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: N1M4Q

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 OptH
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 -2132934.21271
FMO2-HF: Nuclear repulsion 2048823.685648
FMO2-HF: Total energy -84110.527062
FMO2-MP2: Total energy -84359.368051


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.
-52.16-53.5917.329-6.644-9.254-0.014
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 : 0.926 / q_NPA : 0.961
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].
3A7THR0-0.0240.0093.8060.9563.123-0.025-1.062-1.080-0.003
4A8VAL0-0.010-0.0136.1770.4520.4520.0000.0000.0000.000
5A9ILE00.0670.0369.6080.5100.5100.0000.0000.0000.000
6A10THR0-0.045-0.03713.0440.0700.0700.0000.0000.0000.000
7A11SER0-0.038-0.02116.3080.6040.6040.0000.0000.0000.000
8A12PRO0-0.0240.00916.3040.2490.2490.0000.0000.0000.000
9A13SER00.0330.02618.6510.6110.6110.0000.0000.0000.000
10A14THR00.009-0.02319.720-0.582-0.5820.0000.0000.0000.000
11A15GLU-1-0.886-0.93818.761-13.212-13.2120.0000.0000.0000.000
12A16GLU-1-0.837-0.92915.684-15.046-15.0460.0000.0000.0000.000
13A17LEU0-0.038-0.01015.505-0.869-0.8690.0000.0000.0000.000
14A18VAL00.015-0.01416.419-0.762-0.7620.0000.0000.0000.000
15A19SER0-0.0210.01514.687-0.692-0.6920.0000.0000.0000.000
16A20LEU00.0380.0019.851-0.914-0.9140.0000.0000.0000.000
17A21VAL0-0.028-0.01912.170-1.178-1.1780.0000.0000.0000.000
18A22ASN0-0.018-0.01614.369-0.330-0.3300.0000.0000.0000.000
19A23SER0-0.0330.0009.669-0.344-0.3440.0000.0000.0000.000
20A24ALA0-0.024-0.0189.906-1.261-1.2610.0000.0000.0000.000
21A25LEU0-0.049-0.03410.952-0.466-0.4660.0000.0000.0000.000
22A26LEU0-0.053-0.01312.9430.2470.2470.0000.0000.0000.000
23A27GLU-1-0.962-0.9897.939-26.221-26.2210.0000.0000.0000.000
24A28GLU-1-0.956-0.9599.465-23.539-23.5390.0000.0000.0000.000
25A29ALA0-0.043-0.0216.679-3.281-3.2810.0000.0000.0000.000
26A30MET0-0.071-0.0497.3992.6342.6340.0000.0000.0000.000
27A31LEU00.0110.0178.823-1.258-1.2580.0000.0000.0000.000
28A32THR0-0.025-0.01310.3511.3011.3010.0000.0000.0000.000
29A33ILE00.0050.03612.751-0.304-0.3040.0000.0000.0000.000
30A34PHE0-0.027-0.00313.8330.5020.5020.0000.0000.0000.000
31A35ALA00.0620.01317.8290.1410.1410.0000.0000.0000.000
32A36ARG10.9621.01121.27310.57310.5730.0000.0000.0000.000
33A37CYS0-0.035-0.00224.1200.0610.0610.0000.0000.0000.000
34A38LYS10.9730.99326.2329.4389.4380.0000.0000.0000.000
35A39VAL0-0.041-0.02826.141-0.275-0.2750.0000.0000.0000.000
36A40HIS10.9110.94828.7489.9259.9250.0000.0000.0000.000
37A41TYR0-0.067-0.08228.833-0.491-0.4910.0000.0000.0000.000
38A42ASP-1-0.874-0.93130.915-9.122-9.1220.0000.0000.0000.000
39A43GLY00.0950.02332.641-0.274-0.2740.0000.0000.0000.000
40A44ARG10.8800.94235.1707.9527.9520.0000.0000.0000.000
41A45ALA0-0.0130.00433.9360.2520.2520.0000.0000.0000.000
42A46LYS10.9340.96134.9147.7547.7540.0000.0000.0000.000
43A47SER0-0.023-0.00531.4700.1560.1560.0000.0000.0000.000
44A48GLU-1-0.804-0.89332.840-9.317-9.3170.0000.0000.0000.000
45A49LEU0-0.041-0.02129.1430.0790.0790.0000.0000.0000.000
46A50GLY0-0.004-0.00931.486-0.077-0.0770.0000.0000.0000.000
47A51SER00.0120.00630.126-0.382-0.3820.0000.0000.0000.000
48A52GLY00.0280.01028.6000.2420.2420.0000.0000.0000.000
49A53ASP-1-0.904-0.95123.928-11.628-11.6280.0000.0000.0000.000
50A54ARG10.7610.88022.64411.33711.3370.0000.0000.0000.000
51A55VAL00.0070.01516.247-0.326-0.3260.0000.0000.0000.000
52A56ILE0-0.006-0.00717.7210.3540.3540.0000.0000.0000.000
53A57ILE00.003-0.00112.852-0.854-0.8540.0000.0000.0000.000
54A58VAL00.000-0.00514.2031.1971.1970.0000.0000.0000.000
55A59LYS10.9450.97412.13318.66618.6660.0000.0000.0000.000
56A60PRO00.0780.0399.6211.6141.6140.0000.0000.0000.000
57A61ASP-1-0.778-0.86412.919-17.459-17.4590.0000.0000.0000.000
58A62GLY0-0.021-0.01915.5651.3351.3350.0000.0000.0000.000
59A63SER0-0.115-0.07216.4891.1131.1130.0000.0000.0000.000
60A64PHE0-0.018-0.01317.210-0.765-0.7650.0000.0000.0000.000
61A65LEU0-0.002-0.01316.1540.6710.6710.0000.0000.0000.000
62A66ILE00.0430.03518.942-0.396-0.3960.0000.0000.0000.000
63A67HIS00.0580.02918.0721.0621.0620.0000.0000.0000.000
64A68GLN00.0260.00721.6020.3760.3760.0000.0000.0000.000
65A69SER00.0420.01623.118-0.285-0.2850.0000.0000.0000.000
66A70LYS10.9280.95724.94510.72510.7250.0000.0000.0000.000
67A71LYS10.9470.97225.84110.07510.0750.0000.0000.0000.000
68A72ARG10.9871.00123.74212.36912.3690.0000.0000.0000.000
69A73GLU-1-0.911-0.95823.089-12.110-12.1100.0000.0000.0000.000
70A74PRO0-0.011-0.00521.2740.0600.0600.0000.0000.0000.000
71A75VAL0-0.093-0.04023.5060.5060.5060.0000.0000.0000.000
72A76ASN00.0160.00324.7440.6300.6300.0000.0000.0000.000
73A77TRP0-0.039-0.01922.199-0.458-0.4580.0000.0000.0000.000
74A78GLN0-0.010-0.01122.2510.7070.7070.0000.0000.0000.000
75A79PRO0-0.053-0.02321.555-0.641-0.6410.0000.0000.0000.000
76A80PRO00.0790.03919.2420.0530.0530.0000.0000.0000.000
77A81GLY0-0.0080.01819.9540.7270.7270.0000.0000.0000.000
78A82SER0-0.073-0.03720.9871.0701.0700.0000.0000.0000.000
79A83ARG10.9430.96121.11111.15611.1560.0000.0000.0000.000
80A84VAL00.0170.02418.7870.5860.5860.0000.0000.0000.000
81A85ARG10.9180.96319.75110.80310.8030.0000.0000.0000.000
82A86LEU00.0150.02219.2100.2590.2590.0000.0000.0000.000
83A87GLU-1-0.849-0.89821.703-10.249-10.2490.0000.0000.0000.000
84A88LEU00.0130.00025.043-0.082-0.0820.0000.0000.0000.000
85A89ARG10.7820.85426.61210.30410.3040.0000.0000.0000.000
86A90GLU-1-0.893-0.94829.828-8.899-8.8990.0000.0000.0000.000
87A91ASN0-0.0100.01027.444-0.157-0.1570.0000.0000.0000.000
88A92PRO0-0.035-0.01523.204-0.004-0.0040.0000.0000.0000.000
89A93VAL00.0450.02424.899-0.222-0.2220.0000.0000.0000.000
90A94LEU0-0.025-0.00818.367-0.219-0.2190.0000.0000.0000.000
91A95VAL00.0130.00822.6060.2680.2680.0000.0000.0000.000
92A96SER00.0140.01422.104-0.233-0.2330.0000.0000.0000.000
93A97ILE0-0.073-0.05423.9280.6230.6230.0000.0000.0000.000
94A98ARG11.0621.05225.34110.37010.3700.0000.0000.0000.000
95A99ARG10.8870.91927.08710.68510.6850.0000.0000.0000.000
96A100LYS10.9200.98829.1208.9758.9750.0000.0000.0000.000
97A101PRO00.0920.03830.790-0.144-0.1440.0000.0000.0000.000
98A102ARG10.9120.93030.8579.4319.4310.0000.0000.0000.000
99A103GLU-1-0.853-0.87230.475-9.268-9.2680.0000.0000.0000.000
100A104THR0-0.043-0.02428.510-0.527-0.5270.0000.0000.0000.000
101A105LEU0-0.0030.00224.1540.2300.2300.0000.0000.0000.000
102A106GLU-1-0.853-0.91625.671-10.496-10.4960.0000.0000.0000.000
103A107VAL0-0.021-0.01522.3500.2150.2150.0000.0000.0000.000
104A108GLU-1-0.849-0.92824.876-10.042-10.0420.0000.0000.0000.000
105A109LEU0-0.077-0.05620.477-0.155-0.1550.0000.0000.0000.000
106A110GLU-1-0.922-0.96124.660-9.767-9.7670.0000.0000.0000.000
107A111GLU-1-0.873-0.93624.900-11.091-11.0910.0000.0000.0000.000
108A112VAL0-0.022-0.02318.597-0.446-0.4460.0000.0000.0000.000
109A113TYR0-0.004-0.00519.1990.0530.0530.0000.0000.0000.000
110A114MET0-0.012-0.01111.430-0.213-0.2130.0000.0000.0000.000
111A115VAL00.0050.00712.6800.1530.1530.0000.0000.0000.000
112A116SER0-0.029-0.0598.870-0.930-0.9300.0000.0000.0000.000
113A117VAL00.0490.0315.5840.2870.2870.0000.0000.0000.000
114A118PHE0-0.008-0.0083.242-6.778-5.8570.048-0.344-0.624-0.003
115A119ARG10.9360.9581.86530.69925.66517.299-5.114-7.152-0.006
116A120ALA0-0.046-0.0473.722-0.866-0.4260.008-0.120-0.327-0.002
117A121GLU-1-0.878-0.9064.741-32.680-32.604-0.001-0.004-0.0710.000
118A122ASP-1-0.900-0.9047.597-30.891-30.8910.0000.0000.0000.000
119A123TYR0-0.126-0.1028.8943.9143.9140.0000.0000.0000.000
120A134GLU-1-0.942-0.97929.285-10.507-10.5070.0000.0000.0000.000
121A135MET0-0.029-0.02927.358-0.098-0.0980.0000.0000.0000.000
122A136ALA00.0300.01130.4690.0400.0400.0000.0000.0000.000
123A137GLU-1-0.881-0.94333.284-8.747-8.7470.0000.0000.0000.000
124A138LEU00.0120.00927.2510.0240.0240.0000.0000.0000.000
125A139ILE0-0.075-0.03431.654-0.007-0.0070.0000.0000.0000.000
126A140PHE0-0.050-0.03334.0500.2210.2210.0000.0000.0000.000
127A141GLU-1-0.913-0.94933.575-9.234-9.2340.0000.0000.0000.000
128A142ASN00.0010.00732.4010.1580.1580.0000.0000.0000.000
129A143PRO00.006-0.00133.850-0.212-0.2120.0000.0000.0000.000
130A144GLU-1-0.851-0.91334.881-8.398-8.3980.0000.0000.0000.000
131A145VAL0-0.059-0.02230.003-0.224-0.2240.0000.0000.0000.000
132A146ILE0-0.080-0.02632.045-0.251-0.2510.0000.0000.0000.000
133A147GLU-1-0.880-0.96234.316-8.444-8.4440.0000.0000.0000.000
134A148PRO00.0010.01136.3980.0140.0140.0000.0000.0000.000
135A149GLY0-0.015-0.01638.4820.1960.1960.0000.0000.0000.000
136A150PHE00.0180.00138.5140.1810.1810.0000.0000.0000.000
137A151LYS10.9500.96340.6937.2267.2260.0000.0000.0000.000
138A152PRO00.0130.01938.8810.1120.1120.0000.0000.0000.000
139A153LEU0-0.064-0.02441.3890.1970.1970.0000.0000.0000.000
140A154PHE00.0380.02541.530-0.065-0.0650.0000.0000.0000.000
141A165ALA0-0.027-0.01938.1160.0570.0570.0000.0000.0000.000
142A166VAL0-0.034-0.01336.8000.0110.0110.0000.0000.0000.000
143A167LEU00.0030.00439.6140.0130.0130.0000.0000.0000.000
144A168GLY00.0270.00441.983-0.053-0.0530.0000.0000.0000.000
145A169ARG10.9180.95142.9776.7476.7470.0000.0000.0000.000
146A170ASP-1-0.775-0.90343.117-7.311-7.3110.0000.0000.0000.000
147A171SER0-0.0090.00744.2810.1840.1840.0000.0000.0000.000
148A172ASP-1-0.970-0.96746.175-6.368-6.3680.0000.0000.0000.000
149A173GLY0-0.086-0.04248.1200.1450.1450.0000.0000.0000.000
150A174ASN0-0.052-0.02046.8250.2540.2540.0000.0000.0000.000
151A175ILE0-0.012-0.00446.036-0.153-0.1530.0000.0000.0000.000
152A176VAL00.0190.00340.228-0.045-0.0450.0000.0000.0000.000
153A177VAL0-0.012-0.02440.859-0.059-0.0590.0000.0000.0000.000
154A178LEU00.0110.00835.631-0.209-0.2090.0000.0000.0000.000
155A179GLU-1-0.890-0.96435.743-8.747-8.7470.0000.0000.0000.000
156A180LEU00.0140.01131.681-0.299-0.2990.0000.0000.0000.000
157A181LYS10.8940.94729.1529.6699.6690.0000.0000.0000.000
158A182ARG11.0241.01524.57112.03012.0300.0000.0000.0000.000
159A183ARG10.9550.96020.38714.30914.3090.0000.0000.0000.000
160A184ARG10.9450.97421.51514.30414.3040.0000.0000.0000.000
161A185ALA00.0260.00725.0130.2510.2510.0000.0000.0000.000
162A186GLU-1-0.907-0.97228.398-10.967-10.9670.0000.0000.0000.000
163A187LEU0-0.031-0.02330.6480.1750.1750.0000.0000.0000.000
164A188HIS00.0070.00234.3480.1830.1830.0000.0000.0000.000
165A189ALA00.0530.00034.2240.2440.2440.0000.0000.0000.000
166A190VAL00.0170.03634.5960.0820.0820.0000.0000.0000.000
167A191ARG10.9360.96937.2828.2308.2300.0000.0000.0000.000
168A192GLN00.0030.00337.845-0.006-0.0060.0000.0000.0000.000
169A193LEU00.0100.02537.1350.1790.1790.0000.0000.0000.000
170A194LYS10.9530.97940.3467.5037.5030.0000.0000.0000.000
171A195SER00.0320.00643.0240.1000.1000.0000.0000.0000.000
172A196TYR0-0.019-0.00539.9300.1600.1600.0000.0000.0000.000
173A197VAL00.0200.00143.5390.1280.1280.0000.0000.0000.000
174A198GLU-1-0.983-0.99245.464-6.478-6.4780.0000.0000.0000.000
175A199ILE00.0400.01647.2510.0980.0980.0000.0000.0000.000
176A200LEU0-0.0090.00846.3460.0770.0770.0000.0000.0000.000
177A201ARG10.8420.94546.6556.8126.8120.0000.0000.0000.000
178A202GLU-1-0.960-0.97851.052-5.821-5.8210.0000.0000.0000.000
179A203GLU-1-0.963-0.97952.178-6.050-6.0500.0000.0000.0000.000
180A204TYR0-0.074-0.05350.6720.1130.1130.0000.0000.0000.000
181A205GLY00.0020.02353.0520.0110.0110.0000.0000.0000.000
182A206ASP-1-0.916-0.98550.945-6.508-6.5080.0000.0000.0000.000
183A207LYS10.9250.96248.3376.3256.3250.0000.0000.0000.000
184A208VAL0-0.0070.02446.305-0.170-0.1700.0000.0000.0000.000
185A209ARG10.8190.89740.5467.8127.8120.0000.0000.0000.000
186A210GLY00.0100.01840.960-0.019-0.0190.0000.0000.0000.000
187A211ILE00.008-0.00334.995-0.107-0.1070.0000.0000.0000.000
188A212LEU0-0.067-0.04032.007-0.075-0.0750.0000.0000.0000.000
189A213VAL00.0360.02730.877-0.226-0.2260.0000.0000.0000.000
190A214ALA00.025-0.01027.266-0.018-0.0180.0000.0000.0000.000
191A215PRO0-0.0020.03022.162-0.077-0.0770.0000.0000.0000.000
192A216SER0-0.019-0.02522.669-0.280-0.2800.0000.0000.0000.000
193A217LEU00.0350.05724.7680.2440.2440.0000.0000.0000.000
194A218THR00.0000.00626.239-0.342-0.3420.0000.0000.0000.000
195A219SER00.0340.00728.3180.3220.3220.0000.0000.0000.000
196A220GLY00.0720.03130.2980.3050.3050.0000.0000.0000.000
197A221ALA00.0080.00231.1060.3160.3160.0000.0000.0000.000
198A222LYS10.9110.96430.8039.6649.6640.0000.0000.0000.000
199A223ARG10.9300.95731.6339.7829.7820.0000.0000.0000.000
200A224LEU0-0.033-0.01635.8570.2460.2460.0000.0000.0000.000
201A225LEU0-0.002-0.01833.5390.1760.1760.0000.0000.0000.000
202A226GLU-1-0.922-0.96636.591-8.672-8.6720.0000.0000.0000.000
203A227LYS10.8710.94738.3407.7967.7960.0000.0000.0000.000
204A228GLU-1-0.929-0.98541.120-7.154-7.1540.0000.0000.0000.000
205A229GLY00.0300.03241.6210.1410.1410.0000.0000.0000.000
206A230LEU0-0.058-0.01038.660-0.040-0.0400.0000.0000.0000.000
207A231GLU-1-0.804-0.89536.853-8.321-8.3210.0000.0000.0000.000
208A232PHE0-0.041-0.04527.945-0.161-0.1610.0000.0000.0000.000
209A233ARG10.9230.96631.1189.5809.5800.0000.0000.0000.000
210A234LYS10.9180.96825.44911.99311.9930.0000.0000.0000.000
211A235LEU00.0590.02626.460-0.003-0.0030.0000.0000.0000.000
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