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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: R12Y8

Calculation Name: 7JLT-AB-Xray159

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 7JLT

Chain ID: AB

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2020-09-18

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 217
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2185647.680141
FMO2-HF: Nuclear repulsion 2105592.061571
FMO2-HF: Total energy -80055.61857
FMO2-MP2: Total energy -80280.44967


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:SER )


Summations of interaction energy for fragment #1(A:1:SER )
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.
-63.696-57.0071.231-3.179-4.742-0.007
Interaction energy analysis for fragmet #1(A:1:SER )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.891 / q_NPA : 0.919
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].
3A3MET 00.0610.0622.6010.4674.1130.687-1.753-2.5790.007
4A4SER 0-0.006-0.0052.609-6.363-3.7900.546-1.365-1.755-0.014
5A5ASP -1-0.746-0.8564.424-37.019-36.685-0.001-0.043-0.2900.000
6A6VAL 0-0.0010.0116.5845.4195.4190.0000.0000.0000.000
7A7LYS 10.8050.9117.15535.83335.8330.0000.0000.0000.000
8A8CYS 0-0.019-0.0027.7303.3293.3290.0000.0000.0000.000
9A9THR 00.024-0.01110.4932.8352.8350.0000.0000.0000.000
10A10SER 00.014-0.00412.2782.4022.4020.0000.0000.0000.000
11A11VAL 00.0150.01713.3871.5561.5560.0000.0000.0000.000
12A12VAL 0-0.021-0.01114.6681.4761.4760.0000.0000.0000.000
13A13LEU 00.0050.00516.4571.1671.1670.0000.0000.0000.000
14A14LEU 00.0160.00618.0761.0121.0120.0000.0000.0000.000
15A15SER 00.0290.01519.5601.0091.0090.0000.0000.0000.000
16A16VAL 0-0.047-0.04120.7530.8240.8240.0000.0000.0000.000
17A17LEU 00.0110.00421.6160.7680.7680.0000.0000.0000.000
18A18GLN 0-0.022-0.02224.0370.2040.2040.0000.0000.0000.000
19A19GLN 0-0.076-0.03325.7590.6160.6160.0000.0000.0000.000
20A20LEU 0-0.0050.00725.7290.5730.5730.0000.0000.0000.000
21A21ARG 10.8950.95028.8639.7879.7870.0000.0000.0000.000
22A22VAL 00.0700.03526.6140.3410.3410.0000.0000.0000.000
23A23GLU -1-0.827-0.89728.560-10.994-10.9940.0000.0000.0000.000
24A24SER 0-0.028-0.00629.9570.2500.2500.0000.0000.0000.000
25A25SER 00.0010.01631.1950.3440.3440.0000.0000.0000.000
26A26SER 00.0630.02830.711-0.343-0.3430.0000.0000.0000.000
27A27LYS 10.9340.98729.95310.10610.1060.0000.0000.0000.000
28A28LEU 00.0590.01526.870-0.274-0.2740.0000.0000.0000.000
29A29TRP 00.0500.03523.811-0.630-0.6300.0000.0000.0000.000
30A30ALA 00.0280.01725.171-0.509-0.5090.0000.0000.0000.000
31A31GLN 0-0.027-0.01724.576-0.250-0.2500.0000.0000.0000.000
32A32CYS 0-0.020-0.00121.998-0.643-0.6430.0000.0000.0000.000
33A33VAL 00.019-0.00120.530-0.895-0.8950.0000.0000.0000.000
34A34GLN 0-0.035-0.00920.141-0.735-0.7350.0000.0000.0000.000
35A35LEU 00.0130.00818.342-0.759-0.7590.0000.0000.0000.000
36A36HIS 00.025-0.00416.082-1.734-1.7340.0000.0000.0000.000
37A37ASN 0-0.030-0.02215.182-1.708-1.7080.0000.0000.0000.000
38A38ASP -1-0.767-0.85615.311-17.248-17.2480.0000.0000.0000.000
39A39ILE 0-0.045-0.01011.049-1.665-1.6650.0000.0000.0000.000
40A40LEU 00.001-0.01410.783-3.113-3.1130.0000.0000.0000.000
41A41LEU 0-0.040-0.01211.213-1.639-1.6390.0000.0000.0000.000
42A42ALA 00.0100.0359.9500.0840.0840.0000.0000.0000.000
43A43LYS 10.8360.9279.71318.71118.7110.0000.0000.0000.000
44A44ASP -1-0.858-0.9467.324-26.941-26.9410.0000.0000.0000.000
45A45THR 00.039-0.0174.140-1.018-0.882-0.001-0.018-0.1180.000
46A46THR 00.0190.0167.0430.4450.4450.0000.0000.0000.000
47A47GLU -1-0.847-0.93110.578-20.597-20.5970.0000.0000.0000.000
48A48ALA 00.0260.0148.6900.8210.8210.0000.0000.0000.000
49A49PHE 00.013-0.0217.2910.0450.0450.0000.0000.0000.000
50A50GLU -1-0.886-0.92611.685-15.887-15.8870.0000.0000.0000.000
51A51LYS 10.8850.93014.33217.80617.8060.0000.0000.0000.000
52A52MET 0-0.029-0.01313.0530.8350.8350.0000.0000.0000.000
53A53VAL 00.0290.01715.1120.8370.8370.0000.0000.0000.000
54A54SER 0-0.007-0.01117.4770.6520.6520.0000.0000.0000.000
55A55LEU 00.0090.01516.8070.7250.7250.0000.0000.0000.000
56A56LEU 0-0.002-0.01117.6560.6660.6660.0000.0000.0000.000
57A57SER 00.010-0.01619.9230.8880.8880.0000.0000.0000.000
58A58VAL 00.0340.00322.7990.7100.7100.0000.0000.0000.000
59A59LEU 00.0030.00122.0480.5080.5080.0000.0000.0000.000
60A60LEU 0-0.017-0.01721.9980.4140.4140.0000.0000.0000.000
61A61SER 0-0.0460.00425.8930.5010.5010.0000.0000.0000.000
62A62MET 0-0.0130.00527.1500.4570.4570.0000.0000.0000.000
63A63GLN 00.0370.02830.153-0.075-0.0750.0000.0000.0000.000
64A64GLY 0-0.021-0.01532.5840.1590.1590.0000.0000.0000.000
65A65ALA 0-0.065-0.02528.7680.0160.0160.0000.0000.0000.000
66A66VAL 0-0.023-0.01725.118-0.297-0.2970.0000.0000.0000.000
67A67ASP -1-0.776-0.84028.506-9.678-9.6780.0000.0000.0000.000
68A68ILE 00.0410.01624.949-0.221-0.2210.0000.0000.0000.000
69A69ASN 00.0850.06127.295-0.607-0.6070.0000.0000.0000.000
70A70LYS 10.9700.99429.7419.1339.1330.0000.0000.0000.000
71A71LEU 0-0.067-0.03723.504-0.041-0.0410.0000.0000.0000.000
72A72CYS 0-0.057-0.06924.893-0.448-0.4480.0000.0000.0000.000
73A73GLU -1-0.922-0.94326.378-9.646-9.6460.0000.0000.0000.000
74A74GLU -1-0.862-0.91826.600-11.768-11.7680.0000.0000.0000.000
75A75MET 0-0.095-0.03820.914-0.440-0.4400.0000.0000.0000.000
76A76LEU 0-0.045-0.02025.315-0.219-0.2190.0000.0000.0000.000
77A77ASP -1-0.910-0.94727.036-9.801-9.8010.0000.0000.0000.000
78A78ASN 0-0.120-0.05526.6250.4820.4820.0000.0000.0000.000
79A79ARG 0-0.100-0.03923.654-2.209-2.2090.0000.0000.0000.000
80B77GLU 0-0.083-0.04537.2200.7790.7790.0000.0000.0000.000
81B78ASP -1-0.757-0.89135.461-8.574-8.5740.0000.0000.0000.000
82B79LYS 10.9390.97230.02910.10210.1020.0000.0000.0000.000
83B80ARG 10.9420.96730.4119.9739.9730.0000.0000.0000.000
84B81ALA 00.0620.03030.473-0.333-0.3330.0000.0000.0000.000
85B82LYS 10.9840.99330.6389.2429.2420.0000.0000.0000.000
86B83VAL 0-0.023-0.00126.055-0.334-0.3340.0000.0000.0000.000
87B84THR 00.0260.01725.965-0.420-0.4200.0000.0000.0000.000
88B85SER 0-0.036-0.01525.793-0.331-0.3310.0000.0000.0000.000
89B86ALA 00.0420.01124.868-0.338-0.3380.0000.0000.0000.000
90B87MET 0-0.028-0.01621.204-0.615-0.6150.0000.0000.0000.000
91B88GLN 00.019-0.00820.892-0.836-0.8360.0000.0000.0000.000
92B89THR 00.025-0.00121.678-0.753-0.7530.0000.0000.0000.000
93B90MET 00.0050.00117.782-0.662-0.6620.0000.0000.0000.000
94B91LEU 0-0.0140.02016.771-1.281-1.2810.0000.0000.0000.000
95B92PHE 00.0930.02816.820-1.144-1.1440.0000.0000.0000.000
96B93THR 0-0.0400.01216.565-0.897-0.8970.0000.0000.0000.000
97B94MET 0-0.042-0.01611.518-0.832-0.8320.0000.0000.0000.000
98B95LEU 0-0.008-0.01412.658-1.757-1.7570.0000.0000.0000.000
99B96ARG 10.9520.95414.48215.21315.2130.0000.0000.0000.000
100B97LYS 10.8230.9117.27035.82035.8200.0000.0000.0000.000
101B98LEU 0-0.146-0.0828.327-2.810-2.8100.0000.0000.0000.000
102B99ASP -1-0.875-0.91410.018-22.312-22.3120.0000.0000.0000.000
103B100ASN 00.000-0.00510.7860.9460.9460.0000.0000.0000.000
104B101ASP -1-0.824-0.89612.566-17.873-17.8730.0000.0000.0000.000
105B102ALA 0-0.038-0.02314.7991.1111.1110.0000.0000.0000.000
106B103LEU 0-0.033-0.04412.9340.7630.7630.0000.0000.0000.000
107B104ASN 0-0.011-0.01815.5050.8590.8590.0000.0000.0000.000
108B105ASN 00.0050.01418.0711.0161.0160.0000.0000.0000.000
109B106ILE 00.0100.00719.0220.6350.6350.0000.0000.0000.000
110B107ILE 00.0000.00518.0510.5090.5090.0000.0000.0000.000
111B108ASN 0-0.022-0.03621.2670.6420.6420.0000.0000.0000.000
112B109ASN 00.0260.01823.8710.8030.8030.0000.0000.0000.000
113B110ALA 00.0240.02125.4100.4950.4950.0000.0000.0000.000
114B111ARG 10.8000.89923.73912.83112.8310.0000.0000.0000.000
115B112ASP -1-0.891-0.93827.901-10.527-10.5270.0000.0000.0000.000
116B113GLY 0-0.019-0.00630.1140.3940.3940.0000.0000.0000.000
117B114CYS 0-0.094-0.03128.9380.1380.1380.0000.0000.0000.000
118B115VAL 00.0400.03328.072-0.570-0.5700.0000.0000.0000.000
119B116PRO 0-0.043-0.01425.3390.2960.2960.0000.0000.0000.000
120B117LEU 00.015-0.00628.5170.0840.0840.0000.0000.0000.000
121B118ASN 0-0.062-0.03429.1690.2110.2110.0000.0000.0000.000
122B119ILE 0-0.021-0.00424.011-0.219-0.2190.0000.0000.0000.000
123B120ILE 0-0.0010.01521.7480.3280.3280.0000.0000.0000.000
124B121PRO 0-0.012-0.00822.857-0.602-0.6020.0000.0000.0000.000
125B122LEU 00.019-0.00318.232-0.241-0.2410.0000.0000.0000.000
126B123THR 0-0.053-0.01821.628-0.385-0.3850.0000.0000.0000.000
127B124THR 00.0460.03024.3560.0970.0970.0000.0000.0000.000
128B125ALA 0-0.035-0.02126.3190.2880.2880.0000.0000.0000.000
129B126ALA 00.0340.00426.9110.2400.2400.0000.0000.0000.000
130B127LYS 10.8990.95428.5158.9868.9860.0000.0000.0000.000
131B128LEU 0-0.029-0.01526.073-0.299-0.2990.0000.0000.0000.000
132B129MET 0-0.039-0.01729.4130.3590.3590.0000.0000.0000.000
133B130VAL 00.0420.01528.060-0.348-0.3480.0000.0000.0000.000
134B131VAL 00.0070.01531.1660.3510.3510.0000.0000.0000.000
135B132ILE 00.0320.00932.162-0.345-0.3450.0000.0000.0000.000
136B133PRO 0-0.001-0.00633.2040.3310.3310.0000.0000.0000.000
137B134ASP -1-0.763-0.87735.807-8.438-8.4380.0000.0000.0000.000
138B135TYR 00.0410.01836.556-0.191-0.1910.0000.0000.0000.000
139B136ASN 0-0.100-0.06235.477-0.068-0.0680.0000.0000.0000.000
140B137THR 00.009-0.01730.981-0.322-0.3220.0000.0000.0000.000
141B138TYR 00.0670.01232.280-0.286-0.2860.0000.0000.0000.000
142B139LYS 10.9110.96133.6608.2328.2320.0000.0000.0000.000
143B140ASN 0-0.0300.00227.819-0.071-0.0710.0000.0000.0000.000
144B141THR 0-0.031-0.01628.012-0.315-0.3150.0000.0000.0000.000
145B142CYS 0-0.071-0.02229.926-0.218-0.2180.0000.0000.0000.000
146B143ASP -1-0.898-0.94032.192-8.855-8.8550.0000.0000.0000.000
147B144GLY 00.0120.01133.813-0.056-0.0560.0000.0000.0000.000
148B145THR 0-0.078-0.05434.8320.0870.0870.0000.0000.0000.000
149B146THR 0-0.0180.00129.158-0.145-0.1450.0000.0000.0000.000
150B147PHE 0-0.018-0.01228.106-0.010-0.0100.0000.0000.0000.000
151B148THR 0-0.010-0.01424.395-0.328-0.3280.0000.0000.0000.000
152B149TYR 00.0190.00124.2730.0040.0040.0000.0000.0000.000
153B150ALA 00.0090.01120.029-0.186-0.1860.0000.0000.0000.000
154B151SER 0-0.033-0.01517.203-0.410-0.4100.0000.0000.0000.000
155B152ALA 0-0.0110.00819.295-0.388-0.3880.0000.0000.0000.000
156B153LEU 00.0400.01721.7180.3240.3240.0000.0000.0000.000
157B154TRP 0-0.012-0.02722.892-0.001-0.0010.0000.0000.0000.000
158B155GLU -1-0.794-0.86528.160-9.296-9.2960.0000.0000.0000.000
159B156ILE 0-0.039-0.04231.8170.0440.0440.0000.0000.0000.000
160B157GLN 0-0.096-0.04034.2120.3060.3060.0000.0000.0000.000
161B158GLN 0-0.013-0.01336.8010.1780.1780.0000.0000.0000.000
162B159VAL 00.0340.01437.321-0.272-0.2720.0000.0000.0000.000
163B160VAL 0-0.0370.00839.4830.2430.2430.0000.0000.0000.000
164B161ASP -1-0.751-0.87640.405-7.203-7.2030.0000.0000.0000.000
165B162ALA 00.0060.00542.515-0.034-0.0340.0000.0000.0000.000
166B163ASP -1-0.877-0.89743.423-6.552-6.5520.0000.0000.0000.000
167B164SER 0-0.058-0.04443.7590.0680.0680.0000.0000.0000.000
168B165LYS 10.8270.92144.8296.4986.4980.0000.0000.0000.000
169B166ILE 0-0.073-0.03643.420-0.143-0.1430.0000.0000.0000.000
170B167VAL 00.0180.01342.5550.1400.1400.0000.0000.0000.000
171B168GLN 0-0.010-0.01842.645-0.264-0.2640.0000.0000.0000.000
172B169LEU 00.0590.01837.8850.0140.0140.0000.0000.0000.000
173B170SER 0-0.053-0.02841.7970.0110.0110.0000.0000.0000.000
174B171GLU -1-0.875-0.93544.612-6.652-6.6520.0000.0000.0000.000
175B172ILE 0-0.0270.01139.3430.0270.0270.0000.0000.0000.000
176B173SER 00.000-0.02241.265-0.179-0.1790.0000.0000.0000.000
177B174MET 0-0.026-0.01641.573-0.024-0.0240.0000.0000.0000.000
178B175ASP -1-0.906-0.93443.597-6.657-6.6570.0000.0000.0000.000
179B176ASN 00.0060.00246.5100.2520.2520.0000.0000.0000.000
180B177SER 00.022-0.00742.738-0.068-0.0680.0000.0000.0000.000
181B178PRO 0-0.0240.00244.803-0.098-0.0980.0000.0000.0000.000
182B179ASN 0-0.050-0.00546.8920.0300.0300.0000.0000.0000.000
183B180LEU 00.0050.01643.1090.0590.0590.0000.0000.0000.000
184B181ALA 00.0020.00945.488-0.013-0.0130.0000.0000.0000.000
185B182TRP 0-0.0110.01537.624-0.258-0.2580.0000.0000.0000.000
186B183PRO 0-0.027-0.02437.5640.1080.1080.0000.0000.0000.000
187B184LEU 00.0200.01836.8750.1190.1190.0000.0000.0000.000
188B185ILE 0-0.026-0.02835.092-0.294-0.2940.0000.0000.0000.000
189B186VAL 00.0350.02532.4530.2170.2170.0000.0000.0000.000
190B187THR 0-0.046-0.02333.099-0.293-0.2930.0000.0000.0000.000
191B188ALA 00.0220.01030.1390.2090.2090.0000.0000.0000.000
192B189LEU 0-0.031-0.01529.939-0.165-0.1650.0000.0000.0000.000
193B190ARG 10.8230.93019.03014.22514.2250.0000.0000.0000.000
194B191ALA 00.0670.03826.6110.2640.2640.0000.0000.0000.000
195B192ASN -1-0.882-0.94921.946-12.905-12.9050.0000.0000.0000.000
196A101HOH 0-0.043-0.00822.825-0.050-0.0500.0000.0000.0000.000
197A102HOH 00.011-0.00830.879-0.086-0.0860.0000.0000.0000.000
198A103HOH 0-0.040-0.03431.9790.1260.1260.0000.0000.0000.000
199A104HOH 0-0.050-0.05034.9810.1150.1150.0000.0000.0000.000
200A105HOH 0-0.042-0.03829.734-0.055-0.0550.0000.0000.0000.000
201A106HOH 0-0.048-0.03434.5250.0570.0570.0000.0000.0000.000
202A107HOH 0-0.003-0.00530.0420.1370.1370.0000.0000.0000.000
203A108HOH 0-0.020-0.01519.6390.2230.2230.0000.0000.0000.000
204A109HOH 0-0.010-0.01020.830-0.064-0.0640.0000.0000.0000.000
205A110HOH 0-0.022-0.01630.979-0.024-0.0240.0000.0000.0000.000
206B201HOH 0-0.015-0.01751.008-0.007-0.0070.0000.0000.0000.000
207B202HOH 0-0.051-0.05448.0740.0640.0640.0000.0000.0000.000
208B203HOH 00.008-0.00528.569-0.161-0.1610.0000.0000.0000.000
209B204HOH 0-0.010-0.01548.9110.0650.0650.0000.0000.0000.000
210B205HOH 0-0.023-0.04525.595-0.200-0.2000.0000.0000.0000.000
211B206HOH 0-0.004-0.00829.4850.1760.1760.0000.0000.0000.000
212B207HOH 0-0.020-0.01329.763-0.019-0.0190.0000.0000.0000.000
213B208HOH 00.0260.01812.715-0.589-0.5890.0000.0000.0000.000
214B209HOH 00.0120.00949.9780.0340.0340.0000.0000.0000.000
215B210HOH 0-0.021-0.01916.828-0.470-0.4700.0000.0000.0000.000
216B211HOH 0-0.046-0.03950.9100.0300.0300.0000.0000.0000.000
217B212HOH 0-0.035-0.02650.665-0.002-0.0020.0000.0000.0000.000