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: 6YY6Z

Calculation Name: 3TCV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3TCV

Chain ID: A

ChEMBL ID:

UniProt ID: Q2YIN4

Base Structure: X-ray

Registration Date: 2023-09-21

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 OptAll
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 221
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2874744.902974
FMO2-HF: Nuclear repulsion 2785721.592065
FMO2-HF: Total energy -89023.310909
FMO2-MP2: Total energy -89287.79729


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:4:LEU)


Summations of interaction energy for fragment #1(A:4:LEU)
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.
-5.003-0.1331.313-1.804-4.378-0.006
Interaction energy analysis for fragmet #1(A:4:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.022 / q_NPA : -0.011
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].
3A6ASN00.0140.0083.579-2.051-0.3020.004-0.772-0.9800.000
4A7TRP0-0.037-0.0142.721-1.4000.2240.243-0.481-1.386-0.002
5A8THR0-0.005-0.0094.7340.2310.285-0.001-0.013-0.0400.000
6A9PRO00.0060.0008.010-0.036-0.0360.0000.0000.0000.000
7A10ARG10.8050.9247.8580.5410.5410.0000.0000.0000.000
8A11PRO00.0150.00611.5640.0200.0200.0000.0000.0000.000
9A12LYS10.8490.92914.8040.1290.1290.0000.0000.0000.000
10A13PRO00.0190.01716.9720.0140.0140.0000.0000.0000.000
11A14GLU-1-0.815-0.92219.052-0.141-0.1410.0000.0000.0000.000
12A15ARG10.8220.87822.5260.1100.1100.0000.0000.0000.000
13A16LYS10.8290.92422.3060.0860.0860.0000.0000.0000.000
14A17ILE00.0160.00226.295-0.004-0.0040.0000.0000.0000.000
15A18PHE0-0.0080.00321.5850.0010.0010.0000.0000.0000.000
16A19GLU-1-0.762-0.86026.898-0.038-0.0380.0000.0000.0000.000
17A20GLY00.0370.02728.0790.0000.0000.0000.0000.0000.000
18A21ARG10.8420.92029.5060.0220.0220.0000.0000.0000.000
19A22TYR0-0.070-0.06530.9760.0030.0030.0000.0000.0000.000
20A23VAL0-0.025-0.00928.9640.0000.0000.0000.0000.0000.000
21A24ARG10.8190.88830.3880.0460.0460.0000.0000.0000.000
22A25LEU0-0.0280.00225.266-0.002-0.0020.0000.0000.0000.000
23A26GLU-1-0.748-0.83928.886-0.049-0.0490.0000.0000.0000.000
24A27PRO0-0.0050.00127.313-0.002-0.0020.0000.0000.0000.000
25A28LEU0-0.033-0.00529.2960.0060.0060.0000.0000.0000.000
26A29ASN00.012-0.00731.7610.0010.0010.0000.0000.0000.000
27A30ALA00.0560.02635.0710.0030.0030.0000.0000.0000.000
28A31GLN0-0.004-0.00438.1610.0030.0030.0000.0000.0000.000
29A32LYS10.8350.90435.7660.0500.0500.0000.0000.0000.000
30A33HIS00.019-0.02233.3490.0000.0000.0000.0000.0000.000
31A34GLY00.0330.01438.0450.0000.0000.0000.0000.0000.000
32A35ASP-1-0.843-0.91939.872-0.044-0.0440.0000.0000.0000.000
33A36GLU-1-0.831-0.91840.247-0.040-0.0400.0000.0000.0000.000
34A37LEU0-0.006-0.00334.748-0.001-0.0010.0000.0000.0000.000
35A38PHE00.0260.02238.666-0.001-0.0010.0000.0000.0000.000
36A39ALA00.0230.03241.4320.0000.0000.0000.0000.0000.000
37A40ALA0-0.006-0.00438.3470.0000.0000.0000.0000.0000.000
38A41SER0-0.089-0.04537.873-0.003-0.0030.0000.0000.0000.000
39A42SER0-0.031-0.03939.6330.0000.0000.0000.0000.0000.000
40A43VAL0-0.021-0.00440.9320.0020.0020.0000.0000.0000.000
41A44GLU-1-0.922-0.96543.983-0.036-0.0360.0000.0000.0000.000
42A45ASP-1-0.796-0.86141.117-0.046-0.0460.0000.0000.0000.000
43A46ALA00.0020.00240.130-0.003-0.0030.0000.0000.0000.000
44A47GLU-1-0.851-0.94139.361-0.056-0.0560.0000.0000.0000.000
45A48GLN0-0.010-0.00539.201-0.003-0.0030.0000.0000.0000.000
46A49ARG10.7080.82136.1270.0470.0470.0000.0000.0000.000
47A50PHE00.0490.01034.781-0.005-0.0050.0000.0000.0000.000
48A51THR0-0.076-0.03335.261-0.003-0.0030.0000.0000.0000.000
49A52TRP0-0.062-0.05431.166-0.003-0.0030.0000.0000.0000.000
50A53LEU0-0.0400.01330.065-0.007-0.0070.0000.0000.0000.000
51A54PHE00.022-0.00126.2200.0030.0030.0000.0000.0000.000
52A55GLU-1-0.776-0.86631.586-0.088-0.0880.0000.0000.0000.000
53A56THR00.0120.00634.971-0.001-0.0010.0000.0000.0000.000
54A57PRO00.0160.01738.437-0.002-0.0020.0000.0000.0000.000
55A58PRO0-0.074-0.02439.5650.0010.0010.0000.0000.0000.000
56A59ALA00.0500.02342.3850.0020.0020.0000.0000.0000.000
57A60THR0-0.058-0.06245.9850.0020.0020.0000.0000.0000.000
58A61ARG10.7960.86542.5680.0460.0460.0000.0000.0000.000
59A62ALA00.0070.00544.381-0.002-0.0020.0000.0000.0000.000
60A63GLU-1-0.825-0.89643.667-0.049-0.0490.0000.0000.0000.000
61A64PHE00.0200.00736.695-0.003-0.0030.0000.0000.0000.000
62A65GLU-1-0.801-0.88839.310-0.057-0.0570.0000.0000.0000.000
63A66PRO0-0.011-0.01439.213-0.003-0.0030.0000.0000.0000.000
64A67TRP0-0.060-0.02231.538-0.002-0.0020.0000.0000.0000.000
65A68LEU00.0020.03134.776-0.005-0.0050.0000.0000.0000.000
66A69ASP-1-0.805-0.87435.238-0.071-0.0710.0000.0000.0000.000
67A70LYS10.9770.98331.0210.0940.0940.0000.0000.0000.000
68A71ALA0-0.006-0.00630.752-0.006-0.0060.0000.0000.0000.000
69A72SER0-0.010-0.03430.362-0.004-0.0040.0000.0000.0000.000
70A73LYS10.7790.87831.1650.0680.0680.0000.0000.0000.000
71A74SER0-0.062-0.02526.657-0.005-0.0050.0000.0000.0000.000
72A75ASP-1-0.809-0.90323.875-0.135-0.1350.0000.0000.0000.000
73A76ASP-1-0.804-0.88219.917-0.219-0.2190.0000.0000.0000.000
74A77PRO00.005-0.01523.1700.0050.0050.0000.0000.0000.000
75A78LEU0-0.0470.01922.3080.0120.0120.0000.0000.0000.000
76A79PHE00.030-0.00324.5990.0000.0000.0000.0000.0000.000
77A80PHE0-0.045-0.02523.5400.0050.0050.0000.0000.0000.000
78A81ALA00.0150.01828.4720.0000.0000.0000.0000.0000.000
79A82VAL0-0.038-0.02929.2410.0000.0000.0000.0000.0000.000
80A83ILE0-0.006-0.00831.7180.0030.0030.0000.0000.0000.000
81A84ASP-1-0.752-0.85733.756-0.037-0.0370.0000.0000.0000.000
82A85LYS10.7790.86533.3380.0340.0340.0000.0000.0000.000
83A86ALA0-0.055-0.01436.9690.0030.0030.0000.0000.0000.000
84A87SER0-0.032-0.04639.7430.0010.0010.0000.0000.0000.000
85A88GLY00.0080.01739.2180.0010.0010.0000.0000.0000.000
86A89LYS10.8440.91438.9980.0340.0340.0000.0000.0000.000
87A90VAL0-0.028-0.01635.189-0.002-0.0020.0000.0000.0000.000
88A91ALA00.0180.01235.5960.0010.0010.0000.0000.0000.000
89A92GLY00.005-0.01733.2970.0000.0000.0000.0000.0000.000
90A93ARG10.7770.89930.3800.0860.0860.0000.0000.0000.000
91A94GLN00.011-0.00124.7120.0060.0060.0000.0000.0000.000
92A95ALA00.0160.00824.5750.0040.0040.0000.0000.0000.000
93A96LEU0-0.0060.01418.365-0.004-0.0040.0000.0000.0000.000
94A97MET0-0.057-0.01119.6480.0140.0140.0000.0000.0000.000
95A98ARG10.7730.84316.0850.2310.2310.0000.0000.0000.000
96A99ILE0-0.025-0.00815.733-0.031-0.0310.0000.0000.0000.000
97A100ASP-1-0.769-0.86311.355-0.571-0.5710.0000.0000.0000.000
98A101PRO00.020-0.00111.274-0.068-0.0680.0000.0000.0000.000
99A102ALA0-0.0290.00010.385-0.064-0.0640.0000.0000.0000.000
100A103ASN0-0.055-0.0506.661-0.342-0.3420.0000.0000.0000.000
101A104GLY0-0.0160.0086.467-0.135-0.1350.0000.0000.0000.000
102A105VAL00.002-0.0078.8010.0230.0230.0000.0000.0000.000
103A106ILE0-0.0070.00910.8870.0330.0330.0000.0000.0000.000
104A107GLU-1-0.779-0.88214.601-0.185-0.1850.0000.0000.0000.000
105A108ILE0-0.050-0.01317.7030.0110.0110.0000.0000.0000.000
106A109GLY00.0760.01320.8520.0030.0030.0000.0000.0000.000
107A110SER0-0.028-0.03223.5910.0090.0090.0000.0000.0000.000
108A111ILE0-0.0170.01124.1520.0070.0070.0000.0000.0000.000
109A112TYR0-0.049-0.03928.2640.0020.0020.0000.0000.0000.000
110A113TRP0-0.022-0.02326.2620.0030.0030.0000.0000.0000.000
111A114GLY00.1070.05933.3540.0010.0010.0000.0000.0000.000
112A115PRO00.024-0.00636.7020.0000.0000.0000.0000.0000.000
113A116LEU0-0.0050.00938.2940.0010.0010.0000.0000.0000.000
114A117ILE00.0050.00432.2430.0010.0010.0000.0000.0000.000
115A118SER0-0.038-0.00333.511-0.001-0.0010.0000.0000.0000.000
116A119ARG10.9030.94031.2500.0620.0620.0000.0000.0000.000
117A120ARG10.9010.95633.8720.0350.0350.0000.0000.0000.000
118A121PRO00.0260.00231.360-0.004-0.0040.0000.0000.0000.000
119A122ALA00.0690.03430.093-0.003-0.0030.0000.0000.0000.000
120A123ALA00.0460.03129.724-0.004-0.0040.0000.0000.0000.000
121A124THR0-0.0010.00125.805-0.006-0.0060.0000.0000.0000.000
122A125GLU-1-0.764-0.87625.346-0.046-0.0460.0000.0000.0000.000
123A126ALA00.0040.00825.509-0.004-0.0040.0000.0000.0000.000
124A127GLN00.0460.01819.569-0.018-0.0180.0000.0000.0000.000
125A128PHE0-0.022-0.00621.224-0.009-0.0090.0000.0000.0000.000
126A129LEU0-0.027-0.02020.919-0.004-0.0040.0000.0000.0000.000
127A130PHE00.0370.02220.224-0.003-0.0030.0000.0000.0000.000
128A131MET0-0.0070.03316.127-0.017-0.0170.0000.0000.0000.000
129A132GLN00.0320.01016.177-0.002-0.0020.0000.0000.0000.000
130A133TYR0-0.0030.00317.019-0.001-0.0010.0000.0000.0000.000
131A134VAL00.0500.01313.119-0.010-0.0100.0000.0000.0000.000
132A135PHE0-0.0030.0009.919-0.032-0.0320.0000.0000.0000.000
133A136ASP-1-0.806-0.88112.386-0.057-0.0570.0000.0000.0000.000
134A137VAL0-0.076-0.02914.9320.0230.0230.0000.0000.0000.000
135A138LEU0-0.0220.00613.7830.0010.0010.0000.0000.0000.000
136A139GLY00.0040.01710.081-0.037-0.0370.0000.0000.0000.000
137A140TYR0-0.062-0.0618.321-0.127-0.1270.0000.0000.0000.000
138A141ARG10.8220.8852.857-0.1361.1871.068-0.529-1.862-0.004
139A142ARG10.7290.8267.5520.3700.3700.0000.0000.0000.000
140A143TYR00.005-0.0189.9300.0120.0120.0000.0000.0000.000
141A144GLU-1-0.750-0.87013.699-0.294-0.2940.0000.0000.0000.000
142A145TRP00.008-0.00616.0460.0210.0210.0000.0000.0000.000
143A146GLU-1-0.836-0.88719.613-0.153-0.1530.0000.0000.0000.000
144A147CYS0-0.027-0.01521.7650.0100.0100.0000.0000.0000.000
145A148HIS00.0840.04125.469-0.006-0.0060.0000.0000.0000.000
146A149ASN00.0460.01926.9470.0000.0000.0000.0000.0000.000
147A150GLU-1-0.788-0.87628.081-0.068-0.0680.0000.0000.0000.000
148A151ASN00.0180.02329.0620.0100.0100.0000.0000.0000.000
149A152GLY00.018-0.00329.349-0.003-0.0030.0000.0000.0000.000
150A153PRO0-0.039-0.03730.0900.0000.0000.0000.0000.0000.000
151A154SER00.0010.01726.642-0.002-0.0020.0000.0000.0000.000
152A155ARG10.8640.93224.1470.0960.0960.0000.0000.0000.000
153A156ARG10.9990.99725.3510.0590.0590.0000.0000.0000.000
154A157ALA0-0.052-0.00827.0280.0030.0030.0000.0000.0000.000
155A158ALA00.0570.03221.6540.0010.0010.0000.0000.0000.000
156A159GLU-1-0.781-0.89922.136-0.090-0.0900.0000.0000.0000.000
157A160ARG10.8170.93323.5750.0600.0600.0000.0000.0000.000
158A161PHE0-0.050-0.03021.9120.0070.0070.0000.0000.0000.000
159A162GLY00.0430.02619.3750.0010.0010.0000.0000.0000.000
160A163PHE0-0.055-0.00816.993-0.002-0.0020.0000.0000.0000.000
161A164ARG10.9000.94413.8910.1480.1480.0000.0000.0000.000
162A165PHE00.020-0.01217.020-0.015-0.0150.0000.0000.0000.000
163A166GLU-1-0.784-0.83213.284-0.283-0.2830.0000.0000.0000.000
164A167GLY00.0080.00917.475-0.001-0.0010.0000.0000.0000.000
165A168ILE0-0.034-0.02920.4600.0010.0010.0000.0000.0000.000
166A169PHE00.0050.02217.6730.0040.0040.0000.0000.0000.000
167A170ARG10.9740.97223.4120.1080.1080.0000.0000.0000.000
168A171GLN0-0.051-0.04427.091-0.004-0.0040.0000.0000.0000.000
169A172HIS0-0.057-0.00522.450-0.007-0.0070.0000.0000.0000.000
170A173MET00.0110.01026.447-0.004-0.0040.0000.0000.0000.000
171A174VAL0-0.003-0.00128.9900.0050.0050.0000.0000.0000.000
172A175VAL00.0150.00030.521-0.002-0.0020.0000.0000.0000.000
173A176LYS10.8130.90833.6930.0780.0780.0000.0000.0000.000
174A177GLY00.0250.02337.3070.0030.0030.0000.0000.0000.000
175A178ARG10.8100.88535.6050.0710.0710.0000.0000.0000.000
176A179ASN00.0360.00531.537-0.005-0.0050.0000.0000.0000.000
177A180ARG10.7980.85724.4540.1320.1320.0000.0000.0000.000
178A181ASP-1-0.793-0.89027.729-0.105-0.1050.0000.0000.0000.000
179A182THR0-0.0400.00122.3480.0050.0050.0000.0000.0000.000
180A183ALA0-0.041-0.00823.049-0.006-0.0060.0000.0000.0000.000
181A184TRP00.0160.00617.563-0.005-0.0050.0000.0000.0000.000
182A185PHE0-0.036-0.03617.6800.0130.0130.0000.0000.0000.000
183A186SER0-0.068-0.04312.649-0.019-0.0190.0000.0000.0000.000
184A187VAL00.0150.02312.9980.0290.0290.0000.0000.0000.000
185A188LEU00.0230.0057.883-0.047-0.0470.0000.0000.0000.000
186A189ASP-1-0.747-0.8664.457-0.820-0.700-0.001-0.009-0.1100.000
187A190SER0-0.056-0.0397.1190.1040.1040.0000.0000.0000.000
188A191GLU-1-0.861-0.9149.061-0.153-0.1530.0000.0000.0000.000
189A192TRP00.011-0.01712.0250.0310.0310.0000.0000.0000.000
190A193PRO00.0110.00511.9380.0160.0160.0000.0000.0000.000
191A194ALA00.0090.02614.8670.0150.0150.0000.0000.0000.000
192A195LEU0-0.013-0.00416.5030.0050.0050.0000.0000.0000.000
193A196LYS10.8160.89617.5120.0380.0380.0000.0000.0000.000
194A197GLN00.015-0.00918.5100.0050.0050.0000.0000.0000.000
195A198ALA00.0220.02321.4300.0020.0020.0000.0000.0000.000
196A199TYR0-0.031-0.04220.7260.0000.0000.0000.0000.0000.000
197A200GLN0-0.039-0.02222.3510.0030.0030.0000.0000.0000.000
198A201ALA00.0070.00925.4000.0020.0020.0000.0000.0000.000
199A202TRP0-0.034-0.02226.928-0.002-0.0020.0000.0000.0000.000
200A203LEU00.007-0.00425.8990.0000.0000.0000.0000.0000.000
201A204ALA00.0240.03629.4670.0000.0000.0000.0000.0000.000
202A205PRO00.0140.00231.523-0.001-0.0010.0000.0000.0000.000
203A206GLU-1-0.838-0.91934.127-0.006-0.0060.0000.0000.0000.000
204A207ASN0-0.016-0.00531.8120.0030.0030.0000.0000.0000.000
205A208PHE0-0.020-0.00832.207-0.002-0.0020.0000.0000.0000.000
206A209ASP-1-0.812-0.90037.258-0.014-0.0140.0000.0000.0000.000
207A210SER0-0.011-0.01540.997-0.001-0.0010.0000.0000.0000.000
208A211ALA0-0.0110.00543.3630.0000.0000.0000.0000.0000.000
209A212GLY0-0.0150.00539.838-0.002-0.0020.0000.0000.0000.000
210A213GLN0-0.031-0.01838.343-0.005-0.0050.0000.0000.0000.000
211A214GLN00.0050.01032.7240.0000.0000.0000.0000.0000.000
212A215LYS10.8300.89435.8250.0100.0100.0000.0000.0000.000
213A216LYS10.8860.96630.0830.0110.0110.0000.0000.0000.000
214A217THR0-0.062-0.06930.445-0.004-0.0040.0000.0000.0000.000
215A218LEU0-0.023-0.01023.8490.0020.0020.0000.0000.0000.000
216A219GLN00.0500.00625.5800.0000.0000.0000.0000.0000.000
217A220GLU-1-0.723-0.83226.030-0.018-0.0180.0000.0000.0000.000
218A221PHE0-0.031-0.01825.7990.0060.0060.0000.0000.0000.000
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