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: 4JGQN

Calculation Name: 4HYE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4HYE

Chain ID: A

ChEMBL ID:

UniProt ID: Q8DNC2

Base Structure: X-ray

Registration Date: 2023-09-23

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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2197556.303757
FMO2-HF: Nuclear repulsion 2118248.063815
FMO2-HF: Total energy -79308.239942
FMO2-MP2: Total energy -79537.038083


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:0:HIS)


Summations of interaction energy for fragment #1(A:0:HIS)
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.
-231.254-227.59523.785-12.893-14.551-0.139
Interaction energy analysis for fragmet #1(A:0:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.829 / q_NPA : 0.904
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].
3A2LYS10.8630.9433.71841.91543.705-0.004-0.890-0.8960.002
4A3VAL0-0.017-0.0206.8801.2841.2840.0000.0000.0000.000
5A4LEU00.0080.0159.4901.5931.5930.0000.0000.0000.000
6A5VAL0-0.002-0.00613.232-0.036-0.0360.0000.0000.0000.000
7A6ALA0-0.004-0.00115.6440.8200.8200.0000.0000.0000.000
8A7GLH00.006-0.03719.3150.3530.3530.0000.0000.0000.000
9A8ASP-1-0.822-0.90021.664-11.529-11.5290.0000.0000.0000.000
10A9GLN0-0.016-0.01324.6570.1050.1050.0000.0000.0000.000
11A10SER00.0440.00423.043-0.608-0.6080.0000.0000.0000.000
12A11MET00.0030.02022.256-0.319-0.3190.0000.0000.0000.000
13A12LEU00.0040.00420.633-0.398-0.3980.0000.0000.0000.000
14A13ARG10.8210.89518.29813.20513.2050.0000.0000.0000.000
15A14ASP-1-0.862-0.92117.447-16.297-16.2970.0000.0000.0000.000
16A15ALA00.0240.01217.069-0.900-0.9000.0000.0000.0000.000
17A16MET0-0.001-0.00715.436-0.550-0.5500.0000.0000.0000.000
18A17CYS0-0.010-0.00212.974-1.550-1.5500.0000.0000.0000.000
19A18GLN0-0.042-0.00212.330-1.533-1.5330.0000.0000.0000.000
20A19LEU0-0.009-0.01313.078-0.943-0.9430.0000.0000.0000.000
21A20LEU00.013-0.0059.302-1.569-1.5690.0000.0000.0000.000
22A21THR0-0.027-0.0328.186-3.085-3.0850.0000.0000.0000.000
23A22LEU0-0.046-0.0128.902-0.602-0.6020.0000.0000.0000.000
24A23GLN0-0.044-0.0196.848-0.647-0.6470.0000.0000.0000.000
25A24PRO00.0170.0045.429-2.502-2.5020.0000.0000.0000.000
26A25ASP-1-0.812-0.9101.865-112.225-110.55612.296-6.917-7.047-0.082
27A26VAL0-0.055-0.0141.971-17.329-18.1939.040-3.860-4.317-0.053
28A27GLU-1-0.871-0.9031.921-38.290-37.7562.444-1.065-1.913-0.005
29A28SER0-0.002-0.0143.7066.0176.3020.009-0.103-0.192-0.001
30A29VAL0-0.002-0.0017.198-1.313-1.3130.0000.0000.0000.000
31A30LEU0-0.0030.01110.2091.8061.8060.0000.0000.0000.000
32A31GLN0-0.003-0.01013.6140.7960.7960.0000.0000.0000.000
33A32ALA00.0060.00516.9540.5050.5050.0000.0000.0000.000
34A33LYS10.8140.86819.92312.64912.6490.0000.0000.0000.000
35A34ASN0-0.017-0.01423.2250.4710.4710.0000.0000.0000.000
36A35GLY00.1140.05222.849-0.488-0.4880.0000.0000.0000.000
37A36GLN00.010-0.00123.2140.0180.0180.0000.0000.0000.000
38A37GLU-1-0.804-0.88721.447-12.932-12.9320.0000.0000.0000.000
39A38ALA00.0330.00719.084-0.440-0.4400.0000.0000.0000.000
40A39ILE00.0020.01419.310-0.555-0.5550.0000.0000.0000.000
41A40GLN0-0.041-0.02221.046-0.105-0.1050.0000.0000.0000.000
42A41LEU0-0.010-0.00616.989-0.018-0.0180.0000.0000.0000.000
43A42LEU00.0320.01015.092-0.498-0.4980.0000.0000.0000.000
44A43GLU-1-0.896-0.94717.624-12.192-12.1920.0000.0000.0000.000
45A44LYS10.7440.86618.41913.58713.5870.0000.0000.0000.000
46A45GLU-1-0.901-0.92412.482-19.258-19.2580.0000.0000.0000.000
47A46SER0-0.035-0.01010.1620.0960.0960.0000.0000.0000.000
48A47VAL00.006-0.01310.069-1.436-1.4360.0000.0000.0000.000
49A48ASP-1-0.785-0.8715.543-37.745-37.7450.0000.0000.0000.000
50A49ILE0-0.022-0.0216.4801.6661.6660.0000.0000.0000.000
51A50ALA00.0090.00910.0740.0550.0550.0000.0000.0000.000
52A51ILE00.0060.00011.3830.7140.7140.0000.0000.0000.000
53A52LEU0-0.012-0.01014.9910.7280.7280.0000.0000.0000.000
54A53ASP-1-0.735-0.83118.785-12.660-12.6600.0000.0000.0000.000
55A54VAL0-0.020-0.01622.0160.2170.2170.0000.0000.0000.000
56A55GLU-1-0.925-0.97124.724-9.753-9.7530.0000.0000.0000.000
57A56MET0-0.0170.00421.707-0.453-0.4530.0000.0000.0000.000
58A57PRO00.0200.01827.0230.3190.3190.0000.0000.0000.000
59A58VAL0-0.038-0.02428.068-0.330-0.3300.0000.0000.0000.000
60A59LYS10.8530.92226.30810.56410.5640.0000.0000.0000.000
61A60THR00.025-0.00526.251-0.433-0.4330.0000.0000.0000.000
62A61GLY00.0440.00822.254-0.180-0.1800.0000.0000.0000.000
63A62LEU0-0.021-0.01122.139-0.416-0.4160.0000.0000.0000.000
64A63GLU-1-0.777-0.87224.483-10.509-10.5090.0000.0000.0000.000
65A64VAL0-0.049-0.00219.735-0.047-0.0470.0000.0000.0000.000
66A65LEU0-0.009-0.00319.385-0.370-0.3700.0000.0000.0000.000
67A66GLU-1-0.797-0.87621.160-11.028-11.0280.0000.0000.0000.000
68A67TRP00.0220.01519.786-0.032-0.0320.0000.0000.0000.000
69A68ILE0-0.004-0.00116.789-0.031-0.0310.0000.0000.0000.000
70A69ARG10.7790.88816.52815.88115.8810.0000.0000.0000.000
71A70SER0-0.067-0.06822.3290.1590.1590.0000.0000.0000.000
72A71GLU-1-0.885-0.91622.410-11.012-11.0120.0000.0000.0000.000
73A72LYS10.7980.89221.33711.30211.3020.0000.0000.0000.000
74A73LEU00.0140.02016.761-0.360-0.3600.0000.0000.0000.000
75A74GLU-1-0.958-0.98513.624-18.401-18.4010.0000.0000.0000.000
76A75THR0-0.069-0.02512.238-0.633-0.6330.0000.0000.0000.000
77A76LYS10.8390.93110.76622.17522.1750.0000.0000.0000.000
78A77VAL0-0.034-0.02612.867-0.374-0.3740.0000.0000.0000.000
79A78VAL00.0030.00012.5550.5790.5790.0000.0000.0000.000
80A79VAL00.0060.00315.6710.2290.2290.0000.0000.0000.000
81A80VAL0-0.0040.00517.753-0.058-0.0580.0000.0000.0000.000
82A81THR00.0260.00120.4780.7590.7590.0000.0000.0000.000
83A82THR00.0240.00424.230-0.180-0.1800.0000.0000.0000.000
84A83PHE00.0630.01027.2380.1680.1680.0000.0000.0000.000
85A84LYS10.7610.89830.3719.3979.3970.0000.0000.0000.000
86A85ARG10.8830.92128.43910.62510.6250.0000.0000.0000.000
87A86ALA00.0330.03427.870-0.175-0.1750.0000.0000.0000.000
88A87GLY00.0330.01528.625-0.203-0.2030.0000.0000.0000.000
89A88TYR00.010-0.00428.1000.2350.2350.0000.0000.0000.000
90A89PHE0-0.0020.01023.714-0.215-0.2150.0000.0000.0000.000
91A90GLU-1-0.793-0.87726.837-9.737-9.7370.0000.0000.0000.000
92A91ARG10.7920.85127.84110.39610.3960.0000.0000.0000.000
93A92ALA00.0270.00923.267-0.216-0.2160.0000.0000.0000.000
94A93VAL0-0.015-0.00423.728-0.481-0.4810.0000.0000.0000.000
95A94LYS10.7830.88025.3589.3609.3600.0000.0000.0000.000
96A95ALA0-0.0080.00924.1410.0270.0270.0000.0000.0000.000
97A96GLY00.0270.00922.355-0.516-0.5160.0000.0000.0000.000
98A97VAL0-0.035-0.00118.729-0.786-0.7860.0000.0000.0000.000
99A98ASP-1-0.766-0.86914.999-18.015-18.0150.0000.0000.0000.000
100A99ALA00.017-0.00215.759-0.163-0.1630.0000.0000.0000.000
101A100TYR0-0.035-0.02917.5210.2820.2820.0000.0000.0000.000
102A101VAL00.0300.01317.2250.4990.4990.0000.0000.0000.000
103A102LEU00.001-0.01020.5140.3870.3870.0000.0000.0000.000
104A103LYS10.7930.86920.43412.20512.2050.0000.0000.0000.000
105A104GLU-1-0.992-0.97820.777-13.569-13.5690.0000.0000.0000.000
106A105ARG10.8530.90216.15117.58617.5860.0000.0000.0000.000
107A106SER0-0.019-0.03017.216-0.543-0.5430.0000.0000.0000.000
108A107ILE00.0310.00111.339-0.354-0.3540.0000.0000.0000.000
109A108ALA00.0210.01412.557-1.864-1.8640.0000.0000.0000.000
110A109ASP-1-0.815-0.87712.788-18.204-18.2040.0000.0000.0000.000
111A110LEU0-0.020-0.00412.503-0.480-0.4800.0000.0000.0000.000
112A111MET00.0290.0055.812-0.402-0.4020.0000.0000.0000.000
113A112GLN0-0.0100.0138.919-2.735-2.7350.0000.0000.0000.000
114A113THR00.006-0.02911.163-0.112-0.1120.0000.0000.0000.000
115A114LEU0-0.032-0.0267.6440.4010.4010.0000.0000.0000.000
116A115HIS0-0.029-0.0123.4821.8562.1010.000-0.058-0.1860.000
117A116THR0-0.0030.0037.9381.3681.3680.0000.0000.0000.000
118A117VAL0-0.051-0.02710.2761.3701.3700.0000.0000.0000.000
119A118LEU00.0280.0135.0751.0771.0770.0000.0000.0000.000
120A119GLU-1-0.863-0.8879.072-25.426-25.4260.0000.0000.0000.000
121A120GLY0-0.028-0.01711.0902.1142.1140.0000.0000.0000.000
122A121ARG10.7280.82611.93824.06724.0670.0000.0000.0000.000
123A122LYS10.8500.93215.34015.07215.0720.0000.0000.0000.000
124A123GLU-1-0.779-0.85615.331-19.024-19.0240.0000.0000.0000.000
125A124TYR0-0.041-0.03218.0540.1990.1990.0000.0000.0000.000
126A125SER00.015-0.00921.525-0.051-0.0510.0000.0000.0000.000
127A126PRO00.0200.01821.9170.6080.6080.0000.0000.0000.000
128A127GLU-1-0.771-0.87323.687-12.772-12.7720.0000.0000.0000.000
129A128LEU0-0.050-0.03223.7920.5450.5450.0000.0000.0000.000
130A129MET0-0.055-0.01925.1800.4340.4340.0000.0000.0000.000
131A130GLU-1-0.907-0.94828.317-9.537-9.5370.0000.0000.0000.000
132A131MET0-0.0050.00730.3430.5320.5320.0000.0000.0000.000
133A132VAL0-0.059-0.04329.8330.3700.3700.0000.0000.0000.000
134A133MET0-0.055-0.01132.4100.2410.2410.0000.0000.0000.000
135A134THR0-0.036-0.02434.2690.3450.3450.0000.0000.0000.000
136A135ARG10.8570.94333.6099.4289.4280.0000.0000.0000.000
137A136PRO00.0040.00937.3590.0040.0040.0000.0000.0000.000
138A137ASN00.032-0.00540.184-0.141-0.1410.0000.0000.0000.000
139A138PRO00.0050.02140.3070.1940.1940.0000.0000.0000.000
140A139LEU0-0.049-0.01942.1780.1940.1940.0000.0000.0000.000
141A140THR00.022-0.02645.4270.0770.0770.0000.0000.0000.000
142A141GLU-1-0.887-0.95848.433-6.182-6.1820.0000.0000.0000.000
143A142GLN00.0320.01550.287-0.052-0.0520.0000.0000.0000.000
144A143GLU-1-0.800-0.85646.903-6.694-6.6940.0000.0000.0000.000
145A144ILE00.0340.01544.812-0.102-0.1020.0000.0000.0000.000
146A145ALA0-0.012-0.00446.841-0.066-0.0660.0000.0000.0000.000
147A146VAL00.005-0.00447.8830.0080.0080.0000.0000.0000.000
148A147LEU00.0090.00541.957-0.032-0.0320.0000.0000.0000.000
149A148LYS10.9020.95245.0346.8106.8100.0000.0000.0000.000
150A149GLY0-0.0120.00446.7650.0790.0790.0000.0000.0000.000
151A150ILE0-0.027-0.02943.409-0.006-0.0060.0000.0000.0000.000
152A151ALA0-0.017-0.01142.600-0.061-0.0610.0000.0000.0000.000
153A152ARG10.8220.91843.5156.1566.1560.0000.0000.0000.000
154A153GLY00.0150.00845.7880.1170.1170.0000.0000.0000.000
155A154LEU0-0.0510.00846.9250.0710.0710.0000.0000.0000.000
156A155SER0-0.007-0.03849.131-0.101-0.1010.0000.0000.0000.000
157A156ASN00.046-0.01250.235-0.080-0.0800.0000.0000.0000.000
158A157GLN0-0.0290.00052.7100.0300.0300.0000.0000.0000.000
159A158GLU-1-0.754-0.84353.499-5.908-5.9080.0000.0000.0000.000
160A159ILE0-0.015-0.00549.4440.0250.0250.0000.0000.0000.000
161A160ALA0-0.029-0.01653.9260.0320.0320.0000.0000.0000.000
162A161ASP-1-0.832-0.90856.994-5.257-5.2570.0000.0000.0000.000
163A162GLN0-0.001-0.00254.522-0.028-0.0280.0000.0000.0000.000
164A163LEU0-0.034-0.01452.874-0.015-0.0150.0000.0000.0000.000
165A164TYR0-0.0260.00257.2810.0810.0810.0000.0000.0000.000
166A165LEU0-0.0220.00256.0210.0330.0330.0000.0000.0000.000
167A166SER00.0520.03259.784-0.006-0.0060.0000.0000.0000.000
168A167ASN00.042-0.00356.302-0.175-0.1750.0000.0000.0000.000
169A168GLY00.0160.00155.747-0.110-0.1100.0000.0000.0000.000
170A169THR00.0100.00155.607-0.079-0.0790.0000.0000.0000.000
171A170ILE00.0360.02951.692-0.118-0.1180.0000.0000.0000.000
172A171ARG10.8580.92451.4655.7385.7380.0000.0000.0000.000
173A172ASN00.0290.02950.738-0.181-0.1810.0000.0000.0000.000
174A173TYR00.0170.00550.483-0.098-0.0980.0000.0000.0000.000
175A174VAL00.004-0.00646.166-0.141-0.1410.0000.0000.0000.000
176A175THR0-0.019-0.01546.081-0.177-0.1770.0000.0000.0000.000
177A176ASN0-0.028-0.01346.045-0.152-0.1520.0000.0000.0000.000
178A177ILE0-0.009-0.00443.225-0.145-0.1450.0000.0000.0000.000
179A178LEU0-0.010-0.01241.519-0.157-0.1570.0000.0000.0000.000
180A179SER0-0.0100.00840.867-0.262-0.2620.0000.0000.0000.000
181A180LYS10.7900.86841.1606.6936.6930.0000.0000.0000.000
182A181LEU0-0.055-0.02038.168-0.129-0.1290.0000.0000.0000.000
183A182ASP-1-0.855-0.93134.484-9.271-9.2710.0000.0000.0000.000
184A183ALA0-0.0390.00136.469-0.203-0.2030.0000.0000.0000.000
185A184GLY00.0380.01637.2980.1980.1980.0000.0000.0000.000
186A185ASN0-0.032-0.03037.4940.2640.2640.0000.0000.0000.000
187A186ARG10.8960.92440.4146.6386.6380.0000.0000.0000.000
188A187THR00.0390.01538.5080.0770.0770.0000.0000.0000.000
189A188GLU-1-0.749-0.85533.735-9.202-9.2020.0000.0000.0000.000
190A189ALA00.0270.01736.901-0.131-0.1310.0000.0000.0000.000
191A190ALA00.0070.00139.242-0.016-0.0160.0000.0000.0000.000
192A191ASN00.0070.00034.5350.1090.1090.0000.0000.0000.000
193A192ILE00.0230.01833.823-0.097-0.0970.0000.0000.0000.000
194A193ALA00.0210.01735.461-0.101-0.1010.0000.0000.0000.000
195A194LYS10.8510.91234.2268.9308.9300.0000.0000.0000.000
196A195GLU-1-0.855-0.92031.672-9.668-9.6680.0000.0000.0000.000
197A196SER0-0.040-0.02233.420-0.258-0.2580.0000.0000.0000.000
198A197GLY00.0150.02134.9080.0970.0970.0000.0000.0000.000
199A198TRP0-0.012-0.01037.4120.2350.2350.0000.0000.0000.000
200A199LEU0-0.059-0.01940.2460.4290.4290.0000.0000.0000.000