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: 3Q56L

Calculation Name: 5GKJ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5GKJ

Chain ID: A

ChEMBL ID:

UniProt ID: Q5JER9

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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2134478.609435
FMO2-HF: Nuclear repulsion 2050364.964771
FMO2-HF: Total energy -84113.644664
FMO2-MP2: Total energy -84362.452371


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:5:LYS)


Summations of interaction energy for fragment #1(A:5:LYS)
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.
-77.038-67.6817.096-6.19-10.264-0.048
Interaction energy analysis for fragmet #1(A:5:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 1.005 / q_NPA : 1.018
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].
3A7THR00.0120.0143.889-0.0621.848-0.010-1.009-0.8910.003
4A8VAL0-0.009-0.0146.240-0.131-0.1310.0000.0000.0000.000
5A9ILE00.0460.03010.0460.4970.4970.0000.0000.0000.000
6A10THR0-0.006-0.00913.507-0.210-0.2100.0000.0000.0000.000
7A11SER0-0.020-0.01616.8300.3000.3000.0000.0000.0000.000
8A12PRO0-0.050-0.00116.3310.3420.3420.0000.0000.0000.000
9A13SER00.0440.01718.4410.6000.6000.0000.0000.0000.000
10A14THR00.030-0.01019.487-0.524-0.5240.0000.0000.0000.000
11A15GLU-1-0.895-0.92018.083-13.960-13.9600.0000.0000.0000.000
12A16GLU-1-0.818-0.91615.475-15.195-15.1950.0000.0000.0000.000
13A17LEU0-0.032-0.01015.032-1.070-1.0700.0000.0000.0000.000
14A18VAL00.012-0.00716.202-0.746-0.7460.0000.0000.0000.000
15A19SER00.0110.00013.973-0.708-0.7080.0000.0000.0000.000
16A20LEU0-0.033-0.0159.226-1.141-1.1410.0000.0000.0000.000
17A21VAL0-0.011-0.00611.538-1.486-1.4860.0000.0000.0000.000
18A22ASN0-0.071-0.05513.975-0.289-0.2890.0000.0000.0000.000
19A23SER0-0.024-0.0248.4130.3290.3290.0000.0000.0000.000
20A24ALA0-0.017-0.0209.662-1.103-1.1030.0000.0000.0000.000
21A25LEU0-0.056-0.03210.707-0.529-0.5290.0000.0000.0000.000
22A26LEU0-0.046-0.00312.3890.5930.5930.0000.0000.0000.000
23A27GLU-1-0.846-0.8956.075-31.551-31.5510.0000.0000.0000.000
24A28GLU-1-0.958-0.9658.997-24.354-24.3540.0000.0000.0000.000
25A29ALA0-0.036-0.0116.819-3.284-3.2840.0000.0000.0000.000
26A30MET0-0.047-0.0287.2312.5162.5160.0000.0000.0000.000
27A31LEU00.0230.0258.290-1.596-1.5960.0000.0000.0000.000
28A32THR0-0.063-0.04710.7840.5700.5700.0000.0000.0000.000
29A33ILE00.0030.02212.383-0.315-0.3150.0000.0000.0000.000
30A34PHE0-0.030-0.01014.4530.2510.2510.0000.0000.0000.000
31A35ALA00.0510.01317.9470.1150.1150.0000.0000.0000.000
32A36ARG10.8630.94221.44611.07211.0720.0000.0000.0000.000
33A37CYS0-0.041-0.00823.745-0.166-0.1660.0000.0000.0000.000
34A38LYS10.8870.93325.8389.7529.7520.0000.0000.0000.000
35A39VAL0-0.036-0.01925.601-0.342-0.3420.0000.0000.0000.000
36A40HIS10.8360.88628.07610.41310.4130.0000.0000.0000.000
37A41TYR0-0.016-0.00827.223-0.522-0.5220.0000.0000.0000.000
38A42ASP-1-0.908-0.95730.297-9.212-9.2120.0000.0000.0000.000
39A43GLY00.0800.02431.967-0.332-0.3320.0000.0000.0000.000
40A44ARG10.8710.93834.3888.2218.2210.0000.0000.0000.000
41A45ALA0-0.006-0.00232.8940.2440.2440.0000.0000.0000.000
42A46LYS10.9060.94233.7658.1608.1600.0000.0000.0000.000
43A47SER0-0.007-0.00130.1120.1520.1520.0000.0000.0000.000
44A48GLU-1-0.754-0.84431.737-9.682-9.6820.0000.0000.0000.000
45A49LEU0-0.023-0.00628.2510.1300.1300.0000.0000.0000.000
46A50GLY00.0150.00231.6040.0140.0140.0000.0000.0000.000
47A51SER0-0.018-0.03729.721-0.337-0.3370.0000.0000.0000.000
48A52GLY0-0.005-0.01328.1650.2680.2680.0000.0000.0000.000
49A53ASP-1-0.834-0.86524.491-11.906-11.9060.0000.0000.0000.000
50A54ARG10.7330.85422.31811.65311.6530.0000.0000.0000.000
51A55VAL00.0150.01516.038-0.361-0.3610.0000.0000.0000.000
52A56ILE0-0.0050.00117.2500.4750.4750.0000.0000.0000.000
53A57ILE0-0.007-0.00812.089-0.889-0.8890.0000.0000.0000.000
54A58VAL0-0.001-0.00813.3121.4701.4700.0000.0000.0000.000
55A59LYS10.8250.90111.25919.38619.3860.0000.0000.0000.000
56A60PRO00.1010.0509.5691.9411.9410.0000.0000.0000.000
57A61ASP-1-0.749-0.82812.764-19.291-19.2910.0000.0000.0000.000
58A62GLY00.0410.01515.6041.4301.4300.0000.0000.0000.000
59A63SER0-0.105-0.06915.6980.9520.9520.0000.0000.0000.000
60A64PHE00.0070.00016.339-0.981-0.9810.0000.0000.0000.000
61A65LEU00.001-0.00715.0540.9800.9800.0000.0000.0000.000
62A66ILE00.0430.02918.486-0.405-0.4050.0000.0000.0000.000
63A67HIS00.0390.01417.3901.1781.1780.0000.0000.0000.000
64A68GLN00.0790.03421.0770.3640.3640.0000.0000.0000.000
65A69SER00.0220.00722.949-0.135-0.1350.0000.0000.0000.000
66A70LYS10.9200.95624.63611.18211.1820.0000.0000.0000.000
67A71LYS10.8900.94225.46311.21211.2120.0000.0000.0000.000
68A72ARG10.9590.97622.88012.38512.3850.0000.0000.0000.000
69A73GLU-1-0.838-0.90321.699-12.655-12.6550.0000.0000.0000.000
70A74PRO0-0.007-0.00520.0150.3390.3390.0000.0000.0000.000
71A75VAL0-0.060-0.01822.6570.4980.4980.0000.0000.0000.000
72A76ASN00.008-0.00124.2430.6740.6740.0000.0000.0000.000
73A77TRP0-0.031-0.01621.166-0.496-0.4960.0000.0000.0000.000
74A78GLN00.000-0.00421.4120.7920.7920.0000.0000.0000.000
75A79PRO0-0.018-0.00120.602-0.711-0.7110.0000.0000.0000.000
76A80PRO00.0690.03018.0760.0360.0360.0000.0000.0000.000
77A81GLY0-0.0110.00519.6820.8370.8370.0000.0000.0000.000
78A82SER0-0.102-0.05221.1751.0241.0240.0000.0000.0000.000
79A83ARG10.9410.95920.78411.53111.5310.0000.0000.0000.000
80A84VAL00.0010.00318.1730.7130.7130.0000.0000.0000.000
81A85ARG10.8290.89420.07811.40911.4090.0000.0000.0000.000
82A86LEU00.0130.01418.6110.0100.0100.0000.0000.0000.000
83A87GLU-1-0.809-0.85721.704-10.619-10.6190.0000.0000.0000.000
84A88LEU00.009-0.00524.485-0.273-0.2730.0000.0000.0000.000
85A89ARG10.7510.84026.43210.62110.6210.0000.0000.0000.000
86A90GLU-1-0.891-0.95029.596-9.508-9.5080.0000.0000.0000.000
87A91ASN0-0.016-0.00427.722-0.088-0.0880.0000.0000.0000.000
88A92PRO00.0040.00422.9200.0100.0100.0000.0000.0000.000
89A93VAL00.005-0.00424.753-0.107-0.1070.0000.0000.0000.000
90A94LEU00.0220.01717.772-0.198-0.1980.0000.0000.0000.000
91A95VAL00.003-0.00922.2830.4320.4320.0000.0000.0000.000
92A96SER00.0100.01121.417-0.368-0.3680.0000.0000.0000.000
93A97ILE0-0.032-0.01623.4040.6720.6720.0000.0000.0000.000
94A98ARG10.9050.94825.16410.77810.7780.0000.0000.0000.000
95A99ARG10.9120.91826.64111.16111.1610.0000.0000.0000.000
96A100LYS10.9350.98628.8529.1619.1610.0000.0000.0000.000
97A101PRO00.0910.04330.459-0.109-0.1090.0000.0000.0000.000
98A102ARG10.9090.94830.3509.6089.6080.0000.0000.0000.000
99A103GLU-1-0.762-0.83929.820-9.481-9.4810.0000.0000.0000.000
100A104THR0-0.031-0.01127.844-0.625-0.6250.0000.0000.0000.000
101A105LEU0-0.0040.01323.2620.2640.2640.0000.0000.0000.000
102A106GLU-1-0.820-0.88125.016-11.011-11.0110.0000.0000.0000.000
103A107VAL0-0.014-0.02221.3790.2210.2210.0000.0000.0000.000
104A108GLU-1-0.790-0.87724.332-10.320-10.3200.0000.0000.0000.000
105A109LEU0-0.039-0.03520.548-0.070-0.0700.0000.0000.0000.000
106A110GLU-1-0.804-0.88724.519-10.417-10.4170.0000.0000.0000.000
107A111GLU-1-0.876-0.93924.524-11.730-11.7300.0000.0000.0000.000
108A112VAL0-0.029-0.01218.659-0.457-0.4570.0000.0000.0000.000
109A113TYR0-0.023-0.03719.876-0.175-0.1750.0000.0000.0000.000
110A114MET0-0.014-0.00912.402-0.158-0.1580.0000.0000.0000.000
111A115VAL00.0040.01312.5820.1130.1130.0000.0000.0000.000
112A116SER0-0.050-0.0379.386-0.923-0.9230.0000.0000.0000.000
113A117VAL00.0560.0266.4960.6970.6970.0000.0000.0000.000
114A118PHE0-0.023-0.0252.581-9.847-7.6931.130-1.018-2.266-0.013
115A119ARG10.8070.8702.41342.84846.3402.027-1.741-3.778-0.006
116A120ALA0-0.020-0.0282.338-20.863-19.1593.950-2.411-3.244-0.032
117A121GLU-1-0.858-0.8924.530-33.797-33.700-0.001-0.011-0.0850.000
118A122ASP-1-0.937-0.9456.502-36.713-36.7130.0000.0000.0000.000
119A123TYR0-0.140-0.1097.6735.2215.2210.0000.0000.0000.000
120A134GLU-1-0.771-0.85328.107-11.159-11.1590.0000.0000.0000.000
121A135MET0-0.015-0.02327.343-0.068-0.0680.0000.0000.0000.000
122A136ALA00.0190.01230.5470.0460.0460.0000.0000.0000.000
123A137GLU-1-0.856-0.92732.919-8.626-8.6260.0000.0000.0000.000
124A138LEU0-0.036-0.01827.4480.0470.0470.0000.0000.0000.000
125A139ILE0-0.042-0.01731.7350.0160.0160.0000.0000.0000.000
126A140PHE0-0.036-0.02934.3380.2500.2500.0000.0000.0000.000
127A141GLU-1-0.886-0.91433.473-9.213-9.2130.0000.0000.0000.000
128A142ASN0-0.050-0.04432.7450.1730.1730.0000.0000.0000.000
129A143PRO0-0.0020.00734.009-0.197-0.1970.0000.0000.0000.000
130A144GLU-1-0.829-0.92635.208-8.188-8.1880.0000.0000.0000.000
131A145VAL0-0.049-0.01229.759-0.184-0.1840.0000.0000.0000.000
132A146ILE0-0.078-0.02331.851-0.245-0.2450.0000.0000.0000.000
133A147GLU-1-0.800-0.89734.358-8.247-8.2470.0000.0000.0000.000
134A148PRO0-0.0080.01536.1990.0520.0520.0000.0000.0000.000
135A149GLY00.024-0.00338.4700.1860.1860.0000.0000.0000.000
136A150PHE0-0.050-0.02337.6680.1910.1910.0000.0000.0000.000
137A151LYS10.8970.93640.5567.6387.6380.0000.0000.0000.000
138A152PRO0-0.0010.01138.7950.1360.1360.0000.0000.0000.000
139A153LEU0-0.036-0.01141.5980.1860.1860.0000.0000.0000.000
140A154PHE00.0300.02341.806-0.035-0.0350.0000.0000.0000.000
141A165ALA0-0.050-0.03037.722-0.089-0.0890.0000.0000.0000.000
142A166VAL0-0.017-0.00736.9160.0590.0590.0000.0000.0000.000
143A167LEU00.0150.01139.505-0.004-0.0040.0000.0000.0000.000
144A168GLY00.0160.00041.988-0.039-0.0390.0000.0000.0000.000
145A169ARG10.8520.92942.9716.6326.6320.0000.0000.0000.000
146A170ASP-1-0.763-0.85743.387-7.381-7.3810.0000.0000.0000.000
147A171SER00.0220.00844.5240.1370.1370.0000.0000.0000.000
148A172ASP-1-0.868-0.91446.322-6.331-6.3310.0000.0000.0000.000
149A173GLY00.004-0.00148.1980.1340.1340.0000.0000.0000.000
150A174ASN0-0.051-0.05146.2630.2280.2280.0000.0000.0000.000
151A175ILE00.0300.01245.901-0.110-0.1100.0000.0000.0000.000
152A176VAL00.0150.00540.173-0.040-0.0400.0000.0000.0000.000
153A177VAL00.0080.00640.561-0.032-0.0320.0000.0000.0000.000
154A178LEU00.0200.00935.872-0.194-0.1940.0000.0000.0000.000
155A179GLU-1-0.772-0.88135.423-8.708-8.7080.0000.0000.0000.000
156A180LEU00.0140.02431.823-0.308-0.3080.0000.0000.0000.000
157A181LYS10.7830.86429.0559.6099.6090.0000.0000.0000.000
158A182ARG10.8890.89824.00811.81111.8110.0000.0000.0000.000
159A183ARG10.8030.86519.17214.41314.4130.0000.0000.0000.000
160A184ARG10.9090.95720.92614.56114.5610.0000.0000.0000.000
161A185ALA00.0740.04124.9170.2150.2150.0000.0000.0000.000
162A186GLU-1-0.869-0.93828.285-10.951-10.9510.0000.0000.0000.000
163A187LEU0-0.010-0.00330.4560.1990.1990.0000.0000.0000.000
164A188HIS0-0.015-0.01533.8050.3140.3140.0000.0000.0000.000
165A189ALA00.0720.02933.3500.2270.2270.0000.0000.0000.000
166A190VAL0-0.0090.00634.2150.1540.1540.0000.0000.0000.000
167A191ARG10.9190.96636.7858.4648.4640.0000.0000.0000.000
168A192GLN0-0.024-0.01036.525-0.024-0.0240.0000.0000.0000.000
169A193LEU00.0240.01736.7660.1820.1820.0000.0000.0000.000
170A194LYS10.8030.91039.9877.1737.1730.0000.0000.0000.000
171A195SER00.011-0.03942.4850.1300.1300.0000.0000.0000.000
172A196TYR0-0.069-0.03939.3520.1630.1630.0000.0000.0000.000
173A197VAL00.0040.00043.2460.1370.1370.0000.0000.0000.000
174A198GLU-1-0.800-0.86145.254-6.664-6.6640.0000.0000.0000.000
175A199ILE00.0630.02747.4410.1100.1100.0000.0000.0000.000
176A200LEU0-0.021-0.01246.2390.0820.0820.0000.0000.0000.000
177A201ARG10.7550.87746.9206.7246.7240.0000.0000.0000.000
178A202GLU-1-0.985-0.98950.948-5.837-5.8370.0000.0000.0000.000
179A203GLU-1-0.903-0.92951.332-6.111-6.1110.0000.0000.0000.000
180A204TYR0-0.133-0.09450.5710.1030.1030.0000.0000.0000.000
181A205GLY0-0.0020.01653.0670.0090.0090.0000.0000.0000.000
182A206ASP-1-0.814-0.90350.507-6.589-6.5890.0000.0000.0000.000
183A207LYS10.8100.89948.2416.3776.3770.0000.0000.0000.000
184A208VAL0-0.045-0.00446.628-0.195-0.1950.0000.0000.0000.000
185A209ARG10.7780.83639.7487.7737.7730.0000.0000.0000.000
186A210GLY00.0430.01040.5600.0150.0150.0000.0000.0000.000
187A211ILE0-0.008-0.00234.462-0.132-0.1320.0000.0000.0000.000
188A212LEU0-0.035-0.01931.470-0.077-0.0770.0000.0000.0000.000
189A213VAL00.0100.00030.633-0.199-0.1990.0000.0000.0000.000
190A214ALA00.0450.01726.947-0.006-0.0060.0000.0000.0000.000
191A215PRO00.0160.02821.740-0.063-0.0630.0000.0000.0000.000
192A216SER0-0.043-0.02322.310-0.389-0.3890.0000.0000.0000.000
193A217LEU00.0190.01824.5150.2480.2480.0000.0000.0000.000
194A218THR00.0030.00126.031-0.301-0.3010.0000.0000.0000.000
195A219SER00.0200.00228.0620.2500.2500.0000.0000.0000.000
196A220GLY00.0470.02029.9950.3030.3030.0000.0000.0000.000
197A221ALA00.007-0.00130.9200.3210.3210.0000.0000.0000.000
198A222LYS10.8640.93130.4749.7509.7500.0000.0000.0000.000
199A223ARG10.8690.90732.5519.5469.5460.0000.0000.0000.000
200A224LEU0-0.024-0.00335.6750.2260.2260.0000.0000.0000.000
201A225LEU0-0.016-0.01833.4740.1760.1760.0000.0000.0000.000
202A226GLU-1-0.792-0.87135.985-8.912-8.9120.0000.0000.0000.000
203A227LYS10.7960.88938.1317.7817.7810.0000.0000.0000.000
204A228GLU-1-0.809-0.89940.783-7.334-7.3340.0000.0000.0000.000
205A229GLY0-0.0030.01841.5670.1120.1120.0000.0000.0000.000
206A230LEU0-0.044-0.01038.326-0.003-0.0030.0000.0000.0000.000
207A231GLU-1-0.820-0.89136.440-8.347-8.3470.0000.0000.0000.000
208A232PHE0-0.041-0.04327.039-0.177-0.1770.0000.0000.0000.000
209A233ARG10.8510.92130.6279.2629.2620.0000.0000.0000.000
210A234LYS10.9400.97524.40612.20712.2070.0000.0000.0000.000
211A235LEU00.0560.02126.2990.0750.0750.0000.0000.0000.000
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