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: YZ982

Calculation Name: 1HAR-A-Xray372

Preferred Name: Gag-Pol polyprotein

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1HAR

Chain ID: A

ChEMBL ID: CHEMBL5823

UniProt ID: P03366

Base Structure: X-ray

Registration Date: 2023-06-22

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 196
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2133294.028347
FMO2-HF: Nuclear repulsion 2056654.211724
FMO2-HF: Total energy -76639.816623
FMO2-MP2: Total energy -76865.86408


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:1:PRO)


Summations of interaction energy for fragment #1(A:1:PRO)
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.
-6.807-0.2622.881-3.717-5.707-0.024
Interaction energy analysis for fragmet #1(A:1:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.008 / q_NPA : -0.018
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].
3A3SER0-0.040-0.0303.818-0.1571.754-0.014-0.869-1.0270.001
4A4PRO0-0.038-0.0075.4500.2940.2940.0000.0000.0000.000
5A5ILE0-0.044-0.0288.0410.1640.1640.0000.0000.0000.000
6A6GLU-1-0.935-0.97010.772-0.317-0.3170.0000.0000.0000.000
7A7THR0-0.0170.00413.537-0.034-0.0340.0000.0000.0000.000
8A8VAL0-0.027-0.01915.0060.0430.0430.0000.0000.0000.000
9A9PRO0-0.034-0.01218.1820.0070.0070.0000.0000.0000.000
10A10VAL0-0.017-0.00918.9550.0050.0050.0000.0000.0000.000
11A11LYS10.9330.96522.0430.1460.1460.0000.0000.0000.000
12A12LEU00.0040.00125.152-0.005-0.0050.0000.0000.0000.000
13A13LYS10.8560.92427.2220.0760.0760.0000.0000.0000.000
14A14PRO00.032-0.01030.3690.0040.0040.0000.0000.0000.000
15A15GLY0-0.0110.00733.3520.0030.0030.0000.0000.0000.000
16A16MET0-0.071-0.00330.4910.0070.0070.0000.0000.0000.000
17A17ASP-1-0.724-0.83330.017-0.034-0.0340.0000.0000.0000.000
18A18GLY00.0400.00626.932-0.004-0.0040.0000.0000.0000.000
19A19PRO0-0.060-0.02625.0160.0050.0050.0000.0000.0000.000
20A20LYS10.9120.93627.5480.0180.0180.0000.0000.0000.000
21A21VAL0-0.020-0.00127.9220.0020.0020.0000.0000.0000.000
22A22ALA00.0360.02728.5420.0050.0050.0000.0000.0000.000
23A23GLN0-0.017-0.01025.107-0.004-0.0040.0000.0000.0000.000
24A24TRP00.0100.00726.2210.0030.0030.0000.0000.0000.000
25A25PRO00.0600.03528.9120.0080.0080.0000.0000.0000.000
26A26LEU0-0.029-0.01124.744-0.001-0.0010.0000.0000.0000.000
27A27THR00.0230.00028.8970.0010.0010.0000.0000.0000.000
28A28ALA00.0860.03927.9870.0090.0090.0000.0000.0000.000
29A29ALA00.0030.00527.3260.0100.0100.0000.0000.0000.000
30A30LYS10.8980.93924.506-0.065-0.0650.0000.0000.0000.000
31A31ILE00.0010.01223.2940.0140.0140.0000.0000.0000.000
32A32ALA00.0260.01522.6940.0170.0170.0000.0000.0000.000
33A33ALA00.0020.00221.1690.0240.0240.0000.0000.0000.000
34A34LEU00.008-0.00418.8800.0350.0350.0000.0000.0000.000
35A35VAL00.0230.01917.7480.0350.0350.0000.0000.0000.000
36A36ALA00.0030.03017.3930.0320.0320.0000.0000.0000.000
37A37ILE00.0170.00313.7760.0630.0630.0000.0000.0000.000
38A38CYS0-0.041-0.04113.0790.0710.0710.0000.0000.0000.000
39A39THR0-0.0010.00413.2130.0200.0200.0000.0000.0000.000
40A40GLU-1-0.819-0.90410.4000.9150.9150.0000.0000.0000.000
41A41MET00.000-0.0018.9180.1620.1620.0000.0000.0000.000
42A42GLU-1-0.811-0.8858.8820.3120.3120.0000.0000.0000.000
43A43LYS10.8020.9059.012-1.181-1.1810.0000.0000.0000.000
44A44GLU-1-0.891-0.9394.8794.0814.0810.0000.0000.0000.000
45A45GLY00.0070.0085.065-0.093-0.063-0.0010.000-0.0290.000
46A46LYS10.8440.9174.553-3.728-3.595-0.001-0.017-0.1150.000
47A47ILE0-0.043-0.0138.290-0.166-0.1660.0000.0000.0000.000
48A48SER0-0.010-0.00711.7540.0430.0430.0000.0000.0000.000
49A49LYS10.8630.93014.327-0.269-0.2690.0000.0000.0000.000
50A50ILE0-0.060-0.02117.808-0.016-0.0160.0000.0000.0000.000
51A51GLY00.0430.02820.5280.0110.0110.0000.0000.0000.000
52A52PRO0-0.056-0.03724.058-0.005-0.0050.0000.0000.0000.000
53A53GLU-1-0.870-0.93323.6630.0240.0240.0000.0000.0000.000
54A54ASN0-0.0120.00321.519-0.011-0.0110.0000.0000.0000.000
55A55PRO0-0.008-0.00425.3740.0080.0080.0000.0000.0000.000
56A56TYR0-0.058-0.04224.430-0.001-0.0010.0000.0000.0000.000
57A57ASN0-0.009-0.01624.5360.0180.0180.0000.0000.0000.000
58A58THR00.0200.02622.396-0.014-0.0140.0000.0000.0000.000
59A59PRO0-0.028-0.00323.4910.0110.0110.0000.0000.0000.000
60A60VAL00.0180.00219.816-0.007-0.0070.0000.0000.0000.000
61A61PHE0-0.020-0.02521.7630.0010.0010.0000.0000.0000.000
62A62ALA00.0700.04221.2580.0070.0070.0000.0000.0000.000
63A63ILE00.0120.00920.639-0.006-0.0060.0000.0000.0000.000
64A71TRP0-0.035-0.03119.337-0.016-0.0160.0000.0000.0000.000
65A72ALA00.0680.04117.1200.0340.0340.0000.0000.0000.000
66A73LYS10.9030.96015.320-0.155-0.1550.0000.0000.0000.000
67A74LEU00.0020.00017.188-0.013-0.0130.0000.0000.0000.000
68A75VAL00.0080.00717.3690.0140.0140.0000.0000.0000.000
69A76ASP-1-0.779-0.86420.259-0.027-0.0270.0000.0000.0000.000
70A77PHE00.0160.00017.4710.0000.0000.0000.0000.0000.000
71A78ARG10.8620.91023.0570.0020.0020.0000.0000.0000.000
72A79GLU-1-0.773-0.85726.570-0.038-0.0380.0000.0000.0000.000
73A80LEU00.0430.02221.051-0.002-0.0020.0000.0000.0000.000
74A81ASN00.0150.00222.315-0.017-0.0170.0000.0000.0000.000
75A82LYS10.8400.90425.1840.0300.0300.0000.0000.0000.000
76A83ARG10.8050.88127.4090.0380.0380.0000.0000.0000.000
77A84THR00.0140.02122.571-0.004-0.0040.0000.0000.0000.000
78A85GLN00.0310.02924.4950.0050.0050.0000.0000.0000.000
79A86ASP-1-0.853-0.92025.555-0.106-0.1060.0000.0000.0000.000
80A87PHE00.0150.01921.281-0.008-0.0080.0000.0000.0000.000
81A88TRP00.0000.00224.4140.0170.0170.0000.0000.0000.000
82A89GLU-1-0.871-0.94022.829-0.205-0.2050.0000.0000.0000.000
83A90VAL0-0.048-0.01723.0100.0080.0080.0000.0000.0000.000
84A104LYS10.8280.89828.2760.1060.1060.0000.0000.0000.000
85A105SER0-0.045-0.00625.4010.0090.0090.0000.0000.0000.000
86A106VAL00.010-0.02523.431-0.010-0.0100.0000.0000.0000.000
87A107THR0-0.042-0.00818.1620.0140.0140.0000.0000.0000.000
88A108VAL00.0310.01818.786-0.016-0.0160.0000.0000.0000.000
89A109LEU0-0.076-0.03213.2020.0160.0160.0000.0000.0000.000
90A110ASP-1-0.796-0.88513.699-0.194-0.1940.0000.0000.0000.000
91A111VAL0-0.087-0.06110.616-0.053-0.0530.0000.0000.0000.000
92A112GLY00.0970.04910.646-0.112-0.1120.0000.0000.0000.000
93A113ASP-1-0.908-0.9758.0700.1990.1990.0000.0000.0000.000
94A114ALA0-0.035-0.0136.098-0.101-0.1010.0000.0000.0000.000
95A115TYR0-0.056-0.0677.107-0.322-0.3220.0000.0000.0000.000
96A116PHE0-0.057-0.0256.544-0.094-0.0940.0000.0000.0000.000
97A117SER00.0130.0002.349-0.2431.1400.219-0.737-0.865-0.003
98A118VAL0-0.0020.0054.885-0.189-0.145-0.001-0.010-0.0320.000
99A119PRO00.0240.0138.2600.2460.2460.0000.0000.0000.000
100A120LEU0-0.044-0.01110.3980.0630.0630.0000.0000.0000.000
101A121ASP-1-0.811-0.92813.732-0.175-0.1750.0000.0000.0000.000
102A122GLU-1-0.808-0.91214.825-0.160-0.1600.0000.0000.0000.000
103A123ASP-1-0.849-0.91317.371-0.066-0.0660.0000.0000.0000.000
104A124PHE0-0.030-0.01618.9740.0230.0230.0000.0000.0000.000
105A125ARG10.7890.90813.6250.2170.2170.0000.0000.0000.000
106A126LYS10.8640.93417.8980.0970.0970.0000.0000.0000.000
107A127TYR0-0.008-0.01220.9170.0170.0170.0000.0000.0000.000
108A128THR0-0.066-0.04017.2690.0080.0080.0000.0000.0000.000
109A129ALA0-0.0060.01119.2010.0160.0160.0000.0000.0000.000
110A130PHE00.009-0.00515.969-0.001-0.0010.0000.0000.0000.000
111A131THR00.003-0.02021.1030.0110.0110.0000.0000.0000.000
112A132ILE0-0.0190.00318.344-0.004-0.0040.0000.0000.0000.000
113A133PRO0-0.005-0.02222.755-0.002-0.0020.0000.0000.0000.000
114A134SER00.0530.04325.9160.0170.0170.0000.0000.0000.000
115A135ILE0-0.023-0.01428.200-0.007-0.0070.0000.0000.0000.000
116A136ASN00.015-0.00930.068-0.002-0.0020.0000.0000.0000.000
117A137ASN0-0.081-0.04232.260-0.005-0.0050.0000.0000.0000.000
118A138GLU-1-0.913-0.93432.2620.0690.0690.0000.0000.0000.000
119A139THR0-0.014-0.02028.413-0.001-0.0010.0000.0000.0000.000
120A140PRO00.0410.00028.252-0.002-0.0020.0000.0000.0000.000
121A141GLY0-0.0310.00425.755-0.005-0.0050.0000.0000.0000.000
122A142ILE0-0.034-0.01319.625-0.005-0.0050.0000.0000.0000.000
123A143ARG10.8400.91221.442-0.042-0.0420.0000.0000.0000.000
124A144TYR00.011-0.03115.1470.0060.0060.0000.0000.0000.000
125A145GLN00.0340.01515.938-0.022-0.0220.0000.0000.0000.000
126A146TYR00.0450.01012.1630.0620.0620.0000.0000.0000.000
127A147ASN0-0.005-0.02010.089-0.036-0.0360.0000.0000.0000.000
128A148VAL0-0.0120.0147.211-0.077-0.0770.0000.0000.0000.000
129A149LEU0-0.025-0.01210.5160.1600.1600.0000.0000.0000.000
130A150PRO00.0050.01511.5150.0240.0240.0000.0000.0000.000
131A151GLN00.0530.03612.1110.0210.0210.0000.0000.0000.000
132A152GLY00.0200.00815.2320.0360.0360.0000.0000.0000.000
133A153TRP0-0.056-0.02516.6700.0160.0160.0000.0000.0000.000
134A154LYS10.7740.84918.9850.0920.0920.0000.0000.0000.000
135A155GLY00.0680.02019.576-0.002-0.0020.0000.0000.0000.000
136A156SER0-0.049-0.03114.493-0.033-0.0330.0000.0000.0000.000
137A157PRO00.0770.04115.429-0.059-0.0590.0000.0000.0000.000
138A158ALA00.0370.02317.244-0.033-0.0330.0000.0000.0000.000
139A159ILE0-0.027-0.02514.257-0.014-0.0140.0000.0000.0000.000
140A160PHE00.0500.0379.216-0.044-0.0440.0000.0000.0000.000
141A161GLN00.0640.04413.798-0.061-0.0610.0000.0000.0000.000
142A162SER0-0.046-0.01016.456-0.009-0.0090.0000.0000.0000.000
143A163SER0-0.015-0.02212.1870.0060.0060.0000.0000.0000.000
144A164MET00.0050.01110.598-0.026-0.0260.0000.0000.0000.000
145A165THR0-0.056-0.04513.6180.0330.0330.0000.0000.0000.000
146A166LYS10.9390.96915.0130.4090.4090.0000.0000.0000.000
147A167ILE00.0390.0319.2720.0380.0380.0000.0000.0000.000
148A168LEU0-0.029-0.01213.2530.0460.0460.0000.0000.0000.000
149A169ALA0-0.0060.01515.7020.0470.0470.0000.0000.0000.000
150A170PRO00.006-0.00815.7460.0360.0360.0000.0000.0000.000
151A171PHE00.0120.01015.8370.0240.0240.0000.0000.0000.000
152A172LYS10.9600.96618.0010.3360.3360.0000.0000.0000.000
153A173ALA0-0.042-0.00820.7880.0230.0230.0000.0000.0000.000
154A174ALA0-0.005-0.00420.6710.0190.0190.0000.0000.0000.000
155A175ASN0-0.0100.01519.4680.0350.0350.0000.0000.0000.000
156A176PRO00.0210.01923.083-0.007-0.0070.0000.0000.0000.000
157A177ASP-1-0.878-0.94825.252-0.138-0.1380.0000.0000.0000.000
158A178ILE0-0.048-0.03320.8680.0060.0060.0000.0000.0000.000
159A179VAL0-0.015-0.00423.725-0.008-0.0080.0000.0000.0000.000
160A180ILE0-0.032-0.02017.351-0.004-0.0040.0000.0000.0000.000
161A181TYR0-0.015-0.01320.680-0.006-0.0060.0000.0000.0000.000
162A182GLN0-0.002-0.01314.929-0.048-0.0480.0000.0000.0000.000
163A183TYR0-0.0040.02219.3380.0190.0190.0000.0000.0000.000
164A184MET0-0.007-0.01517.540-0.014-0.0140.0000.0000.0000.000
165A185ASP-1-0.807-0.88814.437-0.230-0.2300.0000.0000.0000.000
166A186ASP-1-0.804-0.86214.845-0.178-0.1780.0000.0000.0000.000
167A187LEU0-0.058-0.04913.846-0.012-0.0120.0000.0000.0000.000
168A188TYR0-0.080-0.06016.8680.0310.0310.0000.0000.0000.000
169A189VAL0-0.008-0.01317.386-0.010-0.0100.0000.0000.0000.000
170A190GLY00.0360.02020.6340.0200.0200.0000.0000.0000.000
171A191SER0-0.010-0.01924.187-0.005-0.0050.0000.0000.0000.000
172A192ASP-1-0.812-0.90526.301-0.089-0.0890.0000.0000.0000.000
173A193LEU0-0.0050.02024.6740.0090.0090.0000.0000.0000.000
174A194ALA00.0330.01328.3660.0020.0020.0000.0000.0000.000
175A195ILE00.0640.00926.028-0.007-0.0070.0000.0000.0000.000
176A196GLY00.0070.01325.083-0.004-0.0040.0000.0000.0000.000
177A197ALA00.0390.01424.209-0.006-0.0060.0000.0000.0000.000
178A198HIS00.0590.04421.891-0.010-0.0100.0000.0000.0000.000
179A199ARG10.8190.89116.9430.0910.0910.0000.0000.0000.000
180A200THR00.023-0.01219.296-0.007-0.0070.0000.0000.0000.000
181A201LYS10.8600.94418.7470.1400.1400.0000.0000.0000.000
182A202ILE0-0.027-0.01315.981-0.032-0.0320.0000.0000.0000.000
183A203GLU-1-0.782-0.86314.285-0.210-0.2100.0000.0000.0000.000
184A204GLU-1-0.919-0.95213.955-0.217-0.2170.0000.0000.0000.000
185A205LEU0-0.050-0.01613.404-0.049-0.0490.0000.0000.0000.000
186A206ARG10.8470.88410.6910.1170.1170.0000.0000.0000.000
187A207GLN00.0040.0049.139-0.150-0.1500.0000.0000.0000.000
188A208HIS0-0.056-0.0389.645-0.055-0.0550.0000.0000.0000.000
189A209LEU0-0.008-0.0208.186-0.071-0.0710.0000.0000.0000.000
190A210LEU00.0350.0293.867-0.529-0.3400.001-0.030-0.1600.000
191A211ARG10.8930.9545.1290.0930.167-0.0010.000-0.0730.000
192A212TRP0-0.040-0.0136.5470.1190.1190.0000.0000.0000.000
193A213GLY00.0290.0222.406-0.562-0.0831.033-0.760-0.7530.000
194A214LEU00.0050.0042.559-5.789-4.0931.327-1.115-1.908-0.022
195A215THR00.0100.0062.6750.1370.7500.320-0.178-0.7550.000
196A216THR00.0340.0305.2280.3330.326-0.001-0.0010.0100.000