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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: R1258

Calculation Name: 6M5I-AB-Xray149

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 6M5I

Chain ID: AB

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2020-07-20

Reference: Y.Handa, K. Kato, Y. Kawashima, K. Fukuzawa et.al., FMO calculation for SARS Cov-2 related proteins. To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHSideSolv
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water All crystal waters in PDB.
Procedure Manual calculation
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 229
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2222685.224152
FMO2-HF: Nuclear repulsion 2141601.756254
FMO2-HF: Total energy -81083.467898
FMO2-MP2: Total energy -81311.013797


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(B:82:GLU )


Summations of interaction energy for fragment #1(B:82:GLU )
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.
-35.808-46.835.652-14.869-9.7890.138
Interaction energy analysis for fragmet #1(B:82:GLU )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.066 / q_NPA : 0.051
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].
3B84LYS 11.0061.0013.29714.44316.206-0.003-0.748-1.0120.000
4B85ARG 10.9530.9642.8810.7811.7130.103-0.183-0.8520.000
5B86ALA 00.0620.0533.3685.0635.5690.008-0.164-0.3490.000
6B87LYS 11.0361.0025.0716.4516.576-0.001-0.007-0.1160.000
7B88VAL 0-0.073-0.0207.6590.6210.6210.0000.0000.0000.000
8B89THR 00.0390.0066.8230.9260.9260.0000.0000.0000.000
9B90SER 00.0040.0299.139-0.150-0.1500.0000.0000.0000.000
10B91ALA 00.0310.02610.8020.0450.0450.0000.0000.0000.000
11B92MET 0-0.029-0.01312.2670.2150.2150.0000.0000.0000.000
12B93GLN 00.0490.00611.1090.7360.7360.0000.0000.0000.000
13B94THR 00.017-0.00314.525-0.123-0.1230.0000.0000.0000.000
14B95MET 0-0.0040.01616.678-0.062-0.0620.0000.0000.0000.000
15B96LEU 00.0170.02816.990-0.069-0.0690.0000.0000.0000.000
16B97PHE 00.0900.02617.345-0.104-0.1040.0000.0000.0000.000
17B98THR 0-0.0060.02321.132-0.087-0.0870.0000.0000.0000.000
18B99MET 0-0.054-0.02722.478-0.083-0.0830.0000.0000.0000.000
19B100LEU 00.0000.00421.346-0.042-0.0420.0000.0000.0000.000
20B101ARG 10.9290.94523.081-0.792-0.7920.0000.0000.0000.000
21B102LYS 10.9440.98126.168-0.312-0.3120.0000.0000.0000.000
22B103LEU 0-0.063-0.02726.255-0.040-0.0400.0000.0000.0000.000
23B104ASP -1-0.948-0.95729.7920.4360.4360.0000.0000.0000.000
24B105ASN 00.0220.01130.6010.0090.0090.0000.0000.0000.000
25B106ASP -1-0.813-0.90331.3650.5310.5310.0000.0000.0000.000
26B107ALA 00.0010.00031.7310.0190.0190.0000.0000.0000.000
27B108LEU 0-0.018-0.00726.4870.0700.0700.0000.0000.0000.000
28B109ASN 00.0480.01927.8300.1080.1080.0000.0000.0000.000
29B110ASN 0-0.0160.00829.2730.0470.0470.0000.0000.0000.000
30B111ILE 00.0530.02625.1750.0110.0110.0000.0000.0000.000
31B112ILE 0-0.040-0.02923.2350.0820.0820.0000.0000.0000.000
32B113ASN 0-0.038-0.02225.2120.0240.0240.0000.0000.0000.000
33B114ASN 00.0440.02627.572-0.026-0.0260.0000.0000.0000.000
34B115ALA 00.0150.00722.7120.0040.0040.0000.0000.0000.000
35B116ARG 10.7920.88323.003-0.612-0.6120.0000.0000.0000.000
36B117ASP -1-0.911-0.94124.6420.6210.6210.0000.0000.0000.000
37B118GLY 0-0.033-0.00824.677-0.029-0.0290.0000.0000.0000.000
38B119CYS 0-0.0780.02025.7490.0440.0440.0000.0000.0000.000
39B120VAL 00.0460.03622.0560.0160.0160.0000.0000.0000.000
40B121PRO 0-0.028-0.00423.527-0.068-0.0680.0000.0000.0000.000
41B122LEU 0-0.005-0.02323.7270.1380.1380.0000.0000.0000.000
42B123ASN 0-0.070-0.04123.8880.0990.0990.0000.0000.0000.000
43B124ILE 0-0.023-0.00523.290-0.009-0.0090.0000.0000.0000.000
44B125ILE 00.0640.03325.548-0.095-0.0950.0000.0000.0000.000
45B126PRO 0-0.0440.00928.3930.0400.0400.0000.0000.0000.000
46B127LEU 00.010-0.01230.390-0.052-0.0520.0000.0000.0000.000
47B128THR 0-0.063-0.03533.233-0.031-0.0310.0000.0000.0000.000
48B129THR 00.0600.02036.2610.0020.0020.0000.0000.0000.000
49B130ALA 00.0370.02338.345-0.013-0.0130.0000.0000.0000.000
50B131ALA 0-0.079-0.02633.2160.0210.0210.0000.0000.0000.000
51B132LYS 10.9240.93730.335-1.131-1.1310.0000.0000.0000.000
52B133LEU 0-0.015-0.00330.3210.0920.0920.0000.0000.0000.000
53B134MET 0-0.0010.02728.783-0.012-0.0120.0000.0000.0000.000
54B135VAL 00.0430.03428.0240.0990.0990.0000.0000.0000.000
55B136VAL 0-0.0100.00925.601-0.058-0.0580.0000.0000.0000.000
56B137ILE 00.0210.00328.813-0.012-0.0120.0000.0000.0000.000
57B138PRO 00.010-0.00928.586-0.021-0.0210.0000.0000.0000.000
58B139ASP -1-0.824-0.90230.8270.4570.4570.0000.0000.0000.000
59B140TYR 00.057-0.00433.7520.0170.0170.0000.0000.0000.000
60B141ASN 0-0.048-0.02934.978-0.028-0.0280.0000.0000.0000.000
61B142THR 00.0520.01531.455-0.008-0.0080.0000.0000.0000.000
62B143TYR 00.0750.03334.5590.0100.0100.0000.0000.0000.000
63B144LYS 10.9030.96736.944-0.429-0.4290.0000.0000.0000.000
64B145ASN 0-0.034-0.01635.031-0.037-0.0370.0000.0000.0000.000
65B146THR 0-0.065-0.03533.5290.0160.0160.0000.0000.0000.000
66B147CYS 0-0.064-0.02936.8820.0240.0240.0000.0000.0000.000
67B148ASP -1-0.915-0.95339.5480.3780.3780.0000.0000.0000.000
68B149GLY 0-0.0240.00443.332-0.001-0.0010.0000.0000.0000.000
69B150THR 0-0.026-0.04743.2370.0080.0080.0000.0000.0000.000
70B151THR 00.0120.03441.7220.0300.0300.0000.0000.0000.000
71B152PHE 0-0.021-0.02332.2900.0060.0060.0000.0000.0000.000
72B153THR 0-0.023-0.02537.4290.0320.0320.0000.0000.0000.000
73B154TYR 00.0360.02927.2340.0340.0340.0000.0000.0000.000
74B155ALA 00.0120.01130.6680.0050.0050.0000.0000.0000.000
75B156SER 0-0.042-0.03132.3550.0000.0000.0000.0000.0000.000
76B157ALA 0-0.025-0.00835.696-0.020-0.0200.0000.0000.0000.000
77B158LEU 00.0260.00837.1120.0100.0100.0000.0000.0000.000
78B159TRP 0-0.026-0.04432.7080.0500.0500.0000.0000.0000.000
79B160GLU -1-0.823-0.90238.5030.4940.4940.0000.0000.0000.000
80B161ILE 0-0.034-0.03038.3330.0370.0370.0000.0000.0000.000
81B162GLN 0-0.083-0.03238.571-0.030-0.0300.0000.0000.0000.000
82B163GLN 0-0.043-0.01835.513-0.056-0.0560.0000.0000.0000.000
83B164VAL 00.0100.00036.2110.0420.0420.0000.0000.0000.000
84B165VAL 0-0.047-0.01533.701-0.026-0.0260.0000.0000.0000.000
85B166ASP -1-0.790-0.92434.7040.6760.6760.0000.0000.0000.000
86B167ALA 00.0300.01131.3090.0460.0460.0000.0000.0000.000
87B168ASP -1-0.904-0.90831.8480.6920.6920.0000.0000.0000.000
88B169SER 0-0.074-0.05332.2540.0110.0110.0000.0000.0000.000
89B170LYS 10.8800.95534.408-0.639-0.6390.0000.0000.0000.000
90B171ILE 0-0.017-0.00238.0570.0070.0070.0000.0000.0000.000
91B172VAL 00.0140.01838.493-0.022-0.0220.0000.0000.0000.000
92B173GLN 00.0020.01841.0440.0160.0160.0000.0000.0000.000
93B174LEU 00.0210.00142.386-0.011-0.0110.0000.0000.0000.000
94B175SER 0-0.018-0.00643.842-0.006-0.0060.0000.0000.0000.000
95B176GLU -1-0.918-0.95843.3770.4420.4420.0000.0000.0000.000
96B177ILE 0-0.009-0.01839.156-0.011-0.0110.0000.0000.0000.000
97B178SER 0-0.033-0.01342.216-0.008-0.0080.0000.0000.0000.000
98B179MET 00.0110.02044.2780.0060.0060.0000.0000.0000.000
99B180ASP -1-0.804-0.86446.3990.2710.2710.0000.0000.0000.000
100B181ASN 0-0.009-0.00244.481-0.014-0.0140.0000.0000.0000.000
101B182SER 00.0140.01640.2840.0060.0060.0000.0000.0000.000
102B183PRO 0-0.0160.00039.9430.0260.0260.0000.0000.0000.000
103B184ASN 0-0.063-0.03540.661-0.010-0.0100.0000.0000.0000.000
104B185LEU 0-0.0330.00338.5820.0140.0140.0000.0000.0000.000
105B186ALA 00.0160.01235.253-0.006-0.0060.0000.0000.0000.000
106B187TRP 0-0.0140.00633.0420.0550.0550.0000.0000.0000.000
107B188PRO 0-0.026-0.02428.087-0.004-0.0040.0000.0000.0000.000
108B189LEU 00.0210.01231.3370.0080.0080.0000.0000.0000.000
109B190ILE 0-0.006-0.00928.7850.0620.0620.0000.0000.0000.000
110B191VAL 00.0350.03532.193-0.042-0.0420.0000.0000.0000.000
111B192THR 0-0.043-0.04032.7130.0870.0870.0000.0000.0000.000
112B193ALA 00.0120.01234.364-0.053-0.0530.0000.0000.0000.000
113B194LEU 0-0.014-0.00635.4180.0610.0610.0000.0000.0000.000
114B195ARG 10.8920.96732.644-0.840-0.8400.0000.0000.0000.000
115B196ALA -1-0.896-0.93238.1360.5730.5730.0000.0000.0000.000
116A1SER 10.8310.89036.267-0.405-0.4050.0000.0000.0000.000
117A2LYS 11.1021.06731.833-0.477-0.4770.0000.0000.0000.000
118A3MET 0-0.0500.02431.7290.0550.0550.0000.0000.0000.000
119A4SER 0-0.029-0.03931.6060.0320.0320.0000.0000.0000.000
120A5ASP -1-0.817-0.90628.6780.5080.5080.0000.0000.0000.000
121A6VAL 0-0.0050.01127.1190.0720.0720.0000.0000.0000.000
122A7LYS 10.8200.90726.530-0.611-0.6110.0000.0000.0000.000
123A8CYS 0-0.0030.01724.6410.1070.1070.0000.0000.0000.000
124A9THR 00.041-0.01722.7290.1010.1010.0000.0000.0000.000
125A10SER 0-0.017-0.00321.5770.1750.1750.0000.0000.0000.000
126A11VAL 00.0250.00520.6530.1970.1970.0000.0000.0000.000
127A12VAL 0-0.037-0.01417.5920.2240.2240.0000.0000.0000.000
128A13LEU 00.0130.00116.9220.3180.3180.0000.0000.0000.000
129A14LEU 0-0.0130.00916.7470.3890.3890.0000.0000.0000.000
130A15SER 00.0530.01314.0090.3820.3820.0000.0000.0000.000
131A16VAL 0-0.024-0.01412.7060.6460.6460.0000.0000.0000.000
132A17LEU 00.0160.00111.8100.9390.9390.0000.0000.0000.000
133A18GLN 0-0.083-0.03911.4121.3241.3240.0000.0000.0000.000
134A19GLN 0-0.022-0.0227.563-0.041-0.0410.0000.0000.0000.000
135A20LEU 0-0.066-0.0137.2153.0793.0790.0000.0000.0000.000
136A21ARG 10.8200.8942.287-45.933-43.0961.312-1.991-2.1590.028
137A22VAL 00.0830.0369.873-0.656-0.6560.0000.0000.0000.000
138A23GLU -1-0.875-0.92413.4263.9353.9350.0000.0000.0000.000
139A24SER 0-0.036-0.00812.687-0.179-0.1790.0000.0000.0000.000
140A25SER 00.0420.03314.597-0.290-0.2900.0000.0000.0000.000
141A26SER 00.0490.03517.368-0.202-0.2020.0000.0000.0000.000
142A27LYS 10.8390.88719.889-1.834-1.8340.0000.0000.0000.000
143A28LEU 00.1220.06117.068-0.139-0.1390.0000.0000.0000.000
144A29TRP 00.0780.04215.623-0.025-0.0250.0000.0000.0000.000
145A30ALA 0-0.013-0.00419.142-0.182-0.1820.0000.0000.0000.000
146A31GLN 00.002-0.00122.738-0.027-0.0270.0000.0000.0000.000
147A32CYS 0-0.0050.00919.657-0.082-0.0820.0000.0000.0000.000
148A33VAL 00.0180.00520.258-0.135-0.1350.0000.0000.0000.000
149A34GLN 00.0170.01922.520-0.110-0.1100.0000.0000.0000.000
150A35LEU 0-0.025-0.02724.264-0.114-0.1140.0000.0000.0000.000
151A36HIS 00.002-0.00622.284-0.094-0.0940.0000.0000.0000.000
152A37ASN 0-0.038-0.03624.601-0.066-0.0660.0000.0000.0000.000
153A38ASP -1-0.824-0.89027.2660.9410.9410.0000.0000.0000.000
154A39ILE 0-0.028-0.01526.890-0.101-0.1010.0000.0000.0000.000
155A40LEU 0-0.040-0.01425.254-0.102-0.1020.0000.0000.0000.000
156A41LEU 0-0.0030.00029.257-0.096-0.0960.0000.0000.0000.000
157A42ALA 00.0280.05832.100-0.060-0.0600.0000.0000.0000.000
158A43LYS 10.9480.96034.046-0.509-0.5090.0000.0000.0000.000
159A44ASP -1-0.838-0.94537.0670.5180.5180.0000.0000.0000.000
160A45THR 00.015-0.02934.8020.0250.0250.0000.0000.0000.000
161A46THR 0-0.0290.00134.3450.0330.0330.0000.0000.0000.000
162A47GLU -1-0.787-0.90133.8740.8090.8090.0000.0000.0000.000
163A48ALA 0-0.016-0.01531.2100.0630.0630.0000.0000.0000.000
164A49PHE 0-0.002-0.02129.9900.0670.0670.0000.0000.0000.000
165A50GLU -1-0.858-0.90530.3110.7680.7680.0000.0000.0000.000
166A51LYS 10.7970.88428.815-0.858-0.8580.0000.0000.0000.000
167A52MET 0-0.047-0.01923.3740.1560.1560.0000.0000.0000.000
168A53VAL 00.0150.00725.5710.0990.0990.0000.0000.0000.000
169A54SER 0-0.012-0.01326.0170.0470.0470.0000.0000.0000.000
170A55LEU 0-0.0150.01420.9570.1250.1250.0000.0000.0000.000
171A56LEU 00.0140.00220.5200.2060.2060.0000.0000.0000.000
172A57SER 0-0.030-0.03321.1300.1270.1270.0000.0000.0000.000
173A58VAL 00.0410.01017.9690.0820.0820.0000.0000.0000.000
174A59LEU 00.0080.00314.8440.2310.2310.0000.0000.0000.000
175A60LEU 0-0.017-0.01117.6750.1540.1540.0000.0000.0000.000
176A61SER 0-0.0120.02019.810-0.069-0.0690.0000.0000.0000.000
177A62MET 0-0.097-0.04413.2690.0990.0990.0000.0000.0000.000
178A63GLN 00.0570.05216.506-0.186-0.1860.0000.0000.0000.000
179A64GLY 0-0.007-0.00513.192-0.106-0.1060.0000.0000.0000.000
180A65ALA 0-0.055-0.01911.1600.1030.1030.0000.0000.0000.000
181A66VAL 00.0260.00811.6670.1670.1670.0000.0000.0000.000
182A67ASP -1-0.771-0.85914.1371.0621.0620.0000.0000.0000.000
183A68ILE 00.0590.00016.225-0.156-0.1560.0000.0000.0000.000
184A69ASN 00.0260.02418.750-0.219-0.2190.0000.0000.0000.000
185A70LYS 10.9100.93314.943-1.140-1.1400.0000.0000.0000.000
186A71LEU 0-0.0150.00113.735-0.092-0.0920.0000.0000.0000.000
187A72CYS 0-0.100-0.06817.077-0.175-0.1750.0000.0000.0000.000
188A73GLU -1-0.946-0.96218.5590.0290.0290.0000.0000.0000.000
189A74GLU -1-0.877-0.94214.344-0.413-0.4130.0000.0000.0000.000
190A75MET 0-0.122-0.05118.782-0.069-0.0690.0000.0000.0000.000
191A76LEU 0-0.057-0.02621.128-0.057-0.0570.0000.0000.0000.000
192A77ASP -1-0.871-0.92020.811-0.412-0.4120.0000.0000.0000.000
193A78ASN 0-0.117-0.04320.009-0.135-0.1350.0000.0000.0000.000
194A79ARG 10.8650.91522.4640.2550.2550.0000.0000.0000.000
195A80ALA 0-0.073-0.02525.5790.0380.0380.0000.0000.0000.000
196A81THR -1-0.915-0.95020.511-0.552-0.5520.0000.0000.0000.000
197B301HOH 0-0.005-0.02045.214-0.001-0.0010.0000.0000.0000.000
198B302HOH 00.0110.00734.0170.0010.0010.0000.0000.0000.000
199B303HOH 0-0.036-0.0361.731-14.325-20.49114.860-5.593-3.1010.052
200B304HOH 00.0160.00634.7390.0130.0130.0000.0000.0000.000
201B305HOH 0-0.008-0.01540.8310.0000.0000.0000.0000.0000.000
202B306HOH 00.0720.04138.0160.0140.0140.0000.0000.0000.000
203B307HOH 0-0.013-0.03926.5680.0040.0040.0000.0000.0000.000
204B308HOH 0-0.032-0.03128.2620.0070.0070.0000.0000.0000.000
205B309HOH 00.0120.00523.7670.0000.0000.0000.0000.0000.000
206B310HOH 0-0.054-0.04433.7540.0070.0070.0000.0000.0000.000
207B311HOH 00.002-0.00920.3840.0540.0540.0000.0000.0000.000
208B312HOH 0-0.057-0.04849.573-0.001-0.0010.0000.0000.0000.000
209B313HOH 00.0060.00034.995-0.011-0.0110.0000.0000.0000.000
210B314HOH 00.0190.00034.3530.0120.0120.0000.0000.0000.000
211B315HOH 0-0.063-0.05034.999-0.004-0.0040.0000.0000.0000.000
212B316HOH 0-0.070-0.04651.808-0.006-0.0060.0000.0000.0000.000
213B317HOH 00.002-0.00428.5970.0170.0170.0000.0000.0000.000
214B318HOH 0-0.064-0.03937.618-0.015-0.0150.0000.0000.0000.000
215B319HOH 00.0040.00540.2460.0080.0080.0000.0000.0000.000
216B320HOH 00.015-0.01420.7650.0490.0490.0000.0000.0000.000
217B321HOH 00.003-0.04529.7690.0220.0220.0000.0000.0000.000
218A101HOH 0-0.057-0.04417.139-0.124-0.1240.0000.0000.0000.000
219A102HOH 0-0.025-0.0151.615-12.934-23.92319.373-6.183-2.2000.058
220A103HOH 0-0.038-0.03617.733-0.127-0.1270.0000.0000.0000.000
221A104HOH 00.008-0.00134.9020.0020.0020.0000.0000.0000.000
222A105HOH 0-0.064-0.05036.4280.0110.0110.0000.0000.0000.000
223A106HOH 00.0460.03227.4400.0240.0240.0000.0000.0000.000
224A107HOH 0-0.028-0.02214.972-0.113-0.1130.0000.0000.0000.000
225A108HOH 0-0.025-0.02322.114-0.059-0.0590.0000.0000.0000.000
226A109HOH 00.0280.02114.109-0.121-0.1210.0000.0000.0000.000
227A110HOH 0-0.049-0.03423.606-0.004-0.0040.0000.0000.0000.000
228A111HOH 0-0.022-0.02321.8420.0320.0320.0000.0000.0000.000
229A112HOH 0-0.032-0.02129.1020.0130.0130.0000.0000.0000.000