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: 4JVKN

Calculation Name: 2IMH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2IMH

Chain ID: A

ChEMBL ID:

UniProt ID: Q5LQD5

Base Structure: X-ray

Registration Date: 2023-09-23

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 230
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2542085.278749
FMO2-HF: Nuclear repulsion 2456757.59853
FMO2-HF: Total energy -85327.680219
FMO2-MP2: Total energy -85577.171583


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:SER)


Summations of interaction energy for fragment #1(A:0:SER)
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.
-8.81-1.1223.395-3.952-7.1290.016
Interaction energy analysis for fragmet #1(A:0:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.028 / q_NPA : 0.016
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].
3A2THR0-0.012-0.0163.3232.7705.5280.091-1.429-1.4190.005
4A3PHE00.0280.0085.470-0.193-0.1930.0000.0000.0000.000
5A4SER0-0.035-0.0479.1220.3000.3000.0000.0000.0000.000
6A5ILE0-0.001-0.00111.597-0.049-0.0490.0000.0000.0000.000
7A6LEU0-0.028-0.00515.3710.0500.0500.0000.0000.0000.000
8A7ALA00.032-0.01118.055-0.007-0.0070.0000.0000.0000.000
9A8HIS00.0340.01421.6190.0160.0160.0000.0000.0000.000
10A9ASP-1-0.780-0.87325.177-0.072-0.0720.0000.0000.0000.000
11A10PRO0-0.023-0.01927.5750.0080.0080.0000.0000.0000.000
12A11GLU-1-0.982-0.97530.882-0.044-0.0440.0000.0000.0000.000
13A12THR0-0.042-0.04729.8580.0050.0050.0000.0000.0000.000
14A13GLY00.0170.00930.5070.0040.0040.0000.0000.0000.000
15A14ALA0-0.067-0.01926.474-0.003-0.0030.0000.0000.0000.000
16A15ILE0-0.0080.00423.431-0.013-0.0130.0000.0000.0000.000
17A16GLY00.051-0.00820.7450.0230.0230.0000.0000.0000.000
18A17GLY00.0140.01316.743-0.042-0.0420.0000.0000.0000.000
19A18ALA0-0.031-0.01114.6140.0620.0620.0000.0000.0000.000
20A19ALA00.010-0.0019.341-0.131-0.1310.0000.0000.0000.000
21A20ALA00.0290.0178.2570.1540.1540.0000.0000.0000.000
22A21THR00.0070.0032.719-1.310-0.2680.494-0.559-0.9780.006
23A22GLY00.0450.0312.701-2.820-1.7170.844-0.727-1.2200.004
24A23SER0-0.028-0.0162.641-3.148-1.2891.660-0.912-2.6080.001
25A24LEU00.0170.0254.059-1.345-1.2030.010-0.054-0.0980.000
26A25CYS0-0.080-0.0507.121-0.182-0.1820.0000.0000.0000.000
27A26VAL00.0220.0336.866-0.296-0.2960.0000.0000.0000.000
28A27GLY00.029-0.0118.202-0.251-0.2510.0000.0000.0000.000
29A28GLY0-0.055-0.01811.550-0.075-0.0750.0000.0000.0000.000
30A29TRP0-0.037-0.0137.671-0.214-0.2140.0000.0000.0000.000
31A30VAL0-0.0060.0097.715-0.089-0.0890.0000.0000.0000.000
32A31LEU0-0.040-0.00410.751-0.030-0.0300.0000.0000.0000.000
33A32ARG10.7960.88913.2140.3270.3270.0000.0000.0000.000
34A33GLY00.0370.00017.472-0.027-0.0270.0000.0000.0000.000
35A34ASP-1-0.782-0.88020.924-0.071-0.0710.0000.0000.0000.000
36A35LEU00.0290.02324.645-0.011-0.0110.0000.0000.0000.000
37A36ASN0-0.083-0.02727.629-0.009-0.0090.0000.0000.0000.000
38A37ALA00.007-0.00124.927-0.002-0.0020.0000.0000.0000.000
39A38GLY00.0410.02324.103-0.008-0.0080.0000.0000.0000.000
40A39MET0-0.065-0.02018.5790.0230.0230.0000.0000.0000.000
41A40SER0-0.029-0.03917.195-0.021-0.0210.0000.0000.0000.000
42A41ALA00.0240.01612.2400.0360.0360.0000.0000.0000.000
43A42SER0-0.075-0.04012.252-0.114-0.1140.0000.0000.0000.000
44A43GLN00.0240.0037.2070.1260.1260.0000.0000.0000.000
45A44GLY00.0150.0006.2170.4500.4500.0000.0000.0000.000
46A45ALA0-0.029-0.0154.786-0.643-0.603-0.001-0.003-0.0350.000
47A46ALA0-0.027-0.0145.8420.6430.6430.0000.0000.0000.000
48A47PRO00.0010.0256.6760.1400.1400.0000.0000.0000.000
49A48SER00.0420.0189.4460.2400.2400.0000.0000.0000.000
50A49THR00.0430.00513.224-0.037-0.0370.0000.0000.0000.000
51A50PHE00.0180.01114.8520.0140.0140.0000.0000.0000.000
52A51TRP00.0490.02013.366-0.018-0.0180.0000.0000.0000.000
53A52GLY00.0310.01515.9280.0060.0060.0000.0000.0000.000
54A53GLU-1-0.841-0.90416.674-0.149-0.1490.0000.0000.0000.000
55A54GLU-1-0.934-0.97919.966-0.212-0.2120.0000.0000.0000.000
56A55VAL0-0.025-0.01418.5260.0170.0170.0000.0000.0000.000
57A56LEU00.0050.00220.0470.0150.0150.0000.0000.0000.000
58A57GLN0-0.031-0.02023.0240.0200.0200.0000.0000.0000.000
59A58HIS00.0450.01923.8860.0150.0150.0000.0000.0000.000
60A59LEU0-0.0040.00022.9790.0070.0070.0000.0000.0000.000
61A60ARG10.7240.84324.7220.1330.1330.0000.0000.0000.000
62A61ASP-1-0.915-0.93929.185-0.111-0.1110.0000.0000.0000.000
63A62GLY0-0.036-0.01230.5810.0050.0050.0000.0000.0000.000
64A63SER0-0.064-0.02127.3370.0000.0000.0000.0000.0000.000
65A64HIS00.0630.03226.624-0.012-0.0120.0000.0000.0000.000
66A65PRO00.034-0.00123.025-0.011-0.0110.0000.0000.0000.000
67A66GLU-1-0.957-0.98723.016-0.293-0.2930.0000.0000.0000.000
68A67ASP-1-0.889-0.94323.711-0.223-0.2230.0000.0000.0000.000
69A68ALA0-0.0030.00223.620-0.003-0.0030.0000.0000.0000.000
70A69VAL0-0.005-0.01018.249-0.016-0.0160.0000.0000.0000.000
71A70ASN00.0150.01620.418-0.049-0.0490.0000.0000.0000.000
72A71HIS0-0.050-0.01522.5650.0030.0030.0000.0000.0000.000
73A72VAL00.0070.01718.5140.0060.0060.0000.0000.0000.000
74A73THR0-0.034-0.02516.7390.0010.0010.0000.0000.0000.000
75A74SER0-0.037-0.03619.1380.0090.0090.0000.0000.0000.000
76A75GLN0-0.0200.00222.2530.0170.0170.0000.0000.0000.000
77A76ASP-1-0.783-0.84716.669-0.369-0.3690.0000.0000.0000.000
78A77SER0-0.024-0.02919.150-0.034-0.0340.0000.0000.0000.000
79A78GLY0-0.016-0.00716.0490.0040.0040.0000.0000.0000.000
80A79ARG10.8540.91114.3480.2560.2560.0000.0000.0000.000
81A80ALA00.0030.00213.886-0.104-0.1040.0000.0000.0000.000
82A81TYR0-0.0070.0029.819-0.076-0.0760.0000.0000.0000.000
83A82ARG10.8060.8909.2460.3470.3470.0000.0000.0000.000
84A83GLN0-0.005-0.0108.939-0.303-0.3030.0000.0000.0000.000
85A84LEU0-0.036-0.00211.273-0.039-0.0390.0000.0000.0000.000
86A85ALA00.0380.03114.0020.0240.0240.0000.0000.0000.000
87A86ALA00.0210.00416.1280.0190.0190.0000.0000.0000.000
88A87MET0-0.034-0.00319.413-0.002-0.0020.0000.0000.0000.000
89A88ASP-1-0.759-0.86722.144-0.162-0.1620.0000.0000.0000.000
90A89LEU0-0.009-0.01925.6650.0010.0010.0000.0000.0000.000
91A90LEU0-0.066-0.02927.8770.0130.0130.0000.0000.0000.000
92A91GLY0-0.012-0.00725.3440.0020.0020.0000.0000.0000.000
93A92ASN0-0.082-0.02925.297-0.017-0.0170.0000.0000.0000.000
94A93ALA00.014-0.00420.960-0.006-0.0060.0000.0000.0000.000
95A94ALA0-0.0050.01420.8880.0070.0070.0000.0000.0000.000
96A95ALA00.024-0.00915.556-0.026-0.0260.0000.0000.0000.000
97A96PHE0-0.0110.01514.4450.0440.0440.0000.0000.0000.000
98A97THR00.009-0.01411.217-0.192-0.1920.0000.0000.0000.000
99A98GLY0-0.0120.00912.3930.0950.0950.0000.0000.0000.000
100A99SER0-0.013-0.05411.756-0.155-0.1550.0000.0000.0000.000
101A100GLU-1-0.884-0.92211.096-0.540-0.5400.0000.0000.0000.000
102A101ASN0-0.094-0.0397.199-0.397-0.3970.0000.0000.0000.000
103A102GLN00.0190.0044.4670.5230.625-0.001-0.005-0.0950.000
104A103ASP-1-0.848-0.8926.664-1.308-1.3080.0000.0000.0000.000
105A104ILE00.009-0.0028.034-0.167-0.1670.0000.0000.0000.000
106A105LYS10.8550.8968.9560.7370.7370.0000.0000.0000.000
107A106GLY0-0.019-0.00410.6410.1430.1430.0000.0000.0000.000
108A107SER0-0.007-0.01212.937-0.082-0.0820.0000.0000.0000.000
109A108VAL0-0.0110.00315.6930.0420.0420.0000.0000.0000.000
110A109THR00.0370.03218.825-0.005-0.0050.0000.0000.0000.000
111A110PHE0-0.020-0.01419.2510.0160.0160.0000.0000.0000.000
112A111ALA0-0.017-0.01624.0660.0020.0020.0000.0000.0000.000
113A112SER00.0190.01724.9910.0050.0050.0000.0000.0000.000
114A113GLY00.0760.02121.6180.0140.0140.0000.0000.0000.000
115A114ILE0-0.053-0.01117.254-0.010-0.0100.0000.0000.0000.000
116A115ALA00.0320.03515.4290.0030.0030.0000.0000.0000.000
117A116SER0-0.031-0.02312.426-0.056-0.0560.0000.0000.0000.000
118A117GLY00.0570.0108.9230.0470.0470.0000.0000.0000.000
119A118ASN0-0.069-0.0264.509-1.032-0.955-0.001-0.013-0.0620.000
120A119MET00.0010.0372.722-0.730-0.1650.299-0.250-0.6140.000
121A120LEU0-0.021-0.0035.4840.4720.4720.0000.0000.0000.000
122A121GLY00.0220.0058.6670.1050.1050.0000.0000.0000.000
123A122ASP-1-0.809-0.89610.821-0.300-0.3000.0000.0000.0000.000
124A123ASN0-0.002-0.00713.632-0.136-0.1360.0000.0000.0000.000
125A124SER0-0.070-0.05815.799-0.018-0.0180.0000.0000.0000.000
126A125VAL00.0350.03311.1320.0300.0300.0000.0000.0000.000
127A126LEU00.0250.01012.1490.0560.0560.0000.0000.0000.000
128A127GLY0-0.0140.00415.5230.0580.0580.0000.0000.0000.000
129A128ALA00.0500.02317.3310.0370.0370.0000.0000.0000.000
130A129MET0-0.062-0.01412.649-0.001-0.0010.0000.0000.0000.000
131A130THR0-0.031-0.02917.2390.0290.0290.0000.0000.0000.000
132A131GLU-1-0.970-0.98320.145-0.131-0.1310.0000.0000.0000.000
133A132ALA00.001-0.00219.8150.0230.0230.0000.0000.0000.000
134A133PHE0-0.032-0.02520.1610.0210.0210.0000.0000.0000.000
135A134VAL0-0.054-0.03822.0640.0140.0140.0000.0000.0000.000
136A135ALA0-0.0210.00125.1080.0120.0120.0000.0000.0000.000
137A136SER0-0.070-0.01624.6860.0170.0170.0000.0000.0000.000
138A137ASP-1-0.879-0.94026.633-0.044-0.0440.0000.0000.0000.000
139A138LEU0-0.070-0.02925.2590.0110.0110.0000.0000.0000.000
140A139THR00.0510.00627.200-0.008-0.0080.0000.0000.0000.000
141A140PHE00.0210.01122.5570.0030.0030.0000.0000.0000.000
142A141GLU-1-0.825-0.93522.271-0.027-0.0270.0000.0000.0000.000
143A142ARG10.9630.97321.319-0.013-0.0130.0000.0000.0000.000
144A143ARG10.8620.96022.1190.0850.0850.0000.0000.0000.000
145A144LEU0-0.028-0.00818.164-0.015-0.0150.0000.0000.0000.000
146A145LEU0-0.023-0.01917.272-0.001-0.0010.0000.0000.0000.000
147A146ALA00.0160.00717.6480.0130.0130.0000.0000.0000.000
148A147ALA00.0110.00917.167-0.007-0.0070.0000.0000.0000.000
149A148LEU0-0.031-0.01611.844-0.032-0.0320.0000.0000.0000.000
150A149ILE00.0240.01013.8330.0130.0130.0000.0000.0000.000
151A150ALA0-0.0020.00316.0940.0020.0020.0000.0000.0000.000
152A151ALA0-0.029-0.01412.450-0.029-0.0290.0000.0000.0000.000
153A152GLU-1-0.923-0.98811.3800.3080.3080.0000.0000.0000.000
154A153GLY0-0.038-0.01512.610-0.005-0.0050.0000.0000.0000.000
155A154ALA0-0.0260.00315.077-0.001-0.0010.0000.0000.0000.000
156A155GLY0-0.038-0.00111.867-0.073-0.0730.0000.0000.0000.000
157A156SER0-0.051-0.0418.955-0.041-0.0410.0000.0000.0000.000
158A157ASP-1-0.827-0.9259.6160.0610.0610.0000.0000.0000.000
159A158PHE0-0.0200.0029.9850.0940.0940.0000.0000.0000.000
160A159ARG10.7510.8374.9420.6670.6670.0000.0000.0000.000
161A160GLY00.0610.0486.0520.2590.2590.0000.0000.0000.000
162A161LEU0-0.022-0.0135.5040.4310.4310.0000.0000.0000.000
163A162LEU0-0.022-0.0165.908-0.376-0.3760.0000.0000.0000.000
164A163SER0-0.058-0.0456.487-0.618-0.6180.0000.0000.0000.000
165A164ALA00.0370.0028.2540.0800.0800.0000.0000.0000.000
166A165ALA0-0.033-0.01410.777-0.022-0.0220.0000.0000.0000.000
167A166MET00.0210.01613.393-0.056-0.0560.0000.0000.0000.000
168A167LEU0-0.023-0.00216.5450.0240.0240.0000.0000.0000.000
169A168VAL0-0.005-0.00618.700-0.029-0.0290.0000.0000.0000.000
170A169LEU0-0.0100.00222.2100.0180.0180.0000.0000.0000.000
171A170HIS00.053-0.00525.093-0.004-0.0040.0000.0000.0000.000
172A171PRO00.0370.01828.7790.0060.0060.0000.0000.0000.000
173A172ASP-1-0.821-0.88031.839-0.026-0.0260.0000.0000.0000.000
174A173ARG10.8460.91927.5050.0330.0330.0000.0000.0000.000
175A174PRO00.0160.02528.341-0.006-0.0060.0000.0000.0000.000
176A175PRO0-0.015-0.01923.679-0.001-0.0010.0000.0000.0000.000
177A176VAL00.0160.02022.0290.0170.0170.0000.0000.0000.000
178A177THR0-0.016-0.00818.969-0.015-0.0150.0000.0000.0000.000
179A178LEU0-0.037-0.01418.2820.0200.0200.0000.0000.0000.000
180A179ARG10.8520.88413.702-0.241-0.2410.0000.0000.0000.000
181A180ILE0-0.0270.01212.675-0.015-0.0150.0000.0000.0000.000
182A181ASP-1-0.736-0.85411.1850.5410.5410.0000.0000.0000.000
183A182TYR00.043-0.0019.9770.1430.1430.0000.0000.0000.000
184A183HIS0-0.0340.00211.038-0.133-0.1330.0000.0000.0000.000
185A184PRO0-0.046-0.01411.1470.1430.1430.0000.0000.0000.000
186A185ASP-1-0.905-0.96611.7380.4870.4870.0000.0000.0000.000
187A186ASN00.0470.02212.920-0.020-0.0200.0000.0000.0000.000
188A187PRO00.0410.0259.471-0.107-0.1070.0000.0000.0000.000
189A188ILE00.0450.02311.373-0.073-0.0730.0000.0000.0000.000
190A189GLY00.0490.02814.146-0.065-0.0650.0000.0000.0000.000
191A190ALA0-0.060-0.03415.654-0.043-0.0430.0000.0000.0000.000
192A191LEU0-0.003-0.00514.211-0.036-0.0360.0000.0000.0000.000
193A192GLU-1-0.845-0.91217.0290.0480.0480.0000.0000.0000.000
194A193GLN0-0.030-0.03219.968-0.029-0.0290.0000.0000.0000.000
195A194LEU0-0.046-0.01818.297-0.020-0.0200.0000.0000.0000.000
196A195TYR00.0670.01720.860-0.020-0.0200.0000.0000.0000.000
197A196GLN0-0.036-0.00822.400-0.021-0.0210.0000.0000.0000.000
198A197LYS10.8680.94723.993-0.164-0.1640.0000.0000.0000.000
199A198ALA0-0.0150.00524.033-0.007-0.0070.0000.0000.0000.000
200A199THR0-0.053-0.04025.388-0.014-0.0140.0000.0000.0000.000
201A200THR0-0.021-0.01528.094-0.008-0.0080.0000.0000.0000.000
202A201GLY00.002-0.00431.0400.0050.0050.0000.0000.0000.000
203A202ASP-1-0.809-0.90533.8560.0600.0600.0000.0000.0000.000
204A203TYR00.0140.01626.5380.0010.0010.0000.0000.0000.000
205A204ALA00.0250.01530.769-0.004-0.0040.0000.0000.0000.000
206A205ASP-1-0.859-0.91931.8580.0230.0230.0000.0000.0000.000
207A206TRP00.006-0.00429.402-0.002-0.0020.0000.0000.0000.000
208A207ALA00.001-0.00330.160-0.004-0.0040.0000.0000.0000.000
209A208ARG10.7380.83432.149-0.025-0.0250.0000.0000.0000.000
210A209GLN0-0.028-0.01534.682-0.005-0.0050.0000.0000.0000.000
211A210VAL0-0.014-0.00231.5590.0010.0010.0000.0000.0000.000
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