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: MV91Z

Calculation Name: 4GM2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4GM2

Chain ID: A

ChEMBL ID:

UniProt ID: Q8IL98

Base Structure: X-ray

Registration Date: 2023-06-22

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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2005078.849863
FMO2-HF: Nuclear repulsion 1932699.272482
FMO2-HF: Total energy -72379.577381
FMO2-MP2: Total energy -72593.105546


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:61:PRO)


Summations of interaction energy for fragment #1(A:61: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.
-5.5431.883.174-3.873-6.7250.007
Interaction energy analysis for fragmet #1(A:61:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.082 / q_NPA : 0.036
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].
3A63LEU00.0390.0162.370-4.874-0.0120.805-2.342-3.3250.006
4A64LEU00.0180.0162.070-2.296-0.2622.366-1.395-3.0060.001
5A65LEU00.0690.0433.8400.4140.9410.003-0.136-0.3940.000
6A66SER0-0.065-0.0315.8080.5780.5780.0000.0000.0000.000
7A67LYS10.8970.9477.4080.6540.6540.0000.0000.0000.000
8A68ARG10.8120.9058.7960.4510.4510.0000.0000.0000.000
9A69ILE0-0.038-0.0096.1830.1820.1820.0000.0000.0000.000
10A70ILE00.0280.0245.637-0.501-0.5010.0000.0000.0000.000
11A71PHE0-0.037-0.0275.2680.1270.1270.0000.0000.0000.000
12A72LEU00.0070.0176.9520.3600.3600.0000.0000.0000.000
13A73SER0-0.033-0.0237.811-0.086-0.0860.0000.0000.0000.000
14A74SER00.0410.01610.4890.0480.0480.0000.0000.0000.000
15A75PRO00.0210.03312.957-0.035-0.0350.0000.0000.0000.000
16A76ILE00.003-0.00814.1400.0480.0480.0000.0000.0000.000
17A77TYR00.0320.01013.345-0.029-0.0290.0000.0000.0000.000
18A78PRO00.0440.01314.8380.0070.0070.0000.0000.0000.000
19A79HIS00.0740.03410.410-0.069-0.0690.0000.0000.0000.000
20A80ILE0-0.046-0.0089.4050.0170.0170.0000.0000.0000.000
21A81SER0-0.015-0.02711.082-0.027-0.0270.0000.0000.0000.000
22A82GLU-1-0.901-0.94112.4660.0930.0930.0000.0000.0000.000
23A83GLN0-0.009-0.0107.1310.0860.0860.0000.0000.0000.000
24A84ILE0-0.009-0.0029.113-0.121-0.1210.0000.0000.0000.000
25A85ILE00.0480.02510.706-0.081-0.0810.0000.0000.0000.000
26A86SER0-0.017-0.00510.211-0.037-0.0370.0000.0000.0000.000
27A87GLN0-0.028-0.0225.723-0.388-0.3880.0000.0000.0000.000
28A88LEU0-0.0020.0019.547-0.058-0.0580.0000.0000.0000.000
29A89LEU0-0.0020.00012.898-0.006-0.0060.0000.0000.0000.000
30A90TYR0-0.005-0.00310.080-0.026-0.0260.0000.0000.0000.000
31A91LEU00.0190.0009.032-0.001-0.0010.0000.0000.0000.000
32A92GLU-1-0.748-0.84912.926-0.129-0.1290.0000.0000.0000.000
33A93TYR0-0.076-0.04816.0530.0290.0290.0000.0000.0000.000
34A94GLU-1-0.984-0.96613.311-0.272-0.2720.0000.0000.0000.000
35A95SER0-0.073-0.05116.1820.0190.0190.0000.0000.0000.000
36A96LYS10.8910.96317.5470.1080.1080.0000.0000.0000.000
37A97ARG11.0081.00619.9330.1070.1070.0000.0000.0000.000
38A98LYS10.9670.98316.0190.2650.2650.0000.0000.0000.000
39A99PRO00.0250.01516.372-0.023-0.0230.0000.0000.0000.000
40A100ILE0-0.0100.00411.032-0.047-0.0470.0000.0000.0000.000
41A101HIS00.0210.04310.7330.0830.0830.0000.0000.0000.000
42A102LEU00.0500.0229.906-0.085-0.0850.0000.0000.0000.000
43A103TYR0-0.015-0.0149.2160.0440.0440.0000.0000.0000.000
44A104ILE00.003-0.01110.5010.0600.0600.0000.0000.0000.000
45A105ASN0-0.028-0.01312.519-0.044-0.0440.0000.0000.0000.000
46A106SER0-0.005-0.02013.6920.0380.0380.0000.0000.0000.000
47A107THR0-0.021-0.03415.704-0.021-0.0210.0000.0000.0000.000
48A108GLY00.0220.01617.794-0.015-0.0150.0000.0000.0000.000
49A109ASP-1-0.820-0.91218.3100.1070.1070.0000.0000.0000.000
50A110ILE0-0.0080.00920.626-0.002-0.0020.0000.0000.0000.000
51A111ASP-1-0.866-0.96119.6460.1950.1950.0000.0000.0000.000
52A112ASN0-0.0160.00021.693-0.016-0.0160.0000.0000.0000.000
53A113ASN0-0.025-0.01824.802-0.004-0.0040.0000.0000.0000.000
54A114LYS10.9200.97224.551-0.086-0.0860.0000.0000.0000.000
55A115ILE00.0450.02323.7850.0090.0090.0000.0000.0000.000
56A116ILE0-0.055-0.01717.772-0.001-0.0010.0000.0000.0000.000
57A117ASN0-0.030-0.04417.8790.0010.0010.0000.0000.0000.000
58A118LEU0-0.010-0.00821.045-0.009-0.0090.0000.0000.0000.000
59A119ASN00.0080.01022.034-0.014-0.0140.0000.0000.0000.000
60A120GLY00.0760.04420.334-0.003-0.0030.0000.0000.0000.000
61A121ILE00.002-0.00821.052-0.005-0.0050.0000.0000.0000.000
62A122THR00.0530.01423.030-0.006-0.0060.0000.0000.0000.000
63A123ASP-1-0.814-0.88918.1220.0730.0730.0000.0000.0000.000
64A124VAL0-0.046-0.03318.480-0.009-0.0090.0000.0000.0000.000
65A125ILE0-0.026-0.01719.861-0.013-0.0130.0000.0000.0000.000
66A126SER00.0270.01019.760-0.011-0.0110.0000.0000.0000.000
67A127ILE0-0.042-0.01215.242-0.011-0.0110.0000.0000.0000.000
68A128VAL0-0.028-0.01418.127-0.018-0.0180.0000.0000.0000.000
69A129ASP-1-0.886-0.94020.516-0.028-0.0280.0000.0000.0000.000
70A130VAL0-0.042-0.02516.561-0.008-0.0080.0000.0000.0000.000
71A131ILE0-0.065-0.03616.131-0.016-0.0160.0000.0000.0000.000
72A132ASN0-0.037-0.02219.066-0.010-0.0100.0000.0000.0000.000
73A133TYR0-0.076-0.01622.0440.0010.0010.0000.0000.0000.000
74A134ILE0-0.071-0.02116.552-0.004-0.0040.0000.0000.0000.000
75A135SER0-0.082-0.06920.7950.0040.0040.0000.0000.0000.000
76A136SER0-0.052-0.03216.858-0.005-0.0050.0000.0000.0000.000
77A137ASP-1-0.861-0.92018.657-0.107-0.1070.0000.0000.0000.000
78A138VAL00.0230.00314.733-0.030-0.0300.0000.0000.0000.000
79A139TYR0-0.039-0.01815.5640.0250.0250.0000.0000.0000.000
80A140THR0-0.004-0.01914.640-0.025-0.0250.0000.0000.0000.000
81A141TYR0-0.017-0.02913.4220.0130.0130.0000.0000.0000.000
82A142CYS0-0.0260.01114.3370.0210.0210.0000.0000.0000.000
83A143LEU0-0.004-0.04011.519-0.010-0.0100.0000.0000.0000.000
84A144GLY00.0090.00615.4710.0110.0110.0000.0000.0000.000
85A145LYS10.9340.99117.144-0.147-0.1470.0000.0000.0000.000
86A146ALA00.0700.03217.1440.0140.0140.0000.0000.0000.000
87A147TYR00.001-0.00419.127-0.013-0.0130.0000.0000.0000.000
88A148GLY00.0790.03620.8650.0100.0100.0000.0000.0000.000
89A149ILE00.0180.00419.098-0.008-0.0080.0000.0000.0000.000
90A150ALA00.0320.01017.074-0.007-0.0070.0000.0000.0000.000
91A151CYS0-0.0570.00018.504-0.015-0.0150.0000.0000.0000.000
92A152ILE00.0400.02121.246-0.011-0.0110.0000.0000.0000.000
93A153LEU0-0.0160.01014.438-0.010-0.0100.0000.0000.0000.000
94A154ALA00.0380.01317.727-0.018-0.0180.0000.0000.0000.000
95A155SER0-0.0290.01318.658-0.015-0.0150.0000.0000.0000.000
96A156SER00.004-0.03019.853-0.003-0.0030.0000.0000.0000.000
97A157GLY0-0.0100.01719.036-0.009-0.0090.0000.0000.0000.000
98A158LYS10.8790.95019.6890.0960.0960.0000.0000.0000.000
99A159LYS10.8900.94822.0010.0330.0330.0000.0000.0000.000
100A160GLY0-0.014-0.00424.944-0.003-0.0030.0000.0000.0000.000
101A161TYR0-0.067-0.05119.842-0.002-0.0020.0000.0000.0000.000
102A162ARG10.7860.92119.3450.0240.0240.0000.0000.0000.000
103A163PHE00.0310.01117.8620.0080.0080.0000.0000.0000.000
104A164SER00.0350.00218.9210.0100.0100.0000.0000.0000.000
105A165LEU0-0.0320.01216.194-0.007-0.0070.0000.0000.0000.000
106A166LYS11.0120.99120.2860.0090.0090.0000.0000.0000.000
107A167ASN0-0.038-0.02322.413-0.001-0.0010.0000.0000.0000.000
108A168SER0-0.036-0.00819.0860.0100.0100.0000.0000.0000.000
109A169SER0-0.025-0.00321.420-0.005-0.0050.0000.0000.0000.000
110A170PHE00.004-0.02220.2680.0070.0070.0000.0000.0000.000
111A171CYS0-0.030-0.00123.6560.0000.0000.0000.0000.0000.000
112A172LEU0-0.010-0.00324.7190.0030.0030.0000.0000.0000.000
113A173ASN00.0320.00725.058-0.001-0.0010.0000.0000.0000.000
114A174GLN00.0070.01328.733-0.002-0.0020.0000.0000.0000.000
115A175SER0-0.035-0.03831.2410.0030.0030.0000.0000.0000.000
116A176TYR0-0.073-0.03724.773-0.003-0.0030.0000.0000.0000.000
117A177SER0-0.012-0.01930.324-0.002-0.0020.0000.0000.0000.000
118A178ILE00.0150.01726.5600.0000.0000.0000.0000.0000.000
119A179ILE0-0.0060.00430.180-0.002-0.0020.0000.0000.0000.000
120A180PRO0-0.011-0.01028.5670.0020.0020.0000.0000.0000.000
121A181PHE00.0010.00330.711-0.003-0.0030.0000.0000.0000.000
122A182ASN0-0.030-0.01930.478-0.004-0.0040.0000.0000.0000.000
123A183GLN00.0400.02233.8400.0000.0000.0000.0000.0000.000
124A184ALA00.0270.02634.7010.0000.0000.0000.0000.0000.000
125A185THR00.004-0.01036.063-0.001-0.0010.0000.0000.0000.000
126A186ASN00.0070.00837.782-0.002-0.0020.0000.0000.0000.000
127A187ILE00.0950.04237.9840.0000.0000.0000.0000.0000.000
128A188GLU-1-0.862-0.92139.2950.0110.0110.0000.0000.0000.000
129A189ILE0-0.021-0.02835.372-0.001-0.0010.0000.0000.0000.000
130A190GLN00.0710.03633.969-0.002-0.0020.0000.0000.0000.000
131A191ASN00.004-0.01335.2640.0020.0020.0000.0000.0000.000
132A192LYS10.8660.93237.466-0.011-0.0110.0000.0000.0000.000
133A193GLU-1-0.936-0.95929.6620.0250.0250.0000.0000.0000.000
134A194ILE0-0.0040.00932.4920.0000.0000.0000.0000.0000.000
135A195MET0-0.016-0.01033.4890.0000.0000.0000.0000.0000.000
136A196ASN0-0.003-0.00433.087-0.003-0.0030.0000.0000.0000.000
137A197THR0-0.032-0.02027.954-0.002-0.0020.0000.0000.0000.000
138A198LYS10.9190.95030.120-0.026-0.0260.0000.0000.0000.000
139A199LYS10.8860.92932.4540.0000.0000.0000.0000.0000.000
140A200LYS10.9790.98228.600-0.008-0.0080.0000.0000.0000.000
141A201VAL00.0140.01926.860-0.003-0.0030.0000.0000.0000.000
142A202ILE00.0340.01728.622-0.002-0.0020.0000.0000.0000.000
143A203GLU-1-0.856-0.89830.797-0.007-0.0070.0000.0000.0000.000
144A204ILE0-0.007-0.00324.486-0.003-0.0030.0000.0000.0000.000
145A205ILE00.0140.01026.542-0.004-0.0040.0000.0000.0000.000
146A206SER00.000-0.00528.302-0.002-0.0020.0000.0000.0000.000
147A207LYS10.9700.99826.4970.0290.0290.0000.0000.0000.000
148A208ASN0-0.070-0.05123.901-0.007-0.0070.0000.0000.0000.000
149A209THR0-0.028-0.02527.442-0.002-0.0020.0000.0000.0000.000
150A210GLU-1-0.971-0.98329.811-0.025-0.0250.0000.0000.0000.000
151A211LYS10.8700.94532.5330.0080.0080.0000.0000.0000.000
152A212ASP-1-0.843-0.92134.906-0.006-0.0060.0000.0000.0000.000
153A213THR00.031-0.00634.7370.0010.0010.0000.0000.0000.000
154A214ASN0-0.036-0.01736.6760.0020.0020.0000.0000.0000.000
155A215VAL00.0400.02436.3590.0020.0020.0000.0000.0000.000
156A216ILE00.0020.00131.7240.0020.0020.0000.0000.0000.000
157A217SER00.013-0.01134.3040.0030.0030.0000.0000.0000.000
158A218ASN0-0.057-0.01336.3470.0010.0010.0000.0000.0000.000
159A219VAL0-0.032-0.01232.7040.0020.0020.0000.0000.0000.000
160A220LEU0-0.0280.00829.9740.0030.0030.0000.0000.0000.000
161A221GLU-1-0.908-0.95133.7450.0170.0170.0000.0000.0000.000
162A222ARG10.8550.91135.163-0.020-0.0200.0000.0000.0000.000
163A223ASP-1-0.801-0.87331.0210.0400.0400.0000.0000.0000.000
164A224LYS10.8980.95630.570-0.015-0.0150.0000.0000.0000.000
165A225TYR0-0.007-0.02426.8880.0020.0020.0000.0000.0000.000
166A226PHE00.0010.00826.563-0.004-0.0040.0000.0000.0000.000
167A227ASN00.0590.03626.3050.0020.0020.0000.0000.0000.000
168A228ALA00.050-0.00324.273-0.002-0.0020.0000.0000.0000.000
169A229ASP-1-0.857-0.93125.702-0.009-0.0090.0000.0000.0000.000
170A230GLU-1-0.892-0.95529.2370.0110.0110.0000.0000.0000.000
171A231ALA0-0.056-0.02825.2310.0000.0000.0000.0000.0000.000
172A232VAL0-0.005-0.00426.362-0.003-0.0030.0000.0000.0000.000
173A233ASP-1-0.942-0.95528.186-0.008-0.0080.0000.0000.0000.000
174A234PHE0-0.072-0.04629.3380.0000.0000.0000.0000.0000.000
175A235LYS10.9560.97228.6950.0160.0160.0000.0000.0000.000
176A236LEU0-0.043-0.02424.582-0.002-0.0020.0000.0000.0000.000
177A237ILE0-0.041-0.02720.917-0.003-0.0030.0000.0000.0000.000
178A238ASP-1-0.798-0.87623.620-0.044-0.0440.0000.0000.0000.000
179A239HIS0-0.005-0.00523.4930.0050.0050.0000.0000.0000.000
180A240ILE00.003-0.00122.948-0.001-0.0010.0000.0000.0000.000
181A241LEU0-0.054-0.02617.779-0.004-0.0040.0000.0000.0000.000
182A242GLU-1-0.932-0.96422.059-0.029-0.0290.0000.0000.0000.000
183A243LYS10.9350.97121.2310.0400.0400.0000.0000.0000.000