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: 436RN

Calculation Name: 1TC5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1TC5

Chain ID: A

ChEMBL ID:

UniProt ID: P84066

Base Structure: X-ray

Registration Date: 2023-03-13

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 187
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2001329.406971
FMO2-HF: Nuclear repulsion 1927407.200974
FMO2-HF: Total energy -73922.205997
FMO2-MP2: Total energy -74135.131537


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:8:HIS)


Summations of interaction energy for fragment #1(A:8:HIS)
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.
-11.92-5.2671.482-3.295-4.839-0.012
Interaction energy analysis for fragmet #1(A:8:HIS)
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 : -0.005
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].
3A10THR0-0.0340.0093.4340.6553.326-0.006-1.234-1.4310.004
4A11ILE00.0100.0035.3450.3390.453-0.001-0.009-0.1040.000
5A12ARG10.7980.8668.8522.1742.1740.0000.0000.0000.000
6A13VAL0-0.002-0.01510.7920.0860.0860.0000.0000.0000.000
7A14MET0-0.026-0.00814.1460.0420.0420.0000.0000.0000.000
8A15LEU0-0.0240.00016.6510.0180.0180.0000.0000.0000.000
9A16GLN00.016-0.00419.5590.0020.0020.0000.0000.0000.000
10A17ALA00.0400.01423.1700.0030.0030.0000.0000.0000.000
11A18MET0-0.0350.00926.276-0.020-0.0200.0000.0000.0000.000
12A19ASP-1-0.819-0.93128.553-0.085-0.0850.0000.0000.0000.000
13A20GLN0-0.007-0.01232.3240.0090.0090.0000.0000.0000.000
14A21GLY00.0140.01030.506-0.015-0.0150.0000.0000.0000.000
15A22HIS0-0.005-0.00531.5420.0040.0040.0000.0000.0000.000
16A23LEU00.0060.00426.129-0.017-0.0170.0000.0000.0000.000
17A24LEU0-0.059-0.00930.4030.0120.0120.0000.0000.0000.000
18A25VAL00.000-0.00629.093-0.024-0.0240.0000.0000.0000.000
19A26ASN00.0640.04131.001-0.017-0.0170.0000.0000.0000.000
20A27ASN00.0110.00430.149-0.012-0.0120.0000.0000.0000.000
21A28VAL0-0.019-0.01032.9870.0000.0000.0000.0000.0000.000
22A29ASP-1-0.906-0.95636.600-0.183-0.1830.0000.0000.0000.000
23A30LYS10.9861.01833.7750.2020.2020.0000.0000.0000.000
24A31TYR0-0.025-0.03133.440-0.022-0.0220.0000.0000.0000.000
25A32VAL0-0.0080.00730.2870.0170.0170.0000.0000.0000.000
26A33ARG10.8340.90432.5280.1270.1270.0000.0000.0000.000
27A34ALA0-0.0200.00129.9820.0030.0030.0000.0000.0000.000
28A35GLY00.0100.00632.0040.0000.0000.0000.0000.0000.000
29A36ARG10.8930.94731.2410.0530.0530.0000.0000.0000.000
30A37GLY00.0430.00928.3920.0090.0090.0000.0000.0000.000
31A38VAL0-0.031-0.00921.6760.0010.0010.0000.0000.0000.000
32A39MET0-0.0050.01723.516-0.007-0.0070.0000.0000.0000.000
33A40VAL0-0.016-0.01417.954-0.011-0.0110.0000.0000.0000.000
34A41TYR00.000-0.00418.536-0.019-0.0190.0000.0000.0000.000
35A42ILE00.0150.00813.618-0.038-0.0380.0000.0000.0000.000
36A43ALA0-0.036-0.00812.6240.0310.0310.0000.0000.0000.000
37A44PHE00.0470.02110.066-0.116-0.1160.0000.0000.0000.000
38A45LEU0-0.017-0.0187.1960.3430.3430.0000.0000.0000.000
39A46SER0-0.020-0.0215.518-0.598-0.5980.0000.0000.0000.000
40A47ASP-1-0.813-0.8992.845-14.410-12.4230.181-1.188-0.980-0.012
41A48ARG10.8070.8885.5273.2083.2080.0000.0000.0000.000
42A49ASP-1-0.865-0.9236.239-0.599-0.5990.0000.0000.0000.000
43A50SER0-0.072-0.0172.4540.1470.8121.099-0.322-1.4410.000
44A51DAL00.0400.0062.700-2.043-1.2240.200-0.321-0.698-0.003
45A52PRO0-0.012-0.0163.663-1.955-1.5580.009-0.221-0.185-0.001
46A53ILE0-0.012-0.0135.9320.2950.2950.0000.0000.0000.000
47A54THR00.0280.0157.4470.1060.1060.0000.0000.0000.000
48A55ASP-1-0.684-0.8329.962-0.262-0.2620.0000.0000.0000.000
49A56GLU-1-0.821-0.90711.4550.1310.1310.0000.0000.0000.000
50A57ALA0-0.0110.0026.9030.0730.0730.0000.0000.0000.000
51A58LEU0-0.005-0.0088.915-0.052-0.0520.0000.0000.0000.000
52A59ARG10.8430.90211.294-0.018-0.0180.0000.0000.0000.000
53A60HIS00.0110.0208.818-0.052-0.0520.0000.0000.0000.000
54A61ALA0-0.006-0.00510.1010.0450.0450.0000.0000.0000.000
55A62VAL0-0.025-0.01011.938-0.018-0.0180.0000.0000.0000.000
56A63GLY00.0670.03015.1100.0030.0030.0000.0000.0000.000
57A64VAL0-0.024-0.00211.8130.0150.0150.0000.0000.0000.000
58A65LEU0-0.036-0.00515.227-0.022-0.0220.0000.0000.0000.000
59A66LEU0-0.007-0.01017.550-0.007-0.0070.0000.0000.0000.000
60A67HIS0-0.035-0.02417.4490.0110.0110.0000.0000.0000.000
61A68THR0-0.072-0.04616.8630.0550.0550.0000.0000.0000.000
62A69LYS10.7980.88219.365-0.163-0.1630.0000.0000.0000.000
63A70ILE0-0.043-0.01218.5150.0110.0110.0000.0000.0000.000
64A71PHE00.000-0.01721.377-0.004-0.0040.0000.0000.0000.000
65A72THR00.0270.01025.2570.0110.0110.0000.0000.0000.000
66A73HIS00.0120.01426.9140.0170.0170.0000.0000.0000.000
67A74PHE00.006-0.00925.034-0.010-0.0100.0000.0000.0000.000
68A75SER0-0.013-0.02331.152-0.003-0.0030.0000.0000.0000.000
69A76PRO0-0.017-0.00634.2780.0070.0070.0000.0000.0000.000
70A77GLU-1-0.824-0.92336.763-0.005-0.0050.0000.0000.0000.000
71A78LYS10.8590.94534.021-0.019-0.0190.0000.0000.0000.000
72A79MET00.0000.01237.586-0.004-0.0040.0000.0000.0000.000
73A80ILE00.007-0.00434.583-0.002-0.0020.0000.0000.0000.000
74A81ASN0-0.029-0.01732.3180.0080.0080.0000.0000.0000.000
75A82GLN0-0.011-0.00629.3220.0070.0070.0000.0000.0000.000
76A83PRO0-0.020-0.02424.650-0.011-0.0110.0000.0000.0000.000
77A84GLN00.0260.03626.3350.0080.0080.0000.0000.0000.000
78A85SER0-0.003-0.00322.842-0.021-0.0210.0000.0000.0000.000
79A86LEU00.0450.00322.045-0.011-0.0110.0000.0000.0000.000
80A87GLU-1-0.908-0.91723.2570.1290.1290.0000.0000.0000.000
81A88GLU-1-0.786-0.86625.2160.0860.0860.0000.0000.0000.000
82A89CYS0-0.062-0.01727.896-0.004-0.0040.0000.0000.0000.000
83A90PRO00.0830.02628.537-0.018-0.0180.0000.0000.0000.000
84A91GLU-1-0.826-0.89629.611-0.049-0.0490.0000.0000.0000.000
85A92MET0-0.0580.00328.382-0.015-0.0150.0000.0000.0000.000
86A93ASP-1-0.692-0.81628.737-0.122-0.1220.0000.0000.0000.000
87A94ILE0-0.017-0.01022.198-0.003-0.0030.0000.0000.0000.000
88A95LEU0-0.0090.00925.136-0.001-0.0010.0000.0000.0000.000
89A96ILE00.0000.00319.559-0.026-0.0260.0000.0000.0000.000
90A97VAL00.017-0.00621.3430.0120.0120.0000.0000.0000.000
91A98PRO0-0.0190.01118.671-0.070-0.0700.0000.0000.0000.000
92A99GLN0-0.036-0.03717.7270.0600.0600.0000.0000.0000.000
93A100ALA00.0720.02615.280-0.097-0.0970.0000.0000.0000.000
94A101SER00.014-0.00215.050-0.192-0.1920.0000.0000.0000.000
95A102LEU00.0520.02614.267-0.011-0.0110.0000.0000.0000.000
96A103GLY00.0050.00612.041-0.128-0.1280.0000.0000.0000.000
97A104GLY0-0.027-0.01112.793-0.132-0.1320.0000.0000.0000.000
98A105LYS10.8840.94210.0582.3532.3530.0000.0000.0000.000
99A106VAL00.0400.01816.1570.0570.0570.0000.0000.0000.000
100A107LYS10.9660.98918.7130.6260.6260.0000.0000.0000.000
101A108GLY0-0.0010.00720.9460.0450.0450.0000.0000.0000.000
102A109ARG10.9710.97824.3330.3450.3450.0000.0000.0000.000
103A110SER0-0.030-0.01423.6030.0130.0130.0000.0000.0000.000
104A111VAL00.0350.01418.836-0.018-0.0180.0000.0000.0000.000
105A112GLN0-0.032-0.00514.194-0.017-0.0170.0000.0000.0000.000
106A113PHE00.0710.01215.450-0.072-0.0720.0000.0000.0000.000
107A114HIS00.0310.01313.182-0.104-0.1040.0000.0000.0000.000
108A115GLN00.0210.0109.214-0.362-0.3620.0000.0000.0000.000
109A116LEU0-0.0340.0059.753-0.503-0.5030.0000.0000.0000.000
110A117VAL0-0.0140.0099.1900.0790.0790.0000.0000.0000.000
111A118ALA00.0250.00611.8290.2230.2230.0000.0000.0000.000
112A119LYS10.9280.94214.8260.5210.5210.0000.0000.0000.000
113A120ASP-1-0.826-0.91317.610-0.562-0.5620.0000.0000.0000.000
114A121VAL00.0180.01610.8560.0510.0510.0000.0000.0000.000
115A122GLY00.0190.00213.922-0.031-0.0310.0000.0000.0000.000
116A123ALA0-0.020-0.01114.7850.0560.0560.0000.0000.0000.000
117A124ALA00.0160.01315.4050.0590.0590.0000.0000.0000.000
118A125LEU00.001-0.00110.1210.0400.0400.0000.0000.0000.000
119A126TYR0-0.007-0.02914.2490.0550.0550.0000.0000.0000.000
120A127ASP-1-0.893-0.94716.794-0.278-0.2780.0000.0000.0000.000
121A128ARG10.8280.89515.4050.2570.2570.0000.0000.0000.000
122A129PHE0-0.003-0.01813.6870.0480.0480.0000.0000.0000.000
123A130CYS0-0.023-0.01816.3590.0590.0590.0000.0000.0000.000
124A131HIS0-0.066-0.03520.0420.0580.0580.0000.0000.0000.000
125A132PHE0-0.029-0.02214.7190.0420.0420.0000.0000.0000.000
126A133VAL00.0000.01118.3980.0420.0420.0000.0000.0000.000
127A134ARG10.9040.93520.7620.2690.2690.0000.0000.0000.000
128A135VAL00.0060.01422.2530.0240.0240.0000.0000.0000.000
129A136ALA0-0.038-0.01821.0540.0220.0220.0000.0000.0000.000
130A137ARG10.7530.86023.1810.0740.0740.0000.0000.0000.000
131A138GLY0-0.0040.01526.0110.0030.0030.0000.0000.0000.000
132A139VAL0-0.024-0.01427.245-0.001-0.0010.0000.0000.0000.000
133A140ASP-1-0.770-0.86329.143-0.070-0.0700.0000.0000.0000.000
134A141GLU-1-0.783-0.90025.217-0.163-0.1630.0000.0000.0000.000
135A142SER0-0.072-0.04830.000-0.010-0.0100.0000.0000.0000.000
136A143ARG10.9370.97133.4150.0680.0680.0000.0000.0000.000
137A144VAL0-0.0240.01029.488-0.002-0.0020.0000.0000.0000.000
138A145ASP-1-0.851-0.94331.435-0.195-0.1950.0000.0000.0000.000
139A146ALA0-0.001-0.01327.921-0.003-0.0030.0000.0000.0000.000
140A147ASN0-0.123-0.07226.763-0.009-0.0090.0000.0000.0000.000
141A148GLY00.0440.02628.315-0.005-0.0050.0000.0000.0000.000
142A149ALA0-0.032-0.01429.0760.0150.0150.0000.0000.0000.000
143A150PRO00.013-0.00532.653-0.001-0.0010.0000.0000.0000.000
144A151ARG10.8200.91331.5930.1260.1260.0000.0000.0000.000
145A152SER0-0.028-0.03236.768-0.002-0.0020.0000.0000.0000.000
146A153GLU-1-0.932-0.97739.894-0.104-0.1040.0000.0000.0000.000
147A154GLY00.0130.01040.935-0.001-0.0010.0000.0000.0000.000
148A155ASP-1-0.901-0.92539.645-0.079-0.0790.0000.0000.0000.000
149A156ALA0-0.084-0.02838.097-0.003-0.0030.0000.0000.0000.000
150A157PRO0-0.021-0.01736.2480.0060.0060.0000.0000.0000.000
151A158LYS10.8750.95339.5370.0940.0940.0000.0000.0000.000
152A159ALA00.0500.02040.388-0.005-0.0050.0000.0000.0000.000
153A160GLU-1-0.828-0.91040.254-0.149-0.1490.0000.0000.0000.000
154A161GLY00.0040.00541.8920.0080.0080.0000.0000.0000.000
155A162TRP00.007-0.00237.203-0.001-0.0010.0000.0000.0000.000
156A163ILE0-0.046-0.02435.5760.0070.0070.0000.0000.0000.000
157A164LYS10.8930.95337.1940.0470.0470.0000.0000.0000.000
158A165TYR0-0.0180.00132.872-0.009-0.0090.0000.0000.0000.000
159A166ASN0-0.090-0.07033.0980.0140.0140.0000.0000.0000.000
160A167SER00.0530.02530.3200.0010.0010.0000.0000.0000.000
161A168ARG10.7790.87629.8050.1160.1160.0000.0000.0000.000
162A169VAL00.0350.00823.478-0.002-0.0020.0000.0000.0000.000
163A170ILE0-0.038-0.00626.446-0.005-0.0050.0000.0000.0000.000
164A171SER00.0200.01123.140-0.015-0.0150.0000.0000.0000.000
165A172GLY00.0360.02224.1560.0210.0210.0000.0000.0000.000
166A173THR00.0040.00624.406-0.012-0.0120.0000.0000.0000.000
167A174PHE00.0340.01417.825-0.019-0.0190.0000.0000.0000.000
168A175GLY0-0.026-0.01022.7530.0280.0280.0000.0000.0000.000
169A176ASN0-0.062-0.02324.1290.0420.0420.0000.0000.0000.000
170A177ARG10.9170.95925.6000.2600.2600.0000.0000.0000.000
171A178GLN00.011-0.01323.6030.0420.0420.0000.0000.0000.000
172A179GLY0-0.025-0.00927.0560.0010.0010.0000.0000.0000.000
173A180LEU00.012-0.00126.4610.0030.0030.0000.0000.0000.000
174A181ARG10.8510.93330.3170.1850.1850.0000.0000.0000.000
175A182PHE00.012-0.00726.776-0.001-0.0010.0000.0000.0000.000
176A183GLU-1-0.901-0.94030.980-0.143-0.1430.0000.0000.0000.000
177A184SER0-0.033-0.05728.7350.0040.0040.0000.0000.0000.000
178A185GLU-1-0.868-0.92231.327-0.096-0.0960.0000.0000.0000.000
179A186GLY00.006-0.01029.9550.0090.0090.0000.0000.0000.000
180A187PRO0-0.055-0.01425.5190.0040.0040.0000.0000.0000.000
181A188PHE00.0440.02323.891-0.004-0.0040.0000.0000.0000.000
182A189THR00.0210.00519.5660.0210.0210.0000.0000.0000.000
183A190HIS10.8550.94217.1510.1160.1160.0000.0000.0000.000
184A191MET0-0.023-0.00710.728-0.088-0.0880.0000.0000.0000.000
185A192PHE00.0070.00511.6510.1100.1100.0000.0000.0000.000
186A193ASP-1-0.753-0.8446.316-2.268-2.2680.0000.0000.0000.000
187A194ILE00.0210.0105.629-0.109-0.1090.0000.0000.0000.000