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: R8468

Calculation Name: 5B23-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5B23

Chain ID: B

ChEMBL ID:

UniProt ID: Q8XN25

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:


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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2184004.920825
FMO2-HF: Nuclear repulsion 2109011.973428
FMO2-HF: Total energy -74992.947397
FMO2-MP2: Total energy -75214.972348


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:67:SER)


Summations of interaction energy for fragment #1(B:67:SER)
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.
-9.578-5.7660.677-1.66-2.8280.003
Interaction energy analysis for fragmet #1(B:67:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.047 / 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].
3B69LYS10.9390.9652.807-4.775-2.6710.107-0.909-1.3010.001
4B70ASN00.0080.0082.491-2.310-0.9770.571-0.687-1.2170.002
5B71LEU00.0480.0284.205-0.2570.0100.000-0.059-0.2080.000
6B72LYS10.8220.8926.309-1.065-1.0650.0000.0000.0000.000
7B73ASN0-0.056-0.0197.349-0.016-0.0160.0000.0000.0000.000
8B74ILE0-0.0280.0027.175-0.075-0.0750.0000.0000.0000.000
9B75ASN00.021-0.00810.0470.0260.0260.0000.0000.0000.000
10B76PRO00.0100.01611.5930.0440.0440.0000.0000.0000.000
11B77ASP-1-0.765-0.84013.1540.2300.2300.0000.0000.0000.000
12B78TYR0-0.047-0.0457.351-0.172-0.1720.0000.0000.0000.000
13B79ARG10.7660.87011.944-0.302-0.3020.0000.0000.0000.000
14B80PHE00.005-0.0079.9210.1020.1020.0000.0000.0000.000
15B81TRP0-0.026-0.0158.048-0.166-0.1660.0000.0000.0000.000
16B82ILE0-0.001-0.00910.5870.0390.0390.0000.0000.0000.000
17B83LYS10.8500.91713.076-0.042-0.0420.0000.0000.0000.000
18B84VAL0-0.016-0.00515.4300.0210.0210.0000.0000.0000.000
19B85GLU-1-0.817-0.89619.246-0.010-0.0100.0000.0000.0000.000
20B86GLY00.0570.02621.0670.0020.0020.0000.0000.0000.000
21B87THR0-0.115-0.05620.745-0.004-0.0040.0000.0000.0000.000
22B88ASN0-0.040-0.04019.6080.0040.0040.0000.0000.0000.000
23B89ILE0-0.021-0.00917.497-0.012-0.0120.0000.0000.0000.000
24B90ASP-1-0.797-0.89412.723-0.008-0.0080.0000.0000.0000.000
25B91PHE0-0.0140.00412.884-0.057-0.0570.0000.0000.0000.000
26B92PRO0-0.0060.0099.7570.0800.0800.0000.0000.0000.000
27B93VAL0-0.0060.00711.473-0.038-0.0380.0000.0000.0000.000
28B94VAL0-0.019-0.01313.2360.0700.0700.0000.0000.0000.000
29B95GLN0-0.015-0.00815.4320.0200.0200.0000.0000.0000.000
30B96GLY00.0280.02118.3540.0090.0090.0000.0000.0000.000
31B97LYS10.9000.93121.032-0.163-0.1630.0000.0000.0000.000
32B98ASP-1-0.779-0.87724.0190.0910.0910.0000.0000.0000.000
33B99ASN00.038-0.00424.3390.0140.0140.0000.0000.0000.000
34B100ASP-1-0.844-0.91626.1330.0500.0500.0000.0000.0000.000
35B101PHE0-0.001-0.00720.246-0.008-0.0080.0000.0000.0000.000
36B102TYR0-0.041-0.05817.505-0.014-0.0140.0000.0000.0000.000
37B103LEU0-0.0080.01522.165-0.010-0.0100.0000.0000.0000.000
38B104HIS0-0.028-0.00824.659-0.015-0.0150.0000.0000.0000.000
39B105HIS10.7820.88020.604-0.057-0.0570.0000.0000.0000.000
40B106ASN00.0210.01417.6340.0180.0180.0000.0000.0000.000
41B107PHE00.0570.0169.5640.0130.0130.0000.0000.0000.000
42B108ASN0-0.034-0.02513.5440.0070.0070.0000.0000.0000.000
43B109LYS10.7890.89715.324-0.156-0.1560.0000.0000.0000.000
44B110GLU-1-0.796-0.86118.123-0.040-0.0400.0000.0000.0000.000
45B111LYS10.9210.94420.735-0.019-0.0190.0000.0000.0000.000
46B112SER0-0.007-0.01521.568-0.012-0.0120.0000.0000.0000.000
47B113PHE00.0380.01723.6470.0070.0070.0000.0000.0000.000
48B114SER00.008-0.01023.1270.0020.0020.0000.0000.0000.000
49B115GLY0-0.0380.00322.4210.0010.0010.0000.0000.0000.000
50B116SER0-0.033-0.04217.346-0.021-0.0210.0000.0000.0000.000
51B117ILE0-0.0130.00016.5770.0030.0030.0000.0000.0000.000
52B118PHE0-0.060-0.03317.1770.0120.0120.0000.0000.0000.000
53B119VAL0-0.022-0.00917.166-0.006-0.0060.0000.0000.0000.000
54B120ASP-1-0.771-0.87519.8230.1240.1240.0000.0000.0000.000
55B121SER0-0.051-0.03522.1300.0180.0180.0000.0000.0000.000
56B122GLU-1-0.857-0.89223.6870.1270.1270.0000.0000.0000.000
57B123ASN0-0.091-0.05920.759-0.001-0.0010.0000.0000.0000.000
58B124ASN0-0.029-0.01620.8480.0480.0480.0000.0000.0000.000
59B125LEU00.023-0.01315.410-0.001-0.0010.0000.0000.0000.000
60B126ASN0-0.073-0.01717.2090.0520.0520.0000.0000.0000.000
61B127ASP-1-0.819-0.90819.7100.1720.1720.0000.0000.0000.000
62B128ASP-1-0.772-0.83622.7370.1480.1480.0000.0000.0000.000
63B129SER00.0230.00523.2440.0090.0090.0000.0000.0000.000
64B130ASN0-0.004-0.00224.6890.0010.0010.0000.0000.0000.000
65B131ILE0-0.0290.00518.5480.0080.0080.0000.0000.0000.000
66B132VAL00.0310.01421.964-0.012-0.0120.0000.0000.0000.000
67B133VAL0-0.019-0.01818.5960.0140.0140.0000.0000.0000.000
68B134TYR0-0.006-0.01421.656-0.021-0.0210.0000.0000.0000.000
69B135GLY00.0580.01321.2580.0050.0050.0000.0000.0000.000
70B136HIS0-0.022-0.00622.748-0.004-0.0040.0000.0000.0000.000
71B137ASN00.008-0.00124.679-0.009-0.0090.0000.0000.0000.000
72B138MET0-0.0300.01127.345-0.001-0.0010.0000.0000.0000.000
73B139ARG10.9550.97629.525-0.006-0.0060.0000.0000.0000.000
74B140ASN00.004-0.00125.679-0.003-0.0030.0000.0000.0000.000
75B141ASP-1-0.770-0.87025.603-0.021-0.0210.0000.0000.0000.000
76B142THR00.0220.04022.202-0.004-0.0040.0000.0000.0000.000
77B143MET0-0.022-0.01517.3910.0140.0140.0000.0000.0000.000
78B144PHE00.0570.01818.814-0.002-0.0020.0000.0000.0000.000
79B145ALA00.0190.02122.9380.0020.0020.0000.0000.0000.000
80B146GLN0-0.028-0.01723.4280.0000.0000.0000.0000.0000.000
81B147ILE00.0190.01822.4950.0000.0000.0000.0000.0000.000
82B148LYS10.7880.87426.0450.0050.0050.0000.0000.0000.000
83B149HIS00.0130.00426.3690.0020.0020.0000.0000.0000.000
84B150PHE0-0.0010.00324.226-0.001-0.0010.0000.0000.0000.000
85B151LYS10.8340.90529.957-0.015-0.0150.0000.0000.0000.000
86B152ASN0-0.024-0.00532.798-0.001-0.0010.0000.0000.0000.000
87B153GLU-1-0.840-0.91433.3490.0140.0140.0000.0000.0000.000
88B154ASN0-0.034-0.02534.5200.0010.0010.0000.0000.0000.000
89B155PHE0-0.0060.00025.617-0.001-0.0010.0000.0000.0000.000
90B156PHE00.0200.01429.5860.0020.0020.0000.0000.0000.000
91B157ASN0-0.020-0.01530.3830.0050.0050.0000.0000.0000.000
92B158ALA0-0.036-0.00930.0270.0010.0010.0000.0000.0000.000
93B159ASN0-0.070-0.04425.324-0.002-0.0020.0000.0000.0000.000
94B160LYS10.8680.91325.406-0.027-0.0270.0000.0000.0000.000
95B161TYR0-0.024-0.01820.8630.0050.0050.0000.0000.0000.000
96B162VAL00.0120.01418.360-0.007-0.0070.0000.0000.0000.000
97B163THR0-0.023-0.02013.7500.0010.0010.0000.0000.0000.000
98B164LEU0-0.0030.00613.453-0.004-0.0040.0000.0000.0000.000
99B165TYR0-0.027-0.0124.568-0.432-0.324-0.001-0.005-0.1020.000
100B166ARG10.9740.9778.868-0.416-0.4160.0000.0000.0000.000
101B167GLU-1-0.878-0.9236.7791.0971.0970.0000.0000.0000.000
102B168GLY0-0.059-0.0355.173-0.506-0.5060.0000.0000.0000.000
103B169LYS10.8630.9326.038-1.010-1.0100.0000.0000.0000.000
104B170LYS10.8480.9189.551-0.031-0.0310.0000.0000.0000.000
105B171SER0-0.001-0.01011.907-0.033-0.0330.0000.0000.0000.000
106B172THR0-0.029-0.02515.1730.0070.0070.0000.0000.0000.000
107B173PHE00.0310.01216.995-0.002-0.0020.0000.0000.0000.000
108B174GLU-1-0.782-0.85921.3840.0380.0380.0000.0000.0000.000
109B175ILE0-0.038-0.02223.9990.0040.0040.0000.0000.0000.000
110B176PHE0-0.009-0.01226.639-0.007-0.0070.0000.0000.0000.000
111B177SER0-0.007-0.01629.593-0.006-0.0060.0000.0000.0000.000
112B178VAL00.002-0.00429.8270.0050.0050.0000.0000.0000.000
113B179TYR0-0.008-0.01031.696-0.005-0.0050.0000.0000.0000.000
114B180GLN0-0.014-0.02832.8310.0000.0000.0000.0000.0000.000
115B181GLH00.002-0.01435.148-0.001-0.0010.0000.0000.0000.000
116B182ASN00.007-0.00236.0900.0010.0010.0000.0000.0000.000
117B183ALA00.002-0.00134.4360.0030.0030.0000.0000.0000.000
118B184LYS10.8380.88135.339-0.043-0.0430.0000.0000.0000.000
119B185ASP-1-0.894-0.92937.8500.0410.0410.0000.0000.0000.000
120B186LEU00.0550.03031.0650.0030.0030.0000.0000.0000.000
121B187GLU-1-0.852-0.91333.0060.0560.0560.0000.0000.0000.000
122B188SER0-0.050-0.01234.3550.0030.0030.0000.0000.0000.000
123B189GLU-1-0.771-0.84635.1170.0510.0510.0000.0000.0000.000
124B190ILE0-0.024-0.00928.6260.0040.0040.0000.0000.0000.000
125B191LYS10.8700.93030.539-0.067-0.0670.0000.0000.0000.000
126B192THR00.0140.01725.142-0.001-0.0010.0000.0000.0000.000
127B193LYS10.7670.85825.506-0.137-0.1370.0000.0000.0000.000
128B194PHE00.0470.01129.036-0.008-0.0080.0000.0000.0000.000
129B195SER0-0.086-0.04631.4700.0060.0060.0000.0000.0000.000
130B196ASN0-0.011-0.01935.060-0.003-0.0030.0000.0000.0000.000
131B197LYS10.8970.94933.291-0.065-0.0650.0000.0000.0000.000
132B198GLU-1-0.860-0.94235.3290.0590.0590.0000.0000.0000.000
133B199ASP-1-0.812-0.89336.2440.0590.0590.0000.0000.0000.000
134B200TYR0-0.079-0.05227.6980.0010.0010.0000.0000.0000.000
135B201GLU-1-0.781-0.88533.8550.0550.0550.0000.0000.0000.000
136B202LYS10.7600.87635.870-0.057-0.0570.0000.0000.0000.000
137B203TYR00.0550.02729.693-0.002-0.0020.0000.0000.0000.000
138B204LEU0-0.006-0.00629.512-0.001-0.0010.0000.0000.0000.000
139B205LYS10.8580.92233.197-0.050-0.0500.0000.0000.0000.000
140B206GLU-1-0.805-0.89336.5360.0500.0500.0000.0000.0000.000
141B207GLN00.0450.03931.586-0.002-0.0020.0000.0000.0000.000
142B208GLU-1-0.829-0.89033.9880.0430.0430.0000.0000.0000.000
143B209SER0-0.097-0.05234.894-0.004-0.0040.0000.0000.0000.000
144B210LYS10.8230.89235.635-0.048-0.0480.0000.0000.0000.000
145B211SER0-0.061-0.03134.523-0.001-0.0010.0000.0000.0000.000
146B212LEU0-0.051-0.02934.883-0.003-0.0030.0000.0000.0000.000
147B213PHE00.0040.00233.958-0.003-0.0030.0000.0000.0000.000
148B214LYS10.8530.94035.076-0.034-0.0340.0000.0000.0000.000
149B215ARG10.8240.91528.815-0.039-0.0390.0000.0000.0000.000
150B216ASP-1-0.882-0.94733.5980.0270.0270.0000.0000.0000.000
151B217GLY0-0.028-0.02733.2710.0010.0010.0000.0000.0000.000
152B218ILE0-0.050-0.02129.1460.0010.0010.0000.0000.0000.000
153B219ASP-1-0.907-0.96530.2580.0560.0560.0000.0000.0000.000
154B220LEU0-0.0260.00430.3230.0050.0050.0000.0000.0000.000
155B221ASN00.0440.02330.946-0.002-0.0020.0000.0000.0000.000
156B222SER00.015-0.00631.0870.0070.0070.0000.0000.0000.000
157B223ASN0-0.071-0.03830.0070.0030.0030.0000.0000.0000.000
158B224ASP-1-0.757-0.84526.9440.0860.0860.0000.0000.0000.000
159B225ARG10.8270.93817.955-0.227-0.2270.0000.0000.0000.000
160B226ILE0-0.014-0.00724.160-0.001-0.0010.0000.0000.0000.000
161B227LEU0-0.018-0.00119.1040.0180.0180.0000.0000.0000.000
162B228THR0-0.008-0.01322.848-0.018-0.0180.0000.0000.0000.000
163B229LEU0-0.011-0.00320.4310.0090.0090.0000.0000.0000.000
164B230ILE00.0320.01424.059-0.012-0.0120.0000.0000.0000.000
165B231THR00.012-0.02425.330-0.001-0.0010.0000.0000.0000.000
166B232CYS0-0.064-0.01527.2690.0020.0020.0000.0000.0000.000
167B233GLY00.0490.02730.409-0.002-0.0020.0000.0000.0000.000
168B234TYR0-0.095-0.09131.231-0.001-0.0010.0000.0000.0000.000
169B235ASP-1-0.796-0.86636.3740.0140.0140.0000.0000.0000.000
170B236PHE00.0240.01238.064-0.001-0.0010.0000.0000.0000.000
171B237VAL00.0210.00238.7730.0010.0010.0000.0000.0000.000
172B238ASN0-0.025-0.02136.5910.0000.0000.0000.0000.0000.000
173B239ALA00.0160.03536.0990.0030.0030.0000.0000.0000.000
174B240ARG10.8880.92527.987-0.050-0.0500.0000.0000.0000.000
175B241ILE0-0.024-0.00729.627-0.003-0.0030.0000.0000.0000.000
176B242VAL0-0.0050.00328.6630.0050.0050.0000.0000.0000.000
177B243VAL00.0140.00825.389-0.006-0.0060.0000.0000.0000.000
178B244VAL0-0.009-0.00126.3090.0100.0100.0000.0000.0000.000
179B245ALA00.0380.02023.316-0.008-0.0080.0000.0000.0000.000
180B246LYS10.7990.89724.704-0.065-0.0650.0000.0000.0000.000
181B247GLU-1-0.855-0.92217.9240.2310.2310.0000.0000.0000.000
182B248ILE0-0.013-0.01021.207-0.013-0.0130.0000.0000.0000.000
183B249ASP-1-0.876-0.91418.0540.1140.1140.0000.0000.0000.000