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: 52R1Z

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 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 196
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2134160.464953
FMO2-HF: Nuclear repulsion 2057521.861318
FMO2-HF: Total energy -76638.603635
FMO2-MP2: Total energy -76864.704053


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.
-4.835-0.4226.208-4.032-6.584-0.031
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 : -0.013 / q_NPA : -0.016
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].
3A3SER0-0.042-0.0153.818-0.3641.718-0.010-0.971-1.1000.001
4A4PRO0-0.029-0.0035.2880.2140.298-0.001-0.003-0.0790.000
5A5ILE0-0.041-0.0307.8770.1780.1780.0000.0000.0000.000
6A6GLU-1-0.934-0.97310.602-0.340-0.3400.0000.0000.0000.000
7A7THR00.0110.00713.024-0.040-0.0400.0000.0000.0000.000
8A8VAL0-0.029-0.01114.8140.0470.0470.0000.0000.0000.000
9A9PRO0-0.018-0.00117.9960.0050.0050.0000.0000.0000.000
10A10VAL0-0.015-0.00619.0730.0060.0060.0000.0000.0000.000
11A11LYS10.9470.97421.9940.1660.1660.0000.0000.0000.000
12A12LEU00.0110.00225.177-0.006-0.0060.0000.0000.0000.000
13A13LYS10.8750.93127.1350.0940.0940.0000.0000.0000.000
14A14PRO00.033-0.00730.2890.0040.0040.0000.0000.0000.000
15A15GLY00.0010.01233.2750.0030.0030.0000.0000.0000.000
16A16MET0-0.062-0.01030.2730.0070.0070.0000.0000.0000.000
17A17ASP-1-0.776-0.86730.021-0.050-0.0500.0000.0000.0000.000
18A18GLY00.007-0.00426.896-0.005-0.0050.0000.0000.0000.000
19A19PRO0-0.068-0.02624.8790.0070.0070.0000.0000.0000.000
20A20LYS10.9940.97827.5090.0230.0230.0000.0000.0000.000
21A21VAL0-0.0150.00327.7120.0030.0030.0000.0000.0000.000
22A22ALA00.0340.02428.4200.0050.0050.0000.0000.0000.000
23A23GLN00.0050.00625.280-0.008-0.0080.0000.0000.0000.000
24A24TRP00.0180.00425.4740.0040.0040.0000.0000.0000.000
25A25PRO00.0360.02428.7260.0080.0080.0000.0000.0000.000
26A26LEU0-0.024-0.01124.488-0.001-0.0010.0000.0000.0000.000
27A27THR00.002-0.00528.5850.0000.0000.0000.0000.0000.000
28A28ALA00.0990.04227.8440.0080.0080.0000.0000.0000.000
29A29ALA00.0110.00527.0850.0100.0100.0000.0000.0000.000
30A30LYS10.9380.96424.317-0.054-0.0540.0000.0000.0000.000
31A31ILE00.0150.01523.1390.0120.0120.0000.0000.0000.000
32A32ALA00.0240.01622.7300.0160.0160.0000.0000.0000.000
33A33ALA0-0.0010.00220.9950.0250.0250.0000.0000.0000.000
34A34LEU00.005-0.01118.7710.0340.0340.0000.0000.0000.000
35A35VAL00.0180.01617.7840.0310.0310.0000.0000.0000.000
36A36ALA00.0120.03617.4220.0320.0320.0000.0000.0000.000
37A37ILE00.0150.00513.6560.0640.0640.0000.0000.0000.000
38A38CYS0-0.047-0.04213.1160.0640.0640.0000.0000.0000.000
39A39THR0-0.0110.00213.2400.0110.0110.0000.0000.0000.000
40A40GLU-1-0.889-0.95910.5030.8210.8210.0000.0000.0000.000
41A41MET0-0.012-0.0038.9600.1750.1750.0000.0000.0000.000
42A42GLU-1-0.882-0.9608.9050.3070.3070.0000.0000.0000.000
43A43LYS10.8900.9708.445-1.443-1.4430.0000.0000.0000.000
44A44GLU-1-0.978-1.0014.8103.5943.5940.0000.0000.0000.000
45A45GLY00.0120.0125.071-0.145-0.101-0.0010.000-0.0420.000
46A46LYS10.8940.9614.391-2.478-2.349-0.001-0.014-0.1140.000
47A47ILE0-0.052-0.0188.309-0.163-0.1630.0000.0000.0000.000
48A48SER00.0270.01311.7630.0490.0490.0000.0000.0000.000
49A49LYS10.9310.97314.333-0.245-0.2450.0000.0000.0000.000
50A50ILE0-0.051-0.01617.816-0.016-0.0160.0000.0000.0000.000
51A51GLY00.0460.02820.5330.0120.0120.0000.0000.0000.000
52A52PRO0-0.052-0.03524.060-0.006-0.0060.0000.0000.0000.000
53A53GLU-1-0.881-0.94023.7820.0090.0090.0000.0000.0000.000
54A54ASN0-0.0220.00621.657-0.011-0.0110.0000.0000.0000.000
55A55PRO0-0.016-0.01025.3800.0080.0080.0000.0000.0000.000
56A56TYR0-0.067-0.03924.448-0.001-0.0010.0000.0000.0000.000
57A57ASN0-0.011-0.01424.5630.0170.0170.0000.0000.0000.000
58A58THR00.0210.02722.234-0.013-0.0130.0000.0000.0000.000
59A59PRO0-0.027-0.00423.3080.0110.0110.0000.0000.0000.000
60A60VAL00.0540.01219.374-0.010-0.0100.0000.0000.0000.000
61A61PHE0-0.040-0.03921.5860.0040.0040.0000.0000.0000.000
62A62ALA00.0290.03421.0700.0050.0050.0000.0000.0000.000
63A63ILE00.000-0.00320.096-0.003-0.0030.0000.0000.0000.000
64A71TRP0-0.034-0.03319.127-0.017-0.0170.0000.0000.0000.000
65A72ALA00.0720.04416.9300.0330.0330.0000.0000.0000.000
66A73LYS10.8970.94414.981-0.111-0.1110.0000.0000.0000.000
67A74LEU00.0170.00717.012-0.019-0.0190.0000.0000.0000.000
68A75VAL00.0040.00117.2070.0170.0170.0000.0000.0000.000
69A76ASP-1-0.866-0.93220.087-0.046-0.0460.0000.0000.0000.000
70A77PHE00.0290.00317.3010.0020.0020.0000.0000.0000.000
71A78ARG10.9380.98022.9100.0190.0190.0000.0000.0000.000
72A79GLU-1-0.871-0.95026.432-0.051-0.0510.0000.0000.0000.000
73A80LEU00.0290.02120.871-0.001-0.0010.0000.0000.0000.000
74A81ASN00.0320.00622.303-0.018-0.0180.0000.0000.0000.000
75A82LYS10.8790.95025.0720.0450.0450.0000.0000.0000.000
76A83ARG10.8500.91327.3730.0550.0550.0000.0000.0000.000
77A84THR00.0220.03622.505-0.004-0.0040.0000.0000.0000.000
78A85GLN0-0.0010.01824.5670.0070.0070.0000.0000.0000.000
79A86ASP-1-0.837-0.91925.492-0.125-0.1250.0000.0000.0000.000
80A87PHE00.0110.00621.059-0.008-0.0080.0000.0000.0000.000
81A88TRP00.0000.00124.3980.0180.0180.0000.0000.0000.000
82A89GLU-1-0.889-0.94523.063-0.225-0.2250.0000.0000.0000.000
83A90VAL0-0.051-0.01923.1650.0100.0100.0000.0000.0000.000
84A104LYS10.8740.95327.8770.1160.1160.0000.0000.0000.000
85A105SER0-0.032-0.01525.4560.0100.0100.0000.0000.0000.000
86A106VAL00.020-0.02123.264-0.011-0.0110.0000.0000.0000.000
87A107THR0-0.0340.00218.1950.0150.0150.0000.0000.0000.000
88A108VAL00.0410.01818.634-0.017-0.0170.0000.0000.0000.000
89A109LEU0-0.077-0.03712.6310.0180.0180.0000.0000.0000.000
90A110ASP-1-0.795-0.89414.094-0.231-0.2310.0000.0000.0000.000
91A111VAL0-0.097-0.06210.642-0.057-0.0570.0000.0000.0000.000
92A112GLY00.1040.06010.640-0.129-0.1290.0000.0000.0000.000
93A113ASP-1-0.923-0.9787.8740.0190.0190.0000.0000.0000.000
94A114ALA0-0.042-0.0176.075-0.170-0.1700.0000.0000.0000.000
95A115TYR00.010-0.0087.086-0.318-0.3180.0000.0000.0000.000
96A116PHE0-0.041-0.0206.380-0.056-0.0560.0000.0000.0000.000
97A117SER00.0140.0102.3070.5041.5860.191-0.565-0.708-0.002
98A118VAL0-0.0050.0054.837-0.102-0.056-0.001-0.010-0.0340.000
99A119PRO00.0170.0158.4200.2250.2250.0000.0000.0000.000
100A120LEU0-0.044-0.01410.3980.0710.0710.0000.0000.0000.000
101A121ASP-1-0.851-0.93913.677-0.208-0.2080.0000.0000.0000.000
102A122GLU-1-0.901-0.96715.472-0.169-0.1690.0000.0000.0000.000
103A123ASP-1-0.878-0.92717.361-0.108-0.1080.0000.0000.0000.000
104A124PHE0-0.048-0.03718.8720.0280.0280.0000.0000.0000.000
105A125ARG10.8920.95612.8270.3000.3000.0000.0000.0000.000
106A126LYS10.9290.98817.9020.1130.1130.0000.0000.0000.000
107A127TYR00.002-0.00720.9230.0190.0190.0000.0000.0000.000
108A128THR0-0.077-0.05417.2040.0070.0070.0000.0000.0000.000
109A129ALA00.0060.01519.1990.0140.0140.0000.0000.0000.000
110A130PHE0-0.013-0.00915.832-0.001-0.0010.0000.0000.0000.000
111A131THR00.000-0.02521.1250.0110.0110.0000.0000.0000.000
112A132ILE0-0.036-0.00518.527-0.005-0.0050.0000.0000.0000.000
113A133PRO0-0.009-0.02422.785-0.001-0.0010.0000.0000.0000.000
114A134SER00.0520.04525.9460.0170.0170.0000.0000.0000.000
115A135ILE0-0.012-0.01128.228-0.007-0.0070.0000.0000.0000.000
116A136ASN00.013-0.01130.099-0.002-0.0020.0000.0000.0000.000
117A137ASN0-0.081-0.04132.284-0.005-0.0050.0000.0000.0000.000
118A138GLU-1-0.910-0.92932.2090.0690.0690.0000.0000.0000.000
119A139THR0-0.007-0.02128.438-0.001-0.0010.0000.0000.0000.000
120A140PRO00.035-0.00228.307-0.002-0.0020.0000.0000.0000.000
121A141GLY0-0.0280.00725.776-0.005-0.0050.0000.0000.0000.000
122A142ILE0-0.031-0.01219.644-0.004-0.0040.0000.0000.0000.000
123A143ARG10.8350.90421.459-0.029-0.0290.0000.0000.0000.000
124A144TYR00.0350.00815.3840.0090.0090.0000.0000.0000.000
125A145GLN00.0480.02215.890-0.016-0.0160.0000.0000.0000.000
126A146TYR00.0440.02312.0100.0720.0720.0000.0000.0000.000
127A147ASN0-0.042-0.0419.981-0.024-0.0240.0000.0000.0000.000
128A148VAL0-0.0110.0087.116-0.084-0.0840.0000.0000.0000.000
129A149LEU0-0.026-0.01410.4020.1740.1740.0000.0000.0000.000
130A150PRO00.0030.01611.3920.0120.0120.0000.0000.0000.000
131A151GLN00.0550.03412.3340.0390.0390.0000.0000.0000.000
132A152GLY00.0240.01215.1040.0410.0410.0000.0000.0000.000
133A153TRP0-0.064-0.03216.5050.0210.0210.0000.0000.0000.000
134A154LYS10.7740.85218.8940.1110.1110.0000.0000.0000.000
135A155GLY00.0630.02519.515-0.001-0.0010.0000.0000.0000.000
136A156SER0-0.041-0.02614.566-0.038-0.0380.0000.0000.0000.000
137A157PRO00.0720.04215.395-0.064-0.0640.0000.0000.0000.000
138A158ALA00.0430.02417.240-0.032-0.0320.0000.0000.0000.000
139A159ILE0-0.025-0.02014.236-0.012-0.0120.0000.0000.0000.000
140A160PHE00.0510.0389.296-0.052-0.0520.0000.0000.0000.000
141A161GLN00.0470.02913.809-0.057-0.0570.0000.0000.0000.000
142A162SER0-0.050-0.01316.498-0.006-0.0060.0000.0000.0000.000
143A163SER00.000-0.02112.1450.0120.0120.0000.0000.0000.000
144A164MET0-0.0010.00910.367-0.016-0.0160.0000.0000.0000.000
145A165THR0-0.057-0.04013.5460.0390.0390.0000.0000.0000.000
146A166LYS10.9250.95914.9510.4250.4250.0000.0000.0000.000
147A167ILE00.0520.0419.2650.0400.0400.0000.0000.0000.000
148A168LEU0-0.012-0.00713.1780.0510.0510.0000.0000.0000.000
149A169ALA0-0.0130.01615.4050.0500.0500.0000.0000.0000.000
150A170PRO0-0.003-0.00915.5600.0400.0400.0000.0000.0000.000
151A171PHE00.0280.01215.6690.0260.0260.0000.0000.0000.000
152A172LYS10.9530.96017.7640.3640.3640.0000.0000.0000.000
153A173ALA0-0.036-0.00320.5360.0240.0240.0000.0000.0000.000
154A174ALA0-0.001-0.00420.4970.0200.0200.0000.0000.0000.000
155A175ASN0-0.0180.00519.4770.0410.0410.0000.0000.0000.000
156A176PRO00.0190.01922.891-0.009-0.0090.0000.0000.0000.000
157A177ASP-1-0.918-0.96225.489-0.140-0.1400.0000.0000.0000.000
158A178ILE0-0.067-0.04020.7560.0060.0060.0000.0000.0000.000
159A179VAL0-0.019-0.00623.517-0.009-0.0090.0000.0000.0000.000
160A180ILE0-0.030-0.02117.099-0.004-0.0040.0000.0000.0000.000
161A181TYR0-0.024-0.01620.463-0.006-0.0060.0000.0000.0000.000
162A182GLN00.014-0.00315.608-0.018-0.0180.0000.0000.0000.000
163A183TYR0-0.0040.02019.2730.0230.0230.0000.0000.0000.000
164A184MET00.001-0.00417.559-0.016-0.0160.0000.0000.0000.000
165A185ASP-1-0.859-0.93714.435-0.261-0.2610.0000.0000.0000.000
166A186ASP-1-0.873-0.91214.849-0.213-0.2130.0000.0000.0000.000
167A187LEU0-0.060-0.05113.295-0.015-0.0150.0000.0000.0000.000
168A188TYR0-0.030-0.01416.6940.0360.0360.0000.0000.0000.000
169A189VAL0-0.002-0.01017.317-0.010-0.0100.0000.0000.0000.000
170A190GLY00.0290.01220.4910.0220.0220.0000.0000.0000.000
171A191SER0-0.042-0.04024.053-0.005-0.0050.0000.0000.0000.000
172A192ASP-1-0.830-0.92726.175-0.091-0.0910.0000.0000.0000.000
173A193LEU0-0.0160.01724.3980.0090.0090.0000.0000.0000.000
174A194ALA00.0330.01328.2990.0020.0020.0000.0000.0000.000
175A195ILE00.0660.01126.062-0.007-0.0070.0000.0000.0000.000
176A196GLY0-0.0040.00625.097-0.004-0.0040.0000.0000.0000.000
177A197ALA00.0470.00724.223-0.005-0.0050.0000.0000.0000.000
178A198HIS00.0580.03621.846-0.010-0.0100.0000.0000.0000.000
179A199ARG10.8560.91317.5000.0740.0740.0000.0000.0000.000
180A200THR00.0250.00519.310-0.006-0.0060.0000.0000.0000.000
181A201LYS10.9070.97118.7240.1510.1510.0000.0000.0000.000
182A202ILE0-0.041-0.01515.982-0.033-0.0330.0000.0000.0000.000
183A203GLU-1-0.806-0.88214.804-0.193-0.1930.0000.0000.0000.000
184A204GLU-1-0.918-0.95613.946-0.214-0.2140.0000.0000.0000.000
185A205LEU0-0.051-0.00913.138-0.050-0.0500.0000.0000.0000.000
186A206ARG10.8560.90210.4870.1120.1120.0000.0000.0000.000
187A207GLN00.0080.0059.081-0.149-0.1490.0000.0000.0000.000
188A208HIS0-0.058-0.0459.487-0.056-0.0560.0000.0000.0000.000
189A209LEU0-0.017-0.0217.848-0.073-0.0730.0000.0000.0000.000
190A210LEU00.0360.0273.857-0.546-0.3490.001-0.028-0.1700.000
191A211ARG10.8870.9524.8970.0680.152-0.001-0.001-0.0820.000
192A212TRP0-0.043-0.0176.5110.0930.0930.0000.0000.0000.000
193A213GLY00.0230.0092.439-0.648-0.1301.229-0.814-0.9320.000
194A214LEU00.0020.0032.215-4.417-4.8584.355-1.431-2.483-0.030
195A215THR0-0.002-0.0052.7570.1650.7560.448-0.193-0.8460.000
196A216THR00.0410.0245.2300.2130.210-0.001-0.0020.0060.000