Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: QVK8Y

Calculation Name: 3R3H-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3R3H

Chain ID: A

ChEMBL ID:

UniProt ID: Q5ZT85

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 OptH
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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2662108.101224
FMO2-HF: Nuclear repulsion 2576163.965042
FMO2-HF: Total energy -85944.136182
FMO2-MP2: Total energy -86196.368857


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:4:LYS)


Summations of interaction energy for fragment #1(A:4:LYS)
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.
-71.316-65.5671.635-3.482-3.903-0.041
Interaction energy analysis for fragmet #1(A:4:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.942 / q_NPA : 0.959
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].
3A6LEU0-0.026-0.0212.300-33.558-28.2751.628-3.403-3.509-0.041
4A7SER00.0010.0093.31910.61911.0350.008-0.078-0.3460.000
5A8LEU00.0220.0155.069-0.516-0.466-0.001-0.001-0.0480.000
6A9THR00.0540.0307.2221.6781.6780.0000.0000.0000.000
7A10PRO00.032-0.0049.7750.9680.9680.0000.0000.0000.000
8A11GLU-1-0.860-0.94511.950-22.556-22.5560.0000.0000.0000.000
9A12LEU0-0.0060.0067.6900.7340.7340.0000.0000.0000.000
10A13TYR0-0.045-0.03711.5991.2881.2880.0000.0000.0000.000
11A14LYS10.9310.95613.74219.32819.3280.0000.0000.0000.000
12A15TYR00.0190.02112.9740.7110.7110.0000.0000.0000.000
13A16LEU00.0030.00412.8380.8290.8290.0000.0000.0000.000
14A17LEU0-0.020-0.03315.3001.1181.1180.0000.0000.0000.000
15A18ASP-1-0.934-0.95218.593-14.220-14.2200.0000.0000.0000.000
16A19ILE0-0.029-0.00215.6160.6790.6790.0000.0000.0000.000
17A20SER0-0.109-0.04818.4220.4850.4850.0000.0000.0000.000
18A21LEU0-0.020-0.00920.5440.6800.6800.0000.0000.0000.000
19A22ARG10.8920.95222.53912.59812.5980.0000.0000.0000.000
20A23GLU-1-0.765-0.83126.115-11.800-11.8000.0000.0000.0000.000
21A24HIS00.0600.03427.8030.1300.1300.0000.0000.0000.000
22A25PRO00.0520.00831.571-0.137-0.1370.0000.0000.0000.000
23A26ALA00.0830.04633.539-0.040-0.0400.0000.0000.0000.000
24A27LEU0-0.022-0.00528.7890.0460.0460.0000.0000.0000.000
25A28ALA00.0090.01629.191-0.101-0.1010.0000.0000.0000.000
26A29ALA0-0.045-0.01530.192-0.096-0.0960.0000.0000.0000.000
27A30LEU00.0090.01332.1250.0480.0480.0000.0000.0000.000
28A31ARG10.8370.88224.54212.48212.4820.0000.0000.0000.000
29A32LYS10.9580.97629.6899.8129.8120.0000.0000.0000.000
30A33GLU-1-0.993-0.99130.577-8.561-8.5610.0000.0000.0000.000
31A34THR0-0.095-0.06031.5280.1590.1590.0000.0000.0000.000
32A35SER0-0.051-0.03727.701-0.265-0.2650.0000.0000.0000.000
33A36THR0-0.039-0.02128.555-0.217-0.2170.0000.0000.0000.000
34A37MET0-0.0020.01930.9040.0730.0730.0000.0000.0000.000
35A38GLU-1-0.849-0.92829.830-10.954-10.9540.0000.0000.0000.000
36A39LEU0-0.020-0.02229.345-0.276-0.2760.0000.0000.0000.000
37A40ALA0-0.029-0.01327.017-0.212-0.2120.0000.0000.0000.000
38A41ASN0-0.0180.00324.390-0.854-0.8540.0000.0000.0000.000
39A42MET0-0.031-0.00824.576-0.458-0.4580.0000.0000.0000.000
40A43GLN0-0.015-0.00226.5400.3750.3750.0000.0000.0000.000
41A44VAL00.0530.03823.140-0.532-0.5320.0000.0000.0000.000
42A45ALA00.0240.00520.1010.1640.1640.0000.0000.0000.000
43A46PRO00.016-0.00821.2000.1520.1520.0000.0000.0000.000
44A47GLU-1-0.768-0.89817.665-17.077-17.0770.0000.0000.0000.000
45A48GLN00.0380.03617.797-0.270-0.2700.0000.0000.0000.000
46A49ALA00.002-0.00421.2900.4420.4420.0000.0000.0000.000
47A50GLN00.0180.01322.6120.5740.5740.0000.0000.0000.000
48A51PHE0-0.030-0.01520.5560.2850.2850.0000.0000.0000.000
49A52MET00.0490.00622.6620.4000.4000.0000.0000.0000.000
50A53GLN0-0.052-0.02025.7400.1900.1900.0000.0000.0000.000
51A54MET0-0.066-0.03623.7840.3780.3780.0000.0000.0000.000
52A55LEU00.0230.01423.2760.4440.4440.0000.0000.0000.000
53A56ILE00.0590.05927.0540.3700.3700.0000.0000.0000.000
54A57ARG10.9250.96926.53711.76611.7660.0000.0000.0000.000
55A58LEU0-0.079-0.05525.0280.3170.3170.0000.0000.0000.000
56A59THR0-0.035-0.00629.4130.1730.1730.0000.0000.0000.000
57A60ARG10.8500.92731.3729.7099.7090.0000.0000.0000.000
58A61ALA00.0190.01333.6740.2900.2900.0000.0000.0000.000
59A62LYS10.8570.94335.4528.2108.2100.0000.0000.0000.000
60A63LYS10.8920.96938.1127.6657.6650.0000.0000.0000.000
61A64VAL0-0.019-0.01333.039-0.171-0.1710.0000.0000.0000.000
62A65LEU0-0.0100.00134.6470.2580.2580.0000.0000.0000.000
63A66GLU-1-0.791-0.88231.604-10.368-10.3680.0000.0000.0000.000
64A67LEU0-0.002-0.01532.1420.3820.3820.0000.0000.0000.000
65A68GLY00.0710.03131.436-0.400-0.4000.0000.0000.0000.000
66A69THR00.004-0.00231.1840.3170.3170.0000.0000.0000.000
67A70PHE0-0.0060.01629.833-0.335-0.3350.0000.0000.0000.000
68A71THR00.0300.02030.9810.2520.2520.0000.0000.0000.000
69A72GLY00.013-0.00833.1450.2990.2990.0000.0000.0000.000
70A73TYR0-0.037-0.05726.5870.0630.0630.0000.0000.0000.000
71A74SER00.0390.00528.371-0.079-0.0790.0000.0000.0000.000
72A75ALA00.0630.03730.0680.0320.0320.0000.0000.0000.000
73A76LEU0-0.038-0.00533.0450.2160.2160.0000.0000.0000.000
74A77ALA00.014-0.00528.8440.1020.1020.0000.0000.0000.000
75A78MET00.0210.01329.1780.0860.0860.0000.0000.0000.000
76A79SER00.0150.00932.0680.1940.1940.0000.0000.0000.000
77A80LEU0-0.036-0.01832.2190.1840.1840.0000.0000.0000.000
78A81ALA0-0.089-0.02630.7390.0080.0080.0000.0000.0000.000
79A82LEU0-0.025-0.00432.8170.0010.0010.0000.0000.0000.000
80A83PRO0-0.041-0.01536.0370.0570.0570.0000.0000.0000.000
81A84ASP-1-0.912-0.95939.201-7.672-7.6720.0000.0000.0000.000
82A85ASP-1-0.898-0.95642.430-7.528-7.5280.0000.0000.0000.000
83A86GLY0-0.053-0.02439.8020.0390.0390.0000.0000.0000.000
84A87GLN0-0.038-0.03239.7960.0870.0870.0000.0000.0000.000
85A88VAL00.0040.00335.263-0.169-0.1690.0000.0000.0000.000
86A89ILE0-0.045-0.01837.8740.2090.2090.0000.0000.0000.000
87A90THR0-0.034-0.02234.979-0.114-0.1140.0000.0000.0000.000
88A91CYS0-0.043-0.03636.1500.3760.3760.0000.0000.0000.000
89A92ASP-1-0.817-0.92636.038-9.143-9.1430.0000.0000.0000.000
90A93ILE0-0.009-0.02134.0350.2410.2410.0000.0000.0000.000
91A94ASN0-0.022-0.00235.6780.1400.1400.0000.0000.0000.000
92A95GLU-1-0.954-0.96237.379-7.544-7.5440.0000.0000.0000.000
93A96GLY0-0.036-0.00738.4990.1670.1670.0000.0000.0000.000
94A97TRP0-0.049-0.03737.9050.1450.1450.0000.0000.0000.000
95A98THR00.0330.01137.039-0.198-0.1980.0000.0000.0000.000
96A99LYS10.9330.96237.5548.6168.6160.0000.0000.0000.000
97A100HIS00.0180.01538.694-0.253-0.2530.0000.0000.0000.000
98A101ALA00.0820.04537.001-0.012-0.0120.0000.0000.0000.000
99A102HIS00.024-0.00338.740-0.091-0.0910.0000.0000.0000.000
100A103PRO0-0.026-0.01040.8370.0780.0780.0000.0000.0000.000
101A104TYR00.1150.04536.6820.0870.0870.0000.0000.0000.000
102A105TRP0-0.007-0.01435.9400.1150.1150.0000.0000.0000.000
103A106ARG10.9200.97239.5157.1787.1780.0000.0000.0000.000
104A107GLU-1-0.968-0.96238.258-8.388-8.3880.0000.0000.0000.000
105A108ALA0-0.043-0.02737.117-0.014-0.0140.0000.0000.0000.000
106A109LYS10.8850.93539.0747.3127.3120.0000.0000.0000.000
107A110GLN00.0800.02737.0730.0800.0800.0000.0000.0000.000
108A111GLU-1-0.906-0.95440.451-7.393-7.3930.0000.0000.0000.000
109A112HIS0-0.041-0.01942.6240.1720.1720.0000.0000.0000.000
110A113LYS10.8510.94737.9928.4328.4320.0000.0000.0000.000
111A114ILE0-0.044-0.01237.330-0.110-0.1100.0000.0000.0000.000
112A115LYS10.9380.97540.4657.3267.3260.0000.0000.0000.000
113A116LEU00.003-0.00739.176-0.106-0.1060.0000.0000.0000.000
114A117ARG10.8370.91740.5827.5877.5870.0000.0000.0000.000
115A118LEU00.0420.01840.719-0.155-0.1550.0000.0000.0000.000
116A119GLY00.0390.03341.2760.1960.1960.0000.0000.0000.000
117A120PRO00.0310.00840.011-0.228-0.2280.0000.0000.0000.000
118A121ALA00.0720.02236.7350.1270.1270.0000.0000.0000.000
119A122LEU00.0130.01238.3780.0530.0530.0000.0000.0000.000
120A123ASP-1-0.879-0.93240.351-7.168-7.1680.0000.0000.0000.000
121A124THR0-0.034-0.02340.6940.1930.1930.0000.0000.0000.000
122A125LEU00.009-0.00436.5500.0600.0600.0000.0000.0000.000
123A126HIS0-0.014-0.00741.1920.0460.0460.0000.0000.0000.000
124A127SER0-0.0360.00544.0520.1010.1010.0000.0000.0000.000
125A128LEU0-0.002-0.01740.5510.1260.1260.0000.0000.0000.000
126A129LEU00.0070.01341.3820.0270.0270.0000.0000.0000.000
127A130ASN0-0.082-0.03644.3400.0100.0100.0000.0000.0000.000
128A131GLU-1-0.979-0.99547.589-6.268-6.2680.0000.0000.0000.000
129A132GLY0-0.019-0.00445.7940.1020.1020.0000.0000.0000.000
130A133GLY0-0.0130.00845.621-0.024-0.0240.0000.0000.0000.000
131A134GLU-1-0.956-1.00541.276-7.531-7.5310.0000.0000.0000.000
132A135HIS0-0.077-0.02439.412-0.149-0.1490.0000.0000.0000.000
133A136GLN0-0.0080.00839.8640.1790.1790.0000.0000.0000.000
134A137PHE00.0130.00135.8530.0190.0190.0000.0000.0000.000
135A138ASP-1-0.795-0.91534.521-8.669-8.6690.0000.0000.0000.000
136A139PHE00.008-0.00827.226-0.314-0.3140.0000.0000.0000.000
137A140ILE00.0010.01331.0340.2600.2600.0000.0000.0000.000
138A141PHE00.004-0.00425.160-0.334-0.3340.0000.0000.0000.000
139A142ILE0-0.022-0.03128.4220.4000.4000.0000.0000.0000.000
140A143ASP-1-0.845-0.92826.571-12.520-12.5200.0000.0000.0000.000
141A144ALA0-0.0300.00728.5950.1520.1520.0000.0000.0000.000
142A145ASP-1-0.797-0.88130.384-9.481-9.4810.0000.0000.0000.000
143A146LYS10.9300.95026.41811.93111.9310.0000.0000.0000.000
144A147THR0-0.067-0.04430.382-0.073-0.0730.0000.0000.0000.000
145A148ASN00.0180.02133.2960.4050.4050.0000.0000.0000.000
146A149TYR0-0.014-0.02426.1180.2680.2680.0000.0000.0000.000
147A150LEU0-0.0080.01130.664-0.093-0.0930.0000.0000.0000.000
148A151ASN0-0.021-0.01132.9090.0120.0120.0000.0000.0000.000
149A152TYR0-0.026-0.06032.6240.2510.2510.0000.0000.0000.000
150A153TYR0-0.025-0.00128.409-0.081-0.0810.0000.0000.0000.000
151A154GLU-1-0.824-0.92832.017-8.784-8.7840.0000.0000.0000.000
152A155LEU0-0.041-0.02935.0170.1650.1650.0000.0000.0000.000
153A156ALA00.0130.01032.6010.1430.1430.0000.0000.0000.000
154A157LEU0-0.030-0.01530.8720.0150.0150.0000.0000.0000.000
155A158LYS10.9040.96734.4807.9037.9030.0000.0000.0000.000
156A159LEU0-0.006-0.01736.9590.1370.1370.0000.0000.0000.000
157A160VAL0-0.0200.01232.1660.0160.0160.0000.0000.0000.000
158A161THR0-0.0210.00435.4570.2550.2550.0000.0000.0000.000
159A162PRO00.0230.00634.315-0.245-0.2450.0000.0000.0000.000
160A163LYS10.9460.95832.6198.4798.4790.0000.0000.0000.000
161A164GLY00.0110.00231.541-0.228-0.2280.0000.0000.0000.000
162A165LEU0-0.047-0.02725.010-0.170-0.1700.0000.0000.0000.000
163A166ILE00.0240.01227.9200.2040.2040.0000.0000.0000.000
164A167ALA0-0.006-0.00625.032-0.444-0.4440.0000.0000.0000.000
165A168ILE0-0.039-0.01724.5200.4510.4510.0000.0000.0000.000
166A169ASP-1-0.787-0.90721.699-15.213-15.2130.0000.0000.0000.000
167A170ASN0-0.049-0.04021.1101.0341.0340.0000.0000.0000.000
168A171ILE0-0.060-0.01119.6570.3800.3800.0000.0000.0000.000
169A172PHE0-0.030-0.04814.7680.1430.1430.0000.0000.0000.000
170A173TRP00.0110.00719.128-0.196-0.1960.0000.0000.0000.000
171A174ASP-1-0.844-0.93418.131-16.257-16.2570.0000.0000.0000.000
172A175GLY0-0.052-0.01417.248-0.612-0.6120.0000.0000.0000.000
173A176LYS10.9210.95917.96213.97913.9790.0000.0000.0000.000
174A177VAL0-0.060-0.02618.8120.6620.6620.0000.0000.0000.000
175A178ILE0-0.063-0.03715.8900.3170.3170.0000.0000.0000.000
176A179ASP-1-0.873-0.93219.123-13.616-13.6160.0000.0000.0000.000
177A180PRO0-0.079-0.05121.4280.5610.5610.0000.0000.0000.000
178A181ASN0-0.017-0.00624.6050.8100.8100.0000.0000.0000.000
179A182ASP-1-0.794-0.87325.225-11.481-11.4810.0000.0000.0000.000
180A183THR0-0.005-0.01727.1520.2150.2150.0000.0000.0000.000
181A184SER0-0.056-0.02328.6640.3610.3610.0000.0000.0000.000
182A185GLY00.007-0.03630.161-0.176-0.1760.0000.0000.0000.000
183A186GLN00.0420.01628.765-0.139-0.1390.0000.0000.0000.000
184A187THR00.0370.04125.035-0.125-0.1250.0000.0000.0000.000
185A188ARG10.9280.96826.2759.1949.1940.0000.0000.0000.000
186A189GLU-1-0.886-0.94928.955-9.532-9.5320.0000.0000.0000.000
187A190ILE00.0280.04723.3660.0450.0450.0000.0000.0000.000
188A191LYS10.9350.97123.31011.96911.9690.0000.0000.0000.000
189A192LYS10.8490.93525.1309.3319.3310.0000.0000.0000.000
190A193LEU00.0710.02626.4780.1460.1460.0000.0000.0000.000
191A194ASN0-0.004-0.01321.4260.1780.1780.0000.0000.0000.000
192A195GLN0-0.077-0.04123.390-0.176-0.1760.0000.0000.0000.000
193A196VAL0-0.013-0.00725.8450.1350.1350.0000.0000.0000.000
194A197ILE00.0420.02523.7440.1570.1570.0000.0000.0000.000
195A198LYS10.8870.97321.70812.13712.1370.0000.0000.0000.000
196A199ASN0-0.053-0.04023.935-0.236-0.2360.0000.0000.0000.000
197A200ASP-1-0.792-0.86726.897-9.266-9.2660.0000.0000.0000.000
198A201SER0-0.032-0.02127.521-0.200-0.2000.0000.0000.0000.000
199A202ARG10.7960.87129.7909.1419.1410.0000.0000.0000.000
200A203VAL0-0.015-0.00226.8050.1490.1490.0000.0000.0000.000
201A204PHE00.0000.00324.596-0.192-0.1920.0000.0000.0000.000
202A205VAL00.035-0.00520.551-0.030-0.0300.0000.0000.0000.000
203A206SER0-0.035-0.01118.008-0.382-0.3820.0000.0000.0000.000
204A207LEU0-0.0180.00316.1380.3180.3180.0000.0000.0000.000
205A208LEU0-0.016-0.00414.889-1.095-1.0950.0000.0000.0000.000
206A209ALA0-0.010-0.00811.7620.7080.7080.0000.0000.0000.000
207A210ILE0-0.050-0.03112.349-2.039-2.0390.0000.0000.0000.000
208A211ALA00.0380.02314.684-0.334-0.3340.0000.0000.0000.000
209A212ASP-1-0.760-0.85815.915-17.278-17.2780.0000.0000.0000.000
210A213GLY0-0.015-0.01616.9160.3410.3410.0000.0000.0000.000
211A214MET00.0060.00217.7500.8890.8890.0000.0000.0000.000
212A215PHE00.010-0.00819.289-0.636-0.6360.0000.0000.0000.000
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