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: R5MY8

Calculation Name: 2AJ2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2AJ2

Chain ID: A

ChEMBL ID:

UniProt ID: Q9KUP8

Base Structure: X-ray

Registration Date: 2023-03-13

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 187
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1971653.830763
FMO2-HF: Nuclear repulsion 1897663.348891
FMO2-HF: Total energy -73990.481872
FMO2-MP2: Total energy -74203.276041


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:6:SER)


Summations of interaction energy for fragment #1(A:6: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.
-4.885-0.434-0.035-2.415-2.001-0.003
Interaction energy analysis for fragmet #1(A:6:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.097 / q_NPA : -0.065
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].
3A8ILE0-0.031-0.0033.584-1.5622.889-0.035-2.415-2.001-0.003
4A9GLU-1-0.904-0.9545.958-2.430-2.4300.0000.0000.0000.000
5A10VAL0-0.053-0.0198.9160.5310.5310.0000.0000.0000.000
6A11GLY00.0200.00211.029-0.018-0.0180.0000.0000.0000.000
7A12HIS0-0.045-0.04414.0790.0880.0880.0000.0000.0000.000
8A13SER0-0.0200.00217.8140.0260.0260.0000.0000.0000.000
9A14MET00.0350.03019.8690.0150.0150.0000.0000.0000.000
10A15ASN0-0.016-0.00323.1400.0530.0530.0000.0000.0000.000
11A16LEU00.0410.00325.5190.0140.0140.0000.0000.0000.000
12A17THR00.0110.00928.8820.0310.0310.0000.0000.0000.000
13A18ASN0-0.0260.00130.6860.0090.0090.0000.0000.0000.000
14A19HIS0-0.005-0.00728.7680.0050.0050.0000.0000.0000.000
15A20PHE0-0.047-0.01532.8360.0110.0110.0000.0000.0000.000
16A21LEU0-0.0020.00532.413-0.010-0.0100.0000.0000.0000.000
17A22VAL0-0.034-0.02335.3670.0150.0150.0000.0000.0000.000
18A23ALA00.0090.02336.484-0.005-0.0050.0000.0000.0000.000
19A24MET00.0310.01935.2070.0090.0090.0000.0000.0000.000
20A25PRO0-0.030-0.03338.4090.0060.0060.0000.0000.0000.000
21A26SER0-0.045-0.01537.4270.0070.0070.0000.0000.0000.000
22A27MET0-0.0150.03037.629-0.002-0.0020.0000.0000.0000.000
23A28LYS10.8510.90335.0620.1860.1860.0000.0000.0000.000
24A29ASP-1-0.783-0.90240.818-0.131-0.1310.0000.0000.0000.000
25A30PRO0-0.047-0.03442.551-0.001-0.0010.0000.0000.0000.000
26A31TYR0-0.0020.00543.8320.0030.0030.0000.0000.0000.000
27A32PHE00.0400.01640.784-0.002-0.0020.0000.0000.0000.000
28A33LYS10.7930.88842.2540.1140.1140.0000.0000.0000.000
29A34ARG10.8960.95243.2340.1060.1060.0000.0000.0000.000
30A35SER00.0180.02141.2570.0010.0010.0000.0000.0000.000
31A36VAL00.013-0.00839.419-0.005-0.0050.0000.0000.0000.000
32A37ILE0-0.0020.00837.2170.0060.0060.0000.0000.0000.000
33A38TYR0-0.006-0.00936.261-0.006-0.0060.0000.0000.0000.000
34A39ILE0-0.0030.00231.6950.0070.0070.0000.0000.0000.000
35A40CYS0-0.057-0.03934.5970.0000.0000.0000.0000.0000.000
36A41GLU-1-0.863-0.95531.422-0.263-0.2630.0000.0000.0000.000
37A42HIS0-0.029-0.01326.3090.0070.0070.0000.0000.0000.000
38A43ASN0-0.006-0.01126.035-0.030-0.0300.0000.0000.0000.000
39A44GLN00.0250.00320.1070.0320.0320.0000.0000.0000.000
40A45ASP-1-0.905-0.93825.180-0.310-0.3100.0000.0000.0000.000
41A46GLY0-0.052-0.02728.5510.0210.0210.0000.0000.0000.000
42A47ALA0-0.020-0.00429.790-0.016-0.0160.0000.0000.0000.000
43A48MET00.0060.02232.1170.0170.0170.0000.0000.0000.000
44A49GLY00.0280.00235.570-0.009-0.0090.0000.0000.0000.000
45A50LEU00.0120.02437.8310.0110.0110.0000.0000.0000.000
46A51MET0-0.033-0.01240.977-0.003-0.0030.0000.0000.0000.000
47A52ILE0-0.017-0.00341.2820.0080.0080.0000.0000.0000.000
48A53ASN0-0.049-0.05544.3280.0010.0010.0000.0000.0000.000
49A54ALA00.0410.02846.9560.0040.0040.0000.0000.0000.000
50A55PRO0-0.052-0.00448.7600.0000.0000.0000.0000.0000.000
51A56ILE00.003-0.01552.1180.0020.0020.0000.0000.0000.000
52A57ASP-1-0.966-0.97754.238-0.076-0.0760.0000.0000.0000.000
53A58ILE0-0.008-0.00256.1090.0010.0010.0000.0000.0000.000
54A59THR00.0290.01157.110-0.003-0.0030.0000.0000.0000.000
55A60VAL00.0080.01255.1930.0000.0000.0000.0000.0000.000
56A61GLY00.0570.01657.0400.0000.0000.0000.0000.0000.000
57A62GLY0-0.052-0.01960.5710.0020.0020.0000.0000.0000.000
58A63MET00.0070.00553.9750.0010.0010.0000.0000.0000.000
59A64LEU00.0470.02756.5130.0000.0000.0000.0000.0000.000
60A65LYS10.9660.97159.3240.0680.0680.0000.0000.0000.000
61A66GLN0-0.091-0.02659.7800.0020.0020.0000.0000.0000.000
62A67VAL0-0.071-0.04956.1930.0010.0010.0000.0000.0000.000
63A68ASP-1-0.955-0.96859.526-0.069-0.0690.0000.0000.0000.000
64A69ILE0-0.076-0.03156.7970.0000.0000.0000.0000.0000.000
65A70GLU-1-0.954-0.97260.530-0.067-0.0670.0000.0000.0000.000
66A71PRO0-0.057-0.02360.920-0.002-0.0020.0000.0000.0000.000
67A72ALA00.0230.01060.0330.0020.0020.0000.0000.0000.000
68A73TYR0-0.032-0.02758.9010.0030.0030.0000.0000.0000.000
69A74PRO00.000-0.00863.7250.0000.0000.0000.0000.0000.000
70A75GLN00.0330.01362.501-0.003-0.0030.0000.0000.0000.000
71A76SER0-0.001-0.01762.8250.0010.0010.0000.0000.0000.000
72A77HIS10.7820.88757.4300.0840.0840.0000.0000.0000.000
73A78GLN0-0.018-0.05061.034-0.002-0.0020.0000.0000.0000.000
74A79GLU-1-0.803-0.90361.568-0.068-0.0680.0000.0000.0000.000
75A80ASN0-0.049-0.03356.5500.0000.0000.0000.0000.0000.000
76A81LEU00.0380.01557.521-0.003-0.0030.0000.0000.0000.000
77A82LYS10.8010.88659.9150.0690.0690.0000.0000.0000.000
78A83LYS10.9190.98654.4350.0920.0920.0000.0000.0000.000
79A84PRO00.0250.01053.9510.0010.0010.0000.0000.0000.000
80A85VAL00.0170.02251.765-0.003-0.0030.0000.0000.0000.000
81A86PHE0-0.027-0.04348.3890.0030.0030.0000.0000.0000.000
82A87ASN0-0.033-0.01547.273-0.004-0.0040.0000.0000.0000.000
83A88GLY00.0180.00145.041-0.004-0.0040.0000.0000.0000.000
84A89GLY00.041-0.00643.080-0.010-0.0100.0000.0000.0000.000
85A90PRO00.0070.02042.3430.0040.0040.0000.0000.0000.000
86A91VAL0-0.029-0.00739.9990.0050.0050.0000.0000.0000.000
87A92SER00.007-0.00943.467-0.003-0.0030.0000.0000.0000.000
88A93GLU-1-0.821-0.92845.835-0.116-0.1160.0000.0000.0000.000
89A94ASP-1-0.960-0.95748.525-0.112-0.1120.0000.0000.0000.000
90A95ARG10.8890.94144.4270.1370.1370.0000.0000.0000.000
91A96GLY0-0.010-0.00148.029-0.001-0.0010.0000.0000.0000.000
92A97PHE0-0.014-0.02142.156-0.006-0.0060.0000.0000.0000.000
93A98ILE0-0.0200.00246.0480.0020.0020.0000.0000.0000.000
94A99LEU00.0310.03141.039-0.006-0.0060.0000.0000.0000.000
95A100HIS0-0.019-0.02644.4440.0050.0050.0000.0000.0000.000
96A101ARG10.8230.89943.9680.1230.1230.0000.0000.0000.000
97A102PRO0-0.092-0.02942.2210.0060.0060.0000.0000.0000.000
98A103ARG10.8450.92845.3640.1010.1010.0000.0000.0000.000
99A104ASP-1-0.853-0.91148.943-0.102-0.1020.0000.0000.0000.000
100A105HIS0-0.079-0.02845.468-0.002-0.0020.0000.0000.0000.000
101A106TYR0-0.015-0.03946.8480.0040.0040.0000.0000.0000.000
102A107GLU-1-0.930-0.99246.382-0.113-0.1130.0000.0000.0000.000
103A108SER0-0.037-0.02843.735-0.008-0.0080.0000.0000.0000.000
104A109SER0-0.013-0.02342.983-0.001-0.0010.0000.0000.0000.000
105A110MET00.0130.01635.465-0.004-0.0040.0000.0000.0000.000
106A111LYS10.8540.90638.5100.1760.1760.0000.0000.0000.000
107A112MET0-0.0210.00433.930-0.012-0.0120.0000.0000.0000.000
108A113THR00.0310.00435.011-0.006-0.0060.0000.0000.0000.000
109A114ASP-1-0.907-0.93937.321-0.170-0.1700.0000.0000.0000.000
110A115ASP-1-0.835-0.92740.000-0.135-0.1350.0000.0000.0000.000
111A116ILE0-0.014-0.01338.4240.0070.0070.0000.0000.0000.000
112A117ALA0-0.0040.01339.734-0.010-0.0100.0000.0000.0000.000
113A118VAL00.0310.01440.2080.0070.0070.0000.0000.0000.000
114A119THR00.0010.00942.437-0.004-0.0040.0000.0000.0000.000
115A120THR0-0.051-0.02243.0460.0040.0040.0000.0000.0000.000
116A121SER00.005-0.01445.9540.0010.0010.0000.0000.0000.000
117A122LYS10.9490.97148.6360.1000.1000.0000.0000.0000.000
118A123ASP-1-0.768-0.84750.403-0.112-0.1120.0000.0000.0000.000
119A124ILE00.0330.02948.6940.0040.0040.0000.0000.0000.000
120A125LEU0-0.013-0.02052.2500.0020.0020.0000.0000.0000.000
121A126THR0-0.048-0.02554.8480.0030.0030.0000.0000.0000.000
122A127VAL00.0230.01553.8630.0040.0040.0000.0000.0000.000
123A128LEU00.0470.04752.8510.0010.0010.0000.0000.0000.000
124A129GLY0-0.010-0.01156.8100.0030.0030.0000.0000.0000.000
125A130THR0-0.087-0.06658.6760.0040.0040.0000.0000.0000.000
126A131GLU-1-0.796-0.86758.333-0.078-0.0780.0000.0000.0000.000
127A132ALA0-0.029-0.02256.813-0.002-0.0020.0000.0000.0000.000
128A133GLU-1-0.758-0.80354.468-0.094-0.0940.0000.0000.0000.000
129A134PRO00.004-0.01449.5350.0010.0010.0000.0000.0000.000
130A135GLU-1-0.877-0.94150.903-0.095-0.0950.0000.0000.0000.000
131A136GLY0-0.027-0.01148.9520.0020.0020.0000.0000.0000.000
132A137TYR0-0.086-0.06248.063-0.006-0.0060.0000.0000.0000.000
133A138ILE0-0.0270.00445.2810.0050.0050.0000.0000.0000.000
134A139VAL00.0170.01148.005-0.005-0.0050.0000.0000.0000.000
135A140ALA00.0030.00746.0520.0030.0030.0000.0000.0000.000
136A141LEU0-0.001-0.00348.1380.0000.0000.0000.0000.0000.000
137A142GLY00.0700.03945.6530.0010.0010.0000.0000.0000.000
138A143TYR0-0.048-0.03538.250-0.004-0.0040.0000.0000.0000.000
139A144SER0-0.032-0.02539.1190.0060.0060.0000.0000.0000.000
140A145GLY00.0010.00736.637-0.008-0.0080.0000.0000.0000.000
141A146TRP0-0.053-0.02732.3990.0060.0060.0000.0000.0000.000
142A147SER00.011-0.00932.0070.0000.0000.0000.0000.0000.000
143A148ALA00.0920.04527.074-0.008-0.0080.0000.0000.0000.000
144A149GLY00.0010.02426.0410.0050.0050.0000.0000.0000.000
145A150GLN0-0.032-0.05026.673-0.009-0.0090.0000.0000.0000.000
146A151LEU00.0140.02129.6580.0120.0120.0000.0000.0000.000
147A152GLU-1-0.848-0.93824.184-0.393-0.3930.0000.0000.0000.000
148A153VAL0-0.025-0.01326.323-0.007-0.0070.0000.0000.0000.000
149A154GLU-1-0.811-0.89627.779-0.192-0.1920.0000.0000.0000.000
150A155LEU0-0.036-0.01026.5440.0140.0140.0000.0000.0000.000
151A156THR0-0.105-0.03724.4170.0030.0030.0000.0000.0000.000
152A157GLU-1-0.864-0.90827.414-0.180-0.1800.0000.0000.0000.000
153A158ASN0-0.030-0.02231.065-0.008-0.0080.0000.0000.0000.000
154A159SER0-0.020-0.01133.3990.0180.0180.0000.0000.0000.000
155A160TRP00.019-0.01832.7420.0140.0140.0000.0000.0000.000
156A161LEU00.0150.01131.074-0.007-0.0070.0000.0000.0000.000
157A162THR00.002-0.00129.4740.0020.0020.0000.0000.0000.000
158A163ILE0-0.047-0.02331.248-0.002-0.0020.0000.0000.0000.000
159A164GLU-1-0.874-0.92131.026-0.263-0.2630.0000.0000.0000.000
160A165ALA0-0.028-0.01732.7060.0150.0150.0000.0000.0000.000
161A166ASP-1-0.817-0.92736.160-0.158-0.1580.0000.0000.0000.000
162A167PRO00.0660.02239.1000.0030.0030.0000.0000.0000.000
163A168GLU-1-0.793-0.87742.113-0.130-0.1300.0000.0000.0000.000
164A169LEU0-0.099-0.03641.0400.0080.0080.0000.0000.0000.000
165A170ILE00.009-0.00540.0800.0030.0030.0000.0000.0000.000
166A171PHE0-0.026-0.01243.5180.0060.0060.0000.0000.0000.000
167A172ASN0-0.018-0.01447.3290.0010.0010.0000.0000.0000.000
168A173THR0-0.0380.00646.0620.0050.0050.0000.0000.0000.000
169A174PRO00.0210.00848.860-0.003-0.0030.0000.0000.0000.000
170A175VAL00.0790.02949.203-0.003-0.0030.0000.0000.0000.000
171A176HIS0-0.028-0.02148.811-0.006-0.0060.0000.0000.0000.000
172A177GLU-1-0.886-0.94948.547-0.097-0.0970.0000.0000.0000.000
173A178LYS10.7660.90944.7650.1220.1220.0000.0000.0000.000
174A179TRP00.022-0.00141.0170.0020.0020.0000.0000.0000.000
175A180GLN0-0.022-0.01442.866-0.006-0.0060.0000.0000.0000.000
176A181LYS10.9700.97643.4900.1180.1180.0000.0000.0000.000
177A182ALA00.0060.00839.417-0.004-0.0040.0000.0000.0000.000
178A183ILE00.0550.01538.646-0.005-0.0050.0000.0000.0000.000
179A184GLN0-0.0220.00439.0210.0010.0010.0000.0000.0000.000
180A185LYS10.8650.94437.1780.1650.1650.0000.0000.0000.000
181A186LEU0-0.066-0.03233.526-0.007-0.0070.0000.0000.0000.000
182A187GLY0-0.0100.00435.917-0.001-0.0010.0000.0000.0000.000
183A188ILE0-0.032-0.01036.7320.0050.0050.0000.0000.0000.000
184A189SER0-0.019-0.03639.5750.0050.0050.0000.0000.0000.000
185A190PRO0-0.037-0.02042.8280.0000.0000.0000.0000.0000.000
186A191ALA00.0110.00244.2150.0030.0030.0000.0000.0000.000
187A192GLN00.0090.03345.0720.0030.0030.0000.0000.0000.000