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: MNYNZ

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 OptHSide
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 -2025506.115253
FMO2-HF: Nuclear repulsion 1952396.897466
FMO2-HF: Total energy -73109.217788
FMO2-MP2: Total energy -73319.394192


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.
89.96391.07118.125-10.479-8.7550.054
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 : -0.907 / q_NPA : -0.932
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].
3A4THR00.0390.0101.658-38.665-40.62115.191-7.794-5.4410.073
4A5ILE0-0.042-0.0354.011-6.357-6.0950.006-0.127-0.1420.001
5A6LEU00.0080.0137.650-2.625-2.6250.0000.0000.0000.000
6A7ILE0-0.008-0.01010.269-1.725-1.7250.0000.0000.0000.000
7A8LEU00.003-0.00313.560-0.960-0.9600.0000.0000.0000.000
8A9GLY00.0730.02316.364-0.705-0.7050.0000.0000.0000.000
9A10ASP-1-0.813-0.89819.35912.92512.9250.0000.0000.0000.000
10A11MIR-1-0.776-0.87222.36011.75211.7520.0000.0000.0000.000
11A12LEU0-0.088-0.03723.526-0.125-0.1250.0000.0000.0000.000
12A13SER00.008-0.01518.4240.2670.2670.0000.0000.0000.000
13A14ALA0-0.0230.00119.5310.7610.7610.0000.0000.0000.000
14A15ALA0-0.026-0.00421.656-0.309-0.3090.0000.0000.0000.000
15A16TYR00.0300.01623.937-0.384-0.3840.0000.0000.0000.000
16A17GLY0-0.007-0.00227.098-0.191-0.1910.0000.0000.0000.000
17A18LEU0-0.084-0.02726.096-0.328-0.3280.0000.0000.0000.000
18A19GLN00.0260.01426.330-0.101-0.1010.0000.0000.0000.000
19A20GLN00.0480.02218.174-0.317-0.3170.0000.0000.0000.000
20A21GLU-1-0.919-0.98321.20613.91713.9170.0000.0000.0000.000
21A22GLU-1-0.879-0.93022.27611.09611.0960.0000.0000.0000.000
22A23GLY00.0100.00321.661-0.277-0.2770.0000.0000.0000.000
23A24TRP00.016-0.00215.7410.8720.8720.0000.0000.0000.000
24A25VAL00.0060.01114.3340.4700.4700.0000.0000.0000.000
25A26LYS10.8220.90715.603-14.729-14.7290.0000.0000.0000.000
26A27LEU0-0.005-0.00317.2040.1920.1920.0000.0000.0000.000
27A28LEU0-0.059-0.02613.871-0.260-0.2600.0000.0000.0000.000
28A29GLN0-0.006-0.0219.4611.4371.4370.0000.0000.0000.000
29A30ASP-1-0.766-0.86713.70416.53916.5390.0000.0000.0000.000
30A31LYS10.7580.86315.816-16.187-16.1870.0000.0000.0000.000
31A32TYR00.044-0.01010.524-0.181-0.1810.0000.0000.0000.000
32A33ASP-1-0.835-0.90611.87524.04824.0480.0000.0000.0000.000
33A34ALA0-0.087-0.04213.370-0.600-0.6000.0000.0000.0000.000
34A35GLU-1-0.864-0.90413.69315.86115.8610.0000.0000.0000.000
35A36GLN0-0.089-0.03211.399-0.227-0.2270.0000.0000.0000.000
36A37SER0-0.0120.0018.5241.1481.1480.0000.0000.0000.000
37A38ASP-1-0.836-0.9092.20135.06136.1822.349-1.757-1.712-0.026
38A39ILE0-0.051-0.0164.4336.1536.262-0.001-0.014-0.0950.000
39A40VAL00.0040.0165.426-4.573-4.5730.0000.0000.0000.000
40A41LEU0-0.043-0.0176.8692.1892.1890.0000.0000.0000.000
41A42ILE00.0260.0227.330-1.806-1.8060.0000.0000.0000.000
42A43ASN0-0.016-0.01710.742-0.854-0.8540.0000.0000.0000.000
43A44ALA00.0260.02714.351-0.594-0.5940.0000.0000.0000.000
44A45SER0-0.022-0.01416.062-0.961-0.9610.0000.0000.0000.000
45A46ILE0-0.040-0.01619.025-0.294-0.2940.0000.0000.0000.000
46A47SER00.009-0.01622.536-0.242-0.2420.0000.0000.0000.000
47A48GLY00.0020.00125.776-0.181-0.1810.0000.0000.0000.000
48A49GLU-1-0.830-0.88622.04013.23413.2340.0000.0000.0000.000
49A50THR0-0.070-0.04125.355-0.312-0.3120.0000.0000.0000.000
50A51SER00.041-0.01723.9940.3720.3720.0000.0000.0000.000
51A52GLY0-0.029-0.02224.2430.3610.3610.0000.0000.0000.000
52A53GLY0-0.061-0.03925.6000.0590.0590.0000.0000.0000.000
53A54ALA00.0810.04420.2960.3270.3270.0000.0000.0000.000
54A55LEU0-0.036-0.01720.7860.5660.5660.0000.0000.0000.000
55A56ARG10.8740.93222.153-11.466-11.4660.0000.0000.0000.000
56A57ARG10.8440.90118.660-16.149-16.1490.0000.0000.0000.000
57A58LEU0-0.0070.01314.7750.4280.4280.0000.0000.0000.000
58A59ASP-1-0.806-0.88316.21017.39517.3950.0000.0000.0000.000
59A60ALA00.0310.01616.2370.8440.8440.0000.0000.0000.000
60A61LEU0-0.021-0.01013.8900.6870.6870.0000.0000.0000.000
61A62LEU0-0.021-0.01711.7431.9251.9250.0000.0000.0000.000
62A63GLU-1-0.950-0.96411.21920.80820.8080.0000.0000.0000.000
63A64GLN0-0.083-0.04112.3280.5000.5000.0000.0000.0000.000
64A65TYR0-0.049-0.0478.561-0.248-0.2480.0000.0000.0000.000
65A66GLU-1-0.955-0.9497.11338.63138.6310.0000.0000.0000.000
66A67PRO0-0.048-0.0095.6466.8086.8080.0000.0000.0000.000
67A68THR00.0880.0192.866-2.676-1.1040.580-0.787-1.3650.006
68A69HIS0-0.0210.0145.496-3.957-3.9570.0000.0000.0000.000
69A70VAL0-0.011-0.0018.1990.6670.6670.0000.0000.0000.000
70A71LEU0-0.008-0.00411.314-1.538-1.5380.0000.0000.0000.000
71A72ILE00.001-0.00113.849-0.555-0.5550.0000.0000.0000.000
72A73GLH0-0.017-0.03317.276-0.422-0.4220.0000.0000.0000.000
73A74LEU00.0120.00419.992-0.419-0.4190.0000.0000.0000.000
74A75GLY00.0820.03222.769-0.123-0.1230.0000.0000.0000.000
75A76ALA00.0250.01626.210-0.568-0.5680.0000.0000.0000.000
76A77ASN0-0.019-0.03426.714-0.875-0.8750.0000.0000.0000.000
77A78ASP-1-0.762-0.87627.85111.06011.0600.0000.0000.0000.000
78A79GLY00.0180.01330.505-0.385-0.3850.0000.0000.0000.000
79A80LEU00.016-0.00331.238-0.419-0.4190.0000.0000.0000.000
80A81ARG10.9090.97531.495-10.160-10.1600.0000.0000.0000.000
81A82GLY00.0290.03135.379-0.224-0.2240.0000.0000.0000.000
82A83PHE0-0.051-0.01531.780-0.180-0.1800.0000.0000.0000.000
83A84PRO0-0.002-0.00234.7500.0570.0570.0000.0000.0000.000
84A85VAL00.0830.04831.4710.2390.2390.0000.0000.0000.000
85A86LYS11.0021.00931.456-8.618-8.6180.0000.0000.0000.000
86A87LYS10.8800.94429.616-10.452-10.4520.0000.0000.0000.000
87A88MET00.0150.02927.3700.2860.2860.0000.0000.0000.000
88A89GLN00.0560.02427.0830.3020.3020.0000.0000.0000.000
89A90THR0-0.071-0.03626.7020.3290.3290.0000.0000.0000.000
90A91ASN0-0.037-0.02625.7080.1900.1900.0000.0000.0000.000
91A92LEU00.0580.02422.3120.5410.5410.0000.0000.0000.000
92A93THR00.0120.00521.7580.7300.7300.0000.0000.0000.000
93A94ALA0-0.039-0.01522.0260.5210.5210.0000.0000.0000.000
94A95LEU0-0.0050.00118.8900.5330.5330.0000.0000.0000.000
95A96VAL00.0280.01717.5271.1931.1930.0000.0000.0000.000
96A97LYS10.9460.97317.299-12.574-12.5740.0000.0000.0000.000
97A98LYS10.8060.88217.681-15.243-15.2430.0000.0000.0000.000
98A99SER00.0350.00513.3501.0501.0500.0000.0000.0000.000
99A100GLN0-0.025-0.02013.1200.8230.8230.0000.0000.0000.000
100A101ALA0-0.065-0.02214.4000.5440.5440.0000.0000.0000.000
101A102ALA0-0.037-0.01111.942-0.280-0.2800.0000.0000.0000.000
102A103ASN0-0.070-0.0419.6921.4131.4130.0000.0000.0000.000
103A104ALA00.0820.0689.2082.8992.8990.0000.0000.0000.000
104A105MET0-0.018-0.0109.441-4.731-4.7310.0000.0000.0000.000
105A106THR0-0.022-0.02311.0130.9740.9740.0000.0000.0000.000
106A107ALA0-0.028-0.00713.754-1.239-1.2390.0000.0000.0000.000
107A108LEU0-0.040-0.02215.7290.1630.1630.0000.0000.0000.000
108A109MET0-0.0370.00018.769-0.663-0.6630.0000.0000.0000.000
109A110GLU-1-0.838-0.89820.83511.06311.0630.0000.0000.0000.000
110A111ILE0-0.032-0.00423.0770.0050.0050.0000.0000.0000.000
111A112TYR0-0.056-0.05226.668-0.649-0.6490.0000.0000.0000.000
112A113ILE0-0.028-0.00330.3100.1090.1090.0000.0000.0000.000
113A114PRO00.0610.03232.876-0.179-0.1790.0000.0000.0000.000
114A115PRO00.0100.00836.4260.0500.0500.0000.0000.0000.000
115A116ASN0-0.016-0.02037.892-0.295-0.2950.0000.0000.0000.000
116A117TYR0-0.028-0.01936.953-0.266-0.2660.0000.0000.0000.000
117A118GLY00.0050.00940.846-0.091-0.0910.0000.0000.0000.000
118A119PRO00.0450.00139.8400.2250.2250.0000.0000.0000.000
119A120ARG10.9320.97138.225-7.972-7.9720.0000.0000.0000.000
120A121TYR00.045-0.00734.6750.1830.1830.0000.0000.0000.000
121A122SER00.0700.03235.1700.1710.1710.0000.0000.0000.000
122A123LYS10.9590.98234.120-7.905-7.9050.0000.0000.0000.000
123A124MET0-0.080-0.03034.1460.1130.1130.0000.0000.0000.000
124A125PHE00.0390.01228.5660.1970.1970.0000.0000.0000.000
125A126THR00.0230.01129.2700.1660.1660.0000.0000.0000.000
126A127SER0-0.040-0.03629.1460.2780.2780.0000.0000.0000.000
127A128SER0-0.061-0.04029.1240.2710.2710.0000.0000.0000.000
128A129PHE00.0410.00523.6690.1780.1780.0000.0000.0000.000
129A130THR00.0360.02625.0280.4540.4540.0000.0000.0000.000
130A131GLN00.0040.00126.7350.0630.0630.0000.0000.0000.000
131A132ILE00.0060.01222.5610.1100.1100.0000.0000.0000.000
132A133SER0-0.052-0.02121.7630.2500.2500.0000.0000.0000.000
133A134GLU-1-0.919-0.96623.25111.01311.0130.0000.0000.0000.000
134A135ASP-1-0.985-0.97725.51211.45911.4590.0000.0000.0000.000
135A136THR0-0.126-0.09720.5580.3660.3660.0000.0000.0000.000
136A137ASN0-0.0190.00017.9660.2580.2580.0000.0000.0000.000
137A138ALA00.0060.02517.5990.7860.7860.0000.0000.0000.000
138A139HIS00.0560.04216.196-1.110-1.1100.0000.0000.0000.000
139A140LEU0-0.009-0.00318.1930.4540.4540.0000.0000.0000.000
140A141MET0-0.037-0.01014.4040.0190.0190.0000.0000.0000.000
141A142ASN00.032-0.00220.353-0.824-0.8240.0000.0000.0000.000
142A143PHE00.0300.01322.3390.4120.4120.0000.0000.0000.000
143A144PHE00.0830.02020.275-0.449-0.4490.0000.0000.0000.000
144A145MET0-0.021-0.00724.158-0.231-0.2310.0000.0000.0000.000
145A146LEU0-0.046-0.00827.381-0.505-0.5050.0000.0000.0000.000
146A147ASP-1-0.827-0.91128.6679.7159.7150.0000.0000.0000.000
147A148ILE0-0.0220.00226.926-0.214-0.2140.0000.0000.0000.000
148A149ALA00.018-0.02330.331-0.335-0.3350.0000.0000.0000.000
149A150GLY0-0.035-0.00632.589-0.251-0.2510.0000.0000.0000.000
150A151LYS10.8210.91132.370-9.917-9.9170.0000.0000.0000.000
151A152SER00.0620.02634.9540.1190.1190.0000.0000.0000.000
152A153ASP-1-0.871-0.92135.4729.0059.0050.0000.0000.0000.000
153A154LEU0-0.0240.00030.3680.1940.1940.0000.0000.0000.000
154A155MET0-0.0040.02431.2610.5370.5370.0000.0000.0000.000
155A156GLN0-0.057-0.04629.787-0.482-0.4820.0000.0000.0000.000
156A157ASN00.016-0.00334.440-0.067-0.0670.0000.0000.0000.000
157A158ASP-1-0.790-0.87534.0669.3669.3660.0000.0000.0000.000
158A159SER0-0.061-0.02735.942-0.100-0.1000.0000.0000.0000.000
159A160LEU0-0.049-0.01632.4650.0520.0520.0000.0000.0000.000
160A161HIS10.7840.85328.408-10.093-10.0930.0000.0000.0000.000
161A162PRO00.0890.04526.435-0.340-0.3400.0000.0000.0000.000
162A163ASN0-0.038-0.02728.9720.3770.3770.0000.0000.0000.000
163A164LYS10.9470.94827.926-10.438-10.4380.0000.0000.0000.000
164A165LYS10.8280.90527.825-8.899-8.8990.0000.0000.0000.000
165A166ALA00.0170.00727.7270.1130.1130.0000.0000.0000.000
166A167GLN00.0060.00723.3600.8870.8870.0000.0000.0000.000
167A168PRO00.006-0.00523.0470.5540.5540.0000.0000.0000.000
168A169LEU00.0080.01123.2580.2430.2430.0000.0000.0000.000
169A170ILE00.0530.03020.9110.1860.1860.0000.0000.0000.000
170A171ARG10.8090.88518.281-13.698-13.6980.0000.0000.0000.000
171A172ASP-1-0.797-0.87518.78714.78814.7880.0000.0000.0000.000
172A173GLU-1-0.906-0.96019.92712.83512.8350.0000.0000.0000.000
173A174MET0-0.028-0.00916.2210.1140.1140.0000.0000.0000.000
174A175TYR0-0.046-0.02613.9120.9290.9290.0000.0000.0000.000
175A176ASP-1-0.855-0.92115.20415.07215.0720.0000.0000.0000.000
176A177SER0-0.073-0.04816.954-0.041-0.0410.0000.0000.0000.000
177A178ILE0-0.002-0.00311.2310.2870.2870.0000.0000.0000.000
178A179LYS10.9780.99912.240-15.562-15.5620.0000.0000.0000.000
179A180LYS10.8670.91613.311-14.191-14.1910.0000.0000.0000.000
180A181TRP00.0150.00511.2120.1410.1410.0000.0000.0000.000
181A182LEU0-0.001-0.0057.680-0.201-0.2010.0000.0000.0000.000
182A183ASN0-0.108-0.04510.421-0.439-0.4390.0000.0000.0000.000
183A184ASN0-0.104-0.04013.017-1.373-1.3730.0000.0000.0000.000