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: V5641

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 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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2341860.426696
FMO2-HF: Nuclear repulsion 2258112.74265
FMO2-HF: Total energy -83747.684046
FMO2-MP2: Total energy -83986.029339


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.
-4.096-1.9130.029-1.151-1.061-0.004
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 : -0.030 / q_NPA : -0.034
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-1-0.845-0.9393.178-5.300-3.1170.029-1.151-1.061-0.004
4B64ALA00.0180.0015.8890.7310.7310.0000.0000.0000.000
5B65GLY0-0.0050.0027.9270.3320.3320.0000.0000.0000.000
6B66LEU00.0290.0009.4740.2000.2000.0000.0000.0000.000
7B67VAL0-0.038-0.0028.0440.1940.1940.0000.0000.0000.000
8B68ALA00.0420.02210.9110.1970.1970.0000.0000.0000.000
9B69GLU-1-0.963-0.98013.650-0.632-0.6320.0000.0000.0000.000
10B70ALA0-0.032-0.01813.7870.1090.1090.0000.0000.0000.000
11B71GLU-1-0.961-0.98913.999-0.311-0.3110.0000.0000.0000.000
12B72ALA0-0.0030.00916.7990.0700.0700.0000.0000.0000.000
13B73VAL0-0.035-0.02118.8640.0560.0560.0000.0000.0000.000
14B74ALA0-0.012-0.00619.0380.0490.0490.0000.0000.0000.000
15B75ALA00.0400.02320.9580.0440.0440.0000.0000.0000.000
16B76GLY00.0180.00522.9390.0300.0300.0000.0000.0000.000
17B77TRP0-0.032-0.02319.5640.0250.0250.0000.0000.0000.000
18B78MET0-0.031-0.01322.0120.0320.0320.0000.0000.0000.000
19B79LEU00.0100.01626.4650.0200.0200.0000.0000.0000.000
20B80ASP-1-0.783-0.89028.923-0.128-0.1280.0000.0000.0000.000
21B81PHE0-0.026-0.01128.9310.0140.0140.0000.0000.0000.000
22B82LEU00.022-0.00228.5490.0140.0140.0000.0000.0000.000
23B83CYS00.0020.01032.0820.0110.0110.0000.0000.0000.000
24B84LEU00.0130.00733.2290.0100.0100.0000.0000.0000.000
25B85SER0-0.054-0.03133.3920.0100.0100.0000.0000.0000.000
26B86LEU0-0.0160.00536.0470.0070.0070.0000.0000.0000.000
27B87CYS0-0.014-0.01437.9520.0050.0050.0000.0000.0000.000
28B88ARG10.9000.91135.1820.0720.0720.0000.0000.0000.000
29B89ALA0-0.0040.00939.8060.0040.0040.0000.0000.0000.000
30B90PHE00.0180.00241.6720.0040.0040.0000.0000.0000.000
31B91ARG10.8310.89843.5160.0490.0490.0000.0000.0000.000
32B92ASP-1-0.805-0.86743.467-0.039-0.0390.0000.0000.0000.000
33B93GLY00.0240.02046.3210.0030.0030.0000.0000.0000.000
34B94ARG10.7640.86239.6020.0440.0440.0000.0000.0000.000
35B95SER00.0770.02142.851-0.003-0.0030.0000.0000.0000.000
36B96GLU-1-0.794-0.86541.112-0.034-0.0340.0000.0000.0000.000
37B97ASP-1-0.817-0.90538.674-0.037-0.0370.0000.0000.0000.000
38B98PHE00.0110.02338.054-0.005-0.0050.0000.0000.0000.000
39B99ARG10.8870.91838.5300.0320.0320.0000.0000.0000.000
40B100ARG10.8440.91635.3330.0280.0280.0000.0000.0000.000
41B101THR0-0.001-0.01533.959-0.005-0.0050.0000.0000.0000.000
42B102ARG10.9270.95833.7790.0550.0550.0000.0000.0000.000
43B103ASN00.0000.00433.369-0.007-0.0070.0000.0000.0000.000
44B104SER0-0.0080.00229.913-0.004-0.0040.0000.0000.0000.000
45B105ALA00.002-0.01029.284-0.010-0.0100.0000.0000.0000.000
46B106GLU-1-0.956-0.97329.984-0.105-0.1050.0000.0000.0000.000
47B107ALA00.0100.00327.139-0.008-0.0080.0000.0000.0000.000
48B108ILE0-0.017-0.01624.786-0.012-0.0120.0000.0000.0000.000
49B109ILE0-0.0040.00125.212-0.021-0.0210.0000.0000.0000.000
50B110HIS0-0.072-0.04025.006-0.010-0.0100.0000.0000.0000.000
51B111GLY00.0120.02121.497-0.012-0.0120.0000.0000.0000.000
52B112LEU0-0.075-0.03421.160-0.034-0.0340.0000.0000.0000.000
53B113SER00.0460.02420.2880.0140.0140.0000.0000.0000.000
54B114SER0-0.045-0.02522.4420.0100.0100.0000.0000.0000.000
55B115LEU00.0120.00225.5870.0070.0070.0000.0000.0000.000
56B116THR00.006-0.00527.8040.0130.0130.0000.0000.0000.000
57B117ALA00.0820.02430.3800.0080.0080.0000.0000.0000.000
58B118CYS0-0.033-0.02531.8690.0110.0110.0000.0000.0000.000
59B119GLN00.0910.06225.7610.0080.0080.0000.0000.0000.000
60B120LEU00.0550.04131.4790.0050.0050.0000.0000.0000.000
61B121ARG10.8280.89133.9880.1110.1110.0000.0000.0000.000
62B122THR0-0.033-0.03932.5500.0100.0100.0000.0000.0000.000
63B123ILE00.0430.02630.3630.0080.0080.0000.0000.0000.000
64B124TYR00.0460.02434.6420.0070.0070.0000.0000.0000.000
65B125ILE0-0.0020.00737.9760.0080.0080.0000.0000.0000.000
66B126CYS0-0.033-0.01735.4210.0060.0060.0000.0000.0000.000
67B127GLN00.019-0.00336.4630.0070.0070.0000.0000.0000.000
68B128PHE00.0100.00439.3160.0060.0060.0000.0000.0000.000
69B129LEU00.006-0.00340.4860.0050.0050.0000.0000.0000.000
70B130THR0-0.050-0.03638.6220.0050.0050.0000.0000.0000.000
71B131ARG10.8640.94239.4790.0810.0810.0000.0000.0000.000
72B132ILE00.008-0.00144.7380.0040.0040.0000.0000.0000.000
73B133ALA0-0.063-0.02944.3360.0040.0040.0000.0000.0000.000
74B134ALA0-0.027-0.00844.9920.0030.0030.0000.0000.0000.000
75B135GLY00.0250.00346.9980.0010.0010.0000.0000.0000.000
76B136LYS10.7920.86850.1490.0340.0340.0000.0000.0000.000
77B137THR0-0.072-0.02347.6630.0020.0020.0000.0000.0000.000
78B138LEU00.0260.00249.649-0.003-0.0030.0000.0000.0000.000
79B139ASP-1-0.902-0.94948.889-0.037-0.0370.0000.0000.0000.000
80B140ALA0-0.083-0.03145.255-0.001-0.0010.0000.0000.0000.000
81B141GLN00.0250.02144.9400.0020.0020.0000.0000.0000.000
82B142PHE0-0.031-0.04441.439-0.002-0.0020.0000.0000.0000.000
83B143GLU-1-0.809-0.86542.286-0.081-0.0810.0000.0000.0000.000
84B144ASN00.005-0.00640.8980.0030.0030.0000.0000.0000.000
85B145ASP-1-0.835-0.89844.473-0.052-0.0520.0000.0000.0000.000
86B146GLU-1-0.912-0.96248.178-0.047-0.0470.0000.0000.0000.000
87B147ARG10.8330.89449.2930.0520.0520.0000.0000.0000.000
88B148ILE0-0.088-0.02948.3020.0010.0010.0000.0000.0000.000
89B149THR00.0560.00949.250-0.001-0.0010.0000.0000.0000.000
90B150PRO00.0380.01647.297-0.003-0.0030.0000.0000.0000.000
91B151LEU00.0230.01147.931-0.003-0.0030.0000.0000.0000.000
92B152GLU-1-0.740-0.81550.085-0.051-0.0510.0000.0000.0000.000
93B153SER0-0.022-0.02544.477-0.003-0.0030.0000.0000.0000.000
94B154ALA0-0.019-0.02445.560-0.003-0.0030.0000.0000.0000.000
95B155LEU0-0.046-0.02646.575-0.003-0.0030.0000.0000.0000.000
96B156MET00.0060.00345.712-0.001-0.0010.0000.0000.0000.000
97B157ILE00.0070.01941.387-0.003-0.0030.0000.0000.0000.000
98B158TRP0-0.072-0.04243.917-0.004-0.0040.0000.0000.0000.000
99B159GLY0-0.020-0.01146.2310.0000.0000.0000.0000.0000.000
100B160SER0-0.049-0.02842.086-0.002-0.0020.0000.0000.0000.000
101B161ILE0-0.080-0.04040.917-0.005-0.0050.0000.0000.0000.000
102B162GLU-1-0.909-0.94239.829-0.098-0.0980.0000.0000.0000.000
103B163LYS10.7930.89442.1900.0670.0670.0000.0000.0000.000
104B164GLU-1-0.925-0.95644.943-0.065-0.0650.0000.0000.0000.000
105B165HIS0-0.015-0.01647.7900.0030.0030.0000.0000.0000.000
106B166ASP-1-0.762-0.88551.325-0.055-0.0550.0000.0000.0000.000
107B167LYS10.9770.98253.4880.0410.0410.0000.0000.0000.000
108B168LEU0-0.024-0.01550.3870.0010.0010.0000.0000.0000.000
109B169HIS00.0380.02247.8610.0010.0010.0000.0000.0000.000
110B170GLU-1-0.893-0.94251.766-0.047-0.0470.0000.0000.0000.000
111B171GLU-1-0.868-0.92254.940-0.040-0.0400.0000.0000.0000.000
112B172ILE0-0.016-0.01649.7070.0020.0020.0000.0000.0000.000
113B173GLN0-0.019-0.00352.406-0.001-0.0010.0000.0000.0000.000
114B174ASN00.032-0.00653.2710.0000.0000.0000.0000.0000.000
115B175LEU0-0.020-0.00655.2050.0020.0020.0000.0000.0000.000
116B176ILE00.0340.01149.7510.0010.0010.0000.0000.0000.000
117B177LYS10.8750.95453.8730.0500.0500.0000.0000.0000.000
118B178ILE0-0.023-0.01056.2060.0010.0010.0000.0000.0000.000
119B179GLN00.008-0.02355.3170.0020.0020.0000.0000.0000.000
120B180ALA00.001-0.00354.0920.0010.0010.0000.0000.0000.000
121B181ILE0-0.0050.00155.5350.0010.0010.0000.0000.0000.000
122B182ALA00.001-0.00459.1320.0010.0010.0000.0000.0000.000
123B183VAL00.0250.01254.4270.0020.0020.0000.0000.0000.000
124B184CYS0-0.0280.00257.1360.0010.0010.0000.0000.0000.000
125B185MET0-0.070-0.01858.9650.0010.0010.0000.0000.0000.000
126B186GLU-1-0.861-0.91558.627-0.030-0.0300.0000.0000.0000.000
127B187ASN0-0.071-0.04156.9060.0020.0020.0000.0000.0000.000
128B188GLY0-0.0170.00560.7170.0000.0000.0000.0000.0000.000
129B189ASN0-0.032-0.01457.9400.0020.0020.0000.0000.0000.000
130B190PHE00.005-0.02261.747-0.001-0.0010.0000.0000.0000.000
131B191LYS10.8440.91663.0830.0340.0340.0000.0000.0000.000
132B192GLU-1-0.741-0.86556.112-0.039-0.0390.0000.0000.0000.000
133B193ALA00.0380.01359.415-0.002-0.0020.0000.0000.0000.000
134B194GLU-1-0.908-0.96961.039-0.032-0.0320.0000.0000.0000.000
135B195GLU-1-0.884-0.92558.773-0.039-0.0390.0000.0000.0000.000
136B196VAL00.0040.00955.695-0.002-0.0020.0000.0000.0000.000
137B197PHE0-0.006-0.02057.788-0.001-0.0010.0000.0000.0000.000
138B198GLU-1-0.942-0.96560.160-0.042-0.0420.0000.0000.0000.000
139B199ARG10.8320.88954.0120.0460.0460.0000.0000.0000.000
140B200ILE0-0.034-0.00654.156-0.002-0.0020.0000.0000.0000.000
141B201PHE0-0.063-0.04956.516-0.001-0.0010.0000.0000.0000.000
142B202GLY00.0760.05359.6870.0010.0010.0000.0000.0000.000
143B203ASP-1-0.833-0.90557.919-0.049-0.0490.0000.0000.0000.000
144B204PRO0-0.031-0.01860.1990.0010.0010.0000.0000.0000.000
145B205ASN0-0.062-0.04258.9170.0020.0020.0000.0000.0000.000
146B206SER0-0.031-0.00857.8960.0000.0000.0000.0000.0000.000
147B207HIS0-0.045-0.00959.5210.0040.0040.0000.0000.0000.000
148B208MET00.0600.01461.062-0.001-0.0010.0000.0000.0000.000
149B209PRO00.0080.00863.0730.0010.0010.0000.0000.0000.000
150B210PHE0-0.004-0.01865.3540.0000.0000.0000.0000.0000.000
151B211LYS10.8630.95962.1850.0420.0420.0000.0000.0000.000
152B212SER00.0410.00065.4940.0000.0000.0000.0000.0000.000
153B213LYS10.9250.96868.6770.0270.0270.0000.0000.0000.000
154B214LEU00.0120.01661.6780.0010.0010.0000.0000.0000.000
155B215LEU00.0500.03665.3660.0000.0000.0000.0000.0000.000
156B216MET0-0.025-0.01167.0010.0010.0010.0000.0000.0000.000
157B217ILE0-0.021-0.02067.0790.0010.0010.0000.0000.0000.000
158B218ILE00.0700.03363.1940.0010.0010.0000.0000.0000.000
159B219SER0-0.026-0.00567.0870.0010.0010.0000.0000.0000.000
160B220GLN0-0.058-0.03769.8340.0010.0010.0000.0000.0000.000
161B221LYS10.7780.90068.4050.0290.0290.0000.0000.0000.000
162B222ASP-1-0.867-0.92969.470-0.024-0.0240.0000.0000.0000.000
163B223THR00.004-0.01364.205-0.001-0.0010.0000.0000.0000.000
164B224PHE0-0.011-0.01065.534-0.001-0.0010.0000.0000.0000.000
165B225HIS00.0370.04068.1410.0000.0000.0000.0000.0000.000
166B226SER00.004-0.01367.874-0.001-0.0010.0000.0000.0000.000
167B227PHE00.010-0.00663.2730.0000.0000.0000.0000.0000.000
168B228PHE00.0420.00862.080-0.001-0.0010.0000.0000.0000.000
169B229GLN0-0.053-0.01763.1780.0000.0000.0000.0000.0000.000
170B230HIS0-0.048-0.00964.2380.0000.0000.0000.0000.0000.000
171B231PHE0-0.043-0.01960.933-0.001-0.0010.0000.0000.0000.000
172B232SER00.0380.03060.169-0.001-0.0010.0000.0000.0000.000
173B233TYR00.0750.02150.398-0.001-0.0010.0000.0000.0000.000
174B234ASN00.010-0.00755.144-0.002-0.0020.0000.0000.0000.000
175B235HIS00.0160.02255.835-0.001-0.0010.0000.0000.0000.000
176B236MET00.0110.01451.735-0.002-0.0020.0000.0000.0000.000
177B237MET0-0.011-0.00648.458-0.003-0.0030.0000.0000.0000.000
178B238GLU-1-0.836-0.89251.340-0.039-0.0390.0000.0000.0000.000
179B239LYS10.8240.90452.5760.0390.0390.0000.0000.0000.000
180B240ILE00.0500.02647.422-0.002-0.0020.0000.0000.0000.000
181B241LYS10.8200.88347.7060.0350.0350.0000.0000.0000.000
182B242SER0-0.031-0.00647.855-0.001-0.0010.0000.0000.0000.000
183B243TYR00.0270.00642.767-0.001-0.0010.0000.0000.0000.000
184B244VAL0-0.003-0.00842.755-0.004-0.0040.0000.0000.0000.000
185B245ASN0-0.007-0.01543.322-0.003-0.0030.0000.0000.0000.000
186B246TYR0-0.024-0.01541.7620.0000.0000.0000.0000.0000.000
187B247VAL00.0430.02639.125-0.004-0.0040.0000.0000.0000.000
188B248LEU0-0.060-0.02939.130-0.005-0.0050.0000.0000.0000.000
189B249SER0-0.040-0.02939.191-0.001-0.0010.0000.0000.0000.000
190B250GLU-1-0.789-0.82837.834-0.100-0.1000.0000.0000.0000.000
191B251LYS10.9020.92333.2450.1210.1210.0000.0000.0000.000
192B252SER0-0.071-0.00734.319-0.006-0.0060.0000.0000.0000.000
193B253SER0-0.020-0.00134.010-0.002-0.0020.0000.0000.0000.000
194B254THR0-0.012-0.02330.272-0.009-0.0090.0000.0000.0000.000
195B255PHE0-0.009-0.00822.1200.0110.0110.0000.0000.0000.000
196B256LEU00.0750.03924.6670.0090.0090.0000.0000.0000.000
197B257MET00.0420.06427.2620.0130.0130.0000.0000.0000.000
198B258LYS10.9390.98129.7340.1320.1320.0000.0000.0000.000
199B259ALA0-0.005-0.00625.9580.0090.0090.0000.0000.0000.000
200B260ALA00.000-0.00528.0470.0100.0100.0000.0000.0000.000
201B261ALA0-0.009-0.01829.6120.0100.0100.0000.0000.0000.000
202B262LYS10.9250.97529.7260.0650.0650.0000.0000.0000.000
203B263VAL0-0.054-0.02227.2190.0070.0070.0000.0000.0000.000
204B264VAL0-0.047-0.02330.3240.0080.0080.0000.0000.0000.000
205B265GLU-1-0.962-0.96333.735-0.042-0.0420.0000.0000.0000.000