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: 896MY

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 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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2212293.282612
FMO2-HF: Nuclear repulsion 2136842.358427
FMO2-HF: Total energy -75450.924184
FMO2-MP2: Total energy -75669.380955


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.
-29.947-12.13113.868-10.529-21.155-0.068
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 : -0.039 / 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].
3A4VAL00.0380.0142.2090.7473.7431.737-1.431-3.303-0.004
4A5ILE0-0.023-0.0074.320-1.123-0.9750.004-0.033-0.1190.000
5A6MET0-0.005-0.0058.044-0.020-0.0200.0000.0000.0000.000
6A7ASP-1-0.865-0.94810.5060.5550.5550.0000.0000.0000.000
7A8ASN0-0.013-0.02213.310-0.135-0.1350.0000.0000.0000.000
8A9GLY00.0450.02016.496-0.058-0.0580.0000.0000.0000.000
9A10GLY0-0.039-0.01017.813-0.032-0.0320.0000.0000.0000.000
10A11GLN00.017-0.00618.3940.0280.0280.0000.0000.0000.000
11A12TYR0-0.044-0.02618.2440.0040.0040.0000.0000.0000.000
12A13VAL00.0720.04612.3760.0780.0780.0000.0000.0000.000
13A14HIS00.0580.01212.9280.2220.2220.0000.0000.0000.000
14A15ARG10.8980.95713.596-0.435-0.4350.0000.0000.0000.000
15A16ILE00.0780.05210.6430.0230.0230.0000.0000.0000.000
16A17TRP0-0.010-0.0096.436-0.329-0.3290.0000.0000.0000.000
17A18ARG10.9330.94910.211-0.581-0.5810.0000.0000.0000.000
18A19THR00.0200.01312.859-0.076-0.0760.0000.0000.0000.000
19A20LEU00.0330.0186.875-0.022-0.0220.0000.0000.0000.000
20A21ARG10.8890.9427.276-1.687-1.6870.0000.0000.0000.000
21A22TYR0-0.089-0.0319.913-0.165-0.1650.0000.0000.0000.000
22A23LEU0-0.024-0.01610.528-0.113-0.1130.0000.0000.0000.000
23A24GLY0-0.0380.0059.897-0.005-0.0050.0000.0000.0000.000
24A25VAL00.000-0.0044.662-0.0370.052-0.001-0.007-0.0820.000
25A26GLU-1-0.926-0.9592.428-13.303-7.8412.491-3.424-4.528-0.030
26A27THR0-0.023-0.0252.487-0.5931.1253.155-2.376-2.496-0.017
27A28LYS10.9810.9842.064-2.726-2.8534.149-0.214-3.8080.003
28A29ILE0-0.0060.0224.683-0.066-0.003-0.0010.044-0.1060.000
29A30ILE0-0.024-0.0096.184-0.122-0.1220.0000.0000.0000.000
30A31PRO00.0520.0128.987-0.006-0.0060.0000.0000.0000.000
31A32ASN00.0310.02511.865-0.069-0.0690.0000.0000.0000.000
32A33THR00.0150.00813.918-0.058-0.0580.0000.0000.0000.000
33A34THR0-0.047-0.0109.047-0.042-0.0420.0000.0000.0000.000
34A35PRO00.0500.02212.461-0.013-0.0130.0000.0000.0000.000
35A36LEU00.0860.04612.006-0.075-0.0750.0000.0000.0000.000
36A37GLU-1-0.912-0.94511.099-0.781-0.7810.0000.0000.0000.000
37A38GLU-1-0.956-0.9899.573-0.653-0.6530.0000.0000.0000.000
38A39ILE0-0.010-0.0187.005-0.320-0.3200.0000.0000.0000.000
39A40LYS10.9670.9856.3180.7060.7060.0000.0000.0000.000
40A41ALA0-0.075-0.0437.580-0.438-0.4380.0000.0000.0000.000
41A42MET0-0.061-0.0202.439-1.0980.1210.526-0.249-1.496-0.001
42A43ASN0-0.081-0.0252.831-5.152-3.2570.302-0.974-1.223-0.011
43A44PRO00.0220.0102.441-4.374-2.4060.842-1.186-1.623-0.008
44A45LYS10.9360.9492.3152.2834.3950.666-0.624-2.1540.000
45A46GLY00.0760.0274.2740.9281.216-0.001-0.040-0.2470.000
46A47ILE0-0.054-0.0184.776-0.593-0.608-0.001-0.0150.0300.000
47A48ILE00.0060.0097.2470.1110.1110.0000.0000.0000.000
48A49PHE00.0280.0259.7860.0660.0660.0000.0000.0000.000
49A50SER00.034-0.00212.674-0.005-0.0050.0000.0000.0000.000
50A51GLY00.0010.00214.414-0.087-0.0870.0000.0000.0000.000
51A52GLY00.017-0.00917.6680.0400.0400.0000.0000.0000.000
52A53PRO0-0.031-0.01020.355-0.015-0.0150.0000.0000.0000.000
53A54SER00.0520.02222.711-0.022-0.0220.0000.0000.0000.000
54A55LEU00.0450.01022.0130.0080.0080.0000.0000.0000.000
55A56GLU-1-0.982-0.96823.1590.0700.0700.0000.0000.0000.000
56A57ASN0-0.052-0.03419.555-0.028-0.0280.0000.0000.0000.000
57A58THR0-0.004-0.02718.0840.0390.0390.0000.0000.0000.000
58A59GLY0-0.0190.00516.8190.0060.0060.0000.0000.0000.000
59A60ASN0-0.031-0.04314.284-0.011-0.0110.0000.0000.0000.000
60A61CYS0-0.026-0.00613.780-0.018-0.0180.0000.0000.0000.000
61A62GLU-1-0.800-0.89114.8440.0370.0370.0000.0000.0000.000
62A63LYS10.8440.93016.0370.1750.1750.0000.0000.0000.000
63A64VAL00.013-0.00510.855-0.049-0.0490.0000.0000.0000.000
64A65LEU0-0.061-0.02013.785-0.034-0.0340.0000.0000.0000.000
65A66GLU-1-0.929-0.97216.214-0.182-0.1820.0000.0000.0000.000
66A67HIS00.0440.04115.4540.0210.0210.0000.0000.0000.000
67A68TYR0-0.013-0.01612.589-0.086-0.0860.0000.0000.0000.000
68A69ASP-1-0.894-0.95814.118-0.430-0.4300.0000.0000.0000.000
69A70GLU-1-0.933-0.95713.676-0.604-0.6040.0000.0000.0000.000
70A71PHE0-0.130-0.0778.455-0.232-0.2320.0000.0000.0000.000
71A72ASN0-0.089-0.05010.654-0.008-0.0080.0000.0000.0000.000
72A73VAL0-0.0090.0127.1570.0080.0080.0000.0000.0000.000
73A74PRO00.0210.0158.5220.0310.0310.0000.0000.0000.000
74A75ILE0-0.005-0.0029.421-0.031-0.0310.0000.0000.0000.000
75A76LEU00.0120.01311.2820.0250.0250.0000.0000.0000.000
76A77GLY00.002-0.00112.6340.0530.0530.0000.0000.0000.000
77A78ILE0-0.009-0.01214.186-0.007-0.0070.0000.0000.0000.000
78A79CYS0-0.072-0.03617.153-0.016-0.0160.0000.0000.0000.000
79A80LEU00.0450.02819.004-0.020-0.0200.0000.0000.0000.000
80A81GLY00.0370.01316.380-0.034-0.0340.0000.0000.0000.000
81A82HIS00.0120.01117.297-0.026-0.0260.0000.0000.0000.000
82A83GLN0-0.004-0.02219.541-0.040-0.0400.0000.0000.0000.000
83A84LEU0-0.028-0.00416.331-0.023-0.0230.0000.0000.0000.000
84A85ILE00.0020.00515.368-0.034-0.0340.0000.0000.0000.000
85A86ALA0-0.0020.00219.498-0.027-0.0270.0000.0000.0000.000
86A87LYS10.9610.97623.101-0.084-0.0840.0000.0000.0000.000
87A88PHE0-0.0080.00220.621-0.013-0.0130.0000.0000.0000.000
88A89PHE0-0.004-0.01918.188-0.017-0.0170.0000.0000.0000.000
89A90GLY0-0.0030.00823.586-0.005-0.0050.0000.0000.0000.000
90A91GLY00.0330.03326.172-0.001-0.0010.0000.0000.0000.000
91A92LYS10.8640.92027.798-0.058-0.0580.0000.0000.0000.000
92A93VAL00.0400.02425.2090.0110.0110.0000.0000.0000.000
93A94GLY0-0.056-0.02828.556-0.014-0.0140.0000.0000.0000.000
94A95ARG11.0130.99930.551-0.088-0.0880.0000.0000.0000.000
95A96GLY0-0.008-0.00631.898-0.008-0.0080.0000.0000.0000.000
96A97GLU-1-0.964-0.95633.0120.1190.1190.0000.0000.0000.000
97A98LYS10.9780.97233.158-0.171-0.1710.0000.0000.0000.000
98A99ALA00.017-0.00131.8060.0110.0110.0000.0000.0000.000
99A100GLU-1-0.962-0.97030.8970.1800.1800.0000.0000.0000.000
100A101TYR0-0.017-0.01724.3900.0160.0160.0000.0000.0000.000
101A102SER0-0.056-0.03029.491-0.018-0.0180.0000.0000.0000.000
102A103LEU0-0.006-0.00727.4480.0160.0160.0000.0000.0000.000
103A104VAL0-0.037-0.01529.136-0.020-0.0200.0000.0000.0000.000
104A105GLU-1-0.846-0.91929.4090.2390.2390.0000.0000.0000.000
105A106ILE0-0.021-0.01024.935-0.013-0.0130.0000.0000.0000.000
106A107GLU-1-0.885-0.95929.5720.1610.1610.0000.0000.0000.000
107A108ILE0-0.029-0.01524.408-0.002-0.0020.0000.0000.0000.000
108A109ILE0-0.078-0.05727.899-0.011-0.0110.0000.0000.0000.000
109A110ASP-1-0.886-0.94225.5650.1720.1720.0000.0000.0000.000
110A111GLU-1-0.933-0.97423.1490.2790.2790.0000.0000.0000.000
111A112ASP-1-0.756-0.87919.9600.3720.3720.0000.0000.0000.000
112A113GLU-1-0.823-0.90916.5090.2840.2840.0000.0000.0000.000
113A114ILE0-0.022-0.02815.2760.0690.0690.0000.0000.0000.000
114A115PHE0-0.022-0.01417.6090.0510.0510.0000.0000.0000.000
115A116LYS10.9921.00319.269-0.361-0.3610.0000.0000.0000.000
116A117GLY0-0.044-0.01320.8400.0360.0360.0000.0000.0000.000
117A118LEU0-0.0390.00120.399-0.005-0.0050.0000.0000.0000.000
118A119PRO0-0.048-0.04324.348-0.029-0.0290.0000.0000.0000.000
119A120LYS10.9670.98227.103-0.216-0.2160.0000.0000.0000.000
120A121ARG10.9190.97629.661-0.179-0.1790.0000.0000.0000.000
121A122LEU00.0380.03623.7730.0110.0110.0000.0000.0000.000
122A123LYS10.9110.96827.911-0.231-0.2310.0000.0000.0000.000
123A124VAL0-0.0020.00124.1660.0290.0290.0000.0000.0000.000
124A125TRP00.003-0.01423.562-0.030-0.0300.0000.0000.0000.000
125A126GLH0-0.044-0.09924.1890.0230.0230.0000.0000.0000.000
126A127SER00.0040.01226.213-0.016-0.0160.0000.0000.0000.000
127A128HIS10.8370.92127.367-0.196-0.1960.0000.0000.0000.000
128A129MET00.0060.01828.646-0.010-0.0100.0000.0000.0000.000
129A130ASP-1-0.900-0.94826.9440.1350.1350.0000.0000.0000.000
130A131GLU-1-0.809-0.91026.8100.1750.1750.0000.0000.0000.000
131A132VAL00.0370.01424.314-0.015-0.0150.0000.0000.0000.000
132A133LYS10.7350.85127.526-0.124-0.1240.0000.0000.0000.000
133A134GLU-1-0.964-0.96329.7790.0550.0550.0000.0000.0000.000
134A135LEU00.012-0.00125.9470.0060.0060.0000.0000.0000.000
135A136PRO0-0.030-0.00923.774-0.010-0.0100.0000.0000.0000.000
136A137PRO00.013-0.00426.8990.0050.0050.0000.0000.0000.000
137A138LYS10.9740.99325.3200.0040.0040.0000.0000.0000.000
138A139PHE00.0080.01820.1440.0040.0040.0000.0000.0000.000
139A140LYS10.9710.99523.438-0.154-0.1540.0000.0000.0000.000
140A141ILE0-0.030-0.01624.8980.0170.0170.0000.0000.0000.000
141A142LEU0-0.031-0.01221.158-0.007-0.0070.0000.0000.0000.000
142A143ALA0-0.015-0.01425.4660.0070.0070.0000.0000.0000.000
143A144ARG10.8630.95227.076-0.154-0.1540.0000.0000.0000.000
144A145SER00.013-0.03629.9260.0050.0050.0000.0000.0000.000
145A146GLU-1-0.957-0.98432.0590.1210.1210.0000.0000.0000.000
146A147THR0-0.0130.00533.545-0.006-0.0060.0000.0000.0000.000
147A148CYS0-0.047-0.00828.412-0.007-0.0070.0000.0000.0000.000
148A149PRO00.0310.00930.8390.0110.0110.0000.0000.0000.000
149A150ILE00.010-0.00125.4870.0020.0020.0000.0000.0000.000
150A151GLU-1-0.689-0.77625.9400.2510.2510.0000.0000.0000.000
151A152ALA0-0.019-0.02121.9420.0350.0350.0000.0000.0000.000
152A153MET0-0.065-0.00220.918-0.036-0.0360.0000.0000.0000.000
153A154LYS10.9050.96418.186-0.123-0.1230.0000.0000.0000.000
154A155HIS00.0420.04419.763-0.014-0.0140.0000.0000.0000.000
155A156GLU-1-0.937-0.99621.2910.0850.0850.0000.0000.0000.000
156A157GLU-1-0.968-0.99221.9530.0170.0170.0000.0000.0000.000
157A158LEU0-0.0130.01117.304-0.024-0.0240.0000.0000.0000.000
158A159PRO0-0.040-0.01013.5360.0490.0490.0000.0000.0000.000
159A160ILE00.0250.00314.1810.0380.0380.0000.0000.0000.000
160A161TYR0-0.063-0.06114.7730.0040.0040.0000.0000.0000.000
161A162GLY00.0000.00316.2980.0170.0170.0000.0000.0000.000
162A163VAL0-0.0150.00017.756-0.008-0.0080.0000.0000.0000.000
163A164GLN00.022-0.01120.2000.0100.0100.0000.0000.0000.000
164A165PHE0-0.007-0.01320.4850.0000.0000.0000.0000.0000.000
165A166HIS10.8100.88118.810-0.439-0.4390.0000.0000.0000.000
166A167PRO00.0290.02916.150-0.020-0.0200.0000.0000.0000.000
167A168GLU-1-0.717-0.85215.2960.6680.6680.0000.0000.0000.000
168A169VAL0-0.131-0.06216.919-0.010-0.0100.0000.0000.0000.000
169A170ALA00.0490.02420.531-0.018-0.0180.0000.0000.0000.000
170A171HIS0-0.049-0.03321.912-0.021-0.0210.0000.0000.0000.000
171A172THR0-0.0110.00121.549-0.046-0.0460.0000.0000.0000.000
172A173GLU-1-0.847-0.91922.7650.3130.3130.0000.0000.0000.000
173A174LYS10.9420.96121.617-0.373-0.3730.0000.0000.0000.000
174A175GLY00.0320.02219.4170.0300.0300.0000.0000.0000.000
175A176GLU-1-0.908-0.96715.5020.7750.7750.0000.0000.0000.000
176A177GLU-1-0.952-0.98615.3990.6650.6650.0000.0000.0000.000
177A178ILE00.0430.04116.4370.0400.0400.0000.0000.0000.000
178A179LEU0-0.017-0.00811.8050.0540.0540.0000.0000.0000.000
179A180ARG10.9340.96211.805-0.640-0.6400.0000.0000.0000.000
180A181ASN0-0.082-0.04012.2380.1360.1360.0000.0000.0000.000
181A182PHE00.0310.0188.7980.0530.0530.0000.0000.0000.000
182A183ALA0-0.005-0.0137.9890.0720.0720.0000.0000.0000.000
183A184LYS10.8960.9298.203-0.464-0.4640.0000.0000.0000.000
184A185LEU0-0.0010.00710.790-0.087-0.0870.0000.0000.0000.000
185A186CYS0-0.068-0.0145.879-0.214-0.2140.0000.0000.0000.000
186A187GLY0-0.048-0.0106.7390.0270.0270.0000.0000.0000.000
187A188GLU-1-0.971-0.9657.8350.0550.0550.0000.0000.0000.000
188A189LEU0-0.029-0.01711.048-0.052-0.0520.0000.0000.0000.000