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

tag_button

FMODB ID: K3873

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 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 187
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1999443.909979
FMO2-HF: Nuclear repulsion 1925522.650713
FMO2-HF: Total energy -73921.259266
FMO2-MP2: Total energy -74134.137344


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.
-13.14-6.3631.994-3.388-5.381-0.018
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 : 0.008 / q_NPA : -0.010
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].
3A10THR0-0.0340.0083.241-0.3382.4810.013-1.280-1.5510.002
4A11ILE00.0210.0074.8470.8861.012-0.001-0.011-0.1140.000
5A12ARG10.8040.8748.3162.5062.5060.0000.0000.0000.000
6A13VAL0-0.003-0.01510.4170.1560.1560.0000.0000.0000.000
7A14MET0-0.028-0.00713.7860.0350.0350.0000.0000.0000.000
8A15LEU0-0.026-0.00516.2700.0280.0280.0000.0000.0000.000
9A16GLN00.012-0.00719.240-0.006-0.0060.0000.0000.0000.000
10A17ALA00.037-0.01022.8630.0010.0010.0000.0000.0000.000
11A18MET0-0.041-0.00625.977-0.015-0.0150.0000.0000.0000.000
12A19ASP-1-0.873-0.93828.223-0.141-0.1410.0000.0000.0000.000
13A20GLN0-0.024-0.02331.9950.0130.0130.0000.0000.0000.000
14A21GLY00.0190.01030.134-0.017-0.0170.0000.0000.0000.000
15A22HIS0-0.009-0.00531.1710.0050.0050.0000.0000.0000.000
16A23LEU00.0050.00625.633-0.016-0.0160.0000.0000.0000.000
17A24LEU0-0.065-0.01729.9310.0130.0130.0000.0000.0000.000
18A25VAL0-0.003-0.00328.961-0.026-0.0260.0000.0000.0000.000
19A26ASN00.0770.03530.580-0.015-0.0150.0000.0000.0000.000
20A27ASN00.0160.00129.713-0.009-0.0090.0000.0000.0000.000
21A28VAL0-0.045-0.02532.5800.0020.0020.0000.0000.0000.000
22A29ASP-1-0.918-0.96236.188-0.203-0.2030.0000.0000.0000.000
23A30LYS11.0101.02434.9140.2250.2250.0000.0000.0000.000
24A31TYR0-0.015-0.02332.940-0.017-0.0170.0000.0000.0000.000
25A32VAL0-0.0150.00730.0150.0190.0190.0000.0000.0000.000
26A33ARG10.8130.88232.0220.1630.1630.0000.0000.0000.000
27A34ALA0-0.0130.00429.6640.0020.0020.0000.0000.0000.000
28A35GLY00.0000.00131.6670.0030.0030.0000.0000.0000.000
29A36ARG10.9170.94930.8840.1070.1070.0000.0000.0000.000
30A37GLY00.0200.00528.0500.0090.0090.0000.0000.0000.000
31A38VAL0-0.013-0.00521.3610.0000.0000.0000.0000.0000.000
32A39MET0-0.0060.01623.132-0.003-0.0030.0000.0000.0000.000
33A40VAL0-0.016-0.01217.566-0.020-0.0200.0000.0000.0000.000
34A41TYR0-0.003-0.00418.102-0.003-0.0030.0000.0000.0000.000
35A42ILE00.0160.01013.427-0.062-0.0620.0000.0000.0000.000
36A43ALA0-0.035-0.01212.2630.0770.0770.0000.0000.0000.000
37A44PHE00.0410.0249.593-0.185-0.1850.0000.0000.0000.000
38A45LEU0-0.022-0.0256.7920.4770.4770.0000.0000.0000.000
39A46SER0-0.022-0.0335.515-0.706-0.7060.0000.0000.0000.000
40A47ASP-1-0.812-0.9022.649-13.804-11.5600.364-1.370-1.238-0.017
41A48ARG10.7850.8765.5602.8322.8320.0000.0000.0000.000
42A49ASP-1-0.863-0.9246.419-0.123-0.1230.0000.0000.0000.000
43A50SER0-0.0530.0042.5190.3450.5991.364-0.075-1.5420.001
44A51DAL00.0380.0042.646-2.978-2.0510.244-0.422-0.748-0.003
45A52PRO0-0.007-0.0053.645-2.042-1.6350.010-0.230-0.188-0.001
46A53ILE0-0.012-0.0116.0150.2590.2590.0000.0000.0000.000
47A54THR00.0270.0137.3960.1330.1330.0000.0000.0000.000
48A55ASP-1-0.744-0.8949.922-0.428-0.4280.0000.0000.0000.000
49A56GLU-1-0.867-0.93311.467-0.008-0.0080.0000.0000.0000.000
50A57ALA0-0.014-0.0046.8660.0470.0470.0000.0000.0000.000
51A58LEU00.001-0.0088.878-0.114-0.1140.0000.0000.0000.000
52A59ARG10.9070.94611.2430.0830.0830.0000.0000.0000.000
53A60HIS00.0130.0249.1110.0130.0130.0000.0000.0000.000
54A61ALA0-0.008-0.01010.1110.0340.0340.0000.0000.0000.000
55A62VAL0-0.029-0.01211.895-0.001-0.0010.0000.0000.0000.000
56A63GLY00.0690.03415.0740.0210.0210.0000.0000.0000.000
57A64VAL0-0.0220.00312.0830.0330.0330.0000.0000.0000.000
58A65LEU0-0.034-0.00315.4350.0020.0020.0000.0000.0000.000
59A66LEU0-0.018-0.01417.4170.0160.0160.0000.0000.0000.000
60A67HIS00.0160.01117.8680.0210.0210.0000.0000.0000.000
61A68THR0-0.067-0.04716.9930.0630.0630.0000.0000.0000.000
62A69LYS10.8730.93719.561-0.073-0.0730.0000.0000.0000.000
63A70ILE0-0.036-0.00418.1560.0080.0080.0000.0000.0000.000
64A71PHE00.004-0.01821.0140.0040.0040.0000.0000.0000.000
65A72THR00.0190.00525.0170.0110.0110.0000.0000.0000.000
66A73HIS00.0300.04326.6920.0130.0130.0000.0000.0000.000
67A74PHE0-0.004-0.01724.908-0.007-0.0070.0000.0000.0000.000
68A75SER0-0.011-0.00930.874-0.001-0.0010.0000.0000.0000.000
69A76PRO0-0.021-0.01234.0170.0080.0080.0000.0000.0000.000
70A77GLU-1-0.866-0.93836.508-0.057-0.0570.0000.0000.0000.000
71A78LYS10.8940.95533.8620.0340.0340.0000.0000.0000.000
72A79MET0-0.0020.01337.423-0.003-0.0030.0000.0000.0000.000
73A80ILE00.000-0.00734.419-0.001-0.0010.0000.0000.0000.000
74A81ASN0-0.008-0.00432.1030.0080.0080.0000.0000.0000.000
75A82GLN0-0.016-0.01029.2350.0030.0030.0000.0000.0000.000
76A83PRO0-0.028-0.02724.508-0.010-0.0100.0000.0000.0000.000
77A84GLN00.0500.04926.1650.0090.0090.0000.0000.0000.000
78A85SER0-0.038-0.00923.249-0.020-0.0200.0000.0000.0000.000
79A86LEU00.0470.00021.710-0.002-0.0020.0000.0000.0000.000
80A87GLU-1-0.955-0.95623.2800.0150.0150.0000.0000.0000.000
81A88GLU-1-0.841-0.92125.180-0.001-0.0010.0000.0000.0000.000
82A89CYS0-0.066-0.02427.9280.0040.0040.0000.0000.0000.000
83A90PRO00.0770.02628.502-0.021-0.0210.0000.0000.0000.000
84A91GLU-1-0.940-0.96929.569-0.099-0.0990.0000.0000.0000.000
85A92MET0-0.0610.00228.197-0.013-0.0130.0000.0000.0000.000
86A93ASP-1-0.689-0.83328.689-0.185-0.1850.0000.0000.0000.000
87A94ILE0-0.014-0.00922.134-0.010-0.0100.0000.0000.0000.000
88A95LEU0-0.0130.00624.7710.0050.0050.0000.0000.0000.000
89A96ILE00.0030.00519.287-0.034-0.0340.0000.0000.0000.000
90A97VAL00.013-0.01020.8510.0250.0250.0000.0000.0000.000
91A98PRO0-0.0160.01218.202-0.088-0.0880.0000.0000.0000.000
92A99GLN0-0.033-0.03617.3020.0830.0830.0000.0000.0000.000
93A100ALA00.0730.02514.933-0.110-0.1100.0000.0000.0000.000
94A101SER00.002-0.01014.790-0.193-0.1930.0000.0000.0000.000
95A102LEU00.0580.03013.8130.0050.0050.0000.0000.0000.000
96A103GLY0-0.0010.00711.913-0.142-0.1420.0000.0000.0000.000
97A104GLY0-0.021-0.01512.641-0.085-0.0850.0000.0000.0000.000
98A105LYS10.9210.96510.6871.9271.9270.0000.0000.0000.000
99A106VAL00.0550.02716.0090.0590.0590.0000.0000.0000.000
100A107LYS10.9740.99018.6480.5550.5550.0000.0000.0000.000
101A108GLY0-0.008-0.00420.9130.0390.0390.0000.0000.0000.000
102A109ARG10.9630.97124.2660.3170.3170.0000.0000.0000.000
103A110SER0-0.0200.00123.5950.0090.0090.0000.0000.0000.000
104A111VAL00.0420.02318.745-0.018-0.0180.0000.0000.0000.000
105A112GLN0-0.039-0.00714.280-0.036-0.0360.0000.0000.0000.000
106A113PHE00.0640.00715.425-0.079-0.0790.0000.0000.0000.000
107A114HIS00.0210.00813.242-0.114-0.1140.0000.0000.0000.000
108A115GLN0-0.010-0.0078.555-0.386-0.3860.0000.0000.0000.000
109A116LEU0-0.0510.0009.626-0.562-0.5620.0000.0000.0000.000
110A117VAL0-0.0110.0189.2230.1210.1210.0000.0000.0000.000
111A118ALA00.0290.00311.8170.2180.2180.0000.0000.0000.000
112A119LYS10.9890.98114.8160.5110.5110.0000.0000.0000.000
113A120ASP-1-0.856-0.93317.597-0.562-0.5620.0000.0000.0000.000
114A121VAL0-0.0040.00610.8280.0370.0370.0000.0000.0000.000
115A122GLY00.013-0.00413.906-0.059-0.0590.0000.0000.0000.000
116A123ALA0-0.021-0.01214.7690.0370.0370.0000.0000.0000.000
117A124ALA00.0330.01915.3570.0500.0500.0000.0000.0000.000
118A125LEU00.007-0.00110.0350.0280.0280.0000.0000.0000.000
119A126TYR0-0.011-0.02514.1880.0380.0380.0000.0000.0000.000
120A127ASP-1-0.918-0.95616.733-0.352-0.3520.0000.0000.0000.000
121A128ARG10.8710.94615.2820.3490.3490.0000.0000.0000.000
122A129PHE00.002-0.01513.8200.0460.0460.0000.0000.0000.000
123A130CYS0-0.023-0.02116.3010.0600.0600.0000.0000.0000.000
124A131HIS0-0.080-0.04019.9830.0640.0640.0000.0000.0000.000
125A132PHE0-0.007-0.01214.5200.0490.0490.0000.0000.0000.000
126A133VAL0-0.0080.00818.3520.0430.0430.0000.0000.0000.000
127A134ARG10.9150.94620.7090.3470.3470.0000.0000.0000.000
128A135VAL00.0000.01322.2130.0290.0290.0000.0000.0000.000
129A136ALA0-0.037-0.01821.0170.0260.0260.0000.0000.0000.000
130A137ARG10.7670.87023.1360.1700.1700.0000.0000.0000.000
131A138GLY00.0010.01925.9640.0080.0080.0000.0000.0000.000
132A139VAL0-0.019-0.01227.2420.0050.0050.0000.0000.0000.000
133A140ASP-1-0.802-0.89629.091-0.111-0.1110.0000.0000.0000.000
134A141GLU-1-0.794-0.91025.151-0.226-0.2260.0000.0000.0000.000
135A142SER0-0.088-0.04129.944-0.007-0.0070.0000.0000.0000.000
136A143ARG10.9610.97233.3530.1070.1070.0000.0000.0000.000
137A144VAL0-0.0190.01929.3130.0000.0000.0000.0000.0000.000
138A145ASP-1-0.874-0.95431.452-0.234-0.2340.0000.0000.0000.000
139A146ALA0-0.003-0.01727.836-0.007-0.0070.0000.0000.0000.000
140A147ASN0-0.101-0.06926.701-0.008-0.0080.0000.0000.0000.000
141A148GLY00.0220.01328.255-0.010-0.0100.0000.0000.0000.000
142A149ALA0-0.043-0.01629.0170.0150.0150.0000.0000.0000.000
143A150PRO00.013-0.00432.5940.0000.0000.0000.0000.0000.000
144A151ARG10.8750.94931.6060.1690.1690.0000.0000.0000.000
145A152SER0-0.0050.00736.7080.0010.0010.0000.0000.0000.000
146A153GLU-1-0.943-0.98839.834-0.130-0.1300.0000.0000.0000.000
147A154GLY00.0470.03640.875-0.002-0.0020.0000.0000.0000.000
148A155ASP-1-0.959-0.98239.567-0.110-0.1100.0000.0000.0000.000
149A156ALA0-0.092-0.03538.046-0.006-0.0060.0000.0000.0000.000
150A157PRO0-0.024-0.01836.1560.0070.0070.0000.0000.0000.000
151A158LYS10.9180.97939.4710.1260.1260.0000.0000.0000.000
152A159ALA00.0540.02939.899-0.008-0.0080.0000.0000.0000.000
153A160GLU-1-0.917-0.95239.766-0.163-0.1630.0000.0000.0000.000
154A161GLY00.002-0.00741.5410.0080.0080.0000.0000.0000.000
155A162TRP00.0500.02037.149-0.002-0.0020.0000.0000.0000.000
156A163ILE0-0.056-0.03035.1730.0100.0100.0000.0000.0000.000
157A164LYS10.9871.01137.0010.0870.0870.0000.0000.0000.000
158A165TYR0-0.038-0.01132.763-0.007-0.0070.0000.0000.0000.000
159A166ASN0-0.081-0.07133.0340.0190.0190.0000.0000.0000.000
160A167SER00.0760.04630.2730.0020.0020.0000.0000.0000.000
161A168ARG10.7920.89529.7510.1680.1680.0000.0000.0000.000
162A169VAL00.0380.01123.477-0.009-0.0090.0000.0000.0000.000
163A170ILE0-0.039-0.00626.391-0.001-0.0010.0000.0000.0000.000
164A171SER0-0.006-0.00523.079-0.033-0.0330.0000.0000.0000.000
165A172GLY00.0560.03023.7910.0300.0300.0000.0000.0000.000
166A173THR00.0090.02024.224-0.017-0.0170.0000.0000.0000.000
167A174PHE00.0380.01917.765-0.017-0.0170.0000.0000.0000.000
168A175GLY0-0.040-0.01722.3360.0340.0340.0000.0000.0000.000
169A176ASN0-0.060-0.02523.7460.0510.0510.0000.0000.0000.000
170A177ARG10.9460.97825.2100.2890.2890.0000.0000.0000.000
171A178GLN00.017-0.00723.1880.0410.0410.0000.0000.0000.000
172A179GLY0-0.035-0.01426.6490.0010.0010.0000.0000.0000.000
173A180LEU00.0200.00726.1990.0010.0010.0000.0000.0000.000
174A181ARG10.9170.96929.9060.2310.2310.0000.0000.0000.000
175A182PHE00.019-0.00726.549-0.005-0.0050.0000.0000.0000.000
176A183GLU-1-0.896-0.93330.632-0.181-0.1810.0000.0000.0000.000
177A184SER0-0.026-0.04528.471-0.001-0.0010.0000.0000.0000.000
178A185GLU-1-0.867-0.92231.024-0.139-0.1390.0000.0000.0000.000
179A186GLY00.001-0.01129.7020.0120.0120.0000.0000.0000.000
180A187PRO0-0.055-0.01325.211-0.003-0.0030.0000.0000.0000.000
181A188PHE00.0370.01924.124-0.014-0.0140.0000.0000.0000.000
182A189THR00.0200.00119.3690.0130.0130.0000.0000.0000.000
183A190HIS10.8700.95116.9030.2590.2590.0000.0000.0000.000
184A191MET0-0.0120.00010.782-0.093-0.0930.0000.0000.0000.000
185A192PHE00.0050.00311.3800.1250.1250.0000.0000.0000.000
186A193ASP-1-0.758-0.8486.006-2.642-2.6420.0000.0000.0000.000
187A194ILE00.0060.0005.658-0.163-0.1630.0000.0000.0000.000