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

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FMODB ID: MNRJZ

Calculation Name: 3MGK-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 3MGK

Chain ID: A

ChEMBL ID:
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UniProt ID: Q97FB4

Base Structure: X-ray

Registration Date: 2023-09-22

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 OptHSide
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 199
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2371662.67681
FMO2-HF: Nuclear repulsion 2293399.810091
FMO2-HF: Total energy -78262.866719
FMO2-MP2: Total energy -78494.862032


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:SER)


Summations of interaction energy for fragment #1(A:2:SER)
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.
-13.425-9.4884.61-3.736-4.81-0.032
Interaction energy analysis for fragmet #1(A:2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.030 / q_NPA : -0.022
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].
3A4ARG10.8570.9313.826-1.0790.647-0.025-0.891-0.8090.001
4A5ILE0-0.036-0.0236.6490.1520.1520.0000.0000.0000.000
5A6ASP-1-0.780-0.8739.648-0.164-0.1640.0000.0000.0000.000
6A7VAL0-0.028-0.01912.8130.0250.0250.0000.0000.0000.000
7A8LEU0-0.0110.00015.4180.0590.0590.0000.0000.0000.000
8A9LEU0-0.021-0.00518.7160.0010.0010.0000.0000.0000.000
9A10PHE0-0.021-0.02421.5840.0340.0340.0000.0000.0000.000
10A11ASN00.021-0.00825.195-0.014-0.0140.0000.0000.0000.000
11A12LYS10.8270.89428.5100.1190.1190.0000.0000.0000.000
12A13PHE00.0490.04123.0530.0030.0030.0000.0000.0000.000
13A14GLU-1-0.847-0.92425.685-0.201-0.2010.0000.0000.0000.000
14A15THR00.016-0.03024.251-0.022-0.0220.0000.0000.0000.000
15A16LEU0-0.0050.00122.629-0.026-0.0260.0000.0000.0000.000
16A17ASP-1-0.798-0.92021.881-0.314-0.3140.0000.0000.0000.000
17A18VAL0-0.008-0.00118.499-0.040-0.0400.0000.0000.0000.000
18A19PHE00.011-0.03418.166-0.044-0.0440.0000.0000.0000.000
19A20GLY00.0210.02218.955-0.020-0.0200.0000.0000.0000.000
20A21PRO00.002-0.00715.463-0.037-0.0370.0000.0000.0000.000
21A22VAL0-0.017-0.00414.183-0.103-0.1030.0000.0000.0000.000
22A23GLU-1-0.896-0.93014.173-0.662-0.6620.0000.0000.0000.000
23A24ILE0-0.011-0.00312.590-0.052-0.0520.0000.0000.0000.000
24A25PHE00.0250.0028.892-0.049-0.0490.0000.0000.0000.000
25A26GLY0-0.0080.0119.576-0.253-0.2530.0000.0000.0000.000
26A27ASN0-0.072-0.05111.9150.0920.0920.0000.0000.0000.000
27A28LEU0-0.055-0.0257.2060.0450.0450.0000.0000.0000.000
28A29GLN0-0.037-0.0316.723-0.596-0.5960.0000.0000.0000.000
29A30ASP-1-0.916-0.9366.129-1.285-1.2850.0000.0000.0000.000
30A31ASP-1-0.910-0.9382.433-6.623-5.8870.615-0.476-0.875-0.003
31A32PHE0-0.020-0.0412.256-5.070-4.5083.889-2.049-2.402-0.032
32A33GLU-1-0.882-0.9235.0070.6580.769-0.001-0.007-0.1030.000
33A34LEU0-0.042-0.0386.5900.0960.0960.0000.0000.0000.000
34A35ASN00.006-0.01010.1690.2000.2000.0000.0000.0000.000
35A36PHE00.0030.01312.272-0.010-0.0100.0000.0000.0000.000
36A37ILE00.0160.00815.2520.0680.0680.0000.0000.0000.000
37A38SER0-0.020-0.03317.902-0.014-0.0140.0000.0000.0000.000
38A39SER0-0.073-0.06221.4450.0110.0110.0000.0000.0000.000
39A40ASP-1-0.916-0.93823.953-0.060-0.0600.0000.0000.0000.000
40A41GLY00.0080.02022.1960.0150.0150.0000.0000.0000.000
41A42GLY00.0230.00822.7750.0030.0030.0000.0000.0000.000
42A43LEU0-0.030-0.02123.562-0.019-0.0190.0000.0000.0000.000
43A44VAL00.0050.01623.5350.0120.0120.0000.0000.0000.000
44A45GLU-1-0.854-0.91625.693-0.138-0.1380.0000.0000.0000.000
45A46SER00.0090.01126.2290.0110.0110.0000.0000.0000.000
46A47SER0-0.030-0.03127.9190.0210.0210.0000.0000.0000.000
47A48GLN0-0.075-0.03428.7900.0020.0020.0000.0000.0000.000
48A49LYS10.8400.91930.9300.1260.1260.0000.0000.0000.000
49A50VAL00.0420.03925.1390.0060.0060.0000.0000.0000.000
50A51ARG10.8690.92226.8640.1200.1200.0000.0000.0000.000
51A52VAL00.0340.02620.495-0.004-0.0040.0000.0000.0000.000
52A53GLU-1-0.943-0.96921.028-0.111-0.1110.0000.0000.0000.000
53A54THR0-0.042-0.00718.988-0.028-0.0280.0000.0000.0000.000
54A55SER00.0190.00716.4200.0440.0440.0000.0000.0000.000
55A56LEU00.0340.01319.129-0.018-0.0180.0000.0000.0000.000
56A57TYR0-0.041-0.02714.0810.0080.0080.0000.0000.0000.000
57A58THR00.004-0.00514.8610.0450.0450.0000.0000.0000.000
58A59ARG10.7080.83014.135-0.276-0.2760.0000.0000.0000.000
59A60ASP-1-0.720-0.8759.3071.2161.2160.0000.0000.0000.000
60A61GLU-1-0.919-0.94311.2240.3110.3110.0000.0000.0000.000
61A62ASN0-0.097-0.0458.9650.0160.0160.0000.0000.0000.000
62A63ILE00.0260.0353.034-0.1670.6350.132-0.313-0.6210.002
63A64GLU-1-0.809-0.8814.944-0.139-0.1390.0000.0000.0000.000
64A65LYS10.8710.9326.137-0.848-0.8480.0000.0000.0000.000
65A66ILE00.0080.0096.3810.0770.0770.0000.0000.0000.000
66A67LEU00.0100.02410.0540.0320.0320.0000.0000.0000.000
67A68PHE00.003-0.00513.6800.0030.0030.0000.0000.0000.000
68A69VAL00.004-0.01715.3880.0540.0540.0000.0000.0000.000
69A70PRO00.0220.02119.1630.0030.0030.0000.0000.0000.000
70A71GLY00.0440.00821.6270.0290.0290.0000.0000.0000.000
71A72GLY00.0710.03125.291-0.005-0.0050.0000.0000.0000.000
72A73SER0-0.040-0.03028.3730.0090.0090.0000.0000.0000.000
73A74GLY00.0200.02629.5290.0110.0110.0000.0000.0000.000
74A75THR0-0.001-0.00326.7230.0100.0100.0000.0000.0000.000
75A76ARG10.8680.94429.3890.1360.1360.0000.0000.0000.000
76A77GLU-1-0.838-0.91333.053-0.093-0.0930.0000.0000.0000.000
77A78LYS10.8980.94827.2440.1100.1100.0000.0000.0000.000
78A79VAL00.0130.01129.3140.0020.0020.0000.0000.0000.000
79A80ASN0-0.056-0.03730.7460.0100.0100.0000.0000.0000.000
80A81ASP-1-0.781-0.87429.966-0.062-0.0620.0000.0000.0000.000
81A82ASP-1-0.804-0.90329.787-0.056-0.0560.0000.0000.0000.000
82A83ASN0-0.053-0.02529.1710.0080.0080.0000.0000.0000.000
83A84PHE00.0050.00323.855-0.001-0.0010.0000.0000.0000.000
84A85ILE00.0280.00925.096-0.009-0.0090.0000.0000.0000.000
85A86ASN0-0.016-0.01225.0720.0030.0030.0000.0000.0000.000
86A87PHE00.0100.00620.1600.0070.0070.0000.0000.0000.000
87A88ILE00.0240.01320.525-0.002-0.0020.0000.0000.0000.000
88A89GLY00.0530.03220.198-0.009-0.0090.0000.0000.0000.000
89A90ASN0-0.076-0.04020.7860.0260.0260.0000.0000.0000.000
90A91MET00.0280.02216.7360.0100.0100.0000.0000.0000.000
91A92VAL0-0.024-0.01816.200-0.014-0.0140.0000.0000.0000.000
92A93LYS10.8190.90116.630-0.029-0.0290.0000.0000.0000.000
93A94GLU-1-0.827-0.88914.0150.1840.1840.0000.0000.0000.000
94A95SER0-0.047-0.01312.035-0.006-0.0060.0000.0000.0000.000
95A96LYS10.7960.8957.110-0.168-0.1680.0000.0000.0000.000
96A97TYR0-0.007-0.0057.4310.0650.0650.0000.0000.0000.000
97A98ILE0-0.0080.00411.745-0.004-0.0040.0000.0000.0000.000
98A99ILE00.0270.01711.3260.0200.0200.0000.0000.0000.000
99A100SER00.0340.02115.7340.0260.0260.0000.0000.0000.000
100A101VAL0-0.0090.01118.905-0.011-0.0110.0000.0000.0000.000
101A102CYS0-0.0270.01021.3900.0350.0350.0000.0000.0000.000
102A103THR0-0.034-0.05825.022-0.001-0.0010.0000.0000.0000.000
103A104GLY00.0570.06122.6180.0170.0170.0000.0000.0000.000
104A105SER0-0.021-0.03923.1470.0090.0090.0000.0000.0000.000
105A106ALA0-0.013-0.01624.1220.0170.0170.0000.0000.0000.000
106A107LEU0-0.0150.00124.0660.0170.0170.0000.0000.0000.000
107A108LEU00.0170.01119.0860.0160.0160.0000.0000.0000.000
108A109SER0-0.022-0.00823.1970.0200.0200.0000.0000.0000.000
109A110LYS10.9030.97326.3460.0890.0890.0000.0000.0000.000
110A111ALA0-0.029-0.01223.8060.0140.0140.0000.0000.0000.000
111A112GLY00.002-0.00825.6170.0090.0090.0000.0000.0000.000
112A113ILE0-0.030-0.01420.0200.0050.0050.0000.0000.0000.000
113A114LEU0-0.029-0.01521.665-0.007-0.0070.0000.0000.0000.000
114A115ASN00.0560.04124.550-0.007-0.0070.0000.0000.0000.000
115A116GLY0-0.008-0.00126.5290.0050.0050.0000.0000.0000.000
116A117LYS10.8390.93021.6460.1040.1040.0000.0000.0000.000
117A118ARG10.8260.90421.8960.1720.1720.0000.0000.0000.000
118A119ALA00.0080.00923.302-0.020-0.0200.0000.0000.0000.000
119A120THR00.000-0.02523.9890.0190.0190.0000.0000.0000.000
120A121THR00.0410.03425.126-0.005-0.0050.0000.0000.0000.000
121A122ASN00.001-0.00926.8070.0030.0030.0000.0000.0000.000
122A123LYS10.7990.90028.0500.2070.2070.0000.0000.0000.000
123A124ARG10.9270.96531.9250.1590.1590.0000.0000.0000.000
124A125SER0-0.014-0.00430.9190.0120.0120.0000.0000.0000.000
125A126PHE00.0660.04130.1150.0040.0040.0000.0000.0000.000
126A127LYS10.9140.99132.8390.0850.0850.0000.0000.0000.000
127A128TRP00.0500.02130.553-0.001-0.0010.0000.0000.0000.000
128A129VAL00.0080.00828.4420.0040.0040.0000.0000.0000.000
129A130THR0-0.068-0.06131.1630.0060.0060.0000.0000.0000.000
130A131GLU-1-0.866-0.95032.908-0.080-0.0800.0000.0000.0000.000
131A132GLN0-0.088-0.04432.2520.0060.0060.0000.0000.0000.000
132A133ASN0-0.028-0.02929.2810.0120.0120.0000.0000.0000.000
133A134GLU-1-0.922-0.95432.558-0.073-0.0730.0000.0000.0000.000
134A135ASP-1-0.927-0.95331.581-0.060-0.0600.0000.0000.0000.000
135A136VAL0-0.076-0.02926.784-0.003-0.0030.0000.0000.0000.000
136A137LEU00.0020.00528.3060.0040.0040.0000.0000.0000.000
137A138TRP0-0.023-0.02926.459-0.021-0.0210.0000.0000.0000.000
138A139VAL00.0090.00727.0300.0090.0090.0000.0000.0000.000
139A140LYS10.8500.94429.0260.1190.1190.0000.0000.0000.000
140A141GLU-1-0.866-0.94731.085-0.136-0.1360.0000.0000.0000.000
141A142ALA00.0390.06025.576-0.005-0.0050.0000.0000.0000.000
142A143ARG10.7550.88423.9210.2950.2950.0000.0000.0000.000
143A144TRP00.042-0.00218.584-0.010-0.0100.0000.0000.0000.000
144A145VAL0-0.015-0.00121.3030.0180.0180.0000.0000.0000.000
145A146LYS10.8720.94814.4190.3530.3530.0000.0000.0000.000
146A147ASP-1-0.820-0.91618.962-0.118-0.1180.0000.0000.0000.000
147A148GLY00.0320.02817.6490.0070.0070.0000.0000.0000.000
148A149ASN0-0.045-0.03612.973-0.018-0.0180.0000.0000.0000.000
149A150ILE00.0190.00814.269-0.059-0.0590.0000.0000.0000.000
150A151TYR0-0.042-0.04613.1520.0170.0170.0000.0000.0000.000
151A152THR0-0.0040.00917.2170.0000.0000.0000.0000.0000.000
152A153SER00.0910.01520.0540.0020.0020.0000.0000.0000.000
153A154SER0-0.059-0.02722.0230.0200.0200.0000.0000.0000.000
154A155GLY00.003-0.00925.063-0.001-0.0010.0000.0000.0000.000
155A156VAL00.0560.01924.300-0.015-0.0150.0000.0000.0000.000
156A157SER00.0380.02023.366-0.017-0.0170.0000.0000.0000.000
157A158ALA0-0.020-0.00222.909-0.020-0.0200.0000.0000.0000.000
158A159GLY00.0230.01620.369-0.024-0.0240.0000.0000.0000.000
159A160ILE00.0360.03518.650-0.053-0.0530.0000.0000.0000.000
160A161ASP-1-0.724-0.82718.197-0.406-0.4060.0000.0000.0000.000
161A162MET0-0.0200.00116.420-0.003-0.0030.0000.0000.0000.000
162A163THR0-0.050-0.02113.309-0.048-0.0480.0000.0000.0000.000
163A164LEU00.0400.01913.495-0.118-0.1180.0000.0000.0000.000
164A165GLY00.0110.01214.512-0.036-0.0360.0000.0000.0000.000
165A166PHE0-0.014-0.0138.2800.0260.0260.0000.0000.0000.000
166A167ILE00.0160.0068.876-0.097-0.0970.0000.0000.0000.000
167A168GLU-1-0.841-0.92510.534-0.526-0.5260.0000.0000.0000.000
168A169ASP-1-0.865-0.89912.437-0.446-0.4460.0000.0000.0000.000
169A170LEU0-0.098-0.0415.5380.0820.0820.0000.0000.0000.000
170A171ILE0-0.045-0.0264.872-0.088-0.0880.0000.0000.0000.000
171A172GLY00.0100.0248.5100.1110.1110.0000.0000.0000.000
172A173LYS10.7830.86312.0430.3300.3300.0000.0000.0000.000
173A174GLU-1-0.847-0.90514.794-0.459-0.4590.0000.0000.0000.000
174A175LYS10.9210.9586.4982.5382.5380.0000.0000.0000.000
175A176ALA00.0160.01612.802-0.016-0.0160.0000.0000.0000.000
176A177LEU0-0.022-0.02314.7300.0430.0430.0000.0000.0000.000
177A178GLU-1-0.947-0.96213.368-0.745-0.7450.0000.0000.0000.000
178A179ILE00.0530.03711.5580.0500.0500.0000.0000.0000.000
179A180SER0-0.082-0.03615.9510.0770.0770.0000.0000.0000.000
180A181ARG10.8260.87618.7790.4840.4840.0000.0000.0000.000
181A182SER0-0.044-0.02617.6500.0210.0210.0000.0000.0000.000
182A183ILE0-0.032-0.01317.5670.0340.0340.0000.0000.0000.000
183A184GLU-1-0.995-0.98420.628-0.252-0.2520.0000.0000.0000.000
184A185TYR0-0.084-0.04920.5580.0300.0300.0000.0000.0000.000
185A186PHE0-0.063-0.04222.560-0.008-0.0080.0000.0000.0000.000
186A187TRP00.0230.00717.163-0.005-0.0050.0000.0000.0000.000
187A188ASN0-0.100-0.06522.7370.0410.0410.0000.0000.0000.000
188A189GLU-1-0.803-0.91121.275-0.356-0.3560.0000.0000.0000.000
189A190ASP-1-0.834-0.90322.612-0.219-0.2190.0000.0000.0000.000
190A191SER00.0270.02021.902-0.004-0.0040.0000.0000.0000.000
191A192ASN0-0.077-0.05923.8870.0110.0110.0000.0000.0000.000
192A193TYR0-0.034-0.02727.3230.0130.0130.0000.0000.0000.000
193A194ASP-1-0.827-0.94628.434-0.217-0.2170.0000.0000.0000.000
194A195PRO0-0.012-0.00430.0650.0150.0150.0000.0000.0000.000
195A196PHE0-0.006-0.01929.6690.0140.0140.0000.0000.0000.000
196A197SER0-0.029-0.03031.9120.0080.0080.0000.0000.0000.000
197A198LYS10.9400.96834.2500.1470.1470.0000.0000.0000.000
198A199ILE0-0.0190.00535.8890.0060.0060.0000.0000.0000.000
199A200TYR00.0330.03334.7910.0080.0080.0000.0000.0000.000