FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: Z244N

Calculation Name: 7JJC-BF-Xray89

Preferred Name:

Target Type:

Ligand Name: glycerol

ligand 3-letter code: GOL

PDB ID: 7JJC

Chain ID: BF

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2021-02-22

Reference: T. Ohyama, K. Kamisaka, C. Watanabe, T. Honma et. al., FMO-based interaction energy analysis of SARS-Cov-2 related protein and ligand complexes, To be published.

DOI:

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHLSideSolv
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water Waters within average of the temperature factors of receptor.
Procedure Auto-FMO protocol ver. 1.20200406
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 192
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software MIZUHO/ABINIT-MP 4.0(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1879690.169503
FMO2-HF: Nuclear repulsion 1810476.621297
FMO2-HF: Total energy -69213.548206
FMO2-MP2: Total energy -69414.61275


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:-10:GLY )


Summations of interaction energy for fragment #1(B:-10:GLY )
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.
-11.983-5.8064.437-5.862-4.753-0.05
Interaction energy analysis for fragmet #1(B:-10:GLY )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.015 / q_NPA : -0.001
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].
3B-8GLU -1-0.810-0.9152.360-14.134-8.0894.438-5.831-4.652-0.050
4B-7ASN 0-0.0090.0054.2961.3951.527-0.001-0.031-0.1010.000
5B-6LEU 0-0.032-0.0086.7920.4230.4230.0000.0000.0000.000
6B-5TYR 0-0.062-0.0569.039-0.030-0.0300.0000.0000.0000.000
7B-4GLN 00.0250.01410.2120.0740.0740.0000.0000.0000.000
8B-3GLY 00.0270.01513.1480.0350.0350.0000.0000.0000.000
9B-2GLY 00.012-0.01316.2580.0320.0320.0000.0000.0000.000
10B-1HIS 0-0.090-0.05113.8640.0690.0690.0000.0000.0000.000
11B0MET 0-0.045-0.00316.0840.0080.0080.0000.0000.0000.000
12B273PHE 00.0270.00119.2600.0070.0070.0000.0000.0000.000
13B274LYS 10.8290.90223.0140.1360.1360.0000.0000.0000.000
14B424CYS 0-0.057-0.00921.1280.0080.0080.0000.0000.0000.000
15B276MET 00.0040.02221.323-0.014-0.0140.0000.0000.0000.000
16B277GLU -1-0.816-0.88623.938-0.110-0.1100.0000.0000.0000.000
17B278ALA 0-0.011-0.00627.2530.0000.0000.0000.0000.0000.000
18B279LEU 0-0.049-0.03326.1510.0030.0030.0000.0000.0000.000
19B280GLY 00.0760.03430.3370.0040.0040.0000.0000.0000.000
20B281MET 0-0.0180.00331.9120.0050.0050.0000.0000.0000.000
21B282GLU -1-0.892-0.93834.147-0.050-0.0500.0000.0000.0000.000
22B283SER 0-0.064-0.04435.7670.0030.0030.0000.0000.0000.000
23B284GLY 00.0130.00037.3840.0020.0020.0000.0000.0000.000
24B285GLU -1-0.966-0.95734.959-0.054-0.0540.0000.0000.0000.000
25B286ILE 0-0.087-0.01832.2850.0010.0010.0000.0000.0000.000
26B287HIS 00.0970.04836.9380.0020.0020.0000.0000.0000.000
27B288SER 0-0.037-0.06939.1110.0000.0000.0000.0000.0000.000
28B289ASP -1-0.883-0.93140.603-0.016-0.0160.0000.0000.0000.000
29B290GLN 0-0.063-0.03535.3990.0020.0020.0000.0000.0000.000
30B291ILE 0-0.042-0.00435.5850.0000.0000.0000.0000.0000.000
31B292THR 00.0170.00136.1240.0020.0020.0000.0000.0000.000
32B293ALA 0-0.014-0.02535.907-0.001-0.0010.0000.0000.0000.000
33B294SER 0-0.033-0.02736.1570.0000.0000.0000.0000.0000.000
34B295SER 00.006-0.02437.9220.0000.0000.0000.0000.0000.000
35B296GLN 0-0.020-0.02039.995-0.003-0.0030.0000.0000.0000.000
36B297TYR 0-0.0110.00442.4950.0010.0010.0000.0000.0000.000
37B298SER 00.013-0.01344.5310.0000.0000.0000.0000.0000.000
38B299THR 00.0760.03145.6500.0000.0000.0000.0000.0000.000
39B300ASN 0-0.069-0.03946.407-0.001-0.0010.0000.0000.0000.000
40B301TRP 0-0.032-0.02540.822-0.002-0.0020.0000.0000.0000.000
41B302SER 00.0700.04141.7860.0010.0010.0000.0000.0000.000
42B303ALA 00.0680.01438.291-0.001-0.0010.0000.0000.0000.000
43B304GLU -1-0.883-0.89438.352-0.020-0.0200.0000.0000.0000.000
44B305ARG 10.8060.89140.3350.0120.0120.0000.0000.0000.000
45B306SER 0-0.035-0.04034.720-0.002-0.0020.0000.0000.0000.000
46B307ARG 10.8560.92534.7590.0280.0280.0000.0000.0000.000
47B308LEU 0-0.019-0.00731.1500.0020.0020.0000.0000.0000.000
48B309ASN 0-0.047-0.03934.5860.0020.0020.0000.0000.0000.000
49B310TYR 00.0240.02937.4080.0020.0020.0000.0000.0000.000
50B311PRO 00.0280.01640.0420.0010.0010.0000.0000.0000.000
51B312GLU -1-0.877-0.92343.045-0.014-0.0140.0000.0000.0000.000
52B313ASN 0-0.017-0.02142.515-0.001-0.0010.0000.0000.0000.000
53B314GLY 00.0690.03138.843-0.003-0.0030.0000.0000.0000.000
54B315TRP 0-0.0180.01033.7960.0010.0010.0000.0000.0000.000
55B316THR 0-0.034-0.05337.661-0.001-0.0010.0000.0000.0000.000
56B317PRO 0-0.0300.01036.739-0.001-0.0010.0000.0000.0000.000
57B318GLY 00.005-0.00639.8300.0000.0000.0000.0000.0000.000
58B319GLU -1-0.911-0.95340.5290.0160.0160.0000.0000.0000.000
59B320ASP -1-0.756-0.83737.9050.0070.0070.0000.0000.0000.000
60B321SER 00.023-0.00936.2670.0040.0040.0000.0000.0000.000
61B322TYR 00.0260.00330.543-0.002-0.0020.0000.0000.0000.000
62B323ARG 10.8710.92731.612-0.038-0.0380.0000.0000.0000.000
63B324GLU -1-0.824-0.83334.0250.0130.0130.0000.0000.0000.000
64B325TRP 0-0.019-0.03331.6580.0010.0010.0000.0000.0000.000
65B326ILE 0-0.0120.01631.745-0.001-0.0010.0000.0000.0000.000
66B327GLN 0-0.007-0.00931.2900.0030.0030.0000.0000.0000.000
67B328VAL 00.0280.01630.2130.0000.0000.0000.0000.0000.000
68B329ASP -1-0.762-0.83831.189-0.027-0.0270.0000.0000.0000.000
69B330LEU 0-0.016-0.01127.184-0.002-0.0020.0000.0000.0000.000
70B331GLY 00.0350.02331.778-0.003-0.0030.0000.0000.0000.000
71B332LEU 0-0.068-0.04531.3430.0030.0030.0000.0000.0000.000
72B333LEU 0-0.0070.00826.065-0.003-0.0030.0000.0000.0000.000
73B334ARG 10.8880.94226.6100.0610.0610.0000.0000.0000.000
74B335PHE 00.0450.02020.648-0.002-0.0020.0000.0000.0000.000
75B336VAL 0-0.022-0.01121.7220.0050.0050.0000.0000.0000.000
76B337THR 0-0.009-0.02318.528-0.005-0.0050.0000.0000.0000.000
77B338ALA 00.0480.02418.863-0.018-0.0180.0000.0000.0000.000
78B339VAL 00.0030.00521.3180.0110.0110.0000.0000.0000.000
79B340GLY 00.0160.02824.184-0.006-0.0060.0000.0000.0000.000
80B341THR 0-0.014-0.01426.8650.0060.0060.0000.0000.0000.000
81B342GLN 00.0100.00129.121-0.002-0.0020.0000.0000.0000.000
82B343GLY 00.0230.03532.3030.0050.0050.0000.0000.0000.000
83B344ALA 0-0.0060.00734.856-0.003-0.0030.0000.0000.0000.000
84B345ILE 0-0.023-0.01338.5380.0020.0020.0000.0000.0000.000
85B346SER 00.000-0.02341.741-0.001-0.0010.0000.0000.0000.000
86B347LYS 10.8440.92442.8780.0190.0190.0000.0000.0000.000
87B348GLU -1-0.806-0.87647.542-0.009-0.0090.0000.0000.0000.000
88B349THR 0-0.052-0.06246.7390.0000.0000.0000.0000.0000.000
89B350LYS 10.8740.93945.9290.0120.0120.0000.0000.0000.000
90B351LYS 10.8810.95943.470-0.001-0.0010.0000.0000.0000.000
91B352LYS 10.9400.96338.8320.0070.0070.0000.0000.0000.000
92B353TYR 0-0.043-0.02837.9450.0030.0030.0000.0000.0000.000
93B354TYR 00.0640.02131.809-0.004-0.0040.0000.0000.0000.000
94B355VAL 0-0.004-0.00129.0100.0050.0050.0000.0000.0000.000
95B356LYS 10.8320.91128.277-0.019-0.0190.0000.0000.0000.000
96B357THR 00.0080.02424.310-0.003-0.0030.0000.0000.0000.000
97B358TYR 00.0500.02523.8400.0040.0040.0000.0000.0000.000
98B359LYS 10.8780.95322.747-0.075-0.0750.0000.0000.0000.000
99B360ILE 00.0300.01321.991-0.007-0.0070.0000.0000.0000.000
100B361ASP -1-0.765-0.81922.6620.0420.0420.0000.0000.0000.000
101B362VAL 0-0.017-0.00621.687-0.009-0.0090.0000.0000.0000.000
102B363SER 00.0220.00424.7710.0080.0080.0000.0000.0000.000
103B364SER 00.033-0.00825.401-0.011-0.0110.0000.0000.0000.000
104B365ASN 0-0.025-0.03727.885-0.004-0.0040.0000.0000.0000.000
105B366GLY 00.0160.02430.4950.0000.0000.0000.0000.0000.000
106B367GLU -1-0.976-0.98531.7790.0100.0100.0000.0000.0000.000
107B368ASP -1-0.867-0.90228.1550.0250.0250.0000.0000.0000.000
108B369TRP 0-0.056-0.02826.835-0.007-0.0070.0000.0000.0000.000
109B370ILE 0-0.0010.00020.4830.0130.0130.0000.0000.0000.000
110B371THR 0-0.075-0.06221.121-0.006-0.0060.0000.0000.0000.000
111B372ILE 00.0250.02917.1380.0160.0160.0000.0000.0000.000
112B373LYS 10.8730.92215.888-0.079-0.0790.0000.0000.0000.000
113B374GLU -1-0.780-0.85110.7770.1860.1860.0000.0000.0000.000
114B375GLY 00.0210.01111.2530.0810.0810.0000.0000.0000.000
115B376ASN 0-0.007-0.01412.0020.0070.0070.0000.0000.0000.000
116B377LYS 10.8700.93812.645-0.438-0.4380.0000.0000.0000.000
117B378PRO 0-0.044-0.04316.690-0.011-0.0110.0000.0000.0000.000
118B379VAL 00.0240.03015.5230.0200.0200.0000.0000.0000.000
119B380LEU 0-0.012-0.00818.233-0.014-0.0140.0000.0000.0000.000
120B381PHE 00.0240.00917.8270.0000.0000.0000.0000.0000.000
121B382GLN 0-0.021-0.02420.1610.0120.0120.0000.0000.0000.000
122B383GLY 00.0270.00822.764-0.012-0.0120.0000.0000.0000.000
123B384ASN 0-0.0270.00026.225-0.001-0.0010.0000.0000.0000.000
124B385THR 00.0500.01127.9240.0060.0060.0000.0000.0000.000
125B386ASN 0-0.004-0.01130.6710.0030.0030.0000.0000.0000.000
126B387PRO 0-0.024-0.01333.450-0.002-0.0020.0000.0000.0000.000
127B388THR 0-0.015-0.02135.3700.0010.0010.0000.0000.0000.000
128B389ASP -1-0.797-0.85831.498-0.046-0.0460.0000.0000.0000.000
129B390VAL 00.0310.01928.3440.0040.0040.0000.0000.0000.000
130B391VAL 0-0.023-0.00324.550-0.006-0.0060.0000.0000.0000.000
131B392VAL 00.0210.01621.7300.0040.0040.0000.0000.0000.000
132B393ALA 0-0.0190.00720.615-0.005-0.0050.0000.0000.0000.000
133B394VAL 00.010-0.00515.9650.0020.0020.0000.0000.0000.000
134B395PHE 0-0.016-0.01416.8030.0140.0140.0000.0000.0000.000
135B396PRO 00.0580.02511.897-0.053-0.0530.0000.0000.0000.000
136B397LYS 10.8830.9537.8770.4790.4790.0000.0000.0000.000
137B398PRO 00.0890.05013.7050.0540.0540.0000.0000.0000.000
138B399LEU 0-0.069-0.02116.6750.0060.0060.0000.0000.0000.000
139B400ILE 00.0320.02519.169-0.002-0.0020.0000.0000.0000.000
140B401THR 0-0.007-0.02122.1560.0160.0160.0000.0000.0000.000
141B402ARG 10.8320.89024.6570.0200.0200.0000.0000.0000.000
142B403PHE 0-0.0100.01728.013-0.001-0.0010.0000.0000.0000.000
143B404VAL 00.004-0.00325.3320.0000.0000.0000.0000.0000.000
144B405ARG 10.8900.93227.069-0.008-0.0080.0000.0000.0000.000
145B406ILE 0-0.0020.00326.7870.0030.0030.0000.0000.0000.000
146B407LYS 10.8560.90525.866-0.035-0.0350.0000.0000.0000.000
147B408PRO 0-0.008-0.00727.8040.0040.0040.0000.0000.0000.000
148B409ALA 0-0.036-0.01526.8820.0060.0060.0000.0000.0000.000
149B410THR 0-0.010-0.01127.8560.0030.0030.0000.0000.0000.000
150B411TRP 00.0450.03430.268-0.005-0.0050.0000.0000.0000.000
151B412GLU -1-0.849-0.90132.8320.0130.0130.0000.0000.0000.000
152B413THR 0-0.047-0.01835.370-0.003-0.0030.0000.0000.0000.000
153B414GLY 0-0.007-0.03238.1120.0020.0020.0000.0000.0000.000
154B415ILE 0-0.045-0.01234.211-0.003-0.0030.0000.0000.0000.000
155B416SER 00.010-0.00335.582-0.001-0.0010.0000.0000.0000.000
156B417MET 0-0.054-0.01228.7950.0010.0010.0000.0000.0000.000
157B418ARG 10.8070.91933.6390.0310.0310.0000.0000.0000.000
158B419PHE 0-0.024-0.03729.047-0.001-0.0010.0000.0000.0000.000
159B420GLU -1-0.701-0.81529.241-0.057-0.0570.0000.0000.0000.000
160B421VAL 0-0.029-0.02225.580-0.002-0.0020.0000.0000.0000.000
161B422TYR 00.0300.01523.7730.0010.0010.0000.0000.0000.000
162B423GLY 00.0490.01723.134-0.006-0.0060.0000.0000.0000.000
163B425LYS 10.9480.96526.0110.0760.0760.0000.0000.0000.000
164B426ILE 0-0.040-0.01625.127-0.009-0.0090.0000.0000.0000.000
165B427THR -1-0.926-0.94426.538-0.073-0.0730.0000.0000.0000.000
166F683ARG 10.9620.96448.590-0.007-0.0070.0000.0000.0000.000
167F684ALA 00.0280.00549.9810.0000.0000.0000.0000.0000.000
168F685ARG 00.1140.13339.957-0.008-0.0080.0000.0000.0000.000
169B601HOH 0-0.034-0.02931.505-0.002-0.0020.0000.0000.0000.000
170B602HOH 0-0.022-0.02810.9920.0350.0350.0000.0000.0000.000
171B603HOH 0-0.023-0.03033.3460.0020.0020.0000.0000.0000.000
172B604HOH 00.026-0.00129.356-0.002-0.0020.0000.0000.0000.000
173B605HOH 0-0.006-0.01915.683-0.002-0.0020.0000.0000.0000.000
174B606HOH 0-0.021-0.02932.5320.0010.0010.0000.0000.0000.000
175B607HOH 00.012-0.00127.228-0.003-0.0030.0000.0000.0000.000
176B608HOH 00.0290.02837.082-0.001-0.0010.0000.0000.0000.000
177B609HOH 0-0.027-0.02228.638-0.002-0.0020.0000.0000.0000.000
178B610HOH 0-0.016-0.03730.8680.0030.0030.0000.0000.0000.000
179B611HOH 00.002-0.00323.4160.0050.0050.0000.0000.0000.000
180B612HOH 0-0.019-0.01835.2320.0000.0000.0000.0000.0000.000
181B613HOH 0-0.019-0.02127.746-0.001-0.0010.0000.0000.0000.000
182B614HOH 0-0.024-0.02020.254-0.002-0.0020.0000.0000.0000.000
183B615HOH 0-0.049-0.04015.709-0.011-0.0110.0000.0000.0000.000
184B616HOH 0-0.020-0.00935.3360.0020.0020.0000.0000.0000.000
185B617HOH 00.0460.02533.267-0.001-0.0010.0000.0000.0000.000
186B618HOH 0-0.037-0.02540.8650.0000.0000.0000.0000.0000.000
187B619HOH 0-0.007-0.01025.991-0.003-0.0030.0000.0000.0000.000
188B620HOH 0-0.028-0.02834.5500.0010.0010.0000.0000.0000.000
189B621HOH 00.0310.02231.620-0.001-0.0010.0000.0000.0000.000
190B622HOH 0-0.019-0.02319.152-0.005-0.0050.0000.0000.0000.000
191B623HOH 00.0300.02127.5280.0010.0010.0000.0000.0000.000
192F701HOH 0-0.023-0.01552.2120.0000.0000.0000.0000.0000.000