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: G51L1

Calculation Name: 1W8A-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1W8A

Chain ID: A

ChEMBL ID:

UniProt ID: P24014

Base Structure: X-ray

Registration Date: 2023-09-24

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 187
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2065867.388959
FMO2-HF: Nuclear repulsion 1989057.474415
FMO2-HF: Total energy -76809.914544
FMO2-MP2: Total energy -77026.84857


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(A:542:ASP)


Summations of interaction energy for fragment #1(A:542:ASP)
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.
36.19138.556-0.014-0.953-1.3970.004
Interaction energy analysis for fragmet #1(A:542:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.974 / q_NPA : -0.998
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].
3A544PRO00.0020.0143.813-2.604-1.135-0.021-0.650-0.7980.002
4A545ALA00.010-0.0036.281-1.828-1.8280.0000.0000.0000.000
5A546MET0-0.043-0.0167.656-1.060-1.0600.0000.0000.0000.000
6A547CYS0-0.107-0.0498.973-0.838-0.8380.0000.0000.0000.000
7A548HIS00.0310.0059.1681.6701.6700.0000.0000.0000.000
8A550GLU-1-0.870-0.9018.65821.91221.9120.0000.0000.0000.000
9A551GLY00.0070.0029.894-0.794-0.7940.0000.0000.0000.000
10A552THR0-0.013-0.0108.3652.8362.8360.0000.0000.0000.000
11A553THR00.015-0.00210.258-0.184-0.1840.0000.0000.0000.000
12A554VAL00.000-0.0028.5871.6641.6640.0000.0000.0000.000
13A555ASP-1-0.826-0.87710.92216.31816.3180.0000.0000.0000.000
14A557THR0-0.050-0.07613.909-1.094-1.0940.0000.0000.0000.000
15A558GLY00.0220.02017.4300.2480.2480.0000.0000.0000.000
16A559ARG10.8210.91612.604-19.374-19.3740.0000.0000.0000.000
17A560GLY00.0210.01717.3950.0590.0590.0000.0000.0000.000
18A561LEU0-0.044-0.02413.784-0.219-0.2190.0000.0000.0000.000
19A562LYS10.9330.96017.921-13.546-13.5460.0000.0000.0000.000
20A563GLU-1-0.932-0.96715.87116.20216.2020.0000.0000.0000.000
21A564ILE0-0.032-0.01312.9020.5640.5640.0000.0000.0000.000
22A565PRO00.0320.0159.7040.0540.0540.0000.0000.0000.000
23A566ARG11.0110.98010.487-20.796-20.7960.0000.0000.0000.000
24A567ASP-1-0.968-0.9755.15535.99836.064-0.001-0.001-0.0630.000
25A568ILE00.0290.0275.3113.4193.4190.0000.0000.0000.000
26A569PRO00.0450.0203.704-2.022-1.2550.009-0.301-0.4750.002
27A570LEU00.010-0.0075.242-6.363-6.300-0.001-0.001-0.0610.000
28A571HIS0-0.052-0.0446.761-6.104-6.1040.0000.0000.0000.000
29A572THR0-0.0090.0167.764-1.621-1.6210.0000.0000.0000.000
30A573THR0-0.025-0.0089.793-1.604-1.6040.0000.0000.0000.000
31A574GLU-1-0.865-0.92313.04815.61115.6110.0000.0000.0000.000
32A575LEU00.0120.01011.6371.5401.5400.0000.0000.0000.000
33A576LEU0-0.006-0.00614.316-1.561-1.5610.0000.0000.0000.000
34A577LEU00.0310.00913.5180.6310.6310.0000.0000.0000.000
35A578ASN00.0090.00017.079-0.828-0.8280.0000.0000.0000.000
36A579ASP-1-0.802-0.85819.80213.10813.1080.0000.0000.0000.000
37A580ASN0-0.044-0.01617.1770.3860.3860.0000.0000.0000.000
38A581GLU-1-0.960-1.00520.88811.58611.5860.0000.0000.0000.000
39A582LEU0-0.020-0.00517.760-0.287-0.2870.0000.0000.0000.000
40A583GLY00.0340.04021.598-0.135-0.1350.0000.0000.0000.000
41A584ARG10.8850.89923.582-11.705-11.7050.0000.0000.0000.000
42A585ILE0-0.0040.01720.6300.4240.4240.0000.0000.0000.000
43A586SER00.0480.01220.052-0.763-0.7630.0000.0000.0000.000
44A587SER0-0.062-0.04721.3140.5580.5580.0000.0000.0000.000
45A588ASP-1-0.865-0.93117.06516.81316.8130.0000.0000.0000.000
46A589GLY0-0.004-0.00918.7780.4160.4160.0000.0000.0000.000
47A590LEU0-0.027-0.00911.6390.5550.5550.0000.0000.0000.000
48A591PHE00.0880.02514.9870.8950.8950.0000.0000.0000.000
49A592GLY0-0.0390.00616.6210.4060.4060.0000.0000.0000.000
50A593ARG10.8930.93713.262-20.438-20.4380.0000.0000.0000.000
51A594LEU0-0.024-0.00210.1901.6371.6370.0000.0000.0000.000
52A595PRO0-0.011-0.01712.202-1.026-1.0260.0000.0000.0000.000
53A596HIS00.0110.00911.332-1.861-1.8610.0000.0000.0000.000
54A597LEU0-0.0110.01413.423-0.284-0.2840.0000.0000.0000.000
55A598VAL00.0340.00915.172-1.214-1.2140.0000.0000.0000.000
56A599LYS10.8280.91917.431-16.343-16.3430.0000.0000.0000.000
57A600LEU0-0.0020.00616.5661.0051.0050.0000.0000.0000.000
58A601GLU-1-0.920-0.96918.37313.27213.2720.0000.0000.0000.000
59A602LEU00.0330.01118.4270.5520.5520.0000.0000.0000.000
60A603LYS10.9210.96221.389-13.015-13.0150.0000.0000.0000.000
61A604ARG10.7750.85823.493-11.283-11.2830.0000.0000.0000.000
62A605ASN00.0480.00720.7120.4470.4470.0000.0000.0000.000
63A606GLN0-0.066-0.03324.542-0.484-0.4840.0000.0000.0000.000
64A607LEU0-0.0070.03623.174-0.168-0.1680.0000.0000.0000.000
65A608THR0-0.022-0.01227.118-0.400-0.4000.0000.0000.0000.000
66A609GLY00.009-0.00628.494-0.312-0.3120.0000.0000.0000.000
67A610ILE0-0.033-0.01624.6980.3840.3840.0000.0000.0000.000
68A611GLU-1-0.883-0.92724.61311.59211.5920.0000.0000.0000.000
69A612PRO0-0.002-0.01626.3700.1900.1900.0000.0000.0000.000
70A613ASN0-0.0070.00026.5830.0720.0720.0000.0000.0000.000
71A614ALA00.0520.04322.2950.3690.3690.0000.0000.0000.000
72A615PHE0-0.036-0.02620.8250.6920.6920.0000.0000.0000.000
73A616GLU-1-0.871-0.94023.07311.46411.4640.0000.0000.0000.000
74A617GLY00.001-0.00721.7120.5820.5820.0000.0000.0000.000
75A618ALA0-0.022-0.01619.8910.6800.6800.0000.0000.0000.000
76A619SER0-0.035-0.01020.808-0.068-0.0680.0000.0000.0000.000
77A620HIS00.0090.00617.142-0.879-0.8790.0000.0000.0000.000
78A621ILE0-0.0100.00618.711-0.168-0.1680.0000.0000.0000.000
79A622GLN0-0.069-0.05120.727-0.328-0.3280.0000.0000.0000.000
80A623GLU-1-0.917-0.96622.06012.37212.3720.0000.0000.0000.000
81A624LEU00.0210.01621.8860.5900.5900.0000.0000.0000.000
82A625GLN0-0.005-0.00223.030-1.058-1.0580.0000.0000.0000.000
83A626LEU00.0420.00723.8160.3600.3600.0000.0000.0000.000
84A627GLY0-0.0190.01926.243-0.326-0.3260.0000.0000.0000.000
85A628GLU-1-0.855-0.92827.60510.85510.8550.0000.0000.0000.000
86A629ASN0-0.068-0.04925.6430.4140.4140.0000.0000.0000.000
87A630LYS10.9310.96329.406-9.898-9.8980.0000.0000.0000.000
88A631ILE00.0160.01528.119-0.137-0.1370.0000.0000.0000.000
89A632LYS10.9820.97332.361-8.535-8.5350.0000.0000.0000.000
90A633GLU-1-0.869-0.94934.9757.9717.9710.0000.0000.0000.000
91A634ILE00.000-0.00433.1140.3010.3010.0000.0000.0000.000
92A635SER00.0550.00132.753-0.282-0.2820.0000.0000.0000.000
93A636ASN00.0100.02134.0280.2760.2760.0000.0000.0000.000
94A637LYS10.9460.98031.307-8.863-8.8630.0000.0000.0000.000
95A638MET0-0.0150.00929.0080.1930.1930.0000.0000.0000.000
96A639PHE00.0420.00927.3750.3460.3460.0000.0000.0000.000
97A640LEU0-0.027-0.00728.313-0.031-0.0310.0000.0000.0000.000
98A641GLY00.0750.03925.8910.3460.3460.0000.0000.0000.000
99A642LEU0-0.034-0.00223.0930.2620.2620.0000.0000.0000.000
100A643HIS0-0.002-0.00526.173-0.047-0.0470.0000.0000.0000.000
101A644GLN00.0040.00224.783-0.755-0.7550.0000.0000.0000.000
102A645LEU0-0.0260.01824.4090.0970.0970.0000.0000.0000.000
103A646LYS10.8880.94226.396-11.230-11.2300.0000.0000.0000.000
104A647THR00.022-0.00626.683-0.652-0.6520.0000.0000.0000.000
105A648LEU00.0380.03326.8360.3990.3990.0000.0000.0000.000
106A649ASN0-0.027-0.01827.872-0.728-0.7280.0000.0000.0000.000
107A650LEU00.0390.00728.6430.2800.2800.0000.0000.0000.000
108A651TYR0-0.033-0.01231.163-0.316-0.3160.0000.0000.0000.000
109A652ASP-1-0.892-0.97231.9189.2069.2060.0000.0000.0000.000
110A653ASN0-0.0070.02329.6900.2710.2710.0000.0000.0000.000
111A654GLN0-0.038-0.04133.568-0.028-0.0280.0000.0000.0000.000
112A655ILE0-0.021-0.00133.134-0.160-0.1600.0000.0000.0000.000
113A656SER00.0220.00937.081-0.203-0.2030.0000.0000.0000.000
114A733CYS0-0.0550.03439.605-0.112-0.1120.0000.0000.0000.000
115A658VAL00.019-0.00237.1940.2410.2410.0000.0000.0000.000
116A659MET00.0020.01737.046-0.194-0.1940.0000.0000.0000.000
117A660PRO00.025-0.00938.8970.1460.1460.0000.0000.0000.000
118A661GLY00.0350.01138.8320.0700.0700.0000.0000.0000.000
119A662SER0-0.023-0.04934.9630.1260.1260.0000.0000.0000.000
120A663PHE0-0.013-0.01032.7650.2550.2550.0000.0000.0000.000
121A664GLU-1-0.984-0.97634.7038.5588.5580.0000.0000.0000.000
122A665HIS00.0590.03430.4420.2570.2570.0000.0000.0000.000
123A666LEU0-0.040-0.00329.0440.3460.3460.0000.0000.0000.000
124A667ASN00.025-0.00231.767-0.290-0.2900.0000.0000.0000.000
125A668SER0-0.050-0.03129.368-0.331-0.3310.0000.0000.0000.000
126A669LEU0-0.0450.00030.1680.0050.0050.0000.0000.0000.000
127A670THR0-0.070-0.04231.414-0.281-0.2810.0000.0000.0000.000
128A671SER0-0.025-0.01131.007-0.336-0.3360.0000.0000.0000.000
129A672LEU00.0420.02131.6080.2720.2720.0000.0000.0000.000
130A673ASN0-0.050-0.01432.384-0.491-0.4910.0000.0000.0000.000
131A674LEU00.033-0.00433.4970.1740.1740.0000.0000.0000.000
132A675ALA00.0510.02736.181-0.230-0.2300.0000.0000.0000.000
133A676SER0-0.027-0.01136.4650.1290.1290.0000.0000.0000.000
134A677ASN00.0300.02434.6680.1130.1130.0000.0000.0000.000
135A678PRO0-0.0130.01338.708-0.201-0.2010.0000.0000.0000.000
136A679PHE0-0.0010.01237.779-0.007-0.0070.0000.0000.0000.000
137A680ASN0-0.008-0.02942.654-0.303-0.3030.0000.0000.0000.000
138A681CYS0-0.080-0.02243.5130.1750.1750.0000.0000.0000.000
139A682ASN00.0540.03047.714-0.104-0.1040.0000.0000.0000.000
140A683CYS0-0.029-0.03349.0910.0660.0660.0000.0000.0000.000
141A684HIS0-0.0030.00645.4540.0640.0640.0000.0000.0000.000
142A685LEU0-0.065-0.01741.7050.1650.1650.0000.0000.0000.000
143A686ALA00.0340.01045.4800.0410.0410.0000.0000.0000.000
144A687TRP0-0.029-0.00439.238-0.020-0.0200.0000.0000.0000.000
145A688PHE00.016-0.00338.5240.0680.0680.0000.0000.0000.000
146A689ALA00.0500.03443.2270.1090.1090.0000.0000.0000.000
147A690GLU-1-0.850-0.96245.3956.4976.4970.0000.0000.0000.000
148A691TRP0-0.0130.00036.1640.0180.0180.0000.0000.0000.000
149A692LEU0-0.007-0.00539.5680.1370.1370.0000.0000.0000.000
150A693ARG10.8170.91042.196-6.460-6.4600.0000.0000.0000.000
151A694LYS10.9541.00743.041-7.224-7.2240.0000.0000.0000.000
152A695LYS10.8770.94835.183-8.850-8.8500.0000.0000.0000.000
153A696SER0-0.037-0.01140.4130.0040.0040.0000.0000.0000.000
154A697LEU00.0420.02236.1410.1970.1970.0000.0000.0000.000
155A698ASN0-0.030-0.00635.998-0.331-0.3310.0000.0000.0000.000
156A699GLY0-0.001-0.01839.625-0.111-0.1110.0000.0000.0000.000
157A700GLY00.0480.02437.412-0.031-0.0310.0000.0000.0000.000
158A701ALA0-0.030-0.01638.0310.1050.1050.0000.0000.0000.000
159A702ALA00.0030.01739.655-0.048-0.0480.0000.0000.0000.000
160A703ARG10.9170.94441.046-7.164-7.1640.0000.0000.0000.000
161A705GLY00.012-0.00244.870-0.062-0.0620.0000.0000.0000.000
162A706ALA00.008-0.00145.8600.0260.0260.0000.0000.0000.000
163A707PRO00.0100.02348.208-0.137-0.1370.0000.0000.0000.000
164A708SER00.012-0.00851.464-0.005-0.0050.0000.0000.0000.000
165A709LYS10.8980.95453.341-5.746-5.7460.0000.0000.0000.000
166A710VAL00.0530.02050.123-0.036-0.0360.0000.0000.0000.000
167A711ARG10.9760.99148.213-6.264-6.2640.0000.0000.0000.000
168A712ASP-1-0.873-0.94446.8396.6566.6560.0000.0000.0000.000
169A713VAL0-0.052-0.00648.1410.0500.0500.0000.0000.0000.000
170A714GLN0-0.014-0.01045.4400.2430.2430.0000.0000.0000.000
171A715ILE00.0460.02143.192-0.121-0.1210.0000.0000.0000.000
172A716LYS10.9360.95844.233-7.055-7.0550.0000.0000.0000.000
173A717ASP-1-0.976-0.98946.7176.4876.4870.0000.0000.0000.000
174A718LEU0-0.0040.00249.600-0.164-0.1640.0000.0000.0000.000
175A719PRO00.0160.03350.7050.1240.1240.0000.0000.0000.000
176A720HIS00.0720.02250.829-0.004-0.0040.0000.0000.0000.000
177A721SER0-0.004-0.01052.231-0.010-0.0100.0000.0000.0000.000
178A722GLU-1-0.951-0.98254.0025.4855.4850.0000.0000.0000.000
179A723PHE0-0.117-0.04147.2120.0600.0600.0000.0000.0000.000
180A724LYS10.9490.98152.102-5.557-5.5570.0000.0000.0000.000
181A726SER00.011-0.02653.275-0.100-0.1000.0000.0000.0000.000
182A727SER00.0030.01156.205-0.010-0.0100.0000.0000.0000.000
183A728GLU-1-0.844-0.89454.8935.7195.7190.0000.0000.0000.000
184A729ASN0-0.101-0.06251.2910.1760.1760.0000.0000.0000.000
185A730SER0-0.038-0.03551.0480.1180.1180.0000.0000.0000.000
186A731GLU-1-0.872-0.94547.0696.6226.6220.0000.0000.0000.000
187A732GLY00.023-0.00345.019-0.023-0.0230.0000.0000.0000.000