FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 6NV7Z

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 OptHSide
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
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1703396.815654
FMO2-HF: Nuclear repulsion 1632398.140067
FMO2-HF: Total energy -70998.675587
FMO2-MP2: Total energy -71209.140696


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.
-2.1970.8540.089-1.268-1.8740.002
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 : 0.033 / q_NPA : -0.018
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].
3A89GLY0-0.018-0.0102.617-1.3661.3410.084-1.182-1.6100.002
4A90SER00.010-0.0113.8260.3020.6460.005-0.086-0.2640.000
5A91HIS0-0.070-0.0406.130-0.135-0.1350.0000.0000.0000.000
6A92MET00.0850.0619.3760.0920.0920.0000.0000.0000.000
7A93GLU-1-0.991-0.9918.847-0.512-0.5120.0000.0000.0000.000
8A94VAL0-0.007-0.00910.1600.0450.0450.0000.0000.0000.000
9A95PRO0-0.024-0.01012.3300.0110.0110.0000.0000.0000.000
10A96GLN00.0930.06215.116-0.018-0.0180.0000.0000.0000.000
11A97PRO00.0020.00316.6870.0050.0050.0000.0000.0000.000
12A98THR0-0.028-0.04420.382-0.005-0.0050.0000.0000.0000.000
13A99ASP-1-0.882-0.92023.078-0.093-0.0930.0000.0000.0000.000
14A100LEU0-0.0180.02423.2210.0020.0020.0000.0000.0000.000
15A101SER0-0.058-0.03826.2210.0060.0060.0000.0000.0000.000
16A102PHE00.0650.02226.168-0.003-0.0030.0000.0000.0000.000
17A103VAL0-0.076-0.01431.5860.0030.0030.0000.0000.0000.000
18A104ASP-1-0.734-0.91534.497-0.054-0.0540.0000.0000.0000.000
19A105ILE00.019-0.00536.9780.0010.0010.0000.0000.0000.000
20A106THR0-0.078-0.03639.6930.0000.0000.0000.0000.0000.000
21A107ASP-1-0.978-0.96341.976-0.034-0.0340.0000.0000.0000.000
22A108SER0-0.0290.00338.6290.0010.0010.0000.0000.0000.000
23A109SER00.0020.00636.572-0.002-0.0020.0000.0000.0000.000
24A110ILE0-0.0200.02330.9080.0000.0000.0000.0000.0000.000
25A111GLY0-0.026-0.02232.722-0.001-0.0010.0000.0000.0000.000
26A112LEU0-0.0040.00325.186-0.001-0.0010.0000.0000.0000.000
27A113ARG10.9400.95328.5620.0640.0640.0000.0000.0000.000
28A114TRP0-0.0220.01123.3310.0010.0010.0000.0000.0000.000
29A115THR0-0.033-0.02825.3320.0070.0070.0000.0000.0000.000
30A116PRO0-0.037-0.03323.265-0.009-0.0090.0000.0000.0000.000
31A117LEU00.0070.02516.535-0.001-0.0010.0000.0000.0000.000
32A118ASN0-0.001-0.01418.8430.0130.0130.0000.0000.0000.000
33A119SER0-0.037-0.00815.032-0.012-0.0120.0000.0000.0000.000
34A120SER00.0190.01317.1820.0030.0030.0000.0000.0000.000
35A121THR0-0.057-0.04417.875-0.022-0.0220.0000.0000.0000.000
36A122ILE0-0.0040.03017.739-0.018-0.0180.0000.0000.0000.000
37A123ILE0-0.054-0.04517.6960.0120.0120.0000.0000.0000.000
38A124GLY00.0270.01619.0260.0190.0190.0000.0000.0000.000
39A125TYR0-0.019-0.00219.037-0.027-0.0270.0000.0000.0000.000
40A126ARG10.8240.88915.7480.1590.1590.0000.0000.0000.000
41A127ILE0-0.023-0.01220.062-0.009-0.0090.0000.0000.0000.000
42A128THR00.0390.02120.2640.0020.0020.0000.0000.0000.000
43A129VAL00.0080.01423.028-0.002-0.0020.0000.0000.0000.000
44A130VAL0-0.003-0.01823.2260.0030.0030.0000.0000.0000.000
45A131ALA00.0290.03226.626-0.001-0.0010.0000.0000.0000.000
46A132ALA00.000-0.01628.201-0.001-0.0010.0000.0000.0000.000
47A133GLY0-0.022-0.02328.9730.0030.0030.0000.0000.0000.000
48A134GLU-1-0.992-0.98029.034-0.029-0.0290.0000.0000.0000.000
49A135GLY0-0.007-0.01526.802-0.004-0.0040.0000.0000.0000.000
50A136ILE0-0.047-0.04327.4090.0030.0030.0000.0000.0000.000
51A137PRO0-0.009-0.01028.099-0.002-0.0020.0000.0000.0000.000
52A138ILE0-0.0190.04622.421-0.001-0.0010.0000.0000.0000.000
53A139PHE0-0.008-0.01326.1460.0030.0030.0000.0000.0000.000
54A140GLU-1-0.858-0.93220.166-0.114-0.1140.0000.0000.0000.000
55A141ASP-1-0.867-0.92223.920-0.067-0.0670.0000.0000.0000.000
56A142PHE0-0.066-0.04021.763-0.011-0.0110.0000.0000.0000.000
57A143VAL0-0.0030.01723.4080.0070.0070.0000.0000.0000.000
58A144ASP-1-0.847-0.93123.154-0.101-0.1010.0000.0000.0000.000
59A145SER0-0.031-0.02821.8790.0040.0040.0000.0000.0000.000
60A146SER0-0.058-0.02523.544-0.001-0.0010.0000.0000.0000.000
61A147VAL0-0.042-0.01626.1470.0080.0080.0000.0000.0000.000
62A148GLY00.0340.01325.791-0.008-0.0080.0000.0000.0000.000
63A149TYR0-0.065-0.05527.4500.0020.0020.0000.0000.0000.000
64A150TYR00.0230.00626.640-0.002-0.0020.0000.0000.0000.000
65A151THR0-0.010-0.00229.6070.0010.0010.0000.0000.0000.000
66A152VAL00.0100.02028.881-0.001-0.0010.0000.0000.0000.000
67A153THR0-0.021-0.01832.0710.0020.0020.0000.0000.0000.000
68A154GLY00.034-0.00434.8650.0000.0000.0000.0000.0000.000
69A155LEU0-0.0070.01132.0620.0000.0000.0000.0000.0000.000
70A156GLU-1-0.833-0.90835.629-0.029-0.0290.0000.0000.0000.000
71A157PRO0-0.020-0.03337.159-0.002-0.0020.0000.0000.0000.000
72A158GLY0-0.007-0.00839.0950.0010.0010.0000.0000.0000.000
73A159ILE0-0.0270.01033.7740.0000.0000.0000.0000.0000.000
74A160ASP-1-0.848-0.91330.632-0.056-0.0560.0000.0000.0000.000
75A161TYR00.0410.03329.3920.0010.0010.0000.0000.0000.000
76A162ASP-1-0.797-0.88923.129-0.093-0.0930.0000.0000.0000.000
77A163ILE0-0.053-0.04124.868-0.001-0.0010.0000.0000.0000.000
78A164SER00.0030.00119.402-0.008-0.0080.0000.0000.0000.000
79A165VAL00.0010.00620.2910.0010.0010.0000.0000.0000.000
80A166TYR0-0.018-0.01714.190-0.016-0.0160.0000.0000.0000.000
81A167THR0-0.033-0.03215.4370.0030.0030.0000.0000.0000.000
82A168VAL00.0310.01614.505-0.038-0.0380.0000.0000.0000.000
83A169LYS10.8950.91513.2220.3290.3290.0000.0000.0000.000
84A170ASN0-0.021-0.01613.364-0.023-0.0230.0000.0000.0000.000
85A171GLY00.0170.01612.896-0.028-0.0280.0000.0000.0000.000
86A172GLY00.0170.0249.920-0.072-0.0720.0000.0000.0000.000
87A173GLU-1-0.840-0.90510.149-0.160-0.1600.0000.0000.0000.000
88A174SER0-0.037-0.00710.015-0.067-0.0670.0000.0000.0000.000
89A175THR00.003-0.00311.3600.0060.0060.0000.0000.0000.000
90A176PRO00.0200.01512.792-0.002-0.0020.0000.0000.0000.000
91A177THR0-0.045-0.01016.4790.0050.0050.0000.0000.0000.000
92A178THR0-0.063-0.06919.698-0.002-0.0020.0000.0000.0000.000
93A179LEU0-0.018-0.01722.3990.0020.0020.0000.0000.0000.000
94A180THR0-0.007-0.00925.982-0.002-0.0020.0000.0000.0000.000
95A181GLN0-0.062-0.02828.7870.0020.0020.0000.0000.0000.000
96A182GLN0-0.050-0.02531.9690.0030.0030.0000.0000.0000.000
97A183THR00.0180.01635.2290.0010.0010.0000.0000.0000.000
98A184ALA0-0.025-0.00637.3330.0020.0020.0000.0000.0000.000
99A185VAL00.0570.03440.9080.0000.0000.0000.0000.0000.000
100A186PRO00.006-0.01343.6820.0000.0000.0000.0000.0000.000
101A187PRO00.0020.02746.2470.0010.0010.0000.0000.0000.000
102A188PRO00.0160.02049.3270.0000.0000.0000.0000.0000.000
103A189THR0-0.041-0.04752.0290.0000.0000.0000.0000.0000.000
104A190ASP-1-0.840-0.90954.605-0.018-0.0180.0000.0000.0000.000
105A191LEU00.0450.03758.0070.0010.0010.0000.0000.0000.000
106A192ARG10.7720.86359.8050.0180.0180.0000.0000.0000.000
107A193PHE00.0380.01161.8040.0000.0000.0000.0000.0000.000
108A194THR0-0.033-0.01666.3840.0000.0000.0000.0000.0000.000
109A195ASN00.0160.00169.9540.0000.0000.0000.0000.0000.000
110A196ILE0-0.037-0.02871.9610.0000.0000.0000.0000.0000.000
111A197GLY00.0230.01274.4770.0000.0000.0000.0000.0000.000
112A198PRO0-0.034-0.02175.1470.0000.0000.0000.0000.0000.000
113A199ASP-1-0.869-0.91874.097-0.011-0.0110.0000.0000.0000.000
114A200THR0-0.039-0.03171.8120.0000.0000.0000.0000.0000.000
115A201MET0-0.042-0.00867.2880.0000.0000.0000.0000.0000.000
116A202ARG10.9320.98066.7720.0140.0140.0000.0000.0000.000
117A203VAL00.0210.00961.7510.0000.0000.0000.0000.0000.000
118A204THR0-0.004-0.01062.4790.0000.0000.0000.0000.0000.000
119A205TRP0-0.024-0.00156.4020.0000.0000.0000.0000.0000.000
120A206ALA00.0150.02056.6380.0010.0010.0000.0000.0000.000
121A207PRO00.0260.00853.984-0.001-0.0010.0000.0000.0000.000
122A208PRO0-0.0070.01548.8980.0000.0000.0000.0000.0000.000
123A209PRO0-0.022-0.02049.6380.0010.0010.0000.0000.0000.000
124A210SER0-0.032-0.03947.0660.0000.0000.0000.0000.0000.000
125A211ILE00.0380.02544.782-0.001-0.0010.0000.0000.0000.000
126A212ASP-1-0.937-0.94847.460-0.020-0.0200.0000.0000.0000.000
127A213LEU0-0.060-0.03348.1600.0000.0000.0000.0000.0000.000
128A214THR00.0150.00048.1020.0000.0000.0000.0000.0000.000
129A215ASN0-0.062-0.04750.5860.0010.0010.0000.0000.0000.000
130A216PHE00.0170.01752.045-0.001-0.0010.0000.0000.0000.000
131A217LEU0-0.015-0.00353.0730.0010.0010.0000.0000.0000.000
132A218VAL0-0.039-0.03854.877-0.001-0.0010.0000.0000.0000.000
133A219ARG10.8120.87151.3830.0220.0220.0000.0000.0000.000
134A220TYR0-0.006-0.02758.1260.0000.0000.0000.0000.0000.000
135A221SER00.0930.06460.2210.0000.0000.0000.0000.0000.000
136A222PRO0-0.0030.01262.9910.0000.0000.0000.0000.0000.000
137A223VAL0-0.028-0.02663.0590.0000.0000.0000.0000.0000.000
138A224LYS10.8520.92463.4320.0140.0140.0000.0000.0000.000
139A225ASN0-0.023-0.00663.6920.0000.0000.0000.0000.0000.000
140A226GLU-1-0.868-0.94158.164-0.019-0.0190.0000.0000.0000.000
141A227GLU-1-0.887-0.95157.835-0.019-0.0190.0000.0000.0000.000
142A228ASP-1-0.975-0.97160.532-0.014-0.0140.0000.0000.0000.000
143A229VAL0-0.070-0.04757.6190.0000.0000.0000.0000.0000.000
144A230ALA0-0.0100.00860.9110.0000.0000.0000.0000.0000.000
145A231GLU-1-0.845-0.93755.458-0.019-0.0190.0000.0000.0000.000
146A232LEU0-0.027-0.01958.8620.0010.0010.0000.0000.0000.000
147A233SER0-0.0060.02355.609-0.001-0.0010.0000.0000.0000.000
148A234ILE0-0.036-0.02757.2780.0010.0010.0000.0000.0000.000
149A235SER00.0580.02456.735-0.001-0.0010.0000.0000.0000.000
150A236PRO00.0440.02953.2220.0000.0000.0000.0000.0000.000
151A237SER0-0.030-0.01355.2200.0000.0000.0000.0000.0000.000
152A238ASP-1-0.955-0.97057.888-0.014-0.0140.0000.0000.0000.000
153A239ASN0-0.048-0.03558.6170.0000.0000.0000.0000.0000.000
154A240ALA0-0.042-0.04060.0710.0000.0000.0000.0000.0000.000
155A241VAL00.0380.02761.9830.0000.0000.0000.0000.0000.000
156A242VAL0-0.043-0.02664.3580.0000.0000.0000.0000.0000.000
157A243LEU00.0080.02463.4900.0000.0000.0000.0000.0000.000
158A244THR00.031-0.01267.5950.0000.0000.0000.0000.0000.000
159A245ASN0-0.032-0.01270.0860.0000.0000.0000.0000.0000.000
160A246LEU0-0.0140.01967.6510.0000.0000.0000.0000.0000.000
161A247LEU00.0440.01371.1760.0000.0000.0000.0000.0000.000
162A248PRO00.0750.03073.1260.0000.0000.0000.0000.0000.000
163A249GLY0-0.038-0.00774.8870.0000.0000.0000.0000.0000.000
164A250THR0-0.047-0.01969.1680.0000.0000.0000.0000.0000.000
165A251GLU-1-0.909-0.97466.074-0.016-0.0160.0000.0000.0000.000
166A252TYR00.0400.01264.9280.0000.0000.0000.0000.0000.000
167A253VAL0-0.025-0.01558.6800.0000.0000.0000.0000.0000.000
168A254VAL00.012-0.00560.1260.0000.0000.0000.0000.0000.000
169A255SER0-0.025-0.02554.847-0.001-0.0010.0000.0000.0000.000
170A256VAL00.0040.00655.2310.0010.0010.0000.0000.0000.000
171A257SER0-0.003-0.00150.413-0.001-0.0010.0000.0000.0000.000
172A258SER00.012-0.01848.5520.0010.0010.0000.0000.0000.000
173A259VAL0-0.021-0.00347.966-0.001-0.0010.0000.0000.0000.000
174A260TYR0-0.022-0.03141.2960.0020.0020.0000.0000.0000.000
175A261GLU-1-0.810-0.90242.987-0.023-0.0230.0000.0000.0000.000
176A262GLN0-0.075-0.04143.419-0.002-0.0020.0000.0000.0000.000
177A263HIS0-0.033-0.00540.067-0.001-0.0010.0000.0000.0000.000
178A264GLU-1-0.779-0.86744.125-0.023-0.0230.0000.0000.0000.000
179A265SER0-0.0230.02644.960-0.001-0.0010.0000.0000.0000.000
180A266THR00.004-0.00845.0750.0000.0000.0000.0000.0000.000
181A267PRO0-0.031-0.02047.5170.0010.0010.0000.0000.0000.000
182A268LEU0-0.0190.02551.2700.0000.0000.0000.0000.0000.000
183A269ARG10.9160.93252.5070.0230.0230.0000.0000.0000.000
184A270GLY0-0.0110.00056.3310.0000.0000.0000.0000.0000.000
185A271ARG10.8980.94358.4200.0190.0190.0000.0000.0000.000
186A272GLN00.0380.04263.0410.0000.0000.0000.0000.0000.000
187A273LYS10.9150.97666.7020.0150.0150.0000.0000.0000.000
188A274THR0-0.070-0.03869.9940.0000.0000.0000.0000.0000.000