.0000.000
182A295GLN0-0.066-0.03539.8850.0010.0010.0000.0000.0000.000
183A296LEU0-0.054-0.01041.4140.0030.0030.0000.0000.0000.000
184A297HIS10.6940.81645.1630.0360.0360.0000.0000.0000.000
185A298GLY00.0350.03748.4100.0020.0020.0000.0000.0000.000
186A299THR0-0.038-0.04249.752-0.001-0.0010.0000.0000.0000.000
187A300ARG10.7700.86947.2960.0390.0390.0000.0000.0000.000
188A301PRO00.0210.01652.484-0.001-0.0010.0000.0000.0000.000