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: J3Z59

Calculation Name: 5EFT-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5EFT

Chain ID: B

ChEMBL ID:

UniProt ID: B6SCH3

Base Structure: X-ray

Registration Date: 2023-06-20

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 262
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3727267.122191
FMO2-HF: Nuclear repulsion 3621401.484952
FMO2-HF: Total energy -105865.637239
FMO2-MP2: Total energy -106178.211135


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(B:4:LEU)


Summations of interaction energy for fragment #1(B: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.
-4.517-2.348-0.01-0.891-1.2670.001
Interaction energy analysis for fragmet #1(B:4:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.024 / q_NPA : -0.026
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].
3B6ARG10.8340.9103.4020.1071.835-0.010-0.757-0.9600.000
4B7ARG10.7910.8884.321-0.172-0.031-0.001-0.021-0.1190.000
5B8THR00.0330.0336.970-0.388-0.3880.0000.0000.0000.000
6B9PHE00.0410.00510.5070.1060.1060.0000.0000.0000.000
7B10GLY00.0460.01913.274-0.018-0.0180.0000.0000.0000.000
8B11SER0-0.081-0.02910.1080.1080.1080.0000.0000.0000.000
9B12TYR00.0380.01511.592-0.012-0.0120.0000.0000.0000.000
10B13LYS10.9500.9694.066-7.008-6.7080.001-0.113-0.1880.001
11B14ILE0-0.033-0.01310.220-0.241-0.2410.0000.0000.0000.000
12B15GLU-1-0.876-0.9337.8161.4191.4190.0000.0000.0000.000
13B16GLU-1-0.901-0.96911.8070.2850.2850.0000.0000.0000.000
14B17LEU00.0070.01714.717-0.044-0.0440.0000.0000.0000.000
15B18THR0-0.020-0.02916.8880.0060.0060.0000.0000.0000.000
16B19ILE0-0.0160.00019.787-0.023-0.0230.0000.0000.0000.000
17B43LYS10.9480.97023.996-0.141-0.1410.0000.0000.0000.000
18B44LYS10.9580.98017.835-0.229-0.2290.0000.0000.0000.000
19B45ILE0-0.047-0.02219.566-0.006-0.0060.0000.0000.0000.000
20B46PRO00.0310.03516.7870.0090.0090.0000.0000.0000.000
21B47LEU0-0.016-0.02013.991-0.058-0.0580.0000.0000.0000.000
22B48LEU0-0.028-0.00113.6410.0970.0970.0000.0000.0000.000
23B49ASP-1-0.815-0.8969.0780.6980.6980.0000.0000.0000.000
24B50ASP-1-0.864-0.95512.1990.4480.4480.0000.0000.0000.000
25B51GLY00.0600.03712.6170.0270.0270.0000.0000.0000.000
26B52ILE0-0.049-0.03313.265-0.062-0.0620.0000.0000.0000.000
27B53PHE0-0.010-0.00614.507-0.048-0.0480.0000.0000.0000.000
28B54GLU-1-0.857-0.95810.8810.0940.0940.0000.0000.0000.000
29B55LEU0-0.0050.01414.265-0.040-0.0400.0000.0000.0000.000
30B56LEU0-0.014-0.02316.461-0.028-0.0280.0000.0000.0000.000
31B57ASN00.0180.01415.887-0.014-0.0140.0000.0000.0000.000
32B58TYR00.010-0.01210.896-0.061-0.0610.0000.0000.0000.000
33B59LEU00.0090.00917.776-0.010-0.0100.0000.0000.0000.000
34B60ILE00.0020.01121.166-0.005-0.0050.0000.0000.0000.000
35B61ASP-1-0.903-0.95718.632-0.115-0.1150.0000.0000.0000.000
36B62GLY00.0210.03021.399-0.011-0.0110.0000.0000.0000.000
37B63THR0-0.075-0.02615.973-0.018-0.0180.0000.0000.0000.000
38B64ASN00.0710.04119.0580.0320.0320.0000.0000.0000.000
39B65PHE00.0230.01815.089-0.024-0.0240.0000.0000.0000.000
40B66ASN00.0240.01915.090-0.003-0.0030.0000.0000.0000.000
41B67LYS10.8770.93714.1690.1500.1500.0000.0000.0000.000
42B68THR00.0080.00012.820-0.022-0.0220.0000.0000.0000.000
43B69CYS0-0.062-0.0277.549-0.012-0.0120.0000.0000.0000.000
44B70TYR00.0680.0298.3100.1200.1200.0000.0000.0000.000
45B71CYS00.0210.05410.9730.0450.0450.0000.0000.0000.000
46B72GLY00.0400.02910.631-0.010-0.0100.0000.0000.0000.000
47B73PHE0-0.0080.0006.7060.0450.0450.0000.0000.0000.000
48B74ASN00.0150.03112.747-0.039-0.0390.0000.0000.0000.000
49B75TYR00.057-0.02912.2540.0650.0650.0000.0000.0000.000
50B76SER0-0.065-0.04518.006-0.014-0.0140.0000.0000.0000.000
51B77HIS0-0.002-0.01415.888-0.019-0.0190.0000.0000.0000.000
52B78LEU0-0.071-0.03516.781-0.002-0.0020.0000.0000.0000.000
53B79PRO00.0740.01920.806-0.012-0.0120.0000.0000.0000.000
54B80ASN0-0.010-0.01023.699-0.006-0.0060.0000.0000.0000.000
55B81LEU00.0130.02516.076-0.008-0.0080.0000.0000.0000.000
56B82GLU-1-0.919-0.96519.2190.0020.0020.0000.0000.0000.000
57B83ARG10.8700.91220.379-0.069-0.0690.0000.0000.0000.000
58B84ASP-1-0.741-0.86123.8810.0630.0630.0000.0000.0000.000
59B85PHE0-0.015-0.01917.3720.0000.0000.0000.0000.0000.000
60B86ASN00.0430.01921.093-0.016-0.0160.0000.0000.0000.000
61B87ILE00.0200.02423.093-0.007-0.0070.0000.0000.0000.000
62B88ALA00.0060.00323.533-0.005-0.0050.0000.0000.0000.000
63B89SER0-0.071-0.07021.198-0.005-0.0050.0000.0000.0000.000
64B90LEU00.0200.02123.515-0.009-0.0090.0000.0000.0000.000
65B91TYR00.0710.04126.786-0.004-0.0040.0000.0000.0000.000
66B92VAL0-0.051-0.02124.4600.0000.0000.0000.0000.0000.000
67B93ARG10.8540.94024.3720.0540.0540.0000.0000.0000.000
68B94GLU-1-0.883-0.95226.664-0.016-0.0160.0000.0000.0000.000
69B95ASN00.0070.00630.047-0.004-0.0040.0000.0000.0000.000
70B96PHE0-0.018-0.05026.834-0.002-0.0020.0000.0000.0000.000
71B97GLU-1-0.890-0.95028.728-0.047-0.0470.0000.0000.0000.000
72B98ILE00.0470.04131.0170.0000.0000.0000.0000.0000.000
73B99CYS0-0.098-0.05432.0040.0020.0020.0000.0000.0000.000
74B100THR0-0.132-0.07729.469-0.003-0.0030.0000.0000.0000.000
75B101ASP-1-0.850-0.91432.757-0.036-0.0360.0000.0000.0000.000
76B102GLN0-0.117-0.05235.159-0.001-0.0010.0000.0000.0000.000
77B103LEU0-0.066-0.03833.4680.0020.0020.0000.0000.0000.000
78B104ASP-1-0.889-0.93235.010-0.051-0.0510.0000.0000.0000.000
79B105LEU0-0.021-0.04329.5600.0010.0010.0000.0000.0000.000
80B106ALA00.0280.02730.045-0.007-0.0070.0000.0000.0000.000
81B107ASN0-0.015-0.00730.617-0.010-0.0100.0000.0000.0000.000
82B108TYR0-0.117-0.06929.239-0.002-0.0020.0000.0000.0000.000
83B109VAL0-0.021-0.01823.724-0.010-0.0100.0000.0000.0000.000
84B110ARG10.8600.93719.7460.0830.0830.0000.0000.0000.000
85B111GLN00.0380.02522.131-0.026-0.0260.0000.0000.0000.000
86B112PRO0-0.035-0.00817.3960.0030.0030.0000.0000.0000.000
87B113ASN0-0.062-0.05718.7990.0070.0070.0000.0000.0000.000
88B114ILE00.0410.03819.436-0.006-0.0060.0000.0000.0000.000
89B115SER0-0.039-0.02922.3890.0190.0190.0000.0000.0000.000
90B116ILE00.0190.02322.785-0.003-0.0030.0000.0000.0000.000
91B117LYS10.8620.92126.601-0.025-0.0250.0000.0000.0000.000
92B118SER0-0.0150.00529.7010.0050.0050.0000.0000.0000.000
93B119PRO0-0.002-0.01731.736-0.003-0.0030.0000.0000.0000.000
94B120ASP-1-0.747-0.86833.1970.0480.0480.0000.0000.0000.000
95B121PHE0-0.015-0.01123.4830.0020.0020.0000.0000.0000.000
96B122THR00.0530.03529.057-0.004-0.0040.0000.0000.0000.000
97B123VAL00.0410.02924.3500.0050.0050.0000.0000.0000.000
98B124CYS0-0.080-0.03126.631-0.007-0.0070.0000.0000.0000.000
99B125LEU00.004-0.00724.1500.0020.0020.0000.0000.0000.000
100B126GLU-1-0.904-0.96025.745-0.012-0.0120.0000.0000.0000.000
101B127TYR00.0160.00026.136-0.013-0.0130.0000.0000.0000.000
102B128VAL00.0280.00526.5750.0080.0080.0000.0000.0000.000
103B129LEU00.0260.02428.371-0.009-0.0090.0000.0000.0000.000
104B130LYS10.9530.97324.3190.1290.1290.0000.0000.0000.000
105B131THR0-0.029-0.02728.554-0.006-0.0060.0000.0000.0000.000
106B132VAL00.0150.01630.116-0.001-0.0010.0000.0000.0000.000
107B133VAL0-0.056-0.00224.050-0.004-0.0040.0000.0000.0000.000
108B160GLN00.019-0.00737.3660.0020.0020.0000.0000.0000.000
109B161GLU-1-0.888-0.92834.517-0.040-0.0400.0000.0000.0000.000
110B162THR0-0.031-0.02731.217-0.005-0.0050.0000.0000.0000.000
111B163LYS10.9240.97531.5140.0360.0360.0000.0000.0000.000
112B164PHE0-0.019-0.00429.993-0.003-0.0030.0000.0000.0000.000
113B165VAL00.0350.02229.145-0.001-0.0010.0000.0000.0000.000
114B166GLU-1-0.890-0.95129.9240.0250.0250.0000.0000.0000.000
115B167MET00.0690.05526.461-0.003-0.0030.0000.0000.0000.000
116B168SER0-0.078-0.04430.0010.0040.0040.0000.0000.0000.000
117B169LEU0-0.009-0.00325.817-0.001-0.0010.0000.0000.0000.000
118B170LEU0-0.025-0.01128.1100.0020.0020.0000.0000.0000.000
119B171PRO0-0.0030.01431.9110.0050.0050.0000.0000.0000.000
120B172LEU0-0.027-0.02633.7370.0010.0010.0000.0000.0000.000
121B173LEU0-0.081-0.04437.1950.0000.0000.0000.0000.0000.000
122B174ASN0-0.045-0.02139.983-0.002-0.0020.0000.0000.0000.000
123B175ARG10.8290.91035.979-0.040-0.0400.0000.0000.0000.000
124B176GLU-1-0.905-0.95541.6010.0180.0180.0000.0000.0000.000
125B177SER0-0.064-0.04043.950-0.001-0.0010.0000.0000.0000.000
126B178GLU-1-0.900-0.93740.5610.0350.0350.0000.0000.0000.000
127B179GLU-1-0.941-0.98943.1500.0200.0200.0000.0000.0000.000
128B180SER0-0.077-0.02845.293-0.002-0.0020.0000.0000.0000.000
129B181LEU0-0.022-0.02139.224-0.001-0.0010.0000.0000.0000.000
130B182THR00.0060.00938.4280.0010.0010.0000.0000.0000.000
131B183GLU-1-0.887-0.94737.1260.0200.0200.0000.0000.0000.000
132B184GLU-1-0.896-0.95835.1310.0080.0080.0000.0000.0000.000
133B185ILE0-0.020-0.00233.8080.0020.0020.0000.0000.0000.000
134B186LEU00.0250.00733.9760.0050.0050.0000.0000.0000.000
135B187GLU-1-0.951-0.96631.8890.0290.0290.0000.0000.0000.000
136B188GLY00.013-0.00229.8720.0050.0050.0000.0000.0000.000
137B189GLU-1-0.791-0.87829.0670.0470.0470.0000.0000.0000.000
138B190GLY00.018-0.00129.6170.0100.0100.0000.0000.0000.000
139B191ALA0-0.0100.00926.5180.0110.0110.0000.0000.0000.000
140B192VAL0-0.001-0.01225.1570.0140.0140.0000.0000.0000.000
141B193VAL0-0.0020.00025.0190.0170.0170.0000.0000.0000.000
142B194ASN0-0.038-0.01925.5910.0200.0200.0000.0000.0000.000
143B195VAL00.0250.01020.1430.0230.0230.0000.0000.0000.000
144B196LEU00.0060.00020.9790.0320.0320.0000.0000.0000.000
145B197LYS10.8170.90122.216-0.082-0.0820.0000.0000.0000.000
146B198LEU0-0.041-0.00720.0230.0250.0250.0000.0000.0000.000
147B199PHE0-0.0160.00614.9520.0360.0360.0000.0000.0000.000
148B200ILE00.0110.00318.1360.0470.0470.0000.0000.0000.000
149B201LYS10.8990.95820.407-0.185-0.1850.0000.0000.0000.000
150B202GLY00.0260.01416.5440.0130.0130.0000.0000.0000.000
151B203PHE0-0.006-0.00116.2240.0510.0510.0000.0000.0000.000
152B204LEU0-0.061-0.03517.2190.0260.0260.0000.0000.0000.000
153B205MET0-0.023-0.00317.620-0.018-0.0180.0000.0000.0000.000
154B206HIS00.0440.03411.5320.1300.1300.0000.0000.0000.000
155B207LEU0-0.0140.00215.4990.0170.0170.0000.0000.0000.000
156B208GLY0-0.034-0.02917.964-0.019-0.0190.0000.0000.0000.000
157B209GLU-1-0.974-0.98215.7200.4650.4650.0000.0000.0000.000
158B210ASN0-0.088-0.03713.3810.0780.0780.0000.0000.0000.000
159B211PRO0-0.035-0.01516.2580.0200.0200.0000.0000.0000.000
160B212ASN00.0810.04614.450-0.035-0.0350.0000.0000.0000.000
161B213SER00.0090.00917.879-0.034-0.0340.0000.0000.0000.000
162B214TYR0-0.071-0.06416.885-0.065-0.0650.0000.0000.0000.000
163B215ASP-1-0.747-0.86118.6960.4250.4250.0000.0000.0000.000
164B216ARG10.9150.96720.883-0.243-0.2430.0000.0000.0000.000
165B217GLN0-0.084-0.04622.138-0.021-0.0210.0000.0000.0000.000
166B218LEU0-0.0160.00817.639-0.003-0.0030.0000.0000.0000.000
167B219THR00.0200.00921.835-0.006-0.0060.0000.0000.0000.000
168B220VAL00.0180.00921.9400.0200.0200.0000.0000.0000.000
169B221GLU-1-0.853-0.92723.1960.1670.1670.0000.0000.0000.000
170B222LYS10.8930.94419.808-0.188-0.1880.0000.0000.0000.000
171B223TYR00.0690.05116.935-0.007-0.0070.0000.0000.0000.000
172B224ARG10.8430.93422.635-0.132-0.1320.0000.0000.0000.000
173B225PRO00.0330.01524.611-0.007-0.0070.0000.0000.0000.000
174B226LEU00.0490.02420.717-0.009-0.0090.0000.0000.0000.000
175B227LEU0-0.023-0.00424.678-0.009-0.0090.0000.0000.0000.000
176B228VAL0-0.004-0.01127.186-0.008-0.0080.0000.0000.0000.000
177B229SER00.0260.01228.265-0.011-0.0110.0000.0000.0000.000
178B230ILE0-0.0290.00524.791-0.005-0.0050.0000.0000.0000.000
179B231VAL0-0.062-0.03529.316-0.005-0.0050.0000.0000.0000.000
180B232GLY00.005-0.02032.404-0.006-0.0060.0000.0000.0000.000
181B233TYR00.000-0.01432.091-0.003-0.0030.0000.0000.0000.000
182B234GLU-1-0.771-0.85931.2540.0880.0880.0000.0000.0000.000
183B235TYR0-0.072-0.02334.554-0.004-0.0040.0000.0000.0000.000
184B236LEU0-0.055-0.05737.561-0.003-0.0030.0000.0000.0000.000
185B237VAL00.0380.03136.171-0.004-0.0040.0000.0000.0000.000
186B238GLY00.0280.03636.9710.0040.0040.0000.0000.0000.000
187B239THR0-0.003-0.01233.5100.0050.0050.0000.0000.0000.000
188B240THR0-0.061-0.04130.4070.0020.0020.0000.0000.0000.000
189B241VAL0-0.031-0.02432.7170.0020.0020.0000.0000.0000.000
190B242PRO0-0.085-0.01734.192-0.003-0.0030.0000.0000.0000.000
191B243GLU-1-0.780-0.89237.2940.0440.0440.0000.0000.0000.000
192B244LYS10.8510.93140.146-0.051-0.0510.0000.0000.0000.000
193B245LYS10.8500.90937.733-0.066-0.0660.0000.0000.0000.000
194B246ILE00.0840.04635.3180.0010.0010.0000.0000.0000.000
195B247ASN00.0040.01030.5370.0050.0050.0000.0000.0000.000
196B248HIS00.0760.03132.7170.0000.0000.0000.0000.0000.000
197B249ILE00.0300.02227.1870.0040.0040.0000.0000.0000.000
198B250TYR00.024-0.00125.0670.0000.0000.0000.0000.0000.000
199B251TYR0-0.004-0.06029.2580.0010.0010.0000.0000.0000.000
200B252GLN00.0100.01331.122-0.007-0.0070.0000.0000.0000.000
201B253LEU0-0.014-0.00624.8250.0000.0000.0000.0000.0000.000
202B254ALA00.0120.02628.2600.0030.0030.0000.0000.0000.000
203B255THR0-0.035-0.02629.885-0.010-0.0100.0000.0000.0000.000
204B256PHE0-0.040-0.02230.895-0.008-0.0080.0000.0000.0000.000
205B257ASP-1-0.907-0.94427.6170.1460.1460.0000.0000.0000.000
206B258ASN00.018-0.00526.9810.0140.0140.0000.0000.0000.000
207B259TYR0-0.017-0.01726.378-0.001-0.0010.0000.0000.0000.000
208B260PRO00.0240.01425.1230.0180.0180.0000.0000.0000.000
209B261PHE00.0570.01217.236-0.007-0.0070.0000.0000.0000.000
210B262ASP-1-0.866-0.92222.6490.2380.2380.0000.0000.0000.000
211B263LEU0-0.012-0.02124.248-0.009-0.0090.0000.0000.0000.000
212B264LEU0-0.007-0.01023.037-0.010-0.0100.0000.0000.0000.000
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