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: LJ2K9

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 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 262
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3740221.099341
FMO2-HF: Nuclear repulsion 3634353.229126
FMO2-HF: Total energy -105867.870215
FMO2-MP2: Total energy -106180.668878


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.
-0.6061.1790.003-0.687-1.10
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 : -0.001 / q_NPA : -0.014
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].
3B6ARG10.7970.9003.4971.3332.636-0.002-0.515-0.7860.000
4B7ARG10.7730.8744.0560.8290.9650.000-0.050-0.0860.000
5B8THR00.0370.0326.886-0.369-0.3690.0000.0000.0000.000
6B9PHE00.0520.01910.4610.0750.0750.0000.0000.0000.000
7B10GLY00.0180.01013.2980.0260.0260.0000.0000.0000.000
8B11SER0-0.076-0.04510.0190.1040.1040.0000.0000.0000.000
9B12TYR00.0330.01311.538-0.055-0.0550.0000.0000.0000.000
10B13LYS10.9240.9693.616-4.314-3.9680.005-0.122-0.2280.000
11B14ILE0-0.038-0.02810.003-0.254-0.2540.0000.0000.0000.000
12B15GLU-1-0.832-0.9087.7581.3831.3830.0000.0000.0000.000
13B16GLU-1-0.827-0.89611.4120.2990.2990.0000.0000.0000.000
14B17LEU00.0140.02414.579-0.026-0.0260.0000.0000.0000.000
15B18THR0-0.065-0.06016.9650.0070.0070.0000.0000.0000.000
16B19ILE00.0220.01920.079-0.020-0.0200.0000.0000.0000.000
17B43LYS10.9290.96023.508-0.177-0.1770.0000.0000.0000.000
18B44LYS10.8660.93316.875-0.335-0.3350.0000.0000.0000.000
19B45ILE0-0.020-0.01519.153-0.017-0.0170.0000.0000.0000.000
20B46PRO00.0350.03616.4290.0150.0150.0000.0000.0000.000
21B47LEU0-0.032-0.02213.395-0.059-0.0590.0000.0000.0000.000
22B48LEU0-0.0050.00013.2410.0790.0790.0000.0000.0000.000
23B49ASP-1-0.834-0.8788.5160.4650.4650.0000.0000.0000.000
24B50ASP-1-0.782-0.93212.0140.2550.2550.0000.0000.0000.000
25B51GLY00.0700.03712.4620.0080.0080.0000.0000.0000.000
26B52ILE0-0.057-0.03113.196-0.061-0.0610.0000.0000.0000.000
27B53PHE0-0.0030.00814.763-0.033-0.0330.0000.0000.0000.000
28B54GLU-1-0.833-0.93510.629-0.144-0.1440.0000.0000.0000.000
29B55LEU0-0.0060.01114.058-0.037-0.0370.0000.0000.0000.000
30B56LEU00.0340.00016.410-0.018-0.0180.0000.0000.0000.000
31B57ASN0-0.0090.01016.040-0.008-0.0080.0000.0000.0000.000
32B58TYR0-0.003-0.03210.741-0.067-0.0670.0000.0000.0000.000
33B59LEU00.0020.01817.579-0.003-0.0030.0000.0000.0000.000
34B60ILE00.0140.01121.1160.0030.0030.0000.0000.0000.000
35B61ASP-1-0.802-0.85718.923-0.178-0.1780.0000.0000.0000.000
36B62GLY00.0320.03821.228-0.012-0.0120.0000.0000.0000.000
37B63THR0-0.081-0.03415.695-0.021-0.0210.0000.0000.0000.000
38B64ASN00.0150.01119.1350.0270.0270.0000.0000.0000.000
39B65PHE00.0470.01914.515-0.046-0.0460.0000.0000.0000.000
40B66ASN0-0.044-0.02014.666-0.069-0.0690.0000.0000.0000.000
41B67LYS10.8260.90214.3720.2560.2560.0000.0000.0000.000
42B68THR00.0080.01712.544-0.020-0.0200.0000.0000.0000.000
43B69CYS0-0.030-0.0117.374-0.015-0.0150.0000.0000.0000.000
44B70TYR00.0700.0348.0890.0370.0370.0000.0000.0000.000
45B71CYS0-0.0160.02610.7840.0720.0720.0000.0000.0000.000
46B72GLY00.0490.02010.192-0.048-0.0480.0000.0000.0000.000
47B73PHE0-0.009-0.0076.5020.0420.0420.0000.0000.0000.000
48B74ASN00.0300.02812.634-0.038-0.0380.0000.0000.0000.000
49B75TYR00.036-0.00712.0220.0640.0640.0000.0000.0000.000
50B76SER0-0.017-0.01417.677-0.001-0.0010.0000.0000.0000.000
51B77HIS0-0.030-0.03415.810-0.014-0.0140.0000.0000.0000.000
52B78LEU0-0.050-0.01916.6720.0040.0040.0000.0000.0000.000
53B79PRO00.0620.01520.615-0.018-0.0180.0000.0000.0000.000
54B80ASN0-0.002-0.00923.510-0.006-0.0060.0000.0000.0000.000
55B81LEU00.0170.03216.121-0.011-0.0110.0000.0000.0000.000
56B82GLU-1-0.811-0.90818.577-0.139-0.1390.0000.0000.0000.000
57B83ARG10.8580.91420.175-0.011-0.0110.0000.0000.0000.000
58B84ASP-1-0.739-0.84223.4330.0040.0040.0000.0000.0000.000
59B85PHE0-0.010-0.01716.675-0.002-0.0020.0000.0000.0000.000
60B86ASN00.0250.00420.607-0.021-0.0210.0000.0000.0000.000
61B87ILE00.0370.03422.749-0.006-0.0060.0000.0000.0000.000
62B88ALA00.0110.00723.103-0.001-0.0010.0000.0000.0000.000
63B89SER0-0.033-0.05320.500-0.001-0.0010.0000.0000.0000.000
64B90LEU0-0.0300.00023.166-0.007-0.0070.0000.0000.0000.000
65B91TYR00.0670.04226.479-0.001-0.0010.0000.0000.0000.000
66B92VAL0-0.053-0.03524.1510.0030.0030.0000.0000.0000.000
67B93ARG10.7730.87723.8690.1120.1120.0000.0000.0000.000
68B94GLU-1-0.860-0.94326.457-0.055-0.0550.0000.0000.0000.000
69B95ASN0-0.0020.00029.7680.0020.0020.0000.0000.0000.000
70B96PHE00.005-0.01726.5300.0020.0020.0000.0000.0000.000
71B97GLU-1-0.835-0.89028.011-0.096-0.0960.0000.0000.0000.000
72B98ILE00.0630.04630.6820.0030.0030.0000.0000.0000.000
73B99CYS0-0.130-0.06731.5010.0060.0060.0000.0000.0000.000
74B100THR0-0.102-0.08729.645-0.001-0.0010.0000.0000.0000.000
75B101ASP-1-0.867-0.92732.788-0.060-0.0600.0000.0000.0000.000
76B102GLN0-0.095-0.03935.2610.0030.0030.0000.0000.0000.000
77B103LEU0-0.044-0.02733.4300.0030.0030.0000.0000.0000.000
78B104ASP-1-0.858-0.91534.472-0.070-0.0700.0000.0000.0000.000
79B105LEU00.0440.00729.1590.0020.0020.0000.0000.0000.000
80B106ALA00.0190.01629.967-0.007-0.0070.0000.0000.0000.000
81B107ASN0-0.069-0.03430.655-0.007-0.0070.0000.0000.0000.000
82B108TYR0-0.083-0.05228.8570.0020.0020.0000.0000.0000.000
83B109VAL0-0.006-0.00123.320-0.011-0.0110.0000.0000.0000.000
84B110ARG10.7940.86118.8840.1580.1580.0000.0000.0000.000
85B111GLN0-0.031-0.01721.892-0.025-0.0250.0000.0000.0000.000
86B112PRO0-0.041-0.01717.502-0.006-0.0060.0000.0000.0000.000
87B113ASN0-0.057-0.05618.7450.0100.0100.0000.0000.0000.000
88B114ILE00.0220.01619.551-0.006-0.0060.0000.0000.0000.000
89B115SER0-0.059-0.03922.6540.0180.0180.0000.0000.0000.000
90B116ILE00.0210.01822.496-0.006-0.0060.0000.0000.0000.000
91B117LYS10.7840.86826.7200.0070.0070.0000.0000.0000.000
92B118SER0-0.042-0.01629.6180.0050.0050.0000.0000.0000.000
93B119PRO00.0320.00631.930-0.001-0.0010.0000.0000.0000.000
94B120ASP-1-0.796-0.87532.3810.0190.0190.0000.0000.0000.000
95B121PHE00.0570.00623.508-0.004-0.0040.0000.0000.0000.000
96B122THR00.0110.00429.013-0.004-0.0040.0000.0000.0000.000
97B123VAL00.0340.03424.4180.0050.0050.0000.0000.0000.000
98B124CYS0-0.084-0.03126.586-0.004-0.0040.0000.0000.0000.000
99B125LEU00.0200.00424.1560.0000.0000.0000.0000.0000.000
100B126GLU-1-0.845-0.91425.353-0.030-0.0300.0000.0000.0000.000
101B127TYR00.0260.01025.733-0.015-0.0150.0000.0000.0000.000
102B128VAL00.0080.00426.0900.0090.0090.0000.0000.0000.000
103B129LEU00.0410.03328.342-0.009-0.0090.0000.0000.0000.000
104B130LYS10.9020.93824.7530.1110.1110.0000.0000.0000.000
105B131THR0-0.025-0.02328.651-0.006-0.0060.0000.0000.0000.000
106B132VAL0-0.0060.01129.9100.0020.0020.0000.0000.0000.000
107B133VAL0-0.0320.00123.693-0.005-0.0050.0000.0000.0000.000
108B160GLN00.0170.00137.3940.0010.0010.0000.0000.0000.000
109B161GLU-1-0.860-0.92734.266-0.048-0.0480.0000.0000.0000.000
110B162THR0-0.039-0.02231.298-0.004-0.0040.0000.0000.0000.000
111B163LYS10.8380.91931.2180.0560.0560.0000.0000.0000.000
112B164PHE0-0.008-0.01430.215-0.003-0.0030.0000.0000.0000.000
113B165VAL00.0350.02828.8620.0000.0000.0000.0000.0000.000
114B166GLU-1-0.822-0.90429.610-0.005-0.0050.0000.0000.0000.000
115B167MET00.0560.03525.944-0.002-0.0020.0000.0000.0000.000
116B168SER0-0.017-0.02029.8460.0020.0020.0000.0000.0000.000
117B169LEU0-0.0260.00225.954-0.001-0.0010.0000.0000.0000.000
118B170LEU0-0.0090.00328.3190.0010.0010.0000.0000.0000.000
119B171PRO00.0020.01732.1250.0050.0050.0000.0000.0000.000
120B172LEU0-0.022-0.02833.8750.0020.0020.0000.0000.0000.000
121B173LEU0-0.087-0.05637.2090.0020.0020.0000.0000.0000.000
122B174ASN0-0.068-0.03039.800-0.001-0.0010.0000.0000.0000.000
123B175ARG10.7470.80135.863-0.009-0.0090.0000.0000.0000.000
124B176GLU-1-0.898-0.93641.647-0.001-0.0010.0000.0000.0000.000
125B177SER0-0.067-0.05744.1000.0000.0000.0000.0000.0000.000
126B178GLU-1-0.809-0.87039.6950.0080.0080.0000.0000.0000.000
127B179GLU-1-0.922-0.96542.8750.0000.0000.0000.0000.0000.000
128B180SER0-0.104-0.04744.909-0.002-0.0020.0000.0000.0000.000
129B181LEU0-0.029-0.00737.809-0.002-0.0020.0000.0000.0000.000
130B182THR0-0.021-0.03138.5520.0010.0010.0000.0000.0000.000
131B183GLU-1-0.908-0.95737.406-0.011-0.0110.0000.0000.0000.000
132B184GLU-1-0.829-0.90234.679-0.023-0.0230.0000.0000.0000.000
133B185ILE0-0.0140.00433.538-0.001-0.0010.0000.0000.0000.000
134B186LEU00.0210.01433.6490.0030.0030.0000.0000.0000.000
135B187GLU-1-0.949-0.97330.924-0.018-0.0180.0000.0000.0000.000
136B188GLY00.0240.00429.5280.0010.0010.0000.0000.0000.000
137B189GLU-1-0.768-0.84328.8740.0080.0080.0000.0000.0000.000
138B190GLY00.0290.00929.4780.0070.0070.0000.0000.0000.000
139B191ALA0-0.011-0.00226.2090.0090.0090.0000.0000.0000.000
140B192VAL00.003-0.00124.9180.0070.0070.0000.0000.0000.000
141B193VAL00.0020.00324.9870.0130.0130.0000.0000.0000.000
142B194ASN0-0.041-0.04025.9690.0210.0210.0000.0000.0000.000
143B195VAL00.0020.00520.0070.0160.0160.0000.0000.0000.000
144B196LEU00.001-0.00221.0640.0220.0220.0000.0000.0000.000
145B197LYS10.8110.89722.350-0.032-0.0320.0000.0000.0000.000
146B198LEU0-0.043-0.01320.0380.0240.0240.0000.0000.0000.000
147B199PHE00.0040.00714.7340.0360.0360.0000.0000.0000.000
148B200ILE00.005-0.00218.2180.0440.0440.0000.0000.0000.000
149B201LYS10.8560.92320.540-0.124-0.1240.0000.0000.0000.000
150B202GLY00.0230.00616.5420.0190.0190.0000.0000.0000.000
151B203PHE00.0030.01116.2210.0550.0550.0000.0000.0000.000
152B204LEU0-0.033-0.02517.2820.0340.0340.0000.0000.0000.000
153B205MET0-0.0290.01617.823-0.017-0.0170.0000.0000.0000.000
154B206HIS00.0180.02011.4680.1450.1450.0000.0000.0000.000
155B207LEU00.0100.01115.5050.0410.0410.0000.0000.0000.000
156B208GLY0-0.017-0.01017.9920.0010.0010.0000.0000.0000.000
157B209GLU-1-0.946-0.98815.5960.4240.4240.0000.0000.0000.000
158B210ASN0-0.080-0.03213.2500.0960.0960.0000.0000.0000.000
159B211PRO0-0.044-0.02616.047-0.001-0.0010.0000.0000.0000.000
160B212ASN00.0450.02014.852-0.011-0.0110.0000.0000.0000.000
161B213SER0-0.001-0.00318.196-0.037-0.0370.0000.0000.0000.000
162B214TYR0-0.059-0.07016.966-0.063-0.0630.0000.0000.0000.000
163B215ASP-1-0.724-0.85318.8150.4030.4030.0000.0000.0000.000
164B216ARG10.8510.92220.854-0.264-0.2640.0000.0000.0000.000
165B217GLN0-0.082-0.04521.736-0.019-0.0190.0000.0000.0000.000
166B218LEU0-0.0300.00117.186-0.003-0.0030.0000.0000.0000.000
167B219THR00.000-0.01021.353-0.006-0.0060.0000.0000.0000.000
168B220VAL00.0090.00021.6510.0120.0120.0000.0000.0000.000
169B221GLU-1-0.857-0.91023.0850.1120.1120.0000.0000.0000.000
170B222LYS10.8940.95618.832-0.143-0.1430.0000.0000.0000.000
171B223TYR00.0470.02115.950-0.010-0.0100.0000.0000.0000.000
172B224ARG10.8040.92422.494-0.103-0.1030.0000.0000.0000.000
173B225PRO00.0530.02024.516-0.005-0.0050.0000.0000.0000.000
174B226LEU00.0270.03920.691-0.007-0.0070.0000.0000.0000.000
175B227LEU0-0.011-0.00724.846-0.005-0.0050.0000.0000.0000.000
176B228VAL00.000-0.01027.162-0.005-0.0050.0000.0000.0000.000
177B229SER00.007-0.00527.957-0.009-0.0090.0000.0000.0000.000
178B230ILE0-0.037-0.00624.898-0.004-0.0040.0000.0000.0000.000
179B231VAL0-0.060-0.03729.488-0.004-0.0040.0000.0000.0000.000
180B232GLY00.015-0.00832.490-0.003-0.0030.0000.0000.0000.000
181B233TYR00.021-0.00232.096-0.002-0.0020.0000.0000.0000.000
182B234GLU-1-0.782-0.86031.1750.0450.0450.0000.0000.0000.000
183B235TYR0-0.085-0.02934.305-0.001-0.0010.0000.0000.0000.000
184B236LEU0-0.031-0.03237.275-0.002-0.0020.0000.0000.0000.000
185B237VAL00.0260.01036.249-0.003-0.0030.0000.0000.0000.000
186B238GLY00.0060.01036.3270.0020.0020.0000.0000.0000.000
187B239THR00.009-0.00833.9280.0030.0030.0000.0000.0000.000
188B240THR0-0.063-0.05229.6720.0000.0000.0000.0000.0000.000
189B241VAL0-0.058-0.02632.2850.0020.0020.0000.0000.0000.000
190B242PRO0-0.092-0.01633.6640.0000.0000.0000.0000.0000.000
191B243GLU-1-0.749-0.88236.7320.0190.0190.0000.0000.0000.000
192B244LYS10.8280.93139.647-0.026-0.0260.0000.0000.0000.000
193B245LYS10.8300.89737.830-0.041-0.0410.0000.0000.0000.000
194B246ILE00.0860.05134.7860.0000.0000.0000.0000.0000.000
195B247ASN00.0210.02129.7910.0060.0060.0000.0000.0000.000
196B248HIS00.0490.00432.575-0.002-0.0020.0000.0000.0000.000
197B249ILE00.0270.02927.4850.0030.0030.0000.0000.0000.000
198B250TYR00.025-0.00224.8810.0010.0010.0000.0000.0000.000
199B251TYR00.024-0.00329.1650.0000.0000.0000.0000.0000.000
200B252GLN00.0250.01531.593-0.004-0.0040.0000.0000.0000.000
201B253LEU0-0.011-0.00425.0840.0020.0020.0000.0000.0000.000
202B254ALA00.0170.02228.4530.0020.0020.0000.0000.0000.000
203B255THR0-0.061-0.03330.244-0.009-0.0090.0000.0000.0000.000
204B256PHE0-0.045-0.02431.019-0.006-0.0060.0000.0000.0000.000
205B257ASP-1-0.766-0.88526.7580.1180.1180.0000.0000.0000.000
206B258ASN00.0260.00526.3570.0100.0100.0000.0000.0000.000
207B259TYR0-0.032-0.04426.3850.0020.0020.0000.0000.0000.000
208B260PRO00.0120.00825.0110.0150.0150.0000.0000.0000.000
209B261PHE00.0410.02217.011-0.010-0.0100.0000.0000.0000.000
210B262ASP-1-0.815-0.90422.6250.2330.2330.0000.0000.0000.000
211B263LEU0-0.019-0.01024.251-0.009-0.0090.0000.0000.0000.000
212B264LEU00.0150.00323.409-0.011-0.0110.0000.0000.0000.000
213B265ARG10.7490.86318.765-0.389-0.3890.0000.0000.0000.000
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