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

tag_button

FMODB ID: 7MMKK

Calculation Name: 4O7H-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4O7H

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-09-27

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 222
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2879672.954989
FMO2-HF: Nuclear repulsion 2790684.443744
FMO2-HF: Total energy -88988.511244
FMO2-MP2: Total energy -89251.125544


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.
-12.308-5.9795.579-3.372-8.535-0.023
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 : 0.008 / q_NPA : 0.016
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].
3A3ARG10.9080.9582.596-2.3911.8451.078-2.699-2.615-0.014
4A4LEU0-0.022-0.0064.7370.8240.934-0.001-0.014-0.0950.000
5A5TYR00.0470.0318.2210.0610.0610.0000.0000.0000.000
6A6HIS00.004-0.02710.9170.1440.1440.0000.0000.0000.000
7A7HIS00.1060.04613.4770.0760.0760.0000.0000.0000.000
8A8GLY00.0530.02416.3950.0010.0010.0000.0000.0000.000
9A9LEU00.008-0.00617.9810.0320.0320.0000.0000.0000.000
10A10SER00.0200.03417.9010.0190.0190.0000.0000.0000.000
11A11PRO00.0500.01018.643-0.033-0.0330.0000.0000.0000.000
12A12ALA00.0360.01518.793-0.017-0.0170.0000.0000.0000.000
13A13ALA00.0420.01714.461-0.062-0.0620.0000.0000.0000.000
14A14ARG10.8290.89714.1570.2900.2900.0000.0000.0000.000
15A15LYS10.8960.92115.3000.4630.4630.0000.0000.0000.000
16A16VAL00.0320.00711.2440.0050.0050.0000.0000.0000.000
17A17ARG10.7940.88810.0280.6260.6260.0000.0000.0000.000
18A18VAL0-0.004-0.00711.508-0.001-0.0010.0000.0000.0000.000
19A19ALA00.009-0.00613.7950.0390.0390.0000.0000.0000.000
20A20LEU00.0120.0157.5070.0380.0380.0000.0000.0000.000
21A21ALA00.0090.01210.2310.0380.0380.0000.0000.0000.000
22A22GLU-1-0.815-0.87611.131-0.251-0.2510.0000.0000.0000.000
23A23LYS10.7810.88812.1620.6280.6280.0000.0000.0000.000
24A24ARG10.8380.91610.5420.3680.3680.0000.0000.0000.000
25A25LEU0-0.0180.0117.6060.0280.0280.0000.0000.0000.000
26A26ASP-1-0.902-0.9482.922-1.470-0.9660.121-0.110-0.5140.000
27A27TYR0-0.042-0.0302.183-1.081-0.7381.945-0.937-1.351-0.002
28A28GLU-1-0.846-0.9202.762-2.424-2.0182.1230.658-3.187-0.007
29A29ALA0-0.038-0.0313.997-1.130-1.0420.0130.017-0.1180.000
30A30VAL0-0.004-0.0086.8110.3280.3280.0000.0000.0000.000
31A31ILE0-0.033-0.0219.449-0.033-0.0330.0000.0000.0000.000
32A32GLU-1-0.831-0.91813.227-0.670-0.6700.0000.0000.0000.000
33A33GLU-1-0.942-0.98315.443-0.293-0.2930.0000.0000.0000.000
34A34THR00.0290.01418.2530.0270.0270.0000.0000.0000.000
35A35TRP0-0.052-0.02320.5700.0120.0120.0000.0000.0000.000
36A36ILE0-0.050-0.02221.8720.0450.0450.0000.0000.0000.000
37A37ARG10.8470.90921.8660.2600.2600.0000.0000.0000.000
38A38ASN00.0520.01416.4360.0510.0510.0000.0000.0000.000
39A39GLU-1-0.832-0.91220.070-0.341-0.3410.0000.0000.0000.000
40A40SER0-0.003-0.00315.808-0.003-0.0030.0000.0000.0000.000
41A41PHE0-0.033-0.00514.028-0.074-0.0740.0000.0000.0000.000
42A42LEU00.012-0.00316.801-0.035-0.0350.0000.0000.0000.000
43A43ALA0-0.054-0.01817.5060.0090.0090.0000.0000.0000.000
44A44MET0-0.0420.00212.150-0.087-0.0870.0000.0000.0000.000
45A45ASN0-0.010-0.01615.6880.0210.0210.0000.0000.0000.000
46A46PRO00.0160.01018.0410.0370.0370.0000.0000.0000.000
47A47GLU-1-0.972-0.99221.322-0.426-0.4260.0000.0000.0000.000
48A48GLY0-0.026-0.01420.3570.0250.0250.0000.0000.0000.000
49A49GLU-1-0.949-0.96019.733-0.436-0.4360.0000.0000.0000.000
50A50VAL0-0.074-0.01014.794-0.096-0.0960.0000.0000.0000.000
51A51PRO0-0.057-0.04813.6590.0890.0890.0000.0000.0000.000
52A52VAL00.0120.00511.9530.0830.0830.0000.0000.0000.000
53A53LEU0-0.032-0.0177.917-0.219-0.2190.0000.0000.0000.000
54A54VAL00.0050.0096.4150.4040.4040.0000.0000.0000.000
55A55GLU-1-0.715-0.8036.166-3.709-3.7090.0000.0000.0000.000
56A56ALA0-0.011-0.0112.721-0.965-0.4770.298-0.269-0.5170.000
57A57ASP-1-0.920-0.9594.124-0.430-0.2760.002-0.018-0.1380.000
58A58GLY0-0.007-0.0046.5210.2460.2460.0000.0000.0000.000
59A59LEU0-0.0120.0097.9800.1080.1080.0000.0000.0000.000
60A60THR0-0.009-0.0129.752-0.410-0.4100.0000.0000.0000.000
61A61ILE0-0.046-0.01211.8200.2420.2420.0000.0000.0000.000
62A62THR00.0590.00813.914-0.181-0.1810.0000.0000.0000.000
63A63ASP-1-0.748-0.86816.597-0.471-0.4710.0000.0000.0000.000
64A64GLY00.008-0.00117.067-0.051-0.0510.0000.0000.0000.000
65A65TRP0-0.101-0.06917.9070.0050.0050.0000.0000.0000.000
66A66ALA00.0210.01518.7170.0070.0070.0000.0000.0000.000
67A67ILE0-0.020-0.00812.856-0.026-0.0260.0000.0000.0000.000
68A68CYS0-0.061-0.03315.414-0.010-0.0100.0000.0000.0000.000
69A69GLU-1-0.774-0.87117.128-0.377-0.3770.0000.0000.0000.000
70A70TYR00.034-0.00110.8630.0830.0830.0000.0000.0000.000
71A71LEU0-0.029-0.03511.0230.0030.0030.0000.0000.0000.000
72A72GLU-1-0.771-0.82614.799-0.346-0.3460.0000.0000.0000.000
73A73GLU-1-0.982-0.98918.106-0.399-0.3990.0000.0000.0000.000
74A74VAL0-0.023-0.00812.7130.0650.0650.0000.0000.0000.000
75A75TYR0-0.083-0.0699.5760.0450.0450.0000.0000.0000.000
76A76PRO00.0270.02515.123-0.005-0.0050.0000.0000.0000.000
77A77GLU-1-0.930-0.95117.528-0.216-0.2160.0000.0000.0000.000
78A78PRO0-0.045-0.02515.598-0.025-0.0250.0000.0000.0000.000
79A79SER0-0.024-0.05918.031-0.046-0.0460.0000.0000.0000.000
80A80LEU0-0.037-0.03316.2880.0150.0150.0000.0000.0000.000
81A81LEU0-0.043-0.02820.5330.0130.0130.0000.0000.0000.000
82A82GLY00.0510.02223.5560.0250.0250.0000.0000.0000.000
83A83GLY00.0010.00325.908-0.009-0.0090.0000.0000.0000.000
84A84PRO00.0390.01128.219-0.001-0.0010.0000.0000.0000.000
85A85ALA00.0470.01030.653-0.010-0.0100.0000.0000.0000.000
86A86ALA00.005-0.00331.702-0.008-0.0080.0000.0000.0000.000
87A87MET00.0100.02427.1790.0020.0020.0000.0000.0000.000
88A88ARG10.9660.97924.0860.2730.2730.0000.0000.0000.000
89A89ALA0-0.010-0.00828.197-0.016-0.0160.0000.0000.0000.000
90A90GLU-1-0.732-0.82330.833-0.183-0.1830.0000.0000.0000.000
91A91VAL00.0110.00224.375-0.005-0.0050.0000.0000.0000.000
92A92ARG10.8050.87724.2450.3160.3160.0000.0000.0000.000
93A93ARG10.7710.87727.5070.1770.1770.0000.0000.0000.000
94A94LEU0-0.009-0.01028.6600.0010.0010.0000.0000.0000.000
95A95VAL00.0070.00423.499-0.002-0.0020.0000.0000.0000.000
96A96ALA00.0190.01226.106-0.006-0.0060.0000.0000.0000.000
97A97TRP0-0.077-0.04628.5620.0110.0110.0000.0000.0000.000
98A98PHE0-0.006-0.02026.5620.0110.0110.0000.0000.0000.000
99A99ASP-1-0.687-0.84523.264-0.408-0.4080.0000.0000.0000.000
100A100ARG10.9210.98126.4200.2350.2350.0000.0000.0000.000
101A101LYS10.8170.90329.9570.1750.1750.0000.0000.0000.000
102A102PHE00.0070.00128.4820.0100.0100.0000.0000.0000.000
103A103ASN00.0230.00326.7820.0010.0010.0000.0000.0000.000
104A104ARG10.9300.97629.0220.2280.2280.0000.0000.0000.000
105A105GLU-1-0.846-0.89632.231-0.158-0.1580.0000.0000.0000.000
106A106VAL00.000-0.01431.0150.0150.0150.0000.0000.0000.000
107A107THR00.007-0.03025.5160.0120.0120.0000.0000.0000.000
108A108GLU-1-0.900-0.94528.757-0.258-0.2580.0000.0000.0000.000
109A109PRO0-0.047-0.01329.8350.0030.0030.0000.0000.0000.000
110A110LEU0-0.025-0.02230.7830.0080.0080.0000.0000.0000.000
111A111VAL00.0590.03525.0260.0080.0080.0000.0000.0000.000
112A112ARG10.8690.93228.2590.2010.2010.0000.0000.0000.000
113A113GLU-1-0.817-0.91129.935-0.158-0.1580.0000.0000.0000.000
114A114LYS10.8410.90131.0910.1530.1530.0000.0000.0000.000
115A115LEU0-0.030-0.00725.2780.0080.0080.0000.0000.0000.000
116A116LEU00.0460.01625.0710.0060.0060.0000.0000.0000.000
117A117LYS10.8360.91827.5860.1620.1620.0000.0000.0000.000
118A118ARG10.9010.95929.6970.1430.1430.0000.0000.0000.000
119A119VAL0-0.0230.00123.9350.0090.0090.0000.0000.0000.000
120A120ILE00.0230.03126.5210.0040.0040.0000.0000.0000.000
121A121SER00.006-0.02128.8430.0090.0090.0000.0000.0000.000
122A122GLY0-0.018-0.00931.5760.0090.0090.0000.0000.0000.000
123A123GLY00.0090.02533.1850.0030.0030.0000.0000.0000.000
124A124ALA0-0.024-0.02036.020-0.003-0.0030.0000.0000.0000.000
125A125PRO00.0280.00935.576-0.005-0.0050.0000.0000.0000.000
126A126ASP-1-0.821-0.89537.173-0.121-0.1210.0000.0000.0000.000
127A127SER00.011-0.03038.662-0.002-0.0020.0000.0000.0000.000
128A128ARG10.8720.93540.8310.1030.1030.0000.0000.0000.000
129A129GLN00.0700.04936.321-0.009-0.0090.0000.0000.0000.000
130A130ILE00.0450.02935.390-0.004-0.0040.0000.0000.0000.000
131A131ARG10.8620.92037.3590.1090.1090.0000.0000.0000.000
132A132ALA00.0320.02738.7770.0020.0020.0000.0000.0000.000
133A133GLY00.0700.04135.207-0.001-0.0010.0000.0000.0000.000
134A134ARG10.8870.91735.6530.1190.1190.0000.0000.0000.000
135A135ALA0-0.067-0.02937.1500.0040.0040.0000.0000.0000.000
136A136ASN00.0130.00536.4740.0090.0090.0000.0000.0000.000
137A137VAL00.0050.00532.448-0.003-0.0030.0000.0000.0000.000
138A138HIS00.0180.02935.097-0.002-0.0020.0000.0000.0000.000
139A139THR0-0.047-0.02737.9170.0050.0050.0000.0000.0000.000
140A140HIS0-0.011-0.01732.751-0.004-0.0040.0000.0000.0000.000
141A141LEU00.0320.03131.929-0.005-0.0050.0000.0000.0000.000
142A142ARG10.9941.00334.8280.1180.1180.0000.0000.0000.000
143A143TYR0-0.027-0.00633.9330.0010.0010.0000.0000.0000.000
144A144ILE00.0190.00629.9450.0000.0000.0000.0000.0000.000
145A145SER00.008-0.00133.5400.0020.0020.0000.0000.0000.000
146A146TRP0-0.0100.00436.0970.0060.0060.0000.0000.0000.000
147A147LEU0-0.066-0.04232.3810.0040.0040.0000.0000.0000.000
148A148ILE0-0.050-0.01830.5110.0000.0000.0000.0000.0000.000
149A149ASP-1-0.904-0.93634.003-0.094-0.0940.0000.0000.0000.000
150A150ARG10.8730.94136.9270.1150.1150.0000.0000.0000.000
151A151ARG10.7490.86632.5960.1630.1630.0000.0000.0000.000
152A152ARG10.9170.97829.1190.1300.1300.0000.0000.0000.000
153A153TRP00.0260.01225.105-0.005-0.0050.0000.0000.0000.000
154A154LEU0-0.018-0.01527.3030.0080.0080.0000.0000.0000.000
155A155ALA0-0.013-0.00627.9040.0080.0080.0000.0000.0000.000
156A156GLY0-0.013-0.01029.8260.0050.0050.0000.0000.0000.000
157A157ASP-1-0.877-0.93929.877-0.164-0.1640.0000.0000.0000.000
158A158MET0-0.003-0.00423.6190.0120.0120.0000.0000.0000.000
159A159LEU00.0000.01020.468-0.003-0.0030.0000.0000.0000.000
160A160THR0-0.016-0.00622.252-0.015-0.0150.0000.0000.0000.000
161A161TYR00.0880.01116.844-0.012-0.0120.0000.0000.0000.000
162A162ALA0-0.0250.01021.551-0.004-0.0040.0000.0000.0000.000
163A163ASP-1-0.732-0.88023.326-0.233-0.2330.0000.0000.0000.000
164A164ILE00.0370.02217.3990.0050.0050.0000.0000.0000.000
165A165THR0-0.003-0.00520.919-0.021-0.0210.0000.0000.0000.000
166A166ALA00.0230.02522.3890.0050.0050.0000.0000.0000.000
167A167ALA00.0180.01222.2650.0130.0130.0000.0000.0000.000
168A168CYS0-0.0150.00618.878-0.004-0.0040.0000.0000.0000.000
169A169HIS00.0020.01621.3900.0240.0240.0000.0000.0000.000
170A170LEU00.0040.00124.4920.0150.0150.0000.0000.0000.000
171A171SER0-0.0050.01221.5830.0080.0080.0000.0000.0000.000
172A172LEU00.0060.00121.4320.0170.0170.0000.0000.0000.000
173A173ILE0-0.039-0.02324.6050.0180.0180.0000.0000.0000.000
174A174ASP-1-0.817-0.90126.369-0.146-0.1460.0000.0000.0000.000
175A175TYR0-0.0020.00022.2640.0140.0140.0000.0000.0000.000
176A176ALA0-0.038-0.02626.3540.0140.0140.0000.0000.0000.000
177A177GLY0-0.039-0.01129.4850.0120.0120.0000.0000.0000.000
178A178ASP-1-0.859-0.90931.433-0.133-0.1330.0000.0000.0000.000
179A179VAL00.0220.00729.641-0.001-0.0010.0000.0000.0000.000
180A180PRO0-0.044-0.00132.9660.0060.0060.0000.0000.0000.000
181A181TRP00.045-0.02528.4290.0020.0020.0000.0000.0000.000
182A182GLU-1-0.859-0.93234.865-0.089-0.0890.0000.0000.0000.000
183A183ASP-1-0.899-0.93738.078-0.093-0.0930.0000.0000.0000.000
184A184HIS0-0.121-0.08136.015-0.001-0.0010.0000.0000.0000.000
185A185PRO00.0800.03435.704-0.008-0.0080.0000.0000.0000.000
186A186GLN00.0140.01235.344-0.004-0.0040.0000.0000.0000.000
187A187ALA00.0090.00032.425-0.006-0.0060.0000.0000.0000.000
188A188LYS10.8520.92731.0920.0870.0870.0000.0000.0000.000
189A189GLU-1-0.906-0.95330.530-0.111-0.1110.0000.0000.0000.000
190A190TRP0-0.051-0.02025.849-0.006-0.0060.0000.0000.0000.000
191A191TYR0-0.021-0.02724.180-0.023-0.0230.0000.0000.0000.000
192A192ALA00.0400.02325.671-0.013-0.0130.0000.0000.0000.000
193A193LEU00.0050.01125.669-0.002-0.0020.0000.0000.0000.000
194A194VAL0-0.056-0.03321.421-0.010-0.0100.0000.0000.0000.000
195A195LYS10.8070.89821.1580.1330.1330.0000.0000.0000.000
196A196SER00.0200.00821.0400.0040.0040.0000.0000.0000.000
197A197ARG10.7730.88618.7260.2810.2810.0000.0000.0000.000
198A198PRO0-0.020-0.02714.999-0.014-0.0140.0000.0000.0000.000
199A199SER0-0.038-0.02613.500-0.006-0.0060.0000.0000.0000.000
200A200PHE00.0590.01814.409-0.059-0.0590.0000.0000.0000.000
201A201ARG10.9730.99614.7270.1380.1380.0000.0000.0000.000
202A202PRO00.0200.00111.6840.0350.0350.0000.0000.0000.000
203A203LEU0-0.015-0.00114.3700.0090.0090.0000.0000.0000.000
204A204LEU0-0.0500.00417.1990.0260.0260.0000.0000.0000.000
205A205THR00.001-0.01216.0610.0230.0230.0000.0000.0000.000
206A206GLU-1-0.850-0.88212.719-0.366-0.3660.0000.0000.0000.000
207A207THR0-0.060-0.04017.6000.0070.0070.0000.0000.0000.000
208A208ILE00.0140.01519.669-0.020-0.0200.0000.0000.0000.000
209A209SER0-0.0450.00421.8270.0240.0240.0000.0000.0000.000
210A210PRO00.0920.04124.346-0.016-0.0160.0000.0000.0000.000
211A211ILE0-0.034-0.03026.1860.0170.0170.0000.0000.0000.000
212A212ARG10.8470.92423.8560.1120.1120.0000.0000.0000.000
213A213PRO00.0670.05024.0890.0000.0000.0000.0000.0000.000
214A214PRO00.0110.00127.1310.0160.0160.0000.0000.0000.000
215A215ARG10.9600.96628.3550.0580.0580.0000.0000.0000.000
216A216HIS00.020-0.00129.2140.0140.0140.0000.0000.0000.000
217A217TYR0-0.061-0.01920.771-0.012-0.0120.0000.0000.0000.000
218A218ALA00.005-0.01222.731-0.014-0.0140.0000.0000.0000.000
219A219ASP-1-0.887-0.93424.176-0.074-0.0740.0000.0000.0000.000
220A220LEU0-0.022-0.02622.146-0.013-0.0130.0000.0000.0000.000
221A221ASP-1-0.904-0.93626.183-0.077-0.0770.0000.0000.0000.000
222A222PHE0-0.074-0.03328.3280.0040.0040.0000.0000.0000.000