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: 52G9Z

Calculation Name: 1JN6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1JN6

Chain ID: A

ChEMBL ID:

UniProt ID: P01843

Base Structure: X-ray

Registration Date: 2023-06-26

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 208
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2026600.264669
FMO2-HF: Nuclear repulsion 1947025.657873
FMO2-HF: Total energy -79574.606796
FMO2-MP2: Total energy -79806.184211


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:GLN)


Summations of interaction energy for fragment #1(A:1:GLN)
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.
-10.171-6.2066.884-4.124-6.726-0.021
Interaction energy analysis for fragmet #1(A:1:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.008 / q_NPA : 0.003
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].
3A3VAL00.0270.0223.7200.1032.723-0.008-1.454-1.1580.004
4A4VAL00.0340.0176.253-0.704-0.7040.0000.0000.0000.000
5A5THR0-0.042-0.0328.6990.1340.1340.0000.0000.0000.000
6A6GLN00.051-0.00112.314-0.030-0.0300.0000.0000.0000.000
7A7GLU-1-0.773-0.84815.8680.1600.1600.0000.0000.0000.000
8A8SER00.0200.01519.0450.0060.0060.0000.0000.0000.000
9A9ALA00.006-0.00919.9750.0180.0180.0000.0000.0000.000
10A10LEU0-0.018-0.00722.833-0.013-0.0130.0000.0000.0000.000
11A11THR0-0.017-0.00625.7040.0000.0000.0000.0000.0000.000
12A12THR0-0.021-0.01329.352-0.010-0.0100.0000.0000.0000.000
13A13SER00.0510.02631.6420.0050.0050.0000.0000.0000.000
14A14PRO0-0.001-0.00434.195-0.001-0.0010.0000.0000.0000.000
15A15GLY0-0.053-0.02435.478-0.004-0.0040.0000.0000.0000.000
16A16GLU-1-0.870-0.93233.2230.0310.0310.0000.0000.0000.000
17A17THR0-0.060-0.02630.523-0.002-0.0020.0000.0000.0000.000
18A18VAL00.0030.01626.2690.0010.0010.0000.0000.0000.000
19A19THR0-0.023-0.03623.225-0.006-0.0060.0000.0000.0000.000
20A20LEU0-0.0080.01720.0810.0100.0100.0000.0000.0000.000
21A21THR0-0.074-0.07018.545-0.033-0.0330.0000.0000.0000.000
22A22CYS0-0.035-0.01213.1980.0050.0050.0000.0000.0000.000
23A23ARG10.9410.95513.012-0.130-0.1300.0000.0000.0000.000
24A24SER00.0410.0157.196-0.059-0.0590.0000.0000.0000.000
25A25SER00.000-0.0056.9950.0410.0410.0000.0000.0000.000
26A26SER0-0.034-0.0185.584-0.152-0.1520.0000.0000.0000.000
27A27GLY0-0.0010.0127.5240.0680.0680.0000.0000.0000.000
28A28ALA0-0.053-0.02511.2430.0770.0770.0000.0000.0000.000
29A29ILE0-0.044-0.01111.082-0.062-0.0620.0000.0000.0000.000
30A30THR00.005-0.00712.8790.0360.0360.0000.0000.0000.000
31A31THR00.0460.01014.099-0.010-0.0100.0000.0000.0000.000
32A32SER0-0.0050.01112.1640.0120.0120.0000.0000.0000.000
33A33HIS00.0440.0348.0700.0370.0370.0000.0000.0000.000
34A34TYR0-0.049-0.03211.2140.0380.0380.0000.0000.0000.000
35A35ALA00.0210.02313.5330.0240.0240.0000.0000.0000.000
36A36ASN00.005-0.00514.302-0.039-0.0390.0000.0000.0000.000
37A37TRP0-0.018-0.01415.3890.0710.0710.0000.0000.0000.000
38A38ILE00.004-0.00414.878-0.042-0.0420.0000.0000.0000.000
39A39GLN00.0300.03218.6960.0390.0390.0000.0000.0000.000
40A40GLU-1-0.879-0.95518.8870.3440.3440.0000.0000.0000.000
41A41LYS10.8060.89021.718-0.108-0.1080.0000.0000.0000.000
42A42PRO00.004-0.02024.1180.0120.0120.0000.0000.0000.000
43A43ASP-1-0.889-0.94325.1600.1570.1570.0000.0000.0000.000
44A44HIS00.0010.00220.4180.0040.0040.0000.0000.0000.000
45A45LEU0-0.0010.02121.801-0.019-0.0190.0000.0000.0000.000
46A46PHE0-0.015-0.00917.384-0.007-0.0070.0000.0000.0000.000
47A47THR0-0.043-0.02521.017-0.030-0.0300.0000.0000.0000.000
48A48GLY0-0.0190.00019.8520.0110.0110.0000.0000.0000.000
49A49LEU0-0.007-0.00920.618-0.007-0.0070.0000.0000.0000.000
50A50ILE0-0.024-0.00819.648-0.014-0.0140.0000.0000.0000.000
51A51SER00.0250.02618.2630.0020.0020.0000.0000.0000.000
52A52GLY00.0330.01117.0800.0000.0000.0000.0000.0000.000
53A53THR0-0.046-0.02117.368-0.022-0.0220.0000.0000.0000.000
54A54ASN0-0.011-0.02618.3730.0150.0150.0000.0000.0000.000
55A55ASN0-0.044-0.00721.1960.0170.0170.0000.0000.0000.000
56A56ARG10.8960.93223.0120.0280.0280.0000.0000.0000.000
57A57ALA00.0220.02722.816-0.011-0.0110.0000.0000.0000.000
58A58PRO0-0.013-0.02224.7000.0060.0060.0000.0000.0000.000
59A59GLY00.0350.01627.8970.0050.0050.0000.0000.0000.000
60A60VAL0-0.0430.00125.4080.0090.0090.0000.0000.0000.000
61A61PRO00.0150.01728.819-0.008-0.0080.0000.0000.0000.000
62A62ALA00.016-0.02530.2910.0020.0020.0000.0000.0000.000
63A63ARG10.7670.86130.339-0.049-0.0490.0000.0000.0000.000
64A64PHE00.0370.03625.6290.0020.0020.0000.0000.0000.000
65A65SER0-0.022-0.02126.015-0.012-0.0120.0000.0000.0000.000
66A66GLY00.0060.02321.7350.0110.0110.0000.0000.0000.000
67A67SER0-0.032-0.02520.944-0.011-0.0110.0000.0000.0000.000
68A68LEU00.0160.00716.6180.0030.0030.0000.0000.0000.000
69A69ILE00.0180.01019.6270.0060.0060.0000.0000.0000.000
70A70GLY00.0020.00120.1850.0050.0050.0000.0000.0000.000
71A71ASP-1-0.847-0.92315.621-0.154-0.1540.0000.0000.0000.000
72A72LYS10.8370.92314.8710.0640.0640.0000.0000.0000.000
73A73ALA00.0310.01915.303-0.014-0.0140.0000.0000.0000.000
74A74ALA0-0.020-0.03216.9300.0320.0320.0000.0000.0000.000
75A75LEU0-0.0180.00520.069-0.018-0.0180.0000.0000.0000.000
76A76THR00.0170.00822.0320.0170.0170.0000.0000.0000.000
77A77ILE00.0020.00525.128-0.004-0.0040.0000.0000.0000.000
78A78THR00.0210.00228.2650.0020.0020.0000.0000.0000.000
79A79GLY00.0040.01031.687-0.004-0.0040.0000.0000.0000.000
80A80ALA0-0.0160.00030.6910.0000.0000.0000.0000.0000.000
81A81GLN00.000-0.00832.226-0.001-0.0010.0000.0000.0000.000
82A82THR00.0360.00132.7250.0060.0060.0000.0000.0000.000
83A83GLU-1-0.847-0.89832.7160.0540.0540.0000.0000.0000.000
84A84ASP-1-0.786-0.85928.6850.0630.0630.0000.0000.0000.000
85A85GLU-1-0.821-0.89427.7830.1310.1310.0000.0000.0000.000
86A86ALA0-0.047-0.01824.611-0.004-0.0040.0000.0000.0000.000
87A87ILE00.0130.02019.3820.0050.0050.0000.0000.0000.000
88A88TYR0-0.016-0.03020.023-0.031-0.0310.0000.0000.0000.000
89A89ILE00.0050.02213.7980.0290.0290.0000.0000.0000.000
90A91ALA00.0210.00010.9070.1550.1550.0000.0000.0000.000
91A92LEU0-0.016-0.0098.459-0.148-0.1480.0000.0000.0000.000
92A93TRP0-0.015-0.0028.173-0.058-0.0580.0000.0000.0000.000
93A94PHE00.019-0.0163.600-0.467-0.0100.008-0.096-0.3690.000
94A95SER0-0.033-0.0084.748-0.943-0.733-0.001-0.007-0.2030.000
95A96ASN00.003-0.0013.635-0.581-0.398-0.001-0.021-0.1600.000
96A97GLN00.0010.0032.080-5.997-6.5415.161-1.900-2.717-0.023
97A98PHE00.0140.0006.0420.1400.1400.0000.0000.0000.000
98A99ILE0-0.0120.0082.366-1.677-0.6381.725-0.646-2.119-0.002
99A100PHE00.016-0.0046.659-0.601-0.6010.0000.0000.0000.000
100A101GLY00.0310.0259.2440.3310.3310.0000.0000.0000.000
101A102SER0-0.034-0.03711.601-0.041-0.0410.0000.0000.0000.000
102A103GLY00.0250.02413.957-0.048-0.0480.0000.0000.0000.000
103A104THR0-0.059-0.02716.963-0.002-0.0020.0000.0000.0000.000
104A105LYS10.8850.93518.805-0.433-0.4330.0000.0000.0000.000
105A106VAL00.0060.01123.093-0.012-0.0120.0000.0000.0000.000
106A107THR00.0140.01025.738-0.003-0.0030.0000.0000.0000.000
107A108VAL0-0.009-0.00729.290-0.006-0.0060.0000.0000.0000.000
108A109LEU0-0.024-0.00132.250-0.003-0.0030.0000.0000.0000.000
109A110GLY00.032-0.01435.212-0.003-0.0030.0000.0000.0000.000
110A111GLN0-0.039-0.02538.6240.0030.0030.0000.0000.0000.000
111A112PRO0-0.0170.02039.4380.0000.0000.0000.0000.0000.000
112A113LYS10.8560.93441.450-0.075-0.0750.0000.0000.0000.000
113A114SER0-0.044-0.04242.475-0.006-0.0060.0000.0000.0000.000
114A115SER00.0490.02542.9260.0050.0050.0000.0000.0000.000
115A116PRO0-0.030-0.00642.473-0.001-0.0010.0000.0000.0000.000
116A117SER00.0060.00944.235-0.005-0.0050.0000.0000.0000.000
117A118VAL00.0080.01045.3160.0040.0040.0000.0000.0000.000
118A119THR0-0.036-0.02646.040-0.006-0.0060.0000.0000.0000.000
119A120LEU0-0.0030.00146.4460.0040.0040.0000.0000.0000.000
120A121PHE0-0.004-0.00246.402-0.004-0.0040.0000.0000.0000.000
121A122PRO00.003-0.00148.9730.0030.0030.0000.0000.0000.000
122A123PRO0-0.0080.01549.2140.0010.0010.0000.0000.0000.000
123A124SER00.004-0.02649.741-0.004-0.0040.0000.0000.0000.000
124A125SER0-0.007-0.01851.5710.0010.0010.0000.0000.0000.000
125A126GLU-1-0.782-0.87550.8110.0650.0650.0000.0000.0000.000
126A127GLU-1-0.815-0.87546.2820.0900.0900.0000.0000.0000.000
127A128LEU00.0140.00849.9890.0010.0010.0000.0000.0000.000
128A129GLU-1-0.933-0.94552.9410.0600.0600.0000.0000.0000.000
129A130THR0-0.092-0.06048.9860.0010.0010.0000.0000.0000.000
130A131ASN0-0.056-0.04050.1260.0020.0020.0000.0000.0000.000
131A132LYS10.8990.95844.554-0.096-0.0960.0000.0000.0000.000
132A133ALA00.0350.00447.627-0.004-0.0040.0000.0000.0000.000
133A134THR0-0.038-0.03742.4870.0050.0050.0000.0000.0000.000
134A135LEU0-0.0300.00545.670-0.003-0.0030.0000.0000.0000.000
135A136VAL00.0210.01142.7380.0060.0060.0000.0000.0000.000
136A137CYS0-0.042-0.00343.194-0.002-0.0020.0000.0000.0000.000
137A138THR00.0150.02041.7610.0050.0050.0000.0000.0000.000
138A139ILE00.003-0.00339.484-0.006-0.0060.0000.0000.0000.000
139A140THR00.014-0.02040.5240.0030.0030.0000.0000.0000.000
140A141ASP-1-0.752-0.88641.6060.0690.0690.0000.0000.0000.000
141A142PHE0-0.0090.04136.405-0.004-0.0040.0000.0000.0000.000
142A143TYR00.034-0.00135.4400.0020.0020.0000.0000.0000.000
143A144PRO00.0700.03035.482-0.006-0.0060.0000.0000.0000.000
144A145GLY00.019-0.01034.164-0.002-0.0020.0000.0000.0000.000
145A146VAL0-0.032-0.02533.5130.0130.0130.0000.0000.0000.000
146A147VAL0-0.013-0.00835.172-0.010-0.0100.0000.0000.0000.000
147A148THR0-0.035-0.00536.2650.0090.0090.0000.0000.0000.000
148A149VAL0-0.023-0.01238.088-0.008-0.0080.0000.0000.0000.000
149A150ASP-1-0.834-0.89539.9580.1110.1110.0000.0000.0000.000
150A151TRP00.012-0.02041.830-0.008-0.0080.0000.0000.0000.000
151A152LYS10.7770.86645.468-0.074-0.0740.0000.0000.0000.000
152A153VAL0-0.004-0.01649.011-0.001-0.0010.0000.0000.0000.000
153A154ASP-1-0.780-0.87651.7610.0610.0610.0000.0000.0000.000
154A155GLY0-0.0230.00053.393-0.002-0.0020.0000.0000.0000.000
155A156THR0-0.018-0.00650.7550.0010.0010.0000.0000.0000.000
156A157PRO0-0.006-0.00846.4810.0010.0010.0000.0000.0000.000
157A158VAL0-0.0070.00845.139-0.001-0.0010.0000.0000.0000.000
158A159THR0-0.019-0.02140.0220.0020.0020.0000.0000.0000.000
159A160GLN00.0420.02140.4990.0090.0090.0000.0000.0000.000
160A161GLY00.0230.00940.261-0.006-0.0060.0000.0000.0000.000
161A162MET0-0.048-0.00839.379-0.005-0.0050.0000.0000.0000.000
162A163GLU-1-0.900-0.94134.4920.1760.1760.0000.0000.0000.000
163A164THR0-0.011-0.01335.191-0.014-0.0140.0000.0000.0000.000
164A165THR00.0150.02032.7560.0100.0100.0000.0000.0000.000
165A166GLN00.0330.00328.139-0.008-0.0080.0000.0000.0000.000
166A167PRO0-0.040-0.02631.529-0.007-0.0070.0000.0000.0000.000
167A168SER00.0260.03131.7350.0090.0090.0000.0000.0000.000
168A169LYS10.8200.90631.798-0.118-0.1180.0000.0000.0000.000
169A170GLN0-0.022-0.00333.522-0.003-0.0030.0000.0000.0000.000
170A171SER00.037-0.00136.062-0.001-0.0010.0000.0000.0000.000
171A172ASN0-0.034-0.01337.0340.0000.0000.0000.0000.0000.000
172A173ASN00.015-0.00735.9460.0040.0040.0000.0000.0000.000
173A174LYS10.8560.95037.749-0.066-0.0660.0000.0000.0000.000
174A175TYR0-0.037-0.00832.1020.0030.0030.0000.0000.0000.000
175A176MET0-0.039-0.01436.341-0.008-0.0080.0000.0000.0000.000
176A177ALA00.0160.01235.9480.0090.0090.0000.0000.0000.000
177A178SER0-0.014-0.00436.903-0.009-0.0090.0000.0000.0000.000
178A179SER00.0260.01937.5200.0070.0070.0000.0000.0000.000
179A180TYR0-0.006-0.01937.503-0.010-0.0100.0000.0000.0000.000
180A181LEU00.0100.00741.3250.0040.0040.0000.0000.0000.000
181A182THR0-0.0070.00240.988-0.005-0.0050.0000.0000.0000.000
182A183LEU0-0.053-0.02443.7140.0000.0000.0000.0000.0000.000
183A184THR0-0.027-0.02647.0540.0010.0010.0000.0000.0000.000
184A185ALA00.0720.04349.742-0.001-0.0010.0000.0000.0000.000
185A186ARG10.9590.97253.041-0.066-0.0660.0000.0000.0000.000
186A187ALA0-0.084-0.03650.645-0.001-0.0010.0000.0000.0000.000
187A188TRP00.0810.03151.6770.0000.0000.0000.0000.0000.000
188A189GLU-1-0.865-0.93753.0710.0600.0600.0000.0000.0000.000
189A190ARG10.7930.91252.721-0.072-0.0720.0000.0000.0000.000
190A191HIS10.8210.90852.566-0.069-0.0690.0000.0000.0000.000
191A192SER00.0310.00856.925-0.002-0.0020.0000.0000.0000.000
192A193SER0-0.054-0.02055.550-0.001-0.0010.0000.0000.0000.000
193A194TYR0-0.006-0.00349.7310.0030.0030.0000.0000.0000.000
194A195SER0-0.028-0.03350.270-0.003-0.0030.0000.0000.0000.000
195A197GLN0-0.011-0.03244.857-0.009-0.0090.0000.0000.0000.000
196A198VAL00.0370.00441.4050.0060.0060.0000.0000.0000.000
197A199THR00.0250.02241.942-0.008-0.0080.0000.0000.0000.000
198A200HIS0-0.013-0.02239.3370.0030.0030.0000.0000.0000.000
199A201GLU-1-0.879-0.94738.9010.0850.0850.0000.0000.0000.000
200A202GLY00.0030.00441.634-0.005-0.0050.0000.0000.0000.000
201A203HIS0-0.032-0.00644.192-0.006-0.0060.0000.0000.0000.000
202A204THR00.007-0.00945.3280.0030.0030.0000.0000.0000.000
203A205VAL0-0.0120.00346.578-0.005-0.0050.0000.0000.0000.000
204A206GLU-1-0.797-0.86247.0510.0760.0760.0000.0000.0000.000
205A207LYS10.8560.93249.278-0.069-0.0690.0000.0000.0000.000
206A208SER00.015-0.00850.2670.0030.0030.0000.0000.0000.000
207A209LEU0-0.049-0.00751.227-0.002-0.0020.0000.0000.0000.000
208A210SER00.025-0.00754.7020.0010.0010.0000.0000.0000.000