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: 8JZ7Y

Calculation Name: 1I39-A-Xray309

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1I39

Chain ID: A

ChEMBL ID:

UniProt ID: O29634

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 202
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2268148.049933
FMO2-HF: Nuclear repulsion 2188392.908729
FMO2-HF: Total energy -79755.141204
FMO2-MP2: Total energy -79986.356965


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:0:ACE )


Summations of interaction energy for fragment #1(A:0: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.
1.2782.2230.006-0.417-0.5330
Interaction energy analysis for fragmet #1(A:0:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.027 / q_NPA : 0.006
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].
3A2LYS 10.9931.0303.8621.8522.556-0.005-0.347-0.3510.000
4A3ALA 00.024-0.0127.080-0.058-0.0580.0000.0000.0000.000
5A4GLY 0-0.0120.01510.1320.0900.0900.0000.0000.0000.000
6A5ILE 0-0.032-0.02913.0340.0060.0060.0000.0000.0000.000
7A6ASP -1-0.783-0.90116.515-0.131-0.1310.0000.0000.0000.000
8A7GLU -1-0.907-0.98520.265-0.078-0.0780.0000.0000.0000.000
9A8ALA 00.0360.02823.451-0.002-0.0020.0000.0000.0000.000
10A9GLY 00.010-0.00326.7200.0050.0050.0000.0000.0000.000
11A10LYS 10.9560.99627.5080.0790.0790.0000.0000.0000.000
12A11GLY 0-0.023-0.01930.1310.0050.0050.0000.0000.0000.000
13A12CYS 0-0.1000.01533.2210.0020.0020.0000.0000.0000.000
14A13VAL 0-0.003-0.01035.1270.0020.0020.0000.0000.0000.000
15A14ILE 00.0130.00637.2800.0030.0030.0000.0000.0000.000
16A15GLY 00.0540.03734.328-0.004-0.0040.0000.0000.0000.000
17A16PRO 0-0.013-0.01529.4430.0020.0020.0000.0000.0000.000
18A17LEU 0-0.0440.00726.230-0.002-0.0020.0000.0000.0000.000
19A18VAL 0-0.024-0.01723.3900.0030.0030.0000.0000.0000.000
20A19VAL 00.0260.01019.485-0.004-0.0040.0000.0000.0000.000
21A20ALA 0-0.003-0.00618.5910.0050.0050.0000.0000.0000.000
22A21GLY 00.0320.01314.495-0.001-0.0010.0000.0000.0000.000
23A22VAL 0-0.028-0.01112.9530.0050.0050.0000.0000.0000.000
24A23ALA 00.0390.0267.550-0.028-0.0280.0000.0000.0000.000
25A24CYS 0-0.041-0.0338.9430.1620.1620.0000.0000.0000.000
26A25SER 00.0310.0176.962-0.339-0.3390.0000.0000.0000.000
27A26ASP -1-0.850-0.9257.977-0.430-0.4300.0000.0000.0000.000
28A27GLU -1-0.898-0.97010.617-0.533-0.5330.0000.0000.0000.000
29A28ASP -1-0.889-0.95312.740-0.199-0.1990.0000.0000.0000.000
30A29ARG 10.9580.98214.9280.3610.3610.0000.0000.0000.000
31A30LEU 00.006-0.01013.8960.0440.0440.0000.0000.0000.000
32A31ARG 10.8450.92414.3010.4260.4260.0000.0000.0000.000
33A32LYS 10.9480.99318.8160.2140.2140.0000.0000.0000.000
34A33LEU 0-0.028-0.01018.7410.0240.0240.0000.0000.0000.000
35A34GLY 0-0.0030.00621.7440.0180.0180.0000.0000.0000.000
36A35VAL 00.0070.00118.3420.0140.0140.0000.0000.0000.000
37A36LYS 10.9590.99521.6980.1670.1670.0000.0000.0000.000
38A37ASP -1-0.943-0.96422.832-0.128-0.1280.0000.0000.0000.000
39A38SER 00.062-0.00223.7090.0120.0120.0000.0000.0000.000
40A39LYS 10.8400.90926.1940.1310.1310.0000.0000.0000.000
41A40LYS 10.9300.97728.7680.1150.1150.0000.0000.0000.000
42A41LEU 0-0.032-0.00126.8900.0070.0070.0000.0000.0000.000
43A42SER 00.0300.01730.9330.0010.0010.0000.0000.0000.000
44A43GLN 00.0540.01331.249-0.005-0.0050.0000.0000.0000.000
45A44GLY 00.0370.01931.016-0.004-0.0040.0000.0000.0000.000
46A45ARG 10.8770.91030.0140.0880.0880.0000.0000.0000.000
47A46ARG 10.8310.90227.1680.0900.0900.0000.0000.0000.000
48A47GLU -1-0.924-0.96126.078-0.101-0.1010.0000.0000.0000.000
49A48GLU -1-0.841-0.90626.257-0.106-0.1060.0000.0000.0000.000
50A49LEU 00.0030.00422.040-0.010-0.0100.0000.0000.0000.000
51A50ALA 00.001-0.00821.854-0.022-0.0220.0000.0000.0000.000
52A51GLU -1-0.906-0.95721.135-0.149-0.1490.0000.0000.0000.000
53A52GLU -1-0.977-0.98721.443-0.176-0.1760.0000.0000.0000.000
54A53ILE 0-0.042-0.02716.627-0.030-0.0300.0000.0000.0000.000
55A54ARG 10.9230.95116.6480.1190.1190.0000.0000.0000.000
56A55LYS 10.9340.98416.9730.1390.1390.0000.0000.0000.000
57A56ILE 0-0.047-0.02715.033-0.002-0.0020.0000.0000.0000.000
58A57CYS 0-0.0390.02011.989-0.088-0.0880.0000.0000.0000.000
59A58ARG 10.8910.9609.1470.2730.2730.0000.0000.0000.000
60A59THR 0-0.025-0.02912.123-0.014-0.0140.0000.0000.0000.000
61A60GLU -1-0.826-0.90513.597-0.092-0.0920.0000.0000.0000.000
62A61VAL 00.007-0.00216.165-0.006-0.0060.0000.0000.0000.000
63A62LEU 00.0000.01819.7610.0140.0140.0000.0000.0000.000
64A63LYS 10.9450.96322.0880.0600.0600.0000.0000.0000.000
65A64VAL 00.0000.00625.8380.0070.0070.0000.0000.0000.000
66A65SER 00.0320.00828.479-0.002-0.0020.0000.0000.0000.000
67A66PRO 00.021-0.00332.0440.0020.0020.0000.0000.0000.000
68A67GLU -1-0.887-0.92735.013-0.018-0.0180.0000.0000.0000.000
69A68ASN 00.0690.02231.0900.0040.0040.0000.0000.0000.000
70A69LEU 0-0.078-0.03629.8140.0020.0020.0000.0000.0000.000
71A70ASP -1-0.764-0.88533.086-0.022-0.0220.0000.0000.0000.000
72A71GLU -1-0.972-0.97034.723-0.007-0.0070.0000.0000.0000.000
73A72ARG 10.9260.95725.8040.0240.0240.0000.0000.0000.000
74A73MET 0-0.053-0.03333.4120.0000.0000.0000.0000.0000.000
75A74ALA 0-0.079-0.01935.0640.0010.0010.0000.0000.0000.000
76A75ALA 0-0.007-0.00734.7560.0010.0010.0000.0000.0000.000
77A76LYS 10.8600.92728.5510.0030.0030.0000.0000.0000.000
78A77THR 00.0050.00431.890-0.004-0.0040.0000.0000.0000.000
79A78ILE 00.0400.00029.9910.0000.0000.0000.0000.0000.000
80A79ASN 00.0350.00128.203-0.006-0.0060.0000.0000.0000.000
81A80GLU -1-0.878-0.92726.791-0.015-0.0150.0000.0000.0000.000
82A81ILE 00.0020.00426.3860.0010.0010.0000.0000.0000.000
83A82LEU 00.009-0.00523.551-0.001-0.0010.0000.0000.0000.000
84A83LYS 10.9591.00522.4980.0030.0030.0000.0000.0000.000
85A84GLU -1-0.816-0.89621.422-0.007-0.0070.0000.0000.0000.000
86A85CYS 0-0.062-0.02521.2920.0030.0030.0000.0000.0000.000
87A86TYR 0-0.007-0.02018.523-0.009-0.0090.0000.0000.0000.000
88A87ALA 00.0370.02316.883-0.011-0.0110.0000.0000.0000.000
89A88GLU -1-0.856-0.91716.338-0.019-0.0190.0000.0000.0000.000
90A89ILE 0-0.015-0.01414.4210.0020.0020.0000.0000.0000.000
91A90ILE 00.008-0.00111.768-0.025-0.0250.0000.0000.0000.000
92A91LEU 00.0030.00611.4360.0210.0210.0000.0000.0000.000
93A92ARG 10.7620.89212.5130.0970.0970.0000.0000.0000.000
94A93LEU 0-0.064-0.0449.1270.0110.0110.0000.0000.0000.000
95A94LYS 10.8880.9597.579-0.295-0.2950.0000.0000.0000.000
96A95PRO 0-0.027-0.0065.4560.1640.1640.0000.0000.0000.000
97A96GLU -1-0.949-0.9713.434-0.553-0.3510.011-0.068-0.1440.000
98A97ILE 0-0.018-0.0255.3570.0470.0860.000-0.002-0.0380.000
99A98ALA 0-0.017-0.0078.740-0.181-0.1810.0000.0000.0000.000
100A99TYR 00.000-0.00110.2630.0300.0300.0000.0000.0000.000
101A100VAL 00.012-0.00514.409-0.014-0.0140.0000.0000.0000.000
102A101ASP -1-0.829-0.91417.680-0.116-0.1160.0000.0000.0000.000
103A102SER 00.002-0.00421.2330.0120.0120.0000.0000.0000.000
104A103PRO 0-0.102-0.06723.8610.0020.0020.0000.0000.0000.000
105A104ASP -1-0.914-0.94827.237-0.042-0.0420.0000.0000.0000.000
106A105VAL 00.004-0.02327.613-0.005-0.0050.0000.0000.0000.000
107A106ILE 0-0.058-0.01127.516-0.001-0.0010.0000.0000.0000.000
108A107PRO 00.0570.04422.6640.0030.0030.0000.0000.0000.000
109A108GLU -1-0.852-0.94522.761-0.037-0.0370.0000.0000.0000.000
110A109ARG 10.8580.92723.0750.0190.0190.0000.0000.0000.000
111A110LEU 00.0480.02921.2300.0060.0060.0000.0000.0000.000
112A111SER 00.014-0.00318.770-0.004-0.0040.0000.0000.0000.000
113A112ARG 10.9740.98419.0830.0120.0120.0000.0000.0000.000
114A113GLU -1-0.874-0.94020.8540.0010.0010.0000.0000.0000.000
115A114LEU 00.0110.00017.6100.0060.0060.0000.0000.0000.000
116A115GLU -1-0.899-0.95215.6200.0360.0360.0000.0000.0000.000
117A116GLU -1-1.021-0.99017.2310.0670.0670.0000.0000.0000.000
118A117ILE 0-0.005-0.00219.4420.0080.0080.0000.0000.0000.000
119A118THR 0-0.109-0.06414.2310.0130.0130.0000.0000.0000.000
120A119GLY 00.0380.02714.9470.0300.0300.0000.0000.0000.000
121A120LEU 0-0.076-0.0389.4530.0500.0500.0000.0000.0000.000
122A121ARG 10.9500.99010.237-0.037-0.0370.0000.0000.0000.000
123A122VAL 0-0.025-0.02311.560-0.054-0.0540.0000.0000.0000.000
124A123VAL 0-0.028-0.01414.0220.0180.0180.0000.0000.0000.000
125A124ALA 0-0.0020.01216.120-0.028-0.0280.0000.0000.0000.000
126A125GLU -1-0.845-0.92618.987-0.126-0.1260.0000.0000.0000.000
127A126HIS 00.006-0.01621.4210.0030.0030.0000.0000.0000.000
128A127LYS 10.9450.99024.1530.0760.0760.0000.0000.0000.000
129A128ALA 00.0560.02418.995-0.005-0.0050.0000.0000.0000.000
130A129ASP -1-0.785-0.90319.948-0.159-0.1590.0000.0000.0000.000
131A130GLU -1-1.039-1.01321.640-0.123-0.1230.0000.0000.0000.000
132A131LYS 10.8540.93918.6040.1760.1760.0000.0000.0000.000
133A132TYR 0-0.072-0.06014.792-0.024-0.0240.0000.0000.0000.000
134A133PRO 00.0300.00915.7080.0090.0090.0000.0000.0000.000
135A134LEU 00.0340.0119.9900.0210.0210.0000.0000.0000.000
136A135VAL 00.0040.01814.6540.0100.0100.0000.0000.0000.000
137A136ALA 00.0360.02717.3320.0240.0240.0000.0000.0000.000
138A137ALA 0-0.020-0.01616.3150.0210.0210.0000.0000.0000.000
139A138ALA 00.0000.00416.5260.0180.0180.0000.0000.0000.000
140A139SER 00.0170.00818.2220.0310.0310.0000.0000.0000.000
141A140ILE 0-0.063-0.03021.3130.0210.0210.0000.0000.0000.000
142A141ILE 0-0.008-0.00118.2480.0180.0180.0000.0000.0000.000
143A142ALA 00.0180.00621.5310.0180.0180.0000.0000.0000.000
144A143LYS 10.9400.95323.1830.1310.1310.0000.0000.0000.000
145A144VAL 00.0100.02924.9870.0110.0110.0000.0000.0000.000
146A145GLU -1-0.903-0.95723.599-0.084-0.0840.0000.0000.0000.000
147A146ARG 10.8380.88926.4500.0780.0780.0000.0000.0000.000
148A147GLU -1-0.849-0.93128.912-0.079-0.0790.0000.0000.0000.000
149A148ARG 10.9570.99326.0780.1040.1040.0000.0000.0000.000
150A149GLU -1-0.834-0.87830.992-0.043-0.0430.0000.0000.0000.000
151A150ILE 0-0.064-0.03832.6560.0060.0060.0000.0000.0000.000
152A151GLU -1-0.870-0.94534.743-0.051-0.0510.0000.0000.0000.000
153A152ARG 10.8710.91434.3630.0460.0460.0000.0000.0000.000
154A153LEU 0-0.074-0.05235.9380.0040.0040.0000.0000.0000.000
155A154LYS 10.8540.94638.7800.0500.0500.0000.0000.0000.000
156A155GLU -1-0.948-0.95039.679-0.039-0.0390.0000.0000.0000.000
157A156LYS 10.8750.95241.4180.0290.0290.0000.0000.0000.000
158A157PHE 0-0.076-0.07340.5990.0030.0030.0000.0000.0000.000
159A158GLY 00.0540.04344.3380.0010.0010.0000.0000.0000.000
160A159ASP -1-0.851-0.93143.346-0.042-0.0420.0000.0000.0000.000
161A160PHE 00.003-0.00238.3330.0020.0020.0000.0000.0000.000
162A161GLY 00.016-0.00342.3380.0000.0000.0000.0000.0000.000
163A162SER 0-0.050-0.05137.553-0.002-0.0020.0000.0000.0000.000
164A163GLY 00.0570.02437.175-0.003-0.0030.0000.0000.0000.000
165A164TYR 00.043-0.00132.1340.0010.0010.0000.0000.0000.000
166A165ALA 00.002-0.01238.7340.0020.0020.0000.0000.0000.000
167A166SER 0-0.017-0.01740.6980.0010.0010.0000.0000.0000.000
168A167ASP -1-0.792-0.87341.352-0.040-0.0400.0000.0000.0000.000
169A168PRO 0-0.048-0.06043.1600.0020.0020.0000.0000.0000.000
170A169ARG 11.0671.04845.0130.0320.0320.0000.0000.0000.000
171A170THR 00.0030.00241.3360.0000.0000.0000.0000.0000.000
172A171ARG 10.8990.97344.3650.0330.0330.0000.0000.0000.000
173A172GLU -1-0.969-0.98046.775-0.026-0.0260.0000.0000.0000.000
174A173VAL 00.0480.03046.0580.0010.0010.0000.0000.0000.000
175A174LEU 0-0.004-0.01042.8510.0010.0010.0000.0000.0000.000
176A175LYS 10.9130.96246.8900.0220.0220.0000.0000.0000.000
177A176GLU -1-0.918-0.96050.422-0.023-0.0230.0000.0000.0000.000
178A177TRP 00.0420.01043.0440.0010.0010.0000.0000.0000.000
179A178ILE 0-0.040-0.01747.2110.0010.0010.0000.0000.0000.000
180A179ALA 0-0.039-0.01750.3540.0010.0010.0000.0000.0000.000
181A180SER 0-0.033-0.01251.3660.0010.0010.0000.0000.0000.000
182A181GLY 0-0.0070.00252.3980.0010.0010.0000.0000.0000.000
183A182ARG 10.8730.93350.0270.0170.0170.0000.0000.0000.000
184A183ILE 00.0060.00044.528-0.001-0.0010.0000.0000.0000.000
185A184PRO 00.0120.02042.7470.0010.0010.0000.0000.0000.000
186A185SER 00.0690.01739.886-0.001-0.0010.0000.0000.0000.000
187A186CYS 0-0.064-0.00937.8000.0000.0000.0000.0000.0000.000
188A187VAL 00.0310.00638.022-0.003-0.0030.0000.0000.0000.000
189A188ARG 10.7990.91431.5880.0480.0480.0000.0000.0000.000
190A189MET 00.026-0.00438.6010.0000.0000.0000.0000.0000.000
191A190ARG 10.8480.91838.5410.0150.0150.0000.0000.0000.000
192A191TRP 0-0.0070.01033.5920.0010.0010.0000.0000.0000.000
193A192LYS 10.9880.98939.9710.0260.0260.0000.0000.0000.000
194A193THR 0-0.009-0.01641.7900.0010.0010.0000.0000.0000.000
195A194VAL 00.0530.03242.0840.0010.0010.0000.0000.0000.000
196A195SER 00.0360.02144.0650.0020.0020.0000.0000.0000.000
197A196ASN 0-0.031-0.03246.3230.0000.0000.0000.0000.0000.000
198A197LEU 0-0.009-0.00446.6930.0010.0010.0000.0000.0000.000
199A198ARG 10.9630.98446.9170.0170.0170.0000.0000.0000.000
200A199GLN 0-0.049-0.01949.2860.0010.0010.0000.0000.0000.000
201A200LYS 10.8830.96151.8300.0200.0200.0000.0000.0000.000
202A201NME 00.0100.01853.2910.0010.0010.0000.0000.0000.000