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: QV5KY

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 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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2190015.050071
FMO2-HF: Nuclear repulsion 2110708.689
FMO2-HF: Total energy -79306.361071
FMO2-MP2: Total energy -79535.193996


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.
-237.299-226.0529.212-9.814-10.648-0.109
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 : 0.839 / q_NPA : 0.917
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].
3A2LYS10.9290.9783.65136.31338.485-0.008-1.126-1.0390.002
4A3VAL00.007-0.0026.8552.0722.0720.0000.0000.0000.000
5A4LEU00.0320.0329.4561.4961.4960.0000.0000.0000.000
6A5VAL0-0.002-0.00713.214-0.047-0.0470.0000.0000.0000.000
7A6ALA0-0.028-0.01715.5900.7720.7720.0000.0000.0000.000
8A7GLH0-0.076-0.11419.0860.3700.3700.0000.0000.0000.000
9A8ASP-1-0.808-0.90221.640-11.257-11.2570.0000.0000.0000.000
10A9GLN00.0230.01924.9620.1940.1940.0000.0000.0000.000
11A10SER0-0.015-0.02923.652-0.573-0.5730.0000.0000.0000.000
12A11MET00.0340.03322.800-0.284-0.2840.0000.0000.0000.000
13A12LEU00.0400.01921.016-0.421-0.4210.0000.0000.0000.000
14A13ARG10.8190.89818.82712.75012.7500.0000.0000.0000.000
15A14ASP-1-0.905-0.95218.002-15.376-15.3760.0000.0000.0000.000
16A15ALA0-0.005-0.00117.813-0.835-0.8350.0000.0000.0000.000
17A16MET0-0.007-0.01015.666-0.526-0.5260.0000.0000.0000.000
18A17CYS0-0.037-0.01113.390-1.496-1.4960.0000.0000.0000.000
19A18GLN00.0220.02312.916-1.436-1.4360.0000.0000.0000.000
20A19LEU0-0.030-0.02813.655-0.844-0.8440.0000.0000.0000.000
21A20LEU00.006-0.0179.702-1.334-1.3340.0000.0000.0000.000
22A21THR0-0.033-0.0228.633-2.853-2.8530.0000.0000.0000.000
23A22LEU0-0.054-0.0238.861-1.074-1.0740.0000.0000.0000.000
24A23GLN0-0.028-0.0097.499-1.833-1.8330.0000.0000.0000.000
25A24PRO00.0070.0016.060-1.624-1.6240.0000.0000.0000.000
26A25ASP-1-0.846-0.9402.020-104.632-100.4595.963-4.917-5.219-0.067
27A26VAL0-0.064-0.0262.224-18.342-15.3582.931-3.151-2.763-0.042
28A27GLU-1-0.946-0.9482.403-40.420-38.9140.328-0.566-1.269-0.002
29A28SER00.005-0.0174.1806.1636.3130.000-0.037-0.1140.000
30A29VAL00.0030.0057.698-1.388-1.3880.0000.0000.0000.000
31A30LEU0-0.0050.01310.6541.7841.7840.0000.0000.0000.000
32A31GLN00.0540.01113.9110.6620.6620.0000.0000.0000.000
33A32ALA0-0.0030.01217.1410.6150.6150.0000.0000.0000.000
34A33LYS10.8870.92920.17711.97711.9770.0000.0000.0000.000
35A34ASN00.010-0.00723.3670.3160.3160.0000.0000.0000.000
36A35GLY00.1110.04622.888-0.517-0.5170.0000.0000.0000.000
37A36GLN0-0.031-0.02123.3080.0150.0150.0000.0000.0000.000
38A37GLU-1-0.855-0.92521.663-12.930-12.9300.0000.0000.0000.000
39A38ALA00.037-0.00118.991-0.466-0.4660.0000.0000.0000.000
40A39ILE0-0.0010.01619.415-0.525-0.5250.0000.0000.0000.000
41A40GLN00.0040.00521.114-0.046-0.0460.0000.0000.0000.000
42A41LEU0-0.048-0.03917.096-0.095-0.0950.0000.0000.0000.000
43A42LEU0-0.005-0.00315.235-0.644-0.6440.0000.0000.0000.000
44A43GLU-1-0.922-0.95417.553-12.458-12.4580.0000.0000.0000.000
45A44LYS10.8220.91318.64613.70313.7030.0000.0000.0000.000
46A45GLU-1-0.928-0.94912.809-19.135-19.1350.0000.0000.0000.000
47A46SER0-0.059-0.01710.207-0.421-0.4210.0000.0000.0000.000
48A47VAL00.006-0.01410.164-1.044-1.0440.0000.0000.0000.000
49A48ASP-1-0.817-0.8945.575-37.727-37.7270.0000.0000.0000.000
50A49ILE0-0.027-0.0296.3401.5851.5850.0000.0000.0000.000
51A50ALA00.0030.01110.075-0.044-0.0440.0000.0000.0000.000
52A51ILE0-0.029-0.02711.2890.5710.5710.0000.0000.0000.000
53A52LEU00.005-0.01014.9720.7290.7290.0000.0000.0000.000
54A53ASP-1-0.756-0.82418.643-12.564-12.5640.0000.0000.0000.000
55A54VAL00.011-0.01321.7980.2150.2150.0000.0000.0000.000
56A55GLU-1-1.031-1.02624.285-9.858-9.8580.0000.0000.0000.000
57A56MET0-0.0390.01221.773-0.412-0.4120.0000.0000.0000.000
58A57PRO00.0320.01826.8770.2880.2880.0000.0000.0000.000
59A58VAL0-0.046-0.02928.070-0.320-0.3200.0000.0000.0000.000
60A59LYS10.8850.94726.14710.72310.7230.0000.0000.0000.000
61A60THR00.0490.03126.178-0.445-0.4450.0000.0000.0000.000
62A61GLY00.0460.01022.325-0.277-0.2770.0000.0000.0000.000
63A62LEU0-0.003-0.00922.360-0.377-0.3770.0000.0000.0000.000
64A63GLU-1-0.857-0.92324.693-10.361-10.3610.0000.0000.0000.000
65A64VAL0-0.0200.00019.920-0.041-0.0410.0000.0000.0000.000
66A65LEU0-0.020-0.00619.449-0.317-0.3170.0000.0000.0000.000
67A66GLU-1-0.793-0.88921.356-10.932-10.9320.0000.0000.0000.000
68A67TRP00.0000.02319.901-0.154-0.1540.0000.0000.0000.000
69A68ILE00.0480.00816.9570.0630.0630.0000.0000.0000.000
70A69ARG10.7420.86416.37416.12316.1230.0000.0000.0000.000
71A70SER0-0.111-0.05121.7900.3050.3050.0000.0000.0000.000
72A71GLU-1-0.927-0.96121.903-11.180-11.1800.0000.0000.0000.000
73A72LYS10.8350.91420.88311.64411.6440.0000.0000.0000.000
74A73LEU00.0340.02516.339-0.306-0.3060.0000.0000.0000.000
75A74GLU-1-0.980-0.98813.085-18.593-18.5930.0000.0000.0000.000
76A75THR0-0.0360.00212.228-1.040-1.0400.0000.0000.0000.000
77A76LYS10.9460.97810.19723.48623.4860.0000.0000.0000.000
78A77VAL0-0.011-0.01312.918-0.293-0.2930.0000.0000.0000.000
79A78VAL0-0.003-0.00112.9310.5710.5710.0000.0000.0000.000
80A79VAL00.0160.00915.7600.2140.2140.0000.0000.0000.000
81A80VAL0-0.017-0.00717.8220.0920.0920.0000.0000.0000.000
82A81THR00.0560.02220.4420.6780.6780.0000.0000.0000.000
83A82THR00.0190.01324.198-0.224-0.2240.0000.0000.0000.000
84A83PHE00.0910.01427.0310.0840.0840.0000.0000.0000.000
85A84LYS10.8360.94229.9639.4189.4180.0000.0000.0000.000
86A85ARG10.9300.97128.33410.54710.5470.0000.0000.0000.000
87A86ALA00.0260.01127.993-0.279-0.2790.0000.0000.0000.000
88A87GLY00.010-0.00428.775-0.158-0.1580.0000.0000.0000.000
89A88TYR00.0070.00727.8060.2090.2090.0000.0000.0000.000
90A89PHE00.0200.01624.067-0.238-0.2380.0000.0000.0000.000
91A90GLU-1-0.893-0.94926.714-9.753-9.7530.0000.0000.0000.000
92A91ARG10.7560.84627.87710.27910.2790.0000.0000.0000.000
93A92ALA00.0250.00623.078-0.194-0.1940.0000.0000.0000.000
94A93VAL0-0.013-0.01023.681-0.485-0.4850.0000.0000.0000.000
95A94LYS10.9030.95825.2989.3809.3800.0000.0000.0000.000
96A95ALA00.0120.02923.9950.1310.1310.0000.0000.0000.000
97A96GLY00.006-0.00321.881-0.502-0.5020.0000.0000.0000.000
98A97VAL0-0.055-0.00818.729-0.847-0.8470.0000.0000.0000.000
99A98ASP-1-0.818-0.90915.081-18.195-18.1950.0000.0000.0000.000
100A99ALA0-0.001-0.01115.865-0.120-0.1200.0000.0000.0000.000
101A100TYR0-0.034-0.01117.6390.1680.1680.0000.0000.0000.000
102A101VAL00.0290.01017.1530.3500.3500.0000.0000.0000.000
103A102LEU00.003-0.01220.4340.3370.3370.0000.0000.0000.000
104A103LYS10.8540.92120.44311.83811.8380.0000.0000.0000.000
105A104GLU-1-0.992-0.97521.000-13.587-13.5870.0000.0000.0000.000
106A105ARG10.9300.95615.91817.66217.6620.0000.0000.0000.000
107A106SER00.0380.02817.901-0.539-0.5390.0000.0000.0000.000
108A107ILE00.0470.01412.091-0.407-0.4070.0000.0000.0000.000
109A108ALA00.000-0.00112.997-1.595-1.5950.0000.0000.0000.000
110A109ASP-1-0.867-0.93413.041-18.196-18.1960.0000.0000.0000.000
111A110LEU0-0.059-0.02112.440-0.474-0.4740.0000.0000.0000.000
112A111MET00.023-0.0026.605-0.107-0.1070.0000.0000.0000.000
113A112GLN0-0.0180.0069.108-2.601-2.6010.0000.0000.0000.000
114A113THR00.0330.01411.275-0.011-0.0110.0000.0000.0000.000
115A114LEU0-0.032-0.0317.6030.2490.2490.0000.0000.0000.000
116A115HIS0-0.0060.0014.038-1.087-0.961-0.001-0.009-0.1170.000
117A116THR0-0.0060.0157.9331.0671.0670.0000.0000.0000.000
118A117VAL0-0.029-0.02110.2090.9210.9210.0000.0000.0000.000
119A118LEU0-0.008-0.0104.4180.7300.866-0.001-0.008-0.1270.000
120A119GLU-1-0.991-0.9838.738-27.109-27.1090.0000.0000.0000.000
121A120GLY0-0.072-0.03310.7352.0002.0000.0000.0000.0000.000
122A121ARG10.8670.94512.48223.50523.5050.0000.0000.0000.000
123A122LYS10.9320.97815.14814.75114.7510.0000.0000.0000.000
124A123GLU-1-0.834-0.92415.270-19.113-19.1130.0000.0000.0000.000
125A124TYR0-0.002-0.00818.0690.1110.1110.0000.0000.0000.000
126A125SER00.0290.01020.7750.0690.0690.0000.0000.0000.000
127A126PRO00.0440.01421.9120.5590.5590.0000.0000.0000.000
128A127GLU-1-0.807-0.90723.968-12.457-12.4570.0000.0000.0000.000
129A128LEU0-0.059-0.03223.5300.5640.5640.0000.0000.0000.000
130A129MET0-0.057-0.02225.4460.5120.5120.0000.0000.0000.000
131A130GLU-1-0.891-0.93728.301-9.514-9.5140.0000.0000.0000.000
132A131MET00.0140.01930.4400.5400.5400.0000.0000.0000.000
133A132VAL0-0.095-0.06129.9180.4040.4040.0000.0000.0000.000
134A133MET0-0.043-0.01432.4730.2800.2800.0000.0000.0000.000
135A134THR0-0.030-0.00934.3270.3380.3380.0000.0000.0000.000
136A135ARG10.8830.94733.1159.4679.4670.0000.0000.0000.000
137A136PRO00.0120.01937.7080.0060.0060.0000.0000.0000.000
138A137ASN00.025-0.01340.050-0.151-0.1510.0000.0000.0000.000
139A138PRO0-0.0050.02240.0810.1830.1830.0000.0000.0000.000
140A139LEU0-0.008-0.00442.1070.1790.1790.0000.0000.0000.000
141A140THR00.0310.01545.1430.0890.0890.0000.0000.0000.000
142A141GLU-1-0.899-0.96048.298-6.200-6.2000.0000.0000.0000.000
143A142GLN00.0230.00050.132-0.065-0.0650.0000.0000.0000.000
144A143GLU-1-0.826-0.89846.840-6.714-6.7140.0000.0000.0000.000
145A144ILE00.0490.02444.823-0.070-0.0700.0000.0000.0000.000
146A145ALA0-0.025-0.00646.882-0.051-0.0510.0000.0000.0000.000
147A146VAL00.0260.00247.7970.0090.0090.0000.0000.0000.000
148A147LEU0-0.008-0.01342.026-0.028-0.0280.0000.0000.0000.000
149A148LYS10.9280.97744.8276.7266.7260.0000.0000.0000.000
150A149GLY0-0.014-0.00446.2790.0060.0060.0000.0000.0000.000
151A150ILE0-0.045-0.02743.4880.0030.0030.0000.0000.0000.000
152A151ALA0-0.0060.00042.514-0.058-0.0580.0000.0000.0000.000
153A152ARG10.8700.94343.6766.1646.1640.0000.0000.0000.000
154A153GLY00.0020.00045.8700.1160.1160.0000.0000.0000.000
155A154LEU0-0.068-0.00247.0030.0880.0880.0000.0000.0000.000
156A155SER00.004-0.02249.292-0.084-0.0840.0000.0000.0000.000
157A156ASN00.052-0.01950.573-0.062-0.0620.0000.0000.0000.000
158A157GLN00.0170.00252.8380.0180.0180.0000.0000.0000.000
159A158GLU-1-0.793-0.86752.875-5.899-5.8990.0000.0000.0000.000
160A159ILE0-0.0010.00249.5220.0350.0350.0000.0000.0000.000
161A160ALA0-0.056-0.03954.0300.0440.0440.0000.0000.0000.000
162A161ASP-1-0.838-0.92256.884-5.249-5.2490.0000.0000.0000.000
163A162GLN0-0.049-0.02454.435-0.039-0.0390.0000.0000.0000.000
164A163LEU0-0.037-0.02252.947-0.003-0.0030.0000.0000.0000.000
165A164TYR0-0.0280.00757.4890.0790.0790.0000.0000.0000.000
166A165LEU0-0.021-0.00256.0810.0360.0360.0000.0000.0000.000
167A166SER00.0440.03559.817-0.025-0.0250.0000.0000.0000.000
168A167ASN00.0640.01356.408-0.177-0.1770.0000.0000.0000.000
169A168GLY00.019-0.00755.879-0.110-0.1100.0000.0000.0000.000
170A169THR00.0040.00155.848-0.066-0.0660.0000.0000.0000.000
171A170ILE00.0090.03051.887-0.121-0.1210.0000.0000.0000.000
172A171ARG10.8870.93951.4545.7855.7850.0000.0000.0000.000
173A172ASN00.0340.02450.756-0.161-0.1610.0000.0000.0000.000
174A173TYR00.0180.00650.355-0.092-0.0920.0000.0000.0000.000
175A174VAL0-0.017-0.00945.981-0.145-0.1450.0000.0000.0000.000
176A175THR0-0.0040.00146.090-0.179-0.1790.0000.0000.0000.000
177A176ASN0-0.001-0.00946.005-0.154-0.1540.0000.0000.0000.000
178A177ILE0-0.026-0.00643.083-0.140-0.1400.0000.0000.0000.000
179A178LEU0-0.022-0.02741.807-0.160-0.1600.0000.0000.0000.000
180A179SER0-0.0300.00240.944-0.256-0.2560.0000.0000.0000.000
181A180LYS10.7980.87241.1346.7336.7330.0000.0000.0000.000
182A181LEU0-0.059-0.01938.047-0.143-0.1430.0000.0000.0000.000
183A182ASP-1-0.941-0.95235.172-9.157-9.1570.0000.0000.0000.000
184A183ALA0-0.030-0.02636.357-0.232-0.2320.0000.0000.0000.000
185A184GLY00.0040.00737.3120.1890.1890.0000.0000.0000.000
186A185ASN0-0.011-0.01437.4990.2600.2600.0000.0000.0000.000
187A186ARG10.9540.96640.4776.6366.6360.0000.0000.0000.000
188A187THR00.0320.01137.9490.0740.0740.0000.0000.0000.000
189A188GLU-1-0.807-0.90634.126-9.096-9.0960.0000.0000.0000.000
190A189ALA00.0200.01437.013-0.118-0.1180.0000.0000.0000.000
191A190ALA00.0180.00439.172-0.032-0.0320.0000.0000.0000.000
192A191ASN00.007-0.00134.7380.1060.1060.0000.0000.0000.000
193A192ILE00.0350.02233.705-0.144-0.1440.0000.0000.0000.000
194A193ALA00.0270.03035.419-0.073-0.0730.0000.0000.0000.000
195A194LYS10.9020.96034.7578.8488.8480.0000.0000.0000.000
196A195GLU-1-0.901-0.97332.267-9.589-9.5890.0000.0000.0000.000
197A196SER0-0.077-0.03733.654-0.253-0.2530.0000.0000.0000.000
198A197GLY00.0080.02234.9150.0070.0070.0000.0000.0000.000
199A198TRP0-0.016-0.01736.5320.2020.2020.0000.0000.0000.000
200A199LEU0-0.036-0.01540.4600.3260.3260.0000.0000.0000.000