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: K31Y3

Calculation Name: 2WD5-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2WD5

Chain ID: B

ChEMBL ID:

UniProt ID: Q9CU62

Base Structure: X-ray

Registration Date: 2023-06-21

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 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2137460.328799
FMO2-HF: Nuclear repulsion 2058804.796382
FMO2-HF: Total energy -78655.532417
FMO2-MP2: Total energy -78881.470565


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:492:LYS)


Summations of interaction energy for fragment #1(B:492:LYS)
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.
36.23939.7730.164-1.337-2.3610.001
Interaction energy analysis for fragmet #1(B:492:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 1.017 / q_NPA : 0.986
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].
3B494GLN0-0.056-0.0293.0550.3132.4780.004-0.985-1.1840.003
4B495LEU00.0320.0132.9982.3783.4040.161-0.296-0.891-0.002
5B496LEU00.0710.0515.5593.0903.0900.0000.0000.0000.000
6B497ARG10.9010.9447.95222.95922.9590.0000.0000.0000.000
7B498ALA00.0320.0248.5221.9281.9280.0000.0000.0000.000
8B499ALA0-0.022-0.00910.2331.4991.4990.0000.0000.0000.000
9B500THR0-0.068-0.03812.2121.1741.1740.0000.0000.0000.000
10B501GLY00.0380.02914.1380.9760.9760.0000.0000.0000.000
11B502LYS10.9820.96616.12913.27513.2750.0000.0000.0000.000
12B503ALA00.0000.00417.0920.0900.0900.0000.0000.0000.000
13B504ILE00.0440.02917.3280.2920.2920.0000.0000.0000.000
14B505LEU0-0.022-0.01012.472-0.130-0.1300.0000.0000.0000.000
15B506ASN00.006-0.00116.311-0.570-0.5700.0000.0000.0000.000
16B507GLY00.0840.06119.1190.3380.3380.0000.0000.0000.000
17B508ILE0-0.033-0.01915.6070.1670.1670.0000.0000.0000.000
18B509ASP-1-0.823-0.93115.088-17.213-17.2130.0000.0000.0000.000
19B510SER0-0.042-0.03317.9040.1870.1870.0000.0000.0000.000
20B511ILE00.0040.01620.3410.4010.4010.0000.0000.0000.000
21B512ASN00.001-0.00316.4800.5600.5600.0000.0000.0000.000
22B513LYS10.9140.96619.14313.99313.9930.0000.0000.0000.000
23B514VAL00.0220.01022.3940.3290.3290.0000.0000.0000.000
24B515LEU0-0.0150.00021.4580.3810.3810.0000.0000.0000.000
25B516GLU-1-0.831-0.90119.825-14.117-14.1170.0000.0000.0000.000
26B517HIS0-0.0150.00623.5170.2010.2010.0000.0000.0000.000
27B518PHE00.014-0.01026.8280.4070.4070.0000.0000.0000.000
28B519ARG10.8530.91720.37013.80713.8070.0000.0000.0000.000
29B520ARG10.9110.95323.61712.31112.3110.0000.0000.0000.000
30B521LYS10.8840.93527.80110.06110.0610.0000.0000.0000.000
31B522GLY00.0260.04430.1490.2980.2980.0000.0000.0000.000
32B523ILE0-0.047-0.02631.4360.3490.3490.0000.0000.0000.000
33B524ASN0-0.020-0.01331.242-0.021-0.0210.0000.0000.0000.000
34B525GLN00.0790.04030.534-0.312-0.3120.0000.0000.0000.000
35B526HIS00.0260.00330.158-0.365-0.3650.0000.0000.0000.000
36B527VAL00.0150.00727.489-0.123-0.1230.0000.0000.0000.000
37B528GLN00.0240.00822.711-0.566-0.5660.0000.0000.0000.000
38B529ASN0-0.035-0.01625.656-0.619-0.6190.0000.0000.0000.000
39B530GLY00.0740.04527.8770.0770.0770.0000.0000.0000.000
40B531TYR0-0.063-0.03719.668-0.068-0.0680.0000.0000.0000.000
41B532HIS00.000-0.02822.394-0.624-0.6240.0000.0000.0000.000
42B533GLY00.0480.04718.882-0.490-0.4900.0000.0000.0000.000
43B534ILE0-0.039-0.01714.9720.5960.5960.0000.0000.0000.000
44B535VAL00.014-0.00218.977-0.266-0.2660.0000.0000.0000.000
45B536MET0-0.037-0.01113.156-0.083-0.0830.0000.0000.0000.000
46B537ASN0-0.042-0.02512.844-0.853-0.8530.0000.0000.0000.000
47B538ASN0-0.046-0.03315.757-0.030-0.0300.0000.0000.0000.000
48B539PHE0-0.009-0.00418.1980.6150.6150.0000.0000.0000.000
49B540GLU-1-0.853-0.93115.995-17.093-17.0930.0000.0000.0000.000
50B541CYS00.0070.00318.4590.6870.6870.0000.0000.0000.000
51B542GLU-1-0.893-0.93718.798-13.937-13.9370.0000.0000.0000.000
52B543PRO00.0450.00217.0230.3590.3590.0000.0000.0000.000
53B544ALA0-0.0140.01319.2680.0100.0100.0000.0000.0000.000
54B545PHE0-0.004-0.02122.0690.4010.4010.0000.0000.0000.000
55B546TYR00.0060.00514.3940.2560.2560.0000.0000.0000.000
56B547THR00.0610.02619.781-0.299-0.2990.0000.0000.0000.000
57B548CYS00.0450.03921.6530.0910.0910.0000.0000.0000.000
58B549VAL00.0280.01521.4920.2580.2580.0000.0000.0000.000
59B550GLU-1-0.765-0.86917.077-15.220-15.2200.0000.0000.0000.000
60B551VAL0-0.048-0.03921.0100.0280.0280.0000.0000.0000.000
61B552THR0-0.0230.00123.8110.4020.4020.0000.0000.0000.000
62B553ALA0-0.0100.00622.7460.2650.2650.0000.0000.0000.000
63B554GLY00.0160.00722.6320.0630.0630.0000.0000.0000.000
64B555ASN00.005-0.01721.048-1.046-1.0460.0000.0000.0000.000
65B556ARG10.9490.98122.3399.5959.5950.0000.0000.0000.000
66B557LEU00.0250.00717.439-0.025-0.0250.0000.0000.0000.000
67B558PHE0-0.001-0.03515.192-0.601-0.6010.0000.0000.0000.000
68B559TYR0-0.0020.02420.1310.2920.2920.0000.0000.0000.000
69B560HIS00.0660.04019.969-0.574-0.5740.0000.0000.0000.000
70B561ILE00.0090.01721.9590.5700.5700.0000.0000.0000.000
71B562VAL0-0.025-0.01024.508-0.313-0.3130.0000.0000.0000.000
72B563ASP-1-0.787-0.88727.230-9.707-9.7070.0000.0000.0000.000
73B564SER0-0.043-0.03630.2760.2180.2180.0000.0000.0000.000
74B565ASP-1-0.778-0.90032.277-8.226-8.2260.0000.0000.0000.000
75B566GLU-1-0.871-0.92934.513-8.173-8.1730.0000.0000.0000.000
76B567VAL0-0.073-0.01328.831-0.109-0.1090.0000.0000.0000.000
77B568SER0-0.032-0.04429.851-0.326-0.3260.0000.0000.0000.000
78B569THR0-0.0050.00430.843-0.238-0.2380.0000.0000.0000.000
79B570LYS10.9100.95632.2888.4018.4010.0000.0000.0000.000
80B571ILE00.021-0.00426.165-0.097-0.0970.0000.0000.0000.000
81B572LEU00.0330.01528.990-0.213-0.2130.0000.0000.0000.000
82B573MET0-0.0110.00531.0090.0300.0300.0000.0000.0000.000
83B574GLU-1-0.812-0.91130.511-8.843-8.8430.0000.0000.0000.000
84B575PHE00.0160.01523.909-0.151-0.1510.0000.0000.0000.000
85B576ASN0-0.014-0.02428.987-0.268-0.2680.0000.0000.0000.000
86B577LYS10.8280.92331.7268.8298.8290.0000.0000.0000.000
87B578MET0-0.116-0.05228.806-0.025-0.0250.0000.0000.0000.000
88B579ASN0-0.033-0.01329.382-0.014-0.0140.0000.0000.0000.000
89B580LEU0-0.0260.00024.758-0.314-0.3140.0000.0000.0000.000
90B581PRO0-0.059-0.04022.6390.1950.1950.0000.0000.0000.000
91B582GLY00.0300.04023.653-0.303-0.3030.0000.0000.0000.000
92B583GLU-1-0.923-0.98023.550-10.353-10.3530.0000.0000.0000.000
93B584VAL0-0.043-0.02823.438-0.516-0.5160.0000.0000.0000.000
94B585THR0-0.0060.00125.0930.3390.3390.0000.0000.0000.000
95B586PHE00.0330.00525.589-0.421-0.4210.0000.0000.0000.000
96B587LEU0-0.0140.00425.3490.3110.3110.0000.0000.0000.000
97B588PRO00.0000.00128.238-0.203-0.2030.0000.0000.0000.000
98B589LEU00.014-0.00227.8190.2820.2820.0000.0000.0000.000
99B590ASN0-0.041-0.02931.6620.0800.0800.0000.0000.0000.000
100B591LYS10.8920.95334.4257.8217.8210.0000.0000.0000.000
101B592LEU0-0.059-0.01230.0730.1400.1400.0000.0000.0000.000
102B593ASP-1-0.903-0.94934.763-7.277-7.2770.0000.0000.0000.000
103B594VAL0-0.040-0.00733.139-0.067-0.0670.0000.0000.0000.000
104B595ARG10.9450.96436.5737.0847.0840.0000.0000.0000.000
105B596ASP-1-0.901-0.94638.285-7.440-7.4400.0000.0000.0000.000
106B597THR0-0.064-0.02537.8140.1250.1250.0000.0000.0000.000
107B598ALA00.0270.01639.246-0.122-0.1220.0000.0000.0000.000
108B599TYR0-0.041-0.05434.277-0.023-0.0230.0000.0000.0000.000
109B600PRO00.0250.01539.6890.0970.0970.0000.0000.0000.000
110B601GLU-1-0.941-0.94440.762-6.833-6.8330.0000.0000.0000.000
111B602THR0-0.088-0.07439.3250.1130.1130.0000.0000.0000.000
112B603ASN00.0350.00239.925-0.287-0.2870.0000.0000.0000.000
113B604ASP-1-0.935-0.95338.336-7.441-7.4410.0000.0000.0000.000
114B605ALA00.0250.00035.543-0.147-0.1470.0000.0000.0000.000
115B606ILE0-0.0050.01230.2440.0680.0680.0000.0000.0000.000
116B607PRO00.0570.02332.649-0.184-0.1840.0000.0000.0000.000
117B608MET00.0250.04726.913-0.290-0.2900.0000.0000.0000.000
118B609ILE00.0290.00527.459-0.355-0.3550.0000.0000.0000.000
119B610SER0-0.097-0.05028.145-0.184-0.1840.0000.0000.0000.000
120B611LYS10.9110.95625.9879.6379.6370.0000.0000.0000.000
121B612LEU0-0.0110.02322.193-0.517-0.5170.0000.0000.0000.000
122B613ARG10.8770.93819.86813.55113.5510.0000.0000.0000.000
123B614TYR00.026-0.00621.794-0.659-0.6590.0000.0000.0000.000
124B615ASN00.0190.01423.3870.7500.7500.0000.0000.0000.000
125B616PRO00.0840.03225.2080.0320.0320.0000.0000.0000.000
126B617ARG10.8990.96724.98011.22811.2280.0000.0000.0000.000
127B618PHE0-0.050-0.03822.4960.2090.2090.0000.0000.0000.000
128B619ASP-1-0.726-0.84927.277-9.254-9.2540.0000.0000.0000.000
129B620LYS10.9230.95329.7898.0288.0280.0000.0000.0000.000
130B621ALA00.0200.01326.6830.0710.0710.0000.0000.0000.000
131B622PHE00.0200.00921.571-0.033-0.0330.0000.0000.0000.000
132B623LYS10.8890.92027.2158.7128.7120.0000.0000.0000.000
133B624HIS0-0.0150.00929.5950.2770.2770.0000.0000.0000.000
134B625VAL0-0.098-0.05424.8290.0920.0920.0000.0000.0000.000
135B626PHE00.025-0.00622.742-0.059-0.0590.0000.0000.0000.000
136B627GLY00.0040.01728.8830.1240.1240.0000.0000.0000.000
137B628LYS10.8710.94732.1928.0318.0310.0000.0000.0000.000
138B629THR00.0080.00629.3760.1550.1550.0000.0000.0000.000
139B630LEU00.0140.00631.870-0.126-0.1260.0000.0000.0000.000
140B631ILE0-0.016-0.01627.462-0.168-0.1680.0000.0000.0000.000
141B632CYS0-0.044-0.02131.6650.1880.1880.0000.0000.0000.000
142B633ARG10.9410.98133.1787.5227.5220.0000.0000.0000.000
143B634SER0-0.003-0.02434.741-0.141-0.1410.0000.0000.0000.000
144B635MET00.0520.01434.0100.1020.1020.0000.0000.0000.000
145B636GLU-1-0.868-0.92335.969-7.190-7.1900.0000.0000.0000.000
146B637VAL00.0580.03138.0620.1160.1160.0000.0000.0000.000
147B638SER0-0.018-0.02735.317-0.013-0.0130.0000.0000.0000.000
148B639THR0-0.014-0.00837.5350.1030.1030.0000.0000.0000.000
149B640GLN0-0.024-0.00240.4790.0600.0600.0000.0000.0000.000
150B641LEU00.023-0.00338.7250.1320.1320.0000.0000.0000.000
151B642ALA0-0.027-0.01238.1200.0540.0540.0000.0000.0000.000
152B643ARG10.9090.96440.1016.7136.7130.0000.0000.0000.000
153B644ALA0-0.027-0.00943.6420.1010.1010.0000.0000.0000.000
154B645PHE00.0170.00641.7630.1100.1100.0000.0000.0000.000
155B646THR0-0.009-0.00841.320-0.033-0.0330.0000.0000.0000.000
156B647MET0-0.042-0.02536.925-0.115-0.1150.0000.0000.0000.000
157B648ASP-1-0.819-0.87333.481-8.158-8.1580.0000.0000.0000.000
158B649CYS0-0.0070.01133.956-0.004-0.0040.0000.0000.0000.000
159B650ILE0-0.016-0.00826.990-0.090-0.0900.0000.0000.0000.000
160B651THR00.0380.04530.455-0.032-0.0320.0000.0000.0000.000
161B652LEU00.023-0.00526.584-0.273-0.2730.0000.0000.0000.000
162B653GLU-1-0.905-0.96425.566-10.198-10.1980.0000.0000.0000.000
163B654GLY0-0.024-0.01526.310-0.205-0.2050.0000.0000.0000.000
164B655ASP-1-0.938-0.96027.100-9.126-9.1260.0000.0000.0000.000
165B656GLN0-0.013-0.02728.0910.1010.1010.0000.0000.0000.000
166B657VAL0-0.024-0.01532.1430.1810.1810.0000.0000.0000.000
167B658SER0-0.037-0.01535.4060.0330.0330.0000.0000.0000.000
168B659HIS0-0.037-0.03836.4460.3170.3170.0000.0000.0000.000
169B660ARG10.9120.94639.1447.3857.3850.0000.0000.0000.000
170B661GLY00.0180.01139.8930.1340.1340.0000.0000.0000.000
171B662ALA0-0.046-0.01036.110-0.007-0.0070.0000.0000.0000.000
172B663LEU00.0500.02535.768-0.079-0.0790.0000.0000.0000.000
173B664THR0-0.064-0.03929.447-0.122-0.1220.0000.0000.0000.000
174B665GLY00.0670.02630.093-0.021-0.0210.0000.0000.0000.000
175B666GLY0-0.0120.00028.6710.1360.1360.0000.0000.0000.000
176B667TYR0-0.051-0.01522.0460.1860.1860.0000.0000.0000.000
177B668TYR0-0.018-0.01222.310-0.374-0.3740.0000.0000.0000.000
178B669ASP-1-0.818-0.90218.203-13.993-13.9930.0000.0000.0000.000
179B670THR0-0.021-0.01315.777-0.173-0.1730.0000.0000.0000.000
180B671ARG10.9100.93812.80616.75416.7540.0000.0000.0000.000
181B672LYS10.7930.92015.13013.39013.3900.0000.0000.0000.000
182B673SER00.053-0.00215.049-0.492-0.4920.0000.0000.0000.000
183B674ARG10.9130.95613.03314.09914.0990.0000.0000.0000.000
184B675LEU0-0.038-0.03412.432-1.354-1.3540.0000.0000.0000.000
185B676GLU-1-0.881-0.92811.798-18.592-18.5920.0000.0000.0000.000
186B677LEU00.0320.0057.215-1.253-1.2530.0000.0000.0000.000
187B678GLN0-0.021-0.0067.833-2.460-2.4600.0000.0000.0000.000
188B679LYS10.8960.9539.84018.08318.0830.0000.0000.0000.000
189B680ASP-1-0.864-0.9576.620-26.959-26.9590.0000.0000.0000.000
190B681VAL0-0.102-0.0563.775-3.594-3.3680.000-0.037-0.1900.000
191B682ARG10.8640.9435.62717.91517.9150.0000.0000.0000.000
192B683LYS10.8850.9827.64424.14524.1450.0000.0000.0000.000
193B684ALA0-0.087-0.0214.242-0.764-0.647-0.001-0.019-0.0960.000
194B685GLU-1-0.965-1.0026.361-21.841-21.8410.0000.0000.0000.000