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: NN4VQ

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 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 187
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2069968.95225
FMO2-HF: Nuclear repulsion 1993156.974464
FMO2-HF: Total energy -76811.977786
FMO2-MP2: Total energy -77028.750312


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.
23.46628.3911.054-2.685-3.2950.026
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 : -0.944 / q_NPA : -0.987
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].
3A544PRO00.0040.0033.871-2.020-0.582-0.016-0.669-0.7540.002
4A545ALA00.0010.0036.354-2.361-2.3610.0000.0000.0000.000
5A546MET0-0.034-0.0017.925-1.513-1.5130.0000.0000.0000.000
6A547CYS0-0.090-0.0459.078-0.755-0.7550.0000.0000.0000.000
7A548HIS0-0.007-0.0229.2321.4591.4590.0000.0000.0000.000
8A550GLU-1-0.828-0.8828.36221.73521.7350.0000.0000.0000.000
9A551GLY00.0010.0018.810-1.131-1.1310.0000.0000.0000.000
10A552THR0-0.005-0.0097.8893.1783.1780.0000.0000.0000.000
11A553THR0-0.050-0.03810.0910.0710.0710.0000.0000.0000.000
12A554VAL0-0.013-0.0217.8541.1111.1110.0000.0000.0000.000
13A555ASP-1-0.777-0.84811.09517.23717.2370.0000.0000.0000.000
14A557THR0-0.028-0.02813.907-1.277-1.2770.0000.0000.0000.000
15A558GLY00.0290.01517.5190.2850.2850.0000.0000.0000.000
16A559ARG10.7240.84612.685-19.880-19.8800.0000.0000.0000.000
17A560GLY00.0250.03017.628-0.017-0.0170.0000.0000.0000.000
18A561LEU0-0.034-0.01913.751-0.203-0.2030.0000.0000.0000.000
19A562LYS10.8410.88717.904-13.988-13.9880.0000.0000.0000.000
20A563GLU-1-0.946-0.97015.88016.38316.3830.0000.0000.0000.000
21A564ILE0-0.012-0.00812.9570.3990.3990.0000.0000.0000.000
22A565PRO00.0290.0139.744-0.004-0.0040.0000.0000.0000.000
23A566ARG10.9630.96610.442-20.599-20.5990.0000.0000.0000.000
24A567ASP-1-0.870-0.9405.21133.88433.8840.0000.0000.0000.000
25A568ILE00.0010.0034.7936.0516.070-0.001-0.003-0.0150.000
26A569PRO00.0470.0292.632-8.006-4.7151.068-1.958-2.4010.024
27A570LEU0-0.020-0.0214.151-9.450-9.2730.003-0.055-0.1250.000
28A571HIS0-0.019-0.0176.185-8.690-8.6900.0000.0000.0000.000
29A572THR0-0.0210.0067.282-1.618-1.6180.0000.0000.0000.000
30A573THR0-0.013-0.0199.243-2.236-2.2360.0000.0000.0000.000
31A574GLU-1-0.839-0.89612.57715.98515.9850.0000.0000.0000.000
32A575LEU00.0110.00611.1011.8521.8520.0000.0000.0000.000
33A576LEU0-0.022-0.00813.784-1.739-1.7390.0000.0000.0000.000
34A577LEU00.0730.01614.0940.5800.5800.0000.0000.0000.000
35A578ASN0-0.024-0.00617.192-0.927-0.9270.0000.0000.0000.000
36A579ASP-1-0.820-0.87220.02513.30913.3090.0000.0000.0000.000
37A580ASN0-0.032-0.02317.3780.2980.2980.0000.0000.0000.000
38A581GLU-1-0.886-0.94521.18611.95111.9510.0000.0000.0000.000
39A582LEU00.0060.01617.807-0.212-0.2120.0000.0000.0000.000
40A583GLY00.0250.04221.765-0.188-0.1880.0000.0000.0000.000
41A584ARG10.7810.85224.024-12.231-12.2310.0000.0000.0000.000
42A585ILE00.0290.03220.6730.4920.4920.0000.0000.0000.000
43A586SER00.0250.00220.237-0.741-0.7410.0000.0000.0000.000
44A587SER0-0.053-0.05120.9870.7080.7080.0000.0000.0000.000
45A588ASP-1-0.750-0.86516.13018.56518.5650.0000.0000.0000.000
46A589GLY00.0140.00818.4960.1770.1770.0000.0000.0000.000
47A590LEU0-0.031-0.02510.9210.4360.4360.0000.0000.0000.000
48A591PHE00.0310.00513.9251.0361.0360.0000.0000.0000.000
49A592GLY0-0.0020.01216.0410.1680.1680.0000.0000.0000.000
50A593ARG10.7590.87712.196-20.979-20.9790.0000.0000.0000.000
51A594LEU0-0.0020.0048.9182.0342.0340.0000.0000.0000.000
52A595PRO00.0140.00011.404-0.883-0.8830.0000.0000.0000.000
53A596HIS00.0150.00910.882-2.023-2.0230.0000.0000.0000.000
54A597LEU0-0.0520.01112.925-0.651-0.6510.0000.0000.0000.000
55A598VAL00.0420.01414.336-1.375-1.3750.0000.0000.0000.000
56A599LYS10.7980.89116.872-16.829-16.8290.0000.0000.0000.000
57A600LEU00.0190.01716.0091.0831.0830.0000.0000.0000.000
58A601GLU-1-0.847-0.88718.01613.45713.4570.0000.0000.0000.000
59A602LEU00.0320.01118.3510.6760.6760.0000.0000.0000.000
60A603LYS10.9120.95921.429-13.567-13.5670.0000.0000.0000.000
61A604ARG10.7670.83323.598-11.358-11.3580.0000.0000.0000.000
62A605ASN0-0.008-0.02720.7210.5490.5490.0000.0000.0000.000
63A606GLN0-0.016-0.00524.273-0.501-0.5010.0000.0000.0000.000
64A607LEU00.0050.01422.806-0.251-0.2510.0000.0000.0000.000
65A608THR0-0.014-0.02326.916-0.392-0.3920.0000.0000.0000.000
66A609GLY0-0.018-0.01628.246-0.421-0.4210.0000.0000.0000.000
67A610ILE0-0.017-0.01024.5260.4360.4360.0000.0000.0000.000
68A611GLU-1-0.803-0.87224.60612.01712.0170.0000.0000.0000.000
69A612PRO0-0.002-0.01526.1170.2170.2170.0000.0000.0000.000
70A613ASN00.0120.00125.8290.0330.0330.0000.0000.0000.000
71A614ALA00.0300.03821.8800.4020.4020.0000.0000.0000.000
72A615PHE0-0.016-0.01719.9410.7300.7300.0000.0000.0000.000
73A616GLU-1-0.836-0.91921.92012.19712.1970.0000.0000.0000.000
74A617GLY0-0.038-0.02520.7410.7010.7010.0000.0000.0000.000
75A618ALA0-0.025-0.01818.6110.6470.6470.0000.0000.0000.000
76A619SER0-0.028-0.00819.6040.1120.1120.0000.0000.0000.000
77A620HIS0-0.0120.00116.005-1.108-1.1080.0000.0000.0000.000
78A621ILE0-0.033-0.00517.5130.0020.0020.0000.0000.0000.000
79A622GLN0-0.055-0.03519.893-0.734-0.7340.0000.0000.0000.000
80A623GLU-1-0.860-0.92221.36312.05612.0560.0000.0000.0000.000
81A624LEU00.0210.01521.1260.6990.6990.0000.0000.0000.000
82A625GLN0-0.037-0.03322.361-1.128-1.1280.0000.0000.0000.000
83A626LEU00.0440.01123.2190.4130.4130.0000.0000.0000.000
84A627GLY00.0070.01425.754-0.324-0.3240.0000.0000.0000.000
85A628GLU-1-0.866-0.92327.63011.42411.4240.0000.0000.0000.000
86A629ASN0-0.074-0.04325.3030.3480.3480.0000.0000.0000.000
87A630LYS10.8860.93229.540-10.112-10.1120.0000.0000.0000.000
88A631ILE00.0250.03027.766-0.205-0.2050.0000.0000.0000.000
89A632LYS10.9740.97332.031-8.927-8.9270.0000.0000.0000.000
90A633GLU-1-0.828-0.90834.6858.0658.0650.0000.0000.0000.000
91A634ILE0-0.001-0.00431.9980.3210.3210.0000.0000.0000.000
92A635SER00.0760.02432.510-0.186-0.1860.0000.0000.0000.000
93A636ASN0-0.044-0.04332.8310.4070.4070.0000.0000.0000.000
94A637LYS10.9220.94930.186-9.116-9.1160.0000.0000.0000.000
95A638MET0-0.0380.01628.4050.2990.2990.0000.0000.0000.000
96A639PHE00.0570.00326.1270.3520.3520.0000.0000.0000.000
97A640LEU0-0.034-0.00427.110-0.002-0.0020.0000.0000.0000.000
98A641GLY00.0860.03924.4190.3700.3700.0000.0000.0000.000
99A642LEU0-0.0240.00421.8360.1650.1650.0000.0000.0000.000
100A643HIS0-0.004-0.01524.878-0.037-0.0370.0000.0000.0000.000
101A644GLN0-0.0120.00723.853-0.813-0.8130.0000.0000.0000.000
102A645LEU00.0070.01823.7120.1270.1270.0000.0000.0000.000
103A646LYS10.8490.91225.648-11.295-11.2950.0000.0000.0000.000
104A647THR0-0.002-0.01425.862-0.685-0.6850.0000.0000.0000.000
105A648LEU00.0120.01526.0280.4430.4430.0000.0000.0000.000
106A649ASN0-0.032-0.03227.112-0.856-0.8560.0000.0000.0000.000
107A650LEU00.0290.00227.8660.3540.3540.0000.0000.0000.000
108A651TYR0-0.024-0.00630.514-0.247-0.2470.0000.0000.0000.000
109A652ASP-1-0.801-0.88131.7649.0869.0860.0000.0000.0000.000
110A653ASN0-0.036-0.00129.6500.3850.3850.0000.0000.0000.000
111A654GLN0-0.018-0.01933.654-0.151-0.1510.0000.0000.0000.000
112A655ILE0-0.039-0.00332.454-0.182-0.1820.0000.0000.0000.000
113A656SER00.0350.02236.658-0.207-0.2070.0000.0000.0000.000
114A733CYS0-0.132-0.05238.872-0.212-0.2120.0000.0000.0000.000
115A658VAL00.0220.00335.9640.2630.2630.0000.0000.0000.000
116A659MET00.0430.06236.759-0.165-0.1650.0000.0000.0000.000
117A660PRO00.010-0.00437.8730.1660.1660.0000.0000.0000.000
118A661GLY00.1060.05437.3550.0700.0700.0000.0000.0000.000
119A662SER0-0.052-0.05133.7290.1390.1390.0000.0000.0000.000
120A663PHE0-0.017-0.00531.6810.2820.2820.0000.0000.0000.000
121A664GLU-1-0.972-0.97833.6648.5338.5330.0000.0000.0000.000
122A665HIS00.0660.03328.4870.2110.2110.0000.0000.0000.000
123A666LEU0-0.0150.01027.8730.3160.3160.0000.0000.0000.000
124A667ASN00.0180.00330.650-0.358-0.3580.0000.0000.0000.000
125A668SER0-0.019-0.01528.477-0.373-0.3730.0000.0000.0000.000
126A669LEU0-0.0300.01029.4140.0420.0420.0000.0000.0000.000
127A670THR0-0.032-0.02630.648-0.313-0.3130.0000.0000.0000.000
128A671SER0-0.0270.00030.121-0.362-0.3620.0000.0000.0000.000
129A672LEU00.0300.01130.7260.2750.2750.0000.0000.0000.000
130A673ASN0-0.043-0.01331.789-0.538-0.5380.0000.0000.0000.000
131A674LEU00.0490.01332.5950.2450.2450.0000.0000.0000.000
132A675ALA00.0290.02235.347-0.226-0.2260.0000.0000.0000.000
133A676SER0-0.033-0.05336.3300.1640.1640.0000.0000.0000.000
134A677ASN0-0.040-0.00534.2560.0170.0170.0000.0000.0000.000
135A678PRO00.0120.01538.264-0.200-0.2000.0000.0000.0000.000
136A679PHE0-0.018-0.01537.230-0.088-0.0880.0000.0000.0000.000
137A680ASN00.0420.00942.418-0.326-0.3260.0000.0000.0000.000
138A681CYS0-0.051-0.00943.1010.1830.1830.0000.0000.0000.000
139A682ASN00.0400.01147.205-0.182-0.1820.0000.0000.0000.000
140A683CYS00.0090.00947.9860.1020.1020.0000.0000.0000.000
141A684HIS0-0.021-0.01944.7120.0890.0890.0000.0000.0000.000
142A685LEU0-0.056-0.01941.1100.1980.1980.0000.0000.0000.000
143A686ALA00.0270.00944.6320.0680.0680.0000.0000.0000.000
144A687TRP0-0.037-0.02937.898-0.023-0.0230.0000.0000.0000.000
145A688PHE00.0250.01237.5010.0990.0990.0000.0000.0000.000
146A689ALA00.0500.03042.2050.1120.1120.0000.0000.0000.000
147A690GLU-1-0.805-0.90544.7416.5796.5790.0000.0000.0000.000
148A691TRP0-0.024-0.01235.0810.0340.0340.0000.0000.0000.000
149A692LEU0-0.027-0.01338.3770.1140.1140.0000.0000.0000.000
150A693ARG10.7500.84341.194-6.584-6.5840.0000.0000.0000.000
151A694LYS10.9430.99042.474-7.310-7.3100.0000.0000.0000.000
152A695LYS10.8510.89934.190-9.108-9.1080.0000.0000.0000.000
153A696SER0-0.065-0.00938.7810.0990.0990.0000.0000.0000.000
154A697LEU00.0400.03534.8460.1590.1590.0000.0000.0000.000
155A698ASN00.0370.01835.596-0.382-0.3820.0000.0000.0000.000
156A699GLY0-0.027-0.04238.990-0.048-0.0480.0000.0000.0000.000
157A700GLY00.0070.01536.444-0.058-0.0580.0000.0000.0000.000
158A701ALA0-0.007-0.01037.0930.1380.1380.0000.0000.0000.000
159A702ALA0-0.0050.02438.776-0.052-0.0520.0000.0000.0000.000
160A703ARG10.9000.92040.259-7.324-7.3240.0000.0000.0000.000
161A705GLY00.0400.01044.388-0.065-0.0650.0000.0000.0000.000
162A706ALA0-0.027-0.00545.398-0.037-0.0370.0000.0000.0000.000
163A707PRO00.0280.02047.744-0.126-0.1260.0000.0000.0000.000
164A708SER00.013-0.00150.939-0.037-0.0370.0000.0000.0000.000
165A709LYS10.8220.90252.937-5.789-5.7890.0000.0000.0000.000
166A710VAL00.0190.01150.238-0.063-0.0630.0000.0000.0000.000
167A711ARG10.8390.91048.022-6.428-6.4280.0000.0000.0000.000
168A712ASP-1-0.805-0.87846.6486.6356.6350.0000.0000.0000.000
169A713VAL0-0.0070.00947.2290.0840.0840.0000.0000.0000.000
170A714GLN0-0.028-0.02744.0150.3090.3090.0000.0000.0000.000
171A715ILE00.010-0.00241.858-0.142-0.1420.0000.0000.0000.000
172A716LYS10.8820.92843.332-7.192-7.1920.0000.0000.0000.000
173A717ASP-1-0.852-0.89345.6206.6966.6960.0000.0000.0000.000
174A718LEU00.0200.02348.869-0.171-0.1710.0000.0000.0000.000
175A719PRO00.0250.02949.6890.1410.1410.0000.0000.0000.000
176A720HIS00.0700.01749.968-0.046-0.0460.0000.0000.0000.000
177A721SER0-0.030-0.02751.2870.0040.0040.0000.0000.0000.000
178A722GLU-1-0.821-0.88353.1265.5645.5640.0000.0000.0000.000
179A723PHE0-0.067-0.00646.0160.0620.0620.0000.0000.0000.000
180A724LYS10.8030.88150.990-5.657-5.6570.0000.0000.0000.000
181A726SER00.031-0.00852.979-0.109-0.1090.0000.0000.0000.000
182A727SER0-0.014-0.01955.7380.0280.0280.0000.0000.0000.000
183A728GLU-1-0.794-0.84154.5985.8165.8160.0000.0000.0000.000
184A729ASN0-0.070-0.05151.2520.1770.1770.0000.0000.0000.000
185A730SER0-0.040-0.03651.1930.0940.0940.0000.0000.0000.000
186A731GLU-1-0.881-0.94147.2926.6226.6220.0000.0000.0000.000
187A732GLY0-0.003-0.01244.7120.0050.0050.0000.0000.0000.000