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: K9633

Calculation Name: 2QM4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2QM4

Chain ID: A

ChEMBL ID:

UniProt ID: Q9H9Q4

Base Structure: X-ray

Registration Date: 2023-09-20

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 232
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2579786.465629
FMO2-HF: Nuclear repulsion 2485919.081502
FMO2-HF: Total energy -93867.384127
FMO2-MP2: Total energy -94133.720399


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:SER)


Summations of interaction energy for fragment #1(A:-1: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.
-39.684-43.51832.059-16.809-11.415-0.076
Interaction energy analysis for fragmet #1(A:-1:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.002 / q_NPA : -0.023
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].
3A1MET0-0.0050.0063.105-5.213-1.1480.098-2.139-2.0230.010
4A2GLU-1-0.850-0.9011.635-31.830-40.89631.951-14.212-8.672-0.084
5A3GLU-1-0.931-0.9743.589-4.561-3.3940.010-0.458-0.720-0.002
6A4LEU0-0.097-0.0375.7490.7010.7010.0000.0000.0000.000
7A5GLU-1-0.781-0.8927.579-0.006-0.0060.0000.0000.0000.000
8A6GLN0-0.010-0.0047.1010.3400.3400.0000.0000.0000.000
9A7GLY00.0100.0019.6290.2370.2370.0000.0000.0000.000
10A8LEU0-0.042-0.01911.6720.1530.1530.0000.0000.0000.000
11A9LEU0-0.033-0.01813.1090.1130.1130.0000.0000.0000.000
12A10MET0-0.037-0.01312.2330.0790.0790.0000.0000.0000.000
13A11GLN0-0.066-0.01615.9370.1030.1030.0000.0000.0000.000
14A12PRO00.0180.00218.2750.0010.0010.0000.0000.0000.000
15A13TRP0-0.048-0.04121.1090.0110.0110.0000.0000.0000.000
16A14ALA00.0140.01223.7480.0060.0060.0000.0000.0000.000
17A15TRP00.002-0.00925.8790.0050.0050.0000.0000.0000.000
18A16LEU0-0.0020.00225.0000.0020.0020.0000.0000.0000.000
19A17GLN00.0380.01428.7960.0050.0050.0000.0000.0000.000
20A18LEU0-0.054-0.03327.9440.0060.0060.0000.0000.0000.000
21A19ALA0-0.058-0.03332.084-0.001-0.0010.0000.0000.0000.000
22A20GLU-1-0.952-0.95134.460-0.002-0.0020.0000.0000.0000.000
23A21ASN00.009-0.00531.708-0.005-0.0050.0000.0000.0000.000
24A22SER0-0.004-0.00531.231-0.002-0.0020.0000.0000.0000.000
25A23LEU0-0.031-0.02025.3170.0030.0030.0000.0000.0000.000
26A24LEU00.0090.01925.205-0.005-0.0050.0000.0000.0000.000
27A25ALA0-0.001-0.01722.2360.0100.0100.0000.0000.0000.000
28A26LYS10.8750.97217.2790.3510.3510.0000.0000.0000.000
29A27VAL00.015-0.01116.6360.0260.0260.0000.0000.0000.000
30A28PHE00.0030.02210.118-0.047-0.0470.0000.0000.0000.000
31A29ILE00.0120.00513.4570.0620.0620.0000.0000.0000.000
32A30THR00.0400.0249.881-0.002-0.0020.0000.0000.0000.000
33A31LYS10.9360.95510.3230.0090.0090.0000.0000.0000.000
34A32GLN0-0.026-0.0395.6340.1130.1130.0000.0000.0000.000
35A33GLY00.0520.0239.1700.2530.2530.0000.0000.0000.000
36A34TYR0-0.064-0.05711.156-0.140-0.1400.0000.0000.0000.000
37A35ALA00.0460.03410.5510.1430.1430.0000.0000.0000.000
38A36LEU0-0.038-0.02512.534-0.079-0.0790.0000.0000.0000.000
39A37LEU00.003-0.00816.0870.0230.0230.0000.0000.0000.000
40A38VAL00.0040.00718.111-0.013-0.0130.0000.0000.0000.000
41A39SER00.004-0.00921.744-0.003-0.0030.0000.0000.0000.000
42A40ASP-1-0.773-0.89624.700-0.042-0.0420.0000.0000.0000.000
43A41LEU0-0.058-0.03227.5060.0000.0000.0000.0000.0000.000
44A42GLN0-0.064-0.00928.967-0.002-0.0020.0000.0000.0000.000
45A43GLN0-0.024-0.01425.6510.0030.0030.0000.0000.0000.000
46A44VAL0-0.007-0.00220.255-0.009-0.0090.0000.0000.0000.000
47A45TRP00.012-0.00320.4040.0080.0080.0000.0000.0000.000
48A46HIS0-0.066-0.05611.625-0.024-0.0240.0000.0000.0000.000
49A47GLU-1-0.700-0.82914.7720.2590.2590.0000.0000.0000.000
50A48GLN0-0.033-0.0127.3990.3690.3690.0000.0000.0000.000
51A49VAL0-0.048-0.01011.4960.0900.0900.0000.0000.0000.000
52A50ASP-1-0.781-0.9067.9521.1261.1260.0000.0000.0000.000
53A51THR0-0.003-0.0249.765-0.142-0.1420.0000.0000.0000.000
54A52SER00.0130.00411.493-0.145-0.1450.0000.0000.0000.000
55A53VAL00.0230.02212.635-0.102-0.1020.0000.0000.0000.000
56A54VAL0-0.018-0.00214.109-0.078-0.0780.0000.0000.0000.000
57A55SER0-0.036-0.02616.003-0.063-0.0630.0000.0000.0000.000
58A56GLN0-0.056-0.03417.366-0.029-0.0290.0000.0000.0000.000
59A57ARG10.8860.94517.557-0.290-0.2900.0000.0000.0000.000
60A58ALA0-0.0030.00120.081-0.033-0.0330.0000.0000.0000.000
61A59LYS10.9390.95821.971-0.200-0.2000.0000.0000.0000.000
62A60GLU-1-0.942-0.96422.3470.2210.2210.0000.0000.0000.000
63A61LEU0-0.064-0.01623.364-0.018-0.0180.0000.0000.0000.000
64A62ASN0-0.0110.00024.536-0.033-0.0330.0000.0000.0000.000
65A63LYS10.9640.97127.520-0.111-0.1110.0000.0000.0000.000
66A64ARG10.9230.95830.280-0.061-0.0610.0000.0000.0000.000
67A65LEU00.0540.04327.091-0.005-0.0050.0000.0000.0000.000
68A66THR0-0.023-0.02024.3120.0150.0150.0000.0000.0000.000
69A67ALA00.0110.01123.209-0.014-0.0140.0000.0000.0000.000
70A68PRO00.0160.00619.3590.0200.0200.0000.0000.0000.000
71A69PRO00.0680.03014.946-0.024-0.0240.0000.0000.0000.000
72A70ALA00.0450.01715.494-0.021-0.0210.0000.0000.0000.000
73A71ALA0-0.0180.00316.636-0.036-0.0360.0000.0000.0000.000
74A72PHE00.0220.00318.991-0.022-0.0220.0000.0000.0000.000
75A73LEU0-0.032-0.00613.364-0.009-0.0090.0000.0000.0000.000
76A74CYS0-0.014-0.00917.522-0.040-0.0400.0000.0000.0000.000
77A75HIS0-0.010-0.00219.902-0.022-0.0220.0000.0000.0000.000
78A76LEU00.019-0.00218.157-0.013-0.0130.0000.0000.0000.000
79A77ASP-1-0.902-0.93918.783-0.167-0.1670.0000.0000.0000.000
80A78ASN00.004-0.02020.720-0.028-0.0280.0000.0000.0000.000
81A79LEU0-0.054-0.01724.099-0.003-0.0030.0000.0000.0000.000
82A80LEU0-0.019-0.02020.360-0.005-0.0050.0000.0000.0000.000
83A81ARG10.9070.97520.2620.1690.1690.0000.0000.0000.000
84A82PRO0-0.007-0.01724.070-0.010-0.0100.0000.0000.0000.000
85A83LEU00.0090.00227.647-0.001-0.0010.0000.0000.0000.000
86A84LEU0-0.013-0.00323.022-0.003-0.0030.0000.0000.0000.000
87A85LYS10.9040.96426.5760.1110.1110.0000.0000.0000.000
88A86ASP-1-0.861-0.94528.452-0.084-0.0840.0000.0000.0000.000
89A87ALA0-0.0080.00231.7200.0040.0040.0000.0000.0000.000
90A88ALA0-0.035-0.01133.3600.0070.0070.0000.0000.0000.000
91A89HIS0-0.026-0.01632.6020.0030.0030.0000.0000.0000.000
92A90PRO0-0.036-0.01834.4640.0030.0030.0000.0000.0000.000
93A91SER00.0150.01031.0770.0020.0020.0000.0000.0000.000
94A92GLU-1-0.926-0.96433.0500.0040.0040.0000.0000.0000.000
95A93ALA0-0.067-0.01929.4240.0080.0080.0000.0000.0000.000
96A94THR0-0.040-0.03331.326-0.003-0.0030.0000.0000.0000.000
97A95PHE00.0310.01025.1790.0070.0070.0000.0000.0000.000
98A96SER0-0.015-0.01029.163-0.002-0.0020.0000.0000.0000.000
99A97CYS00.005-0.00527.3920.0040.0040.0000.0000.0000.000
100A98ASP-1-0.807-0.88628.2340.0560.0560.0000.0000.0000.000
101A99CYS00.0150.00427.7500.0070.0070.0000.0000.0000.000
102A100VAL0-0.021-0.00627.380-0.001-0.0010.0000.0000.0000.000
103A101ALA0-0.024-0.01727.1180.0100.0100.0000.0000.0000.000
104A102ASP-1-0.879-0.93023.5140.0290.0290.0000.0000.0000.000
105A103ALA0-0.028-0.02822.9560.0050.0050.0000.0000.0000.000
106A104LEU00.0060.00822.962-0.013-0.0130.0000.0000.0000.000
107A105ILE0-0.025-0.02122.9020.0160.0160.0000.0000.0000.000
108A106LEU00.0130.01922.687-0.013-0.0130.0000.0000.0000.000
109A107ARG10.8030.89824.156-0.062-0.0620.0000.0000.0000.000
110A108VAL00.0430.01524.552-0.013-0.0130.0000.0000.0000.000
111A109ARG10.9500.98627.253-0.021-0.0210.0000.0000.0000.000
112A110SER00.0230.00727.584-0.010-0.0100.0000.0000.0000.000
113A111GLU-1-0.953-0.98230.1160.0270.0270.0000.0000.0000.000
114A112LEU00.0440.01124.615-0.004-0.0040.0000.0000.0000.000
115A113SER0-0.048-0.02729.0920.0040.0040.0000.0000.0000.000
116A114GLY00.0420.03731.2910.0020.0020.0000.0000.0000.000
117A115LEU0-0.056-0.02531.7250.0010.0010.0000.0000.0000.000
118A116PRO0-0.039-0.02531.815-0.003-0.0030.0000.0000.0000.000
119A117PHE0-0.0110.00722.2930.0090.0090.0000.0000.0000.000
120A118TYR0-0.025-0.02127.055-0.016-0.0160.0000.0000.0000.000
121A119TRP00.0080.00317.4420.0220.0220.0000.0000.0000.000
122A120ASN00.0230.01222.582-0.029-0.0290.0000.0000.0000.000
123A121PHE00.0070.00818.2590.0250.0250.0000.0000.0000.000
124A122HIS0-0.048-0.03719.138-0.028-0.0280.0000.0000.0000.000
125A123CYS0-0.040-0.00118.3830.0240.0240.0000.0000.0000.000
126A124MET00.0270.02617.907-0.002-0.0020.0000.0000.0000.000
127A125LEU00.0190.00919.155-0.020-0.0200.0000.0000.0000.000
128A126ALA0-0.0290.00317.4980.0130.0130.0000.0000.0000.000
129A127SER00.0380.01314.517-0.020-0.0200.0000.0000.0000.000
130A128PRO00.0800.01317.546-0.029-0.0290.0000.0000.0000.000
131A129SER0-0.031-0.01715.156-0.026-0.0260.0000.0000.0000.000
132A130LEU00.0480.04212.305-0.058-0.0580.0000.0000.0000.000
133A131VAL00.0460.02616.060-0.018-0.0180.0000.0000.0000.000
134A132SER0-0.059-0.03419.233-0.012-0.0120.0000.0000.0000.000
135A133GLN00.0340.00412.4560.0460.0460.0000.0000.0000.000
136A134HIS00.0690.04413.6670.0140.0140.0000.0000.0000.000
137A135LEU00.0060.01318.7240.0200.0200.0000.0000.0000.000
138A136ILE00.0120.00322.3820.0020.0020.0000.0000.0000.000
139A137ARG10.8870.92519.8160.3860.3860.0000.0000.0000.000
140A138PRO00.0360.02220.4740.0130.0130.0000.0000.0000.000
141A139LEU00.0470.01923.3830.0150.0150.0000.0000.0000.000
142A140MET0-0.036-0.00826.2600.0130.0130.0000.0000.0000.000
143A141GLY00.014-0.01026.0150.0100.0100.0000.0000.0000.000
144A142MET0-0.0290.00726.2570.0050.0050.0000.0000.0000.000
145A143SER00.0190.01228.6550.0160.0160.0000.0000.0000.000
146A144LEU0-0.032-0.01129.2410.0110.0110.0000.0000.0000.000
147A145ALA00.0160.01229.3920.0090.0090.0000.0000.0000.000
148A146LEU00.0250.00331.5060.0080.0080.0000.0000.0000.000
149A147GLN0-0.0120.00134.1350.0140.0140.0000.0000.0000.000
150A148CYS0-0.023-0.02333.9270.0070.0070.0000.0000.0000.000
151A149GLN00.0260.01532.4930.0140.0140.0000.0000.0000.000
152A150VAL00.0300.01736.9120.0070.0070.0000.0000.0000.000
153A151ARG10.9030.95839.2420.1140.1140.0000.0000.0000.000
154A152GLU-1-0.914-0.95336.901-0.136-0.1360.0000.0000.0000.000
155A153LEU0-0.017-0.01939.9730.0060.0060.0000.0000.0000.000
156A154ALA00.0010.01242.8330.0050.0050.0000.0000.0000.000
157A155THR0-0.047-0.03343.5980.0050.0050.0000.0000.0000.000
158A156LEU0-0.029-0.02042.3480.0040.0040.0000.0000.0000.000
159A157LEU0-0.014-0.00446.2910.0040.0040.0000.0000.0000.000
160A158HIS10.8480.92048.2690.0800.0800.0000.0000.0000.000
161A159MET00.0040.01448.6130.0030.0030.0000.0000.0000.000
162A160LYS10.9640.97848.4200.0800.0800.0000.0000.0000.000
163A161ASP-1-0.808-0.90452.389-0.062-0.0620.0000.0000.0000.000
164A162LEU0-0.034-0.00753.7580.0020.0020.0000.0000.0000.000
165A163GLU-1-0.914-0.95153.902-0.063-0.0630.0000.0000.0000.000
166A164ILE0-0.048-0.03255.7030.0030.0030.0000.0000.0000.000
167A165GLN0-0.053-0.03158.5420.0010.0010.0000.0000.0000.000
168A166ASP-1-0.874-0.93658.567-0.054-0.0540.0000.0000.0000.000
169A167TYR0-0.057-0.02758.6380.0030.0030.0000.0000.0000.000
170A168GLN0-0.095-0.05862.5910.0020.0020.0000.0000.0000.000
171A169GLU-1-0.928-0.96363.813-0.044-0.0440.0000.0000.0000.000
172A170SER0-0.096-0.03464.8830.0010.0010.0000.0000.0000.000
173A171GLY0-0.018-0.01067.4290.0010.0010.0000.0000.0000.000
174A172ALA0-0.047-0.00665.6540.0010.0010.0000.0000.0000.000
175A173THR0-0.047-0.03066.0090.0010.0010.0000.0000.0000.000
176A174LEU00.0190.00868.6670.0000.0000.0000.0000.0000.000
177A175ILE0-0.007-0.00171.5330.0000.0000.0000.0000.0000.000
178A176ARG10.9700.98463.9180.0410.0410.0000.0000.0000.000
179A177ASP-1-0.808-0.89267.750-0.038-0.0380.0000.0000.0000.000
180A178ARG10.8190.89063.8720.0410.0410.0000.0000.0000.000
181A179LEU0-0.041-0.01861.2820.0000.0000.0000.0000.0000.000
182A180LYS10.9590.98060.2970.0460.0460.0000.0000.0000.000
183A181THR00.0180.00154.6040.0010.0010.0000.0000.0000.000
184A182GLU-1-0.944-0.96857.050-0.049-0.0490.0000.0000.0000.000
185A183PRO0-0.0070.00655.778-0.002-0.0020.0000.0000.0000.000
186A184PHE0-0.016-0.01747.0660.0000.0000.0000.0000.0000.000
187A185GLU-1-0.822-0.90952.473-0.067-0.0670.0000.0000.0000.000
188A186GLU-1-0.855-0.92247.273-0.081-0.0810.0000.0000.0000.000
189A187ASN0-0.036-0.02948.751-0.004-0.0040.0000.0000.0000.000
190A188SER00.0010.00450.6650.0000.0000.0000.0000.0000.000
191A189PHE00.0080.00044.4110.0000.0000.0000.0000.0000.000
192A190LEU0-0.036-0.02843.989-0.001-0.0010.0000.0000.0000.000
193A191GLU-1-0.927-0.96847.587-0.056-0.0560.0000.0000.0000.000
194A192GLN00.0070.00150.1630.0010.0010.0000.0000.0000.000
195A193PHE0-0.0130.00442.2730.0010.0010.0000.0000.0000.000
196A194MET0-0.038-0.02742.2290.0000.0000.0000.0000.0000.000
197A195ILE0-0.0230.01146.9380.0020.0020.0000.0000.0000.000
198A196GLU-1-0.968-0.99150.021-0.054-0.0540.0000.0000.0000.000
199A197LYS10.9090.94345.5940.0680.0680.0000.0000.0000.000
200A198LEU0-0.017-0.00241.037-0.002-0.0020.0000.0000.0000.000
201A199PRO0-0.001-0.00142.591-0.003-0.0030.0000.0000.0000.000
202A200GLU-1-0.934-0.97242.743-0.057-0.0570.0000.0000.0000.000
203A201ALA0-0.033-0.01240.942-0.003-0.0030.0000.0000.0000.000
204A202CYS0-0.084-0.03937.965-0.005-0.0050.0000.0000.0000.000
205A203SER0-0.0240.00037.312-0.002-0.0020.0000.0000.0000.000
206A204ILE00.0200.01232.687-0.003-0.0030.0000.0000.0000.000
207A205GLY00.0110.00034.955-0.001-0.0010.0000.0000.0000.000
208A206ASP-1-0.861-0.94234.104-0.064-0.0640.0000.0000.0000.000
209A207GLY00.0260.00930.993-0.002-0.0020.0000.0000.0000.000
210A208LYS10.8810.94731.2310.0650.0650.0000.0000.0000.000
211A209PRO00.0450.01832.984-0.007-0.0070.0000.0000.0000.000
212A210PHE00.0280.01625.408-0.008-0.0080.0000.0000.0000.000
213A211VAL0-0.012-0.01327.303-0.012-0.0120.0000.0000.0000.000
214A212MET0-0.058-0.02729.515-0.002-0.0020.0000.0000.0000.000
215A213ASN00.0010.01032.4130.0000.0000.0000.0000.0000.000
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