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: 6NY1Z

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 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 222
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2826768.40938
FMO2-HF: Nuclear repulsion 2735714.330238
FMO2-HF: Total energy -91054.079142
FMO2-MP2: Total energy -91321.408863


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.
-14.559-9.4793.008-1.773-6.3140.011
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 : 0.062 / q_NPA : 0.047
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].
3A3ILE00.0380.0262.252-3.247-0.9022.514-0.549-4.309-0.004
4A4MET0-0.0090.0234.5030.3450.413-0.001-0.017-0.0500.000
5A5LEU00.0220.0005.914-0.197-0.1970.0000.0000.0000.000
6A6ASP-1-0.681-0.8259.1580.2600.2600.0000.0000.0000.000
7A7PRO0-0.0240.01312.4940.0600.0600.0000.0000.0000.000
8A8PHE00.0240.00014.243-0.029-0.0290.0000.0000.0000.000
9A9SER0-0.041-0.01812.1770.0040.0040.0000.0000.0000.000
10A10GLU-1-0.816-0.91614.0590.2770.2770.0000.0000.0000.000
11A11LYS10.9000.9636.739-1.111-1.1110.0000.0000.0000.000
12A12ALA00.008-0.01412.067-0.047-0.0470.0000.0000.0000.000
13A13LYS10.8360.91313.627-0.357-0.3570.0000.0000.0000.000
14A14GLU-1-0.964-0.99114.5290.3640.3640.0000.0000.0000.000
15A15LEU0-0.052-0.02211.403-0.015-0.0150.0000.0000.0000.000
16A16LEU0-0.016-0.00715.397-0.043-0.0430.0000.0000.0000.000
17A17LYS10.9310.98718.311-0.198-0.1980.0000.0000.0000.000
18A18GLY0-0.012-0.00719.191-0.013-0.0130.0000.0000.0000.000
19A19PHE0-0.064-0.02516.597-0.018-0.0180.0000.0000.0000.000
20A20GLY00.0120.01521.785-0.015-0.0150.0000.0000.0000.000
21A21SER0-0.070-0.07224.5120.0130.0130.0000.0000.0000.000
22A22ILE00.0490.00223.914-0.003-0.0030.0000.0000.0000.000
23A23ASN00.0620.02325.500-0.012-0.0120.0000.0000.0000.000
24A24ASP-1-0.822-0.85925.7660.0430.0430.0000.0000.0000.000
25A25PHE0-0.023-0.02017.609-0.009-0.0090.0000.0000.0000.000
26A26MET00.0010.00822.701-0.018-0.0180.0000.0000.0000.000
27A27ASP-1-0.844-0.90024.801-0.025-0.0250.0000.0000.0000.000
28A28ALA0-0.037-0.03421.657-0.013-0.0130.0000.0000.0000.000
29A29ILE00.0020.01619.637-0.019-0.0190.0000.0000.0000.000
30A30PRO00.001-0.00521.256-0.022-0.0220.0000.0000.0000.000
31A31LYS10.7540.89223.2310.0130.0130.0000.0000.0000.000
32A32ILE0-0.062-0.02516.586-0.006-0.0060.0000.0000.0000.000
33A33VAL0-0.043-0.01816.869-0.037-0.0370.0000.0000.0000.000
34A34SER0-0.016-0.03219.5430.0290.0290.0000.0000.0000.000
35A35VAL00.034-0.00921.830-0.001-0.0010.0000.0000.0000.000
36A36ASP-1-0.893-0.94823.318-0.153-0.1530.0000.0000.0000.000
37A37ASP-1-0.859-0.89418.322-0.288-0.2880.0000.0000.0000.000
38A38VAL0-0.045-0.02518.876-0.020-0.0200.0000.0000.0000.000
39A39ILE00.003-0.00120.332-0.002-0.0020.0000.0000.0000.000
40A40GLU-1-0.797-0.88017.507-0.357-0.3570.0000.0000.0000.000
41A41ARG10.7770.86912.5690.1910.1910.0000.0000.0000.000
42A42ILE00.022-0.00118.0670.0090.0090.0000.0000.0000.000
43A43ARG10.8030.87921.2720.1500.1500.0000.0000.0000.000
44A44VAL0-0.008-0.00916.662-0.004-0.0040.0000.0000.0000.000
45A45VAL0-0.071-0.03419.8270.0060.0060.0000.0000.0000.000
46A46LYN00.0050.03322.6870.0160.0160.0000.0000.0000.000
47A47ASN00.0070.00221.8650.0040.0040.0000.0000.0000.000
48A48GLU-1-0.840-0.91719.852-0.198-0.1980.0000.0000.0000.000
49A49LYS10.9180.93917.9140.2150.2150.0000.0000.0000.000
50A50LEU0-0.079-0.02217.043-0.054-0.0540.0000.0000.0000.000
51A51ILE00.0330.00513.183-0.048-0.0480.0000.0000.0000.000
52A52ASP-1-0.900-0.96811.925-0.866-0.8660.0000.0000.0000.000
53A53LYS10.7670.88410.4780.2750.2750.0000.0000.0000.000
54A54PHE00.004-0.00110.352-0.093-0.0930.0000.0000.0000.000
55A55LEU0-0.067-0.0127.782-0.033-0.0330.0000.0000.0000.000
56A56ASP-1-0.962-0.9783.947-3.437-3.2440.001-0.033-0.1600.000
57A57GLN00.0370.0085.4090.3860.3860.0000.0000.0000.000
58A58ASP-1-0.817-0.9226.598-0.135-0.1350.0000.0000.0000.000
59A59ASN0-0.026-0.0395.9910.3980.3980.0000.0000.0000.000
60A60VAL00.0560.0329.2030.0340.0340.0000.0000.0000.000
61A61MET00.0140.01511.1210.0210.0210.0000.0000.0000.000
62A62ASP-1-0.767-0.82110.312-0.108-0.1080.0000.0000.0000.000
63A63LEU00.0140.00612.4260.0350.0350.0000.0000.0000.000
64A64ALA00.0400.02714.9730.0100.0100.0000.0000.0000.000
65A65GLN00.0910.04014.692-0.010-0.0100.0000.0000.0000.000
66A66PHE0-0.023-0.01915.9550.0220.0220.0000.0000.0000.000
67A67TYR0-0.016-0.04217.4930.0060.0060.0000.0000.0000.000
68A68ALA00.0390.04220.0920.0060.0060.0000.0000.0000.000
69A69LEU0-0.015-0.01419.4780.0080.0080.0000.0000.0000.000
70A70LEU0-0.038-0.01720.7390.0080.0080.0000.0000.0000.000
71A71GLY00.0550.02623.9960.0060.0060.0000.0000.0000.000
72A72ALA0-0.040-0.01125.7350.0010.0010.0000.0000.0000.000
73A73LEU00.0210.00525.5780.0000.0000.0000.0000.0000.000
74A74SER0-0.058-0.01828.7400.0050.0050.0000.0000.0000.000
75A75TYR0-0.053-0.05030.6740.0000.0000.0000.0000.0000.000
76A76SER0-0.079-0.06131.9650.0000.0000.0000.0000.0000.000
77A77PRO0-0.008-0.00630.739-0.002-0.0020.0000.0000.0000.000
78A78TYR0-0.054-0.02731.4800.0050.0050.0000.0000.0000.000
79A79GLY00.0600.03932.1810.0010.0010.0000.0000.0000.000
80A80ILE00.0790.02530.6980.0030.0030.0000.0000.0000.000
81A81GLU-1-0.810-0.87028.532-0.026-0.0260.0000.0000.0000.000
82A82LEU00.0130.00726.199-0.002-0.0020.0000.0000.0000.000
83A83GLU-1-0.975-0.98926.228-0.003-0.0030.0000.0000.0000.000
84A84LEU0-0.019-0.02225.309-0.002-0.0020.0000.0000.0000.000
85A85VAL00.0140.01321.756-0.009-0.0090.0000.0000.0000.000
86A86LYS10.8140.91321.223-0.053-0.0530.0000.0000.0000.000
87A87LYS10.9800.99020.7370.0520.0520.0000.0000.0000.000
88A88ALA00.0160.01019.660-0.005-0.0050.0000.0000.0000.000
89A89ASN00.000-0.01316.668-0.040-0.0400.0000.0000.0000.000
90A90LEU00.0150.03615.8640.0110.0110.0000.0000.0000.000
91A91ILE0-0.0180.00216.3980.0280.0280.0000.0000.0000.000
92A92ILE00.0070.01211.932-0.013-0.0130.0000.0000.0000.000
93A93TYR0-0.051-0.06411.056-0.036-0.0360.0000.0000.0000.000
94A94SER00.003-0.01311.4730.1060.1060.0000.0000.0000.000
95A95GLU-1-0.873-0.89112.480-0.085-0.0850.0000.0000.0000.000
96A96ARG10.7920.8847.4190.4990.4990.0000.0000.0000.000
97A97LEU00.0490.0258.1540.2260.2260.0000.0000.0000.000
98A98LYS10.7800.8869.7840.1640.1640.0000.0000.0000.000
99A99ARG10.8030.8847.8140.3940.3940.0000.0000.0000.000
100A100LYS10.8320.9252.797-12.883-11.1010.420-0.921-1.2820.015
101A101LYS10.8730.9365.824-0.431-0.4310.0000.0000.0000.000
102A102GLU-1-0.845-0.9195.7360.8220.8220.0000.0000.0000.000
103A103ILE0-0.044-0.0446.2351.0241.0240.0000.0000.0000.000
104A104LYS10.9110.9682.947-1.085-0.4150.075-0.241-0.5050.000
105A105PRO00.0730.0347.641-0.007-0.0070.0000.0000.0000.000
106A106GLU-1-0.850-0.9288.5670.7890.7890.0000.0000.0000.000
107A107GLU-1-0.871-0.9464.9654.3064.328-0.001-0.012-0.0080.000
108A108ILE0-0.044-0.0269.361-0.090-0.0900.0000.0000.0000.000
109A109SER0-0.083-0.06612.420-0.048-0.0480.0000.0000.0000.000
110A110ILE0-0.0110.00115.660-0.058-0.0580.0000.0000.0000.000
111A111ASP-1-0.824-0.91815.6540.4530.4530.0000.0000.0000.000
112A112VAL0-0.018-0.01514.001-0.049-0.0490.0000.0000.0000.000
113A113SER00.0220.00812.5130.0700.0700.0000.0000.0000.000
114A114THR0-0.015-0.01410.644-0.094-0.0940.0000.0000.0000.000
115A115ALA0-0.018-0.01413.410-0.022-0.0220.0000.0000.0000.000
116A116ILE0-0.013-0.00312.560-0.023-0.0230.0000.0000.0000.000
117A117GLU-1-0.948-0.96715.9430.1790.1790.0000.0000.0000.000
118A118PHE0-0.022-0.02819.6850.0090.0090.0000.0000.0000.000
119A119PRO00.0310.02322.603-0.015-0.0150.0000.0000.0000.000
120A120THR00.017-0.01426.194-0.004-0.0040.0000.0000.0000.000
121A121GLU-1-0.992-0.98628.0980.0880.0880.0000.0000.0000.000
122A122ASP-1-0.836-0.89228.8220.1060.1060.0000.0000.0000.000
123A123VAL0-0.0040.00525.833-0.003-0.0030.0000.0000.0000.000
124A124ARG10.8350.90128.292-0.065-0.0650.0000.0000.0000.000
125A125LYS10.9530.97231.293-0.072-0.0720.0000.0000.0000.000
126A126ILE00.0500.04126.036-0.004-0.0040.0000.0000.0000.000
127A127GLU-1-0.689-0.82227.5060.0720.0720.0000.0000.0000.000
128A128ARG10.7720.89329.490-0.053-0.0530.0000.0000.0000.000
129A129VAL0-0.034-0.02631.428-0.006-0.0060.0000.0000.0000.000
130A130TYR0-0.042-0.03027.285-0.003-0.0030.0000.0000.0000.000
131A131GLY0-0.006-0.00327.2520.0030.0030.0000.0000.0000.000
132A132LYS10.9090.94521.685-0.068-0.0680.0000.0000.0000.000
133A133ILE00.0390.01621.691-0.005-0.0050.0000.0000.0000.000
134A134PRO0-0.075-0.01920.8590.0060.0060.0000.0000.0000.000
135A135GLU-1-0.775-0.89815.4590.2380.2380.0000.0000.0000.000
136A136TYR0-0.0030.01811.6230.0060.0060.0000.0000.0000.000
137A137THR00.0100.02116.730-0.066-0.0660.0000.0000.0000.000
138A138MET0-0.009-0.00217.2960.0410.0410.0000.0000.0000.000
139A139LYS10.8270.93119.493-0.313-0.3130.0000.0000.0000.000
140A140ILE00.0310.00821.740-0.010-0.0100.0000.0000.0000.000
141A141SER00.012-0.00624.996-0.006-0.0060.0000.0000.0000.000
142A142ASP-1-0.765-0.88120.5750.2700.2700.0000.0000.0000.000
143A143PHE00.0590.02023.689-0.012-0.0120.0000.0000.0000.000
144A144LEU0-0.060-0.03824.830-0.014-0.0140.0000.0000.0000.000
145A145ASP-1-0.859-0.90225.8350.1470.1470.0000.0000.0000.000
146A146LEU0-0.038-0.02021.459-0.009-0.0090.0000.0000.0000.000
147A147VAL0-0.041-0.01825.527-0.012-0.0120.0000.0000.0000.000
148A148PRO00.0170.00728.073-0.003-0.0030.0000.0000.0000.000
149A149ASP-1-0.897-0.94131.6200.0730.0730.0000.0000.0000.000
150A150GLU-1-0.823-0.85727.8230.1130.1130.0000.0000.0000.000
151A151LYS10.8370.89031.776-0.087-0.0870.0000.0000.0000.000
152A152LEU00.0570.03127.8590.0000.0000.0000.0000.0000.000
153A153ALA0-0.023-0.00730.6980.0030.0030.0000.0000.0000.000
154A154ASN0-0.030-0.00731.081-0.006-0.0060.0000.0000.0000.000
155A155TYR0-0.061-0.03225.5370.0030.0030.0000.0000.0000.000
156A156TYR0-0.018-0.02625.130-0.004-0.0040.0000.0000.0000.000
157A157ILE0-0.020-0.02425.7860.0170.0170.0000.0000.0000.000
158A158TYR0-0.023-0.04123.993-0.018-0.0180.0000.0000.0000.000
159A159GLU-1-0.862-0.91123.6590.2140.2140.0000.0000.0000.000
160A160GLY0-0.023-0.00624.4460.0120.0120.0000.0000.0000.000
161A161ARG10.8130.90616.935-0.374-0.3740.0000.0000.0000.000
162A162VAL00.003-0.00422.977-0.017-0.0170.0000.0000.0000.000
163A163TYR00.0240.00521.0160.0310.0310.0000.0000.0000.000
164A164LEU0-0.045-0.03219.650-0.026-0.0260.0000.0000.0000.000
165A165LYS10.9020.95619.559-0.091-0.0910.0000.0000.0000.000
166A166ARG10.8950.93913.223-0.180-0.1800.0000.0000.0000.000
167A167GLU-1-0.930-0.97117.5310.1440.1440.0000.0000.0000.000
168A168ASP-1-0.785-0.90320.1550.1460.1460.0000.0000.0000.000
169A169LEU0-0.0090.02814.1050.0010.0010.0000.0000.0000.000
170A170ILE00.0390.01915.229-0.002-0.0020.0000.0000.0000.000
171A171ARG10.7770.88117.697-0.141-0.1410.0000.0000.0000.000
172A172ILE00.006-0.01521.083-0.013-0.0130.0000.0000.0000.000
173A173TRP0-0.001-0.01914.671-0.017-0.0170.0000.0000.0000.000
174A174SER0-0.020-0.04018.772-0.014-0.0140.0000.0000.0000.000
175A175LYS10.8580.92520.120-0.112-0.1120.0000.0000.0000.000
176A176ALA00.0290.01519.443-0.011-0.0110.0000.0000.0000.000
177A177PHE0-0.026-0.00616.649-0.012-0.0120.0000.0000.0000.000
178A178GLU-1-0.810-0.89519.7150.0540.0540.0000.0000.0000.000
179A179ARG10.8500.91323.043-0.157-0.1570.0000.0000.0000.000
180A180ASN0-0.022-0.00519.125-0.024-0.0240.0000.0000.0000.000
181A181VAL00.0050.00420.658-0.010-0.0100.0000.0000.0000.000
182A182GLU-1-0.858-0.91422.8540.0500.0500.0000.0000.0000.000
183A183ARG10.8850.93924.925-0.132-0.1320.0000.0000.0000.000
184A184GLY00.009-0.00323.903-0.003-0.0030.0000.0000.0000.000
185A185VAL00.0140.00424.933-0.006-0.0060.0000.0000.0000.000
186A186ASN0-0.042-0.03727.029-0.012-0.0120.0000.0000.0000.000
187A187MET0-0.059-0.01627.2570.0020.0020.0000.0000.0000.000
188A188LEU0-0.011-0.00824.766-0.001-0.0010.0000.0000.0000.000
189A189TYR0-0.023-0.01329.272-0.011-0.0110.0000.0000.0000.000
190A190GLU-1-0.959-0.97932.6610.0410.0410.0000.0000.0000.000
191A191ILE00.0420.01928.828-0.002-0.0020.0000.0000.0000.000
192A192ARG10.7940.89331.916-0.019-0.0190.0000.0000.0000.000
193A193ASP-1-0.844-0.90532.9460.0030.0030.0000.0000.0000.000
194A194GLU-1-0.949-0.97233.0080.0160.0160.0000.0000.0000.000
195A195LEU0-0.050-0.00328.322-0.003-0.0030.0000.0000.0000.000
196A196PRO00.018-0.00228.542-0.004-0.0040.0000.0000.0000.000
197A197GLU-1-0.859-0.92831.087-0.053-0.0530.0000.0000.0000.000
198A198PHE00.0230.00122.758-0.002-0.0020.0000.0000.0000.000
199A199TYR00.0500.00524.347-0.007-0.0070.0000.0000.0000.000
200A200ARG10.9340.96728.3590.0140.0140.0000.0000.0000.000
201A201LYS10.8270.90829.8250.0600.0600.0000.0000.0000.000
202A202VAL00.0070.00624.363-0.005-0.0050.0000.0000.0000.000
203A203LEU0-0.022-0.00327.392-0.004-0.0040.0000.0000.0000.000
204A204GLY00.004-0.00329.541-0.001-0.0010.0000.0000.0000.000
205A205GLU-1-0.909-0.95927.384-0.097-0.0970.0000.0000.0000.000
206A206ILE0-0.045-0.01625.229-0.006-0.0060.0000.0000.0000.000
207A207GLN0-0.037-0.02528.1810.0030.0030.0000.0000.0000.000
208A208ALA00.0810.04631.2370.0010.0010.0000.0000.0000.000
209A209PHE0-0.007-0.00225.622-0.005-0.0050.0000.0000.0000.000
210A210ALA00.0130.00329.6640.0000.0000.0000.0000.0000.000
211A211GLU-1-0.915-0.94631.150-0.047-0.0470.0000.0000.0000.000
212A212GLU-1-0.784-0.84930.127-0.109-0.1090.0000.0000.0000.000
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