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: Q83NY

Calculation Name: 1D02-A-Xray309

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1D02

Chain ID: A

ChEMBL ID:

UniProt ID: P43642

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 198
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2230249.462469
FMO2-HF: Nuclear repulsion 2151634.741774
FMO2-HF: Total energy -78614.720695
FMO2-MP2: Total energy -78849.847515


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:5:ACE )


Summations of interaction energy for fragment #1(A:5:ACE )
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.
0.4241.5930.015-0.595-0.589-0.003
Interaction energy analysis for fragmet #1(A:5:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.032 / q_NPA : 0.010
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].
3A7SER 0-0.0330.0083.8601.6292.182-0.004-0.222-0.3270.000
4A8GLY 00.0870.0356.626-0.078-0.0780.0000.0000.0000.000
5A9ARG 10.9050.9499.6270.3910.3910.0000.0000.0000.000
6A10LEU 00.0400.02812.074-0.058-0.0580.0000.0000.0000.000
7A11ASN 0-0.012-0.00715.2250.0450.0450.0000.0000.0000.000
8A12TRP 00.051-0.00417.3500.0260.0260.0000.0000.0000.000
9A13GLN 0-0.023-0.00919.2420.0130.0130.0000.0000.0000.000
10A14ALA 00.0680.04620.6910.0180.0180.0000.0000.0000.000
11A15LEU 0-0.014-0.00122.0060.0160.0160.0000.0000.0000.000
12A16ALA 0-0.014-0.01623.8850.0150.0150.0000.0000.0000.000
13A17GLY 00.0310.01825.5250.0120.0120.0000.0000.0000.000
14A18LEU 00.0030.01426.3730.0090.0090.0000.0000.0000.000
15A19LYS 10.9210.97328.1530.0850.0850.0000.0000.0000.000
16A20ALA 0-0.023-0.01729.8850.0070.0070.0000.0000.0000.000
17A21SER 0-0.085-0.04931.0970.0050.0050.0000.0000.0000.000
18A22GLY 0-0.028-0.01732.8430.0030.0030.0000.0000.0000.000
19A23ALA 0-0.0060.00931.8040.0030.0030.0000.0000.0000.000
20A24GLU -1-0.948-0.96533.180-0.078-0.0780.0000.0000.0000.000
21A25GLN 00.0420.01628.487-0.001-0.0010.0000.0000.0000.000
22A26ASN 00.0100.00229.6180.0000.0000.0000.0000.0000.000
23A27LEU 00.0580.01424.928-0.006-0.0060.0000.0000.0000.000
24A28TYR 0-0.003-0.03025.505-0.008-0.0080.0000.0000.0000.000
25A29ASN 00.0130.00224.934-0.015-0.0150.0000.0000.0000.000
26A30VAL 00.0200.02124.120-0.010-0.0100.0000.0000.0000.000
27A31PHE 00.006-0.01919.926-0.010-0.0100.0000.0000.0000.000
28A32ASN 00.0040.00020.231-0.039-0.0390.0000.0000.0000.000
29A33ALA 00.0240.02720.674-0.020-0.0200.0000.0000.0000.000
30A34VAL 0-0.043-0.01418.519-0.020-0.0200.0000.0000.0000.000
31A35PHE 00.012-0.00616.197-0.030-0.0300.0000.0000.0000.000
32A36GLU -1-0.904-0.93015.693-0.280-0.2800.0000.0000.0000.000
33A37GLY 00.0010.00214.2450.0020.0020.0000.0000.0000.000
34A38THR 0-0.077-0.03011.468-0.101-0.1010.0000.0000.0000.000
35A39LYS 10.9220.9585.7730.9610.9610.0000.0000.0000.000
36A40TYR 0-0.009-0.01010.1040.0440.0440.0000.0000.0000.000
37A41VAL 00.0370.02913.3740.0040.0040.0000.0000.0000.000
38A42LEU 0-0.017-0.00316.6160.0240.0240.0000.0000.0000.000
39A43TYR 0-0.092-0.08717.6960.0100.0100.0000.0000.0000.000
40A44GLU -1-0.903-0.96122.713-0.088-0.0880.0000.0000.0000.000
41A45LYS 10.8900.94926.4170.0700.0700.0000.0000.0000.000
42A46PRO 0-0.0210.00723.721-0.001-0.0010.0000.0000.0000.000
43A47LYS 10.9610.94925.4220.0980.0980.0000.0000.0000.000
44A48HIS 00.0650.03420.2660.0210.0210.0000.0000.0000.000
45A49LEU 00.0280.03325.0990.0080.0080.0000.0000.0000.000
46A50LYS 10.9070.95328.0320.0590.0590.0000.0000.0000.000
47A51ASN 0-0.018-0.01330.3250.0050.0050.0000.0000.0000.000
48A52LEU 0-0.050-0.03329.4470.0020.0020.0000.0000.0000.000
49A53TYR 00.020-0.02433.2480.0020.0020.0000.0000.0000.000
50A54ALA 00.0210.04437.0170.0020.0020.0000.0000.0000.000
51A55GLN 00.0400.01633.2620.0020.0020.0000.0000.0000.000
52A56VAL 0-0.061-0.02537.5820.0020.0020.0000.0000.0000.000
53A57VAL 00.0110.00839.4070.0000.0000.0000.0000.0000.000
54A58LEU 0-0.021-0.01042.1820.0010.0010.0000.0000.0000.000
55A59PRO 00.0160.00645.3930.0010.0010.0000.0000.0000.000
56A60ASP -1-0.845-0.93948.333-0.008-0.0080.0000.0000.0000.000
57A61ASP -1-1.001-1.00751.217-0.007-0.0070.0000.0000.0000.000
58A62VAL 00.0210.01348.1840.0000.0000.0000.0000.0000.000
59A63ILE 0-0.017-0.00647.193-0.001-0.0010.0000.0000.0000.000
60A64LYS 10.9120.95650.8800.0060.0060.0000.0000.0000.000
61A65GLU -1-0.899-0.93453.664-0.009-0.0090.0000.0000.0000.000
62A66ILE 0-0.087-0.02248.267-0.001-0.0010.0000.0000.0000.000
63A67PHE 0-0.038-0.02550.4480.0000.0000.0000.0000.0000.000
64A68ASN 0-0.007-0.01849.823-0.001-0.0010.0000.0000.0000.000
65A69PRO 0-0.037-0.01347.4880.0000.0000.0000.0000.0000.000
66A70LEU 00.0140.01049.2630.0000.0000.0000.0000.0000.000
67A71ILE 0-0.030-0.02843.194-0.001-0.0010.0000.0000.0000.000
68A72ASP -1-0.755-0.84242.305-0.023-0.0230.0000.0000.0000.000
69A73LEU 0-0.004-0.00441.580-0.002-0.0020.0000.0000.0000.000
70A74SER 0-0.074-0.04439.183-0.001-0.0010.0000.0000.0000.000
71A75THR 0-0.046-0.03337.412-0.002-0.0020.0000.0000.0000.000
72A76THR 0-0.051-0.01937.800-0.003-0.0030.0000.0000.0000.000
73A77GLN 0-0.032-0.01831.524-0.003-0.0030.0000.0000.0000.000
74A78TRP 00.0120.00235.633-0.002-0.0020.0000.0000.0000.000
75A79GLY 00.0350.02032.8750.0010.0010.0000.0000.0000.000
76A80VAL 0-0.057-0.02529.9710.0010.0010.0000.0000.0000.000
77A81SER 0-0.059-0.04930.117-0.003-0.0030.0000.0000.0000.000
78A82PRO 00.0150.03326.5850.0020.0020.0000.0000.0000.000
79A83ALA 00.0280.02528.818-0.004-0.0040.0000.0000.0000.000
80A84PHE 00.0130.01122.985-0.005-0.0050.0000.0000.0000.000
81A85ALA 00.0050.01221.0880.0110.0110.0000.0000.0000.000
82A86ILE 0-0.0010.01416.388-0.011-0.0110.0000.0000.0000.000
83A87GLU -1-0.815-0.87114.203-0.218-0.2180.0000.0000.0000.000
84A88ASN 00.0470.0478.575-0.164-0.1640.0000.0000.0000.000
85A89THR 0-0.054-0.06710.655-0.009-0.0090.0000.0000.0000.000
86A90GLU -1-0.936-0.9653.504-2.397-1.7810.019-0.373-0.262-0.003
87A91THR 0-0.039-0.0368.1370.1160.1160.0000.0000.0000.000
88A92HIS 10.8200.90910.0580.3530.3530.0000.0000.0000.000
89A93LYS 10.8860.98112.8650.0420.0420.0000.0000.0000.000
90A94ILE 0-0.049-0.04614.853-0.037-0.0370.0000.0000.0000.000
91A95LEU 00.0040.01717.6900.0230.0230.0000.0000.0000.000
92A96PHE 0-0.021-0.02519.994-0.011-0.0110.0000.0000.0000.000
93A97GLY 00.0490.01223.4550.0070.0070.0000.0000.0000.000
94A98GLU -1-0.955-0.99125.878-0.059-0.0590.0000.0000.0000.000
95A99ILE 00.0410.02328.674-0.001-0.0010.0000.0000.0000.000
96A100LYS 10.8370.91931.5340.0500.0500.0000.0000.0000.000
97A101ARG 10.9590.98733.1130.0640.0640.0000.0000.0000.000
98A102GLN 0-0.052-0.04237.3570.0010.0010.0000.0000.0000.000
99A103ASP -1-0.855-0.91540.759-0.034-0.0340.0000.0000.0000.000
100A104GLY 0-0.003-0.03143.3020.0000.0000.0000.0000.0000.000
101A105TRP 0-0.098-0.03444.8570.0010.0010.0000.0000.0000.000
102A106VAL 00.0330.00143.8820.0000.0000.0000.0000.0000.000
103A107GLU -1-0.765-0.86346.159-0.024-0.0240.0000.0000.0000.000
104A108GLY 0-0.015-0.00949.492-0.001-0.0010.0000.0000.0000.000
105A109LYS 10.8910.96247.7410.0270.0270.0000.0000.0000.000
106A110ASP -1-0.822-0.90552.098-0.017-0.0170.0000.0000.0000.000
107A111PRO 0-0.001-0.02750.820-0.001-0.0010.0000.0000.0000.000
108A112SER 0-0.0150.00050.484-0.001-0.0010.0000.0000.0000.000
109A113ALA 0-0.0050.00049.127-0.001-0.0010.0000.0000.0000.000
110A114GLY 00.0520.03046.521-0.002-0.0020.0000.0000.0000.000
111A115ARG 10.8560.91646.8170.0220.0220.0000.0000.0000.000
112A116GLY 0-0.0340.00045.9910.0000.0000.0000.0000.0000.000
113A117ASN 00.0640.01343.961-0.001-0.0010.0000.0000.0000.000
114A118ALA 00.0550.03342.1120.0000.0000.0000.0000.0000.000
115A119HIS 0-0.005-0.00938.078-0.003-0.0030.0000.0000.0000.000
116A120GLU -1-0.854-0.92137.860-0.023-0.0230.0000.0000.0000.000
117A121ARG 10.9190.96036.9880.0380.0380.0000.0000.0000.000
118A122SER 0-0.104-0.06233.487-0.001-0.0010.0000.0000.0000.000
119A123CYS 00.0500.01633.806-0.001-0.0010.0000.0000.0000.000
120A124LYS 10.9620.99333.9010.0400.0400.0000.0000.0000.000
121A125LEU 0-0.024-0.01628.9640.0020.0020.0000.0000.0000.000
122A126PHE 00.0410.03431.0370.0000.0000.0000.0000.0000.000
123A127THR 0-0.052-0.01833.2860.0040.0040.0000.0000.0000.000
124A128PRO 00.0720.02033.019-0.001-0.0010.0000.0000.0000.000
125A129GLY 0-0.020-0.00732.2920.0000.0000.0000.0000.0000.000
126A130LEU 00.001-0.00730.990-0.002-0.0020.0000.0000.0000.000
127A131LEU 00.0340.03328.472-0.004-0.0040.0000.0000.0000.000
128A132LYS 10.9780.99227.2830.0040.0040.0000.0000.0000.000
129A133ALA 00.004-0.00127.0250.0000.0000.0000.0000.0000.000
130A134TYR 00.019-0.01124.966-0.004-0.0040.0000.0000.0000.000
131A135ARG 10.8540.92722.8600.0010.0010.0000.0000.0000.000
132A136THR 0-0.055-0.01921.9250.0010.0010.0000.0000.0000.000
133A137ILE 0-0.060-0.04121.914-0.003-0.0030.0000.0000.0000.000
134A138GLY 00.0050.01419.773-0.011-0.0110.0000.0000.0000.000
135A139GLY 00.0570.03617.587-0.015-0.0150.0000.0000.0000.000
136A140ILE 0-0.015-0.00117.6880.0150.0150.0000.0000.0000.000
137A141ASN 0-0.019-0.03619.229-0.003-0.0030.0000.0000.0000.000
138A142ASP -1-0.852-0.91019.2110.0420.0420.0000.0000.0000.000
139A143GLU -1-0.930-0.98621.219-0.002-0.0020.0000.0000.0000.000
140A144GLU -1-0.908-0.88321.6410.0260.0260.0000.0000.0000.000
141A145ILE 0-0.064-0.01120.823-0.006-0.0060.0000.0000.0000.000
142A146LEU 0-0.037-0.01724.0690.0020.0020.0000.0000.0000.000
143A147PRO 00.000-0.00622.591-0.006-0.0060.0000.0000.0000.000
144A148PHE 0-0.009-0.00523.261-0.010-0.0100.0000.0000.0000.000
145A149TRP 00.0170.00722.4890.0010.0010.0000.0000.0000.000
146A150VAL 0-0.037-0.01325.811-0.005-0.0050.0000.0000.0000.000
147A151VAL 00.0270.02127.0340.0020.0020.0000.0000.0000.000
148A152PHE 00.000-0.01329.8860.0010.0010.0000.0000.0000.000
149A153GLU -1-0.837-0.94331.725-0.070-0.0700.0000.0000.0000.000
150A154GLY 00.0580.02335.3020.0030.0030.0000.0000.0000.000
151A155ASP -1-0.848-0.92938.928-0.034-0.0340.0000.0000.0000.000
152A156ILE 0-0.0270.00238.0180.0020.0020.0000.0000.0000.000
153A157THR 0-0.043-0.03635.3040.0020.0020.0000.0000.0000.000
154A158ARG 10.7930.86038.0630.0300.0300.0000.0000.0000.000
155A159ASP -1-0.747-0.83240.863-0.021-0.0210.0000.0000.0000.000
156A160PRO 0-0.002-0.01042.3120.0000.0000.0000.0000.0000.000
157A161LYS 10.9560.97743.9050.0180.0180.0000.0000.0000.000
158A162ARG 10.8700.92940.9120.0240.0240.0000.0000.0000.000
159A163VAL 00.0290.02837.6070.0000.0000.0000.0000.0000.000
160A164ARG 10.9020.95238.6330.0160.0160.0000.0000.0000.000
161A165GLU -1-0.804-0.88140.390-0.021-0.0210.0000.0000.0000.000
162A166ILE 00.0010.00035.0190.0010.0010.0000.0000.0000.000
163A167THR 0-0.038-0.02635.6400.0000.0000.0000.0000.0000.000
164A168PHE 0-0.023-0.02336.3480.0020.0020.0000.0000.0000.000
165A169TRP 0-0.022-0.02336.7760.0000.0000.0000.0000.0000.000
166A170TYR 0-0.012-0.00730.126-0.001-0.0010.0000.0000.0000.000
167A171ASP -1-0.845-0.89332.922-0.001-0.0010.0000.0000.0000.000
168A172HIS 10.8690.93729.748-0.003-0.0030.0000.0000.0000.000
169A173TYR 00.0030.00427.3370.0020.0020.0000.0000.0000.000
170A174GLN 0-0.030-0.03529.504-0.008-0.0080.0000.0000.0000.000
171A175ASP -1-0.815-0.89924.604-0.027-0.0270.0000.0000.0000.000
172A176ASN 0-0.023-0.02124.425-0.002-0.0020.0000.0000.0000.000
173A177TYR 0-0.041-0.03526.936-0.005-0.0050.0000.0000.0000.000
174A178PHE 0-0.0010.01127.3140.0000.0000.0000.0000.0000.000
175A179MET 0-0.045-0.01229.423-0.001-0.0010.0000.0000.0000.000
176A180TRP 0-0.001-0.00229.655-0.001-0.0010.0000.0000.0000.000
177A181ARG 10.8740.92432.1290.0370.0370.0000.0000.0000.000
178A182PRO 00.0390.00335.117-0.003-0.0030.0000.0000.0000.000
179A183ASN 0-0.018-0.01236.9130.0000.0000.0000.0000.0000.000
180A184GLU -1-0.815-0.87632.035-0.052-0.0520.0000.0000.0000.000
181A185SER 0-0.034-0.00729.240-0.004-0.0040.0000.0000.0000.000
182A186GLY 00.0790.02227.3990.0000.0000.0000.0000.0000.000
183A187GLU -1-0.991-0.99224.271-0.097-0.0970.0000.0000.0000.000
184A188LYS 10.8810.92424.7880.0490.0490.0000.0000.0000.000
185A189LEU 0-0.0090.01424.8740.0020.0020.0000.0000.0000.000
186A190VAL 00.003-0.01420.093-0.003-0.0030.0000.0000.0000.000
187A191GLN 00.016-0.00721.030-0.003-0.0030.0000.0000.0000.000
188A192HIS 00.0080.02421.9900.0060.0060.0000.0000.0000.000
189A193PHE 00.0460.01415.5010.0060.0060.0000.0000.0000.000
190A194ASN 00.0260.01016.217-0.027-0.0270.0000.0000.0000.000
191A195GLU -1-0.978-0.98717.394-0.051-0.0510.0000.0000.0000.000
192A196LYS 10.8860.94919.9920.0520.0520.0000.0000.0000.000
193A197LEU 0-0.016-0.01419.1750.0070.0070.0000.0000.0000.000
194A198LYS 10.8060.90512.5040.2270.2270.0000.0000.0000.000
195A199LYS 10.9350.98013.386-0.004-0.0040.0000.0000.0000.000
196A200TYR 0-0.099-0.08913.8750.0140.0140.0000.0000.0000.000
197A201LEU 0-0.071-0.04613.2270.0010.0010.0000.0000.0000.000
198A202ASP -2-1.788-1.8849.594-0.131-0.1310.0000.0000.0000.000