Manual

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: J2L89

Calculation Name: 1D3U-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1D3U

Chain ID: A

ChEMBL ID:

UniProt ID: P62001

Base Structure: X-ray

Registration Date: 2023-09-27

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 180
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1738826.822265
FMO2-HF: Nuclear repulsion 1668239.113022
FMO2-HF: Total energy -70587.709244
FMO2-MP2: Total energy -70792.97835


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.
-0.5020.758-0.009-0.468-0.7840.001
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 : -0.010 / q_NPA : -0.031
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].
3A3ASP-1-0.775-0.8433.879-2.815-1.702-0.007-0.440-0.6660.001
4A4MET0-0.013-0.0174.2750.9041.018-0.001-0.009-0.1040.000
5A5SER0-0.076-0.0678.2020.3510.3510.0000.0000.0000.000
6A6LYS10.8550.91510.7811.2551.2550.0000.0000.0000.000
7A7VAL0-0.0090.01110.5820.1100.1100.0000.0000.0000.000
8A8LYS10.8190.90713.3840.3210.3210.0000.0000.0000.000
9A9LEU0-0.005-0.00316.3940.0310.0310.0000.0000.0000.000
10A10ARG10.9200.95718.8160.1220.1220.0000.0000.0000.000
11A11ILE00.0470.02122.5130.0150.0150.0000.0000.0000.000
12A12GLU-1-0.859-0.90924.656-0.089-0.0890.0000.0000.0000.000
13A13ASN00.0490.01727.4100.0000.0000.0000.0000.0000.000
14A14ILE0-0.0270.01127.7590.0080.0080.0000.0000.0000.000
15A15VAL00.0010.00029.821-0.001-0.0010.0000.0000.0000.000
16A16ALA00.0010.00131.5370.0050.0050.0000.0000.0000.000
17A17SER00.0310.03034.0540.0000.0000.0000.0000.0000.000
18A18VAL0-0.006-0.01736.922-0.001-0.0010.0000.0000.0000.000
19A19ASP-1-0.796-0.88439.7220.0230.0230.0000.0000.0000.000
20A20LEU00.0310.01142.744-0.002-0.0020.0000.0000.0000.000
21A21PHE0-0.049-0.03142.421-0.001-0.0010.0000.0000.0000.000
22A22ALA00.003-0.02047.682-0.001-0.0010.0000.0000.0000.000
23A23GLN00.0000.01350.2750.0000.0000.0000.0000.0000.000
24A24LEU0-0.057-0.03148.778-0.002-0.0020.0000.0000.0000.000
25A25ASP-1-0.856-0.92252.8960.0060.0060.0000.0000.0000.000
26A26LEU0-0.003-0.01150.104-0.001-0.0010.0000.0000.0000.000
27A27GLU-1-0.785-0.88353.8160.0050.0050.0000.0000.0000.000
28A28LYS10.8760.94956.933-0.002-0.0020.0000.0000.0000.000
29A29VAL0-0.040-0.03750.742-0.001-0.0010.0000.0000.0000.000
30A30LEU0-0.0090.00452.778-0.001-0.0010.0000.0000.0000.000
31A31ASP-1-0.866-0.92353.647-0.006-0.0060.0000.0000.0000.000
32A32LEU0-0.101-0.04451.664-0.002-0.0020.0000.0000.0000.000
33A33CYS0-0.093-0.03844.830-0.004-0.0040.0000.0000.0000.000
34A34PRO00.0420.02450.5530.0010.0010.0000.0000.0000.000
35A35ASN0-0.015-0.00947.1910.0020.0020.0000.0000.0000.000
36A36SER0-0.010-0.01847.9060.0010.0010.0000.0000.0000.000
37A37LYS10.8640.91647.744-0.002-0.0020.0000.0000.0000.000
38A38TYR0-0.060-0.06249.4270.0010.0010.0000.0000.0000.000
39A39ASN00.0290.00251.401-0.001-0.0010.0000.0000.0000.000
40A40PRO0-0.002-0.00351.9110.0010.0010.0000.0000.0000.000
41A41GLU-1-0.961-0.96252.5790.0110.0110.0000.0000.0000.000
42A42GLU-1-0.843-0.88948.6860.0050.0050.0000.0000.0000.000
43A43PHE0-0.025-0.03742.8170.0020.0020.0000.0000.0000.000
44A44PRO0-0.0030.01446.916-0.002-0.0020.0000.0000.0000.000
45A45GLY0-0.005-0.01647.2020.0010.0010.0000.0000.0000.000
46A46ILE0-0.042-0.01248.220-0.001-0.0010.0000.0000.0000.000
47A47ILE00.0000.00343.9850.0000.0000.0000.0000.0000.000
48A49HIS00.0110.00542.529-0.001-0.0010.0000.0000.0000.000
49A50LEU0-0.016-0.00642.1740.0000.0000.0000.0000.0000.000
50A51ASP-1-0.826-0.91442.149-0.027-0.0270.0000.0000.0000.000
51A52ASP-1-0.823-0.89941.872-0.037-0.0370.0000.0000.0000.000
52A53PRO0-0.072-0.02638.650-0.004-0.0040.0000.0000.0000.000
53A54LYS10.8180.88533.9960.0440.0440.0000.0000.0000.000
54A55VAL0-0.065-0.02236.352-0.001-0.0010.0000.0000.0000.000
55A56ALA00.0520.03738.3680.0000.0000.0000.0000.0000.000
56A57LEU0-0.045-0.04539.2400.0020.0020.0000.0000.0000.000
57A58LEU0-0.0010.01640.2630.0000.0000.0000.0000.0000.000
58A59ILE00.013-0.00443.2190.0010.0010.0000.0000.0000.000
59A60PHE00.0440.02242.4770.0000.0000.0000.0000.0000.000
60A61SER00.0790.03447.6640.0000.0000.0000.0000.0000.000
61A62SER0-0.042-0.01746.489-0.001-0.0010.0000.0000.0000.000
62A63GLY00.0400.02448.0650.0010.0010.0000.0000.0000.000
63A64LYS10.7990.89142.879-0.027-0.0270.0000.0000.0000.000
64A65LEU00.009-0.00541.373-0.002-0.0020.0000.0000.0000.000
65A66VAL0-0.030-0.01236.7710.0040.0040.0000.0000.0000.000
66A67VAL0-0.0080.00736.539-0.003-0.0030.0000.0000.0000.000
67A68THR0-0.011-0.00334.4790.0030.0030.0000.0000.0000.000
68A69GLY00.0820.03533.750-0.002-0.0020.0000.0000.0000.000
69A70ALA0-0.0360.00232.736-0.006-0.0060.0000.0000.0000.000
70A71LYS10.8200.90228.9080.0620.0620.0000.0000.0000.000
71A72SER00.008-0.02128.768-0.005-0.0050.0000.0000.0000.000
72A73VAL00.0600.01028.9760.0050.0050.0000.0000.0000.000
73A74GLN00.1200.06931.6930.0060.0060.0000.0000.0000.000
74A75ASP-1-0.783-0.86533.837-0.043-0.0430.0000.0000.0000.000
75A76ILE00.0200.00232.8610.0030.0030.0000.0000.0000.000
76A77GLU-1-0.906-0.95034.462-0.017-0.0170.0000.0000.0000.000
77A78ARG10.8180.89436.6800.0410.0410.0000.0000.0000.000
78A79ALA00.0150.00639.3820.0010.0010.0000.0000.0000.000
79A80VAL00.0170.00539.5600.0020.0020.0000.0000.0000.000
80A81ALA0-0.0050.00541.9180.0020.0020.0000.0000.0000.000
81A82LYS10.8530.91843.1350.0260.0260.0000.0000.0000.000
82A83LEU00.0430.02945.1510.0010.0010.0000.0000.0000.000
83A84ALA00.0540.02045.9390.0010.0010.0000.0000.0000.000
84A85GLN00.0040.01047.7120.0020.0020.0000.0000.0000.000
85A86LYS10.8750.93648.8140.0130.0130.0000.0000.0000.000
86A87LEU00.0650.03348.5770.0010.0010.0000.0000.0000.000
87A88LYS10.8390.91549.7840.0060.0060.0000.0000.0000.000
88A89SER0-0.084-0.05053.7370.0000.0000.0000.0000.0000.000
89A90ILE00.0190.02355.2780.0000.0000.0000.0000.0000.000
90A91GLY0-0.005-0.00457.2940.0010.0010.0000.0000.0000.000
91A92VAL0-0.0250.00352.0860.0010.0010.0000.0000.0000.000
92A93LYS10.9370.95053.688-0.004-0.0040.0000.0000.0000.000
93A94PHE00.0150.01948.6410.0010.0010.0000.0000.0000.000
94A95LYS10.9370.97149.898-0.016-0.0160.0000.0000.0000.000
95A96ARG10.8980.95344.913-0.020-0.0200.0000.0000.0000.000
96A97ALA00.0330.02143.751-0.001-0.0010.0000.0000.0000.000
97A98PRO0-0.001-0.01342.0040.0020.0020.0000.0000.0000.000
98A99GLN0-0.060-0.02337.411-0.002-0.0020.0000.0000.0000.000
99A100ILE0-0.002-0.01434.918-0.001-0.0010.0000.0000.0000.000
100A101ASP-1-0.836-0.89533.3430.0310.0310.0000.0000.0000.000
101A102VAL00.001-0.01228.166-0.001-0.0010.0000.0000.0000.000
102A103GLN0-0.012-0.01329.9540.0140.0140.0000.0000.0000.000
103A104ASN00.0130.00927.3210.0170.0170.0000.0000.0000.000
104A105MET0-0.0410.01124.469-0.013-0.0130.0000.0000.0000.000
105A106VAL00.0010.01424.6560.0080.0080.0000.0000.0000.000
106A107PHE00.0400.00621.158-0.010-0.0100.0000.0000.0000.000
107A108SER0-0.032-0.02922.2400.0070.0070.0000.0000.0000.000
108A109GLY00.037-0.00118.914-0.013-0.0130.0000.0000.0000.000
109A110ASP-1-0.850-0.91017.944-0.255-0.2550.0000.0000.0000.000
110A111ILE00.0400.01512.367-0.037-0.0370.0000.0000.0000.000
111A112GLY00.0050.00813.816-0.095-0.0950.0000.0000.0000.000
112A113ARG10.8430.91412.0750.2920.2920.0000.0000.0000.000
113A114GLU-1-0.871-0.92416.439-0.145-0.1450.0000.0000.0000.000
114A115PHE0-0.011-0.02313.355-0.028-0.0280.0000.0000.0000.000
115A116ASN00.0360.02518.6700.0270.0270.0000.0000.0000.000
116A117LEU00.0320.00819.8650.0160.0160.0000.0000.0000.000
117A118ASP-1-0.793-0.86921.5230.0480.0480.0000.0000.0000.000
118A119VAL0-0.021-0.02217.4360.0200.0200.0000.0000.0000.000
119A120VAL0-0.038-0.01316.2480.0310.0310.0000.0000.0000.000
120A121ALA00.009-0.01618.1400.0480.0480.0000.0000.0000.000
121A122LEU0-0.0470.00119.9250.0160.0160.0000.0000.0000.000
122A123THR00.000-0.00715.3540.0030.0030.0000.0000.0000.000
123A124LEU0-0.037-0.00114.9040.0770.0770.0000.0000.0000.000
124A125PRO00.0280.01915.389-0.043-0.0430.0000.0000.0000.000
125A126ASN0-0.059-0.05218.405-0.027-0.0270.0000.0000.0000.000
126A127CYS0-0.035-0.01520.084-0.018-0.0180.0000.0000.0000.000
127A128GLU-1-0.739-0.80922.0830.1230.1230.0000.0000.0000.000
128A129TYR0-0.050-0.07523.968-0.005-0.0050.0000.0000.0000.000
129A130GLU-1-0.843-0.91926.0220.0520.0520.0000.0000.0000.000
130A131PRO00.0230.01728.261-0.006-0.0060.0000.0000.0000.000
131A132GLU-1-0.933-0.94730.4160.0060.0060.0000.0000.0000.000
132A133GLN0-0.101-0.05532.719-0.002-0.0020.0000.0000.0000.000
133A134PHE0-0.052-0.04126.258-0.005-0.0050.0000.0000.0000.000
134A135PRO00.0130.02128.6690.0040.0040.0000.0000.0000.000
135A136GLY0-0.017-0.02124.655-0.014-0.0140.0000.0000.0000.000
136A137VAL0-0.0090.00220.0570.0120.0120.0000.0000.0000.000
137A138ILE0-0.006-0.00622.581-0.010-0.0100.0000.0000.0000.000
138A139TYR00.0270.01914.5700.0210.0210.0000.0000.0000.000
139A140ARG10.7990.84520.419-0.138-0.1380.0000.0000.0000.000
140A141VAL0-0.0050.00916.7810.0400.0400.0000.0000.0000.000
141A142LYS10.8510.91419.418-0.294-0.2940.0000.0000.0000.000
142A143GLU-1-0.926-0.94619.3170.2240.2240.0000.0000.0000.000
143A144PRO00.0230.01516.7610.0410.0410.0000.0000.0000.000
144A145LYS10.9540.97519.874-0.127-0.1270.0000.0000.0000.000
145A146SER0-0.061-0.04119.669-0.022-0.0220.0000.0000.0000.000
146A147VAL0-0.019-0.01121.6770.0210.0210.0000.0000.0000.000
147A148ILE0-0.020-0.02016.288-0.020-0.0200.0000.0000.0000.000
148A149LEU00.0140.02820.3190.0160.0160.0000.0000.0000.000
149A150LEU00.005-0.00616.788-0.017-0.0170.0000.0000.0000.000
150A151PHE00.0320.01520.4890.0120.0120.0000.0000.0000.000
151A152SER00.0720.03420.943-0.018-0.0180.0000.0000.0000.000
152A153SER00.0440.02721.195-0.020-0.0200.0000.0000.0000.000
153A154GLY00.0240.01018.084-0.033-0.0330.0000.0000.0000.000
154A155LYS10.7740.89317.9650.1990.1990.0000.0000.0000.000
155A156ILE00.0250.01315.9400.0240.0240.0000.0000.0000.000
156A157VAL00.003-0.00320.112-0.018-0.0180.0000.0000.0000.000
157A158CYS0-0.0480.00419.3660.0220.0220.0000.0000.0000.000
158A159SER00.002-0.01121.476-0.018-0.0180.0000.0000.0000.000
159A160GLY00.0040.00223.2110.0180.0180.0000.0000.0000.000
160A161ALA00.0270.01620.8540.0050.0050.0000.0000.0000.000
161A162LYS10.8630.91522.853-0.074-0.0740.0000.0000.0000.000
162A163SER00.005-0.02921.447-0.015-0.0150.0000.0000.0000.000
163A164GLU-1-0.801-0.92418.540-0.106-0.1060.0000.0000.0000.000
164A165ALA0-0.0160.00417.115-0.006-0.0060.0000.0000.0000.000
165A166ASP-1-0.844-0.89916.4030.1040.1040.0000.0000.0000.000
166A167ALA00.0230.00717.0140.0330.0330.0000.0000.0000.000
167A168TRP0-0.019-0.02712.4060.0070.0070.0000.0000.0000.000
168A169GLU-1-0.782-0.85211.5590.3890.3890.0000.0000.0000.000
169A170ALA00.0110.00712.7600.0930.0930.0000.0000.0000.000
170A171VAL00.0310.00312.1070.0550.0550.0000.0000.0000.000
171A172ARG10.8500.9088.401-0.099-0.0990.0000.0000.0000.000
172A173LYS10.7580.8659.087-0.461-0.4610.0000.0000.0000.000
173A174LEU00.0600.03611.5710.1170.1170.0000.0000.0000.000
174A175LEU00.009-0.0018.1890.0410.0410.0000.0000.0000.000
175A176ARG10.8290.8976.399-0.922-0.9220.0000.0000.0000.000
176A177GLU-1-0.863-0.9198.2611.1171.1170.0000.0000.0000.000
177A178LEU0-0.040-0.02511.136-0.057-0.0570.0000.0000.0000.000
178A179ASP-1-0.931-0.9584.4000.3410.374-0.001-0.019-0.0140.000
179A180LYS10.8230.9177.527-1.166-1.1660.0000.0000.0000.000
180A181TYR0-0.0050.0097.050-0.194-0.1940.0000.0000.0000.000