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: Q89QY

Calculation Name: 2QYF-B-Xray316

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2QYF

Chain ID: B

ChEMBL ID:

UniProt ID: Q15013

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 196
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2219501.944271
FMO2-HF: Nuclear repulsion 2141205.271562
FMO2-HF: Total energy -78296.672709
FMO2-MP2: Total energy -78519.597768


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:53:ACE )


Summations of interaction energy for fragment #1(B:53:ACE )
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.
-2.262.0992.187-3.163-3.384-0.026
Interaction energy analysis for fragmet #1(B:53:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / q_NPA : 0.009
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].
3B55MET 00.0170.0073.8590.9261.814-0.005-0.445-0.4380.000
4B56VAL 00.0300.0097.1460.1150.1150.0000.0000.0000.000
5B57PRO 00.0010.02410.2000.1200.1200.0000.0000.0000.000
6B58VAL 00.005-0.00813.6480.0140.0140.0000.0000.0000.000
7B59VAL 0-0.004-0.00416.6520.0180.0180.0000.0000.0000.000
8B60PHE 0-0.031-0.02219.8490.0040.0040.0000.0000.0000.000
9B61PRO 0-0.052-0.03022.8220.0010.0010.0000.0000.0000.000
10B62GLY 00.0620.02225.9040.0080.0080.0000.0000.0000.000
11B63PRO 00.0200.00226.012-0.008-0.0080.0000.0000.0000.000
12B64VAL 00.0670.02422.9280.0020.0020.0000.0000.0000.000
13B65SER 0-0.037-0.02526.4470.0060.0060.0000.0000.0000.000
14B66GLN 00.0540.02025.589-0.005-0.0050.0000.0000.0000.000
15B67GLU -1-0.856-0.92926.336-0.018-0.0180.0000.0000.0000.000
16B68GLY 0-0.029-0.01825.4360.0010.0010.0000.0000.0000.000
17B69CYS 0-0.018-0.01021.885-0.005-0.0050.0000.0000.0000.000
18B70CYS 00.0370.05621.3540.0020.0020.0000.0000.0000.000
19B71GLN 00.0950.03322.5160.0020.0020.0000.0000.0000.000
20B72PHE 0-0.034-0.02918.475-0.003-0.0030.0000.0000.0000.000
21B73THR 00.002-0.00117.7140.0000.0000.0000.0000.0000.000
22B74CYS 0-0.020-0.01918.1870.0150.0150.0000.0000.0000.000
23B75GLU -1-0.833-0.89819.875-0.008-0.0080.0000.0000.0000.000
24B76LEU 0-0.0050.00312.2580.0000.0000.0000.0000.0000.000
25B77LEU 0-0.014-0.00915.3610.0200.0200.0000.0000.0000.000
26B78LYS 10.8530.91116.7450.0150.0150.0000.0000.0000.000
27B79HIS 0-0.0010.00413.6450.0240.0240.0000.0000.0000.000
28B80ILE 00.0060.00511.3860.0100.0100.0000.0000.0000.000
29B81MET 0-0.076-0.02113.8630.0320.0320.0000.0000.0000.000
30B82TYR 00.0130.01616.7840.0110.0110.0000.0000.0000.000
31B83GLN 00.0290.01813.1420.0030.0030.0000.0000.0000.000
32B84ARG 10.7960.8539.880-0.338-0.3380.0000.0000.0000.000
33B85GLN 0-0.031-0.02613.9100.0210.0210.0000.0000.0000.000
34B86GLN 0-0.009-0.00215.875-0.001-0.0010.0000.0000.0000.000
35B87LEU 00.0140.00118.880-0.009-0.0090.0000.0000.0000.000
36B88PRO 00.0130.01820.8170.0000.0000.0000.0000.0000.000
37B89LEU 00.0200.00323.481-0.007-0.0070.0000.0000.0000.000
38B90PRO 00.0010.00521.7540.0050.0050.0000.0000.0000.000
39B91TYR 00.0710.01422.298-0.001-0.0010.0000.0000.0000.000
40B92GLU -1-0.861-0.94724.1570.0010.0010.0000.0000.0000.000
41B93GLN 0-0.042-0.03225.6670.0010.0010.0000.0000.0000.000
42B94LEU 0-0.033-0.01224.9360.0020.0020.0000.0000.0000.000
43B95LYS 10.8740.95728.305-0.017-0.0170.0000.0000.0000.000
44B96HIS 0-0.0340.00930.518-0.001-0.0010.0000.0000.0000.000
45B97NME 0-0.0040.00433.0530.0030.0030.0000.0000.0000.000
46B123ACE 00.001-0.01529.0890.0000.0000.0000.0000.0000.000
47B124CYS 0-0.044-0.02629.2370.0000.0000.0000.0000.0000.000
48B125GLN 00.0950.04630.025-0.001-0.0010.0000.0000.0000.000
49B126GLN 00.0090.00831.018-0.003-0.0030.0000.0000.0000.000
50B127ALA 00.019-0.00225.5860.0010.0010.0000.0000.0000.000
51B128LEU 00.0300.01926.1720.0030.0030.0000.0000.0000.000
52B129ALA 00.0740.03927.719-0.002-0.0020.0000.0000.0000.000
53B130GLU -1-0.939-0.96825.2240.0700.0700.0000.0000.0000.000
54B131LEU 0-0.009-0.00920.9750.0010.0010.0000.0000.0000.000
55B132GLU -1-0.942-0.97824.7380.0220.0220.0000.0000.0000.000
56B133SER 0-0.0050.01927.654-0.005-0.0050.0000.0000.0000.000
57B134VAL 0-0.003-0.00921.324-0.001-0.0010.0000.0000.0000.000
58B135LEU 0-0.055-0.03621.778-0.004-0.0040.0000.0000.0000.000
59B136SER 00.0710.04124.903-0.004-0.0040.0000.0000.0000.000
60B137HIS 10.9240.95826.666-0.039-0.0390.0000.0000.0000.000
61B138LEU 0-0.056-0.03420.536-0.001-0.0010.0000.0000.0000.000
62B139GLU -1-0.938-0.98224.8980.0000.0000.0000.0000.0000.000
63B140ASP -1-0.883-0.92927.6630.0130.0130.0000.0000.0000.000
64B141PHE 0-0.035-0.02322.726-0.002-0.0020.0000.0000.0000.000
65B142PHE 0-0.022-0.04920.610-0.004-0.0040.0000.0000.0000.000
66B143ALA 0-0.0360.00226.703-0.005-0.0050.0000.0000.0000.000
67B144ARG 10.8680.95929.536-0.016-0.0160.0000.0000.0000.000
68B145THR 0-0.027-0.03325.844-0.001-0.0010.0000.0000.0000.000
69B146LEU 0-0.0090.01325.171-0.003-0.0030.0000.0000.0000.000
70B147VAL 00.0370.02819.7870.0070.0070.0000.0000.0000.000
71B148PRO 0-0.0270.00219.395-0.009-0.0090.0000.0000.0000.000
72B149ARG 10.8550.88111.852-0.031-0.0310.0000.0000.0000.000
73B150VAL 00.0140.01115.0790.0150.0150.0000.0000.0000.000
74B151LEU 0-0.038-0.02411.0310.0020.0020.0000.0000.0000.000
75B152ILE 00.0320.02412.388-0.015-0.0150.0000.0000.0000.000
76B153LEU 0-0.009-0.01011.6080.0780.0780.0000.0000.0000.000
77B154LEU 00.0270.01411.522-0.055-0.0550.0000.0000.0000.000
78B155GLY 00.0490.00713.3700.0640.0640.0000.0000.0000.000
79B156GLY 0-0.035-0.01015.7980.0180.0180.0000.0000.0000.000
80B157ASN 00.009-0.01217.048-0.018-0.0180.0000.0000.0000.000
81B158ALA 00.0990.03616.1030.0310.0310.0000.0000.0000.000
82B159LEU 0-0.0160.02515.4340.0160.0160.0000.0000.0000.000
83B160SER 0-0.034-0.01514.3580.0460.0460.0000.0000.0000.000
84B161PRO 00.0440.05711.123-0.020-0.0200.0000.0000.0000.000
85B162LYS 10.8460.91112.302-0.338-0.3380.0000.0000.0000.000
86B163GLU -1-0.783-0.8027.8480.6860.6860.0000.0000.0000.000
87B164PHE 0-0.019-0.0137.544-0.171-0.1710.0000.0000.0000.000
88B165TYR 00.020-0.0326.9340.2390.2390.0000.0000.0000.000
89B166GLU -1-0.818-0.8758.5670.0070.0070.0000.0000.0000.000
90B167LEU 0-0.0220.00010.337-0.084-0.0840.0000.0000.0000.000
91B168ASP -1-0.858-0.92812.879-0.105-0.1050.0000.0000.0000.000
92B169LEU 00.008-0.02014.343-0.030-0.0300.0000.0000.0000.000
93B170SER 0-0.039-0.03417.0250.0040.0040.0000.0000.0000.000
94B171LEU 0-0.031-0.01217.4500.0070.0070.0000.0000.0000.000
95B172LEU 0-0.023-0.01220.195-0.002-0.0020.0000.0000.0000.000
96B173ALA 0-0.054-0.02622.5790.0070.0070.0000.0000.0000.000
97B174PRO 00.0410.02326.2610.0020.0020.0000.0000.0000.000
98B175TYR 0-0.028-0.03127.5520.0010.0010.0000.0000.0000.000
99B176SER 0-0.067-0.02728.9590.0000.0000.0000.0000.0000.000
100B177VAL 00.0750.04030.9850.0020.0020.0000.0000.0000.000
101B178ASP -1-0.895-0.94832.468-0.051-0.0510.0000.0000.0000.000
102B179GLN 0-0.077-0.02628.096-0.007-0.0070.0000.0000.0000.000
103B180SER 0-0.0100.00631.5320.0030.0030.0000.0000.0000.000
104B181LEU 0-0.019-0.01725.9370.0010.0010.0000.0000.0000.000
105B182SER 00.0650.02529.2830.0010.0010.0000.0000.0000.000
106B183THR 00.0880.03725.073-0.009-0.0090.0000.0000.0000.000
107B184ALA 00.0380.02624.805-0.006-0.0060.0000.0000.0000.000
108B185ALA 0-0.025-0.01524.885-0.006-0.0060.0000.0000.0000.000
109B186CYS 0-0.032-0.01222.549-0.013-0.0130.0000.0000.0000.000
110B187LEU 00.0570.02620.354-0.018-0.0180.0000.0000.0000.000
111B188ARG 10.9730.99019.8310.0610.0610.0000.0000.0000.000
112B189ARG 10.8850.96419.6510.1490.1490.0000.0000.0000.000
113B190LEU 00.0170.00615.156-0.028-0.0280.0000.0000.0000.000
114B191PHE 00.023-0.00715.243-0.035-0.0350.0000.0000.0000.000
115B192ARG 10.9330.96615.8950.1600.1600.0000.0000.0000.000
116B193ALA 0-0.020-0.00914.302-0.016-0.0160.0000.0000.0000.000
117B194ILE 00.0220.01310.440-0.067-0.0670.0000.0000.0000.000
118B195PHE 0-0.015-0.00111.238-0.038-0.0380.0000.0000.0000.000
119B196MET 0-0.063-0.03813.2640.0040.0040.0000.0000.0000.000
120B197ALA 0-0.032-0.0028.815-0.021-0.0210.0000.0000.0000.000
121B198ASP -1-0.949-0.9718.783-0.422-0.4220.0000.0000.0000.000
122B199ALA 0-0.0040.0077.349-0.021-0.0210.0000.0000.0000.000
123B200PHE 0-0.088-0.0697.6780.0770.0770.0000.0000.0000.000
124B201SER 00.0600.0568.4710.0890.0890.0000.0000.0000.000
125B202GLU -1-0.893-0.9497.0210.5150.5150.0000.0000.0000.000
126B203LEU 00.0370.01710.749-0.030-0.0300.0000.0000.0000.000
127B204GLN 0-0.071-0.02413.933-0.020-0.0200.0000.0000.0000.000
128B205ALA 00.0480.02314.3680.0200.0200.0000.0000.0000.000
129B206PRO 0-0.040-0.01313.6630.0210.0210.0000.0000.0000.000
130B207PRO 0-0.0090.00515.782-0.027-0.0270.0000.0000.0000.000
131B208LEU 00.0390.02617.4740.0150.0150.0000.0000.0000.000
132B209MET 0-0.096-0.04612.8300.0230.0230.0000.0000.0000.000
133B210GLY 00.0030.00518.380-0.028-0.0280.0000.0000.0000.000
134B211THR 00.027-0.00915.6890.0450.0450.0000.0000.0000.000
135B212VAL 0-0.009-0.00716.748-0.027-0.0270.0000.0000.0000.000
136B213VAL 00.0480.02616.5010.0160.0160.0000.0000.0000.000
137B214MET 0-0.048-0.02516.6630.0010.0010.0000.0000.0000.000
138B215ALA 00.0440.02717.495-0.005-0.0050.0000.0000.0000.000
139B216GLN 0-0.0020.00618.653-0.005-0.0050.0000.0000.0000.000
140B217GLY 00.0840.02120.826-0.008-0.0080.0000.0000.0000.000
141B218HIS 00.0130.00924.3940.0070.0070.0000.0000.0000.000
142B219ARG 10.9490.96227.488-0.010-0.0100.0000.0000.0000.000
143B220ASN 0-0.037-0.02329.0430.0040.0040.0000.0000.0000.000
144B221CYS 0-0.071-0.01228.5900.0000.0000.0000.0000.0000.000
145B222GLY 00.0290.01131.396-0.001-0.0010.0000.0000.0000.000
146B223GLU -1-0.816-0.90027.2440.0320.0320.0000.0000.0000.000
147B224ASP -1-0.919-0.95130.5600.0270.0270.0000.0000.0000.000
148B225TRP 0-0.020-0.01125.0940.0050.0050.0000.0000.0000.000
149B226PHE 0-0.075-0.06322.0110.0090.0090.0000.0000.0000.000
150B227ARG 10.9440.96425.642-0.068-0.0680.0000.0000.0000.000
151B228PRO 00.0620.03924.9280.0070.0070.0000.0000.0000.000
152B229LYS 10.8650.92622.072-0.089-0.0890.0000.0000.0000.000
153B230LEU 00.0440.01122.7120.0050.0050.0000.0000.0000.000
154B231ASN 0-0.0030.00523.470-0.005-0.0050.0000.0000.0000.000
155B232TYR 0-0.056-0.06214.9840.0100.0100.0000.0000.0000.000
156B233ARG 10.9520.96916.651-0.159-0.1590.0000.0000.0000.000
157B234VAL 0-0.0080.00610.7410.0170.0170.0000.0000.0000.000
158B235PRO 0-0.0020.00710.5810.0010.0010.0000.0000.0000.000
159B236SER 00.0120.0099.8060.0440.0440.0000.0000.0000.000
160B237ARG 10.9180.9478.142-0.573-0.5730.0000.0000.0000.000
161B238GLY 00.000-0.0047.498-0.128-0.1280.0000.0000.0000.000
162B239HIS 00.0000.0022.835-1.1990.2920.865-1.146-1.210-0.013
163B240LYS 10.8270.9112.7660.4291.4610.360-0.458-0.935-0.002
164B241LEU 00.008-0.0032.680-2.406-1.5200.967-1.110-0.743-0.011
165B242THR 00.0320.0325.0890.2630.3250.000-0.004-0.0580.000
166B243VAL 0-0.0020.0147.786-0.177-0.1770.0000.0000.0000.000
167B244THR 00.0210.01511.1130.0440.0440.0000.0000.0000.000
168B245LEU 0-0.028-0.01113.375-0.015-0.0150.0000.0000.0000.000
169B246SER 00.0210.00817.0230.0150.0150.0000.0000.0000.000
170B247CYS 0-0.046-0.03219.8780.0000.0000.0000.0000.0000.000
171B248GLY 00.0320.03222.7690.0100.0100.0000.0000.0000.000
172B249ARG 10.9420.98724.3250.0800.0800.0000.0000.0000.000
173B250PRO 00.0190.00824.472-0.008-0.0080.0000.0000.0000.000
174B251SER 00.009-0.00225.166-0.004-0.0040.0000.0000.0000.000
175B252ILE 0-0.012-0.00724.5940.0080.0080.0000.0000.0000.000
176B253ARG 10.9630.97325.4050.0270.0270.0000.0000.0000.000
177B254THR 00.0480.02223.923-0.001-0.0010.0000.0000.0000.000
178B255THR 00.0090.00823.784-0.001-0.0010.0000.0000.0000.000
179B256ALA 0-0.020-0.00123.6860.0040.0040.0000.0000.0000.000
180B257TRP 0-0.022-0.02221.1970.0060.0060.0000.0000.0000.000
181B258GLU -1-0.884-0.94623.904-0.003-0.0030.0000.0000.0000.000
182B259ASP -1-0.950-0.95926.0190.0080.0080.0000.0000.0000.000
183B260TYR 0-0.055-0.02222.9470.0010.0010.0000.0000.0000.000
184B261ILE 0-0.030-0.00722.9470.0050.0050.0000.0000.0000.000
185B262TRP 00.0180.00115.0010.0020.0020.0000.0000.0000.000
186B263PHE 00.0280.01321.2230.0000.0000.0000.0000.0000.000
187B264GLN 0-0.035-0.03720.1580.0160.0160.0000.0000.0000.000
188B265ALA 00.0430.03021.634-0.008-0.0080.0000.0000.0000.000
189B266PRO 0-0.095-0.03223.5360.0120.0120.0000.0000.0000.000
190B267VAL 0-0.0100.00025.2740.0010.0010.0000.0000.0000.000
191B268THR 0-0.042-0.01120.9790.0120.0120.0000.0000.0000.000
192B269PHE 00.0570.02519.682-0.008-0.0080.0000.0000.0000.000
193B270LYS 10.8690.91920.548-0.122-0.1220.0000.0000.0000.000
194B271GLY 00.0270.02320.460-0.009-0.0090.0000.0000.0000.000
195B272PHE 0-0.048-0.05221.168-0.005-0.0050.0000.0000.0000.000
196B273NME 00.0470.03523.1350.0010.0010.0000.0000.0000.000