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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: NNZVQ

Calculation Name: 3M3I-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3M3I

Chain ID: A

ChEMBL ID:

UniProt ID: E9AES8

Base Structure: X-ray

Registration Date: 2023-09-22

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 177
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1928698.847388
FMO2-HF: Nuclear repulsion 1857457.127824
FMO2-HF: Total energy -71241.719565
FMO2-MP2: Total energy -71449.306931


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:10:GLN)


Summations of interaction energy for fragment #1(A:10:GLN)
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.
-14.546-10.8942.034-2.09-3.592-0.006
Interaction energy analysis for fragmet #1(A:10:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.008 / q_NPA : -0.011
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].
3A12THR00.0550.0262.853-8.108-5.5481.121-1.673-2.008-0.006
4A13ALA00.0800.0265.2711.5971.689-0.001-0.004-0.0860.000
5A14GLU-1-0.896-0.9458.493-1.045-1.0450.0000.0000.0000.000
6A15PHE0-0.034-0.0217.9380.6680.6680.0000.0000.0000.000
7A16TRP00.026-0.0106.3020.6600.6600.0000.0000.0000.000
8A17ILE00.0260.03011.1810.1700.1700.0000.0000.0000.000
9A18LYS10.9570.97913.121-0.013-0.0130.0000.0000.0000.000
10A19ARG10.8330.91210.852-0.880-0.8800.0000.0000.0000.000
11A20LEU0-0.0060.01013.1480.0990.0990.0000.0000.0000.000
12A21GLN0-0.057-0.02716.427-0.012-0.0120.0000.0000.0000.000
13A22LEU0-0.0480.00513.640-0.018-0.0180.0000.0000.0000.000
14A23VAL0-0.013-0.01317.897-0.044-0.0440.0000.0000.0000.000
15A24PRO00.011-0.00619.709-0.018-0.0180.0000.0000.0000.000
16A25HIS00.0460.03020.7460.0390.0390.0000.0000.0000.000
17A26PRO0-0.006-0.00322.428-0.036-0.0360.0000.0000.0000.000
18A27GLU-1-0.785-0.85021.326-0.378-0.3780.0000.0000.0000.000
19A28GLY00.0030.02720.621-0.030-0.0300.0000.0000.0000.000
20A29GLY00.0170.01416.4890.0370.0370.0000.0000.0000.000
21A30TYR0-0.044-0.04614.7110.0090.0090.0000.0000.0000.000
22A31TYR0-0.024-0.02217.0020.0390.0390.0000.0000.0000.000
23A32SER00.0420.02618.7970.0060.0060.0000.0000.0000.000
24A33GLU-1-0.895-0.94820.986-0.038-0.0380.0000.0000.0000.000
25A34VAL0-0.0320.00720.4070.0240.0240.0000.0000.0000.000
26A35VAL0-0.029-0.02123.6100.0130.0130.0000.0000.0000.000
27A36ARG10.9750.98026.726-0.007-0.0070.0000.0000.0000.000
28A37SER0-0.0570.00029.7770.0150.0150.0000.0000.0000.000
29A38ALA00.0320.00732.321-0.012-0.0120.0000.0000.0000.000
30A39HIS0-0.0250.00735.616-0.006-0.0060.0000.0000.0000.000
31A40LYS10.9580.96236.141-0.012-0.0120.0000.0000.0000.000
32A41VAL0-0.025-0.01636.1450.0060.0060.0000.0000.0000.000
33A42ASP-1-0.856-0.93738.966-0.008-0.0080.0000.0000.0000.000
34A43ASN00.008-0.00136.1520.0090.0090.0000.0000.0000.000
35A44GLU-1-0.774-0.90434.460-0.035-0.0350.0000.0000.0000.000
36A45GLU-1-0.976-0.98138.012-0.082-0.0820.0000.0000.0000.000
37A46GLY0-0.0240.00040.713-0.001-0.0010.0000.0000.0000.000
38A47ASN0-0.042-0.00639.0130.0080.0080.0000.0000.0000.000
39A48ARG10.8930.94839.502-0.005-0.0050.0000.0000.0000.000
40A49ARG10.7870.87834.2970.0470.0470.0000.0000.0000.000
41A50HIS0-0.029-0.01832.4140.0000.0000.0000.0000.0000.000
42A51ALA00.0160.00933.342-0.007-0.0070.0000.0000.0000.000
43A52TYR00.0510.02727.333-0.005-0.0050.0000.0000.0000.000
44A53THR0-0.0030.00527.0730.0020.0020.0000.0000.0000.000
45A54THR0-0.033-0.00822.669-0.011-0.0110.0000.0000.0000.000
46A55ILE00.0370.01119.883-0.001-0.0010.0000.0000.0000.000
47A56TYR0-0.0150.00115.6600.0700.0700.0000.0000.0000.000
48A57PHE00.0490.01315.797-0.049-0.0490.0000.0000.0000.000
49A58LEU0-0.0130.0019.813-0.031-0.0310.0000.0000.0000.000
50A59CYS0-0.0200.02712.0440.1000.1000.0000.0000.0000.000
51A60THR00.026-0.00910.140-0.216-0.2160.0000.0000.0000.000
52A61PRO00.0170.00110.2930.2270.2270.0000.0000.0000.000
53A62GLU-1-0.947-0.96713.435-1.190-1.1900.0000.0000.0000.000
54A63SER0-0.064-0.01815.0120.1870.1870.0000.0000.0000.000
55A64PRO00.0120.00116.340-0.005-0.0050.0000.0000.0000.000
56A65SER0-0.098-0.07117.8080.0580.0580.0000.0000.0000.000
57A66HIS10.8850.91420.1840.5530.5530.0000.0000.0000.000
58A67LEU0-0.023-0.01423.5680.0300.0300.0000.0000.0000.000
59A68HIS10.8950.95222.7720.3220.3220.0000.0000.0000.000
60A69ARG10.8600.93627.7760.1600.1600.0000.0000.0000.000
61A70LEU00.0130.02825.9890.0010.0010.0000.0000.0000.000
62A71CYS0-0.036-0.04130.4440.0010.0010.0000.0000.0000.000
63A72SER0-0.0160.00930.8510.0100.0100.0000.0000.0000.000
64A73ASP-1-0.836-0.92028.268-0.056-0.0560.0000.0000.0000.000
65A74GLU-1-0.868-0.96522.827-0.176-0.1760.0000.0000.0000.000
66A75THR0-0.078-0.04521.874-0.015-0.0150.0000.0000.0000.000
67A76TRP0-0.008-0.01816.838-0.008-0.0080.0000.0000.0000.000
68A77MET0-0.018-0.02517.0270.0140.0140.0000.0000.0000.000
69A78TYR0-0.036-0.0377.2530.2950.2950.0000.0000.0000.000
70A79HIS0-0.067-0.02911.5540.2230.2230.0000.0000.0000.000
71A80ALA0-0.031-0.0306.4440.5390.5390.0000.0000.0000.000
72A81GLY0-0.0050.0124.005-0.626-0.565-0.001-0.008-0.0510.000
73A82ASP-1-0.719-0.8565.093-3.368-3.306-0.0010.000-0.0610.000
74A83PRO0-0.020-0.0117.1860.3300.3300.0000.0000.0000.000
75A84LEU00.0000.01210.856-0.231-0.2310.0000.0000.0000.000
76A85GLN0-0.013-0.00613.2280.2240.2240.0000.0000.0000.000
77A86LEU00.0090.00016.337-0.031-0.0310.0000.0000.0000.000
78A87HIS0-0.041-0.02218.8020.0840.0840.0000.0000.0000.000
79A88VAL00.0490.01022.5580.0070.0070.0000.0000.0000.000
80A89ILE00.001-0.00225.4640.0120.0120.0000.0000.0000.000
81A90LEU0-0.0060.00428.4180.0060.0060.0000.0000.0000.000
82A91LYS10.9580.98531.2130.1020.1020.0000.0000.0000.000
83A92ASP-1-0.821-0.93134.553-0.083-0.0830.0000.0000.0000.000
84A93PRO0-0.029-0.03833.220-0.004-0.0040.0000.0000.0000.000
85A94GLN00.0280.02432.7610.0010.0010.0000.0000.0000.000
86A95ASP-1-0.851-0.93828.441-0.102-0.1020.0000.0000.0000.000
87A96GLU-1-0.955-0.98330.536-0.026-0.0260.0000.0000.0000.000
88A97ASP-1-0.949-0.96533.353-0.025-0.0250.0000.0000.0000.000
89A98ARG10.8290.93225.7720.0610.0610.0000.0000.0000.000
90A117ARG10.9500.96742.5800.0580.0580.0000.0000.0000.000
91A118PRO00.0460.01541.338-0.001-0.0010.0000.0000.0000.000
92A119LYS10.8630.93437.7100.0860.0860.0000.0000.0000.000
93A120TYR0-0.031-0.03532.548-0.001-0.0010.0000.0000.0000.000
94A121GLN0-0.0120.00834.501-0.016-0.0160.0000.0000.0000.000
95A122VAL0-0.0040.00430.471-0.006-0.0060.0000.0000.0000.000
96A123TYR0-0.028-0.00323.2790.0000.0000.0000.0000.0000.000
97A124ARG10.9100.95525.6590.1390.1390.0000.0000.0000.000
98A125ARG10.9570.99517.7120.4550.4550.0000.0000.0000.000
99A126VAL00.000-0.00419.3320.0320.0320.0000.0000.0000.000
100A127LEU0-0.0050.01114.430-0.059-0.0590.0000.0000.0000.000
101A128VAL00.0260.01614.2470.0870.0870.0000.0000.0000.000
102A129GLY00.036-0.00612.016-0.161-0.1610.0000.0000.0000.000
103A130ALA00.006-0.00310.7650.0960.0960.0000.0000.0000.000
104A131ARG10.8530.9478.5910.2560.2560.0000.0000.0000.000
105A132VAL00.0360.01013.912-0.110-0.1100.0000.0000.0000.000
106A133GLU-1-0.926-0.96415.5250.3190.3190.0000.0000.0000.000
107A134ARG10.8620.92611.9250.1900.1900.0000.0000.0000.000
108A135GLY0-0.0040.00317.799-0.067-0.0670.0000.0000.0000.000
109A136GLU-1-0.887-0.93212.509-0.267-0.2670.0000.0000.0000.000
110A137LEU0-0.006-0.01016.6290.0800.0800.0000.0000.0000.000
111A138LEU00.0220.01014.218-0.037-0.0370.0000.0000.0000.000
112A139GLN0-0.035-0.01916.661-0.013-0.0130.0000.0000.0000.000
113A140TYR00.0350.01519.454-0.016-0.0160.0000.0000.0000.000
114A141THR00.0210.03021.616-0.002-0.0020.0000.0000.0000.000
115A142VAL0-0.017-0.00622.889-0.005-0.0050.0000.0000.0000.000
116A143PRO00.0210.01525.5830.0090.0090.0000.0000.0000.000
117A144GLY00.0720.04229.358-0.020-0.0200.0000.0000.0000.000
118A145GLY0-0.032-0.01531.3440.0050.0050.0000.0000.0000.000
119A146ALA0-0.0240.00528.318-0.008-0.0080.0000.0000.0000.000
120A147ILE0-0.0230.00128.624-0.003-0.0030.0000.0000.0000.000
121A148PHE0-0.047-0.01922.884-0.009-0.0090.0000.0000.0000.000
122A149GLY00.0550.03022.2870.0030.0030.0000.0000.0000.000
123A150SER00.010-0.00816.6420.0390.0390.0000.0000.0000.000
124A151SER00.0170.00116.033-0.023-0.0230.0000.0000.0000.000
125A152VAL00.0240.0099.4400.0700.0700.0000.0000.0000.000
126A153ALA0-0.0040.00712.1670.0330.0330.0000.0000.0000.000
127A154ALA0-0.002-0.00510.719-0.314-0.3140.0000.0000.0000.000
128A155ASP-1-0.901-0.94910.348-1.614-1.6140.0000.0000.0000.000
129A156GLY00.0210.00711.9750.1290.1290.0000.0000.0000.000
130A157ALA0-0.084-0.05810.709-0.225-0.2250.0000.0000.0000.000
131A158ASP-1-0.911-0.9679.984-0.812-0.8120.0000.0000.0000.000
132A159GLY00.0020.0188.710-0.053-0.0530.0000.0000.0000.000
133A160GLN0-0.054-0.0355.3270.6310.6310.0000.0000.0000.000
134A161ALA0-0.073-0.0352.438-3.388-2.6640.910-0.508-1.1250.000
135A162GLY00.0370.0263.296-0.230-0.3200.0030.185-0.0970.000
136A163TYR0-0.070-0.0473.6540.9741.2170.003-0.082-0.1640.000
137A164SER00.0120.0227.016-0.215-0.2150.0000.0000.0000.000
138A165LEU0-0.034-0.0148.8540.1250.1250.0000.0000.0000.000
139A166VAL00.0390.01610.6210.1740.1740.0000.0000.0000.000
140A167SER0-0.0050.00113.8080.0480.0480.0000.0000.0000.000
141A168CYS00.0020.01817.237-0.014-0.0140.0000.0000.0000.000
142A169ILE0-0.013-0.02220.3320.0300.0300.0000.0000.0000.000
143A170VAL00.0180.02323.868-0.011-0.0110.0000.0000.0000.000
144A171SER0-0.070-0.03426.9180.0220.0220.0000.0000.0000.000
145A172PRO00.060-0.00130.1610.0000.0000.0000.0000.0000.000
146A173GLY0-0.067-0.02230.099-0.009-0.0090.0000.0000.0000.000
147A174PHE00.0380.00827.599-0.008-0.0080.0000.0000.0000.000
148A175ASP-1-0.828-0.92029.732-0.057-0.0570.0000.0000.0000.000
149A176TYR00.0130.00826.570-0.013-0.0130.0000.0000.0000.000
150A177ARG10.7780.87732.1260.0560.0560.0000.0000.0000.000
151A178ASP-1-0.761-0.85032.693-0.077-0.0770.0000.0000.0000.000
152A179PHE0-0.064-0.02626.169-0.009-0.0090.0000.0000.0000.000
153A180GLU-1-0.898-0.93931.175-0.161-0.1610.0000.0000.0000.000
154A181ILE0-0.034-0.02726.606-0.016-0.0160.0000.0000.0000.000
155A182PHE00.006-0.00129.6200.0160.0160.0000.0000.0000.000
156A183THR00.006-0.00430.089-0.020-0.0200.0000.0000.0000.000
157A184GLN00.036-0.01127.8990.0350.0350.0000.0000.0000.000
158A185ALA00.0170.01332.2420.0130.0130.0000.0000.0000.000
159A186GLN00.0290.02434.7060.0010.0010.0000.0000.0000.000
160A187LEU0-0.013-0.02130.6550.0120.0120.0000.0000.0000.000
161A188MET0-0.042-0.01434.0280.0050.0050.0000.0000.0000.000
162A189GLU-1-0.951-0.95436.249-0.164-0.1640.0000.0000.0000.000
163A190LEU0-0.069-0.02637.5290.0120.0120.0000.0000.0000.000
164A191TYR0-0.075-0.05234.3350.0150.0150.0000.0000.0000.000
165A192PRO00.0930.04834.845-0.016-0.0160.0000.0000.0000.000
166A193GLN00.002-0.00934.784-0.011-0.0110.0000.0000.0000.000
167A194HIS0-0.084-0.05430.574-0.017-0.0170.0000.0000.0000.000
168A195GLU-1-0.833-0.93330.629-0.290-0.2900.0000.0000.0000.000
169A196ALA0-0.017-0.00527.823-0.019-0.0190.0000.0000.0000.000
170A197VAL00.0260.01525.076-0.032-0.0320.0000.0000.0000.000
171A198ILE0-0.0040.00326.435-0.027-0.0270.0000.0000.0000.000
172A199LYS10.9070.93928.0680.2920.2920.0000.0000.0000.000
173A200GLN0-0.0520.00021.099-0.072-0.0720.0000.0000.0000.000
174A201MET0-0.009-0.00720.021-0.058-0.0580.0000.0000.0000.000
175A202ALA0-0.0190.00624.1940.0050.0050.0000.0000.0000.000
176A203TYR0-0.048-0.03324.597-0.037-0.0370.0000.0000.0000.000
177A204GLU-1-0.940-0.96427.789-0.296-0.2960.0000.0000.0000.000