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: YZM22

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 OptH
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 -2341590.192363
FMO2-HF: Nuclear repulsion 2257843.423619
FMO2-HF: Total energy -83746.768744
FMO2-MP2: Total energy -83985.051074


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.
-4.328-2.0490.031-1.206-1.105-0.004
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 : -0.031 / q_NPA : -0.037
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-1-0.865-0.9533.159-5.601-3.3220.031-1.206-1.105-0.004
4B64ALA00.0280.0025.8730.7790.7790.0000.0000.0000.000
5B65GLY0-0.0040.0027.9060.3600.3600.0000.0000.0000.000
6B66LEU00.0400.0119.0700.2160.2160.0000.0000.0000.000
7B67VAL0-0.0220.0057.8820.2130.2130.0000.0000.0000.000
8B68ALA00.0350.01710.8800.2100.2100.0000.0000.0000.000
9B69GLU-1-0.971-0.98213.622-0.652-0.6520.0000.0000.0000.000
10B70ALA0-0.029-0.01613.7780.1130.1130.0000.0000.0000.000
11B71GLU-1-0.968-0.99113.854-0.305-0.3050.0000.0000.0000.000
12B72ALA00.0040.01116.7660.0720.0720.0000.0000.0000.000
13B73VAL0-0.030-0.01618.7890.0580.0580.0000.0000.0000.000
14B74ALA0-0.019-0.01318.9350.0500.0500.0000.0000.0000.000
15B75ALA00.0390.02320.8290.0440.0440.0000.0000.0000.000
16B76GLY00.0200.00822.9060.0290.0290.0000.0000.0000.000
17B77TRP0-0.014-0.01719.5050.0240.0240.0000.0000.0000.000
18B78MET0-0.037-0.02122.0220.0330.0330.0000.0000.0000.000
19B79LEU00.0070.01726.4820.0200.0200.0000.0000.0000.000
20B80ASP-1-0.841-0.92728.889-0.131-0.1310.0000.0000.0000.000
21B81PHE0-0.049-0.02628.9710.0140.0140.0000.0000.0000.000
22B82LEU00.019-0.00128.5270.0140.0140.0000.0000.0000.000
23B83CYS00.0090.01632.1590.0100.0100.0000.0000.0000.000
24B84LEU00.003-0.00232.9230.0100.0100.0000.0000.0000.000
25B85SER0-0.047-0.02333.5290.0100.0100.0000.0000.0000.000
26B86LEU0-0.0170.00336.1520.0070.0070.0000.0000.0000.000
27B87CYS0-0.012-0.01037.9830.0050.0050.0000.0000.0000.000
28B88ARG10.9340.95935.5240.0610.0610.0000.0000.0000.000
29B89ALA0-0.0030.01239.9400.0040.0040.0000.0000.0000.000
30B90PHE00.0150.00441.7640.0040.0040.0000.0000.0000.000
31B91ARG10.8280.87542.9960.0420.0420.0000.0000.0000.000
32B92ASP-1-0.815-0.86443.785-0.033-0.0330.0000.0000.0000.000
33B93GLY00.0000.00946.4120.0030.0030.0000.0000.0000.000
34B94ARG10.7920.87739.7550.0360.0360.0000.0000.0000.000
35B95SER00.0370.00742.922-0.004-0.0040.0000.0000.0000.000
36B96GLU-1-0.806-0.90141.519-0.030-0.0300.0000.0000.0000.000
37B97ASP-1-0.825-0.90638.728-0.030-0.0300.0000.0000.0000.000
38B98PHE00.0050.01138.118-0.005-0.0050.0000.0000.0000.000
39B99ARG10.8790.93338.0630.0280.0280.0000.0000.0000.000
40B100ARG10.9260.96235.3470.0220.0220.0000.0000.0000.000
41B101THR00.010-0.00334.032-0.004-0.0040.0000.0000.0000.000
42B102ARG10.9270.96533.7440.0520.0520.0000.0000.0000.000
43B103ASN00.000-0.00433.297-0.008-0.0080.0000.0000.0000.000
44B104SER0-0.0080.00729.907-0.004-0.0040.0000.0000.0000.000
45B105ALA0-0.001-0.01229.250-0.010-0.0100.0000.0000.0000.000
46B106GLU-1-0.942-0.96929.950-0.105-0.1050.0000.0000.0000.000
47B107ALA00.0110.00227.062-0.009-0.0090.0000.0000.0000.000
48B108ILE0-0.018-0.01624.799-0.012-0.0120.0000.0000.0000.000
49B109ILE0-0.010-0.00325.179-0.022-0.0220.0000.0000.0000.000
50B110HIS0-0.070-0.03524.944-0.011-0.0110.0000.0000.0000.000
51B111GLY00.0090.01921.466-0.014-0.0140.0000.0000.0000.000
52B112LEU0-0.073-0.03121.130-0.035-0.0350.0000.0000.0000.000
53B113SER00.0400.02020.1970.0130.0130.0000.0000.0000.000
54B114SER0-0.050-0.02622.4180.0080.0080.0000.0000.0000.000
55B115LEU00.0490.01025.5640.0090.0090.0000.0000.0000.000
56B116THR00.0070.02027.7910.0120.0120.0000.0000.0000.000
57B117ALA00.0970.03530.3560.0080.0080.0000.0000.0000.000
58B118CYS0-0.014-0.01231.9690.0110.0110.0000.0000.0000.000
59B119GLN00.0460.01825.7460.0080.0080.0000.0000.0000.000
60B120LEU00.0720.05031.4500.0060.0060.0000.0000.0000.000
61B121ARG10.8300.88933.9600.1090.1090.0000.0000.0000.000
62B122THR0-0.027-0.03432.5160.0110.0110.0000.0000.0000.000
63B123ILE00.0430.01930.4220.0080.0080.0000.0000.0000.000
64B124TYR00.0640.03234.6110.0070.0070.0000.0000.0000.000
65B125ILE0-0.0200.00037.9100.0080.0080.0000.0000.0000.000
66B126CYS0-0.038-0.02235.2550.0070.0070.0000.0000.0000.000
67B127GLN00.024-0.00136.9420.0060.0060.0000.0000.0000.000
68B128PHE00.0050.00739.2840.0060.0060.0000.0000.0000.000
69B129LEU00.001-0.00740.3650.0050.0050.0000.0000.0000.000
70B130THR0-0.052-0.03938.5480.0040.0040.0000.0000.0000.000
71B131ARG10.9110.97939.4240.0810.0810.0000.0000.0000.000
72B132ILE00.0210.00944.7060.0040.0040.0000.0000.0000.000
73B133ALA0-0.075-0.03644.3070.0040.0040.0000.0000.0000.000
74B134ALA0-0.027-0.01244.9980.0030.0030.0000.0000.0000.000
75B135GLY00.0250.00346.9640.0010.0010.0000.0000.0000.000
76B136LYS10.8760.93650.1160.0330.0330.0000.0000.0000.000
77B137THR0-0.064-0.02047.8770.0030.0030.0000.0000.0000.000
78B138LEU00.0290.00249.617-0.003-0.0030.0000.0000.0000.000
79B139ASP-1-0.916-0.94848.992-0.036-0.0360.0000.0000.0000.000
80B140ALA0-0.078-0.03045.201-0.002-0.0020.0000.0000.0000.000
81B141GLN00.0260.00644.6100.0020.0020.0000.0000.0000.000
82B142PHE0-0.050-0.05641.448-0.002-0.0020.0000.0000.0000.000
83B143GLU-1-0.838-0.90842.258-0.082-0.0820.0000.0000.0000.000
84B144ASN00.0010.00340.9460.0030.0030.0000.0000.0000.000
85B145ASP-1-0.920-0.96144.448-0.054-0.0540.0000.0000.0000.000
86B146GLU-1-0.917-0.96448.153-0.047-0.0470.0000.0000.0000.000
87B147ARG10.9280.96649.2660.0510.0510.0000.0000.0000.000
88B148ILE0-0.070-0.01948.3690.0020.0020.0000.0000.0000.000
89B149THR00.0600.03649.221-0.001-0.0010.0000.0000.0000.000
90B150PRO00.0310.01247.360-0.003-0.0030.0000.0000.0000.000
91B151LEU00.0200.00847.901-0.003-0.0030.0000.0000.0000.000
92B152GLU-1-0.729-0.83150.054-0.052-0.0520.0000.0000.0000.000
93B153SER0-0.017-0.01244.678-0.003-0.0030.0000.0000.0000.000
94B154ALA0-0.032-0.03245.529-0.003-0.0030.0000.0000.0000.000
95B155LEU0-0.051-0.02846.545-0.003-0.0030.0000.0000.0000.000
96B156MET00.0010.01046.085-0.001-0.0010.0000.0000.0000.000
97B157ILE0-0.0010.00941.479-0.003-0.0030.0000.0000.0000.000
98B158TRP0-0.072-0.04443.888-0.004-0.0040.0000.0000.0000.000
99B159GLY0-0.021-0.01146.2020.0000.0000.0000.0000.0000.000
100B160SER0-0.033-0.01141.965-0.002-0.0020.0000.0000.0000.000
101B161ILE0-0.086-0.03840.919-0.005-0.0050.0000.0000.0000.000
102B162GLU-1-0.915-0.94939.663-0.100-0.1000.0000.0000.0000.000
103B163LYS10.8040.90942.1620.0670.0670.0000.0000.0000.000
104B164GLU-1-0.929-0.95744.915-0.063-0.0630.0000.0000.0000.000
105B165HIS0-0.036-0.01948.0080.0020.0020.0000.0000.0000.000
106B166ASP-1-0.796-0.88950.834-0.055-0.0550.0000.0000.0000.000
107B167LYS10.9810.96953.4100.0390.0390.0000.0000.0000.000
108B168LEU00.0040.00349.9560.0010.0010.0000.0000.0000.000
109B169HIS00.0440.01047.9060.0010.0010.0000.0000.0000.000
110B170GLU-1-0.917-0.95851.736-0.046-0.0460.0000.0000.0000.000
111B171GLU-1-0.938-0.97654.910-0.039-0.0390.0000.0000.0000.000
112B172ILE0-0.021-0.01949.5430.0020.0020.0000.0000.0000.000
113B173GLN0-0.024-0.00352.373-0.001-0.0010.0000.0000.0000.000
114B174ASN00.030-0.00953.2400.0000.0000.0000.0000.0000.000
115B175LEU0-0.024-0.00955.1550.0020.0020.0000.0000.0000.000
116B176ILE00.0240.01049.6290.0010.0010.0000.0000.0000.000
117B177LYS10.9030.97053.8410.0500.0500.0000.0000.0000.000
118B178ILE0-0.020-0.00756.1750.0010.0010.0000.0000.0000.000
119B179GLN00.019-0.01355.2280.0020.0020.0000.0000.0000.000
120B180ALA00.000-0.00254.1280.0010.0010.0000.0000.0000.000
121B181ILE0-0.0020.00355.5030.0010.0010.0000.0000.0000.000
122B182ALA00.002-0.00859.1340.0010.0010.0000.0000.0000.000
123B183VAL00.0400.02454.4440.0020.0020.0000.0000.0000.000
124B184CYS0-0.0140.02156.9470.0010.0010.0000.0000.0000.000
125B185MET0-0.067-0.02058.9340.0010.0010.0000.0000.0000.000
126B186GLU-1-0.958-0.98358.852-0.029-0.0290.0000.0000.0000.000
127B187ASN0-0.075-0.04756.9800.0020.0020.0000.0000.0000.000
128B188GLY0-0.0190.00460.6850.0000.0000.0000.0000.0000.000
129B189ASN0-0.0040.00757.9500.0020.0020.0000.0000.0000.000
130B190PHE0-0.004-0.02661.717-0.001-0.0010.0000.0000.0000.000
131B191LYS10.8880.94563.0350.0350.0350.0000.0000.0000.000
132B192GLU-1-0.807-0.91355.603-0.040-0.0400.0000.0000.0000.000
133B193ALA00.0200.00359.386-0.002-0.0020.0000.0000.0000.000
134B194GLU-1-0.972-0.98961.009-0.033-0.0330.0000.0000.0000.000
135B195GLU-1-0.911-0.95458.823-0.040-0.0400.0000.0000.0000.000
136B196VAL00.0020.00755.685-0.002-0.0020.0000.0000.0000.000
137B197PHE0-0.007-0.01757.760-0.001-0.0010.0000.0000.0000.000
138B198GLU-1-0.946-0.97159.980-0.043-0.0430.0000.0000.0000.000
139B199ARG10.8240.88153.8740.0470.0470.0000.0000.0000.000
140B200ILE0-0.039-0.00954.213-0.002-0.0020.0000.0000.0000.000
141B201PHE0-0.084-0.07156.4880.0000.0000.0000.0000.0000.000
142B202GLY00.0580.04359.6670.0010.0010.0000.0000.0000.000
143B203ASP-1-0.868-0.92357.491-0.050-0.0500.0000.0000.0000.000
144B204PRO0-0.023-0.01360.1730.0010.0010.0000.0000.0000.000
145B205ASN0-0.014-0.01258.9740.0020.0020.0000.0000.0000.000
146B206SER0-0.074-0.03657.9000.0000.0000.0000.0000.0000.000
147B207HIS0-0.027-0.00859.4940.0030.0030.0000.0000.0000.000
148B208MET00.0750.02161.033-0.001-0.0010.0000.0000.0000.000
149B209PRO0-0.0070.00463.0440.0010.0010.0000.0000.0000.000
150B210PHE00.002-0.01765.3240.0000.0000.0000.0000.0000.000
151B211LYS10.9130.99362.5170.0410.0410.0000.0000.0000.000
152B212SER00.0420.00165.4640.0000.0000.0000.0000.0000.000
153B213LYS10.9040.95768.6470.0260.0260.0000.0000.0000.000
154B214LEU00.0110.01961.6190.0010.0010.0000.0000.0000.000
155B215LEU00.0640.04265.1720.0010.0010.0000.0000.0000.000
156B216MET0-0.024-0.01466.9720.0010.0010.0000.0000.0000.000
157B217ILE0-0.016-0.01767.2440.0010.0010.0000.0000.0000.000
158B218ILE00.0550.02763.2060.0010.0010.0000.0000.0000.000
159B219SER0-0.0320.00367.0570.0010.0010.0000.0000.0000.000
160B220GLN0-0.106-0.05869.8050.0010.0010.0000.0000.0000.000
161B221LYS10.8860.94068.3790.0270.0270.0000.0000.0000.000
162B222ASP-1-0.866-0.92969.439-0.023-0.0230.0000.0000.0000.000
163B223THR00.005-0.01664.341-0.001-0.0010.0000.0000.0000.000
164B224PHE0-0.013-0.01165.782-0.001-0.0010.0000.0000.0000.000
165B225HIS00.0570.06068.1080.0000.0000.0000.0000.0000.000
166B226SER00.020-0.01267.841-0.001-0.0010.0000.0000.0000.000
167B227PHE0-0.002-0.01763.2390.0000.0000.0000.0000.0000.000
168B228PHE00.0400.00961.828-0.001-0.0010.0000.0000.0000.000
169B229GLN0-0.042-0.01263.1450.0000.0000.0000.0000.0000.000
170B230HIS0-0.048-0.00864.2040.0010.0010.0000.0000.0000.000
171B231PHE0-0.051-0.02260.837-0.001-0.0010.0000.0000.0000.000
172B232SER00.0430.02960.135-0.001-0.0010.0000.0000.0000.000
173B233TYR00.0750.01450.518-0.001-0.0010.0000.0000.0000.000
174B234ASN00.011-0.00655.110-0.002-0.0020.0000.0000.0000.000
175B235HIS00.0290.03155.8000.0000.0000.0000.0000.0000.000
176B236MET00.0260.01751.507-0.002-0.0020.0000.0000.0000.000
177B237MET0-0.045-0.02648.622-0.003-0.0030.0000.0000.0000.000
178B238GLU-1-0.941-0.96251.306-0.034-0.0340.0000.0000.0000.000
179B239LYS10.9040.96252.4770.0360.0360.0000.0000.0000.000
180B240ILE00.0490.02647.424-0.002-0.0020.0000.0000.0000.000
181B241LYS10.9130.95447.6670.0340.0340.0000.0000.0000.000
182B242SER0-0.056-0.01247.706-0.002-0.0020.0000.0000.0000.000
183B243TYR00.0900.03342.629-0.002-0.0020.0000.0000.0000.000
184B244VAL0-0.018-0.01542.787-0.003-0.0030.0000.0000.0000.000
185B245ASN0-0.004-0.01743.116-0.003-0.0030.0000.0000.0000.000
186B246TYR00.0120.02042.6050.0000.0000.0000.0000.0000.000
187B247VAL00.0440.02639.057-0.003-0.0030.0000.0000.0000.000
188B248LEU0-0.068-0.03538.996-0.004-0.0040.0000.0000.0000.000
189B249SER0-0.033-0.02138.9930.0000.0000.0000.0000.0000.000
190B250GLU-1-0.793-0.84937.434-0.097-0.0970.0000.0000.0000.000
191B251LYS10.9100.94433.4380.1120.1120.0000.0000.0000.000
192B252SER0-0.089-0.00434.126-0.005-0.0050.0000.0000.0000.000
193B253SER0-0.0060.00433.805-0.001-0.0010.0000.0000.0000.000
194B254THR0-0.002-0.02330.028-0.008-0.0080.0000.0000.0000.000
195B255PHE0-0.020-0.01322.0460.0120.0120.0000.0000.0000.000
196B256LEU00.0700.03724.4440.0100.0100.0000.0000.0000.000
197B257MET00.0320.02327.0530.0130.0130.0000.0000.0000.000
198B258LYS10.9510.98528.6160.1210.1210.0000.0000.0000.000
199B259ALA0-0.016-0.01125.7790.0090.0090.0000.0000.0000.000
200B260ALA00.007-0.00227.8500.0110.0110.0000.0000.0000.000
201B261ALA00.000-0.01529.3950.0100.0100.0000.0000.0000.000
202B262LYS10.9660.98428.8320.0510.0510.0000.0000.0000.000
203B263VAL0-0.062-0.02327.1630.0070.0070.0000.0000.0000.000
204B264VAL0-0.048-0.02230.1180.0080.0080.0000.0000.0000.000
205B265GLU-1-1.011-0.97833.541-0.026-0.0260.0000.0000.0000.000