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: 2J3RR

Calculation Name: 2GEE-A-Xray372

Preferred Name: Fibronectin

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2GEE

Chain ID: A

ChEMBL ID: CHEMBL3810

UniProt ID: P02751

Base Structure: X-ray

Registration Date: 2023-09-19

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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1705179.976877
FMO2-HF: Nuclear repulsion 1634182.784385
FMO2-HF: Total energy -70997.192492
FMO2-MP2: Total energy -71207.881038


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:87:PRO)


Summations of interaction energy for fragment #1(A:87: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.
-2.1370.7770.101-1.166-1.8480.002
Interaction energy analysis for fragmet #1(A:87:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.030 / q_NPA : -0.019
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].
3A89GLY0-0.001-0.0072.588-1.2151.3680.096-1.083-1.5950.002
4A90SER00.005-0.0193.8330.1990.5300.005-0.083-0.2530.000
5A91HIS0-0.073-0.0335.918-0.209-0.2090.0000.0000.0000.000
6A92MET00.0880.0649.3580.0840.0840.0000.0000.0000.000
7A93GLU-1-0.998-0.9998.797-0.462-0.4620.0000.0000.0000.000
8A94VAL00.008-0.0039.9890.0390.0390.0000.0000.0000.000
9A95PRO0-0.054-0.02812.2620.0090.0090.0000.0000.0000.000
10A96GLN00.0890.04014.729-0.020-0.0200.0000.0000.0000.000
11A97PRO0-0.003-0.01316.6740.0040.0040.0000.0000.0000.000
12A98THR0-0.007-0.02120.372-0.006-0.0060.0000.0000.0000.000
13A99ASP-1-0.891-0.92323.063-0.086-0.0860.0000.0000.0000.000
14A100LEU0-0.0140.02423.5630.0020.0020.0000.0000.0000.000
15A101SER0-0.062-0.04226.2480.0060.0060.0000.0000.0000.000
16A102PHE00.0490.00825.958-0.002-0.0020.0000.0000.0000.000
17A103VAL0-0.063-0.00931.6460.0030.0030.0000.0000.0000.000
18A104ASP-1-0.715-0.89334.464-0.052-0.0520.0000.0000.0000.000
19A105ILE00.028-0.00336.9280.0010.0010.0000.0000.0000.000
20A106THR0-0.079-0.04839.2600.0000.0000.0000.0000.0000.000
21A107ASP-1-0.954-0.95641.339-0.034-0.0340.0000.0000.0000.000
22A108SER0-0.0180.01638.5620.0010.0010.0000.0000.0000.000
23A109SER0-0.012-0.00136.403-0.002-0.0020.0000.0000.0000.000
24A110ILE0-0.0180.02431.0680.0000.0000.0000.0000.0000.000
25A111GLY0-0.033-0.02332.656-0.001-0.0010.0000.0000.0000.000
26A112LEU0-0.0290.00125.214-0.001-0.0010.0000.0000.0000.000
27A113ARG10.9440.96028.6630.0600.0600.0000.0000.0000.000
28A114TRP0-0.0160.00823.5120.0000.0000.0000.0000.0000.000
29A115THR0-0.029-0.04225.3170.0060.0060.0000.0000.0000.000
30A116PRO0-0.061-0.04123.241-0.008-0.0080.0000.0000.0000.000
31A117LEU00.0310.02216.123-0.001-0.0010.0000.0000.0000.000
32A118ASN00.006-0.01018.6920.0130.0130.0000.0000.0000.000
33A119SER0-0.054-0.02015.049-0.012-0.0120.0000.0000.0000.000
34A120SER00.0170.01317.0880.0040.0040.0000.0000.0000.000
35A121THR0-0.085-0.05717.780-0.017-0.0170.0000.0000.0000.000
36A122ILE0-0.0230.02117.696-0.015-0.0150.0000.0000.0000.000
37A123ILE0-0.044-0.02117.4990.0110.0110.0000.0000.0000.000
38A124GLY00.0310.01519.0270.0170.0170.0000.0000.0000.000
39A125TYR0-0.0110.00919.056-0.026-0.0260.0000.0000.0000.000
40A126ARG10.8700.93715.2750.1560.1560.0000.0000.0000.000
41A127ILE0-0.035-0.00319.892-0.008-0.0080.0000.0000.0000.000
42A128THR00.0330.01920.0140.0020.0020.0000.0000.0000.000
43A129VAL0-0.021-0.00322.889-0.002-0.0020.0000.0000.0000.000
44A130VAL00.007-0.01523.3140.0030.0030.0000.0000.0000.000
45A131ALA00.0430.04326.525-0.001-0.0010.0000.0000.0000.000
46A132ALA00.004-0.01328.122-0.001-0.0010.0000.0000.0000.000
47A133GLY0-0.028-0.02628.9160.0030.0030.0000.0000.0000.000
48A134GLU-1-0.992-0.98329.004-0.030-0.0300.0000.0000.0000.000
49A135GLY0-0.010-0.01626.792-0.004-0.0040.0000.0000.0000.000
50A136ILE0-0.050-0.04127.4170.0030.0030.0000.0000.0000.000
51A137PRO0-0.011-0.01828.056-0.002-0.0020.0000.0000.0000.000
52A138ILE0-0.0230.04421.695-0.001-0.0010.0000.0000.0000.000
53A139PHE0-0.008-0.00826.0680.0030.0030.0000.0000.0000.000
54A140GLU-1-0.906-0.97420.170-0.106-0.1060.0000.0000.0000.000
55A141ASP-1-0.889-0.93423.788-0.060-0.0600.0000.0000.0000.000
56A142PHE0-0.063-0.03521.679-0.010-0.0100.0000.0000.0000.000
57A143VAL0-0.0030.02123.1970.0080.0080.0000.0000.0000.000
58A144ASP-1-0.867-0.94423.027-0.092-0.0920.0000.0000.0000.000
59A145SER0-0.029-0.04022.0340.0020.0020.0000.0000.0000.000
60A146SER0-0.095-0.03823.534-0.002-0.0020.0000.0000.0000.000
61A147VAL00.0000.01026.1550.0070.0070.0000.0000.0000.000
62A148GLY00.0240.00225.800-0.007-0.0070.0000.0000.0000.000
63A149TYR0-0.066-0.05527.4610.0020.0020.0000.0000.0000.000
64A150TYR00.0610.01126.666-0.001-0.0010.0000.0000.0000.000
65A151THR0-0.020-0.01129.4940.0000.0000.0000.0000.0000.000
66A152VAL00.0540.05428.769-0.001-0.0010.0000.0000.0000.000
67A153THR0-0.024-0.02331.9180.0020.0020.0000.0000.0000.000
68A154GLY00.036-0.00434.736-0.001-0.0010.0000.0000.0000.000
69A155LEU0-0.027-0.00432.1750.0000.0000.0000.0000.0000.000
70A156GLU-1-0.898-0.95935.519-0.029-0.0290.0000.0000.0000.000
71A157PRO0-0.026-0.04437.042-0.002-0.0020.0000.0000.0000.000
72A158GLY0-0.008-0.01138.9620.0010.0010.0000.0000.0000.000
73A159ILE0-0.0170.01533.1370.0000.0000.0000.0000.0000.000
74A160ASP-1-0.867-0.96030.358-0.056-0.0560.0000.0000.0000.000
75A161TYR00.0310.03129.2080.0010.0010.0000.0000.0000.000
76A162ASP-1-0.839-0.92923.015-0.089-0.0890.0000.0000.0000.000
77A163ILE0-0.018-0.01624.775-0.001-0.0010.0000.0000.0000.000
78A164SER00.005-0.03019.272-0.006-0.0060.0000.0000.0000.000
79A165VAL0-0.0080.00020.4180.0010.0010.0000.0000.0000.000
80A166TYR0-0.014-0.01714.113-0.008-0.0080.0000.0000.0000.000
81A167THR0-0.030-0.00114.7200.0060.0060.0000.0000.0000.000
82A168VAL00.0560.01914.532-0.035-0.0350.0000.0000.0000.000
83A169LYS10.9480.94412.9990.3100.3100.0000.0000.0000.000
84A170ASN0-0.015-0.01713.318-0.014-0.0140.0000.0000.0000.000
85A171GLY00.0140.01312.767-0.024-0.0240.0000.0000.0000.000
86A172GLY00.0140.0219.730-0.071-0.0710.0000.0000.0000.000
87A173GLU-1-0.849-0.9139.947-0.152-0.1520.0000.0000.0000.000
88A174SER0-0.0500.00810.065-0.062-0.0620.0000.0000.0000.000
89A175THR00.0120.00911.5490.0030.0030.0000.0000.0000.000
90A176PRO00.0010.00112.846-0.001-0.0010.0000.0000.0000.000
91A177THR0-0.049-0.00616.5430.0050.0050.0000.0000.0000.000
92A178THR00.0220.00519.744-0.002-0.0020.0000.0000.0000.000
93A179LEU0-0.049-0.02422.4710.0010.0010.0000.0000.0000.000
94A180THR00.0040.01926.057-0.002-0.0020.0000.0000.0000.000
95A181GLN0-0.096-0.05028.8040.0020.0020.0000.0000.0000.000
96A182GLN0-0.031-0.00631.9330.0030.0030.0000.0000.0000.000
97A183THR00.0290.02235.1120.0010.0010.0000.0000.0000.000
98A184ALA0-0.030-0.00237.1860.0020.0020.0000.0000.0000.000
99A185VAL00.0530.03340.7880.0000.0000.0000.0000.0000.000
100A186PRO00.000-0.01743.5950.0000.0000.0000.0000.0000.000
101A187PRO00.0030.01146.1000.0010.0010.0000.0000.0000.000
102A188PRO00.0090.01749.2040.0000.0000.0000.0000.0000.000
103A189THR0-0.030-0.04152.0590.0000.0000.0000.0000.0000.000
104A190ASP-1-0.856-0.93954.527-0.017-0.0170.0000.0000.0000.000
105A191LEU00.0460.04457.9700.0010.0010.0000.0000.0000.000
106A192ARG10.7970.89059.7760.0170.0170.0000.0000.0000.000
107A193PHE00.0300.01262.2780.0000.0000.0000.0000.0000.000
108A194THR0-0.037-0.02966.3680.0000.0000.0000.0000.0000.000
109A195ASN00.0130.01169.9060.0000.0000.0000.0000.0000.000
110A196ILE0-0.037-0.02571.6240.0000.0000.0000.0000.0000.000
111A197GLY00.0210.00674.3860.0000.0000.0000.0000.0000.000
112A198PRO0-0.040-0.02775.1280.0000.0000.0000.0000.0000.000
113A199ASP-1-0.869-0.92374.045-0.011-0.0110.0000.0000.0000.000
114A200THR0-0.031-0.02071.6690.0000.0000.0000.0000.0000.000
115A201MET0-0.044-0.00767.2350.0000.0000.0000.0000.0000.000
116A202ARG10.9310.98466.7280.0140.0140.0000.0000.0000.000
117A203VAL00.0220.00761.5980.0000.0000.0000.0000.0000.000
118A204THR0-0.003-0.01062.3540.0000.0000.0000.0000.0000.000
119A205TRP0-0.024-0.00856.2440.0000.0000.0000.0000.0000.000
120A206ALA00.0140.01856.4790.0010.0010.0000.0000.0000.000
121A207PRO00.0210.00053.859-0.001-0.0010.0000.0000.0000.000
122A208PRO0-0.0140.01748.7630.0000.0000.0000.0000.0000.000
123A209PRO0-0.006-0.01549.3530.0010.0010.0000.0000.0000.000
124A210SER0-0.040-0.04246.8980.0000.0000.0000.0000.0000.000
125A211ILE00.0430.02944.773-0.001-0.0010.0000.0000.0000.000
126A212ASP-1-0.933-0.94547.372-0.020-0.0200.0000.0000.0000.000
127A213LEU0-0.071-0.04247.7760.0000.0000.0000.0000.0000.000
128A214THR00.0210.01148.4750.0000.0000.0000.0000.0000.000
129A215ASN0-0.054-0.04550.4960.0010.0010.0000.0000.0000.000
130A216PHE00.0080.01651.936-0.001-0.0010.0000.0000.0000.000
131A217LEU00.004-0.00252.8880.0010.0010.0000.0000.0000.000
132A218VAL0-0.045-0.03654.7620.0000.0000.0000.0000.0000.000
133A219ARG10.8260.90150.9440.0220.0220.0000.0000.0000.000
134A220TYR0-0.005-0.02458.0820.0000.0000.0000.0000.0000.000
135A221SER00.1050.06160.4440.0000.0000.0000.0000.0000.000
136A222PRO00.0360.01963.0780.0000.0000.0000.0000.0000.000
137A223VAL0-0.016-0.01862.6780.0000.0000.0000.0000.0000.000
138A224LYS10.8620.92763.4950.0140.0140.0000.0000.0000.000
139A225ASN0-0.011-0.01063.7170.0000.0000.0000.0000.0000.000
140A226GLU-1-0.923-0.95158.243-0.019-0.0190.0000.0000.0000.000
141A227GLU-1-0.893-0.95857.500-0.019-0.0190.0000.0000.0000.000
142A228ASP-1-1.012-0.98460.616-0.014-0.0140.0000.0000.0000.000
143A229VAL0-0.114-0.05057.7020.0000.0000.0000.0000.0000.000
144A230ALA0-0.0090.00460.9560.0000.0000.0000.0000.0000.000
145A231GLU-1-0.912-0.98455.649-0.019-0.0190.0000.0000.0000.000
146A232LEU0-0.039-0.02258.7490.0010.0010.0000.0000.0000.000
147A233SER0-0.0010.02555.789-0.001-0.0010.0000.0000.0000.000
148A234ILE0-0.025-0.02157.1650.0010.0010.0000.0000.0000.000
149A235SER00.0400.02456.631-0.001-0.0010.0000.0000.0000.000
150A236PRO00.0540.03053.2290.0000.0000.0000.0000.0000.000
151A237SER0-0.017-0.01255.1150.0000.0000.0000.0000.0000.000
152A238ASP-1-0.961-0.97557.782-0.014-0.0140.0000.0000.0000.000
153A239ASN0-0.041-0.02658.4970.0000.0000.0000.0000.0000.000
154A240ALA0-0.052-0.04559.9420.0000.0000.0000.0000.0000.000
155A241VAL00.0390.02861.9200.0000.0000.0000.0000.0000.000
156A242VAL0-0.038-0.02164.2330.0000.0000.0000.0000.0000.000
157A243LEU00.0110.01863.3950.0000.0000.0000.0000.0000.000
158A244THR00.026-0.01467.4690.0000.0000.0000.0000.0000.000
159A245ASN0-0.0160.00169.9880.0000.0000.0000.0000.0000.000
160A246LEU0-0.0230.01067.6990.0000.0000.0000.0000.0000.000
161A247LEU00.0470.00671.3090.0000.0000.0000.0000.0000.000
162A248PRO00.0580.03073.2090.0000.0000.0000.0000.0000.000
163A249GLY0-0.036-0.00774.9660.0000.0000.0000.0000.0000.000
164A250THR0-0.036-0.01069.1560.0000.0000.0000.0000.0000.000
165A251GLU-1-0.905-0.96566.004-0.015-0.0150.0000.0000.0000.000
166A252TYR00.0480.02164.9170.0000.0000.0000.0000.0000.000
167A253VAL0-0.010-0.01258.8550.0000.0000.0000.0000.0000.000
168A254VAL00.0260.00660.0250.0000.0000.0000.0000.0000.000
169A255SER0-0.085-0.04354.795-0.001-0.0010.0000.0000.0000.000
170A256VAL00.0500.01455.0750.0010.0010.0000.0000.0000.000
171A257SER00.0210.00850.265-0.001-0.0010.0000.0000.0000.000
172A258SER00.0230.00648.5150.0010.0010.0000.0000.0000.000
173A259VAL0-0.0040.00747.852-0.001-0.0010.0000.0000.0000.000
174A260TYR00.0380.02240.8390.0020.0020.0000.0000.0000.000
175A261GLU-1-0.837-0.91442.841-0.024-0.0240.0000.0000.0000.000
176A262GLN0-0.069-0.03743.334-0.002-0.0020.0000.0000.0000.000
177A263HIS0-0.036-0.01139.932-0.001-0.0010.0000.0000.0000.000
178A264GLU-1-0.788-0.88244.017-0.023-0.0230.0000.0000.0000.000
179A265SER0-0.0260.01744.844-0.001-0.0010.0000.0000.0000.000
180A266THR00.004-0.00845.1400.0000.0000.0000.0000.0000.000
181A267PRO0-0.045-0.01947.5340.0010.0010.0000.0000.0000.000
182A268LEU0-0.0150.03051.2890.0000.0000.0000.0000.0000.000
183A269ARG10.9510.94852.4250.0230.0230.0000.0000.0000.000
184A270GLY0-0.012-0.00756.4100.0000.0000.0000.0000.0000.000
185A271ARG10.8980.94758.1750.0190.0190.0000.0000.0000.000
186A272GLN00.0540.04063.1130.0000.0000.0000.0000.0000.000
187A273LYS10.9060.97166.7770.0140.0140.0000.0000.0000.000
188A274THR0-0.048-0.03470.0680.0000.0000.0000.0000.0000.000