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: Z65LN

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 OptAll
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 -1699476.455562
FMO2-HF: Nuclear repulsion 1628476.795156
FMO2-HF: Total energy -70999.660406
FMO2-MP2: Total energy -71209.970527


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.
-4.355-1.5910.09-1.176-1.6780.002
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 : -0.023 / q_NPA : -0.031
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].
3A89GLY00.0060.0112.807-1.8210.7410.090-1.136-1.5160.002
4A90SER0-0.030-0.0174.683-0.636-0.4340.000-0.040-0.1620.000
5A91HIS00.000-0.0255.642-0.538-0.5380.0000.0000.0000.000
6A92MET00.0060.0429.4700.0720.0720.0000.0000.0000.000
7A93GLU-1-0.870-0.9338.108-0.294-0.2940.0000.0000.0000.000
8A94VAL00.002-0.01110.7230.0200.0200.0000.0000.0000.000
9A95PRO0-0.031-0.02012.864-0.047-0.0470.0000.0000.0000.000
10A96GLN00.0790.05115.352-0.004-0.0040.0000.0000.0000.000
11A97PRO0-0.0090.00417.3230.0200.0200.0000.0000.0000.000
12A98THR0-0.034-0.05021.093-0.003-0.0030.0000.0000.0000.000
13A99ASP-1-0.862-0.90623.998-0.037-0.0370.0000.0000.0000.000
14A100LEU0-0.0200.01323.4300.0030.0030.0000.0000.0000.000
15A101SER0-0.048-0.01626.6240.0030.0030.0000.0000.0000.000
16A102PHE00.0300.00826.744-0.002-0.0020.0000.0000.0000.000
17A103VAL0-0.063-0.02232.0200.0050.0050.0000.0000.0000.000
18A104ASP-1-0.719-0.86934.448-0.063-0.0630.0000.0000.0000.000
19A105ILE0-0.035-0.02237.1650.0040.0040.0000.0000.0000.000
20A106THR0-0.039-0.02039.5300.0000.0000.0000.0000.0000.000
21A107ASP-1-0.942-0.97541.112-0.040-0.0400.0000.0000.0000.000
22A108SER0-0.022-0.01438.8220.0000.0000.0000.0000.0000.000
23A109SER0-0.044-0.01036.075-0.004-0.0040.0000.0000.0000.000
24A110ILE0-0.0220.02030.8240.0020.0020.0000.0000.0000.000
25A111GLY0-0.026-0.02632.7250.0000.0000.0000.0000.0000.000
26A112LEU0-0.019-0.00425.4960.0010.0010.0000.0000.0000.000
27A113ARG10.9470.95928.8710.0390.0390.0000.0000.0000.000
28A114TRP0-0.0100.00323.664-0.005-0.0050.0000.0000.0000.000
29A115THR0-0.054-0.04425.6600.0050.0050.0000.0000.0000.000
30A116PRO0-0.015-0.02223.754-0.007-0.0070.0000.0000.0000.000
31A117LEU00.0170.02717.0350.0040.0040.0000.0000.0000.000
32A118ASN00.005-0.01219.0570.0190.0190.0000.0000.0000.000
33A119SER0-0.051-0.00915.3620.0230.0230.0000.0000.0000.000
34A120SER00.0180.01017.456-0.014-0.0140.0000.0000.0000.000
35A121THR0-0.036-0.03317.980-0.001-0.0010.0000.0000.0000.000
36A122ILE00.0110.03218.153-0.005-0.0050.0000.0000.0000.000
37A123ILE0-0.067-0.04218.0530.0110.0110.0000.0000.0000.000
38A124GLY00.0230.00319.2170.0090.0090.0000.0000.0000.000
39A125TYR0-0.012-0.00419.270-0.009-0.0090.0000.0000.0000.000
40A126ARG10.7940.85815.7120.2400.2400.0000.0000.0000.000
41A127ILE0-0.037-0.01320.136-0.004-0.0040.0000.0000.0000.000
42A128THR00.0110.00220.139-0.004-0.0040.0000.0000.0000.000
43A129VAL00.0150.02222.9810.0010.0010.0000.0000.0000.000
44A130VAL00.007-0.01522.974-0.004-0.0040.0000.0000.0000.000
45A131ALA00.0430.03226.4040.0030.0030.0000.0000.0000.000
46A132ALA0-0.017-0.01228.479-0.006-0.0060.0000.0000.0000.000
47A133GLY0-0.037-0.02829.2710.0050.0050.0000.0000.0000.000
48A134GLU-1-0.965-0.97429.766-0.085-0.0850.0000.0000.0000.000
49A135GLY0-0.021-0.01426.368-0.005-0.0050.0000.0000.0000.000
50A136ILE0-0.040-0.03626.964-0.003-0.0030.0000.0000.0000.000
51A137PRO0-0.0070.00628.389-0.003-0.0030.0000.0000.0000.000
52A138ILE0-0.0350.01122.7660.0000.0000.0000.0000.0000.000
53A139PHE0-0.005-0.01026.4040.0040.0040.0000.0000.0000.000
54A140GLU-1-0.846-0.91120.163-0.197-0.1970.0000.0000.0000.000
55A141ASP-1-0.862-0.91823.874-0.084-0.0840.0000.0000.0000.000
56A142PHE0-0.082-0.05421.872-0.014-0.0140.0000.0000.0000.000
57A143VAL00.0150.02223.2790.0100.0100.0000.0000.0000.000
58A144ASP-1-0.855-0.93423.286-0.071-0.0710.0000.0000.0000.000
59A145SER0-0.038-0.02622.2820.0010.0010.0000.0000.0000.000
60A146SER0-0.055-0.02423.7080.0040.0040.0000.0000.0000.000
61A147VAL0-0.034-0.00926.2600.0050.0050.0000.0000.0000.000
62A148GLY00.0390.01625.869-0.004-0.0040.0000.0000.0000.000
63A149TYR0-0.062-0.04527.5720.0030.0030.0000.0000.0000.000
64A150TYR00.0170.00426.5870.0000.0000.0000.0000.0000.000
65A151THR0-0.004-0.00529.6660.0040.0040.0000.0000.0000.000
66A152VAL0-0.0080.01129.110-0.003-0.0030.0000.0000.0000.000
67A153THR00.001-0.00532.3340.0020.0020.0000.0000.0000.000
68A154GLY00.0170.00635.206-0.003-0.0030.0000.0000.0000.000
69A155LEU0-0.0110.00131.897-0.002-0.0020.0000.0000.0000.000
70A156GLU-1-0.823-0.88535.751-0.053-0.0530.0000.0000.0000.000
71A157PRO00.005-0.00537.221-0.001-0.0010.0000.0000.0000.000
72A158GLY0-0.021-0.01039.4550.0000.0000.0000.0000.0000.000
73A159ILE0-0.031-0.00133.987-0.001-0.0010.0000.0000.0000.000
74A160ASP-1-0.800-0.88131.067-0.077-0.0770.0000.0000.0000.000
75A161TYR00.0320.01229.311-0.002-0.0020.0000.0000.0000.000
76A162ASP-1-0.784-0.84823.049-0.132-0.1320.0000.0000.0000.000
77A163ILE0-0.021-0.01825.019-0.001-0.0010.0000.0000.0000.000
78A164SER0-0.013-0.03119.640-0.003-0.0030.0000.0000.0000.000
79A165VAL0-0.027-0.00720.636-0.001-0.0010.0000.0000.0000.000
80A166TYR0-0.003-0.00314.381-0.017-0.0170.0000.0000.0000.000
81A167THR0-0.025-0.02215.9850.0190.0190.0000.0000.0000.000
82A168VAL00.0440.02714.834-0.039-0.0390.0000.0000.0000.000
83A169LYS10.8850.91713.6510.0310.0310.0000.0000.0000.000
84A170ASN0-0.012-0.01313.326-0.034-0.0340.0000.0000.0000.000
85A171GLY00.0220.02012.933-0.010-0.0100.0000.0000.0000.000
86A172GLY0-0.0190.0109.791-0.103-0.1030.0000.0000.0000.000
87A173GLU-1-0.831-0.9169.962-0.209-0.2090.0000.0000.0000.000
88A174SER0-0.049-0.02410.285-0.086-0.0860.0000.0000.0000.000
89A175THR0-0.014-0.01111.979-0.059-0.0590.0000.0000.0000.000
90A176PRO00.0190.03313.1000.0330.0330.0000.0000.0000.000
91A177THR0-0.046-0.02116.6500.0100.0100.0000.0000.0000.000
92A178THR0-0.067-0.06319.844-0.006-0.0060.0000.0000.0000.000
93A179LEU0-0.018-0.01322.4490.0090.0090.0000.0000.0000.000
94A180THR0-0.023-0.02626.083-0.007-0.0070.0000.0000.0000.000
95A181GLN0-0.048-0.03728.7510.0060.0060.0000.0000.0000.000
96A182GLN0-0.048-0.03032.0000.0010.0010.0000.0000.0000.000
97A183THR00.004-0.00935.2900.0030.0030.0000.0000.0000.000
98A184ALA0-0.0210.00037.2840.0010.0010.0000.0000.0000.000
99A185VAL00.0350.01740.7180.0000.0000.0000.0000.0000.000
100A186PRO00.0380.00943.3930.0020.0020.0000.0000.0000.000
101A187PRO0-0.0070.02446.1220.0010.0010.0000.0000.0000.000
102A188PRO00.0190.02249.2000.0000.0000.0000.0000.0000.000
103A189THR0-0.027-0.03451.8960.0010.0010.0000.0000.0000.000
104A190ASP-1-0.816-0.88354.548-0.019-0.0190.0000.0000.0000.000
105A191LEU00.0420.03158.0470.0000.0000.0000.0000.0000.000
106A192ARG10.7520.84459.6810.0200.0200.0000.0000.0000.000
107A193PHE00.0280.00261.8250.0000.0000.0000.0000.0000.000
108A194THR0-0.049-0.02966.3430.0000.0000.0000.0000.0000.000
109A195ASN00.0250.00569.901-0.001-0.0010.0000.0000.0000.000
110A196ILE0-0.055-0.03972.0690.0000.0000.0000.0000.0000.000
111A197GLY00.0210.01474.7910.0000.0000.0000.0000.0000.000
112A198PRO0-0.029-0.02475.3470.0000.0000.0000.0000.0000.000
113A199ASP-1-0.815-0.87974.323-0.014-0.0140.0000.0000.0000.000
114A200THR0-0.028-0.03471.793-0.001-0.0010.0000.0000.0000.000
115A201MET0-0.016-0.00267.5090.0000.0000.0000.0000.0000.000
116A202ARG10.9561.00066.1650.0180.0180.0000.0000.0000.000
117A203VAL00.0050.00061.9230.0000.0000.0000.0000.0000.000
118A204THR0-0.016-0.01562.3020.0000.0000.0000.0000.0000.000
119A205TRP00.0010.01056.2940.0010.0010.0000.0000.0000.000
120A206ALA00.0140.01656.3250.0000.0000.0000.0000.0000.000
121A207PRO00.0180.00254.3020.0000.0000.0000.0000.0000.000
122A208PRO0-0.0010.01349.0300.0010.0010.0000.0000.0000.000
123A209PRO0-0.021-0.01749.2150.0000.0000.0000.0000.0000.000
124A210SER0-0.039-0.04146.738-0.001-0.0010.0000.0000.0000.000
125A211ILE00.0330.02344.626-0.002-0.0020.0000.0000.0000.000
126A212ASP-1-0.932-0.95347.478-0.036-0.0360.0000.0000.0000.000
127A213LEU0-0.064-0.02948.084-0.001-0.0010.0000.0000.0000.000
128A214THR00.011-0.01347.8320.0010.0010.0000.0000.0000.000
129A215ASN0-0.079-0.06250.3490.0000.0000.0000.0000.0000.000
130A216PHE00.0420.02451.965-0.001-0.0010.0000.0000.0000.000
131A217LEU0-0.026-0.00352.9320.0000.0000.0000.0000.0000.000
132A218VAL0-0.0100.00054.8120.0000.0000.0000.0000.0000.000
133A219ARG10.8000.85651.2360.0290.0290.0000.0000.0000.000
134A220TYR0-0.020-0.02057.9680.0000.0000.0000.0000.0000.000
135A221SER00.0640.03860.2520.0000.0000.0000.0000.0000.000
136A222PRO00.0000.00962.8970.0000.0000.0000.0000.0000.000
137A223VAL0-0.031-0.03363.2760.0000.0000.0000.0000.0000.000
138A224LYS10.8460.92463.8200.0130.0130.0000.0000.0000.000
139A225ASN0-0.030-0.01563.8710.0010.0010.0000.0000.0000.000
140A226GLU-1-0.759-0.88258.335-0.020-0.0200.0000.0000.0000.000
141A227GLU-1-0.865-0.92758.185-0.020-0.0200.0000.0000.0000.000
142A228ASP-1-0.947-0.94860.439-0.017-0.0170.0000.0000.0000.000
143A229VAL0-0.061-0.04057.7810.0000.0000.0000.0000.0000.000
144A230ALA0-0.019-0.00461.0930.0000.0000.0000.0000.0000.000
145A231GLU-1-0.838-0.92855.306-0.027-0.0270.0000.0000.0000.000
146A232LEU0-0.038-0.02458.8520.0000.0000.0000.0000.0000.000
147A233SER00.0060.01655.651-0.001-0.0010.0000.0000.0000.000
148A234ILE0-0.041-0.02656.9840.0010.0010.0000.0000.0000.000
149A235SER00.0490.01956.685-0.002-0.0020.0000.0000.0000.000
150A236PRO00.0420.02453.2260.0010.0010.0000.0000.0000.000
151A237SER0-0.066-0.04255.2380.0000.0000.0000.0000.0000.000
152A238ASP-1-0.908-0.92358.141-0.023-0.0230.0000.0000.0000.000
153A239ASN0-0.065-0.04458.8450.0000.0000.0000.0000.0000.000
154A240ALA0-0.038-0.03559.8800.0010.0010.0000.0000.0000.000
155A241VAL00.0430.03662.1050.0000.0000.0000.0000.0000.000
156A242VAL0-0.038-0.03964.0770.0010.0010.0000.0000.0000.000
157A243LEU0-0.0010.02563.5210.0000.0000.0000.0000.0000.000
158A244THR00.0390.00367.6420.0000.0000.0000.0000.0000.000
159A245ASN0-0.052-0.02970.3180.0000.0000.0000.0000.0000.000
160A246LEU0-0.0300.00867.6430.0000.0000.0000.0000.0000.000
161A247LEU00.0460.01171.2180.0010.0010.0000.0000.0000.000
162A248PRO00.0790.04073.1290.0000.0000.0000.0000.0000.000
163A249GLY0-0.041-0.00675.3000.0000.0000.0000.0000.0000.000
164A250THR0-0.058-0.02269.6170.0000.0000.0000.0000.0000.000
165A251GLU-1-0.837-0.90566.602-0.014-0.0140.0000.0000.0000.000
166A252TYR00.0520.02565.4920.0000.0000.0000.0000.0000.000
167A253VAL0-0.018-0.00758.8660.0000.0000.0000.0000.0000.000
168A254VAL0-0.001-0.00960.3560.0000.0000.0000.0000.0000.000
169A255SER0-0.007-0.01555.2950.0000.0000.0000.0000.0000.000
170A256VAL0-0.010-0.00354.9510.0000.0000.0000.0000.0000.000
171A257SER0-0.013-0.01350.0570.0000.0000.0000.0000.0000.000
172A258SER00.001-0.02848.5330.0010.0010.0000.0000.0000.000
173A259VAL0-0.048-0.01948.017-0.001-0.0010.0000.0000.0000.000
174A260TYR0-0.030-0.04541.2910.0020.0020.0000.0000.0000.000
175A261GLU-1-0.809-0.89042.890-0.045-0.0450.0000.0000.0000.000
176A262GLN0-0.066-0.03343.212-0.003-0.0030.0000.0000.0000.000
177A263HIS0-0.0290.00839.7340.0000.0000.0000.0000.0000.000
178A264GLU-1-0.782-0.85743.938-0.031-0.0310.0000.0000.0000.000
179A265SER0-0.0210.00344.767-0.001-0.0010.0000.0000.0000.000
180A266THR00.0150.00045.1680.0000.0000.0000.0000.0000.000
181A267PRO0-0.032-0.00447.5500.0000.0000.0000.0000.0000.000
182A268LEU00.0040.02651.3170.0010.0010.0000.0000.0000.000
183A269ARG10.8980.92253.1700.0240.0240.0000.0000.0000.000
184A270GLY0-0.0030.00656.5510.0000.0000.0000.0000.0000.000
185A271ARG10.7880.86958.7160.0180.0180.0000.0000.0000.000
186A272GLN00.0170.03263.1990.0010.0010.0000.0000.0000.000
187A273LYS10.8210.89266.8970.0130.0130.0000.0000.0000.000
188A274THR0-0.069-0.04170.4040.0010.0010.0000.0000.0000.000