Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 2JNVR

Calculation Name: 2DLA-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2DLA

Chain ID: A

ChEMBL ID:

UniProt ID: O57935

Base Structure: X-ray

Registration Date: 2023-06-22

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 222
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2828124.458889
FMO2-HF: Nuclear repulsion 2737072.720036
FMO2-HF: Total energy -91051.738853
FMO2-MP2: Total energy -91319.284101


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-15.122-13.58810.665-3.084-9.1160.005
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.067 / q_NPA : 0.051
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].
3A3ILE00.0320.0122.032-1.964-3.0489.048-1.513-6.452-0.010
4A4MET00.0040.0294.4380.5370.6430.000-0.034-0.0720.000
5A5LEU00.0200.0176.354-0.187-0.1870.0000.0000.0000.000
6A6ASP-1-0.700-0.8469.1210.2110.2110.0000.0000.0000.000
7A7PRO0-0.035-0.00212.4480.0530.0530.0000.0000.0000.000
8A8PHE0-0.019-0.02214.183-0.025-0.0250.0000.0000.0000.000
9A9SER0-0.055-0.01512.0080.0090.0090.0000.0000.0000.000
10A10GLU-1-0.893-0.96914.0000.2590.2590.0000.0000.0000.000
11A11LYS10.9450.9896.389-1.024-1.0240.0000.0000.0000.000
12A12ALA00.010-0.02612.061-0.053-0.0530.0000.0000.0000.000
13A13LYS10.9020.96713.554-0.264-0.2640.0000.0000.0000.000
14A14GLU-1-0.920-0.97614.2510.3090.3090.0000.0000.0000.000
15A15LEU0-0.058-0.02410.788-0.021-0.0210.0000.0000.0000.000
16A16LEU0-0.020-0.01115.043-0.039-0.0390.0000.0000.0000.000
17A17LYS10.9220.98717.615-0.160-0.1600.0000.0000.0000.000
18A18GLY0-0.012-0.00718.779-0.008-0.0080.0000.0000.0000.000
19A19PHE0-0.078-0.03016.321-0.014-0.0140.0000.0000.0000.000
20A20GLY00.0090.01521.399-0.012-0.0120.0000.0000.0000.000
21A21SER0-0.055-0.05023.9320.0100.0100.0000.0000.0000.000
22A22ILE00.035-0.00623.625-0.004-0.0040.0000.0000.0000.000
23A23ASN00.0470.01124.678-0.015-0.0150.0000.0000.0000.000
24A24ASP-1-0.767-0.84125.0730.0220.0220.0000.0000.0000.000
25A25PHE0-0.046-0.03417.121-0.010-0.0100.0000.0000.0000.000
26A26MET0-0.0030.00222.037-0.020-0.0200.0000.0000.0000.000
27A27ASP-1-0.845-0.91024.022-0.033-0.0330.0000.0000.0000.000
28A28ALA0-0.101-0.06621.259-0.012-0.0120.0000.0000.0000.000
29A29ILE0-0.0110.01219.134-0.020-0.0200.0000.0000.0000.000
30A30PRO00.0040.00320.664-0.024-0.0240.0000.0000.0000.000
31A31LYS10.8400.93322.7680.0400.0400.0000.0000.0000.000
32A32ILE0-0.069-0.02716.166-0.005-0.0050.0000.0000.0000.000
33A33VAL0-0.043-0.01516.326-0.039-0.0390.0000.0000.0000.000
34A34SER00.0010.00418.9930.0350.0350.0000.0000.0000.000
35A35VAL00.034-0.00721.105-0.005-0.0050.0000.0000.0000.000
36A36ASP-1-0.895-0.95122.583-0.174-0.1740.0000.0000.0000.000
37A37ASP-1-0.871-0.93117.668-0.320-0.3200.0000.0000.0000.000
38A38VAL0-0.040-0.01918.207-0.026-0.0260.0000.0000.0000.000
39A39ILE0-0.002-0.00619.601-0.005-0.0050.0000.0000.0000.000
40A40GLU-1-0.859-0.93817.661-0.356-0.3560.0000.0000.0000.000
41A41ARG10.7460.86512.2130.2830.2830.0000.0000.0000.000
42A42ILE00.0240.00317.5420.0060.0060.0000.0000.0000.000
43A43ARG10.9050.96520.8000.1870.1870.0000.0000.0000.000
44A44VAL0-0.007-0.01416.572-0.001-0.0010.0000.0000.0000.000
45A45VAL0-0.062-0.02619.6020.0070.0070.0000.0000.0000.000
46A46LYN0-0.0140.02722.5000.0200.0200.0000.0000.0000.000
47A47ASN00.0170.01621.8170.0090.0090.0000.0000.0000.000
48A48GLU-1-0.814-0.91419.610-0.217-0.2170.0000.0000.0000.000
49A49LYS10.8980.92817.6760.2230.2230.0000.0000.0000.000
50A50LEU0-0.105-0.03516.902-0.060-0.0600.0000.0000.0000.000
51A51ILE00.0310.01112.819-0.060-0.0600.0000.0000.0000.000
52A52ASP-1-0.909-0.97911.149-1.014-1.0140.0000.0000.0000.000
53A53LYS10.8980.96810.3720.3300.3300.0000.0000.0000.000
54A54PHE0-0.012-0.00610.003-0.104-0.1040.0000.0000.0000.000
55A55LEU0-0.117-0.0367.594-0.083-0.0830.0000.0000.0000.000
56A56ASP-1-0.965-0.9793.950-3.580-3.3500.002-0.037-0.1950.000
57A57GLN00.0940.0495.0530.6260.6260.0000.0000.0000.000
58A58ASP-1-0.872-0.9325.695-0.430-0.4300.0000.0000.0000.000
59A59ASN00.000-0.0325.1620.5500.5500.0000.0000.0000.000
60A60VAL00.0700.0428.3410.0520.0520.0000.0000.0000.000
61A61MET00.0190.01310.4280.0350.0350.0000.0000.0000.000
62A62ASP-1-0.760-0.8419.466-0.242-0.2420.0000.0000.0000.000
63A63LEU00.0120.00311.5280.0600.0600.0000.0000.0000.000
64A64ALA00.0340.02714.0250.0240.0240.0000.0000.0000.000
65A65GLN00.0690.01012.7770.0170.0170.0000.0000.0000.000
66A66PHE0-0.029-0.02115.1620.0320.0320.0000.0000.0000.000
67A67TYR0-0.014-0.04416.9520.0190.0190.0000.0000.0000.000
68A68ALA00.0270.03619.1960.0130.0130.0000.0000.0000.000
69A69LEU0-0.012-0.01818.6960.0130.0130.0000.0000.0000.000
70A70LEU0-0.022-0.00920.6780.0130.0130.0000.0000.0000.000
71A71GLY00.0480.02623.1910.0100.0100.0000.0000.0000.000
72A72ALA0-0.0370.00524.8870.0050.0050.0000.0000.0000.000
73A73LEU00.0230.01025.1530.0020.0020.0000.0000.0000.000
74A74SER0-0.050-0.02627.9710.0070.0070.0000.0000.0000.000
75A75TYR0-0.087-0.10729.8470.0020.0020.0000.0000.0000.000
76A76SER0-0.054-0.02431.2000.0020.0020.0000.0000.0000.000
77A77PRO0-0.021-0.01430.220-0.003-0.0030.0000.0000.0000.000
78A78TYR0-0.044-0.02031.2560.0060.0060.0000.0000.0000.000
79A79GLY00.0650.03831.9300.0010.0010.0000.0000.0000.000
80A80ILE00.1050.02930.2300.0020.0020.0000.0000.0000.000
81A81GLU-1-0.838-0.90527.970-0.049-0.0490.0000.0000.0000.000
82A82LEU00.006-0.00226.028-0.005-0.0050.0000.0000.0000.000
83A83GLU-1-0.980-0.98825.941-0.020-0.0200.0000.0000.0000.000
84A84LEU0-0.023-0.02224.818-0.003-0.0030.0000.0000.0000.000
85A85VAL00.0010.01421.098-0.014-0.0140.0000.0000.0000.000
86A86LYS10.8380.90720.720-0.031-0.0310.0000.0000.0000.000
87A87LYS10.9940.99920.7090.0650.0650.0000.0000.0000.000
88A88ALA00.0240.01219.205-0.007-0.0070.0000.0000.0000.000
89A89ASN00.0180.00816.227-0.053-0.0530.0000.0000.0000.000
90A90LEU00.0360.04515.7910.0030.0030.0000.0000.0000.000
91A91ILE0-0.0120.02016.1270.0300.0300.0000.0000.0000.000
92A92ILE0-0.0080.00711.675-0.019-0.0190.0000.0000.0000.000
93A93TYR0-0.041-0.06311.104-0.051-0.0510.0000.0000.0000.000
94A94SER0-0.014-0.03211.4630.1150.1150.0000.0000.0000.000
95A95GLU-1-0.903-0.95012.033-0.096-0.0960.0000.0000.0000.000
96A96ARG10.7700.8697.3740.6260.6260.0000.0000.0000.000
97A97LEU00.0560.0178.1740.2720.2720.0000.0000.0000.000
98A98LYS10.7520.8839.8140.2040.2040.0000.0000.0000.000
99A99ARG10.8480.9307.5020.5510.5510.0000.0000.0000.000
100A100LYS10.8870.9632.692-14.825-13.6011.129-0.899-1.4540.013
101A101LYS10.8760.9425.605-0.680-0.6800.0000.0000.0000.000
102A102GLU-1-0.851-0.9255.8420.8010.8010.0000.0000.0000.000
103A103ILE0-0.030-0.0356.2351.0881.0880.0000.0000.0000.000
104A104LYS10.8830.9532.318-0.8300.2120.487-0.592-0.9370.002
105A105PRO00.0650.0317.631-0.006-0.0060.0000.0000.0000.000
106A106GLU-1-0.862-0.9339.0820.6670.6670.0000.0000.0000.000
107A107GLU-1-0.929-0.9905.0733.9833.999-0.001-0.009-0.0060.000
108A108ILE0-0.036-0.0239.350-0.100-0.1000.0000.0000.0000.000
109A109SER0-0.082-0.05212.408-0.043-0.0430.0000.0000.0000.000
110A110ILE0-0.0040.01115.636-0.055-0.0550.0000.0000.0000.000
111A111ASP-1-0.819-0.92515.6420.4490.4490.0000.0000.0000.000
112A112VAL0-0.027-0.02113.945-0.047-0.0470.0000.0000.0000.000
113A113SER00.0080.00012.5020.0780.0780.0000.0000.0000.000
114A114THR0-0.016-0.00810.496-0.088-0.0880.0000.0000.0000.000
115A115ALA0-0.005-0.01813.400-0.025-0.0250.0000.0000.0000.000
116A116ILE00.0020.00712.590-0.022-0.0220.0000.0000.0000.000
117A117GLU-1-0.967-0.97915.9600.1980.1980.0000.0000.0000.000
118A118PHE0-0.013-0.01919.7010.0060.0060.0000.0000.0000.000
119A119PRO00.0240.01822.623-0.014-0.0140.0000.0000.0000.000
120A120THR00.017-0.00926.213-0.004-0.0040.0000.0000.0000.000
121A121GLU-1-1.002-0.99128.1170.0930.0930.0000.0000.0000.000
122A122ASP-1-0.831-0.90628.9470.1110.1110.0000.0000.0000.000
123A123VAL00.0090.01725.881-0.003-0.0030.0000.0000.0000.000
124A124ARG10.9700.97528.317-0.069-0.0690.0000.0000.0000.000
125A125LYS10.9360.96731.319-0.075-0.0750.0000.0000.0000.000
126A126ILE00.0500.04326.144-0.005-0.0050.0000.0000.0000.000
127A127GLU-1-0.790-0.88826.9460.0890.0890.0000.0000.0000.000
128A128ARG10.7500.88929.520-0.058-0.0580.0000.0000.0000.000
129A129VAL0-0.034-0.03031.460-0.006-0.0060.0000.0000.0000.000
130A130TYR0-0.051-0.01327.334-0.003-0.0030.0000.0000.0000.000
131A131GLY0-0.008-0.00827.3220.0030.0030.0000.0000.0000.000
132A132LYS10.9390.95821.977-0.077-0.0770.0000.0000.0000.000
133A133ILE00.0400.02021.434-0.007-0.0070.0000.0000.0000.000
134A134PRO0-0.091-0.03220.8840.0080.0080.0000.0000.0000.000
135A135GLU-1-0.792-0.90715.3890.2510.2510.0000.0000.0000.000
136A136TYR0-0.0120.01512.0600.0110.0110.0000.0000.0000.000
137A137THR00.0020.02016.719-0.072-0.0720.0000.0000.0000.000
138A138MET0-0.007-0.01117.2840.0420.0420.0000.0000.0000.000
139A139LYS10.9140.98719.481-0.276-0.2760.0000.0000.0000.000
140A140ILE00.0320.00721.729-0.011-0.0110.0000.0000.0000.000
141A141SER0-0.012-0.02025.234-0.003-0.0030.0000.0000.0000.000
142A142ASP-1-0.774-0.88920.5680.2570.2570.0000.0000.0000.000
143A143PHE00.0350.00423.677-0.013-0.0130.0000.0000.0000.000
144A144LEU0-0.075-0.04724.817-0.014-0.0140.0000.0000.0000.000
145A145ASP-1-0.895-0.93925.7830.1310.1310.0000.0000.0000.000
146A146LEU0-0.047-0.02521.647-0.011-0.0110.0000.0000.0000.000
147A147VAL0-0.068-0.02625.387-0.013-0.0130.0000.0000.0000.000
148A148PRO00.006-0.00628.063-0.002-0.0020.0000.0000.0000.000
149A149ASP-1-0.917-0.95131.6080.0640.0640.0000.0000.0000.000
150A150GLU-1-0.921-0.94427.7660.1060.1060.0000.0000.0000.000
151A151LYS10.9150.94331.776-0.076-0.0760.0000.0000.0000.000
152A152LEU00.0580.02927.5080.0000.0000.0000.0000.0000.000
153A153ALA0-0.039-0.01430.6860.0030.0030.0000.0000.0000.000
154A154ASN0-0.037-0.01231.178-0.006-0.0060.0000.0000.0000.000
155A155TYR0-0.058-0.03925.3380.0040.0040.0000.0000.0000.000
156A156TYR0-0.025-0.02125.120-0.004-0.0040.0000.0000.0000.000
157A157ILE0-0.011-0.02025.7750.0170.0170.0000.0000.0000.000
158A158TYR00.0200.00723.927-0.019-0.0190.0000.0000.0000.000
159A159GLU-1-0.903-0.96223.1110.2290.2290.0000.0000.0000.000
160A160GLY0-0.026-0.00424.4370.0120.0120.0000.0000.0000.000
161A161ARG10.8240.92017.570-0.363-0.3630.0000.0000.0000.000
162A162VAL00.007-0.00122.954-0.017-0.0170.0000.0000.0000.000
163A163TYR00.0070.00221.1810.0310.0310.0000.0000.0000.000
164A164LEU0-0.038-0.03219.731-0.028-0.0280.0000.0000.0000.000
165A165LYS10.9280.97019.559-0.096-0.0960.0000.0000.0000.000
166A166ARG10.9780.99613.691-0.196-0.1960.0000.0000.0000.000
167A167GLU-1-0.953-0.98817.5830.1450.1450.0000.0000.0000.000
168A168ASP-1-0.803-0.92420.1930.1420.1420.0000.0000.0000.000
169A169LEU00.0150.03214.333-0.002-0.0020.0000.0000.0000.000
170A170ILE00.0330.01915.140-0.005-0.0050.0000.0000.0000.000
171A171ARG10.8660.96117.702-0.137-0.1370.0000.0000.0000.000
172A172ILE0-0.008-0.01720.910-0.016-0.0160.0000.0000.0000.000
173A173TRP00.002-0.02114.625-0.020-0.0200.0000.0000.0000.000
174A174SER0-0.022-0.03018.759-0.019-0.0190.0000.0000.0000.000
175A175LYS10.9510.97920.103-0.104-0.1040.0000.0000.0000.000
176A176ALA00.0130.00819.475-0.012-0.0120.0000.0000.0000.000
177A177PHE0-0.029-0.00216.959-0.014-0.0140.0000.0000.0000.000
178A178GLU-1-0.925-0.97119.6800.0300.0300.0000.0000.0000.000
179A179ARG10.9090.93923.009-0.134-0.1340.0000.0000.0000.000
180A180ASN0-0.0210.00118.946-0.024-0.0240.0000.0000.0000.000
181A181VAL0-0.018-0.00720.706-0.011-0.0110.0000.0000.0000.000
182A182GLU-1-0.824-0.89222.8050.0260.0260.0000.0000.0000.000
183A183ARG10.8870.94824.849-0.105-0.1050.0000.0000.0000.000
184A184GLY00.014-0.00223.843-0.002-0.0020.0000.0000.0000.000
185A185VAL00.0160.00824.874-0.006-0.0060.0000.0000.0000.000
186A186ASN0-0.040-0.02826.741-0.008-0.0080.0000.0000.0000.000
187A187MET0-0.068-0.01727.1810.0040.0040.0000.0000.0000.000
188A188LEU00.0140.00124.173-0.001-0.0010.0000.0000.0000.000
189A189TYR0-0.040-0.02228.680-0.010-0.0100.0000.0000.0000.000
190A190GLU-1-0.955-0.97832.1590.0250.0250.0000.0000.0000.000
191A191ILE00.0560.02327.930-0.001-0.0010.0000.0000.0000.000
192A192ARG10.8990.97430.973-0.002-0.0020.0000.0000.0000.000
193A193ASP-1-0.937-0.93632.008-0.010-0.0100.0000.0000.0000.000
194A194GLU-1-0.933-0.96532.220-0.002-0.0020.0000.0000.0000.000
195A195LEU0-0.067-0.00527.596-0.004-0.0040.0000.0000.0000.000
196A196PRO00.0300.00427.869-0.004-0.0040.0000.0000.0000.000
197A197GLU-1-0.946-0.98730.260-0.063-0.0630.0000.0000.0000.000
198A198PHE00.008-0.00922.065-0.002-0.0020.0000.0000.0000.000
199A199TYR00.0600.01423.229-0.010-0.0100.0000.0000.0000.000
200A200ARG10.9090.96027.4500.0320.0320.0000.0000.0000.000
201A201LYS10.9090.96228.6870.0790.0790.0000.0000.0000.000
202A202VAL00.0110.00923.548-0.005-0.0050.0000.0000.0000.000
203A203LEU0-0.036-0.00726.592-0.005-0.0050.0000.0000.0000.000
204A204GLY0-0.003-0.01228.7790.0000.0000.0000.0000.0000.000
205A205GLU-1-0.883-0.94226.663-0.116-0.1160.0000.0000.0000.000
206A206ILE0-0.061-0.02724.906-0.006-0.0060.0000.0000.0000.000
207A207GLN0-0.012-0.01627.5620.0040.0040.0000.0000.0000.000
208A208ALA00.0750.04330.6040.0020.0020.0000.0000.0000.000
209A209PHE00.0220.01425.437-0.005-0.0050.0000.0000.0000.000
210A210ALA00.0200.00429.1840.0010.0010.0000.0000.0000.000
211A211GLU-1-0.925-0.94930.707-0.059-0.0590.0000.0000.0000.000
212A212GLU-1-0.903-0.94030.405-0.115-0.1150.0000.0000.0000.000
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