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: 52K3Z

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 OptAll
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 -2586499.761001
FMO2-HF: Nuclear repulsion 2492630.631423
FMO2-HF: Total energy -93869.129578
FMO2-MP2: Total energy -94135.607969


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.
-50.13-51.45929.19-16.329-11.53-0.099
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 : -0.015 / q_NPA : -0.026
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].
3A1MET0-0.028-0.0072.879-6.645-1.8090.157-2.657-2.3360.017
4A2GLU-1-0.825-0.8881.633-41.585-50.22328.777-12.511-7.627-0.107
5A3GLU-1-0.940-0.9823.095-3.274-0.9070.257-1.154-1.470-0.009
6A4LEU0-0.081-0.0325.3220.7850.891-0.001-0.007-0.0970.000
7A5GLU-1-0.761-0.8747.796-0.542-0.5420.0000.0000.0000.000
8A6GLN00.0070.0046.6360.6290.6290.0000.0000.0000.000
9A7GLY00.0130.0029.2620.3000.3000.0000.0000.0000.000
10A8LEU0-0.070-0.03611.3100.1900.1900.0000.0000.0000.000
11A9LEU0-0.041-0.02312.5590.1400.1400.0000.0000.0000.000
12A10MET0-0.004-0.00711.6520.1330.1330.0000.0000.0000.000
13A11GLN0-0.0330.01015.5910.1410.1410.0000.0000.0000.000
14A12PRO00.016-0.00117.595-0.013-0.0130.0000.0000.0000.000
15A13TRP0-0.054-0.03020.945-0.001-0.0010.0000.0000.0000.000
16A14ALA00.0300.01623.2240.0170.0170.0000.0000.0000.000
17A15TRP0-0.030-0.04425.319-0.001-0.0010.0000.0000.0000.000
18A16LEU0-0.014-0.00525.4280.0060.0060.0000.0000.0000.000
19A17GLN00.0040.00028.963-0.004-0.0040.0000.0000.0000.000
20A18LEU0-0.039-0.02928.0620.0050.0050.0000.0000.0000.000
21A19ALA0-0.048-0.03632.1840.0000.0000.0000.0000.0000.000
22A20GLU-1-0.944-0.94934.592-0.038-0.0380.0000.0000.0000.000
23A21ASN0-0.024-0.01932.2950.0010.0010.0000.0000.0000.000
24A22SER0-0.0170.00131.8480.0030.0030.0000.0000.0000.000
25A23LEU00.003-0.00225.8910.0010.0010.0000.0000.0000.000
26A24LEU00.0060.02125.573-0.001-0.0010.0000.0000.0000.000
27A25ALA0-0.007-0.01522.394-0.001-0.0010.0000.0000.0000.000
28A26LYS10.8340.93517.1040.5180.5180.0000.0000.0000.000
29A27VAL00.0310.00416.861-0.004-0.0040.0000.0000.0000.000
30A28PHE00.0100.0269.9560.0020.0020.0000.0000.0000.000
31A29ILE00.0280.01113.4580.0350.0350.0000.0000.0000.000
32A30THR00.0370.0259.2340.0650.0650.0000.0000.0000.000
33A31LYS10.9030.9279.266-0.354-0.3540.0000.0000.0000.000
34A32GLN00.0310.0216.161-0.071-0.0710.0000.0000.0000.000
35A33GLY00.0220.0059.3000.2600.2600.0000.0000.0000.000
36A34TYR0-0.043-0.05411.341-0.112-0.1120.0000.0000.0000.000
37A35ALA00.0300.02110.5330.0890.0890.0000.0000.0000.000
38A36LEU0-0.023-0.00812.576-0.018-0.0180.0000.0000.0000.000
39A37LEU00.0040.00016.076-0.009-0.0090.0000.0000.0000.000
40A38VAL00.0140.00018.2250.0150.0150.0000.0000.0000.000
41A39SER0-0.004-0.02721.998-0.009-0.0090.0000.0000.0000.000
42A40ASP-1-0.755-0.87025.076-0.122-0.1220.0000.0000.0000.000
43A41LEU0-0.036-0.01427.9530.0070.0070.0000.0000.0000.000
44A42GLN0-0.090-0.04329.4280.0040.0040.0000.0000.0000.000
45A43GLN0-0.035-0.02025.8400.0020.0020.0000.0000.0000.000
46A44VAL00.0010.00820.467-0.008-0.0080.0000.0000.0000.000
47A45TRP00.0100.01420.495-0.005-0.0050.0000.0000.0000.000
48A46HIS0-0.051-0.04311.5900.0510.0510.0000.0000.0000.000
49A47GLU-1-0.680-0.81014.8500.1270.1270.0000.0000.0000.000
50A48GLN0-0.038-0.0327.6510.2690.2690.0000.0000.0000.000
51A49VAL0-0.027-0.00711.1560.1080.1080.0000.0000.0000.000
52A50ASP-1-0.680-0.8308.6990.9810.9810.0000.0000.0000.000
53A51THR00.0090.00010.356-0.156-0.1560.0000.0000.0000.000
54A52SER0-0.073-0.04811.382-0.146-0.1460.0000.0000.0000.000
55A53VAL00.0200.00313.290-0.107-0.1070.0000.0000.0000.000
56A54VAL0-0.0280.00014.449-0.082-0.0820.0000.0000.0000.000
57A55SER0-0.030-0.04116.043-0.062-0.0620.0000.0000.0000.000
58A56GLN0-0.090-0.04717.778-0.027-0.0270.0000.0000.0000.000
59A57ARG10.8540.90517.396-0.165-0.1650.0000.0000.0000.000
60A58ALA00.0070.00920.297-0.033-0.0330.0000.0000.0000.000
61A59LYS10.8720.92822.169-0.179-0.1790.0000.0000.0000.000
62A60GLU-1-0.895-0.92922.8360.1480.1480.0000.0000.0000.000
63A61LEU0-0.035-0.00123.429-0.018-0.0180.0000.0000.0000.000
64A62ASN0-0.023-0.00324.617-0.025-0.0250.0000.0000.0000.000
65A63LYS10.8780.92427.528-0.096-0.0960.0000.0000.0000.000
66A64ARG10.9440.96930.221-0.050-0.0500.0000.0000.0000.000
67A65LEU00.0590.04427.251-0.003-0.0030.0000.0000.0000.000
68A66THR0-0.021-0.02824.5380.0120.0120.0000.0000.0000.000
69A67ALA00.0320.02622.800-0.013-0.0130.0000.0000.0000.000
70A68PRO00.0320.01218.7280.0190.0190.0000.0000.0000.000
71A69PRO00.0490.03115.036-0.034-0.0340.0000.0000.0000.000
72A70ALA00.0410.00915.080-0.031-0.0310.0000.0000.0000.000
73A71ALA0-0.0160.00216.373-0.044-0.0440.0000.0000.0000.000
74A72PHE00.0120.00019.165-0.028-0.0280.0000.0000.0000.000
75A73LEU0-0.0070.01413.444-0.020-0.0200.0000.0000.0000.000
76A74CYS0-0.0090.00017.620-0.042-0.0420.0000.0000.0000.000
77A75HIS00.0100.00419.657-0.024-0.0240.0000.0000.0000.000
78A76LEU00.009-0.01018.498-0.015-0.0150.0000.0000.0000.000
79A77ASP-1-0.855-0.90318.622-0.183-0.1830.0000.0000.0000.000
80A78ASN0-0.039-0.03520.533-0.019-0.0190.0000.0000.0000.000
81A79LEU0-0.038-0.01623.968-0.002-0.0020.0000.0000.0000.000
82A80LEU0-0.037-0.01620.694-0.004-0.0040.0000.0000.0000.000
83A81ARG10.8220.88618.6010.2350.2350.0000.0000.0000.000
84A82PRO0-0.016-0.01623.333-0.008-0.0080.0000.0000.0000.000
85A83LEU0-0.012-0.00627.101-0.002-0.0020.0000.0000.0000.000
86A84LEU0-0.021-0.00921.824-0.005-0.0050.0000.0000.0000.000
87A85LYS10.7870.89925.8910.0990.0990.0000.0000.0000.000
88A86ASP-1-0.790-0.88828.121-0.091-0.0910.0000.0000.0000.000
89A87ALA00.0060.00531.2950.0040.0040.0000.0000.0000.000
90A88ALA0-0.018-0.00833.3660.0070.0070.0000.0000.0000.000
91A89HIS0-0.041-0.02132.0400.0040.0040.0000.0000.0000.000
92A90PRO0-0.020-0.00634.5800.0000.0000.0000.0000.0000.000
93A91SER00.0250.00731.892-0.001-0.0010.0000.0000.0000.000
94A92GLU-1-0.917-0.95732.549-0.015-0.0150.0000.0000.0000.000
95A93ALA0-0.083-0.04029.0320.0080.0080.0000.0000.0000.000
96A94THR0-0.029-0.01330.846-0.005-0.0050.0000.0000.0000.000
97A95PHE00.0510.01325.6260.0060.0060.0000.0000.0000.000
98A96SER0-0.005-0.00529.1070.0010.0010.0000.0000.0000.000
99A97CYS00.0330.00527.454-0.004-0.0040.0000.0000.0000.000
100A98ASP-1-0.834-0.85628.406-0.007-0.0070.0000.0000.0000.000
101A99CYS00.0220.00527.723-0.003-0.0030.0000.0000.0000.000
102A100VAL0-0.023-0.01027.4530.0070.0070.0000.0000.0000.000
103A101ALA0-0.005-0.00527.1420.0010.0010.0000.0000.0000.000
104A102ASP-1-0.885-0.93723.829-0.090-0.0900.0000.0000.0000.000
105A103ALA0-0.005-0.01723.112-0.013-0.0130.0000.0000.0000.000
106A104LEU0-0.006-0.00323.1440.0000.0000.0000.0000.0000.000
107A105ILE0-0.025-0.02322.9320.0050.0050.0000.0000.0000.000
108A106LEU00.0300.02722.4340.0010.0010.0000.0000.0000.000
109A107ARG10.7730.84724.0760.0070.0070.0000.0000.0000.000
110A108VAL00.0150.00324.357-0.010-0.0100.0000.0000.0000.000
111A109ARG10.8430.92927.4140.0040.0040.0000.0000.0000.000
112A110SER00.0190.00427.847-0.008-0.0080.0000.0000.0000.000
113A111GLU-1-0.865-0.93730.0840.0200.0200.0000.0000.0000.000
114A112LEU00.0050.01124.541-0.003-0.0030.0000.0000.0000.000
115A113SER0-0.022-0.02429.1990.0040.0040.0000.0000.0000.000
116A114GLY00.0390.03531.3020.0020.0020.0000.0000.0000.000
117A115LEU0-0.057-0.02531.6720.0000.0000.0000.0000.0000.000
118A116PRO0-0.023-0.00431.611-0.001-0.0010.0000.0000.0000.000
119A117PHE0-0.020-0.02122.5630.0110.0110.0000.0000.0000.000
120A118TYR00.012-0.00527.299-0.013-0.0130.0000.0000.0000.000
121A119TRP0-0.004-0.00417.7420.0330.0330.0000.0000.0000.000
122A120ASN00.0310.01222.465-0.026-0.0260.0000.0000.0000.000
123A121PHE00.0270.02218.1520.0260.0260.0000.0000.0000.000
124A122HIS0-0.038-0.02919.189-0.021-0.0210.0000.0000.0000.000
125A123CYS0-0.0360.00018.6180.0040.0040.0000.0000.0000.000
126A124MET00.0080.01918.3180.0240.0240.0000.0000.0000.000
127A125LEU00.0000.00519.397-0.033-0.0330.0000.0000.0000.000
128A126ALA0-0.022-0.00417.618-0.014-0.0140.0000.0000.0000.000
129A127SER00.0320.01114.6690.0110.0110.0000.0000.0000.000
130A128PRO00.0570.00517.750-0.026-0.0260.0000.0000.0000.000
131A129SER0-0.014-0.00815.2260.0350.0350.0000.0000.0000.000
132A130LEU00.0310.03512.702-0.033-0.0330.0000.0000.0000.000
133A131VAL00.0490.02316.4390.0060.0060.0000.0000.0000.000
134A132SER0-0.025-0.02219.4280.0160.0160.0000.0000.0000.000
135A133GLN0-0.037-0.02913.567-0.072-0.0720.0000.0000.0000.000
136A134HIS00.0940.05113.7180.0730.0730.0000.0000.0000.000
137A135LEU00.0060.02818.9300.0400.0400.0000.0000.0000.000
138A136ILE00.0020.00822.7250.0130.0130.0000.0000.0000.000
139A137ARG10.8630.91419.6920.4880.4880.0000.0000.0000.000
140A138PRO00.0330.01620.3170.0260.0260.0000.0000.0000.000
141A139LEU00.0550.02623.0190.0240.0240.0000.0000.0000.000
142A140MET0-0.0260.00826.2660.0210.0210.0000.0000.0000.000
143A141GLY00.0250.00825.4250.0170.0170.0000.0000.0000.000
144A142MET0-0.0240.00125.6610.0100.0100.0000.0000.0000.000
145A143SER0-0.006-0.01328.0710.0220.0220.0000.0000.0000.000
146A144LEU0-0.035-0.01528.5780.0160.0160.0000.0000.0000.000
147A145ALA00.0420.02328.7620.0130.0130.0000.0000.0000.000
148A146LEU00.0050.01030.8810.0120.0120.0000.0000.0000.000
149A147GLN0-0.004-0.00633.6600.0170.0170.0000.0000.0000.000
150A148CYS0-0.045-0.03033.2320.0080.0080.0000.0000.0000.000
151A149GLN00.0450.01432.1390.0140.0140.0000.0000.0000.000
152A150VAL00.0020.01036.6350.0090.0090.0000.0000.0000.000
153A151ARG10.8340.91338.9640.1170.1170.0000.0000.0000.000
154A152GLU-1-0.922-0.94936.060-0.134-0.1340.0000.0000.0000.000
155A153LEU0-0.003-0.00839.7000.0070.0070.0000.0000.0000.000
156A154ALA00.0060.00542.3870.0060.0060.0000.0000.0000.000
157A155THR0-0.037-0.02543.2400.0060.0060.0000.0000.0000.000
158A156LEU0-0.019-0.02141.5940.0050.0050.0000.0000.0000.000
159A157LEU0-0.025-0.00645.7520.0050.0050.0000.0000.0000.000
160A158HIS10.7770.86648.2210.0840.0840.0000.0000.0000.000
161A159MET0-0.021-0.00347.8770.0030.0030.0000.0000.0000.000
162A160LYS10.8220.89049.0750.0730.0730.0000.0000.0000.000
163A161ASP-1-0.770-0.87252.000-0.068-0.0680.0000.0000.0000.000
164A162LEU00.0030.00853.6530.0030.0030.0000.0000.0000.000
165A163GLU-1-0.823-0.89053.147-0.062-0.0620.0000.0000.0000.000
166A164ILE0-0.016-0.02255.0580.0030.0030.0000.0000.0000.000
167A165GLN0-0.092-0.03957.8960.0010.0010.0000.0000.0000.000
168A166ASP-1-0.850-0.92358.194-0.052-0.0520.0000.0000.0000.000
169A167TYR0-0.054-0.01157.6770.0030.0030.0000.0000.0000.000
170A168GLN0-0.101-0.05561.2180.0030.0030.0000.0000.0000.000
171A169GLU-1-0.860-0.91962.954-0.046-0.0460.0000.0000.0000.000
172A170SER0-0.123-0.07963.9990.0020.0020.0000.0000.0000.000
173A171GLY0-0.007-0.00366.5700.0010.0010.0000.0000.0000.000
174A172ALA0-0.048-0.02064.8980.0010.0010.0000.0000.0000.000
175A173THR0-0.056-0.04165.9180.0010.0010.0000.0000.0000.000
176A174LEU00.0330.01768.4080.0000.0000.0000.0000.0000.000
177A175ILE0-0.027-0.00870.2540.0000.0000.0000.0000.0000.000
178A176ARG10.8380.88862.1630.0480.0480.0000.0000.0000.000
179A177ASP-1-0.785-0.86766.657-0.042-0.0420.0000.0000.0000.000
180A178ARG10.8280.90363.4340.0430.0430.0000.0000.0000.000
181A179LEU0-0.0080.00060.7250.0000.0000.0000.0000.0000.000
182A180LYS10.8820.91959.9740.0460.0460.0000.0000.0000.000
183A181THR00.0130.00954.2040.0000.0000.0000.0000.0000.000
184A182GLU-1-0.805-0.86956.979-0.051-0.0510.0000.0000.0000.000
185A183PRO0-0.008-0.00955.330-0.002-0.0020.0000.0000.0000.000
186A184PHE00.0030.00346.533-0.001-0.0010.0000.0000.0000.000
187A185GLU-1-0.750-0.85051.394-0.076-0.0760.0000.0000.0000.000
188A186GLU-1-0.788-0.86446.358-0.091-0.0910.0000.0000.0000.000
189A187ASN0-0.095-0.06547.871-0.005-0.0050.0000.0000.0000.000
190A188SER00.000-0.02549.763-0.001-0.0010.0000.0000.0000.000
191A189PHE00.0080.00944.098-0.001-0.0010.0000.0000.0000.000
192A190LEU0-0.011-0.00843.183-0.002-0.0020.0000.0000.0000.000
193A191GLU-1-0.885-0.92946.940-0.071-0.0710.0000.0000.0000.000
194A192GLN0-0.017-0.03149.6070.0010.0010.0000.0000.0000.000
195A193PHE0-0.010-0.00241.5450.0000.0000.0000.0000.0000.000
196A194MET0-0.035-0.03242.562-0.002-0.0020.0000.0000.0000.000
197A195ILE0-0.032-0.00446.7980.0010.0010.0000.0000.0000.000
198A196GLU-1-0.911-0.96049.518-0.068-0.0680.0000.0000.0000.000
199A197LYS10.8170.91145.0670.0760.0760.0000.0000.0000.000
200A198LEU00.0090.01041.033-0.003-0.0030.0000.0000.0000.000
201A199PRO0-0.002-0.00442.528-0.004-0.0040.0000.0000.0000.000
202A200GLU-1-0.946-0.96243.262-0.080-0.0800.0000.0000.0000.000
203A201ALA0-0.016-0.01540.546-0.004-0.0040.0000.0000.0000.000
204A202CYS0-0.097-0.04237.927-0.007-0.0070.0000.0000.0000.000
205A203SER0-0.010-0.00537.580-0.005-0.0050.0000.0000.0000.000
206A204ILE00.0140.00232.637-0.003-0.0030.0000.0000.0000.000
207A205GLY00.0090.00934.759-0.002-0.0020.0000.0000.0000.000
208A206ASP-1-0.794-0.89834.292-0.110-0.1100.0000.0000.0000.000
209A207GLY00.0290.01630.965-0.006-0.0060.0000.0000.0000.000
210A208LYS10.8710.93331.0660.0960.0960.0000.0000.0000.000
211A209PRO00.0270.00832.450-0.005-0.0050.0000.0000.0000.000
212A210PHE00.0160.01325.052-0.006-0.0060.0000.0000.0000.000
213A211VAL0-0.026-0.01027.096-0.012-0.0120.0000.0000.0000.000
214A212MET0-0.051-0.01929.0050.0020.0020.0000.0000.0000.000
215A213ASN00.0070.01131.8550.0050.0050.0000.0000.0000.000
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