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: GNK11

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 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 222
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2595202.545772
FMO2-HF: Nuclear repulsion 2507955.250428
FMO2-HF: Total energy -87247.295345
FMO2-MP2: Total energy -87499.176354


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.
-5.6980.3397.255-4.317-8.973-0.011
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 : -0.050 / q_NPA : -0.027
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].
3A651ASN00.0250.0023.804-0.5671.433-0.029-0.952-1.0190.004
4A652SER0-0.0030.0142.279-1.835-0.3422.533-1.407-2.618-0.015
5A653HIS0-0.004-0.0092.208-0.4990.8793.226-1.341-3.263-0.003
6A654ALA00.0460.0313.8110.2380.5610.007-0.056-0.2740.000
7A655ASP-1-0.875-0.9426.108-0.835-0.8350.0000.0000.0000.000
8A656ASP-1-0.971-0.9767.2140.1470.1470.0000.0000.0000.000
9A657VAL0-0.075-0.0277.4760.2060.2060.0000.0000.0000.000
10A658PHE00.001-0.02110.2930.1260.1260.0000.0000.0000.000
11A659SER00.007-0.00112.1630.0970.0970.0000.0000.0000.000
12A660PRO0-0.092-0.03213.1780.0660.0660.0000.0000.0000.000
13A661ASN0-0.070-0.04516.1380.0400.0400.0000.0000.0000.000
14A662MET00.086-0.08317.8940.0200.0200.0000.0000.0000.000
15A663VAL00.0170.17121.0940.0100.0100.0000.0000.0000.000
16A664GLU-1-0.916-0.94022.328-0.222-0.2220.0000.0000.0000.000
17A665ARG10.8530.91620.7930.2420.2420.0000.0000.0000.000
18A666LEU00.0270.01124.747-0.002-0.0020.0000.0000.0000.000
19A667TRP00.0650.03224.140-0.034-0.0340.0000.0000.0000.000
20A668VAL0-0.065-0.03621.5460.0170.0170.0000.0000.0000.000
21A669LEU00.0710.02120.754-0.021-0.0210.0000.0000.0000.000
22A670ALA00.0190.00819.497-0.043-0.0430.0000.0000.0000.000
23A671LYS10.9110.96018.9230.2600.2600.0000.0000.0000.000
24A672SER00.1010.04515.0050.0250.0250.0000.0000.0000.000
25A673THR00.0090.01713.832-0.105-0.1050.0000.0000.0000.000
26A674ARG10.8590.93712.4470.4050.4050.0000.0000.0000.000
27A675ASP-1-0.853-0.9448.354-1.629-1.6290.0000.0000.0000.000
28A676SER0-0.024-0.0179.054-0.094-0.0940.0000.0000.0000.000
29A677ALA0-0.049-0.02210.111-0.021-0.0210.0000.0000.0000.000
30A678GLN0-0.0120.0027.7720.1360.1360.0000.0000.0000.000
31A679MET0-0.0080.0742.229-0.2440.5991.518-0.561-1.7990.003
32A680SER00.025-0.0235.5170.2100.2100.0000.0000.0000.000
33A681ASP-1-0.851-0.9236.716-1.668-1.6680.0000.0000.0000.000
34A682SER0-0.031-0.0068.7270.2730.2730.0000.0000.0000.000
35A683ILE0-0.040-0.0407.0870.3180.3180.0000.0000.0000.000
36A684ILE00.003-0.02511.6680.1110.1110.0000.0000.0000.000
37A685SER0-0.007-0.00414.8750.1520.1520.0000.0000.0000.000
38A686SER00.0500.00812.2340.1430.1430.0000.0000.0000.000
39A687LEU00.0120.01914.9690.0530.0530.0000.0000.0000.000
40A688SER0-0.032-0.02916.3790.0790.0790.0000.0000.0000.000
41A689ASP-1-0.784-0.90216.801-0.457-0.4570.0000.0000.0000.000
42A690VAL0-0.037-0.01717.1140.0440.0440.0000.0000.0000.000
43A691LEU0-0.056-0.01319.7260.0420.0420.0000.0000.0000.000
44A692VAL0-0.011-0.01623.1060.0360.0360.0000.0000.0000.000
45A693LEU00.0610.03618.3460.0020.0020.0000.0000.0000.000
46A694SER0-0.0100.00021.157-0.005-0.0050.0000.0000.0000.000
47A695PRO00.0300.00219.126-0.023-0.0230.0000.0000.0000.000
48A696LEU00.0100.00918.137-0.008-0.0080.0000.0000.0000.000
49A697GLU-1-0.789-0.90018.338-0.200-0.2000.0000.0000.0000.000
50A698VAL00.0210.02214.140-0.025-0.0250.0000.0000.0000.000
51A699LEU00.0340.01813.334-0.042-0.0420.0000.0000.0000.000
52A700ALA0-0.030-0.01414.8700.0110.0110.0000.0000.0000.000
53A701SER00.009-0.00715.3850.0070.0070.0000.0000.0000.000
54A702TRP00.0230.0287.404-0.029-0.0290.0000.0000.0000.000
55A703TYR0-0.026-0.00812.1260.0110.0110.0000.0000.0000.000
56A704ALA00.0380.00414.1270.0230.0230.0000.0000.0000.000
57A705ALA0-0.003-0.00611.1030.0000.0000.0000.0000.0000.000
58A706ASP-1-0.859-0.9368.448-0.223-0.2230.0000.0000.0000.000
59A707LEU0-0.054-0.03711.1710.0770.0770.0000.0000.0000.000
60A708LEU0-0.038-0.00814.1850.0300.0300.0000.0000.0000.000
61A709ASP-1-0.870-0.9589.463-0.798-0.7980.0000.0000.0000.000
62A710ALA0-0.051-0.02512.3420.0560.0560.0000.0000.0000.000
63A711LEU00.0230.02213.8810.0260.0260.0000.0000.0000.000
64A712LEU0-0.025-0.01314.8790.0060.0060.0000.0000.0000.000
65A713MET0-0.0100.00412.1340.0050.0050.0000.0000.0000.000
66A714GLU-1-0.842-0.89016.4180.1080.1080.0000.0000.0000.000
67A715SER0-0.067-0.04619.3820.0030.0030.0000.0000.0000.000
68A716LEU0-0.037-0.01218.838-0.005-0.0050.0000.0000.0000.000
69A717SER0-0.054-0.01821.3310.0010.0010.0000.0000.0000.000
70A718ARG10.7520.84620.861-0.033-0.0330.0000.0000.0000.000
71A719LYS10.9250.95724.8690.0040.0040.0000.0000.0000.000
72A720VAL0-0.0100.01022.3160.0100.0100.0000.0000.0000.000
73A721GLU-1-0.939-0.98125.634-0.021-0.0210.0000.0000.0000.000
74A722ILE00.0140.00625.988-0.004-0.0040.0000.0000.0000.000
75A723SER00.0020.00526.472-0.009-0.0090.0000.0000.0000.000
76A724GLU-1-0.745-0.87122.389-0.013-0.0130.0000.0000.0000.000
77A725ILE0-0.011-0.01420.851-0.013-0.0130.0000.0000.0000.000
78A726GLU-1-0.884-0.96223.055-0.107-0.1070.0000.0000.0000.000
79A727GLU-1-0.919-0.94523.162-0.021-0.0210.0000.0000.0000.000
80A728ILE0-0.023-0.00917.826-0.007-0.0070.0000.0000.0000.000
81A729ILE0-0.047-0.02720.715-0.025-0.0250.0000.0000.0000.000
82A730SER0-0.079-0.04622.968-0.005-0.0050.0000.0000.0000.000
83A731LEU0-0.044-0.00818.9840.0020.0020.0000.0000.0000.000
84A732CYS0-0.044-0.01018.412-0.029-0.0290.0000.0000.0000.000
85A733PRO0-0.056-0.01319.3860.0160.0160.0000.0000.0000.000
86A734LYS10.8170.87222.3410.1750.1750.0000.0000.0000.000
87A735ASN0-0.015-0.00124.1380.0040.0040.0000.0000.0000.000
88A736SER00.0030.01018.366-0.005-0.0050.0000.0000.0000.000
89A737SER0-0.017-0.02015.0380.0240.0240.0000.0000.0000.000
90A738ILE00.0340.01912.8680.0070.0070.0000.0000.0000.000
91A739ILE00.0340.03216.6930.0310.0310.0000.0000.0000.000
92A740ARG10.8810.94219.2560.4920.4920.0000.0000.0000.000
93A741HIS0-0.066-0.05416.122-0.030-0.0300.0000.0000.0000.000
94A742ALA00.0690.03618.5220.0220.0220.0000.0000.0000.000
95A743LEU00.0070.00819.8430.0270.0270.0000.0000.0000.000
96A744LEU0-0.028-0.01519.9320.0170.0170.0000.0000.0000.000
97A745ALA00.0230.01219.1290.0190.0190.0000.0000.0000.000
98A746LYS10.8420.93221.1870.1540.1540.0000.0000.0000.000
99A747LEU0-0.047-0.01824.5820.0160.0160.0000.0000.0000.000
100A748VAL0-0.012-0.02322.3400.0130.0130.0000.0000.0000.000
101A749LEU0-0.040-0.01720.6630.0170.0170.0000.0000.0000.000
102A750PHE00.0120.02324.5480.0150.0150.0000.0000.0000.000
103A751PRO0-0.031-0.01828.411-0.006-0.0060.0000.0000.0000.000
104A752GLU-1-0.881-0.95431.278-0.080-0.0800.0000.0000.0000.000
105A753ASN0-0.0090.00130.761-0.002-0.0020.0000.0000.0000.000
106A754THR00.0520.01530.321-0.010-0.0100.0000.0000.0000.000
107A755ALA00.0010.00731.882-0.010-0.0100.0000.0000.0000.000
108A756ASP-1-0.870-0.93433.881-0.101-0.1010.0000.0000.0000.000
109A757SER00.0710.04527.617-0.012-0.0120.0000.0000.0000.000
110A758LEU0-0.029-0.02029.289-0.016-0.0160.0000.0000.0000.000
111A759ASN0-0.089-0.06130.699-0.009-0.0090.0000.0000.0000.000
112A760GLU-1-0.793-0.88628.486-0.148-0.1480.0000.0000.0000.000
113A761VAL00.0090.01125.282-0.018-0.0180.0000.0000.0000.000
114A762LEU0-0.023-0.03027.478-0.016-0.0160.0000.0000.0000.000
115A763ALA0-0.034-0.00530.072-0.001-0.0010.0000.0000.0000.000
116A764ALA00.0630.03325.584-0.001-0.0010.0000.0000.0000.000
117A765TYR0-0.010-0.00421.730-0.035-0.0350.0000.0000.0000.000
118A766LYS10.9140.95227.5520.1510.1510.0000.0000.0000.000
119A767ASN00.0040.00928.862-0.002-0.0020.0000.0000.0000.000
120A768THR00.016-0.01223.940-0.008-0.0080.0000.0000.0000.000
121A769LEU0-0.052-0.02127.102-0.007-0.0070.0000.0000.0000.000
122A770ASP-1-0.911-0.95529.615-0.163-0.1630.0000.0000.0000.000
123A771LEU0-0.021-0.00529.1060.0070.0070.0000.0000.0000.000
124A772CYS0-0.067-0.00827.521-0.021-0.0210.0000.0000.0000.000
125A773SER0-0.042-0.03629.4370.0060.0060.0000.0000.0000.000
126A774GLN0-0.062-0.01032.9370.0160.0160.0000.0000.0000.000
127A775ASP-1-0.781-0.89730.754-0.174-0.1740.0000.0000.0000.000
128A776LYS10.9350.95931.1550.1810.1810.0000.0000.0000.000
129A777ARG10.7890.89131.7670.1580.1580.0000.0000.0000.000
130A778LYS10.8110.87426.5030.2290.2290.0000.0000.0000.000
131A779GLN00.0290.00825.690-0.014-0.0140.0000.0000.0000.000
132A780SER00.0270.02226.5180.0100.0100.0000.0000.0000.000
133A781SER00.0010.01227.442-0.013-0.0130.0000.0000.0000.000
134A782VAL0-0.024-0.01926.4600.0130.0130.0000.0000.0000.000
135A783LEU00.0340.02024.914-0.022-0.0220.0000.0000.0000.000
136A784LYS10.9070.94420.1630.4130.4130.0000.0000.0000.000
137A785ILE00.0170.02019.633-0.036-0.0360.0000.0000.0000.000
138A786ASN00.0660.03214.5050.0830.0830.0000.0000.0000.000
139A787LEU00.0690.02418.4560.0210.0210.0000.0000.0000.000
140A788SER00.0870.05613.8730.0560.0560.0000.0000.0000.000
141A789LYS10.9150.96914.7920.7560.7560.0000.0000.0000.000
142A790LEU00.0070.00718.2160.0490.0490.0000.0000.0000.000
143A791PHE00.0470.02118.3970.0340.0340.0000.0000.0000.000
144A792THR0-0.006-0.01517.8240.0070.0070.0000.0000.0000.000
145A793LEU0-0.004-0.00920.2850.0360.0360.0000.0000.0000.000
146A794HIS0-0.073-0.03223.2390.0270.0270.0000.0000.0000.000
147A795SER00.0440.00923.0870.0320.0320.0000.0000.0000.000
148A796CYS0-0.019-0.00423.0220.0240.0240.0000.0000.0000.000
149A797LEU00.0010.02125.0500.0210.0210.0000.0000.0000.000
150A798SER00.0600.02528.3850.0210.0210.0000.0000.0000.000
151A799LEU0-0.0060.01125.6940.0180.0180.0000.0000.0000.000
152A800ALA00.0050.00128.9050.0150.0150.0000.0000.0000.000
153A801LEU0-0.027-0.02630.5010.0120.0120.0000.0000.0000.000
154A802GLN0-0.036-0.02332.4790.0070.0070.0000.0000.0000.000
155A803ARG10.8420.91927.2950.1440.1440.0000.0000.0000.000
156A804LEU0-0.030-0.00434.2650.0060.0060.0000.0000.0000.000
157A805GLY0-0.0030.01336.9440.0040.0040.0000.0000.0000.000
158A806TYR00.0260.01737.4210.0040.0040.0000.0000.0000.000
159A807GLY0-0.0120.00236.877-0.005-0.0050.0000.0000.0000.000
160A808ASP-1-0.920-0.96937.913-0.093-0.0930.0000.0000.0000.000
161A809VAL0-0.026-0.02236.819-0.002-0.0020.0000.0000.0000.000
162A810SER0-0.034-0.04532.715-0.009-0.0090.0000.0000.0000.000
163A811LYS10.9200.96333.4190.0880.0880.0000.0000.0000.000
164A812ARG10.9180.95434.1580.0990.0990.0000.0000.0000.000
165A813MET0-0.0270.00530.905-0.006-0.0060.0000.0000.0000.000
166A814TYR00.043-0.01427.126-0.009-0.0090.0000.0000.0000.000
167A815GLN0-0.016-0.02929.951-0.004-0.0040.0000.0000.0000.000
168A816GLU-1-0.856-0.89831.193-0.149-0.1490.0000.0000.0000.000
169A817ILE0-0.0200.01824.908-0.012-0.0120.0000.0000.0000.000
170A818PHE0-0.024-0.01522.5640.0110.0110.0000.0000.0000.000
171A819VAL0-0.013-0.01222.174-0.028-0.0280.0000.0000.0000.000
172A820PRO0-0.040-0.02717.5620.0070.0070.0000.0000.0000.000
173A821ASP-1-0.882-0.93018.384-0.271-0.2710.0000.0000.0000.000
174A822SER0-0.038-0.02815.440-0.010-0.0100.0000.0000.0000.000
175A823ASP-1-0.944-0.97112.036-0.640-0.6400.0000.0000.0000.000
176A824ALA0-0.026-0.0227.1590.0640.0640.0000.0000.0000.000
177A825ASP-1-0.946-0.9728.210-2.038-2.0380.0000.0000.0000.000
178A826ILE0-0.008-0.0138.9960.3360.3360.0000.0000.0000.000
179A827THR00.0180.02610.1320.1500.1500.0000.0000.0000.000
180A828PRO00.0800.03010.3750.1210.1210.0000.0000.0000.000
181A829LEU00.0370.02513.3140.0840.0840.0000.0000.0000.000
182A830SER0-0.037-0.03314.1500.0280.0280.0000.0000.0000.000
183A831PHE00.0220.02114.7320.0550.0550.0000.0000.0000.000
184A832ILE00.0620.03316.5540.0520.0520.0000.0000.0000.000
185A833ILE0-0.0280.00719.1470.0350.0350.0000.0000.0000.000
186A834SER00.0200.00619.3790.0250.0250.0000.0000.0000.000
187A835TRP00.0370.01720.5590.0280.0280.0000.0000.0000.000
188A836THR0-0.027-0.03122.1680.0220.0220.0000.0000.0000.000
189A837ALA00.0090.01724.1840.0160.0160.0000.0000.0000.000
190A838LEU00.0090.00824.7790.0120.0120.0000.0000.0000.000
191A839ASN0-0.048-0.04325.4540.0270.0270.0000.0000.0000.000
192A840THR0-0.087-0.06128.3660.0070.0070.0000.0000.0000.000
193A841PHE0-0.037-0.02729.2380.0060.0060.0000.0000.0000.000
194A842ALA0-0.0020.01730.1500.0020.0020.0000.0000.0000.000
195A843PRO0-0.041-0.01031.8150.0050.0050.0000.0000.0000.000
196A844ILE0-0.018-0.01334.7030.0020.0020.0000.0000.0000.000
197A845CYS0-0.072-0.02633.3400.0000.0000.0000.0000.0000.000
198A846THR00.0750.05035.2590.0020.0020.0000.0000.0000.000
199A847SER00.0300.05337.8360.0000.0000.0000.0000.0000.000
200A848PRO0-0.048-0.06338.797-0.004-0.0040.0000.0000.0000.000
201A849LYS10.8080.88335.1980.1340.1340.0000.0000.0000.000
202A850GLU-1-0.759-0.88533.435-0.100-0.1000.0000.0000.0000.000
203A851ASN0-0.168-0.10033.582-0.003-0.0030.0000.0000.0000.000
204A852ASP-1-0.787-0.88830.448-0.155-0.1550.0000.0000.0000.000
205A853VAL00.0050.02827.329-0.006-0.0060.0000.0000.0000.000
206A854VAL00.0660.03627.301-0.010-0.0100.0000.0000.0000.000
207A855GLU-1-0.888-0.93827.335-0.103-0.1030.0000.0000.0000.000
208A856LYS10.8510.90425.1730.1720.1720.0000.0000.0000.000
209A857MET0-0.0260.01723.033-0.014-0.0140.0000.0000.0000.000
210A858ALA0-0.014-0.01922.556-0.010-0.0100.0000.0000.0000.000
211A859MET0-0.044-0.03322.8070.0080.0080.0000.0000.0000.000
212A860TYR00.0110.01815.254-0.001-0.0010.0000.0000.0000.000
213A861VAL00.0090.00118.035-0.018-0.0180.0000.0000.0000.000
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219A867THR00.0100.00310.9210.0680.0680.0000.0000.0000.000
220A868LEU0-0.022-0.01413.1010.0380.0380.0000.0000.0000.000
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