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: YVN92

Calculation Name: 2I9D-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2I9D

Chain ID: A

ChEMBL ID:

UniProt ID: Q8A336

Base Structure: X-ray

Registration Date: 2023-09-22

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 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2666798.6915
FMO2-HF: Nuclear repulsion 2580866.12793
FMO2-HF: Total energy -85932.56357
FMO2-MP2: Total energy -86186.370944


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.
-12.238-10.25111.821-7.437-6.371-0.055
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 : 0.005 / q_NPA : 0.001
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].
3A3GLN0-0.060-0.0133.6620.0512.958-0.004-1.621-1.2820.004
4A4ILE00.017-0.0056.3890.0710.0710.0000.0000.0000.000
5A5ILE0-0.041-0.0029.320-0.055-0.0550.0000.0000.0000.000
6A6ASP-1-0.861-0.92712.216-0.093-0.0930.0000.0000.0000.000
7A7ILE0-0.056-0.04915.217-0.028-0.0280.0000.0000.0000.000
8A8GLU-1-0.868-0.90017.914-0.120-0.1200.0000.0000.0000.000
9A9ASN0-0.058-0.03517.945-0.004-0.0040.0000.0000.0000.000
10A10TRP00.0400.00316.1600.0270.0270.0000.0000.0000.000
11A11GLU-1-0.916-0.96118.260-0.429-0.4290.0000.0000.0000.000
12A12ARG10.7790.87118.6070.3810.3810.0000.0000.0000.000
13A13LYS10.8530.94520.8810.1620.1620.0000.0000.0000.000
14A14GLU-1-0.830-0.93621.664-0.120-0.1200.0000.0000.0000.000
15A15ASN0-0.039-0.01822.7540.0190.0190.0000.0000.0000.000
16A16PHE00.008-0.00818.6740.0190.0190.0000.0000.0000.000
17A17ASN0-0.014-0.01522.2330.0300.0300.0000.0000.0000.000
18A18PHE0-0.0410.00124.6300.0220.0220.0000.0000.0000.000
19A19PHE00.001-0.01924.2410.0150.0150.0000.0000.0000.000
20A20ARG10.8850.95820.2200.1110.1110.0000.0000.0000.000
21A21HIS00.0540.02224.8440.0160.0160.0000.0000.0000.000
22A22PHE0-0.024-0.00327.2400.0110.0110.0000.0000.0000.000
23A23GLN0-0.038-0.01427.5200.0060.0060.0000.0000.0000.000
24A24ASN00.0890.03227.065-0.002-0.0020.0000.0000.0000.000
25A25PRO0-0.0210.01623.419-0.005-0.0050.0000.0000.0000.000
26A26GLN0-0.0010.01122.357-0.035-0.0350.0000.0000.0000.000
27A27LEU0-0.046-0.01424.1410.0140.0140.0000.0000.0000.000
28A28SER0-0.008-0.01624.588-0.010-0.0100.0000.0000.0000.000
29A29ILE0-0.019-0.00525.0760.0080.0080.0000.0000.0000.000
30A30THR00.000-0.00726.779-0.001-0.0010.0000.0000.0000.000
31A31SER00.0010.01528.0470.0090.0090.0000.0000.0000.000
32A32GLU-1-0.815-0.88729.445-0.101-0.1010.0000.0000.0000.000
33A33VAL00.0190.02726.133-0.008-0.0080.0000.0000.0000.000
34A34GLU-1-0.800-0.88229.519-0.109-0.1090.0000.0000.0000.000
35A35CYS0-0.051-0.02828.854-0.007-0.0070.0000.0000.0000.000
36A36GLY00.0130.00530.2800.0070.0070.0000.0000.0000.000
37A37GLY00.0470.01431.1660.0070.0070.0000.0000.0000.000
38A38ALA0-0.028-0.02627.1300.0060.0060.0000.0000.0000.000
39A39ARG10.9640.99028.9700.0840.0840.0000.0000.0000.000
40A40GLN0-0.021-0.01431.7020.0110.0110.0000.0000.0000.000
41A41ARG10.8840.93626.1640.1580.1580.0000.0000.0000.000
42A42ALA00.0130.02728.8500.0040.0040.0000.0000.0000.000
43A43LYS10.9520.97430.3250.0650.0650.0000.0000.0000.000
44A44ALA0-0.056-0.02433.7540.0060.0060.0000.0000.0000.000
45A45ALA0-0.020-0.00529.9940.0050.0050.0000.0000.0000.000
46A46GLY00.0070.01131.4780.0040.0040.0000.0000.0000.000
47A47GLN0-0.0040.01226.332-0.004-0.0040.0000.0000.0000.000
48A48SER00.0380.00926.103-0.003-0.0030.0000.0000.0000.000
49A49PHE00.019-0.02426.463-0.009-0.0090.0000.0000.0000.000
50A50PHE00.0180.00522.224-0.015-0.0150.0000.0000.0000.000
51A51LEU00.0630.03720.938-0.016-0.0160.0000.0000.0000.000
52A52HIS0-0.035-0.02421.547-0.031-0.0310.0000.0000.0000.000
53A53TYR00.007-0.00622.558-0.016-0.0160.0000.0000.0000.000
54A54LEU0-0.0130.01018.388-0.026-0.0260.0000.0000.0000.000
55A55TYR00.0210.02316.386-0.040-0.0400.0000.0000.0000.000
56A56ALA0-0.033-0.01517.618-0.050-0.0500.0000.0000.0000.000
57A57VAL00.0190.00217.737-0.036-0.0360.0000.0000.0000.000
58A58LEU00.0020.01512.057-0.048-0.0480.0000.0000.0000.000
59A59ARG10.8050.90613.6440.3220.3220.0000.0000.0000.000
60A60ALA0-0.020-0.02114.837-0.077-0.0770.0000.0000.0000.000
61A61ALA0-0.014-0.00413.607-0.032-0.0320.0000.0000.0000.000
62A62ASN0-0.011-0.0189.009-0.399-0.3990.0000.0000.0000.000
63A63GLU-1-0.810-0.89011.548-0.651-0.6510.0000.0000.0000.000
64A64ILE0-0.044-0.00114.2300.0360.0360.0000.0000.0000.000
65A65PRO00.0470.02712.203-0.035-0.0350.0000.0000.0000.000
66A66GLU-1-0.805-0.93212.694-0.689-0.6890.0000.0000.0000.000
67A67PHE0-0.060-0.04014.2490.0760.0760.0000.0000.0000.000
68A68ARG10.8600.9367.6622.1512.1510.0000.0000.0000.000
69A69TYR0-0.0080.0139.660-0.225-0.2250.0000.0000.0000.000
70A70ARG10.7510.86210.4830.7750.7750.0000.0000.0000.000
71A71ILE0-0.033-0.01112.753-0.007-0.0070.0000.0000.0000.000
72A72ASP-1-0.710-0.8369.2360.2930.2930.0000.0000.0000.000
73A73PRO00.0450.03911.630-0.021-0.0210.0000.0000.0000.000
74A74ASP-1-0.864-0.91312.7960.3880.3880.0000.0000.0000.000
75A75GLY0-0.035-0.02215.689-0.028-0.0280.0000.0000.0000.000
76A76ARG10.8100.89110.736-0.552-0.5520.0000.0000.0000.000
77A77VAL0-0.020-0.00313.109-0.018-0.0180.0000.0000.0000.000
78A78VAL0-0.0050.0008.1750.0170.0170.0000.0000.0000.000
79A79LEU0-0.0110.0008.1190.0790.0790.0000.0000.0000.000
80A80TYR00.0290.0104.873-0.504-0.5040.0000.0000.0000.000
81A81ASP-1-0.867-0.9321.899-17.391-18.57811.825-5.771-4.867-0.059
82A82THR0-0.084-0.0533.7901.7652.0320.000-0.045-0.2220.000
83A83ILE0-0.0420.0015.459-0.064-0.0640.0000.0000.0000.000
84A84ASP-1-0.745-0.8488.338-0.032-0.0320.0000.0000.0000.000
85A85MET0-0.073-0.03910.347-0.027-0.0270.0000.0000.0000.000
86A86LEU00.0550.04114.1060.0580.0580.0000.0000.0000.000
87A87SER0-0.020-0.04716.400-0.035-0.0350.0000.0000.0000.000
88A88PRO00.0070.01619.9850.0220.0220.0000.0000.0000.000
89A89ILE0-0.0050.00322.075-0.013-0.0130.0000.0000.0000.000
90A90LYS10.8180.90525.1080.0240.0240.0000.0000.0000.000
91A91ILE00.0040.00327.720-0.001-0.0010.0000.0000.0000.000
92A92LYS10.8500.91430.405-0.041-0.0410.0000.0000.0000.000
93A93GLU-1-0.807-0.90934.000-0.013-0.0130.0000.0000.0000.000
94A94ASN0-0.054-0.02435.793-0.004-0.0040.0000.0000.0000.000
95A95GLY0-0.006-0.00233.2660.0000.0000.0000.0000.0000.000
96A96LYS10.7940.91230.463-0.056-0.0560.0000.0000.0000.000
97A97PHE00.0470.01425.227-0.006-0.0060.0000.0000.0000.000
98A98PHE00.007-0.00122.0230.0070.0070.0000.0000.0000.000
99A99THR0-0.040-0.02619.289-0.020-0.0200.0000.0000.0000.000
100A100THR0-0.0040.00018.8220.0360.0360.0000.0000.0000.000
101A101ARG10.7980.8687.840-0.380-0.3800.0000.0000.0000.000
102A102PHE0-0.056-0.02414.6710.0210.0210.0000.0000.0000.000
103A103PRO00.0420.03411.057-0.072-0.0720.0000.0000.0000.000
104A104TYR00.033-0.0099.6250.0200.0200.0000.0000.0000.000
105A105HIS00.0380.01710.770-0.013-0.0130.0000.0000.0000.000
106A106ASN00.009-0.01612.910-0.008-0.0080.0000.0000.0000.000
107A107ASP-1-0.829-0.89214.404-0.162-0.1620.0000.0000.0000.000
108A108PHE0-0.038-0.01617.6830.0190.0190.0000.0000.0000.000
109A109ASP-1-0.849-0.92419.699-0.102-0.1020.0000.0000.0000.000
110A110THR0-0.065-0.05516.2530.0300.0300.0000.0000.0000.000
111A111PHE00.0160.01014.8690.0220.0220.0000.0000.0000.000
112A112TYR0-0.019-0.01017.3060.0290.0290.0000.0000.0000.000
113A113GLN0-0.072-0.04920.5520.0300.0300.0000.0000.0000.000
114A114GLU-1-0.875-0.95215.6920.1120.1120.0000.0000.0000.000
115A115ALA0-0.007-0.00118.7750.0190.0190.0000.0000.0000.000
116A116ARG10.8290.89019.7590.0190.0190.0000.0000.0000.000
117A117LEU0-0.0070.00121.2620.0060.0060.0000.0000.0000.000
118A118ILE00.0090.01416.5610.0100.0100.0000.0000.0000.000
119A119ILE0-0.046-0.04221.0620.0040.0040.0000.0000.0000.000
120A120ASP-1-0.887-0.92423.9310.0140.0140.0000.0000.0000.000
121A121ALA0-0.033-0.00723.1070.0040.0040.0000.0000.0000.000
122A122ILE0-0.065-0.01422.8400.0110.0110.0000.0000.0000.000
123A123PRO0-0.0220.00624.724-0.004-0.0040.0000.0000.0000.000
124A124GLU-1-0.904-0.95627.6910.0380.0380.0000.0000.0000.000
125A125ASP-1-0.852-0.92830.5890.0490.0490.0000.0000.0000.000
126A126GLY00.0180.00627.4920.0080.0080.0000.0000.0000.000
127A127ASP-1-0.873-0.93925.2610.1030.1030.0000.0000.0000.000
128A128PRO0-0.023-0.01725.0140.0050.0050.0000.0000.0000.000
129A129TYR00.004-0.01322.811-0.012-0.0120.0000.0000.0000.000
130A130ALA00.0150.03221.5750.0120.0120.0000.0000.0000.000
131A131ALA00.0410.02117.7710.0230.0230.0000.0000.0000.000
132A132GLU-1-0.827-0.90616.8370.0260.0260.0000.0000.0000.000
133A133ASN0-0.038-0.03117.2370.0140.0140.0000.0000.0000.000
134A134GLU-1-0.959-0.96315.1360.3660.3660.0000.0000.0000.000
135A135GLU-1-0.762-0.87511.5770.4690.4690.0000.0000.0000.000
136A136VAL0-0.076-0.04512.8600.0560.0560.0000.0000.0000.000
137A137ALA0-0.097-0.04515.0990.0360.0360.0000.0000.0000.000
138A138ASP-1-0.934-0.9679.9461.1491.1490.0000.0000.0000.000
139A139GLY0-0.092-0.03610.6860.2070.2070.0000.0000.0000.000
140A140ASP-1-0.793-0.8827.5180.3740.3740.0000.0000.0000.000
141A141TYR0-0.019-0.0419.114-0.145-0.1450.0000.0000.0000.000
142A142GLY00.0410.0117.096-0.232-0.2320.0000.0000.0000.000
143A143LEU0-0.018-0.0168.159-0.036-0.0360.0000.0000.0000.000
144A144ILE0-0.039-0.02311.099-0.043-0.0430.0000.0000.0000.000
145A145LEU00.0380.03714.4710.0390.0390.0000.0000.0000.000
146A146LEU0-0.014-0.00617.671-0.011-0.0110.0000.0000.0000.000
147A147SER00.0300.01520.5900.0230.0230.0000.0000.0000.000
148A148ALA0-0.011-0.00724.016-0.011-0.0110.0000.0000.0000.000
149A149THR00.0230.00226.6290.0110.0110.0000.0000.0000.000
150A150PRO00.0220.00729.629-0.004-0.0040.0000.0000.0000.000
151A151ASP-1-0.855-0.92631.689-0.045-0.0450.0000.0000.0000.000
152A152LEU0-0.021-0.00933.3820.0040.0040.0000.0000.0000.000
153A153TYR0-0.045-0.01533.361-0.006-0.0060.0000.0000.0000.000
154A154PHE0-0.0010.00028.3390.0070.0070.0000.0000.0000.000
155A155THR00.010-0.01633.537-0.005-0.0050.0000.0000.0000.000
156A156SER0-0.021-0.02331.870-0.009-0.0090.0000.0000.0000.000
157A157ILE00.0030.01728.2000.0090.0090.0000.0000.0000.000
158A158THR00.0010.00728.478-0.011-0.0110.0000.0000.0000.000
159A159GLY0-0.0100.00325.3070.0080.0080.0000.0000.0000.000
160A160THR00.000-0.00625.4320.0000.0000.0000.0000.0000.000
161A161GLN0-0.050-0.04924.631-0.021-0.0210.0000.0000.0000.000
162A162GLU-1-0.824-0.88720.3910.0670.0670.0000.0000.0000.000
163A163LYS10.8580.91718.609-0.049-0.0490.0000.0000.0000.000
164A164ARG10.9140.95224.4160.0100.0100.0000.0000.0000.000
165A165SER00.0210.01319.937-0.002-0.0020.0000.0000.0000.000
166A166GLY0-0.017-0.01620.993-0.032-0.0320.0000.0000.0000.000
167A167ASN0-0.025-0.03519.7390.0450.0450.0000.0000.0000.000
168A168ASN00.0110.01714.991-0.019-0.0190.0000.0000.0000.000
169A169TYR0-0.015-0.03113.537-0.065-0.0650.0000.0000.0000.000
170A170PRO0-0.058-0.03114.5090.0420.0420.0000.0000.0000.000
171A171LEU00.0130.03117.3600.0080.0080.0000.0000.0000.000
172A172LEU0-0.012-0.02118.092-0.013-0.0130.0000.0000.0000.000
173A173ASN00.0120.00821.9250.0160.0160.0000.0000.0000.000
174A174ALA00.0250.02224.794-0.013-0.0130.0000.0000.0000.000
175A175GLY00.0140.00526.5320.0130.0130.0000.0000.0000.000
176A176LYS10.8060.87630.2820.0480.0480.0000.0000.0000.000
177A177ALA0-0.008-0.01031.707-0.005-0.0050.0000.0000.0000.000
178A178ILE0-0.058-0.03833.4420.0090.0090.0000.0000.0000.000
179A179ILE0-0.013-0.00636.713-0.005-0.0050.0000.0000.0000.000
180A180ARG10.8790.92136.6020.0930.0930.0000.0000.0000.000
181A181GLU-1-0.927-0.96139.824-0.083-0.0830.0000.0000.0000.000
182A182GLY0-0.014-0.00841.962-0.002-0.0020.0000.0000.0000.000
183A183ARG10.8030.88135.6400.1070.1070.0000.0000.0000.000
184A184LEU0-0.045-0.00932.9790.0040.0040.0000.0000.0000.000
185A185VAL00.0660.01832.687-0.008-0.0080.0000.0000.0000.000
186A186MET0-0.007-0.00726.7310.0090.0090.0000.0000.0000.000
187A187PRO0-0.0250.02329.956-0.011-0.0110.0000.0000.0000.000
188A188ILE00.028-0.00823.3860.0010.0010.0000.0000.0000.000
189A189ALA00.0190.03226.141-0.006-0.0060.0000.0000.0000.000
190A190MET0-0.019-0.01019.970-0.007-0.0070.0000.0000.0000.000
191A191THR00.0270.02022.0940.0160.0160.0000.0000.0000.000
192A192ILE00.0030.01418.884-0.020-0.0200.0000.0000.0000.000
193A193HIS00.1020.05418.8760.0120.0120.0000.0000.0000.000
194A194HIS10.8940.93720.4640.1750.1750.0000.0000.0000.000
195A195GLY00.009-0.00221.194-0.004-0.0040.0000.0000.0000.000
196A196PHE0-0.017-0.00615.745-0.020-0.0200.0000.0000.0000.000
197A197ILE00.0180.02416.907-0.033-0.0330.0000.0000.0000.000
198A198ASP-1-0.812-0.88920.565-0.225-0.2250.0000.0000.0000.000
199A199GLY00.0390.00123.738-0.013-0.0130.0000.0000.0000.000
200A200HIS00.0040.00122.7760.0140.0140.0000.0000.0000.000
201A201HIS00.0440.01719.7370.0280.0280.0000.0000.0000.000
202A202LEU00.0260.01221.453-0.015-0.0150.0000.0000.0000.000
203A203SER0-0.041-0.01623.2910.0080.0080.0000.0000.0000.000
204A204LEU00.0090.00321.5940.0060.0060.0000.0000.0000.000
205A205PHE00.0300.00717.638-0.001-0.0010.0000.0000.0000.000
206A206TYR00.018-0.02121.1490.0020.0020.0000.0000.0000.000
207A207LYS10.8340.92024.3890.2210.2210.0000.0000.0000.000
208A208LYS10.8680.93518.1310.4670.4670.0000.0000.0000.000
209A209VAL00.0180.00320.6270.0100.0100.0000.0000.0000.000
210A210GLU-1-0.852-0.92922.753-0.153-0.1530.0000.0000.0000.000
211A211ASP-1-0.858-0.90524.555-0.215-0.2150.0000.0000.0000.000
212A212PHE0-0.042-0.01918.9520.0220.0220.0000.0000.0000.000
213A213LEU00.0130.00824.2760.0220.0220.0000.0000.0000.000
214A214LYS10.9010.98526.9480.2160.2160.0000.0000.0000.000