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: 49GNN

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 OptHSide
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 -2025746.041076
FMO2-HF: Nuclear repulsion 1946172.423548
FMO2-HF: Total energy -79573.617527
FMO2-MP2: Total energy -79805.229123


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.
-8.233-3.7587.343-4.723-7.093-0.018
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 : 0.009 / q_NPA : 0.005
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].
3A3VAL00.0380.0103.703-0.5913.005-0.022-2.037-1.5370.007
4A4VAL00.0110.0106.461-0.528-0.5280.0000.0000.0000.000
5A5THR0-0.042-0.0259.0080.1190.1190.0000.0000.0000.000
6A6GLN00.033-0.01812.485-0.001-0.0010.0000.0000.0000.000
7A7GLU-1-0.805-0.87315.8240.2460.2460.0000.0000.0000.000
8A8SER00.0120.00119.249-0.003-0.0030.0000.0000.0000.000
9A9ALA0-0.015-0.01820.0730.0120.0120.0000.0000.0000.000
10A10LEU00.0050.02522.575-0.016-0.0160.0000.0000.0000.000
11A11THR00.0010.00225.6140.0050.0050.0000.0000.0000.000
12A12THR0-0.011-0.01429.277-0.010-0.0100.0000.0000.0000.000
13A13SER00.0480.04231.7300.0050.0050.0000.0000.0000.000
14A14PRO00.010-0.00734.5620.0000.0000.0000.0000.0000.000
15A15GLY0-0.060-0.02335.270-0.005-0.0050.0000.0000.0000.000
16A16GLU-1-0.904-0.94433.1580.0640.0640.0000.0000.0000.000
17A17THR0-0.037-0.02530.3540.0020.0020.0000.0000.0000.000
18A18VAL0-0.0060.01226.024-0.001-0.0010.0000.0000.0000.000
19A19THR0-0.014-0.02323.320-0.005-0.0050.0000.0000.0000.000
20A20LEU0-0.0130.00920.3080.0080.0080.0000.0000.0000.000
21A21THR0-0.071-0.04918.879-0.016-0.0160.0000.0000.0000.000
22A22CYS0-0.022-0.00813.3770.0040.0040.0000.0000.0000.000
23A23ARG10.9780.98513.096-0.160-0.1600.0000.0000.0000.000
24A24SER00.0530.0117.1900.1750.1750.0000.0000.0000.000
25A25SER00.0090.0136.9940.0070.0070.0000.0000.0000.000
26A26SER0-0.023-0.0075.785-0.122-0.1220.0000.0000.0000.000
27A27GLY00.0030.0027.3890.0770.0770.0000.0000.0000.000
28A28ALA0-0.040-0.00811.1110.0990.0990.0000.0000.0000.000
29A29ILE0-0.042-0.00511.077-0.050-0.0500.0000.0000.0000.000
30A30THR00.007-0.00512.8780.0280.0280.0000.0000.0000.000
31A31THR00.0830.02014.3870.0170.0170.0000.0000.0000.000
32A32SER0-0.0350.00212.3170.0190.0190.0000.0000.0000.000
33A33HIS00.0240.0228.1210.0310.0310.0000.0000.0000.000
34A34TYR0-0.060-0.03511.4940.0560.0560.0000.0000.0000.000
35A35ALA00.0490.03413.3960.0310.0310.0000.0000.0000.000
36A36ASN0-0.012-0.01114.339-0.083-0.0830.0000.0000.0000.000
37A37TRP0-0.015-0.00715.6570.0800.0800.0000.0000.0000.000
38A38ILE00.0200.00814.931-0.046-0.0460.0000.0000.0000.000
39A39GLN00.0380.01818.6840.0280.0280.0000.0000.0000.000
40A40GLU-1-0.892-0.96018.4470.4060.4060.0000.0000.0000.000
41A41LYS10.8390.89721.470-0.164-0.1640.0000.0000.0000.000
42A42PRO0-0.021-0.03224.1170.0120.0120.0000.0000.0000.000
43A43ASP-1-0.878-0.93325.1530.1720.1720.0000.0000.0000.000
44A44HIS0-0.022-0.00420.2150.0150.0150.0000.0000.0000.000
45A45LEU0-0.0030.00721.755-0.017-0.0170.0000.0000.0000.000
46A46PHE00.0040.01417.3250.0030.0030.0000.0000.0000.000
47A47THR0-0.031-0.01821.243-0.035-0.0350.0000.0000.0000.000
48A48GLY0-0.0130.00620.4210.0220.0220.0000.0000.0000.000
49A49LEU00.007-0.00121.134-0.018-0.0180.0000.0000.0000.000
50A50ILE0-0.0280.00119.532-0.023-0.0230.0000.0000.0000.000
51A51SER00.0240.02518.1150.0180.0180.0000.0000.0000.000
52A52GLY00.0390.00717.130-0.015-0.0150.0000.0000.0000.000
53A53THR0-0.052-0.03417.061-0.019-0.0190.0000.0000.0000.000
54A54ASN0-0.032-0.03318.3170.0120.0120.0000.0000.0000.000
55A55ASN0-0.0230.00021.304-0.004-0.0040.0000.0000.0000.000
56A56ARG10.8690.93123.145-0.032-0.0320.0000.0000.0000.000
57A57ALA00.0150.02423.288-0.012-0.0120.0000.0000.0000.000
58A58PRO0-0.023-0.02824.887-0.002-0.0020.0000.0000.0000.000
59A59GLY0-0.0060.01328.1030.0050.0050.0000.0000.0000.000
60A60VAL00.0400.02026.0310.0090.0090.0000.0000.0000.000
61A61PRO00.0150.01229.498-0.008-0.0080.0000.0000.0000.000
62A62ALA00.0490.00030.3910.0060.0060.0000.0000.0000.000
63A63ARG10.7380.85430.248-0.092-0.0920.0000.0000.0000.000
64A64PHE00.0460.01925.5180.0040.0040.0000.0000.0000.000
65A65SER0-0.022-0.01026.033-0.009-0.0090.0000.0000.0000.000
66A66GLY00.0030.01521.7990.0120.0120.0000.0000.0000.000
67A67SER0-0.029-0.02521.233-0.019-0.0190.0000.0000.0000.000
68A68LEU00.0150.00516.3480.0180.0180.0000.0000.0000.000
69A69ILE00.0210.01019.576-0.007-0.0070.0000.0000.0000.000
70A70GLY0-0.006-0.00319.8090.0040.0040.0000.0000.0000.000
71A71ASP-1-0.852-0.92215.722-0.087-0.0870.0000.0000.0000.000
72A72LYS10.8180.90314.9530.0040.0040.0000.0000.0000.000
73A73ALA00.0010.00615.469-0.018-0.0180.0000.0000.0000.000
74A74ALA0-0.002-0.02717.2070.0150.0150.0000.0000.0000.000
75A75LEU0-0.0130.01520.368-0.017-0.0170.0000.0000.0000.000
76A76THR0-0.018-0.02522.1380.0050.0050.0000.0000.0000.000
77A77ILE00.0240.02125.249-0.004-0.0040.0000.0000.0000.000
78A78THR00.002-0.00428.257-0.001-0.0010.0000.0000.0000.000
79A79GLY0-0.0020.00331.769-0.004-0.0040.0000.0000.0000.000
80A80ALA0-0.038-0.00631.0140.0000.0000.0000.0000.0000.000
81A81GLN00.0100.00132.521-0.007-0.0070.0000.0000.0000.000
82A82THR00.0610.00832.7430.0070.0070.0000.0000.0000.000
83A83GLU-1-0.879-0.91932.3900.0960.0960.0000.0000.0000.000
84A84ASP-1-0.784-0.84828.6340.1150.1150.0000.0000.0000.000
85A85GLU-1-0.864-0.89927.7860.1630.1630.0000.0000.0000.000
86A86ALA0-0.047-0.03624.329-0.004-0.0040.0000.0000.0000.000
87A87ILE0-0.0070.00218.9230.0020.0020.0000.0000.0000.000
88A88TYR0-0.032-0.03319.834-0.018-0.0180.0000.0000.0000.000
89A89ILE00.0170.02813.5710.0260.0260.0000.0000.0000.000
90A91ALA00.0100.00510.8760.1680.1680.0000.0000.0000.000
91A92LEU0-0.003-0.0178.239-0.215-0.2150.0000.0000.0000.000
92A93TRP00.0150.0118.0540.1380.1380.0000.0000.0000.000
93A94PHE00.010-0.0203.354-0.659-0.2310.016-0.094-0.3500.000
94A95SER0-0.034-0.0224.830-0.440-0.242-0.001-0.005-0.1920.000
95A96ASN0-0.021-0.0154.218-0.272-0.148-0.001-0.005-0.1170.000
96A97GLN00.0210.0232.073-4.715-5.8106.098-1.997-3.005-0.023
97A98PHE00.0170.0066.4520.2590.2590.0000.0000.0000.000
98A99ILE0-0.0250.0022.404-1.625-0.4011.253-0.585-1.892-0.002
99A100PHE00.000-0.0136.442-0.728-0.7280.0000.0000.0000.000
100A101GLY00.0250.0259.2260.3180.3180.0000.0000.0000.000
101A102SER0-0.028-0.03111.388-0.027-0.0270.0000.0000.0000.000
102A103GLY00.0140.01813.502-0.044-0.0440.0000.0000.0000.000
103A104THR0-0.055-0.02016.710-0.002-0.0020.0000.0000.0000.000
104A105LYS10.9560.96919.851-0.405-0.4050.0000.0000.0000.000
105A106VAL00.0110.01123.081-0.014-0.0140.0000.0000.0000.000
106A107THR00.015-0.00325.625-0.007-0.0070.0000.0000.0000.000
107A108VAL0-0.0060.00329.127-0.008-0.0080.0000.0000.0000.000
108A109LEU0-0.018-0.01032.008-0.003-0.0030.0000.0000.0000.000
109A110GLY00.016-0.01835.072-0.004-0.0040.0000.0000.0000.000
110A111GLN0-0.028-0.02238.4610.0040.0040.0000.0000.0000.000
111A112PRO0-0.0160.02039.192-0.001-0.0010.0000.0000.0000.000
112A113LYS10.9120.97741.004-0.084-0.0840.0000.0000.0000.000
113A114SER0-0.027-0.03541.976-0.005-0.0050.0000.0000.0000.000
114A115SER00.0170.00742.7900.0050.0050.0000.0000.0000.000
115A116PRO0-0.0060.00542.447-0.001-0.0010.0000.0000.0000.000
116A117SER0-0.0270.00544.320-0.006-0.0060.0000.0000.0000.000
117A118VAL00.0170.00445.0320.0040.0040.0000.0000.0000.000
118A119THR0-0.044-0.02545.929-0.006-0.0060.0000.0000.0000.000
119A120LEU0-0.0100.00346.4760.0040.0040.0000.0000.0000.000
120A121PHE00.0090.01346.503-0.003-0.0030.0000.0000.0000.000
121A122PRO0-0.009-0.01048.8300.0030.0030.0000.0000.0000.000
122A123PRO0-0.0010.00949.1000.0010.0010.0000.0000.0000.000
123A124SER00.021-0.00249.408-0.003-0.0030.0000.0000.0000.000
124A125SER00.019-0.01251.1410.0010.0010.0000.0000.0000.000
125A126GLU-1-0.829-0.90850.7710.0590.0590.0000.0000.0000.000
126A127GLU-1-0.826-0.87946.0160.0810.0810.0000.0000.0000.000
127A128LEU00.0220.01549.8070.0010.0010.0000.0000.0000.000
128A129GLU-1-0.950-0.96252.4100.0530.0530.0000.0000.0000.000
129A130THR0-0.092-0.05448.8750.0000.0000.0000.0000.0000.000
130A131ASN0-0.086-0.07149.7400.0020.0020.0000.0000.0000.000
131A132LYS10.9000.96444.663-0.082-0.0820.0000.0000.0000.000
132A133ALA00.0470.01947.523-0.003-0.0030.0000.0000.0000.000
133A134THR0-0.022-0.03142.4580.0040.0040.0000.0000.0000.000
134A135LEU0-0.0410.00645.697-0.003-0.0030.0000.0000.0000.000
135A136VAL00.0150.00242.2710.0050.0050.0000.0000.0000.000
136A137CYS0-0.059-0.01743.168-0.001-0.0010.0000.0000.0000.000
137A138THR00.035-0.00141.2430.0050.0050.0000.0000.0000.000
138A139ILE0-0.020-0.01039.431-0.006-0.0060.0000.0000.0000.000
139A140THR00.028-0.00940.4930.0040.0040.0000.0000.0000.000
140A141ASP-1-0.776-0.89541.9420.0790.0790.0000.0000.0000.000
141A142PHE0-0.0130.04436.186-0.003-0.0030.0000.0000.0000.000
142A143TYR00.0330.00735.1880.0040.0040.0000.0000.0000.000
143A144PRO00.0550.02235.028-0.007-0.0070.0000.0000.0000.000
144A145GLY00.031-0.01934.284-0.003-0.0030.0000.0000.0000.000
145A146VAL0-0.031-0.02333.2170.0130.0130.0000.0000.0000.000
146A147VAL0-0.0120.00234.977-0.009-0.0090.0000.0000.0000.000
147A148THR0-0.026-0.00836.1380.0080.0080.0000.0000.0000.000
148A149VAL0-0.036-0.01838.326-0.007-0.0070.0000.0000.0000.000
149A150ASP-1-0.851-0.90139.8780.1080.1080.0000.0000.0000.000
150A151TRP00.024-0.02241.602-0.007-0.0070.0000.0000.0000.000
151A152LYS10.7970.86445.299-0.072-0.0720.0000.0000.0000.000
152A153VAL00.0040.00548.765-0.001-0.0010.0000.0000.0000.000
153A154ASP-1-0.790-0.88251.3610.0560.0560.0000.0000.0000.000
154A155GLY00.0010.01452.949-0.002-0.0020.0000.0000.0000.000
155A156THR0-0.049-0.02450.2610.0000.0000.0000.0000.0000.000
156A157PRO00.000-0.00346.0990.0010.0010.0000.0000.0000.000
157A158VAL0-0.0180.00645.039-0.002-0.0020.0000.0000.0000.000
158A159THR0-0.008-0.00940.0940.0020.0020.0000.0000.0000.000
159A160GLN00.001-0.00340.3250.0070.0070.0000.0000.0000.000
160A161GLY00.0400.00939.915-0.006-0.0060.0000.0000.0000.000
161A162MET0-0.061-0.02738.875-0.002-0.0020.0000.0000.0000.000
162A163GLU-1-0.906-0.94334.5950.1550.1550.0000.0000.0000.000
163A164THR0-0.0020.00335.100-0.010-0.0100.0000.0000.0000.000
164A165THR00.0070.01732.7090.0090.0090.0000.0000.0000.000
165A166GLN00.0240.00327.681-0.005-0.0050.0000.0000.0000.000
166A167PRO0-0.012-0.01630.919-0.008-0.0080.0000.0000.0000.000
167A168SER00.0060.02131.3320.0120.0120.0000.0000.0000.000
168A169LYS10.8050.91131.825-0.144-0.1440.0000.0000.0000.000
169A170GLN0-0.009-0.01533.586-0.003-0.0030.0000.0000.0000.000
170A171SER00.0520.00235.7410.0000.0000.0000.0000.0000.000
171A172ASN0-0.042-0.02636.7510.0040.0040.0000.0000.0000.000
172A173ASN00.021-0.00335.6200.0030.0030.0000.0000.0000.000
173A174LYS10.8940.95337.289-0.081-0.0810.0000.0000.0000.000
174A175TYR0-0.0280.01731.7900.0010.0010.0000.0000.0000.000
175A176MET0-0.017-0.00436.135-0.009-0.0090.0000.0000.0000.000
176A177ALA00.0030.00835.7670.0100.0100.0000.0000.0000.000
177A178SER0-0.018-0.01936.699-0.009-0.0090.0000.0000.0000.000
178A179SER00.0240.01337.3980.0060.0060.0000.0000.0000.000
179A180TYR00.003-0.00537.123-0.009-0.0090.0000.0000.0000.000
180A181LEU00.0340.03840.8190.0030.0030.0000.0000.0000.000
181A182THR0-0.0030.00340.811-0.005-0.0050.0000.0000.0000.000
182A183LEU0-0.043-0.01243.6220.0000.0000.0000.0000.0000.000
183A184THR0-0.039-0.03647.0450.0000.0000.0000.0000.0000.000
184A185ALA00.0320.01649.506-0.001-0.0010.0000.0000.0000.000
185A186ARG10.9610.97252.657-0.056-0.0560.0000.0000.0000.000
186A187ALA0-0.022-0.01450.694-0.002-0.0020.0000.0000.0000.000
187A188TRP00.0720.03251.5860.0000.0000.0000.0000.0000.000
188A189GLU-1-0.886-0.95153.0740.0520.0520.0000.0000.0000.000
189A190ARG10.8580.93752.804-0.062-0.0620.0000.0000.0000.000
190A191HIS10.7730.90052.123-0.064-0.0640.0000.0000.0000.000
191A192SER00.0450.01656.349-0.002-0.0020.0000.0000.0000.000
192A193SER0-0.037-0.01555.0650.0000.0000.0000.0000.0000.000
193A194TYR00.0020.00249.4890.0030.0030.0000.0000.0000.000
194A195SER0-0.009-0.02149.903-0.001-0.0010.0000.0000.0000.000
195A197GLN0-0.011-0.02244.415-0.007-0.0070.0000.0000.0000.000
196A198VAL00.0460.01040.9330.0060.0060.0000.0000.0000.000
197A199THR0-0.0010.00141.646-0.007-0.0070.0000.0000.0000.000
198A200HIS0-0.032-0.03438.8930.0020.0020.0000.0000.0000.000
199A201GLU-1-0.886-0.95439.0090.0970.0970.0000.0000.0000.000
200A202GLY0-0.018-0.00141.834-0.005-0.0050.0000.0000.0000.000
201A203HIS0-0.030-0.01444.334-0.005-0.0050.0000.0000.0000.000
202A204THR00.001-0.00545.4510.0030.0030.0000.0000.0000.000
203A205VAL0-0.0140.00446.564-0.004-0.0040.0000.0000.0000.000
204A206GLU-1-0.853-0.90947.0970.0730.0730.0000.0000.0000.000
205A207LYS10.8860.95749.273-0.070-0.0700.0000.0000.0000.000
206A208SER00.0140.00650.2010.0030.0030.0000.0000.0000.000
207A209LEU0-0.0330.00050.850-0.002-0.0020.0000.0000.0000.000
208A210SER00.0270.00254.3870.0010.0010.0000.0000.0000.000