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

tag_button

FMODB ID: Z6V4N

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 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 222
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2831159.231119
FMO2-HF: Nuclear repulsion 2740104.085094
FMO2-HF: Total energy -91055.146025
FMO2-MP2: Total energy -91322.290825


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.
-21.266-22.14213.37-4.031-8.4620.022
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 : 0.037 / q_NPA : 0.045
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].
3A3ILE00.0370.0332.450-2.673-0.5913.015-0.625-4.472-0.009
4A4MET00.0060.0274.3160.0050.0940.000-0.025-0.0640.000
5A5LEU00.0240.0065.279-0.255-0.2550.0000.0000.0000.000
6A6ASP-1-0.681-0.8138.6690.4820.4820.0000.0000.0000.000
7A7PRO0-0.0100.02012.0580.0680.0680.0000.0000.0000.000
8A8PHE00.0310.00714.066-0.077-0.0770.0000.0000.0000.000
9A9SER0-0.040-0.01211.923-0.033-0.0330.0000.0000.0000.000
10A10GLU-1-0.805-0.89614.1490.4220.4220.0000.0000.0000.000
11A11LYS10.9140.9696.699-1.550-1.5500.0000.0000.0000.000
12A12ALA0-0.001-0.00812.342-0.047-0.0470.0000.0000.0000.000
13A13LYS10.8030.88613.663-0.559-0.5590.0000.0000.0000.000
14A14GLU-1-0.976-0.99714.3530.4630.4630.0000.0000.0000.000
15A15LEU0-0.026-0.00911.506-0.042-0.0420.0000.0000.0000.000
16A16LEU0-0.014-0.00815.413-0.061-0.0610.0000.0000.0000.000
17A17LYS10.9540.98418.164-0.273-0.2730.0000.0000.0000.000
18A18GLY0-0.032-0.00918.904-0.028-0.0280.0000.0000.0000.000
19A19PHE0-0.033-0.02317.083-0.033-0.0330.0000.0000.0000.000
20A20GLY0-0.0160.00922.098-0.022-0.0220.0000.0000.0000.000
21A21SER0-0.106-0.08924.4960.0210.0210.0000.0000.0000.000
22A22ILE00.0470.00123.4600.0000.0000.0000.0000.0000.000
23A23ASN00.0530.02325.042-0.005-0.0050.0000.0000.0000.000
24A24ASP-1-0.814-0.86126.0460.0960.0960.0000.0000.0000.000
25A25PHE00.000-0.00217.846-0.006-0.0060.0000.0000.0000.000
26A26MET0-0.0130.00823.124-0.011-0.0110.0000.0000.0000.000
27A27ASP-1-0.780-0.87125.3380.0250.0250.0000.0000.0000.000
28A28ALA0-0.026-0.01521.962-0.016-0.0160.0000.0000.0000.000
29A29ILE00.0010.00620.192-0.020-0.0200.0000.0000.0000.000
30A30PRO0-0.014-0.00721.910-0.021-0.0210.0000.0000.0000.000
31A31LYS10.7280.86223.549-0.039-0.0390.0000.0000.0000.000
32A32ILE0-0.066-0.02317.225-0.008-0.0080.0000.0000.0000.000
33A33VAL0-0.046-0.02317.744-0.029-0.0290.0000.0000.0000.000
34A34SER0-0.015-0.02620.3600.0170.0170.0000.0000.0000.000
35A35VAL00.030-0.00922.6990.0100.0100.0000.0000.0000.000
36A36ASP-1-0.865-0.93623.585-0.075-0.0750.0000.0000.0000.000
37A37ASP-1-0.867-0.90018.425-0.161-0.1610.0000.0000.0000.000
38A38VAL0-0.045-0.01819.1270.0000.0000.0000.0000.0000.000
39A39ILE00.0100.00520.9210.0150.0150.0000.0000.0000.000
40A40GLU-1-0.802-0.89617.895-0.204-0.2040.0000.0000.0000.000
41A41ARG10.8230.88713.075-0.119-0.1190.0000.0000.0000.000
42A42ILE0-0.025-0.01518.4600.0210.0210.0000.0000.0000.000
43A43ARG10.8190.86621.6650.0650.0650.0000.0000.0000.000
44A44VAL0-0.023-0.00217.082-0.008-0.0080.0000.0000.0000.000
45A45VAL0-0.051-0.02520.2290.0020.0020.0000.0000.0000.000
46A46LYN00.0150.03523.0600.0070.0070.0000.0000.0000.000
47A47ASN0-0.018-0.01822.341-0.009-0.0090.0000.0000.0000.000
48A48GLU-1-0.862-0.92719.839-0.097-0.0970.0000.0000.0000.000
49A49LYS10.9210.95017.9310.1530.1530.0000.0000.0000.000
50A50LEU0-0.058-0.00417.439-0.049-0.0490.0000.0000.0000.000
51A51ILE00.0490.01913.561-0.017-0.0170.0000.0000.0000.000
52A52ASP-1-0.921-0.97312.397-0.611-0.6110.0000.0000.0000.000
53A53LYS10.7450.85610.7580.1270.1270.0000.0000.0000.000
54A54PHE00.0100.02110.457-0.049-0.0490.0000.0000.0000.000
55A55LEU0-0.047-0.0108.0580.1610.1610.0000.0000.0000.000
56A56ASP-1-0.963-0.9803.763-2.993-2.7540.002-0.052-0.1890.000
57A57GLN00.0540.0015.4130.3340.3340.0000.0000.0000.000
58A58ASP-1-0.803-0.9086.7920.3620.3620.0000.0000.0000.000
59A59ASN0-0.039-0.0376.0920.2490.2490.0000.0000.0000.000
60A60VAL00.0530.0269.8220.0150.0150.0000.0000.0000.000
61A61MET00.0110.00411.7540.0020.0020.0000.0000.0000.000
62A62ASP-1-0.782-0.83610.7650.3470.3470.0000.0000.0000.000
63A63LEU00.0090.00012.8750.0050.0050.0000.0000.0000.000
64A64ALA00.0270.01115.182-0.017-0.0170.0000.0000.0000.000
65A65GLN00.0730.03315.013-0.001-0.0010.0000.0000.0000.000
66A66PHE0-0.007-0.00216.0840.0030.0030.0000.0000.0000.000
67A67TYR0-0.007-0.03416.900-0.019-0.0190.0000.0000.0000.000
68A68ALA00.0290.02920.568-0.012-0.0120.0000.0000.0000.000
69A69LEU0-0.014-0.00119.983-0.006-0.0060.0000.0000.0000.000
70A70LEU0-0.041-0.01820.473-0.003-0.0030.0000.0000.0000.000
71A71GLY00.0590.02323.926-0.004-0.0040.0000.0000.0000.000
72A72ALA0-0.0210.00526.172-0.008-0.0080.0000.0000.0000.000
73A73LEU00.005-0.00625.136-0.005-0.0050.0000.0000.0000.000
74A74SER0-0.045-0.02528.627-0.002-0.0020.0000.0000.0000.000
75A75TYR0-0.063-0.05130.558-0.006-0.0060.0000.0000.0000.000
76A76SER0-0.067-0.05331.927-0.005-0.0050.0000.0000.0000.000
77A77PRO00.0100.00130.3600.0030.0030.0000.0000.0000.000
78A78TYR0-0.067-0.03930.9780.0050.0050.0000.0000.0000.000
79A79GLY00.0510.04832.3440.0000.0000.0000.0000.0000.000
80A80ILE00.0280.00330.6670.0090.0090.0000.0000.0000.000
81A81GLU-1-0.795-0.88128.7610.0580.0580.0000.0000.0000.000
82A82LEU00.0210.01225.7610.0080.0080.0000.0000.0000.000
83A83GLU-1-0.903-0.93625.5850.0930.0930.0000.0000.0000.000
84A84LEU00.013-0.00824.9650.0110.0110.0000.0000.0000.000
85A85VAL00.0240.02221.7710.0030.0030.0000.0000.0000.000
86A86LYS10.7940.88820.922-0.147-0.1470.0000.0000.0000.000
87A87LYS10.8780.92720.180-0.049-0.0490.0000.0000.0000.000
88A88ALA00.0240.01419.9550.0090.0090.0000.0000.0000.000
89A89ASN0-0.012-0.01716.467-0.003-0.0030.0000.0000.0000.000
90A90LEU00.0170.02915.3650.0490.0490.0000.0000.0000.000
91A91ILE0-0.0060.01215.8170.0530.0530.0000.0000.0000.000
92A92ILE00.0150.01312.0160.0210.0210.0000.0000.0000.000
93A93TYR0-0.049-0.05110.601-0.002-0.0020.0000.0000.0000.000
94A94SER00.029-0.01310.9350.1790.1790.0000.0000.0000.000
95A95GLU-1-0.860-0.87712.3400.1340.1340.0000.0000.0000.000
96A96ARG10.7580.8636.999-0.265-0.2650.0000.0000.0000.000
97A97LEU00.0140.0087.8400.2810.2810.0000.0000.0000.000
98A98LYS10.7900.8789.407-0.103-0.1030.0000.0000.0000.000
99A99ARG10.8380.9057.1480.0430.0430.0000.0000.0000.000
100A100LYS10.7740.8841.988-23.329-27.35310.334-3.094-3.2160.031
101A101LYS10.8850.9435.253-0.631-0.6310.0000.0000.0000.000
102A102GLU-1-0.820-0.9055.2561.0561.0560.0000.0000.0000.000
103A103ILE0-0.068-0.0595.5431.6881.777-0.0010.000-0.0870.000
104A104LYS10.9000.9713.110-1.099-0.5820.020-0.178-0.3590.000
105A105PRO00.0600.0277.3890.0460.0460.0000.0000.0000.000
106A106GLU-1-0.843-0.9358.3510.9870.9870.0000.0000.0000.000
107A107GLU-1-0.849-0.9354.4786.6596.7910.000-0.057-0.0750.000
108A108ILE0-0.044-0.0289.047-0.023-0.0230.0000.0000.0000.000
109A109SER0-0.070-0.06312.261-0.105-0.1050.0000.0000.0000.000
110A110ILE0-0.020-0.00915.511-0.091-0.0910.0000.0000.0000.000
111A111ASP-1-0.800-0.88915.4000.6070.6070.0000.0000.0000.000
112A112VAL0-0.017-0.01913.817-0.073-0.0730.0000.0000.0000.000
113A113SER00.0280.01811.9430.0990.0990.0000.0000.0000.000
114A114THR0-0.013-0.01110.367-0.118-0.1180.0000.0000.0000.000
115A115ALA0-0.031-0.01712.844-0.046-0.0460.0000.0000.0000.000
116A116ILE0-0.025-0.01112.063-0.043-0.0430.0000.0000.0000.000
117A117GLU-1-0.939-0.95915.2550.1650.1650.0000.0000.0000.000
118A118PHE0-0.009-0.02719.1060.0230.0230.0000.0000.0000.000
119A119PRO00.0430.02922.122-0.021-0.0210.0000.0000.0000.000
120A120THR00.021-0.00825.880-0.002-0.0020.0000.0000.0000.000
121A121GLU-1-0.987-0.98127.5360.1020.1020.0000.0000.0000.000
122A122ASP-1-0.817-0.88428.2080.1380.1380.0000.0000.0000.000
123A123VAL0-0.0360.00025.137-0.001-0.0010.0000.0000.0000.000
124A124ARG10.8430.88127.668-0.084-0.0840.0000.0000.0000.000
125A125LYS10.9090.95330.947-0.101-0.1010.0000.0000.0000.000
126A126ILE00.0230.02525.107-0.002-0.0020.0000.0000.0000.000
127A127GLU-1-0.756-0.85727.1690.0950.0950.0000.0000.0000.000
128A128ARG10.8590.93028.833-0.076-0.0760.0000.0000.0000.000
129A129VAL0-0.026-0.00930.654-0.008-0.0080.0000.0000.0000.000
130A130TYR0-0.023-0.02826.1900.0000.0000.0000.0000.0000.000
131A131GLY0-0.0370.00326.5080.0060.0060.0000.0000.0000.000
132A132LYS10.8830.92420.555-0.157-0.1570.0000.0000.0000.000
133A133ILE00.0350.01620.746-0.003-0.0030.0000.0000.0000.000
134A134PRO0-0.050-0.01420.3810.0070.0070.0000.0000.0000.000
135A135GLU-1-0.806-0.91215.0200.3430.3430.0000.0000.0000.000
136A136TYR0-0.009-0.00110.7180.0100.0100.0000.0000.0000.000
137A137THR0-0.0060.01616.039-0.092-0.0920.0000.0000.0000.000
138A138MET00.0160.01416.7730.0600.0600.0000.0000.0000.000
139A139LYS10.7970.89919.240-0.445-0.4450.0000.0000.0000.000
140A140ILE00.0340.00121.619-0.004-0.0040.0000.0000.0000.000
141A141SER0-0.010-0.02824.093-0.013-0.0130.0000.0000.0000.000
142A142ASP-1-0.793-0.87820.5550.3850.3850.0000.0000.0000.000
143A143PHE00.0640.01423.320-0.002-0.0020.0000.0000.0000.000
144A144LEU0-0.045-0.02524.435-0.016-0.0160.0000.0000.0000.000
145A145ASP-1-0.842-0.89625.5170.2530.2530.0000.0000.0000.000
146A146LEU0-0.038-0.01821.069-0.009-0.0090.0000.0000.0000.000
147A147VAL0-0.030-0.01325.080-0.008-0.0080.0000.0000.0000.000
148A148PRO00.0250.02427.600-0.010-0.0100.0000.0000.0000.000
149A149ASP-1-0.903-0.95231.0930.1420.1420.0000.0000.0000.000
150A150GLU-1-0.800-0.84327.1530.2070.2070.0000.0000.0000.000
151A151LYS10.8090.88031.051-0.154-0.1540.0000.0000.0000.000
152A152LEU00.0440.01727.7910.0000.0000.0000.0000.0000.000
153A153ALA0-0.0090.00030.1010.0040.0040.0000.0000.0000.000
154A154ASN0-0.0180.00330.218-0.013-0.0130.0000.0000.0000.000
155A155TYR0-0.070-0.03325.2490.0030.0030.0000.0000.0000.000
156A156TYR0-0.009-0.02624.577-0.004-0.0040.0000.0000.0000.000
157A157ILE0-0.022-0.02125.4350.0230.0230.0000.0000.0000.000
158A158TYR0-0.021-0.03223.514-0.026-0.0260.0000.0000.0000.000
159A159GLU-1-0.871-0.91623.0840.2550.2550.0000.0000.0000.000
160A160GLY0-0.0190.00123.7620.0150.0150.0000.0000.0000.000
161A161ARG10.8260.90316.240-0.488-0.4880.0000.0000.0000.000
162A162VAL00.0120.00322.697-0.026-0.0260.0000.0000.0000.000
163A163TYR00.005-0.00520.2420.0440.0440.0000.0000.0000.000
164A164LEU0-0.036-0.02419.042-0.031-0.0310.0000.0000.0000.000
165A165LYS10.8800.92918.991-0.181-0.1810.0000.0000.0000.000
166A166ARG10.8930.93912.699-0.339-0.3390.0000.0000.0000.000
167A167GLU-1-0.872-0.93716.9150.2720.2720.0000.0000.0000.000
168A168ASP-1-0.792-0.90019.6280.2620.2620.0000.0000.0000.000
169A169LEU0-0.0130.00913.1170.0000.0000.0000.0000.0000.000
170A170ILE00.0320.01414.9590.0100.0100.0000.0000.0000.000
171A171ARG10.7540.86817.282-0.258-0.2580.0000.0000.0000.000
172A172ILE00.0230.00320.474-0.020-0.0200.0000.0000.0000.000
173A173TRP0-0.005-0.01914.048-0.014-0.0140.0000.0000.0000.000
174A174SER0-0.007-0.03118.124-0.014-0.0140.0000.0000.0000.000
175A175LYS10.8570.92219.577-0.238-0.2380.0000.0000.0000.000
176A176ALA00.0300.02018.787-0.023-0.0230.0000.0000.0000.000
177A177PHE0-0.026-0.00715.934-0.019-0.0190.0000.0000.0000.000
178A178GLU-1-0.804-0.88719.0230.1700.1700.0000.0000.0000.000
179A179ARG10.8500.91322.523-0.278-0.2780.0000.0000.0000.000
180A180ASN0-0.024-0.01918.928-0.051-0.0510.0000.0000.0000.000
181A181VAL00.0330.02020.161-0.012-0.0120.0000.0000.0000.000
182A182GLU-1-0.869-0.91422.4790.1500.1500.0000.0000.0000.000
183A183ARG10.8940.95124.370-0.257-0.2570.0000.0000.0000.000
184A184GLY00.0220.01223.356-0.010-0.0100.0000.0000.0000.000
185A185VAL00.0130.00424.345-0.013-0.0130.0000.0000.0000.000
186A186ASN0-0.059-0.04426.788-0.023-0.0230.0000.0000.0000.000
187A187MET0-0.059-0.03726.547-0.002-0.0020.0000.0000.0000.000
188A188LEU00.0010.00924.142-0.003-0.0030.0000.0000.0000.000
189A189TYR0-0.023-0.01028.634-0.016-0.0160.0000.0000.0000.000
190A190GLU-1-0.945-0.98132.1010.0960.0960.0000.0000.0000.000
191A191ILE0-0.0200.00328.244-0.003-0.0030.0000.0000.0000.000
192A192ARG10.8460.91132.058-0.071-0.0710.0000.0000.0000.000
193A193ASP-1-0.866-0.91933.0510.0490.0490.0000.0000.0000.000
194A194GLU-1-0.909-0.95633.0840.0620.0620.0000.0000.0000.000
195A195LEU0-0.073-0.01128.543-0.003-0.0030.0000.0000.0000.000
196A196PRO00.0120.00229.144-0.008-0.0080.0000.0000.0000.000
197A197GLU-1-0.841-0.91931.117-0.003-0.0030.0000.0000.0000.000
198A198PHE00.0410.01523.3430.0000.0000.0000.0000.0000.000
199A199TYR00.011-0.01524.9940.0000.0000.0000.0000.0000.000
200A200ARG10.9080.95729.094-0.039-0.0390.0000.0000.0000.000
201A201LYS10.8230.90430.6710.0100.0100.0000.0000.0000.000
202A202VAL00.0210.01525.156-0.004-0.0040.0000.0000.0000.000
203A203LEU0-0.015-0.00228.123-0.001-0.0010.0000.0000.0000.000
204A204GLY00.0290.02030.249-0.001-0.0010.0000.0000.0000.000
205A205GLU-1-0.917-0.96328.040-0.030-0.0300.0000.0000.0000.000
206A206ILE0-0.052-0.02625.794-0.003-0.0030.0000.0000.0000.000
207A207GLN0-0.046-0.02228.6580.0030.0030.0000.0000.0000.000
208A208ALA00.0780.04531.539-0.001-0.0010.0000.0000.0000.000
209A209PHE00.003-0.00125.698-0.006-0.0060.0000.0000.0000.000
210A210ALA00.001-0.01029.894-0.001-0.0010.0000.0000.0000.000
211A211GLU-1-0.935-0.97531.4580.0060.0060.0000.0000.0000.000
212A212GLU-1-0.824-0.87430.562-0.046-0.0460.0000.0000.0000.000
213A213GLU-1-0.841-0.89428.8280.0100.0100.0000.0000.0000.000
214A214PHE0-0.024-0.03231.7100.0020.0020.0000.0000.0000.000
215A215GLY00.0280.01335.1940.0000.0000.0000.0000.0000.000
216A216ARG10.7970.86830.7740.0170.0170.0000.0000.0000.000
217A217LYS10.7740.88031.625-0.019-0.0190.0000.0000.0000.000
218A218PHE0-0.061-0.03436.2850.0030.0030.0000.0000.0000.000
219A219GLY00.0000.01039.3960.0010.0010.0000.0000.0000.000
220A220GLU-1-0.885-0.92934.801-0.026-0.0260.0000.0000.0000.000
221A221ILE0-0.063-0.03039.0290.0010.0010.0000.0000.0000.000
222A222GLN0-0.046-0.01440.853-0.001-0.0010.0000.0000.0000.000