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: ZV9KN

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 OptHSide
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 -2182003.026831
FMO2-HF: Nuclear repulsion 2107010.675512
FMO2-HF: Total energy -74992.351319
FMO2-MP2: Total energy -75214.415648


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.
-13.094-10.0034.422-3.255-4.2570.013
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 : 0.015 / q_NPA : -0.008
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].
3B69LYS10.9480.9702.735-4.999-2.6510.151-1.013-1.4860.003
4B70ASN00.0160.0092.183-4.700-4.3034.251-2.147-2.5000.010
5B71LEU00.0710.0353.722-1.019-0.6730.020-0.095-0.2710.000
6B72LYS10.8110.8876.153-1.231-1.2310.0000.0000.0000.000
7B73ASN0-0.074-0.0366.589-0.167-0.1670.0000.0000.0000.000
8B74ILE0-0.0340.0027.269-0.179-0.1790.0000.0000.0000.000
9B75ASN00.027-0.01010.000-0.062-0.0620.0000.0000.0000.000
10B76PRO00.0120.02111.2880.0520.0520.0000.0000.0000.000
11B77ASP-1-0.796-0.85212.7730.3240.3240.0000.0000.0000.000
12B78TYR00.0090.0037.753-0.161-0.1610.0000.0000.0000.000
13B79ARG10.7790.89111.945-0.374-0.3740.0000.0000.0000.000
14B80PHE0-0.012-0.01610.2300.1210.1210.0000.0000.0000.000
15B81TRP0-0.010-0.0088.770-0.140-0.1400.0000.0000.0000.000
16B82ILE0-0.006-0.00411.3690.0400.0400.0000.0000.0000.000
17B83LYS10.8530.91813.8810.0140.0140.0000.0000.0000.000
18B84VAL0-0.023-0.01116.1660.0190.0190.0000.0000.0000.000
19B85GLU-1-0.854-0.91519.884-0.028-0.0280.0000.0000.0000.000
20B86GLY00.0800.05521.3770.0050.0050.0000.0000.0000.000
21B87THR0-0.082-0.05021.5990.0000.0000.0000.0000.0000.000
22B88ASN0-0.067-0.05220.0810.0020.0020.0000.0000.0000.000
23B89ILE0-0.012-0.00518.090-0.009-0.0090.0000.0000.0000.000
24B90ASP-1-0.779-0.88813.311-0.069-0.0690.0000.0000.0000.000
25B91PHE0-0.0300.00113.636-0.047-0.0470.0000.0000.0000.000
26B92PRO0-0.0120.01110.5010.0590.0590.0000.0000.0000.000
27B93VAL0-0.0040.00012.298-0.026-0.0260.0000.0000.0000.000
28B94VAL0-0.023-0.02013.5730.0740.0740.0000.0000.0000.000
29B95GLN0-0.018-0.00615.5800.0130.0130.0000.0000.0000.000
30B96GLY00.0270.01218.3120.0180.0180.0000.0000.0000.000
31B97LYS10.9040.93521.023-0.217-0.2170.0000.0000.0000.000
32B98ASP-1-0.775-0.87424.0000.1230.1230.0000.0000.0000.000
33B99ASN0-0.004-0.02124.3620.0190.0190.0000.0000.0000.000
34B100ASP-1-0.817-0.92426.2860.0710.0710.0000.0000.0000.000
35B101PHE0-0.030-0.00820.120-0.008-0.0080.0000.0000.0000.000
36B102TYR0-0.020-0.05217.269-0.009-0.0090.0000.0000.0000.000
37B103LEU0-0.0160.01922.043-0.011-0.0110.0000.0000.0000.000
38B104HIS0-0.0180.00224.509-0.016-0.0160.0000.0000.0000.000
39B105HIS10.7880.88220.856-0.102-0.1020.0000.0000.0000.000
40B106ASN00.0210.00818.0070.0210.0210.0000.0000.0000.000
41B107PHE00.0600.0179.6540.0080.0080.0000.0000.0000.000
42B108ASN0-0.019-0.01813.7350.0420.0420.0000.0000.0000.000
43B109LYS10.8100.91315.483-0.264-0.2640.0000.0000.0000.000
44B110GLU-1-0.822-0.87818.5250.0250.0250.0000.0000.0000.000
45B111LYS10.9410.95821.076-0.058-0.0580.0000.0000.0000.000
46B112SER00.000-0.01121.731-0.010-0.0100.0000.0000.0000.000
47B113PHE00.0140.01324.0320.0070.0070.0000.0000.0000.000
48B114SER00.015-0.00422.9680.0000.0000.0000.0000.0000.000
49B115GLY0-0.0450.00122.2790.0020.0020.0000.0000.0000.000
50B116SER0-0.044-0.04917.297-0.014-0.0140.0000.0000.0000.000
51B117ILE0-0.0160.00317.2390.0010.0010.0000.0000.0000.000
52B118PHE0-0.029-0.01217.5780.0230.0230.0000.0000.0000.000
53B119VAL0-0.026-0.00817.874-0.012-0.0120.0000.0000.0000.000
54B120ASP-1-0.781-0.87920.3100.1350.1350.0000.0000.0000.000
55B121SER0-0.022-0.01122.6310.0170.0170.0000.0000.0000.000
56B122GLU-1-0.860-0.91523.6800.1530.1530.0000.0000.0000.000
57B123ASN0-0.124-0.07121.320-0.003-0.0030.0000.0000.0000.000
58B124ASN0-0.020-0.00721.4350.0480.0480.0000.0000.0000.000
59B125LEU00.033-0.00515.653-0.004-0.0040.0000.0000.0000.000
60B126ASN0-0.067-0.03517.3840.0290.0290.0000.0000.0000.000
61B127ASP-1-0.858-0.92319.8750.1770.1770.0000.0000.0000.000
62B128ASP-1-0.776-0.84123.0440.1510.1510.0000.0000.0000.000
63B129SER00.007-0.00323.5800.0070.0070.0000.0000.0000.000
64B130ASN0-0.0020.00725.118-0.002-0.0020.0000.0000.0000.000
65B131ILE0-0.035-0.00518.9200.0100.0100.0000.0000.0000.000
66B132VAL00.0400.01922.391-0.010-0.0100.0000.0000.0000.000
67B133VAL0-0.034-0.02519.0790.0160.0160.0000.0000.0000.000
68B134TYR0-0.010-0.01922.116-0.024-0.0240.0000.0000.0000.000
69B135GLY00.0500.00221.9830.0070.0070.0000.0000.0000.000
70B136HIS0-0.0020.00923.386-0.008-0.0080.0000.0000.0000.000
71B137ASN00.0150.00525.266-0.010-0.0100.0000.0000.0000.000
72B138MET0-0.040-0.00927.688-0.002-0.0020.0000.0000.0000.000
73B139ARG10.9420.96629.504-0.013-0.0130.0000.0000.0000.000
74B140ASN0-0.013-0.01325.880-0.003-0.0030.0000.0000.0000.000
75B141ASP-1-0.770-0.85926.222-0.023-0.0230.0000.0000.0000.000
76B142THR00.0300.03222.728-0.007-0.0070.0000.0000.0000.000
77B143MET0-0.045-0.01917.8360.0150.0150.0000.0000.0000.000
78B144PHE00.0690.03019.296-0.002-0.0020.0000.0000.0000.000
79B145ALA00.0000.00223.6180.0010.0010.0000.0000.0000.000
80B146GLN0-0.054-0.04524.4470.0020.0020.0000.0000.0000.000
81B147ILE00.0510.04123.353-0.002-0.0020.0000.0000.0000.000
82B148LYS10.8560.91826.8770.0030.0030.0000.0000.0000.000
83B149HIS00.0180.01127.2210.0020.0020.0000.0000.0000.000
84B150PHE00.0200.01824.888-0.001-0.0010.0000.0000.0000.000
85B151LYS10.8120.89430.631-0.016-0.0160.0000.0000.0000.000
86B152ASN0-0.043-0.02433.341-0.002-0.0020.0000.0000.0000.000
87B153GLU-1-0.851-0.91633.9590.0080.0080.0000.0000.0000.000
88B154ASN0-0.012-0.01634.9870.0000.0000.0000.0000.0000.000
89B155PHE0-0.0040.00226.249-0.001-0.0010.0000.0000.0000.000
90B156PHE00.0340.01230.2940.0010.0010.0000.0000.0000.000
91B157ASN0-0.019-0.01630.7100.0040.0040.0000.0000.0000.000
92B158ALA0-0.039-0.01030.2890.0000.0000.0000.0000.0000.000
93B159ASN0-0.070-0.04325.821-0.002-0.0020.0000.0000.0000.000
94B160LYS10.8790.91426.034-0.011-0.0110.0000.0000.0000.000
95B161TYR0-0.031-0.00821.2090.0050.0050.0000.0000.0000.000
96B162VAL0-0.0050.00218.825-0.006-0.0060.0000.0000.0000.000
97B163THR0-0.024-0.02213.9410.0040.0040.0000.0000.0000.000
98B164LEU0-0.0060.00113.9600.0010.0010.0000.0000.0000.000
99B165TYR0-0.025-0.0074.928-0.365-0.3650.0000.0000.0000.000
100B166ARG10.9880.9829.402-0.370-0.3700.0000.0000.0000.000
101B167GLU-1-0.883-0.9237.1901.1871.1870.0000.0000.0000.000
102B168GLY0-0.030-0.0195.621-0.408-0.4080.0000.0000.0000.000
103B169LYS10.8610.9306.392-0.844-0.8440.0000.0000.0000.000
104B170LYS10.9550.98710.036-0.023-0.0230.0000.0000.0000.000
105B171SER00.002-0.01112.302-0.035-0.0350.0000.0000.0000.000
106B172THR0-0.043-0.02415.6240.0020.0020.0000.0000.0000.000
107B173PHE00.0230.01017.2770.0010.0010.0000.0000.0000.000
108B174GLU-1-0.762-0.87721.6210.0220.0220.0000.0000.0000.000
109B175ILE0-0.055-0.02124.7230.0040.0040.0000.0000.0000.000
110B176PHE0-0.015-0.00827.114-0.007-0.0070.0000.0000.0000.000
111B177SER0-0.003-0.00929.933-0.004-0.0040.0000.0000.0000.000
112B178VAL00.0000.00630.2120.0050.0050.0000.0000.0000.000
113B179TYR00.003-0.00332.353-0.004-0.0040.0000.0000.0000.000
114B180GLN0-0.019-0.03133.4060.0010.0010.0000.0000.0000.000
115B181GLH0-0.006-0.02935.765-0.002-0.0020.0000.0000.0000.000
116B182ASN00.0270.01736.4370.0020.0020.0000.0000.0000.000
117B183ALA00.0100.00934.8560.0020.0020.0000.0000.0000.000
118B184LYS10.8310.88635.776-0.052-0.0520.0000.0000.0000.000
119B185ASP-1-0.899-0.94038.3300.0450.0450.0000.0000.0000.000
120B186LEU00.0440.00831.6390.0030.0030.0000.0000.0000.000
121B187GLU-1-0.841-0.89833.4510.0650.0650.0000.0000.0000.000
122B188SER0-0.062-0.00734.6010.0040.0040.0000.0000.0000.000
123B189GLU-1-0.773-0.85535.6800.0510.0510.0000.0000.0000.000
124B190ILE0-0.028-0.01128.9770.0020.0020.0000.0000.0000.000
125B191LYS10.8740.95031.081-0.069-0.0690.0000.0000.0000.000
126B192THR00.0180.01725.927-0.001-0.0010.0000.0000.0000.000
127B193LYS10.8050.87325.922-0.147-0.1470.0000.0000.0000.000
128B194PHE00.0420.00129.025-0.009-0.0090.0000.0000.0000.000
129B195SER0-0.095-0.04531.6420.0060.0060.0000.0000.0000.000
130B196ASN0-0.010-0.01335.028-0.002-0.0020.0000.0000.0000.000
131B197LYS11.0010.99233.569-0.061-0.0610.0000.0000.0000.000
132B198GLU-1-0.896-0.95535.5440.0550.0550.0000.0000.0000.000
133B199ASP-1-0.837-0.88936.5610.0620.0620.0000.0000.0000.000
134B200TYR0-0.088-0.06927.9720.0010.0010.0000.0000.0000.000
135B201GLU-1-0.879-0.95634.1630.0500.0500.0000.0000.0000.000
136B202LYS10.8090.89435.924-0.055-0.0550.0000.0000.0000.000
137B203TYR00.0220.02530.099-0.002-0.0020.0000.0000.0000.000
138B204LEU00.008-0.01329.968-0.001-0.0010.0000.0000.0000.000
139B205LYS10.8960.95933.756-0.046-0.0460.0000.0000.0000.000
140B206GLU-1-0.804-0.90237.0600.0490.0490.0000.0000.0000.000
141B207GLN00.0210.03331.907-0.001-0.0010.0000.0000.0000.000
142B208GLU-1-0.813-0.90634.4410.0350.0350.0000.0000.0000.000
143B209SER0-0.116-0.04135.245-0.004-0.0040.0000.0000.0000.000
144B210LYS10.8250.87936.167-0.049-0.0490.0000.0000.0000.000
145B211SER0-0.051-0.02034.765-0.001-0.0010.0000.0000.0000.000
146B212LEU0-0.066-0.04335.798-0.002-0.0020.0000.0000.0000.000
147B213PHE0-0.0120.00134.557-0.003-0.0030.0000.0000.0000.000
148B214LYS10.8740.96135.505-0.027-0.0270.0000.0000.0000.000
149B215ARG10.8200.90929.010-0.028-0.0280.0000.0000.0000.000
150B216ASP-1-0.894-0.95733.8380.0180.0180.0000.0000.0000.000
151B217GLY0-0.034-0.02633.8040.0000.0000.0000.0000.0000.000
152B218ILE0-0.019-0.00729.7810.0000.0000.0000.0000.0000.000
153B219ASP-1-0.944-0.98130.6410.0440.0440.0000.0000.0000.000
154B220LEU0-0.0270.00830.4180.0050.0050.0000.0000.0000.000
155B221ASN00.0530.01330.797-0.001-0.0010.0000.0000.0000.000
156B222SER00.0370.02031.1800.0060.0060.0000.0000.0000.000
157B223ASN0-0.075-0.04729.7130.0060.0060.0000.0000.0000.000
158B224ASP-1-0.753-0.84327.1590.0750.0750.0000.0000.0000.000
159B225ARG10.8620.95718.109-0.210-0.2100.0000.0000.0000.000
160B226ILE0-0.007-0.01024.247-0.003-0.0030.0000.0000.0000.000
161B227LEU0-0.0240.00119.5230.0170.0170.0000.0000.0000.000
162B228THR00.000-0.01523.193-0.019-0.0190.0000.0000.0000.000
163B229LEU0-0.024-0.00621.0280.0120.0120.0000.0000.0000.000
164B230ILE00.0310.01524.793-0.012-0.0120.0000.0000.0000.000
165B231THR00.006-0.03026.0930.0010.0010.0000.0000.0000.000
166B232CYS0-0.056-0.00527.9820.0020.0020.0000.0000.0000.000
167B233GLY00.0500.02230.947-0.003-0.0030.0000.0000.0000.000
168B234TYR0-0.091-0.08631.6100.0000.0000.0000.0000.0000.000
169B235ASP-1-0.799-0.86536.8650.0150.0150.0000.0000.0000.000
170B236PHE00.0180.01138.735-0.001-0.0010.0000.0000.0000.000
171B237VAL00.010-0.00539.1230.0010.0010.0000.0000.0000.000
172B238ASN0-0.023-0.01836.8390.0010.0010.0000.0000.0000.000
173B239ALA00.0230.03536.5750.0030.0030.0000.0000.0000.000
174B240ARG10.9150.94028.739-0.060-0.0600.0000.0000.0000.000
175B241ILE0-0.028-0.00930.280-0.003-0.0030.0000.0000.0000.000
176B242VAL00.0020.00329.2170.0050.0050.0000.0000.0000.000
177B243VAL00.0120.00226.238-0.006-0.0060.0000.0000.0000.000
178B244VAL0-0.010-0.00126.8060.0110.0110.0000.0000.0000.000
179B245ALA00.0200.00223.707-0.009-0.0090.0000.0000.0000.000
180B246LYS10.7970.89824.924-0.050-0.0500.0000.0000.0000.000
181B247GLU-1-0.894-0.94218.3890.1880.1880.0000.0000.0000.000
182B248ILE0-0.012-0.00321.912-0.010-0.0100.0000.0000.0000.000
183B249ASP-1-0.978-0.98420.0070.0560.0560.0000.0000.0000.000