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: 94JK2

Calculation Name: 2B9U-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2B9U

Chain ID: A

ChEMBL ID:

UniProt ID: Q96Z62

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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1973511.157635
FMO2-HF: Nuclear repulsion 1901901.595598
FMO2-HF: Total energy -71609.562037
FMO2-MP2: Total energy -71818.798943


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.
-1.9-0.17710.574-5.084-7.2130.013
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 : 0.040 / q_NPA : 0.009
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].
3A3PHE0-0.045-0.0242.675-2.044-0.0490.318-0.981-1.3320.001
4A4GLU-1-0.954-0.9622.621-4.882-2.4240.825-1.580-1.703-0.018
5A5PHE00.001-0.0155.1180.2060.235-0.001-0.004-0.0240.000
6A6GLU-1-0.840-0.9158.301-0.450-0.4500.0000.0000.0000.000
7A7ASN0-0.043-0.02111.6010.0260.0260.0000.0000.0000.000
8A8LEU00.0280.01114.852-0.006-0.0060.0000.0000.0000.000
9A9GLY00.0110.01717.7100.0100.0100.0000.0000.0000.000
10A10MET0-0.043-0.02320.3600.0030.0030.0000.0000.0000.000
11A11GLY00.0190.00618.8290.0090.0090.0000.0000.0000.000
12A12ILE0-0.0040.01617.8250.0080.0080.0000.0000.0000.000
13A13ILE0-0.040-0.01811.663-0.005-0.0050.0000.0000.0000.000
14A14LEU00.0240.02011.8120.0150.0150.0000.0000.0000.000
15A15ILE0-0.021-0.0188.074-0.030-0.0300.0000.0000.0000.000
16A16LYS10.8860.9417.5500.7160.7160.0000.0000.0000.000
17A17PRO00.0310.0246.453-0.416-0.4160.0000.0000.0000.000
18A18LYS10.8980.9531.7694.0091.2509.432-2.519-4.1540.030
19A19VAL00.0090.0097.7200.2070.2070.0000.0000.0000.000
20A20PHE0-0.040-0.0256.423-0.053-0.0530.0000.0000.0000.000
21A21PRO00.0210.01211.3950.0730.0730.0000.0000.0000.000
22A22ASP-1-0.795-0.90814.395-0.183-0.1830.0000.0000.0000.000
23A23LYS10.9550.96017.1120.1030.1030.0000.0000.0000.000
24A24ARG10.7950.89817.3760.1540.1540.0000.0000.0000.000
25A25GLY00.0290.03319.6570.0150.0150.0000.0000.0000.000
26A26PHE0-0.022-0.01114.968-0.020-0.0200.0000.0000.0000.000
27A27PHE0-0.0150.00112.2410.0370.0370.0000.0000.0000.000
28A28LEU00.0380.01211.262-0.089-0.0890.0000.0000.0000.000
29A29GLU-1-0.891-0.9408.7030.0730.0730.0000.0000.0000.000
30A30VAL00.0140.01110.022-0.094-0.0940.0000.0000.0000.000
31A31PHE00.043-0.00211.1570.0020.0020.0000.0000.0000.000
32A32LYS10.8750.9517.875-0.553-0.5530.0000.0000.0000.000
33A33SER00.0200.01810.9550.1090.1090.0000.0000.0000.000
34A34GLU-1-0.903-0.9289.3650.7500.7500.0000.0000.0000.000
35A35ASP-1-0.854-0.9496.0192.6162.6160.0000.0000.0000.000
36A36PHE00.019-0.0088.260-0.140-0.1400.0000.0000.0000.000
37A37THR00.022-0.00711.028-0.100-0.1000.0000.0000.0000.000
38A38LYS10.9170.9668.097-1.115-1.1150.0000.0000.0000.000
39A39MET0-0.083-0.0247.051-0.117-0.1170.0000.0000.0000.000
40A40ARG10.8830.93311.565-0.216-0.2160.0000.0000.0000.000
41A41ILE0-0.0180.01012.261-0.043-0.0430.0000.0000.0000.000
42A42PRO0-0.0160.00015.5640.0380.0380.0000.0000.0000.000
43A43ASN00.015-0.01017.5770.0210.0210.0000.0000.0000.000
44A44VAL0-0.018-0.01017.510-0.016-0.0160.0000.0000.0000.000
45A45ILE0-0.059-0.03220.2540.0060.0060.0000.0000.0000.000
46A46GLN00.0420.02923.5170.0000.0000.0000.0000.0000.000
47A47THR0-0.015-0.01121.803-0.001-0.0010.0000.0000.0000.000
48A48ASN00.0040.02223.8500.0040.0040.0000.0000.0000.000
49A49MET00.0250.00724.292-0.008-0.0080.0000.0000.0000.000
50A50SER0-0.0540.00226.3330.0070.0070.0000.0000.0000.000
51A51PHE00.0310.01227.220-0.006-0.0060.0000.0000.0000.000
52A52SER0-0.036-0.01028.8630.0100.0100.0000.0000.0000.000
53A53ARG11.0041.01030.4860.0470.0470.0000.0000.0000.000
54A54LYS11.0050.99031.7330.0840.0840.0000.0000.0000.000
55A55GLY00.0260.01532.1200.0050.0050.0000.0000.0000.000
56A56VAL0-0.052-0.01231.7720.0040.0040.0000.0000.0000.000
57A57VAL00.0040.00631.540-0.006-0.0060.0000.0000.0000.000
58A58ARG10.8650.93129.3720.0610.0610.0000.0000.0000.000
59A59GLY00.0040.01929.841-0.005-0.0050.0000.0000.0000.000
60A60LEU0-0.042-0.00829.3620.0010.0010.0000.0000.0000.000
61A61HIS0-0.031-0.05729.5620.0040.0040.0000.0000.0000.000
62A62TYR0-0.034-0.03928.696-0.003-0.0030.0000.0000.0000.000
63A63GLN0-0.004-0.00529.558-0.003-0.0030.0000.0000.0000.000
64A64ARG10.8900.95430.686-0.001-0.0010.0000.0000.0000.000
65A65THR00.0630.03431.3900.0020.0020.0000.0000.0000.000
66A66PRO0-0.102-0.05232.765-0.003-0.0030.0000.0000.0000.000
67A67LYS10.9330.95331.225-0.017-0.0170.0000.0000.0000.000
68A68GLU-1-0.817-0.90127.1090.0220.0220.0000.0000.0000.000
69A69GLN0-0.070-0.06125.273-0.001-0.0010.0000.0000.0000.000
70A70GLY00.0130.02521.357-0.005-0.0050.0000.0000.0000.000
71A71LYS10.9080.94820.6960.0300.0300.0000.0000.0000.000
72A72ILE00.0080.01314.566-0.005-0.0050.0000.0000.0000.000
73A73ILE0-0.0110.01417.6060.0060.0060.0000.0000.0000.000
74A74PHE00.0440.00014.940-0.015-0.0150.0000.0000.0000.000
75A75VAL00.0140.00917.8380.0260.0260.0000.0000.0000.000
76A76PRO0-0.0140.00819.161-0.018-0.0180.0000.0000.0000.000
77A77LYS10.9570.96920.1010.1110.1110.0000.0000.0000.000
78A78GLY00.0370.02823.3550.0110.0110.0000.0000.0000.000
79A79ARG10.8750.90922.7620.1300.1300.0000.0000.0000.000
80A80ILE0-0.037-0.00421.8580.0180.0180.0000.0000.0000.000
81A81LEU0-0.012-0.00123.076-0.013-0.0130.0000.0000.0000.000
82A82ASP-1-0.755-0.89921.268-0.090-0.0900.0000.0000.0000.000
83A83VAL0-0.011-0.01923.153-0.005-0.0050.0000.0000.0000.000
84A84ALA00.0130.01022.6170.0070.0070.0000.0000.0000.000
85A85VAL00.007-0.00724.594-0.003-0.0030.0000.0000.0000.000
86A86ASP-1-0.711-0.78727.024-0.014-0.0140.0000.0000.0000.000
87A87VAL00.0220.01028.1390.0000.0000.0000.0000.0000.000
88A88ARG10.8810.92024.8390.0130.0130.0000.0000.0000.000
89A89LYS11.0020.97931.4960.0070.0070.0000.0000.0000.000
90A90SER0-0.049-0.01833.213-0.001-0.0010.0000.0000.0000.000
91A91SER0-0.046-0.03828.3710.0030.0030.0000.0000.0000.000
92A92PRO0-0.023-0.00828.609-0.002-0.0020.0000.0000.0000.000
93A93THR0-0.092-0.08926.530-0.003-0.0030.0000.0000.0000.000
94A94PHE00.0280.02529.493-0.004-0.0040.0000.0000.0000.000
95A95GLY00.0500.03131.316-0.001-0.0010.0000.0000.0000.000
96A96LYS10.9110.99027.8910.0340.0340.0000.0000.0000.000
97A97TYR00.014-0.00526.2310.0000.0000.0000.0000.0000.000
98A98VAL0-0.0020.01019.788-0.003-0.0030.0000.0000.0000.000
99A99LYS10.9290.96622.9490.0890.0890.0000.0000.0000.000
100A100ALA00.0260.00518.373-0.011-0.0110.0000.0000.0000.000
101A101GLU-1-0.835-0.88720.383-0.158-0.1580.0000.0000.0000.000
102A102LEU0-0.043-0.00616.307-0.027-0.0270.0000.0000.0000.000
103A103ASN00.019-0.00818.2100.0060.0060.0000.0000.0000.000
104A104GLU-1-0.820-0.89818.055-0.192-0.1920.0000.0000.0000.000
105A105GLU-1-0.998-0.98617.286-0.283-0.2830.0000.0000.0000.000
106A106ASN0-0.003-0.01414.578-0.031-0.0310.0000.0000.0000.000
107A107HIS0-0.0240.00113.425-0.071-0.0710.0000.0000.0000.000
108A108TYR0-0.009-0.01611.062-0.067-0.0670.0000.0000.0000.000
109A109MET0-0.055-0.02010.4820.0870.0870.0000.0000.0000.000
110A110LEU00.0220.01913.755-0.024-0.0240.0000.0000.0000.000
111A111TRP0-0.005-0.00714.6240.0310.0310.0000.0000.0000.000
112A112ILE0-0.022-0.01916.307-0.005-0.0050.0000.0000.0000.000
113A113PRO0-0.0050.01219.0230.0110.0110.0000.0000.0000.000
114A114PRO00.0440.00421.231-0.007-0.0070.0000.0000.0000.000
115A115GLY0-0.017-0.01024.9570.0010.0010.0000.0000.0000.000
116A116PHE00.009-0.00823.400-0.005-0.0050.0000.0000.0000.000
117A117ALA0-0.048-0.01326.6180.0030.0030.0000.0000.0000.000
118A118HIS0-0.095-0.06623.5040.0060.0060.0000.0000.0000.000
119A119GLY00.0590.00726.2480.0060.0060.0000.0000.0000.000
120A120PHE0-0.040-0.00425.135-0.008-0.0080.0000.0000.0000.000
121A121GLN00.0040.00527.1460.0040.0040.0000.0000.0000.000
122A122ALA0-0.025-0.00927.517-0.010-0.0100.0000.0000.0000.000
123A123LEU0-0.006-0.02025.2860.0080.0080.0000.0000.0000.000
124A124GLU-1-0.913-0.96526.803-0.133-0.1330.0000.0000.0000.000
125A125ASP-1-0.872-0.94228.922-0.075-0.0750.0000.0000.0000.000
126A126SER0-0.029-0.02925.271-0.012-0.0120.0000.0000.0000.000
127A127ILE0-0.077-0.03623.8860.0130.0130.0000.0000.0000.000
128A128VAL00.0260.02422.299-0.013-0.0130.0000.0000.0000.000
129A129ILE0-0.008-0.01419.9160.0140.0140.0000.0000.0000.000
130A130TYR0-0.013-0.03320.642-0.008-0.0080.0000.0000.0000.000
131A131PHE00.018-0.00216.5470.0120.0120.0000.0000.0000.000
132A132ILE0-0.005-0.00220.098-0.001-0.0010.0000.0000.0000.000
133A133THR00.069-0.00318.6780.0080.0080.0000.0000.0000.000
134A134HIS0-0.0110.02221.182-0.010-0.0100.0000.0000.0000.000
135A135ASN0-0.026-0.01524.8610.0050.0050.0000.0000.0000.000
136A136GLU-1-0.863-0.92227.5180.0180.0180.0000.0000.0000.000
137A137TYR0-0.076-0.03129.300-0.001-0.0010.0000.0000.0000.000
138A138SER0-0.015-0.02831.4910.0030.0030.0000.0000.0000.000
139A139PRO00.0630.02634.467-0.001-0.0010.0000.0000.0000.000
140A140PRO0-0.033-0.00437.075-0.001-0.0010.0000.0000.0000.000
141A141HIS0-0.014-0.00934.510-0.001-0.0010.0000.0000.0000.000
142A142GLU-1-0.862-0.91533.347-0.014-0.0140.0000.0000.0000.000
143A143ARG10.8750.94533.9980.0080.0080.0000.0000.0000.000
144A144CYS0-0.0660.00533.6210.0010.0010.0000.0000.0000.000
145A145ILE00.0350.02531.9260.0020.0020.0000.0000.0000.000
146A146SER0-0.0100.01434.531-0.004-0.0040.0000.0000.0000.000
147A147TYR00.1170.03833.493-0.002-0.0020.0000.0000.0000.000
148A148SER0-0.046-0.03434.266-0.003-0.0030.0000.0000.0000.000
149A149TYR0-0.086-0.08031.5950.0010.0010.0000.0000.0000.000
150A150ILE0-0.046-0.01729.474-0.002-0.0020.0000.0000.0000.000
151A151ASP-1-0.947-0.95732.589-0.061-0.0610.0000.0000.0000.000
152A152TRP0-0.080-0.06127.909-0.008-0.0080.0000.0000.0000.000
153A153PRO00.0180.01129.3810.0020.0020.0000.0000.0000.000
154A154ILE0-0.079-0.02631.4460.0020.0020.0000.0000.0000.000
155A155LYS10.9950.99734.5640.0590.0590.0000.0000.0000.000
156A156GLU-1-0.920-0.96938.053-0.057-0.0570.0000.0000.0000.000
157A157VAL0-0.014-0.00335.602-0.002-0.0020.0000.0000.0000.000
158A158ILE0-0.054-0.01936.1620.0040.0040.0000.0000.0000.000
159A159ILE00.0350.00835.816-0.003-0.0030.0000.0000.0000.000
160A160SER0-0.0140.00336.8680.0030.0030.0000.0000.0000.000
161A161ASP-1-0.811-0.92238.903-0.027-0.0270.0000.0000.0000.000
162A162LYS10.9100.93836.1150.0240.0240.0000.0000.0000.000
163A163ASP-1-0.794-0.90134.396-0.036-0.0360.0000.0000.0000.000
164A164LEU0-0.050-0.02637.595-0.001-0.0010.0000.0000.0000.000
165A165GLN0-0.012-0.00240.6390.0010.0010.0000.0000.0000.000
166A167PRO00.0170.02338.864-0.001-0.0010.0000.0000.0000.000
167A168SER00.024-0.00338.464-0.001-0.0010.0000.0000.0000.000
168A169LEU00.0710.02334.1700.0020.0020.0000.0000.0000.000
169A170GLU-1-0.947-0.98337.325-0.023-0.0230.0000.0000.0000.000
170A171LYS10.8600.93840.3590.0190.0190.0000.0000.0000.000
171A172ALA0-0.0090.01537.4170.0020.0020.0000.0000.0000.000
172A173GLU-1-0.928-0.94838.941-0.005-0.0050.0000.0000.0000.000
173A174VAL0-0.085-0.03834.237-0.001-0.0010.0000.0000.0000.000
174A175PHE00.0130.00929.5490.0030.0030.0000.0000.0000.000
175A176ASP-1-0.928-0.94432.1510.0030.0030.0000.0000.0000.000