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: 82ZLY

Calculation Name: 5GPD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5GPD

Chain ID: A

ChEMBL ID:

UniProt ID: Q9UUD1

Base Structure: X-ray

Registration Date: 2023-06-20

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 222
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2604904.94398
FMO2-HF: Nuclear repulsion 2517654.708268
FMO2-HF: Total energy -87250.235713
FMO2-MP2: Total energy -87501.743218


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:649:ILE)


Summations of interaction energy for fragment #1(A:649:ILE)
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.
-5.6680.1566.462-3.956-8.332-0.003
Interaction energy analysis for fragmet #1(A:649:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.038 / q_NPA : -0.024
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].
3A651ASN0-0.016-0.0173.866-0.5200.944-0.014-0.690-0.7610.004
4A652SER0-0.035-0.0132.424-2.919-0.9901.711-1.331-2.309-0.012
5A653HIS0-0.030-0.0252.359-0.1031.8001.767-0.974-2.697-0.004
6A654ALA00.0540.0324.1420.7220.9590.001-0.042-0.1960.000
7A655ASP-1-0.866-0.9516.515-1.127-1.1270.0000.0000.0000.000
8A656ASP-1-0.966-0.9747.112-0.115-0.1150.0000.0000.0000.000
9A657VAL0-0.051-0.0277.2920.3030.3030.0000.0000.0000.000
10A658PHE0-0.071-0.03110.1230.2270.2270.0000.0000.0000.000
11A659SER00.0410.03512.1890.1440.1440.0000.0000.0000.000
12A660PRO0-0.067-0.03113.1770.0950.0950.0000.0000.0000.000
13A661ASN0-0.041-0.03616.1580.0450.0450.0000.0000.0000.000
14A662MET0-0.042-0.04317.7030.0440.0440.0000.0000.0000.000
15A663VAL00.0130.01720.9470.0290.0290.0000.0000.0000.000
16A664GLU-1-0.851-0.88422.836-0.262-0.2620.0000.0000.0000.000
17A665ARG10.8340.92320.3470.3170.3170.0000.0000.0000.000
18A666LEU00.0290.01624.449-0.003-0.0030.0000.0000.0000.000
19A667TRP00.0690.02523.936-0.039-0.0390.0000.0000.0000.000
20A668VAL0-0.040-0.01921.3680.0230.0230.0000.0000.0000.000
21A669LEU00.0630.02920.300-0.021-0.0210.0000.0000.0000.000
22A670ALA00.0410.02519.209-0.050-0.0500.0000.0000.0000.000
23A671LYS10.9290.96418.5840.2860.2860.0000.0000.0000.000
24A672SER00.0450.00415.196-0.001-0.0010.0000.0000.0000.000
25A673THR0-0.0070.01113.736-0.094-0.0940.0000.0000.0000.000
26A674ARG10.8680.94411.7540.5350.5350.0000.0000.0000.000
27A675ASP-1-0.841-0.9318.170-1.827-1.8270.0000.0000.0000.000
28A676SER0-0.003-0.0128.944-0.055-0.0550.0000.0000.0000.000
29A677ALA0-0.062-0.03210.4580.0400.0400.0000.0000.0000.000
30A678GLN0-0.054-0.0177.0600.2620.2620.0000.0000.0000.000
31A679MET0-0.0050.0591.966-0.0300.2612.997-0.919-2.3690.009
32A680SER00.000-0.0275.1330.4970.4970.0000.0000.0000.000
33A681ASP-1-0.870-0.9516.912-1.428-1.4280.0000.0000.0000.000
34A682SER0-0.072-0.0418.9340.2010.2010.0000.0000.0000.000
35A683ILE00.0880.0586.5790.2740.2740.0000.0000.0000.000
36A684ILE0-0.020-0.02411.2520.1440.1440.0000.0000.0000.000
37A685SER0-0.013-0.00814.8950.1330.1330.0000.0000.0000.000
38A686SER00.0690.02312.8240.1530.1530.0000.0000.0000.000
39A687LEU0-0.0060.00815.2160.0590.0590.0000.0000.0000.000
40A688SER0-0.032-0.02816.5400.0760.0760.0000.0000.0000.000
41A689ASP-1-0.740-0.86716.798-0.571-0.5710.0000.0000.0000.000
42A690VAL0-0.049-0.02616.7390.0560.0560.0000.0000.0000.000
43A691LEU0-0.032-0.00319.2510.0470.0470.0000.0000.0000.000
44A692VAL0-0.020-0.01922.7830.0400.0400.0000.0000.0000.000
45A693LEU00.0340.04218.2240.0180.0180.0000.0000.0000.000
46A694SER00.0150.00421.054-0.010-0.0100.0000.0000.0000.000
47A695PRO00.0320.01318.754-0.025-0.0250.0000.0000.0000.000
48A696LEU00.0140.00717.906-0.021-0.0210.0000.0000.0000.000
49A697GLU-1-0.768-0.88718.851-0.278-0.2780.0000.0000.0000.000
50A698VAL00.0050.00714.192-0.027-0.0270.0000.0000.0000.000
51A699LEU00.0170.01013.343-0.062-0.0620.0000.0000.0000.000
52A700ALA0-0.0030.00814.864-0.003-0.0030.0000.0000.0000.000
53A701SER0-0.006-0.01315.1050.0160.0160.0000.0000.0000.000
54A702TRP00.0190.0227.238-0.025-0.0250.0000.0000.0000.000
55A703TYR0-0.047-0.02512.2180.0070.0070.0000.0000.0000.000
56A704ALA00.0260.00414.1260.0420.0420.0000.0000.0000.000
57A705ALA00.006-0.00111.0300.0290.0290.0000.0000.0000.000
58A706ASP-1-0.823-0.9148.451-0.822-0.8220.0000.0000.0000.000
59A707LEU0-0.037-0.01711.1220.1090.1090.0000.0000.0000.000
60A708LEU0-0.0200.00014.5980.0530.0530.0000.0000.0000.000
61A709ASP-1-0.828-0.93710.171-0.926-0.9260.0000.0000.0000.000
62A710ALA0-0.037-0.01712.6920.0750.0750.0000.0000.0000.000
63A711LEU00.0240.01513.7550.0410.0410.0000.0000.0000.000
64A712LEU0-0.020-0.01415.2520.0240.0240.0000.0000.0000.000
65A713MET0-0.0230.01012.0260.0330.0330.0000.0000.0000.000
66A714GLU-1-0.821-0.87616.2790.0510.0510.0000.0000.0000.000
67A715SER0-0.028-0.01919.1110.0160.0160.0000.0000.0000.000
68A716LEU0-0.035-0.01018.8090.0010.0010.0000.0000.0000.000
69A717SER0-0.155-0.07521.4170.0260.0260.0000.0000.0000.000
70A718ARG10.7340.83220.6640.0260.0260.0000.0000.0000.000
71A719LYS10.9210.95324.9300.0160.0160.0000.0000.0000.000
72A720VAL00.0140.02022.5410.0090.0090.0000.0000.0000.000
73A721GLU-1-0.965-0.99625.737-0.054-0.0540.0000.0000.0000.000
74A722ILE0-0.001-0.00626.089-0.009-0.0090.0000.0000.0000.000
75A723SER0-0.022-0.01226.725-0.012-0.0120.0000.0000.0000.000
76A724GLU-1-0.711-0.85222.547-0.068-0.0680.0000.0000.0000.000
77A725ILE00.010-0.00320.650-0.019-0.0190.0000.0000.0000.000
78A726GLU-1-0.875-0.95122.976-0.156-0.1560.0000.0000.0000.000
79A727GLU-1-0.881-0.90823.406-0.084-0.0840.0000.0000.0000.000
80A728ILE0-0.025-0.00817.710-0.014-0.0140.0000.0000.0000.000
81A729ILE0-0.049-0.03420.769-0.030-0.0300.0000.0000.0000.000
82A730SER0-0.072-0.04922.922-0.006-0.0060.0000.0000.0000.000
83A731LEU0-0.027-0.00619.3570.0080.0080.0000.0000.0000.000
84A732CYS0-0.0440.00519.378-0.043-0.0430.0000.0000.0000.000
85A733PRO0-0.055-0.02019.2300.0290.0290.0000.0000.0000.000
86A734LYS10.8060.88022.1660.2430.2430.0000.0000.0000.000
87A735ASN0-0.024-0.01624.0280.0150.0150.0000.0000.0000.000
88A736SER0-0.004-0.00318.3160.0000.0000.0000.0000.0000.000
89A737SER00.003-0.02815.2220.0510.0510.0000.0000.0000.000
90A738ILE00.0510.03613.3800.0090.0090.0000.0000.0000.000
91A739ILE00.0510.03417.0550.0320.0320.0000.0000.0000.000
92A740ARG10.8620.92319.0120.5570.5570.0000.0000.0000.000
93A741HIS0-0.052-0.04215.985-0.020-0.0200.0000.0000.0000.000
94A742ALA00.0530.02618.7980.0270.0270.0000.0000.0000.000
95A743LEU00.0100.00820.1710.0330.0330.0000.0000.0000.000
96A744LEU0-0.037-0.02120.5440.0220.0220.0000.0000.0000.000
97A745ALA00.0240.00319.2790.0230.0230.0000.0000.0000.000
98A746LYS10.7990.89621.3650.1920.1920.0000.0000.0000.000
99A747LEU0-0.044-0.01924.7810.0200.0200.0000.0000.0000.000
100A748VAL0-0.008-0.01422.1320.0160.0160.0000.0000.0000.000
101A749LEU0-0.026-0.00921.0490.0200.0200.0000.0000.0000.000
102A750PHE0-0.0060.01525.0720.0160.0160.0000.0000.0000.000
103A751PRO0-0.041-0.02128.773-0.004-0.0040.0000.0000.0000.000
104A752GLU-1-0.859-0.94231.517-0.101-0.1010.0000.0000.0000.000
105A753ASN0-0.0090.00330.800-0.002-0.0020.0000.0000.0000.000
106A754THR00.033-0.00230.696-0.012-0.0120.0000.0000.0000.000
107A755ALA0-0.006-0.00432.213-0.010-0.0100.0000.0000.0000.000
108A756ASP-1-0.877-0.93433.767-0.123-0.1230.0000.0000.0000.000
109A757SER00.0850.04627.805-0.015-0.0150.0000.0000.0000.000
110A758LEU0-0.016-0.00329.181-0.019-0.0190.0000.0000.0000.000
111A759ASN0-0.067-0.05130.847-0.010-0.0100.0000.0000.0000.000
112A760GLU-1-0.804-0.88628.499-0.181-0.1810.0000.0000.0000.000
113A761VAL00.0130.01125.303-0.018-0.0180.0000.0000.0000.000
114A762LEU0-0.027-0.02427.534-0.017-0.0170.0000.0000.0000.000
115A763ALA0-0.023-0.00230.333-0.003-0.0030.0000.0000.0000.000
116A764ALA00.0540.03125.717-0.003-0.0030.0000.0000.0000.000
117A765TYR00.0120.01221.504-0.033-0.0330.0000.0000.0000.000
118A766LYS10.9270.96527.5550.1700.1700.0000.0000.0000.000
119A767ASN0-0.005-0.01329.575-0.005-0.0050.0000.0000.0000.000
120A768THR00.002-0.01524.327-0.013-0.0130.0000.0000.0000.000
121A769LEU0-0.048-0.02527.496-0.007-0.0070.0000.0000.0000.000
122A770ASP-1-0.891-0.94329.793-0.190-0.1900.0000.0000.0000.000
123A771LEU00.0080.00729.1520.0050.0050.0000.0000.0000.000
124A772CYS0-0.0560.01427.222-0.014-0.0140.0000.0000.0000.000
125A773SER0-0.084-0.06329.2510.0080.0080.0000.0000.0000.000
126A774GLN00.003-0.00232.8420.0190.0190.0000.0000.0000.000
127A775ASP-1-0.795-0.87330.481-0.202-0.2020.0000.0000.0000.000
128A776LYS10.9180.94130.7050.1920.1920.0000.0000.0000.000
129A777ARG10.7810.88831.5710.1850.1850.0000.0000.0000.000
130A778LYS10.7990.87126.2320.2720.2720.0000.0000.0000.000
131A779GLN00.003-0.01925.378-0.022-0.0220.0000.0000.0000.000
132A780SER00.0170.01726.3950.0120.0120.0000.0000.0000.000
133A781SER0-0.0110.01127.281-0.016-0.0160.0000.0000.0000.000
134A782VAL0-0.024-0.01426.5840.0170.0170.0000.0000.0000.000
135A783LEU00.0350.02124.746-0.027-0.0270.0000.0000.0000.000
136A784LYS10.8930.93420.2060.4210.4210.0000.0000.0000.000
137A785ILE00.0100.01619.290-0.046-0.0460.0000.0000.0000.000
138A786ASN00.0650.03514.0520.0900.0900.0000.0000.0000.000
139A787LEU00.0600.02418.3770.0130.0130.0000.0000.0000.000
140A788SER00.0930.05513.8470.0550.0550.0000.0000.0000.000
141A789LYS10.8830.95114.7920.7560.7560.0000.0000.0000.000
142A790LEU00.002-0.00118.0890.0450.0450.0000.0000.0000.000
143A791PHE00.0420.01618.6780.0300.0300.0000.0000.0000.000
144A792THR00.0000.00217.8890.0120.0120.0000.0000.0000.000
145A793LEU00.0160.00620.3370.0350.0350.0000.0000.0000.000
146A794HIS0-0.041-0.01523.3490.0240.0240.0000.0000.0000.000
147A795SER00.0350.01122.9870.0340.0340.0000.0000.0000.000
148A796CYS0-0.017-0.00423.2190.0220.0220.0000.0000.0000.000
149A797LEU0-0.0140.00125.1780.0200.0200.0000.0000.0000.000
150A798SER00.0390.00928.3230.0210.0210.0000.0000.0000.000
151A799LEU0-0.005-0.00525.4880.0170.0170.0000.0000.0000.000
152A800ALA00.0000.00129.0070.0140.0140.0000.0000.0000.000
153A801LEU0-0.016-0.03130.7070.0130.0130.0000.0000.0000.000
154A802GLN0-0.064-0.02532.3070.0080.0080.0000.0000.0000.000
155A803ARG10.8760.94327.3350.1560.1560.0000.0000.0000.000
156A804LEU0-0.046-0.01434.1040.0070.0070.0000.0000.0000.000
157A805GLY00.0120.01836.6900.0040.0040.0000.0000.0000.000
158A806TYR00.0070.02137.4310.0060.0060.0000.0000.0000.000
159A807GLY00.019-0.00136.830-0.006-0.0060.0000.0000.0000.000
160A808ASP-1-0.939-0.97337.876-0.096-0.0960.0000.0000.0000.000
161A809VAL0-0.014-0.00536.855-0.001-0.0010.0000.0000.0000.000
162A810SER0-0.015-0.02632.862-0.009-0.0090.0000.0000.0000.000
163A811LYS10.8900.94633.5270.0820.0820.0000.0000.0000.000
164A812ARG10.9110.95034.3810.0970.0970.0000.0000.0000.000
165A813MET0-0.0190.00930.713-0.007-0.0070.0000.0000.0000.000
166A814TYR00.066-0.01327.193-0.007-0.0070.0000.0000.0000.000
167A815GLN0-0.044-0.05429.965-0.005-0.0050.0000.0000.0000.000
168A816GLU-1-0.814-0.87231.320-0.135-0.1350.0000.0000.0000.000
169A817ILE0-0.076-0.01324.981-0.016-0.0160.0000.0000.0000.000
170A818PHE0-0.019-0.00822.9340.0120.0120.0000.0000.0000.000
171A819VAL00.002-0.00222.075-0.025-0.0250.0000.0000.0000.000
172A820PRO0-0.047-0.02817.4690.0000.0000.0000.0000.0000.000
173A821ASP-1-0.858-0.92418.583-0.211-0.2110.0000.0000.0000.000
174A822SER0-0.045-0.02815.644-0.025-0.0250.0000.0000.0000.000
175A823ASP-1-0.950-0.96812.367-0.501-0.5010.0000.0000.0000.000
176A824ALA00.001-0.0107.7290.0650.0650.0000.0000.0000.000
177A825ASP-1-0.971-0.9718.180-1.936-1.9360.0000.0000.0000.000
178A826ILE0-0.018-0.0189.0160.2580.2580.0000.0000.0000.000
179A827THR00.0090.02310.0610.1630.1630.0000.0000.0000.000
180A828PRO00.0600.01710.7540.1360.1360.0000.0000.0000.000
181A829LEU00.0220.02713.5640.0850.0850.0000.0000.0000.000
182A830SER0-0.019-0.03913.8660.0490.0490.0000.0000.0000.000
183A831PHE00.0000.02014.7400.0600.0600.0000.0000.0000.000
184A832ILE00.0620.02916.6750.0540.0540.0000.0000.0000.000
185A833ILE0-0.0210.01219.2580.0380.0380.0000.0000.0000.000
186A834SER00.0290.00919.5490.0270.0270.0000.0000.0000.000
187A835TRP00.0330.01520.7740.0310.0310.0000.0000.0000.000
188A836THR0-0.008-0.02322.4710.0230.0230.0000.0000.0000.000
189A837ALA00.0170.02424.4520.0170.0170.0000.0000.0000.000
190A838LEU00.0140.00925.0010.0150.0150.0000.0000.0000.000
191A839ASN0-0.062-0.05325.7730.0250.0250.0000.0000.0000.000
192A840THR0-0.077-0.05028.5720.0080.0080.0000.0000.0000.000
193A841PHE00.000-0.00429.4600.0050.0050.0000.0000.0000.000
194A842ALA0-0.0090.00930.3030.0060.0060.0000.0000.0000.000
195A843PRO0-0.029-0.01032.0990.0050.0050.0000.0000.0000.000
196A844ILE0-0.022-0.01135.0250.0040.0040.0000.0000.0000.000
197A845CYS0-0.065-0.02133.403-0.003-0.0030.0000.0000.0000.000
198A846THR00.0430.03935.372-0.002-0.0020.0000.0000.0000.000
199A847SER0-0.015-0.00437.9360.0040.0040.0000.0000.0000.000
200A848PRO0-0.012-0.01938.148-0.005-0.0050.0000.0000.0000.000
201A849LYS10.7960.87034.9320.1270.1270.0000.0000.0000.000
202A850GLU-1-0.884-0.94134.366-0.085-0.0850.0000.0000.0000.000
203A851ASN0-0.037-0.04133.451-0.007-0.0070.0000.0000.0000.000
204A852ASP-1-0.783-0.86930.619-0.131-0.1310.0000.0000.0000.000
205A853VAL00.0270.02627.431-0.004-0.0040.0000.0000.0000.000
206A854VAL00.0240.01527.386-0.010-0.0100.0000.0000.0000.000
207A855GLU-1-0.891-0.93327.464-0.080-0.0800.0000.0000.0000.000
208A856LYS10.8430.90025.2250.1430.1430.0000.0000.0000.000
209A857MET00.0050.04123.077-0.009-0.0090.0000.0000.0000.000
210A858ALA0-0.009-0.00822.574-0.008-0.0080.0000.0000.0000.000
211A859MET0-0.044-0.02822.8250.0120.0120.0000.0000.0000.000
212A860TYR00.0120.01115.0090.0070.0070.0000.0000.0000.000
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