FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: VR431

Calculation Name: 2WD5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2WD5

Chain ID: A

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 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 177
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1818659.976374
FMO2-HF: Nuclear repulsion 1748761.476343
FMO2-HF: Total energy -69898.500031
FMO2-MP2: Total energy -70102.484215


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:499:ARG)


Summations of interaction energy for fragment #1(A:499:ARG)
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.
-59.065-69.48141.368-17.197-13.754-0.188
Interaction energy analysis for fragmet #1(A:499:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.822 / q_NPA : 0.861
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].
3A501ALA0-0.0050.0073.1404.2447.4230.069-1.584-1.6640.006
4A502GLU-1-0.744-0.8681.794-56.461-61.24615.701-6.022-4.894-0.075
5A503ILE00.0250.0084.9972.9353.047-0.001-0.007-0.1030.000
6A504MET0-0.0150.0196.7952.7112.7110.0000.0000.0000.000
7A505GLU-1-0.799-0.8907.890-18.458-18.4580.0000.0000.0000.000
8A506SER0-0.0030.0029.0241.8501.8500.0000.0000.0000.000
9A507ILE0-0.003-0.00810.9401.6521.6520.0000.0000.0000.000
10A508LYS10.8130.90312.50017.24117.2410.0000.0000.0000.000
11A509ARG10.8290.90012.43719.08719.0870.0000.0000.0000.000
12A510LEU00.001-0.00514.0690.9830.9830.0000.0000.0000.000
13A511TYR0-0.010-0.00316.5771.2221.2220.0000.0000.0000.000
14A512PRO00.0290.02418.5470.0620.0620.0000.0000.0000.000
15A513GLY0-0.001-0.00319.477-0.246-0.2460.0000.0000.0000.000
16A514SER0-0.0200.00020.8890.3440.3440.0000.0000.0000.000
17A515VAL00.0500.02514.827-0.133-0.1330.0000.0000.0000.000
18A516TYR0-0.061-0.05317.9100.1540.1540.0000.0000.0000.000
19A517GLY00.0520.02314.285-0.042-0.0420.0000.0000.0000.000
20A518ARG10.7120.8178.26231.86631.8660.0000.0000.0000.000
21A519LEU00.0270.00213.5940.5720.5720.0000.0000.0000.000
22A520ILE0-0.013-0.00710.4211.0501.0500.0000.0000.0000.000
23A521ASP-1-0.814-0.90812.763-20.523-20.5230.0000.0000.0000.000
24A522LEU00.0140.02915.5170.8830.8830.0000.0000.0000.000
25A523CYS0-0.079-0.03918.4890.9120.9120.0000.0000.0000.000
26A524GLN00.019-0.01518.475-1.129-1.1290.0000.0000.0000.000
27A525PRO00.0170.01920.3830.7040.7040.0000.0000.0000.000
28A526THR0-0.030-0.01523.5240.1420.1420.0000.0000.0000.000
29A527GLN00.0220.01527.0420.1500.1500.0000.0000.0000.000
30A528LYS10.8520.90621.94912.97412.9740.0000.0000.0000.000
31A529LYS10.8970.94325.2679.2339.2330.0000.0000.0000.000
32A530TYR00.0490.00925.985-0.104-0.1040.0000.0000.0000.000
33A531GLN0-0.0030.01220.803-0.366-0.3660.0000.0000.0000.000
34A532ILE00.0360.02620.945-0.822-0.8220.0000.0000.0000.000
35A533ALA00.0280.01321.864-0.403-0.4030.0000.0000.0000.000
36A534VAL00.0330.01120.287-0.189-0.1890.0000.0000.0000.000
37A535THR0-0.040-0.04316.402-0.662-0.6620.0000.0000.0000.000
38A536LYS10.8310.91617.93113.33013.3300.0000.0000.0000.000
39A537VAL0-0.045-0.02020.246-0.159-0.1590.0000.0000.0000.000
40A538LEU00.0390.02218.1240.0740.0740.0000.0000.0000.000
41A539GLY00.0380.02016.214-0.399-0.3990.0000.0000.0000.000
42A540LYS10.9530.9609.96925.34525.3450.0000.0000.0000.000
43A541ASN00.0190.00913.497-1.350-1.3500.0000.0000.0000.000
44A542MET0-0.0260.02313.5910.4160.4160.0000.0000.0000.000
45A543ASP-1-0.792-0.8698.997-30.170-30.1700.0000.0000.0000.000
46A544ALA0-0.042-0.00411.890-1.101-1.1010.0000.0000.0000.000
47A545ILE00.0160.00010.5800.7770.7770.0000.0000.0000.000
48A546ILE0-0.0110.00414.7170.8980.8980.0000.0000.0000.000
49A547VAL0-0.017-0.01317.294-0.348-0.3480.0000.0000.0000.000
50A548ASP-1-0.849-0.89819.821-11.753-11.7530.0000.0000.0000.000
51A549SER00.0240.00022.8630.3840.3840.0000.0000.0000.000
52A550GLU-1-0.790-0.88322.303-13.506-13.5060.0000.0000.0000.000
53A551LYS10.8570.91622.12612.41712.4170.0000.0000.0000.000
54A552THR00.0240.02819.825-0.669-0.6690.0000.0000.0000.000
55A553GLY00.0430.02417.974-0.989-0.9890.0000.0000.0000.000
56A554ARG10.8130.86617.34411.87311.8730.0000.0000.0000.000
57A555ASP-1-0.819-0.88718.344-14.451-14.4510.0000.0000.0000.000
58A556CYS0-0.055-0.02814.357-0.815-0.8150.0000.0000.0000.000
59A557ILE0-0.030-0.01613.694-1.466-1.4660.0000.0000.0000.000
60A558GLN0-0.050-0.03614.189-0.874-0.8740.0000.0000.0000.000
61A559TYR00.0750.03210.923-0.639-0.6390.0000.0000.0000.000
62A560ILE0-0.016-0.0128.791-1.215-1.2150.0000.0000.0000.000
63A561LYS10.8620.93210.66615.72015.7200.0000.0000.0000.000
64A562GLU-1-0.875-0.91413.103-17.440-17.4400.0000.0000.0000.000
65A563GLN0-0.013-0.0129.5641.1051.1050.0000.0000.0000.000
66A564ARG10.8790.9499.66622.46622.4660.0000.0000.0000.000
67A565GLY00.0210.0236.354-2.784-2.7840.0000.0000.0000.000
68A566GLU-1-0.829-0.9061.737-119.688-128.61025.599-9.584-7.093-0.119
69A567PRO0-0.001-0.0065.7611.6051.6050.0000.0000.0000.000
70A568GLU-1-0.776-0.8687.789-40.594-40.5940.0000.0000.0000.000
71A569THR0-0.058-0.03110.0441.6701.6700.0000.0000.0000.000
72A570PHE00.0490.01812.509-0.501-0.5010.0000.0000.0000.000
73A571LEU0-0.029-0.01916.3120.7390.7390.0000.0000.0000.000
74A572PRO00.0050.02219.707-0.003-0.0030.0000.0000.0000.000
75A573LEU00.024-0.00822.3520.5040.5040.0000.0000.0000.000
76A574ASP-1-0.768-0.85925.241-11.724-11.7240.0000.0000.0000.000
77A575TYR0-0.008-0.02825.9360.3950.3950.0000.0000.0000.000
78A576LEU0-0.076-0.02222.9180.0610.0610.0000.0000.0000.000
79A577GLU-1-0.904-0.93525.862-9.853-9.8530.0000.0000.0000.000
80A578VAL0-0.041-0.03127.035-0.294-0.2940.0000.0000.0000.000
81A579LYS10.8590.92229.7219.9889.9880.0000.0000.0000.000
82A580PRO00.0280.00732.059-0.240-0.2400.0000.0000.0000.000
83A581THR0-0.026-0.01031.3510.0000.0000.0000.0000.0000.000
84A582ASP-1-0.844-0.91033.843-7.970-7.9700.0000.0000.0000.000
85A583GLU-1-0.816-0.90936.731-8.061-8.0610.0000.0000.0000.000
86A584LYS10.8830.91838.5307.7957.7950.0000.0000.0000.000
87A585LEU0-0.041-0.02435.0280.0440.0440.0000.0000.0000.000
88A586ARG10.7870.85633.9498.7888.7880.0000.0000.0000.000
89A587GLU-1-0.824-0.87638.658-6.924-6.9240.0000.0000.0000.000
90A588LEU0-0.048-0.02738.1100.1810.1810.0000.0000.0000.000
91A589LYS10.8510.90739.7736.9546.9540.0000.0000.0000.000
92A590GLY0-0.009-0.00939.2360.1220.1220.0000.0000.0000.000
93A591ALA0-0.050-0.01634.560-0.220-0.2200.0000.0000.0000.000
94A592LYS10.9480.97731.9199.5919.5910.0000.0000.0000.000
95A593LEU00.0150.01131.601-0.306-0.3060.0000.0000.0000.000
96A594VAL0-0.019-0.02525.209-0.091-0.0910.0000.0000.0000.000
97A595ILE00.0310.00927.117-0.261-0.2610.0000.0000.0000.000
98A596ASP-1-0.782-0.84528.166-9.455-9.4550.0000.0000.0000.000
99A597VAL0-0.037-0.01926.4770.1950.1950.0000.0000.0000.000
100A598ILE0-0.024-0.00622.761-0.356-0.3560.0000.0000.0000.000
101A599ARG10.8720.94524.18511.92411.9240.0000.0000.0000.000
102A600TYR0-0.027-0.03723.159-0.552-0.5520.0000.0000.0000.000
103A601GLU-1-0.936-0.94622.625-11.801-11.8010.0000.0000.0000.000
104A602PRO00.0790.02622.403-0.551-0.5510.0000.0000.0000.000
105A603PRO00.032-0.00325.804-0.216-0.2160.0000.0000.0000.000
106A604HIS00.0250.00325.9640.2910.2910.0000.0000.0000.000
107A605ILE00.0060.01521.685-0.021-0.0210.0000.0000.0000.000
108A606LYS10.9270.97624.6979.4719.4710.0000.0000.0000.000
109A607LYS10.8620.93026.62311.13411.1340.0000.0000.0000.000
110A608ALA00.0830.03821.158-0.128-0.1280.0000.0000.0000.000
111A609LEU0-0.005-0.00222.287-0.348-0.3480.0000.0000.0000.000
112A610GLN0-0.011-0.03524.2770.1130.1130.0000.0000.0000.000
113A611TYR00.0020.00818.9110.3510.3510.0000.0000.0000.000
114A612ALA0-0.032-0.00421.104-0.046-0.0460.0000.0000.0000.000
115A613CYS0-0.093-0.04122.724-0.068-0.0680.0000.0000.0000.000
116A614GLY00.0160.01025.8060.3370.3370.0000.0000.0000.000
117A615ASN0-0.014-0.00528.8090.1340.1340.0000.0000.0000.000
118A616ALA0-0.020-0.00127.5080.2300.2300.0000.0000.0000.000
119A617LEU00.0220.01529.4620.0440.0440.0000.0000.0000.000
120A618VAL0-0.050-0.02628.683-0.398-0.3980.0000.0000.0000.000
121A619CYS00.0260.02630.5520.3090.3090.0000.0000.0000.000
122A620ASP-1-0.828-0.92231.579-9.439-9.4390.0000.0000.0000.000
123A621ASN0-0.026-0.01832.677-0.136-0.1360.0000.0000.0000.000
124A622VAL00.0380.00530.4190.0070.0070.0000.0000.0000.000
125A623GLU-1-0.914-0.94532.609-8.091-8.0910.0000.0000.0000.000
126A624ASP-1-0.815-0.91236.223-7.977-7.9770.0000.0000.0000.000
127A625ALA0-0.057-0.04131.3610.0010.0010.0000.0000.0000.000
128A626ARG10.9720.98233.5098.5388.5380.0000.0000.0000.000
129A627ARG10.9720.98834.6597.4547.4540.0000.0000.0000.000
130A628ILE00.0340.01235.5520.1500.1500.0000.0000.0000.000
131A629ALA0-0.0500.00732.935-0.039-0.0390.0000.0000.0000.000
132A630PHE0-0.035-0.05531.904-0.060-0.0600.0000.0000.0000.000
133A631GLY00.0240.03537.1420.1360.1360.0000.0000.0000.000
134A632GLY00.002-0.00640.3730.1910.1910.0000.0000.0000.000
135A633HIS00.0200.00840.800-0.236-0.2360.0000.0000.0000.000
136A634GLN00.0130.03138.323-0.163-0.1630.0000.0000.0000.000
137A635ARG10.9230.97134.1618.9308.9300.0000.0000.0000.000
138A636HIS10.8280.88633.4648.5298.5290.0000.0000.0000.000
139A637LYS10.8520.94622.96013.05913.0590.0000.0000.0000.000
140A638THR00.0210.00529.5550.1200.1200.0000.0000.0000.000
141A639VAL0-0.059-0.02224.686-0.194-0.1940.0000.0000.0000.000
142A640ALA00.0570.04328.0060.3300.3300.0000.0000.0000.000
143A641LEU0-0.016-0.02327.225-0.489-0.4890.0000.0000.0000.000
144A642ASP-1-0.794-0.87526.671-11.118-11.1180.0000.0000.0000.000
145A643GLY0-0.011-0.01623.399-0.492-0.4920.0000.0000.0000.000
146A644THR0-0.087-0.06723.643-0.369-0.3690.0000.0000.0000.000
147A645LEU0-0.058-0.03023.0080.0760.0760.0000.0000.0000.000
148A646PHE00.0410.03126.373-0.087-0.0870.0000.0000.0000.000
149A647GLN00.0450.00223.982-0.160-0.1600.0000.0000.0000.000
150A648LYS10.9930.99429.18410.28610.2860.0000.0000.0000.000
151A649SER00.0460.02327.7240.3480.3480.0000.0000.0000.000
152A650GLY00.0100.00930.9400.2170.2170.0000.0000.0000.000
153A651VAL0-0.022-0.00224.8690.0040.0040.0000.0000.0000.000
154A652ILE00.0370.01327.7100.0590.0590.0000.0000.0000.000
155A653SER0-0.0160.00822.478-0.541-0.5410.0000.0000.0000.000
156A654GLY00.0750.02223.3710.3230.3230.0000.0000.0000.000
157A655GLY00.0490.03020.379-0.589-0.5890.0000.0000.0000.000
158A656ALA00.0600.02220.280-0.588-0.5880.0000.0000.0000.000
159A657SER00.0210.01320.4600.0540.0540.0000.0000.0000.000
160A658ASP-1-0.814-0.90816.049-17.194-17.1940.0000.0000.0000.000
161A659LEU0-0.062-0.03416.568-0.901-0.9010.0000.0000.0000.000
162A660LYS10.9490.97018.58813.27613.2760.0000.0000.0000.000
163A661ALA0-0.025-0.00715.585-0.145-0.1450.0000.0000.0000.000
164A662LYS10.9500.97712.85019.11619.1160.0000.0000.0000.000
165A663ALA00.0240.00815.133-0.395-0.3950.0000.0000.0000.000
166A664ARG10.9360.96314.59318.43218.4320.0000.0000.0000.000
167A665ARG10.8930.9399.47526.36926.3690.0000.0000.0000.000
168A666TRP0-0.021-0.02214.1520.0400.0400.0000.0000.0000.000
169A667ASP-1-0.787-0.86817.410-13.390-13.3900.0000.0000.0000.000
170A668GLU-1-0.888-0.94611.553-21.571-21.5710.0000.0000.0000.000
171A669LYS10.8730.93613.78316.40616.4060.0000.0000.0000.000
172A670ALA0-0.052-0.02915.5080.6110.6110.0000.0000.0000.000
173A671VAL00.003-0.00617.4650.5810.5810.0000.0000.0000.000
174A672ASP-1-0.809-0.89014.268-18.282-18.2820.0000.0000.0000.000
175A673LYS10.8920.95216.85412.53712.5370.0000.0000.0000.000
176A674LEU0-0.029-0.00520.1050.6040.6040.0000.0000.0000.000
177A675LYS10.8120.91013.38718.38718.3870.0000.0000.0000.000