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

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FMODB ID: MNZMZ

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 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 231
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2707074.003347
FMO2-HF: Nuclear repulsion 2619056.03421
FMO2-HF: Total energy -88017.969137
FMO2-MP2: Total energy -88274.614192


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.
22.85424.252.996-2.086-2.305-0.013
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 : -0.934 / q_NPA : -0.968
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].
3A4PRO0-0.021-0.0163.886-2.827-1.331-0.008-0.690-0.7980.003
4A5VAL00.0280.0176.339-2.602-2.6020.0000.0000.0000.000
5A6ILE0-0.059-0.0159.332-0.370-0.3700.0000.0000.0000.000
6A7VAL00.0400.00912.428-1.114-1.1140.0000.0000.0000.000
7A8ALA0-0.056-0.03215.662-0.372-0.3720.0000.0000.0000.000
8A9LEU0-0.022-0.02518.724-0.349-0.3490.0000.0000.0000.000
9A10ASP-1-0.847-0.90621.58812.06912.0690.0000.0000.0000.000
10A11LEU0-0.054-0.02723.916-0.166-0.1660.0000.0000.0000.000
11A12ASP-1-0.814-0.89827.0959.7959.7950.0000.0000.0000.000
12A13ASN0-0.018-0.01329.134-0.058-0.0580.0000.0000.0000.000
13A14GLU-1-0.723-0.86527.08311.17711.1770.0000.0000.0000.000
14A15GLU-1-0.891-0.94327.6069.8039.8030.0000.0000.0000.000
15A16GLN0-0.055-0.02627.173-0.032-0.0320.0000.0000.0000.000
16A17LEU00.0110.01221.8160.4280.4280.0000.0000.0000.000
17A18ASN0-0.016-0.02823.3170.9420.9420.0000.0000.0000.000
18A19LYS10.9360.98424.190-9.717-9.7170.0000.0000.0000.000
19A20ILE0-0.0130.00420.6590.2050.2050.0000.0000.0000.000
20A21LEU00.0340.00318.7050.6010.6010.0000.0000.0000.000
21A22SER0-0.080-0.04419.7700.4840.4840.0000.0000.0000.000
22A23LYS10.9310.96121.300-11.817-11.8170.0000.0000.0000.000
23A24LEU0-0.025-0.00916.0640.3710.3710.0000.0000.0000.000
24A25GLY00.0120.00515.8591.0911.0910.0000.0000.0000.000
25A26ASP-1-0.840-0.91914.87717.58017.5800.0000.0000.0000.000
26A27PRO00.0280.00914.5711.3701.3700.0000.0000.0000.000
27A28HIS00.0020.00012.2001.7971.7970.0000.0000.0000.000
28A29ASP-1-0.855-0.90110.15728.65528.6550.0000.0000.0000.000
29A30VAL00.0050.00110.7400.6350.6350.0000.0000.0000.000
30A31PHE0-0.015-0.0158.366-0.166-0.1660.0000.0000.0000.000
31A32VAL00.0230.02011.899-0.344-0.3440.0000.0000.0000.000
32A33LYS10.8450.90915.280-14.286-14.2860.0000.0000.0000.000
33A34VAL00.0400.02517.450-0.544-0.5440.0000.0000.0000.000
34A35GLY00.036-0.00121.0290.3300.3300.0000.0000.0000.000
35A36MET0-0.026-0.00923.909-0.266-0.2660.0000.0000.0000.000
36A37GLU-1-0.897-0.93027.13510.50310.5030.0000.0000.0000.000
37A38LEU00.0580.04723.698-0.218-0.2180.0000.0000.0000.000
38A39PHE0-0.010-0.02125.507-0.257-0.2570.0000.0000.0000.000
39A40TYR0-0.021-0.04227.355-0.077-0.0770.0000.0000.0000.000
40A41ASN0-0.0130.00230.385-0.560-0.5600.0000.0000.0000.000
41A42ALA0-0.0180.00027.909-0.163-0.1630.0000.0000.0000.000
42A43GLY00.0090.01329.420-0.024-0.0240.0000.0000.0000.000
43A44ILE0-0.029-0.03426.4790.4570.4570.0000.0000.0000.000
44A45ASP-1-0.873-0.94125.82610.65410.6540.0000.0000.0000.000
45A46VAL00.0100.01025.0410.3650.3650.0000.0000.0000.000
46A47ILE00.000-0.00320.5610.4920.4920.0000.0000.0000.000
47A48LYS10.8700.93921.567-11.952-11.9520.0000.0000.0000.000
48A49LYS10.8250.89623.025-10.494-10.4940.0000.0000.0000.000
49A50LEU0-0.0160.01219.3650.2970.2970.0000.0000.0000.000
50A51THR00.004-0.02317.3430.4570.4570.0000.0000.0000.000
51A52GLN0-0.020-0.01417.7210.4890.4890.0000.0000.0000.000
52A53GLN0-0.042-0.02519.502-0.082-0.0820.0000.0000.0000.000
53A54GLY00.0260.01115.3580.3090.3090.0000.0000.0000.000
54A55TYR0-0.0080.01213.6401.4561.4560.0000.0000.0000.000
55A56LYS10.8250.9178.876-26.068-26.0680.0000.0000.0000.000
56A57ILE00.0450.02113.140-0.415-0.4150.0000.0000.0000.000
57A58PHE00.005-0.00814.3760.3070.3070.0000.0000.0000.000
58A59LEU00.0540.02716.109-0.598-0.5980.0000.0000.0000.000
59A60ASP-1-0.798-0.87619.46113.55913.5590.0000.0000.0000.000
60A61LEU0-0.011-0.02120.971-0.488-0.4880.0000.0000.0000.000
61A62LYS10.8010.90922.947-13.122-13.1220.0000.0000.0000.000
62A63MET00.0170.01924.074-0.552-0.5520.0000.0000.0000.000
63A64HIS00.024-0.00927.1430.3460.3460.0000.0000.0000.000
64A65ASP-1-0.791-0.86630.0118.6368.6360.0000.0000.0000.000
65A66ILE00.0280.00232.1750.1680.1680.0000.0000.0000.000
66A67PRO00.000-0.01730.9720.1550.1550.0000.0000.0000.000
67A68ASN00.0300.01330.9200.4390.4390.0000.0000.0000.000
68A69THR0-0.005-0.00432.5710.0900.0900.0000.0000.0000.000
69A70VAL00.0230.00326.6960.2400.2400.0000.0000.0000.000
70A71TYR00.0140.03727.6360.3370.3370.0000.0000.0000.000
71A72ASN0-0.043-0.04628.0630.3600.3600.0000.0000.0000.000
72A73GLY00.0300.02628.6620.0670.0670.0000.0000.0000.000
73A74ALA00.014-0.00223.7010.2920.2920.0000.0000.0000.000
74A75LYS10.8750.94924.313-9.947-9.9470.0000.0000.0000.000
75A76ALA0-0.050-0.03126.6150.0230.0230.0000.0000.0000.000
76A77LEU00.024-0.00122.7340.1910.1910.0000.0000.0000.000
77A78ALA00.0270.01721.0210.4290.4290.0000.0000.0000.000
78A79LYS10.9400.98721.474-10.286-10.2860.0000.0000.0000.000
79A80LEU0-0.040-0.01822.207-0.146-0.1460.0000.0000.0000.000
80A81GLY00.0140.02918.9900.2320.2320.0000.0000.0000.000
81A82ILE0-0.047-0.01417.0180.8130.8130.0000.0000.0000.000
82A83THR00.0010.00010.7060.3830.3830.0000.0000.0000.000
83A84PHE00.010-0.0089.6080.7100.7100.0000.0000.0000.000
84A85THR0-0.019-0.01715.159-0.938-0.9380.0000.0000.0000.000
85A86THR00.013-0.00218.5960.2660.2660.0000.0000.0000.000
86A87VAL0-0.028-0.00520.937-0.474-0.4740.0000.0000.0000.000
87A88HIS00.0250.01623.5520.3760.3760.0000.0000.0000.000
88A89ALA00.0050.00124.412-0.146-0.1460.0000.0000.0000.000
89A90LEU00.0060.00126.202-0.258-0.2580.0000.0000.0000.000
90A91GLY00.0100.00328.885-0.355-0.3550.0000.0000.0000.000
91A92GLY0-0.024-0.00929.440-0.227-0.2270.0000.0000.0000.000
92A93SER00.007-0.02927.5620.0880.0880.0000.0000.0000.000
93A94GLN00.0310.00627.7360.3380.3380.0000.0000.0000.000
94A95MET0-0.0090.04426.842-0.011-0.0110.0000.0000.0000.000
95A96ILE0-0.0120.00222.8720.2520.2520.0000.0000.0000.000
96A97LYS10.9570.98324.356-10.320-10.3200.0000.0000.0000.000
97A98SER00.007-0.00625.6240.1320.1320.0000.0000.0000.000
98A99ALA0-0.0010.00024.3690.0270.0270.0000.0000.0000.000
99A100LYS10.8520.92116.718-16.364-16.3640.0000.0000.0000.000
100A101ASP-1-0.880-0.94722.73211.89211.8920.0000.0000.0000.000
101A102GLY0-0.039-0.02825.401-0.082-0.0820.0000.0000.0000.000
102A103LEU0-0.033-0.02218.6360.0150.0150.0000.0000.0000.000
103A104ILE00.0060.00420.7420.4290.4290.0000.0000.0000.000
104A105ALA0-0.034-0.01122.502-0.014-0.0140.0000.0000.0000.000
105A106GLY0-0.016-0.00424.558-0.522-0.5220.0000.0000.0000.000
106A107THR0-0.035-0.02819.3480.4440.4440.0000.0000.0000.000
107A108PRO0-0.022-0.00420.862-0.408-0.4080.0000.0000.0000.000
108A109ALA00.0520.01621.3300.6440.6440.0000.0000.0000.000
109A110GLY0-0.0070.00119.4980.0300.0300.0000.0000.0000.000
110A111HIS0-0.060-0.02017.0880.9690.9690.0000.0000.0000.000
111A112SER0-0.011-0.01113.1910.4330.4330.0000.0000.0000.000
112A113VAL00.0120.01115.298-0.497-0.4970.0000.0000.0000.000
113A114PRO0-0.0050.00415.1751.4891.4890.0000.0000.0000.000
114A115LYS10.8050.91711.091-22.302-22.3020.0000.0000.0000.000
115A116LEU00.0180.00314.885-0.439-0.4390.0000.0000.0000.000
116A117LEU0-0.040-0.01613.6820.3180.3180.0000.0000.0000.000
117A118ALA00.0390.00317.835-0.749-0.7490.0000.0000.0000.000
118A119VAL00.000-0.01820.5260.4300.4300.0000.0000.0000.000
119A120THR0-0.033-0.01022.424-0.603-0.6030.0000.0000.0000.000
120A121GLU-1-0.704-0.86824.3539.5979.5970.0000.0000.0000.000
121A122LEU0-0.036-0.01025.4210.4690.4690.0000.0000.0000.000
122A123THR00.011-0.01224.240-0.257-0.2570.0000.0000.0000.000
123A124SER0-0.0060.00327.262-0.054-0.0540.0000.0000.0000.000
124A125ILE0-0.036-0.00530.227-0.339-0.3390.0000.0000.0000.000
125A126SER00.0630.03031.1110.1970.1970.0000.0000.0000.000
126A127ASP-1-0.858-0.96133.1489.1909.1900.0000.0000.0000.000
127A128ASP-1-0.831-0.90835.0487.3357.3350.0000.0000.0000.000
128A129VAL00.0220.02135.041-0.090-0.0900.0000.0000.0000.000
129A130LEU0-0.039-0.02831.907-0.020-0.0200.0000.0000.0000.000
130A131ARG10.7920.90835.278-7.612-7.6120.0000.0000.0000.000
131A132ASN0-0.026-0.02938.751-0.208-0.2080.0000.0000.0000.000
132A133GLU-1-0.913-0.94538.6447.6357.6350.0000.0000.0000.000
133A134GLN0-0.076-0.03631.721-0.078-0.0780.0000.0000.0000.000
134A135ASN0-0.064-0.03137.409-0.184-0.1840.0000.0000.0000.000
135A136CYS0-0.045-0.00333.323-0.049-0.0490.0000.0000.0000.000
136A137ARG10.9350.96536.239-8.340-8.3400.0000.0000.0000.000
137A138LEU0-0.031-0.02732.199-0.075-0.0750.0000.0000.0000.000
138A139PRO00.0580.04533.150-0.004-0.0040.0000.0000.0000.000
139A140MET00.0770.03428.3150.3440.3440.0000.0000.0000.000
140A141ALA0-0.066-0.03927.7890.3630.3630.0000.0000.0000.000
141A142GLU-1-0.903-0.95627.5799.3569.3560.0000.0000.0000.000
142A143GLN0-0.003-0.01228.7810.1340.1340.0000.0000.0000.000
143A144VAL00.007-0.00223.5290.2550.2550.0000.0000.0000.000
144A145LEU00.0030.00423.3910.5020.5020.0000.0000.0000.000
145A146SER0-0.016-0.00524.7930.3100.3100.0000.0000.0000.000
146A147LEU00.0140.00125.7040.1580.1580.0000.0000.0000.000
147A148ALA0-0.0040.00720.7470.3120.3120.0000.0000.0000.000
148A149LYS10.8450.89821.616-11.673-11.6730.0000.0000.0000.000
149A150MET0-0.0210.00523.516-0.076-0.0760.0000.0000.0000.000
150A151ALA00.0040.00921.192-0.016-0.0160.0000.0000.0000.000
151A152LYS10.8570.92216.099-16.900-16.9000.0000.0000.0000.000
152A153HIS0-0.027-0.01420.6280.3110.3110.0000.0000.0000.000
153A154SER0-0.081-0.05923.027-0.797-0.7970.0000.0000.0000.000
154A155GLY00.0290.02220.654-0.158-0.1580.0000.0000.0000.000
155A156ALA0-0.009-0.00218.9110.4140.4140.0000.0000.0000.000
156A157ASP-1-0.777-0.88013.50918.55618.5560.0000.0000.0000.000
157A158GLY00.0390.01513.7811.4021.4020.0000.0000.0000.000
158A159VAL0-0.037-0.00215.390-1.198-1.1980.0000.0000.0000.000
159A160ILE0-0.029-0.00316.1230.9040.9040.0000.0000.0000.000
160A161CYS0-0.017-0.00517.785-0.545-0.5450.0000.0000.0000.000
161A162SER0-0.021-0.03418.5500.6070.6070.0000.0000.0000.000
162A163PRO00.024-0.01216.1450.2100.2100.0000.0000.0000.000
163A164LEU00.0210.00817.6160.3880.3880.0000.0000.0000.000
164A165GLU-1-0.800-0.87220.33012.37512.3750.0000.0000.0000.000
165A166VAL00.0130.01114.055-0.307-0.3070.0000.0000.0000.000
166A167LYS10.8970.95715.330-17.354-17.3540.0000.0000.0000.000
167A168LYS10.8930.94419.009-12.223-12.2230.0000.0000.0000.000
168A169LEU0-0.005-0.00318.307-0.410-0.4100.0000.0000.0000.000
169A170HIS0-0.047-0.03013.862-0.972-0.9720.0000.0000.0000.000
170A171GLU-1-0.885-0.94817.45513.43213.4320.0000.0000.0000.000
171A172ASN0-0.062-0.02520.432-0.977-0.9770.0000.0000.0000.000
172A173ILE0-0.067-0.02317.232-0.647-0.6470.0000.0000.0000.000
173A174GLY00.0400.04216.5630.1840.1840.0000.0000.0000.000
174A175ASP-1-0.844-0.91811.22621.22921.2290.0000.0000.0000.000
175A176ASP-1-0.869-0.89511.28320.60320.6030.0000.0000.0000.000
176A177PHE0-0.025-0.01912.231-1.631-1.6310.0000.0000.0000.000
177A178LEU0-0.012-0.0108.4931.2981.2980.0000.0000.0000.000
178A179TYR00.030-0.01711.719-2.250-2.2500.0000.0000.0000.000
179A180VAL00.0020.00411.8431.2701.2700.0000.0000.0000.000
180A181THR00.0020.00413.625-1.079-1.0790.0000.0000.0000.000
181A182PRO00.0270.00714.9350.6420.6420.0000.0000.0000.000
182A183GLY0-0.009-0.00717.463-0.502-0.5020.0000.0000.0000.000
183A184ILE0-0.045-0.01513.387-0.586-0.5860.0000.0000.0000.000
184A185ARG10.9180.94716.758-13.744-13.7440.0000.0000.0000.000
185A186PRO00.0120.03015.938-0.472-0.4720.0000.0000.0000.000
186A198ALA00.0290.01517.575-0.242-0.2420.0000.0000.0000.000
187A199THR0-0.013-0.03915.5130.1220.1220.0000.0000.0000.000
188A200PRO00.029-0.00610.9160.2380.2380.0000.0000.0000.000
189A201LYS10.8570.91811.415-16.387-16.3870.0000.0000.0000.000
190A202MET0-0.0140.00212.6420.1460.1460.0000.0000.0000.000
191A203ALA00.0200.01711.9580.0360.0360.0000.0000.0000.000
192A204LYS10.8380.9257.685-24.205-24.2050.0000.0000.0000.000
193A205GLU-1-0.792-0.87510.20919.52619.5260.0000.0000.0000.000
194A206TRP0-0.037-0.04613.200-0.899-0.8990.0000.0000.0000.000
195A207GLY00.0270.01611.489-0.884-0.8840.0000.0000.0000.000
196A208SER0-0.046-0.02311.1170.9440.9440.0000.0000.0000.000
197A209SER00.0490.0317.9361.1841.1840.0000.0000.0000.000
198A210ALA00.0040.0007.1393.2423.2420.0000.0000.0000.000
199A211ILE0-0.0240.0159.358-2.688-2.6880.0000.0000.0000.000
200A212VAL0-0.019-0.01111.6170.4720.4720.0000.0000.0000.000
201A213VAL00.0110.00213.773-0.750-0.7500.0000.0000.0000.000
202A214GLY00.0580.04516.2670.1730.1730.0000.0000.0000.000
203A215ARG10.8940.93119.526-10.957-10.9570.0000.0000.0000.000
204A216PRO0-0.049-0.02818.266-0.218-0.2180.0000.0000.0000.000
205A217ILE00.0060.02114.3440.2500.2500.0000.0000.0000.000
206A218THR00.005-0.02318.771-0.406-0.4060.0000.0000.0000.000
207A219LEU0-0.027-0.00921.522-0.501-0.5010.0000.0000.0000.000
208A220ALA0-0.0110.01220.853-0.398-0.3980.0000.0000.0000.000
209A221SER0-0.015-0.02522.843-0.101-0.1010.0000.0000.0000.000
210A222ASP-1-0.874-0.93120.13314.30114.3010.0000.0000.0000.000
211A223PRO0-0.038-0.01919.2550.5580.5580.0000.0000.0000.000
212A224LYS10.9000.96113.938-19.305-19.3050.0000.0000.0000.000
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