FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 7676K

Calculation Name: 3HP4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3HP4

Chain ID: A

ChEMBL ID:

UniProt ID: Q1G1I7

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 183
LigandCharge MIR=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2030553.754235
FMO2-HF: Nuclear repulsion 1957444.229366
FMO2-HF: Total energy -73109.524869
FMO2-MP2: Total energy -73319.597367


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:2:ASP)


Summations of interaction energy for fragment #1(A:2:ASP)
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.
70.95366.78931.466-15.396-11.9030.073
Interaction energy analysis for fragmet #1(A:2:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.879 / q_NPA : -0.914
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].
3A4THR00.015-0.0091.612-50.023-55.14823.255-11.045-7.0850.099
4A5ILE0-0.048-0.0223.741-8.693-8.2610.025-0.191-0.2660.003
5A6LEU00.0000.0017.415-2.866-2.8660.0000.0000.0000.000
6A7ILE0-0.010-0.00410.258-2.107-2.1070.0000.0000.0000.000
7A8LEU00.0080.00213.268-0.946-0.9460.0000.0000.0000.000
8A9GLY00.0730.01116.248-0.645-0.6450.0000.0000.0000.000
9A10ASP-1-0.800-0.88919.57212.89912.8990.0000.0000.0000.000
10A11MIR-1-0.758-0.85622.37111.83311.8330.0000.0000.0000.000
11A12LEU0-0.088-0.03523.533-0.049-0.0490.0000.0000.0000.000
12A13SER00.0320.00218.2090.4010.4010.0000.0000.0000.000
13A14ALA0-0.042-0.01219.3030.7590.7590.0000.0000.0000.000
14A15ALA0-0.021-0.00321.552-0.339-0.3390.0000.0000.0000.000
15A16TYR0-0.0020.00523.516-0.409-0.4090.0000.0000.0000.000
16A17GLY00.0000.00926.925-0.134-0.1340.0000.0000.0000.000
17A18LEU0-0.082-0.02925.969-0.337-0.3370.0000.0000.0000.000
18A19GLN00.0060.00625.781-0.208-0.2080.0000.0000.0000.000
19A20GLN00.0270.01018.279-0.257-0.2570.0000.0000.0000.000
20A21GLU-1-0.900-0.97820.79013.99113.9910.0000.0000.0000.000
21A22GLU-1-0.863-0.92022.20511.27811.2780.0000.0000.0000.000
22A23GLY00.0160.00721.576-0.160-0.1600.0000.0000.0000.000
23A24TRP0-0.006-0.03115.7900.9670.9670.0000.0000.0000.000
24A25VAL00.0000.00414.3950.4090.4090.0000.0000.0000.000
25A26LYS10.8130.91115.206-14.917-14.9170.0000.0000.0000.000
26A27LEU0-0.023-0.01516.7370.4070.4070.0000.0000.0000.000
27A28LEU0-0.055-0.01513.578-0.389-0.3890.0000.0000.0000.000
28A29GLN00.013-0.0069.0991.3871.3870.0000.0000.0000.000
29A30ASP-1-0.794-0.88213.40816.78416.7840.0000.0000.0000.000
30A31LYS10.7560.86715.592-16.394-16.3940.0000.0000.0000.000
31A32TYR00.0620.00010.179-0.232-0.2320.0000.0000.0000.000
32A33ASP-1-0.828-0.90011.29025.16825.1680.0000.0000.0000.000
33A34ALA0-0.071-0.04012.758-0.653-0.6530.0000.0000.0000.000
34A35GLU-1-0.853-0.88713.49516.11616.1160.0000.0000.0000.000
35A36GLN0-0.109-0.04811.265-0.468-0.4680.0000.0000.0000.000
36A37SER0-0.0140.0058.1521.5271.5270.0000.0000.0000.000
37A38ASP-1-0.818-0.9001.94035.60833.8956.955-2.969-2.273-0.039
38A39ILE0-0.057-0.0174.0477.6807.9070.001-0.051-0.1760.000
39A40VAL00.0010.0125.172-5.137-5.056-0.001-0.001-0.0780.000
40A41LEU0-0.036-0.0186.8292.0192.0190.0000.0000.0000.000
41A42ILE00.0150.0207.243-3.118-3.1180.0000.0000.0000.000
42A43ASN0-0.015-0.00910.395-1.066-1.0660.0000.0000.0000.000
43A44ALA00.0410.02814.019-0.508-0.5080.0000.0000.0000.000
44A45SER0-0.014-0.01516.125-1.118-1.1180.0000.0000.0000.000
45A46ILE0-0.052-0.01918.987-0.293-0.2930.0000.0000.0000.000
46A47SER00.023-0.00822.654-0.228-0.2280.0000.0000.0000.000
47A48GLY0-0.003-0.00225.981-0.216-0.2160.0000.0000.0000.000
48A49GLU-1-0.831-0.88922.01913.37213.3720.0000.0000.0000.000
49A50THR0-0.069-0.04925.425-0.360-0.3600.0000.0000.0000.000
50A51SER00.035-0.01523.9030.3480.3480.0000.0000.0000.000
51A52GLY00.010-0.00324.4540.2800.2800.0000.0000.0000.000
52A53GLY0-0.070-0.02325.649-0.127-0.1270.0000.0000.0000.000
53A54ALA00.1160.05520.2190.2190.2190.0000.0000.0000.000
54A55LEU0-0.038-0.01220.8570.5520.5520.0000.0000.0000.000
55A56ARG10.8220.90022.724-11.610-11.6100.0000.0000.0000.000
56A57ARG10.8160.89318.835-16.222-16.2220.0000.0000.0000.000
57A58LEU00.0090.00914.8750.3280.3280.0000.0000.0000.000
58A59ASP-1-0.813-0.88116.18717.26517.2650.0000.0000.0000.000
59A60ALA00.0430.02216.3040.8690.8690.0000.0000.0000.000
60A61LEU0-0.033-0.01514.1070.6110.6110.0000.0000.0000.000
61A62LEU0-0.022-0.01611.7771.9661.9660.0000.0000.0000.000
62A63GLU-1-0.948-0.97511.41320.52320.5230.0000.0000.0000.000
63A64GLN0-0.078-0.03812.7190.4970.4970.0000.0000.0000.000
64A65TYR0-0.061-0.0488.645-0.558-0.5580.0000.0000.0000.000
65A66GLU-1-0.939-0.9487.29736.70336.7030.0000.0000.0000.000
66A67PRO0-0.057-0.0025.8155.7225.7220.0000.0000.0000.000
67A68THR00.0760.0062.702-2.750-0.9831.232-1.120-1.8790.010
68A69HIS0-0.0140.0165.308-4.046-3.879-0.001-0.019-0.1460.000
69A70VAL0-0.006-0.0047.9600.2080.2080.0000.0000.0000.000
70A71LEU0-0.016-0.00611.222-1.382-1.3820.0000.0000.0000.000
71A72ILE00.0010.00313.761-0.669-0.6690.0000.0000.0000.000
72A73GLH0-0.012-0.03817.228-0.440-0.4400.0000.0000.0000.000
73A74LEU0-0.0050.00620.034-0.419-0.4190.0000.0000.0000.000
74A75GLY00.0730.02422.815-0.137-0.1370.0000.0000.0000.000
75A76ALA00.0130.01726.132-0.566-0.5660.0000.0000.0000.000
76A77ASN0-0.027-0.03326.829-0.886-0.8860.0000.0000.0000.000
77A78ASP-1-0.764-0.87727.72511.15511.1550.0000.0000.0000.000
78A79GLY00.0160.00830.442-0.372-0.3720.0000.0000.0000.000
79A80LEU00.020-0.00131.242-0.420-0.4200.0000.0000.0000.000
80A81ARG10.9010.96831.056-10.324-10.3240.0000.0000.0000.000
81A82GLY00.0370.03235.276-0.197-0.1970.0000.0000.0000.000
82A83PHE0-0.055-0.02031.529-0.183-0.1830.0000.0000.0000.000
83A84PRO00.014-0.00134.6740.0560.0560.0000.0000.0000.000
84A85VAL00.0690.04631.6730.2280.2280.0000.0000.0000.000
85A86LYS11.0041.01131.388-8.653-8.6530.0000.0000.0000.000
86A87LYS10.8760.95029.537-10.512-10.5120.0000.0000.0000.000
87A88MET00.0030.02527.3180.2800.2800.0000.0000.0000.000
88A89GLN00.0470.01626.9970.2710.2710.0000.0000.0000.000
89A90THR0-0.052-0.03226.6660.3320.3320.0000.0000.0000.000
90A91ASN0-0.045-0.02725.6620.1710.1710.0000.0000.0000.000
91A92LEU00.0570.02622.2380.5410.5410.0000.0000.0000.000
92A93THR00.0250.00821.6770.7440.7440.0000.0000.0000.000
93A94ALA0-0.053-0.02322.1780.4640.4640.0000.0000.0000.000
94A95LEU0-0.007-0.00418.9120.4710.4710.0000.0000.0000.000
95A96VAL00.0300.02317.5611.1601.1600.0000.0000.0000.000
96A97LYS10.8940.94617.366-12.477-12.4770.0000.0000.0000.000
97A98LYS10.7990.88018.063-15.184-15.1840.0000.0000.0000.000
98A99SER00.0310.00213.5210.9270.9270.0000.0000.0000.000
99A100GLN0-0.018-0.02413.4590.7000.7000.0000.0000.0000.000
100A101ALA0-0.055-0.02114.8720.4810.4810.0000.0000.0000.000
101A102ALA0-0.022-0.00112.174-0.246-0.2460.0000.0000.0000.000
102A103ASN0-0.055-0.03210.1350.9750.9750.0000.0000.0000.000
103A104ALA00.0460.0509.3001.8321.8320.0000.0000.0000.000
104A105MET00.0090.0179.273-4.592-4.5920.0000.0000.0000.000
105A106THR0-0.040-0.03610.7680.7390.7390.0000.0000.0000.000
106A107ALA0-0.017-0.00413.530-1.228-1.2280.0000.0000.0000.000
107A108LEU0-0.047-0.02415.5470.1290.1290.0000.0000.0000.000
108A109MET0-0.040-0.00818.758-0.723-0.7230.0000.0000.0000.000
109A110GLU-1-0.827-0.89220.69811.12011.1200.0000.0000.0000.000
110A111ILE0-0.037-0.01023.0640.0080.0080.0000.0000.0000.000
111A112TYR0-0.024-0.03526.686-0.638-0.6380.0000.0000.0000.000
112A113ILE0-0.024-0.00230.2990.0760.0760.0000.0000.0000.000
113A114PRO00.0610.03533.047-0.188-0.1880.0000.0000.0000.000
114A115PRO00.0060.00536.6870.0450.0450.0000.0000.0000.000
115A116ASN0-0.026-0.02438.212-0.273-0.2730.0000.0000.0000.000
116A117TYR0-0.028-0.01536.876-0.250-0.2500.0000.0000.0000.000
117A118GLY00.0220.01840.926-0.075-0.0750.0000.0000.0000.000
118A119PRO00.036-0.00439.6500.2140.2140.0000.0000.0000.000
119A120ARG10.9210.96338.827-7.934-7.9340.0000.0000.0000.000
120A121TYR00.0340.00334.5640.1690.1690.0000.0000.0000.000
121A122SER00.0430.01534.9490.1570.1570.0000.0000.0000.000
122A123LYS10.9680.98334.000-7.941-7.9410.0000.0000.0000.000
123A124MET0-0.068-0.01834.3160.0560.0560.0000.0000.0000.000
124A125PHE00.0330.00728.6940.1950.1950.0000.0000.0000.000
125A126THR00.0220.01329.4110.1670.1670.0000.0000.0000.000
126A127SER0-0.033-0.03529.1200.2740.2740.0000.0000.0000.000
127A128SER0-0.062-0.04529.1470.2270.2270.0000.0000.0000.000
128A129PHE00.0310.00423.6760.1950.1950.0000.0000.0000.000
129A130THR00.0350.01724.8660.4430.4430.0000.0000.0000.000
130A131GLN00.0020.00626.4070.0860.0860.0000.0000.0000.000
131A132ILE0-0.0010.00322.3740.1040.1040.0000.0000.0000.000
132A133SER0-0.0400.00521.5360.3150.3150.0000.0000.0000.000
133A134GLU-1-0.906-0.95923.17211.06311.0630.0000.0000.0000.000
134A135ASP-1-0.955-0.97425.53011.45911.4590.0000.0000.0000.000
135A136THR0-0.108-0.09920.4250.3880.3880.0000.0000.0000.000
136A137ASN0-0.0100.01318.3880.1010.1010.0000.0000.0000.000
137A138ALA00.0130.02317.4570.8430.8430.0000.0000.0000.000
138A139HIS00.0110.01716.024-0.991-0.9910.0000.0000.0000.000
139A140LEU00.0180.01817.9610.4400.4400.0000.0000.0000.000
140A141MET0-0.038-0.01214.3580.3100.3100.0000.0000.0000.000
141A142ASN00.0290.00520.405-0.851-0.8510.0000.0000.0000.000
142A143PHE00.0320.01422.2270.4210.4210.0000.0000.0000.000
143A144PHE00.0720.01820.391-0.549-0.5490.0000.0000.0000.000
144A145MET0-0.018-0.00524.354-0.293-0.2930.0000.0000.0000.000
145A146LEU0-0.064-0.01727.366-0.521-0.5210.0000.0000.0000.000
146A147ASP-1-0.855-0.92528.6309.7279.7270.0000.0000.0000.000
147A148ILE00.0010.01126.693-0.264-0.2640.0000.0000.0000.000
148A149ALA00.042-0.01330.080-0.311-0.3110.0000.0000.0000.000
149A150GLY0-0.055-0.01332.439-0.294-0.2940.0000.0000.0000.000
150A151LYS10.8170.90532.625-9.870-9.8700.0000.0000.0000.000
151A152SER00.0510.02134.6530.1440.1440.0000.0000.0000.000
152A153ASP-1-0.865-0.92135.4769.0159.0150.0000.0000.0000.000
153A154LEU0-0.024-0.00130.2140.2000.2000.0000.0000.0000.000
154A155MET00.0060.04430.9000.5420.5420.0000.0000.0000.000
155A156GLN0-0.039-0.04129.329-0.438-0.4380.0000.0000.0000.000
156A157ASN00.009-0.00934.088-0.001-0.0010.0000.0000.0000.000
157A158ASP-1-0.798-0.88433.8019.4589.4580.0000.0000.0000.000
158A159SER0-0.056-0.02935.553-0.107-0.1070.0000.0000.0000.000
159A160LEU0-0.038-0.00932.3190.0430.0430.0000.0000.0000.000
160A161HIS10.8060.86728.279-10.131-10.1310.0000.0000.0000.000
161A162PRO00.0820.04325.975-0.371-0.3710.0000.0000.0000.000
162A163ASN0-0.052-0.04628.6420.3780.3780.0000.0000.0000.000
163A164LYS10.9420.94627.724-10.528-10.5280.0000.0000.0000.000
164A165LYS10.8410.91427.556-8.917-8.9170.0000.0000.0000.000
165A166ALA00.0300.01727.3560.0870.0870.0000.0000.0000.000
166A167GLN00.0110.01523.1190.9280.9280.0000.0000.0000.000
167A168PRO00.008-0.01522.6080.6210.6210.0000.0000.0000.000
168A169LEU0-0.0070.01222.9290.2130.2130.0000.0000.0000.000
169A170ILE00.0420.01420.7300.2300.2300.0000.0000.0000.000
170A171ARG10.8140.89218.096-13.899-13.8990.0000.0000.0000.000
171A172ASP-1-0.771-0.86418.20115.32415.3240.0000.0000.0000.000
172A173GLU-1-0.868-0.94319.39713.08813.0880.0000.0000.0000.000
173A174MET0-0.0230.00216.0780.0660.0660.0000.0000.0000.000
174A175TYR0-0.037-0.02813.6060.8780.8780.0000.0000.0000.000
175A176ASP-1-0.813-0.90614.59715.71115.7110.0000.0000.0000.000
176A177SER0-0.072-0.05016.712-0.287-0.2870.0000.0000.0000.000
177A178ILE0-0.001-0.00210.9020.0440.0440.0000.0000.0000.000
178A179LYS10.9060.95811.748-15.336-15.3360.0000.0000.0000.000
179A180LYS10.8820.93512.766-14.390-14.3900.0000.0000.0000.000
180A181TRP00.0080.00510.9110.0590.0590.0000.0000.0000.000
181A182LEU0-0.0030.0007.370-0.268-0.2680.0000.0000.0000.000
182A183ASN0-0.126-0.05610.234-0.764-0.7640.0000.0000.0000.000
183A184ASN0-0.088-0.04813.019-1.158-1.1580.0000.0000.0000.000