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: MVVKZ

Calculation Name: 5MJW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5MJW

Chain ID: A

ChEMBL ID:

UniProt ID: Q8DJT8

Base Structure: X-ray

Registration Date: 2023-06-21

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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2127734.033729
FMO2-HF: Nuclear repulsion 2049926.934194
FMO2-HF: Total energy -77807.099535
FMO2-MP2: Total energy -78037.003443


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:4:PRO)


Summations of interaction energy for fragment #1(A:4:PRO)
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.
-0.350.965-0.013-0.546-0.7570.003
Interaction energy analysis for fragmet #1(A:4:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.034 / q_NPA : -0.007
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].
3A6THR00.0530.0033.876-0.7350.580-0.013-0.546-0.7570.003
4A7VAL00.0610.0136.3800.4910.4910.0000.0000.0000.000
5A8SER00.0240.0049.7940.1790.1790.0000.0000.0000.000
6A9ASP-1-0.753-0.8336.524-1.145-1.1450.0000.0000.0000.000
7A10THR0-0.058-0.0178.8500.3000.3000.0000.0000.0000.000
8A11LYS10.9821.00011.0990.3140.3140.0000.0000.0000.000
9A12ARG10.8860.9249.2740.5060.5060.0000.0000.0000.000
10A13ALA0-0.015-0.00412.1620.0380.0380.0000.0000.0000.000
11A14PHE00.0030.00714.1210.0190.0190.0000.0000.0000.000
12A15TYR00.018-0.01116.955-0.001-0.0010.0000.0000.0000.000
13A16ALA0-0.027-0.00316.6120.0000.0000.0000.0000.0000.000
14A17ALA0-0.027-0.00318.4770.0120.0120.0000.0000.0000.000
15A18HIS0-0.055-0.02620.1270.0080.0080.0000.0000.0000.000
16A19THR00.0310.01022.384-0.016-0.0160.0000.0000.0000.000
17A20ARG10.9340.97524.077-0.052-0.0520.0000.0000.0000.000
18A21PRO00.0300.00526.607-0.004-0.0040.0000.0000.0000.000
19A22ILE0-0.0070.00723.7920.0060.0060.0000.0000.0000.000
20A23HIS00.0590.02827.692-0.006-0.0060.0000.0000.0000.000
21A24SER00.020-0.00430.015-0.004-0.0040.0000.0000.0000.000
22A25ILE00.0160.01732.3210.0030.0030.0000.0000.0000.000
23A26TYR00.0550.02332.2540.0030.0030.0000.0000.0000.000
24A27ARG10.7750.88729.4700.0300.0300.0000.0000.0000.000
25A28ARG10.8600.92634.6290.0130.0130.0000.0000.0000.000
26A29PHE00.0530.02137.9090.0020.0020.0000.0000.0000.000
27A30ILE00.0110.01534.9020.0000.0000.0000.0000.0000.000
28A31GLU-1-0.855-0.93134.727-0.022-0.0220.0000.0000.0000.000
29A32GLU-1-0.867-0.93339.269-0.014-0.0140.0000.0000.0000.000
30A33LEU0-0.0070.00542.2170.0010.0010.0000.0000.0000.000
31A34LEU00.0040.00738.8240.0000.0000.0000.0000.0000.000
32A35VAL0-0.010-0.00242.7440.0020.0020.0000.0000.0000.000
33A36GLU-1-0.818-0.88045.155-0.019-0.0190.0000.0000.0000.000
34A37ILE0-0.025-0.01045.3880.0010.0010.0000.0000.0000.000
35A38HIS00.0680.04046.1400.0000.0000.0000.0000.0000.000
36A39LEU0-0.050-0.03648.1350.0010.0010.0000.0000.0000.000
37A40LEU0-0.074-0.02650.7560.0010.0010.0000.0000.0000.000
38A41ARG10.8200.90648.6840.0230.0230.0000.0000.0000.000
39A42VAL0-0.036-0.01150.7380.0000.0000.0000.0000.0000.000
40A43ASN0-0.035-0.00453.5150.0020.0020.0000.0000.0000.000
41A44VAL00.0460.01056.810-0.001-0.0010.0000.0000.0000.000
42A45ASP-1-0.830-0.89159.978-0.010-0.0100.0000.0000.0000.000
43A46PHE0-0.049-0.01553.306-0.001-0.0010.0000.0000.0000.000
44A47ARG10.9390.96158.1360.0160.0160.0000.0000.0000.000
45A48TYR0-0.049-0.03851.1850.0000.0000.0000.0000.0000.000
46A49SER00.012-0.00755.5400.0000.0000.0000.0000.0000.000
47A50PRO00.0950.02954.9100.0000.0000.0000.0000.0000.000
48A51LEU0-0.0230.03354.602-0.001-0.0010.0000.0000.0000.000
49A52PHE00.0280.00349.8500.0000.0000.0000.0000.0000.000
50A53ALA0-0.0010.00950.556-0.001-0.0010.0000.0000.0000.000
51A54LEU00.0230.01049.698-0.002-0.0020.0000.0000.0000.000
52A55GLY00.0140.02050.147-0.001-0.0010.0000.0000.0000.000
53A56VAL0-0.022-0.01845.879-0.001-0.0010.0000.0000.0000.000
54A57VAL0-0.027-0.00645.443-0.001-0.0010.0000.0000.0000.000
55A58THR00.006-0.00545.193-0.002-0.0020.0000.0000.0000.000
56A59ALA0-0.048-0.02645.936-0.001-0.0010.0000.0000.0000.000
57A60PHE0-0.021-0.00937.736-0.001-0.0010.0000.0000.0000.000
58A61ASP-1-0.857-0.93941.263-0.050-0.0500.0000.0000.0000.000
59A62GLN00.0370.03341.3580.0000.0000.0000.0000.0000.000
60A63PHE0-0.027-0.01638.8750.0000.0000.0000.0000.0000.000
61A64MET0-0.042-0.02134.601-0.002-0.0020.0000.0000.0000.000
62A65GLU-1-0.849-0.90936.698-0.051-0.0510.0000.0000.0000.000
63A66GLY0-0.007-0.00235.725-0.003-0.0030.0000.0000.0000.000
64A67TYR0-0.083-0.03729.3750.0000.0000.0000.0000.0000.000
65A68GLN00.0380.01328.493-0.006-0.0060.0000.0000.0000.000
66A69PRO0-0.031-0.01026.229-0.001-0.0010.0000.0000.0000.000
67A70GLU-1-0.814-0.91628.677-0.083-0.0830.0000.0000.0000.000
68A71GLY0-0.033-0.00731.1150.0050.0050.0000.0000.0000.000
69A72ASP-1-0.857-0.93628.725-0.106-0.1060.0000.0000.0000.000
70A73ARG10.8370.92332.0410.0800.0800.0000.0000.0000.000
71A74ASP-1-0.770-0.87835.550-0.057-0.0570.0000.0000.0000.000
72A75ARG10.8470.91828.6910.1120.1120.0000.0000.0000.000
73A76ILE00.0110.00232.0990.0040.0040.0000.0000.0000.000
74A77PHE00.0260.02835.8020.0050.0050.0000.0000.0000.000
75A78HIS0-0.004-0.00737.7370.0040.0040.0000.0000.0000.000
76A79ALA00.005-0.00535.7350.0030.0030.0000.0000.0000.000
77A80LEU00.0090.00537.8520.0040.0040.0000.0000.0000.000
78A81CYS0-0.030-0.00640.4290.0040.0040.0000.0000.0000.000
79A82VAL0-0.022-0.01339.2700.0020.0020.0000.0000.0000.000
80A83ALA0-0.039-0.00939.7420.0020.0020.0000.0000.0000.000
81A84GLU-1-0.857-0.94441.724-0.020-0.0200.0000.0000.0000.000
82A85GLU-1-0.919-0.94644.660-0.020-0.0200.0000.0000.0000.000
83A86MET0-0.051-0.02045.8330.0010.0010.0000.0000.0000.000
84A87ASN00.0450.01445.570-0.004-0.0040.0000.0000.0000.000
85A88PRO00.0390.00342.0630.0010.0010.0000.0000.0000.000
86A89GLN0-0.104-0.06244.721-0.003-0.0030.0000.0000.0000.000
87A90GLN00.0070.00646.4040.0000.0000.0000.0000.0000.000
88A91LEU00.0280.01146.7630.0010.0010.0000.0000.0000.000
89A92LYS10.8690.91741.4660.0560.0560.0000.0000.0000.000
90A93GLU-1-0.878-0.91947.770-0.040-0.0400.0000.0000.0000.000
91A94ASP-1-0.800-0.88950.881-0.029-0.0290.0000.0000.0000.000
92A95ALA0-0.030-0.00149.3850.0010.0010.0000.0000.0000.000
93A96ALA00.0440.01649.9290.0010.0010.0000.0000.0000.000
94A97SER0-0.058-0.04151.7900.0010.0010.0000.0000.0000.000
95A98TRP00.000-0.02754.4510.0020.0020.0000.0000.0000.000
96A99GLN0-0.032-0.02951.2420.0000.0000.0000.0000.0000.000
97A100GLN0-0.080-0.02855.6990.0010.0010.0000.0000.0000.000
98A101TYR0-0.047-0.05158.7860.0010.0010.0000.0000.0000.000
99A102GLN0-0.021-0.00153.0640.0000.0000.0000.0000.0000.000
100A103GLY0-0.0120.00258.4010.0000.0000.0000.0000.0000.000
101A104ARG10.8190.90661.1160.0250.0250.0000.0000.0000.000
102A105PRO00.0060.01463.4540.0000.0000.0000.0000.0000.000
103A106LEU00.0780.02864.6670.0000.0000.0000.0000.0000.000
104A107SER00.005-0.00366.4490.0000.0000.0000.0000.0000.000
105A108GLN00.0240.00067.7150.0000.0000.0000.0000.0000.000
106A109ILE00.0010.01563.6700.0000.0000.0000.0000.0000.000
107A110LEU00.0100.00567.0760.0000.0000.0000.0000.0000.000
108A111ASP-1-0.923-0.94769.874-0.016-0.0160.0000.0000.0000.000
109A112GLU-1-0.713-0.81566.680-0.022-0.0220.0000.0000.0000.000
110A113LEU0-0.043-0.01265.7900.0000.0000.0000.0000.0000.000
111A114ASN0-0.040-0.03969.7110.0010.0010.0000.0000.0000.000
112A115SER0-0.055-0.03271.7640.0010.0010.0000.0000.0000.000
113A116GLY0-0.019-0.00473.4760.0000.0000.0000.0000.0000.000
114A117GLN0-0.103-0.05071.5620.0000.0000.0000.0000.0000.000
115A118PRO00.0040.01166.879-0.001-0.0010.0000.0000.0000.000
116A119SER0-0.020-0.02464.6720.0000.0000.0000.0000.0000.000
117A120ALA0-0.0080.01461.2130.0000.0000.0000.0000.0000.000
118A121PRO00.0470.01657.5660.0000.0000.0000.0000.0000.000
119A122LEU00.0310.03560.2550.0010.0010.0000.0000.0000.000
120A123ASN0-0.011-0.02662.6170.0000.0000.0000.0000.0000.000
121A124SER0-0.035-0.04459.8750.0010.0010.0000.0000.0000.000
122A125LEU0-0.007-0.00460.6700.0000.0000.0000.0000.0000.000
123A126ASN0-0.007-0.01162.9860.0010.0010.0000.0000.0000.000
124A127HIS0-0.061-0.03163.2740.0010.0010.0000.0000.0000.000
125A128THR0-0.026-0.01059.9500.0000.0000.0000.0000.0000.000
126A129GLY00.0030.01659.4150.0000.0000.0000.0000.0000.000
127A130LYS10.7810.85258.1580.0100.0100.0000.0000.0000.000
128A131TYR0-0.049-0.04957.438-0.001-0.0010.0000.0000.0000.000
129A132SER00.0270.01452.7610.0010.0010.0000.0000.0000.000
130A133ARG10.8350.88546.6710.0220.0220.0000.0000.0000.000
131A134LEU00.0110.00848.475-0.001-0.0010.0000.0000.0000.000
132A135HIS00.0500.01652.373-0.001-0.0010.0000.0000.0000.000
133A136ALA00.0010.00955.6430.0000.0000.0000.0000.0000.000
134A137VAL00.0070.00049.5880.0000.0000.0000.0000.0000.000
135A138GLY00.0310.02653.091-0.001-0.0010.0000.0000.0000.000
136A139LEU0-0.020-0.01554.193-0.001-0.0010.0000.0000.0000.000
137A140TYR00.008-0.00951.8600.0010.0010.0000.0000.0000.000
138A141ALA00.0240.01051.9340.0000.0000.0000.0000.0000.000
139A142PHE00.026-0.00553.6530.0000.0000.0000.0000.0000.000
140A143LEU0-0.005-0.01556.8300.0000.0000.0000.0000.0000.000
141A144GLN0-0.053-0.03351.1210.0010.0010.0000.0000.0000.000
142A145GLU-1-0.867-0.90452.992-0.035-0.0350.0000.0000.0000.000
143A146LEU0-0.046-0.00356.7330.0000.0000.0000.0000.0000.000
144A147ALA0-0.024-0.01360.3370.0000.0000.0000.0000.0000.000
145A148GLY0-0.014-0.02862.4300.0010.0010.0000.0000.0000.000
146A149GLU-1-0.938-0.96759.039-0.024-0.0240.0000.0000.0000.000
147A150VAL00.0310.01860.6250.0010.0010.0000.0000.0000.000
148A151THR00.0180.02056.4590.0010.0010.0000.0000.0000.000
149A152ILE00.0070.01458.6980.0000.0000.0000.0000.0000.000
150A153HIS00.0030.00060.1650.0010.0010.0000.0000.0000.000
151A154LEU0-0.020-0.01057.6020.0010.0010.0000.0000.0000.000
152A155ASN0-0.012-0.03761.6000.0000.0000.0000.0000.0000.000
153A156GLU-1-0.858-0.90363.904-0.015-0.0150.0000.0000.0000.000
154A157THR00.011-0.00962.8600.0000.0000.0000.0000.0000.000
155A158LEU0-0.049-0.02960.5200.0000.0000.0000.0000.0000.000
156A159ASP-1-0.829-0.89964.900-0.012-0.0120.0000.0000.0000.000
157A160GLN0-0.091-0.06968.2340.0000.0000.0000.0000.0000.000
158A161LEU0-0.004-0.00863.6920.0000.0000.0000.0000.0000.000
159A162ALA00.0020.01167.7740.0000.0000.0000.0000.0000.000
160A163PRO0-0.081-0.03069.2180.0000.0000.0000.0000.0000.000
161A164VAL0-0.032-0.01169.4250.0000.0000.0000.0000.0000.000
162A165ILE00.0130.00963.7660.0000.0000.0000.0000.0000.000
163A166PRO0-0.0170.00465.9690.0010.0010.0000.0000.0000.000
164A167LEU0-0.0010.00560.7670.0000.0000.0000.0000.0000.000
165A168PRO0-0.019-0.01161.9700.0010.0010.0000.0000.0000.000
166A169ILE00.0600.02063.2210.0000.0000.0000.0000.0000.000
167A170GLU-1-0.799-0.89063.197-0.011-0.0110.0000.0000.0000.000
168A171LYS10.8820.94459.6680.0100.0100.0000.0000.0000.000
169A172VAL00.0190.02058.971-0.001-0.0010.0000.0000.0000.000
170A173LYS10.8020.87158.6280.0110.0110.0000.0000.0000.000
171A174ARG10.8640.91656.9380.0100.0100.0000.0000.0000.000
172A175ASP-1-0.795-0.86954.878-0.014-0.0140.0000.0000.0000.000
173A176LEU0-0.0060.00353.861-0.001-0.0010.0000.0000.0000.000
174A177GLU-1-0.881-0.92354.254-0.014-0.0140.0000.0000.0000.000
175A178LEU0-0.049-0.02451.0010.0000.0000.0000.0000.0000.000
176A179TYR0-0.046-0.05447.1700.0000.0000.0000.0000.0000.000
177A180ARG10.9330.96849.3050.0200.0200.0000.0000.0000.000
178A181SER00.0840.05549.678-0.001-0.0010.0000.0000.0000.000
179A182ASN0-0.036-0.01946.4420.0010.0010.0000.0000.0000.000
180A183LEU00.0350.03244.437-0.001-0.0010.0000.0000.0000.000
181A184ASP-1-0.889-0.94245.067-0.027-0.0270.0000.0000.0000.000
182A185LYS10.8190.88644.6140.0160.0160.0000.0000.0000.000
183A186ILE0-0.040-0.01640.288-0.001-0.0010.0000.0000.0000.000
184A187ASN00.0320.00940.567-0.005-0.0050.0000.0000.0000.000
185A188GLN0-0.009-0.00641.133-0.001-0.0010.0000.0000.0000.000
186A189ALA0-0.032-0.00838.255-0.001-0.0010.0000.0000.0000.000
187A190ARG10.8400.90236.5260.0420.0420.0000.0000.0000.000
188A191SER0-0.032-0.00436.423-0.003-0.0030.0000.0000.0000.000
189A192LEU00.0420.02536.669-0.003-0.0030.0000.0000.0000.000
190A193MET0-0.051-0.03430.6520.0000.0000.0000.0000.0000.000
191A194LYS10.7830.88831.9870.0570.0570.0000.0000.0000.000
192A195GLU-1-0.913-0.97732.584-0.044-0.0440.0000.0000.0000.000
193A196LEU0-0.048-0.01128.846-0.001-0.0010.0000.0000.0000.000
194A197VAL0-0.095-0.04026.605-0.003-0.0030.0000.0000.0000.000
195A198GLU-1-0.832-0.89028.360-0.074-0.0740.0000.0000.0000.000