Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 173QZ

Calculation Name: 5WIR-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5WIR

Chain ID: B

ChEMBL ID:

UniProt ID: Q8NA31

Base Structure: X-ray

Registration Date: 2023-06-26

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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2348831.521696
FMO2-HF: Nuclear repulsion 2265083.639937
FMO2-HF: Total energy -83747.881758
FMO2-MP2: Total energy -83986.175349


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:61:SER)


Summations of interaction energy for fragment #1(B:61: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.
-2.902-1.18-0.008-0.932-0.7820
Interaction energy analysis for fragmet #1(B:61:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.040 / q_NPA : -0.039
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].
3B63ASP-1-0.842-0.9283.549-3.660-1.938-0.008-0.932-0.7820.000
4B64ALA00.0300.0126.3450.4740.4740.0000.0000.0000.000
5B65GLY0-0.0140.0008.6580.2270.2270.0000.0000.0000.000
6B66LEU00.017-0.0129.8380.1360.1360.0000.0000.0000.000
7B67VAL0-0.038-0.0048.4020.1280.1280.0000.0000.0000.000
8B68ALA00.0510.02711.2980.1540.1540.0000.0000.0000.000
9B69GLU-1-0.969-0.98714.146-0.588-0.5880.0000.0000.0000.000
10B70ALA0-0.025-0.01414.1540.0880.0880.0000.0000.0000.000
11B71GLU-1-0.947-0.97614.634-0.210-0.2100.0000.0000.0000.000
12B72ALA00.0090.01517.2360.0570.0570.0000.0000.0000.000
13B73VAL0-0.041-0.02419.1680.0450.0450.0000.0000.0000.000
14B74ALA0-0.012-0.00418.9680.0420.0420.0000.0000.0000.000
15B75ALA00.0200.00920.9630.0370.0370.0000.0000.0000.000
16B76GLY00.007-0.00323.3540.0250.0250.0000.0000.0000.000
17B77TRP0-0.047-0.03719.3780.0210.0210.0000.0000.0000.000
18B78MET0-0.017-0.00522.0110.0280.0280.0000.0000.0000.000
19B79LEU00.0120.02226.4800.0170.0170.0000.0000.0000.000
20B80ASP-1-0.748-0.85829.288-0.110-0.1100.0000.0000.0000.000
21B81PHE0-0.0100.00028.8710.0110.0110.0000.0000.0000.000
22B82LEU00.0200.00928.3900.0130.0130.0000.0000.0000.000
23B83CYS0-0.004-0.00132.0250.0090.0090.0000.0000.0000.000
24B84LEU00.0110.00333.2270.0080.0080.0000.0000.0000.000
25B85SER0-0.053-0.03333.1740.0090.0090.0000.0000.0000.000
26B86LEU0-0.0080.01235.8290.0060.0060.0000.0000.0000.000
27B87CYS0-0.005-0.01037.8440.0040.0040.0000.0000.0000.000
28B88ARG10.8700.89534.6670.0620.0620.0000.0000.0000.000
29B89ALA0-0.0110.00139.5440.0040.0040.0000.0000.0000.000
30B90PHE00.010-0.00341.4060.0030.0030.0000.0000.0000.000
31B91ARG10.8240.90043.5490.0400.0400.0000.0000.0000.000
32B92ASP-1-0.798-0.87542.926-0.031-0.0310.0000.0000.0000.000
33B93GLY00.0410.03345.9020.0030.0030.0000.0000.0000.000
34B94ARG10.7880.87939.1490.0330.0330.0000.0000.0000.000
35B95SER00.0580.00442.422-0.002-0.0020.0000.0000.0000.000
36B96GLU-1-0.787-0.85740.614-0.020-0.0200.0000.0000.0000.000
37B97ASP-1-0.810-0.88838.277-0.025-0.0250.0000.0000.0000.000
38B98PHE00.0040.01737.704-0.004-0.0040.0000.0000.0000.000
39B99ARG10.8880.92538.3470.0180.0180.0000.0000.0000.000
40B100ARG10.8230.88835.0930.0150.0150.0000.0000.0000.000
41B101THR0-0.012-0.01733.514-0.003-0.0030.0000.0000.0000.000
42B102ARG10.9450.97033.5760.0400.0400.0000.0000.0000.000
43B103ASN00.0090.00933.593-0.007-0.0070.0000.0000.0000.000
44B104SER0-0.009-0.00329.758-0.001-0.0010.0000.0000.0000.000
45B105ALA00.001-0.00629.345-0.009-0.0090.0000.0000.0000.000
46B106GLU-1-0.947-0.97430.140-0.079-0.0790.0000.0000.0000.000
47B107ALA0-0.0050.00627.149-0.006-0.0060.0000.0000.0000.000
48B108ILE0-0.015-0.01824.966-0.009-0.0090.0000.0000.0000.000
49B109ILE00.001-0.00525.532-0.018-0.0180.0000.0000.0000.000
50B110HIS0-0.070-0.04325.543-0.010-0.0100.0000.0000.0000.000
51B111GLY00.0110.01921.878-0.006-0.0060.0000.0000.0000.000
52B112LEU0-0.072-0.03321.547-0.030-0.0300.0000.0000.0000.000
53B113SER00.0360.01620.2450.0180.0180.0000.0000.0000.000
54B114SER0-0.044-0.02122.3520.0050.0050.0000.0000.0000.000
55B115LEU00.0040.00025.6900.0040.0040.0000.0000.0000.000
56B116THR00.012-0.01228.2480.0120.0120.0000.0000.0000.000
57B117ALA00.0750.02230.7200.0080.0080.0000.0000.0000.000
58B118CYS0-0.034-0.01932.1260.0100.0100.0000.0000.0000.000
59B119GLN00.1010.07726.1030.0060.0060.0000.0000.0000.000
60B120LEU00.0490.02831.7160.0070.0070.0000.0000.0000.000
61B121ARG10.8190.88334.1760.0990.0990.0000.0000.0000.000
62B122THR0-0.040-0.04832.9370.0090.0090.0000.0000.0000.000
63B123ILE00.0360.02530.7260.0080.0080.0000.0000.0000.000
64B124TYR00.0320.01735.0330.0060.0060.0000.0000.0000.000
65B125ILE00.0110.00338.4520.0070.0070.0000.0000.0000.000
66B126CYS0-0.049-0.02535.7800.0060.0060.0000.0000.0000.000
67B127GLN00.0280.00936.3780.0060.0060.0000.0000.0000.000
68B128PHE00.0340.02839.5770.0050.0050.0000.0000.0000.000
69B129LEU00.0130.00340.8300.0040.0040.0000.0000.0000.000
70B130THR0-0.093-0.06839.0950.0040.0040.0000.0000.0000.000
71B131ARG10.8460.92140.0040.0640.0640.0000.0000.0000.000
72B132ILE00.0200.00845.1730.0030.0030.0000.0000.0000.000
73B133ALA0-0.055-0.02944.7080.0030.0030.0000.0000.0000.000
74B134ALA0-0.019-0.00345.5280.0030.0030.0000.0000.0000.000
75B135GLY00.0370.00747.4800.0010.0010.0000.0000.0000.000
76B136LYS10.7820.86250.5960.0270.0270.0000.0000.0000.000
77B137THR0-0.060-0.01448.1400.0010.0010.0000.0000.0000.000
78B138LEU00.017-0.00449.950-0.002-0.0020.0000.0000.0000.000
79B139ASP-1-0.892-0.94049.333-0.026-0.0260.0000.0000.0000.000
80B140ALA0-0.074-0.03545.664-0.001-0.0010.0000.0000.0000.000
81B141GLN00.0090.00845.4630.0000.0000.0000.0000.0000.000
82B142PHE0-0.014-0.03141.830-0.001-0.0010.0000.0000.0000.000
83B143GLU-1-0.806-0.85342.710-0.066-0.0660.0000.0000.0000.000
84B144ASN0-0.008-0.01641.3440.0030.0030.0000.0000.0000.000
85B145ASP-1-0.845-0.88145.031-0.041-0.0410.0000.0000.0000.000
86B146GLU-1-0.907-0.96648.856-0.034-0.0340.0000.0000.0000.000
87B147ARG10.8280.89149.8920.0400.0400.0000.0000.0000.000
88B148ILE0-0.076-0.02348.6760.0010.0010.0000.0000.0000.000
89B149THR00.057-0.00149.510-0.001-0.0010.0000.0000.0000.000
90B150PRO00.0150.00947.748-0.003-0.0030.0000.0000.0000.000
91B151LEU00.0130.01048.245-0.003-0.0030.0000.0000.0000.000
92B152GLU-1-0.735-0.81750.759-0.040-0.0400.0000.0000.0000.000
93B153SER0-0.034-0.03044.843-0.003-0.0030.0000.0000.0000.000
94B154ALA0-0.022-0.02346.120-0.003-0.0030.0000.0000.0000.000
95B155LEU0-0.026-0.01247.162-0.002-0.0020.0000.0000.0000.000
96B156MET00.0110.00546.403-0.001-0.0010.0000.0000.0000.000
97B157ILE00.0060.01741.508-0.003-0.0030.0000.0000.0000.000
98B158TRP0-0.075-0.05344.385-0.004-0.0040.0000.0000.0000.000
99B159GLY0-0.026-0.01346.812-0.001-0.0010.0000.0000.0000.000
100B160SER0-0.034-0.02242.569-0.002-0.0020.0000.0000.0000.000
101B161ILE0-0.081-0.03841.336-0.006-0.0060.0000.0000.0000.000
102B162GLU-1-0.900-0.94640.047-0.086-0.0860.0000.0000.0000.000
103B163LYS10.7790.89342.2860.0570.0570.0000.0000.0000.000
104B164GLU-1-0.910-0.94545.149-0.059-0.0590.0000.0000.0000.000
105B165HIS0-0.009-0.01347.6000.0030.0030.0000.0000.0000.000
106B166ASP-1-0.766-0.88650.948-0.049-0.0490.0000.0000.0000.000
107B167LYS10.9820.98053.1990.0360.0360.0000.0000.0000.000
108B168LEU0-0.015-0.01050.5540.0020.0020.0000.0000.0000.000
109B169HIS00.0560.03647.6690.0010.0010.0000.0000.0000.000
110B170GLU-1-0.848-0.90552.077-0.040-0.0400.0000.0000.0000.000
111B171GLU-1-0.882-0.93855.423-0.034-0.0340.0000.0000.0000.000
112B172ILE0-0.003-0.00449.8750.0020.0020.0000.0000.0000.000
113B173GLN0-0.014-0.00252.823-0.001-0.0010.0000.0000.0000.000
114B174ASN00.0430.00653.6840.0000.0000.0000.0000.0000.000
115B175LEU0-0.028-0.01355.4970.0020.0020.0000.0000.0000.000
116B176ILE00.0200.00749.9840.0010.0010.0000.0000.0000.000
117B177LYS10.8770.95554.1310.0420.0420.0000.0000.0000.000
118B178ILE0-0.041-0.02256.5840.0010.0010.0000.0000.0000.000
119B179GLN00.012-0.03055.6990.0020.0020.0000.0000.0000.000
120B180ALA00.0140.00854.3610.0010.0010.0000.0000.0000.000
121B181ILE0-0.0020.00355.8420.0010.0010.0000.0000.0000.000
122B182ALA0-0.010-0.00759.2560.0010.0010.0000.0000.0000.000
123B183VAL00.0220.00954.5340.0010.0010.0000.0000.0000.000
124B184CYS0-0.039-0.00457.3180.0010.0010.0000.0000.0000.000
125B185MET0-0.076-0.02259.2350.0010.0010.0000.0000.0000.000
126B186GLU-1-0.849-0.91558.673-0.023-0.0230.0000.0000.0000.000
127B187ASN0-0.054-0.03156.9700.0020.0020.0000.0000.0000.000
128B188GLY00.0050.02260.8180.0010.0010.0000.0000.0000.000
129B189ASN0-0.015-0.00157.9840.0020.0020.0000.0000.0000.000
130B190PHE0-0.009-0.03461.905-0.001-0.0010.0000.0000.0000.000
131B191LYS10.8890.95262.8320.0270.0270.0000.0000.0000.000
132B192GLU-1-0.770-0.86756.581-0.030-0.0300.0000.0000.0000.000
133B193ALA00.0430.00959.728-0.001-0.0010.0000.0000.0000.000
134B194GLU-1-0.885-0.94961.143-0.025-0.0250.0000.0000.0000.000
135B195GLU-1-0.928-0.96558.788-0.032-0.0320.0000.0000.0000.000
136B196VAL0-0.0100.00355.976-0.001-0.0010.0000.0000.0000.000
137B197PHE00.009-0.01357.962-0.001-0.0010.0000.0000.0000.000
138B198GLU-1-0.905-0.95860.177-0.035-0.0350.0000.0000.0000.000
139B199ARG10.8260.87654.5640.0360.0360.0000.0000.0000.000
140B200ILE0-0.042-0.00554.500-0.002-0.0020.0000.0000.0000.000
141B201PHE0-0.068-0.04856.893-0.001-0.0010.0000.0000.0000.000
142B202GLY00.0560.04960.3880.0010.0010.0000.0000.0000.000
143B203ASP-1-0.809-0.89258.770-0.042-0.0420.0000.0000.0000.000
144B204PRO0-0.030-0.01860.7890.0000.0000.0000.0000.0000.000
145B205ASN0-0.058-0.03859.4790.0010.0010.0000.0000.0000.000
146B206SER0-0.021-0.00558.2650.0000.0000.0000.0000.0000.000
147B207HIS0-0.090-0.05459.7920.0030.0030.0000.0000.0000.000
148B208MET00.0570.02161.102-0.001-0.0010.0000.0000.0000.000
149B209PRO0-0.009-0.00463.2370.0010.0010.0000.0000.0000.000
150B210PHE0-0.006-0.01765.6190.0000.0000.0000.0000.0000.000
151B211LYS10.8430.95562.2040.0360.0360.0000.0000.0000.000
152B212SER00.0590.01165.9640.0000.0000.0000.0000.0000.000
153B213LYS10.9120.97069.1760.0220.0220.0000.0000.0000.000
154B214LEU00.0150.02062.0630.0010.0010.0000.0000.0000.000
155B215LEU00.0660.03965.7780.0010.0010.0000.0000.0000.000
156B216MET0-0.0230.00267.3370.0010.0010.0000.0000.0000.000
157B217ILE0-0.026-0.01466.8960.0010.0010.0000.0000.0000.000
158B218ILE00.0650.02463.4490.0010.0010.0000.0000.0000.000
159B219SER0-0.072-0.03667.2290.0010.0010.0000.0000.0000.000
160B220GLN0-0.056-0.04570.2430.0000.0000.0000.0000.0000.000
161B221LYS10.7840.89968.6040.0230.0230.0000.0000.0000.000
162B222ASP-1-0.865-0.93069.610-0.019-0.0190.0000.0000.0000.000
163B223THR0-0.009-0.02764.418-0.001-0.0010.0000.0000.0000.000
164B224PHE00.005-0.00265.6480.0000.0000.0000.0000.0000.000
165B225HIS00.0300.03368.3660.0000.0000.0000.0000.0000.000
166B226SER00.002-0.00968.035-0.001-0.0010.0000.0000.0000.000
167B227PHE00.008-0.00563.7260.0000.0000.0000.0000.0000.000
168B228PHE00.0410.00462.422-0.001-0.0010.0000.0000.0000.000
169B229GLN0-0.044-0.01563.3300.0000.0000.0000.0000.0000.000
170B230HIS0-0.0280.00064.0650.0000.0000.0000.0000.0000.000
171B231PHE0-0.054-0.02161.158-0.001-0.0010.0000.0000.0000.000
172B232SER00.0500.03560.098-0.001-0.0010.0000.0000.0000.000
173B233TYR00.0450.01150.556-0.001-0.0010.0000.0000.0000.000
174B234ASN00.0090.00154.924-0.002-0.0020.0000.0000.0000.000
175B235HIS00.0220.01755.481-0.001-0.0010.0000.0000.0000.000
176B236MET00.0110.01651.927-0.002-0.0020.0000.0000.0000.000
177B237MET0-0.0040.00348.255-0.003-0.0030.0000.0000.0000.000
178B238GLU-1-0.833-0.90150.937-0.032-0.0320.0000.0000.0000.000
179B239LYS10.8080.90352.0870.0340.0340.0000.0000.0000.000
180B240ILE00.0560.02547.378-0.002-0.0020.0000.0000.0000.000
181B241LYS10.8230.88647.4310.0290.0290.0000.0000.0000.000
182B242SER0-0.034-0.00847.621-0.001-0.0010.0000.0000.0000.000
183B243TYR00.0270.01243.081-0.001-0.0010.0000.0000.0000.000
184B244VAL00.002-0.00142.482-0.004-0.0040.0000.0000.0000.000
185B245ASN00.008-0.01043.085-0.003-0.0030.0000.0000.0000.000
186B246TYR0-0.030-0.00841.4880.0000.0000.0000.0000.0000.000
187B247VAL00.0340.01838.967-0.004-0.0040.0000.0000.0000.000
188B248LEU0-0.056-0.03538.972-0.004-0.0040.0000.0000.0000.000
189B249SER0-0.034-0.02339.157-0.001-0.0010.0000.0000.0000.000
190B250GLU-1-0.783-0.82537.618-0.091-0.0910.0000.0000.0000.000
191B251LYS10.8960.92233.7090.1040.1040.0000.0000.0000.000
192B252SER0-0.067-0.01734.287-0.005-0.0050.0000.0000.0000.000
193B253SER0-0.026-0.01034.261-0.004-0.0040.0000.0000.0000.000
194B254THR0-0.008-0.02330.245-0.009-0.0090.0000.0000.0000.000
195B255PHE0-0.022-0.00921.8990.0100.0100.0000.0000.0000.000
196B256LEU00.0750.03924.4040.0060.0060.0000.0000.0000.000
197B257MET00.0220.07027.0700.0130.0130.0000.0000.0000.000
198B258LYS10.9220.96229.5450.1230.1230.0000.0000.0000.000
199B259ALA00.0010.00225.6020.0080.0080.0000.0000.0000.000
200B260ALA00.003-0.00527.6790.0100.0100.0000.0000.0000.000
201B261ALA0-0.014-0.01429.2480.0090.0090.0000.0000.0000.000
202B262LYS10.9050.96229.6050.0650.0650.0000.0000.0000.000
203B263VAL0-0.050-0.02126.8620.0060.0060.0000.0000.0000.000
204B264VAL0-0.052-0.02229.9910.0090.0090.0000.0000.0000.000
205B265GLU-1-0.938-0.96133.676-0.042-0.0420.0000.0000.0000.000