FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

tag_button

FMODB ID: 98QY2

Calculation Name: 3TFX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3TFX

Chain ID: A

ChEMBL ID:

UniProt ID: Q5FJB3

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 231
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2699743.255502
FMO2-HF: Nuclear repulsion 2611725.846931
FMO2-HF: Total energy -88017.408571
FMO2-MP2: Total energy -88274.057184


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:2:ASP)


Summations of interaction energy for fragment #1(A:2:ASP)
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.
26.27628.9841.192-1.915-1.985-0.01
Interaction energy analysis for fragmet #1(A:2:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.937 / q_NPA : -0.966
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].
3A4PRO00.0000.0013.860-2.353-0.592-0.012-0.851-0.8990.004
4A5VAL00.0090.0096.366-2.614-2.6140.0000.0000.0000.000
5A6ILE0-0.050-0.0189.344-0.284-0.2840.0000.0000.0000.000
6A7VAL00.032-0.00312.444-1.030-1.0300.0000.0000.0000.000
7A8ALA0-0.059-0.03415.656-0.284-0.2840.0000.0000.0000.000
8A9LEU0-0.031-0.02518.817-0.415-0.4150.0000.0000.0000.000
9A10ASP-1-0.963-0.97321.53312.55212.5520.0000.0000.0000.000
10A11LEU0-0.044-0.03024.140-0.232-0.2320.0000.0000.0000.000
11A12ASP-1-0.833-0.90727.1909.7519.7510.0000.0000.0000.000
12A13ASN0-0.014-0.01629.024-0.138-0.1380.0000.0000.0000.000
13A14GLU-1-0.750-0.89127.17811.10111.1010.0000.0000.0000.000
14A15GLU-1-0.881-0.94027.5429.7579.7570.0000.0000.0000.000
15A16GLN0-0.063-0.02627.395-0.055-0.0550.0000.0000.0000.000
16A17LEU0-0.017-0.00721.7700.4150.4150.0000.0000.0000.000
17A18ASN00.007-0.01523.4260.9660.9660.0000.0000.0000.000
18A19LYS10.9470.98924.515-9.758-9.7580.0000.0000.0000.000
19A20ILE0-0.0210.00020.6900.2250.2250.0000.0000.0000.000
20A21LEU00.0580.02018.9160.5810.5810.0000.0000.0000.000
21A22SER0-0.088-0.03919.8300.4830.4830.0000.0000.0000.000
22A23LYS10.9130.95321.101-11.737-11.7370.0000.0000.0000.000
23A24LEU00.004-0.00515.9810.2870.2870.0000.0000.0000.000
24A25GLY0-0.030-0.03015.3331.1601.1600.0000.0000.0000.000
25A26ASP-1-0.855-0.91514.52817.25117.2510.0000.0000.0000.000
26A27PRO00.0550.01414.1841.2901.2900.0000.0000.0000.000
27A28HIS0-0.0060.00011.8121.8291.8290.0000.0000.0000.000
28A29ASP-1-0.902-0.9329.69829.88929.8890.0000.0000.0000.000
29A30VAL0-0.039-0.01910.6160.3660.3660.0000.0000.0000.000
30A31PHE00.000-0.0038.406-0.160-0.1600.0000.0000.0000.000
31A32VAL00.0130.02011.998-0.412-0.4120.0000.0000.0000.000
32A33LYS10.8550.91815.435-14.242-14.2420.0000.0000.0000.000
33A34VAL00.0330.03117.598-0.526-0.5260.0000.0000.0000.000
34A35GLY00.0500.01521.2020.2730.2730.0000.0000.0000.000
35A36MET0-0.030-0.02123.881-0.225-0.2250.0000.0000.0000.000
36A37GLU-1-0.902-0.93727.11010.44010.4400.0000.0000.0000.000
37A38LEU00.0530.03723.590-0.201-0.2010.0000.0000.0000.000
38A39PHE0-0.006-0.01025.075-0.265-0.2650.0000.0000.0000.000
39A40TYR0-0.012-0.03326.940-0.081-0.0810.0000.0000.0000.000
40A41ASN0-0.0210.00230.057-0.565-0.5650.0000.0000.0000.000
41A42ALA0-0.025-0.01027.590-0.166-0.1660.0000.0000.0000.000
42A43GLY00.0150.02028.830-0.139-0.1390.0000.0000.0000.000
43A44ILE0-0.014-0.03726.4310.4570.4570.0000.0000.0000.000
44A45ASP-1-0.891-0.94025.92210.62910.6290.0000.0000.0000.000
45A46VAL00.0080.00724.5480.3820.3820.0000.0000.0000.000
46A47ILE00.0080.00320.6150.4990.4990.0000.0000.0000.000
47A48LYS10.9350.97221.486-12.051-12.0510.0000.0000.0000.000
48A49LYS10.8480.92122.383-10.425-10.4250.0000.0000.0000.000
49A50LEU0-0.029-0.01119.3370.3850.3850.0000.0000.0000.000
50A51THR0-0.005-0.01817.2530.4940.4940.0000.0000.0000.000
51A52GLN0-0.041-0.01917.7240.4710.4710.0000.0000.0000.000
52A53GLN0-0.051-0.02919.4110.1680.1680.0000.0000.0000.000
53A54GLY00.0160.01015.4630.3720.3720.0000.0000.0000.000
54A55TYR0-0.0210.00113.6491.3181.3180.0000.0000.0000.000
55A56LYS10.8730.9528.120-27.740-27.7400.0000.0000.0000.000
56A57ILE00.0430.01512.979-0.502-0.5020.0000.0000.0000.000
57A58PHE0-0.009-0.01614.3530.2890.2890.0000.0000.0000.000
58A59LEU00.0430.01716.017-0.597-0.5970.0000.0000.0000.000
59A60ASP-1-0.811-0.87719.66213.57713.5770.0000.0000.0000.000
60A61LEU00.004-0.01221.276-0.444-0.4440.0000.0000.0000.000
61A62LYS10.8210.91323.012-13.152-13.1520.0000.0000.0000.000
62A63MET00.0100.01623.928-0.570-0.5700.0000.0000.0000.000
63A64HIS00.022-0.00727.3110.3330.3330.0000.0000.0000.000
64A65ASP-1-0.796-0.87530.1218.6448.6440.0000.0000.0000.000
65A66ILE00.014-0.00832.1510.1860.1860.0000.0000.0000.000
66A67PRO00.009-0.01131.1380.1690.1690.0000.0000.0000.000
67A68ASN00.0260.01031.2430.4060.4060.0000.0000.0000.000
68A69THR00.0160.00832.8210.0890.0890.0000.0000.0000.000
69A70VAL00.0240.00827.0540.2350.2350.0000.0000.0000.000
70A71TYR00.0200.03427.9880.3220.3220.0000.0000.0000.000
71A72ASN0-0.043-0.04028.2360.3790.3790.0000.0000.0000.000
72A73GLY00.0260.02028.7930.0910.0910.0000.0000.0000.000
73A74ALA00.027-0.00224.0660.2970.2970.0000.0000.0000.000
74A75LYS10.9030.96224.195-10.050-10.0500.0000.0000.0000.000
75A76ALA0-0.070-0.04525.6410.2070.2070.0000.0000.0000.000
76A77LEU00.0260.00622.4330.1600.1600.0000.0000.0000.000
77A78ALA00.0090.01420.8010.5080.5080.0000.0000.0000.000
78A79LYS10.9520.99021.386-10.382-10.3820.0000.0000.0000.000
79A80LEU0-0.064-0.03522.019-0.089-0.0890.0000.0000.0000.000
80A81GLY00.0090.03118.7570.1740.1740.0000.0000.0000.000
81A82ILE0-0.0110.00116.8400.7780.7780.0000.0000.0000.000
82A83THR0-0.015-0.00710.5850.5470.5470.0000.0000.0000.000
83A84PHE0-0.004-0.0029.5890.5890.5890.0000.0000.0000.000
84A85THR00.008-0.00715.169-0.867-0.8670.0000.0000.0000.000
85A86THR00.009-0.00718.7890.2280.2280.0000.0000.0000.000
86A87VAL0-0.024-0.00221.036-0.460-0.4600.0000.0000.0000.000
87A88HIS00.0370.01823.6380.4210.4210.0000.0000.0000.000
88A89ALA00.0210.00824.555-0.171-0.1710.0000.0000.0000.000
89A90LEU00.0040.00526.354-0.269-0.2690.0000.0000.0000.000
90A91GLY00.0040.00129.087-0.352-0.3520.0000.0000.0000.000
91A92GLY0-0.030-0.01029.560-0.244-0.2440.0000.0000.0000.000
92A93SER00.008-0.02827.9970.1670.1670.0000.0000.0000.000
93A94GLN00.0400.00727.9990.4860.4860.0000.0000.0000.000
94A95MET0-0.0100.03326.9210.0850.0850.0000.0000.0000.000
95A96ILE0-0.0060.00623.0420.2740.2740.0000.0000.0000.000
96A97LYS10.9640.98724.493-10.267-10.2670.0000.0000.0000.000
97A98SER0-0.010-0.00925.8050.0730.0730.0000.0000.0000.000
98A99ALA0-0.0050.00324.1330.0900.0900.0000.0000.0000.000
99A100LYS10.8630.92316.655-16.732-16.7320.0000.0000.0000.000
100A101ASP-1-0.876-0.94022.61312.11812.1180.0000.0000.0000.000
101A102GLY0-0.040-0.02925.330-0.086-0.0860.0000.0000.0000.000
102A103LEU0-0.038-0.03318.9910.0210.0210.0000.0000.0000.000
103A104ILE0-0.0020.00120.9210.3900.3900.0000.0000.0000.000
104A105ALA0-0.048-0.01722.627-0.044-0.0440.0000.0000.0000.000
105A106GLY0-0.049-0.02224.741-0.323-0.3230.0000.0000.0000.000
106A107THR0-0.019-0.02118.7550.4200.4200.0000.0000.0000.000
107A108PRO0-0.024-0.00220.686-0.380-0.3800.0000.0000.0000.000
108A109ALA00.0710.02920.7720.7030.7030.0000.0000.0000.000
109A110GLY0-0.022-0.00118.957-0.090-0.0900.0000.0000.0000.000
110A111HIS0-0.061-0.03716.6851.1501.1500.0000.0000.0000.000
111A112SER00.0280.01913.0280.3440.3440.0000.0000.0000.000
112A113VAL0-0.018-0.00715.064-0.370-0.3700.0000.0000.0000.000
113A114PRO0-0.019-0.00815.1861.3531.3530.0000.0000.0000.000
114A115LYS10.8440.93011.011-23.168-23.1680.0000.0000.0000.000
115A116LEU0-0.002-0.01114.876-0.471-0.4710.0000.0000.0000.000
116A117LEU0-0.032-0.00913.7180.2560.2560.0000.0000.0000.000
117A118ALA00.014-0.00317.861-0.746-0.7460.0000.0000.0000.000
118A119VAL0-0.007-0.02220.4860.4630.4630.0000.0000.0000.000
119A120THR00.0190.00422.788-0.503-0.5030.0000.0000.0000.000
120A121GLU-1-0.738-0.86824.7989.6409.6400.0000.0000.0000.000
121A122LEU0-0.025-0.01625.5660.4200.4200.0000.0000.0000.000
122A123THR00.016-0.00624.449-0.221-0.2210.0000.0000.0000.000
123A124SER0-0.018-0.00927.416-0.094-0.0940.0000.0000.0000.000
124A125ILE0-0.0310.00230.308-0.336-0.3360.0000.0000.0000.000
125A126SER00.0470.02431.2440.1910.1910.0000.0000.0000.000
126A127ASP-1-0.858-0.95533.6099.0879.0870.0000.0000.0000.000
127A128ASP-1-0.829-0.91235.1867.3557.3550.0000.0000.0000.000
128A129VAL00.0120.02735.297-0.100-0.1000.0000.0000.0000.000
129A130LEU0-0.042-0.03232.113-0.037-0.0370.0000.0000.0000.000
130A131ARG10.8100.91435.457-7.547-7.5470.0000.0000.0000.000
131A132ASN0-0.061-0.06038.782-0.181-0.1810.0000.0000.0000.000
132A133GLU-1-0.918-0.94238.4877.6517.6510.0000.0000.0000.000
133A134GLN0-0.070-0.03831.918-0.074-0.0740.0000.0000.0000.000
134A135ASN0-0.033-0.02037.522-0.180-0.1800.0000.0000.0000.000
135A136CYS0-0.0770.00634.3500.0100.0100.0000.0000.0000.000
136A137ARG10.9920.98736.583-8.320-8.3200.0000.0000.0000.000
137A138LEU0-0.078-0.05432.391-0.127-0.1270.0000.0000.0000.000
138A139PRO00.0760.04333.6590.0350.0350.0000.0000.0000.000
139A140MET00.1010.04528.7700.3290.3290.0000.0000.0000.000
140A141ALA0-0.060-0.03627.7710.3250.3250.0000.0000.0000.000
141A142GLU-1-0.896-0.95927.6309.3299.3290.0000.0000.0000.000
142A143GLN0-0.018-0.01629.2980.0590.0590.0000.0000.0000.000
143A144VAL0-0.001-0.00323.8840.2510.2510.0000.0000.0000.000
144A145LEU0-0.002-0.00123.6000.4460.4460.0000.0000.0000.000
145A146SER0-0.027-0.00825.0270.3210.3210.0000.0000.0000.000
146A147LEU00.0060.00125.6180.1150.1150.0000.0000.0000.000
147A148ALA0-0.0100.00320.9720.3100.3100.0000.0000.0000.000
148A149LYS10.8810.92721.935-11.612-11.6120.0000.0000.0000.000
149A150MET0-0.0110.01423.6600.0050.0050.0000.0000.0000.000
150A151ALA00.0060.00221.600-0.013-0.0130.0000.0000.0000.000
151A152LYS10.8470.92016.473-16.665-16.6650.0000.0000.0000.000
152A153HIS0-0.032-0.02420.7360.3500.3500.0000.0000.0000.000
153A154SER0-0.089-0.05223.363-0.656-0.6560.0000.0000.0000.000
154A155GLY00.0360.01621.103-0.238-0.2380.0000.0000.0000.000
155A156ALA0-0.019-0.00119.2810.4200.4200.0000.0000.0000.000
156A157ASP-1-0.759-0.86713.81818.69218.6920.0000.0000.0000.000
157A158GLY00.0490.01514.0471.4081.4080.0000.0000.0000.000
158A159VAL0-0.0390.00115.458-1.157-1.1570.0000.0000.0000.000
159A160ILE0-0.036-0.01116.2040.8960.8960.0000.0000.0000.000
160A161CYS0-0.030-0.00417.562-0.534-0.5340.0000.0000.0000.000
161A162SER0-0.017-0.04018.3870.6180.6180.0000.0000.0000.000
162A163PRO00.025-0.01316.4620.1920.1920.0000.0000.0000.000
163A164LEU00.0200.00517.8150.3020.3020.0000.0000.0000.000
164A165GLU-1-0.871-0.91020.64412.37312.3730.0000.0000.0000.000
165A166VAL00.0090.01314.436-0.247-0.2470.0000.0000.0000.000
166A167LYS10.9390.99416.146-16.644-16.6440.0000.0000.0000.000
167A168LYS11.0021.00519.435-12.032-12.0320.0000.0000.0000.000
168A169LEU00.005-0.00618.765-0.249-0.2490.0000.0000.0000.000
169A170HIS0-0.068-0.04314.164-0.978-0.9780.0000.0000.0000.000
170A171GLU-1-0.913-0.96117.69513.02213.0220.0000.0000.0000.000
171A172ASN0-0.056-0.01420.821-0.768-0.7680.0000.0000.0000.000
172A173ILE0-0.065-0.03717.378-0.468-0.4680.0000.0000.0000.000
173A174GLY00.0250.03216.8610.1220.1220.0000.0000.0000.000
174A175ASP-1-0.829-0.91311.78920.80020.8000.0000.0000.0000.000
175A176ASP-1-0.900-0.91811.53320.95720.9570.0000.0000.0000.000
176A177PHE0-0.014-0.01212.161-1.699-1.6990.0000.0000.0000.000
177A178LEU0-0.025-0.0078.5351.4511.4510.0000.0000.0000.000
178A179TYR00.025-0.02011.603-2.257-2.2570.0000.0000.0000.000
179A180VAL00.0050.00711.8481.2151.2150.0000.0000.0000.000
180A181THR00.0100.00213.720-1.158-1.1580.0000.0000.0000.000
181A182PRO00.0350.01414.9200.6300.6300.0000.0000.0000.000
182A183GLY0-0.036-0.01417.422-0.338-0.3380.0000.0000.0000.000
183A184ILE0-0.021-0.00613.706-0.659-0.6590.0000.0000.0000.000
184A185ARG10.9170.94416.980-13.307-13.3070.0000.0000.0000.000
185A186PRO00.0300.03916.442-0.235-0.2350.0000.0000.0000.000
186A198ALA00.0290.01317.896-0.204-0.2040.0000.0000.0000.000
187A199THR0-0.009-0.01815.7450.0290.0290.0000.0000.0000.000
188A200PRO00.0420.00711.2010.3400.3400.0000.0000.0000.000
189A201LYS10.8730.92311.696-15.606-15.6060.0000.0000.0000.000
190A202MET0-0.024-0.00713.2230.2440.2440.0000.0000.0000.000
191A203ALA00.0060.01012.2560.0540.0540.0000.0000.0000.000
192A204LYS10.8760.9558.220-22.864-22.8640.0000.0000.0000.000
193A205GLU-1-0.826-0.90510.62318.34018.3400.0000.0000.0000.000
194A206TRP0-0.089-0.07713.664-0.688-0.6880.0000.0000.0000.000
195A207GLY00.0290.02111.476-0.820-0.8200.0000.0000.0000.000
196A208SER0-0.030-0.01211.4040.8140.8140.0000.0000.0000.000
197A209SER00.0380.0178.0581.1381.1380.0000.0000.0000.000
198A210ALA00.0120.0047.3043.1623.1620.0000.0000.0000.000
199A211ILE0-0.0300.0159.576-2.472-2.4720.0000.0000.0000.000
200A212VAL0-0.036-0.01511.8100.5780.5780.0000.0000.0000.000
201A213VAL00.0200.00913.588-0.864-0.8640.0000.0000.0000.000
202A214GLY00.0720.04916.0580.0360.0360.0000.0000.0000.000
203A215ARG10.9770.97719.456-10.785-10.7850.0000.0000.0000.000
204A216PRO0-0.034-0.01418.109-0.192-0.1920.0000.0000.0000.000
205A217ILE00.0320.02714.1130.0570.0570.0000.0000.0000.000
206A218THR00.009-0.00918.588-0.395-0.3950.0000.0000.0000.000
207A219LEU0-0.036-0.02021.285-0.504-0.5040.0000.0000.0000.000
208A220ALA0-0.0140.01420.651-0.415-0.4150.0000.0000.0000.000
209A221SER0-0.003-0.02422.643-0.124-0.1240.0000.0000.0000.000
210A222ASP-1-0.875-0.92820.25313.99013.9900.0000.0000.0000.000
211A223PRO0-0.036-0.01819.4810.5720.5720.0000.0000.0000.000
212A224LYS10.9821.01715.227-17.200-17.2000.0000.0000.0000.000
213A225ALA0-0.001-0.00415.2961.3081.3080.0000.0000.0000.000
214A226ALA0-0.022-0.01515.7240.5990.5990.0000.0000.0000.000
215A227TYR0-0.022-0.03010.8210.8330.8330.0000.0000.0000.000
216A228GLU-1-0.814-0.89510.59026.40526.4050.0000.0000.0000.000
217A229ALA0-0.032-0.01310.7341.5261.5260.0000.0000.0000.000
218A230ILE00.001-0.00610.9030.4630.4630.0000.0000.0000.000
219A231LYS10.8020.8886.968-26.248-26.2480.0000.0000.0000.000
220A232LYS10.9810.9946.586-18.108-18.1080.0000.0000.0000.000
221A233GLU-1-0.838-0.9188.27418.96518.9650.0000.0000.0000.000
222A234PHE0-0.058-0.0426.565-0.192-0.1920.0000.0000.0000.000
223A235ASN0-0.001-0.0132.4513.2374.1101.205-1.064-1.014-0.014
224A236ALA0-0.0080.0135.3071.5621.636-0.0010.000-0.0720.000
225A237GLU-1-0.816-0.9166.13131.02531.0250.0000.0000.0000.000
226A238ASN0-0.048-0.0158.678-3.346-3.3460.0000.0000.0000.000
227A239LEU0-0.054-0.01311.778-0.762-0.7620.0000.0000.0000.000
228A240TYR0-0.001-0.01513.191-0.858-0.8580.0000.0000.0000.000
229A241PHE00.0230.01616.3730.7520.7520.0000.0000.0000.000
230A242GLN00.000-0.01318.253-0.912-0.9120.0000.0000.0000.000
231A243SER00.0080.02319.8810.2240.2240.0000.0000.0000.000