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: JQRG9

Calculation Name: 2D7J-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2D7J

Chain ID: A

ChEMBL ID:

UniProt ID: O59071

Base Structure: X-ray

Registration Date: 2023-09-23

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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2221317.560638
FMO2-HF: Nuclear repulsion 2145864.08118
FMO2-HF: Total energy -75453.479459
FMO2-MP2: Total energy -75671.927955


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:2:MET)


Summations of interaction energy for fragment #1(A:2: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.
-24.953-11.20721.727-10.757-24.716-0.069
Interaction energy analysis for fragmet #1(A:2:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.037 / q_NPA : -0.003
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].
3A4VAL00.0650.0332.2431.0253.3902.341-1.161-3.546-0.003
4A5ILE0-0.048-0.0244.287-1.606-1.6080.0150.134-0.1460.000
5A6MET00.0150.0157.591-0.056-0.0560.0000.0000.0000.000
6A7ASP-1-0.862-0.94510.3040.4090.4090.0000.0000.0000.000
7A8ASN00.011-0.00212.933-0.074-0.0740.0000.0000.0000.000
8A9GLY00.0320.01416.269-0.062-0.0620.0000.0000.0000.000
9A10GLY00.0170.01217.197-0.045-0.0450.0000.0000.0000.000
10A11GLN0-0.021-0.02717.9580.0240.0240.0000.0000.0000.000
11A12TYR0-0.028-0.01917.854-0.024-0.0240.0000.0000.0000.000
12A13VAL00.0550.04411.7070.0080.0080.0000.0000.0000.000
13A14HIS00.0810.02712.5100.0660.0660.0000.0000.0000.000
14A15ARG10.9110.96312.981-0.239-0.2390.0000.0000.0000.000
15A16ILE00.0510.04710.323-0.055-0.0550.0000.0000.0000.000
16A17TRP00.003-0.0025.451-0.220-0.2200.0000.0000.0000.000
17A18ARG10.8880.9359.609-0.385-0.3850.0000.0000.0000.000
18A19THR00.0150.00112.157-0.094-0.0940.0000.0000.0000.000
19A20LEU00.0170.0077.073-0.083-0.0830.0000.0000.0000.000
20A21ARG10.8330.9046.5030.1190.1190.0000.0000.0000.000
21A22TYR0-0.057-0.0169.747-0.116-0.1160.0000.0000.0000.000
22A23LEU0-0.023-0.01810.650-0.044-0.0440.0000.0000.0000.000
23A24GLY00.0090.0149.976-0.018-0.0180.0000.0000.0000.000
24A25VAL0-0.0060.0014.153-0.342-0.230-0.001-0.012-0.0980.000
25A26GLU-1-0.813-0.9052.506-7.964-6.4165.143-2.348-4.343-0.027
26A27THR0-0.012-0.0152.465-2.704-0.4933.635-2.761-3.085-0.018
27A28LYS10.8620.9302.170-1.606-0.7874.239-0.588-4.4710.003
28A29ILE00.0000.0094.1340.8461.0880.0010.003-0.2460.000
29A30ILE0-0.0060.0046.444-0.087-0.0870.0000.0000.0000.000
30A31PRO00.0360.0179.152-0.049-0.0490.0000.0000.0000.000
31A32ASN00.0030.01212.0720.0270.0270.0000.0000.0000.000
32A33THR00.0200.00913.713-0.023-0.0230.0000.0000.0000.000
33A34THR0-0.048-0.0239.775-0.048-0.0480.0000.0000.0000.000
34A35PRO00.0270.02012.6340.0070.0070.0000.0000.0000.000
35A36LEU00.0640.02411.2670.0030.0030.0000.0000.0000.000
36A37GLU-1-0.849-0.89910.695-0.298-0.2980.0000.0000.0000.000
37A38GLU-1-0.897-0.9529.735-0.079-0.0790.0000.0000.0000.000
38A39ILE0-0.002-0.0156.461-0.155-0.1550.0000.0000.0000.000
39A40LYS10.8700.9195.849-0.073-0.0730.0000.0000.0000.000
40A41ALA0-0.020-0.0087.155-0.272-0.2720.0000.0000.0000.000
41A42MET0-0.077-0.0312.478-1.388-0.6001.650-0.459-1.9800.002
42A43ASN0-0.053-0.0222.428-6.056-4.1981.651-1.497-2.012-0.021
43A44PRO00.0130.0152.228-2.194-0.2542.370-1.977-2.333-0.010
44A45LYS10.8490.9052.905-0.8170.6560.6840.017-2.1740.005
45A46GLY00.0710.0374.427-0.949-0.5870.000-0.089-0.2730.000
46A47ILE0-0.039-0.0124.621-0.378-0.348-0.001-0.019-0.0090.000
47A48ILE0-0.007-0.0077.050-0.124-0.1240.0000.0000.0000.000
48A49PHE00.0380.0249.9000.1340.1340.0000.0000.0000.000
49A50SER00.028-0.00512.735-0.056-0.0560.0000.0000.0000.000
50A51GLY00.0210.01814.328-0.055-0.0550.0000.0000.0000.000
51A52GLY00.0150.00217.3450.0440.0440.0000.0000.0000.000
52A53PRO0-0.029-0.01019.885-0.017-0.0170.0000.0000.0000.000
53A54SER00.018-0.01922.699-0.017-0.0170.0000.0000.0000.000
54A55LEU00.0060.00321.9260.0200.0200.0000.0000.0000.000
55A56GLU-1-0.892-0.91823.2340.1320.1320.0000.0000.0000.000
56A57ASN0-0.079-0.04318.917-0.009-0.0090.0000.0000.0000.000
57A58THR00.013-0.02417.8120.0280.0280.0000.0000.0000.000
58A59GLY0-0.0010.01216.3900.0380.0380.0000.0000.0000.000
59A60ASN0-0.017-0.02713.771-0.060-0.0600.0000.0000.0000.000
60A61CYS0-0.048-0.01813.4530.0260.0260.0000.0000.0000.000
61A62GLU-1-0.744-0.86514.5170.2030.2030.0000.0000.0000.000
62A63LYS10.8010.90915.618-0.102-0.1020.0000.0000.0000.000
63A64VAL0-0.011-0.01710.219-0.023-0.0230.0000.0000.0000.000
64A65LEU0-0.068-0.02513.299-0.011-0.0110.0000.0000.0000.000
65A66GLU-1-0.885-0.93515.7330.0780.0780.0000.0000.0000.000
66A67HIS0-0.020-0.01214.9910.0000.0000.0000.0000.0000.000
67A68TYR00.000-0.02011.956-0.027-0.0270.0000.0000.0000.000
68A69ASP-1-0.892-0.94213.4910.0520.0520.0000.0000.0000.000
69A70GLU-1-0.891-0.92312.666-0.050-0.0500.0000.0000.0000.000
70A71PHE0-0.092-0.0587.846-0.065-0.0650.0000.0000.0000.000
71A72ASN0-0.083-0.0549.8110.0580.0580.0000.0000.0000.000
72A73VAL00.0040.0236.6460.0830.0830.0000.0000.0000.000
73A74PRO00.0190.0118.552-0.080-0.0800.0000.0000.0000.000
74A75ILE0-0.010-0.0039.1440.0330.0330.0000.0000.0000.000
75A76LEU0-0.0100.00311.221-0.049-0.0490.0000.0000.0000.000
76A77GLY00.0180.00312.8140.0740.0740.0000.0000.0000.000
77A78ILE0-0.014-0.02513.923-0.039-0.0390.0000.0000.0000.000
78A79CYS0-0.075-0.04417.1120.0060.0060.0000.0000.0000.000
79A80LEU00.0330.02118.950-0.014-0.0140.0000.0000.0000.000
80A81GLY00.0310.01316.334-0.011-0.0110.0000.0000.0000.000
81A82HIS0-0.037-0.01617.229-0.001-0.0010.0000.0000.0000.000
82A83GLN0-0.016-0.01719.599-0.019-0.0190.0000.0000.0000.000
83A84LEU0-0.031-0.00916.091-0.015-0.0150.0000.0000.0000.000
84A85ILE00.0150.01115.085-0.016-0.0160.0000.0000.0000.000
85A86ALA0-0.001-0.00619.197-0.018-0.0180.0000.0000.0000.000
86A87LYS10.8700.92622.562-0.181-0.1810.0000.0000.0000.000
87A88PHE0-0.011-0.00219.944-0.010-0.0100.0000.0000.0000.000
88A89PHE00.007-0.00517.965-0.011-0.0110.0000.0000.0000.000
89A90GLY00.0260.02023.304-0.009-0.0090.0000.0000.0000.000
90A91GLY00.0190.01725.908-0.009-0.0090.0000.0000.0000.000
91A92LYS10.7510.86027.551-0.096-0.0960.0000.0000.0000.000
92A93VAL00.0130.00225.0490.0050.0050.0000.0000.0000.000
93A94GLY0-0.023-0.00128.465-0.008-0.0080.0000.0000.0000.000
94A95ARG10.9880.98930.863-0.094-0.0940.0000.0000.0000.000
95A96GLY00.0280.02132.547-0.005-0.0050.0000.0000.0000.000
96A97GLU-1-0.980-0.96333.4980.0800.0800.0000.0000.0000.000
97A98LYS10.8670.88932.428-0.098-0.0980.0000.0000.0000.000
98A99ALA00.0380.03131.6870.0080.0080.0000.0000.0000.000
99A100GLU-1-0.858-0.89530.6530.0990.0990.0000.0000.0000.000
100A101TYR0-0.006-0.00623.6330.0130.0130.0000.0000.0000.000
101A102SER0-0.022-0.01429.044-0.012-0.0120.0000.0000.0000.000
102A103LEU0-0.028-0.01327.3970.0090.0090.0000.0000.0000.000
103A104VAL0-0.0080.00129.187-0.008-0.0080.0000.0000.0000.000
104A105GLU-1-0.847-0.91029.2020.0950.0950.0000.0000.0000.000
105A106ILE0-0.031-0.00824.5960.0000.0000.0000.0000.0000.000
106A107GLU-1-0.815-0.89029.3050.0740.0740.0000.0000.0000.000
107A108ILE0-0.026-0.01124.1400.0040.0040.0000.0000.0000.000
108A109ILE0-0.040-0.02427.146-0.007-0.0070.0000.0000.0000.000
109A110ASP-1-0.785-0.88724.8570.1150.1150.0000.0000.0000.000
110A111GLU-1-0.860-0.93423.1240.1040.1040.0000.0000.0000.000
111A112ASP-1-0.781-0.90119.1060.1910.1910.0000.0000.0000.000
112A113GLU-1-0.834-0.90016.0020.1750.1750.0000.0000.0000.000
113A114ILE0-0.006-0.02114.4070.0040.0040.0000.0000.0000.000
114A115PHE00.0020.00016.7340.0000.0000.0000.0000.0000.000
115A116LYS10.8690.95418.047-0.128-0.1280.0000.0000.0000.000
116A117GLY00.0060.00220.069-0.002-0.0020.0000.0000.0000.000
117A118LEU0-0.038-0.00319.334-0.008-0.0080.0000.0000.0000.000
118A119PRO0-0.003-0.01923.362-0.004-0.0040.0000.0000.0000.000
119A120LYS10.8850.92925.750-0.086-0.0860.0000.0000.0000.000
120A121ARG10.8330.91328.506-0.077-0.0770.0000.0000.0000.000
121A122LEU00.0100.01623.162-0.001-0.0010.0000.0000.0000.000
122A123LYS10.8190.88927.372-0.085-0.0850.0000.0000.0000.000
123A124VAL0-0.020-0.01024.1170.0060.0060.0000.0000.0000.000
124A125TRP00.020-0.00823.297-0.013-0.0130.0000.0000.0000.000
125A126GLH0-0.031-0.07423.8970.0200.0200.0000.0000.0000.000
126A127SER00.015-0.00226.008-0.010-0.0100.0000.0000.0000.000
127A128HIS10.8500.92427.312-0.117-0.1170.0000.0000.0000.000
128A129MET00.0040.01728.546-0.005-0.0050.0000.0000.0000.000
129A130ASP-1-0.850-0.93427.6680.1190.1190.0000.0000.0000.000
130A131GLU-1-0.785-0.87826.7730.1280.1280.0000.0000.0000.000
131A132VAL00.0220.00524.173-0.005-0.0050.0000.0000.0000.000
132A133LYS10.7200.83627.348-0.111-0.1110.0000.0000.0000.000
133A134GLU-1-0.860-0.91229.5460.0850.0850.0000.0000.0000.000
134A135LEU00.0100.00025.9700.0090.0090.0000.0000.0000.000
135A136PRO0-0.0020.01023.604-0.007-0.0070.0000.0000.0000.000
136A137PRO00.004-0.00226.690-0.002-0.0020.0000.0000.0000.000
137A138LYS10.8090.89724.800-0.087-0.0870.0000.0000.0000.000
138A139PHE00.0070.01519.6450.0140.0140.0000.0000.0000.000
139A140LYS10.8520.93822.018-0.150-0.1500.0000.0000.0000.000
140A141ILE0-0.008-0.01424.4770.0120.0120.0000.0000.0000.000
141A142LEU0-0.046-0.00320.156-0.003-0.0030.0000.0000.0000.000
142A143ALA00.002-0.01624.611-0.008-0.0080.0000.0000.0000.000
143A144ARG10.8000.89726.464-0.079-0.0790.0000.0000.0000.000
144A145SER00.008-0.04929.578-0.003-0.0030.0000.0000.0000.000
145A146GLU-1-0.880-0.93731.9920.0740.0740.0000.0000.0000.000
146A147THR0-0.015-0.00632.859-0.003-0.0030.0000.0000.0000.000
147A148CYS0-0.056-0.01529.3930.0030.0030.0000.0000.0000.000
148A149PRO00.0200.00631.0640.0020.0020.0000.0000.0000.000
149A150ILE00.020-0.00125.3340.0010.0010.0000.0000.0000.000
150A151GLU-1-0.707-0.78225.9930.1490.1490.0000.0000.0000.000
151A152ALA0-0.033-0.02021.4880.0180.0180.0000.0000.0000.000
152A153MET0-0.046-0.01020.439-0.024-0.0240.0000.0000.0000.000
153A154LYS10.8730.93917.894-0.161-0.1610.0000.0000.0000.000
154A155HIS00.0640.04919.258-0.016-0.0160.0000.0000.0000.000
155A156GLU-1-0.896-0.96620.9660.1050.1050.0000.0000.0000.000
156A157GLU-1-0.844-0.91821.8130.1060.1060.0000.0000.0000.000
157A158LEU0-0.0130.00316.8450.0070.0070.0000.0000.0000.000
158A159PRO0-0.0110.01013.250-0.004-0.0040.0000.0000.0000.000
159A160ILE00.009-0.00613.8740.0410.0410.0000.0000.0000.000
160A161TYR0-0.052-0.06214.043-0.020-0.0200.0000.0000.0000.000
161A162GLY00.0070.00416.3000.0310.0310.0000.0000.0000.000
162A163VAL0-0.025-0.00917.818-0.022-0.0220.0000.0000.0000.000
163A164GLN00.022-0.00420.3390.0260.0260.0000.0000.0000.000
164A165PHE0-0.002-0.00520.0210.0030.0030.0000.0000.0000.000
165A166HIS10.8190.88418.595-0.251-0.2510.0000.0000.0000.000
166A167PRO00.0210.02816.142-0.024-0.0240.0000.0000.0000.000
167A168GLU-1-0.769-0.87115.2120.3410.3410.0000.0000.0000.000
168A169VAL0-0.088-0.05017.024-0.012-0.0120.0000.0000.0000.000
169A170ALA00.0320.00620.701-0.011-0.0110.0000.0000.0000.000
170A171HIS0-0.061-0.02522.068-0.014-0.0140.0000.0000.0000.000
171A172THR0-0.010-0.00221.402-0.015-0.0150.0000.0000.0000.000
172A173GLU-1-0.761-0.84922.7450.0960.0960.0000.0000.0000.000
173A174LYS10.8790.91721.017-0.082-0.0820.0000.0000.0000.000
174A175GLY00.0220.01419.3820.0080.0080.0000.0000.0000.000
175A176GLU-1-0.912-0.96515.6640.1270.1270.0000.0000.0000.000
176A177GLU-1-0.849-0.92814.9770.1050.1050.0000.0000.0000.000
177A178ILE00.0190.02715.6900.0050.0050.0000.0000.0000.000
178A179LEU0-0.001-0.00211.5970.0300.0300.0000.0000.0000.000
179A180ARG10.9140.96811.085-0.017-0.0170.0000.0000.0000.000
180A181ASN0-0.063-0.03811.705-0.025-0.0250.0000.0000.0000.000
181A182PHE00.0390.0258.7140.0100.0100.0000.0000.0000.000
182A183ALA00.012-0.0047.4550.0460.0460.0000.0000.0000.000
183A184LYS10.8240.9157.654-0.105-0.1050.0000.0000.0000.000
184A185LEU00.0120.01410.1940.0200.0200.0000.0000.0000.000
185A186CYS0-0.070-0.0275.196-0.038-0.0380.0000.0000.0000.000
186A187GLY0-0.053-0.0226.1420.5210.5210.0000.0000.0000.000
187A188GLU-1-0.938-0.9537.7170.0990.0990.0000.0000.0000.000
188A189LEU0-0.058-0.02511.2950.0250.0250.0000.0000.0000.000