FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 49MGN

Calculation Name: 4Z8Z-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4Z8Z

Chain ID: A

ChEMBL ID:

UniProt ID: A3DBP6

Base Structure: X-ray

Registration Date: 2023-09-20

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 323
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -5474298.982568
FMO2-HF: Nuclear repulsion 5341594.823975
FMO2-HF: Total energy -132704.158593
FMO2-MP2: Total energy -133086.917579


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.
-27.92-20.26318.486-9.524-16.623-0.077
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 : -0.065 / q_NPA : -0.038
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].
3A3GLU-1-0.779-0.8413.420-3.240-1.5230.030-0.828-0.9200.001
4A4ALA00.0180.0026.0130.3170.3170.0000.0000.0000.000
5A5SER0-0.048-0.0274.3060.7680.940-0.001-0.013-0.1580.000
6A6SER00.042-0.0162.671-0.5800.4391.169-0.784-1.405-0.008
7A7LYS10.8700.9334.5541.0181.090-0.001-0.020-0.0520.000
8A8PHE0-0.030-0.0118.0700.0880.0880.0000.0000.0000.000
9A9VAL0-0.028-0.0135.9820.1190.1190.0000.0000.0000.000
10A10ASP-1-0.727-0.8628.585-1.124-1.1240.0000.0000.0000.000
11A11ASN00.015-0.00810.435-0.051-0.0510.0000.0000.0000.000
12A12ILE00.0240.00812.031-0.005-0.0050.0000.0000.0000.000
13A13ALA0-0.033-0.00612.509-0.009-0.0090.0000.0000.0000.000
14A14ILE00.014-0.00114.181-0.031-0.0310.0000.0000.0000.000
15A15GLU-1-0.946-0.96816.6850.0780.0780.0000.0000.0000.000
16A16LYS10.9410.97716.703-0.157-0.1570.0000.0000.0000.000
17A17LEU00.0070.00616.643-0.004-0.0040.0000.0000.0000.000
18A18LEU00.0160.00919.980-0.003-0.0030.0000.0000.0000.000
19A19ASN0-0.027-0.01522.036-0.008-0.0080.0000.0000.0000.000
20A20GLU-1-0.984-1.00121.5970.0910.0910.0000.0000.0000.000
21A21LYS10.8420.91820.3500.0490.0490.0000.0000.0000.000
22A22LEU00.0210.01222.0210.0020.0020.0000.0000.0000.000
23A23LEU0-0.032-0.01025.331-0.006-0.0060.0000.0000.0000.000
24A24ARG10.8520.92927.973-0.003-0.0030.0000.0000.0000.000
25A25VAL0-0.0050.02128.9620.0050.0050.0000.0000.0000.000
26A26SER0-0.094-0.06431.408-0.002-0.0020.0000.0000.0000.000
27A27HIS0-0.032-0.02231.1540.0020.0020.0000.0000.0000.000
28A28ARG10.9470.97734.8110.0750.0750.0000.0000.0000.000
29A29PRO00.0550.04936.466-0.003-0.0030.0000.0000.0000.000
30A30LYS10.9210.95037.5530.0990.0990.0000.0000.0000.000
31A31ASN00.005-0.00240.2250.0060.0060.0000.0000.0000.000
32A32LEU0-0.0020.00237.254-0.005-0.0050.0000.0000.0000.000
33A33PHE0-0.002-0.00940.2770.0020.0020.0000.0000.0000.000
34A34TYR0-0.024-0.01938.2150.0000.0000.0000.0000.0000.000
35A35ASP-1-0.882-0.93940.737-0.118-0.1180.0000.0000.0000.000
36A36ASP-1-0.816-0.93437.606-0.170-0.1700.0000.0000.0000.000
37A37GLU-1-0.989-0.97739.439-0.120-0.1200.0000.0000.0000.000
38A38LYS10.9330.96141.5540.1080.1080.0000.0000.0000.000
39A39VAL0-0.0210.00735.4020.0000.0000.0000.0000.0000.000
40A40PHE00.0120.00032.016-0.007-0.0070.0000.0000.0000.000
41A41ASP-1-0.876-0.94036.938-0.142-0.1420.0000.0000.0000.000
42A42ASP-1-0.941-0.96538.499-0.125-0.1250.0000.0000.0000.000
43A43LEU0-0.036-0.02332.3320.0020.0020.0000.0000.0000.000
44A44CYS0-0.055-0.02236.0360.0000.0000.0000.0000.0000.000
45A45LYS10.9070.94337.6630.1230.1230.0000.0000.0000.000
46A46CYS0-0.056-0.00736.4960.0050.0050.0000.0000.0000.000
47A47GLU-1-0.894-0.94437.328-0.119-0.1190.0000.0000.0000.000
48A48THR0-0.055-0.03733.6020.0040.0040.0000.0000.0000.000
49A49ASP-1-0.869-0.92436.860-0.078-0.0780.0000.0000.0000.000
50A50MET00.031-0.00935.292-0.001-0.0010.0000.0000.0000.000
51A51SER0-0.092-0.03139.0210.0040.0040.0000.0000.0000.000
52A52LYS10.9170.95139.2190.0790.0790.0000.0000.0000.000
53A53VAL0-0.0110.01633.771-0.003-0.0030.0000.0000.0000.000
54A54LYS10.9290.96834.6260.0680.0680.0000.0000.0000.000
55A55LEU00.002-0.00330.129-0.008-0.0080.0000.0000.0000.000
56A56ALA0-0.0100.01130.9600.0090.0090.0000.0000.0000.000
57A57GLU-1-0.850-0.91029.588-0.053-0.0530.0000.0000.0000.000
58A58GLY00.031-0.01229.590-0.001-0.0010.0000.0000.0000.000
59A59ASP-1-0.899-0.93529.2440.0150.0150.0000.0000.0000.000
60A60LYS10.7780.83430.3710.0280.0280.0000.0000.0000.000
61A61ASN0-0.0240.01024.030-0.012-0.0120.0000.0000.0000.000
62A62LEU00.0250.01021.138-0.001-0.0010.0000.0000.0000.000
63A63LYS10.9340.98125.3020.0710.0710.0000.0000.0000.000
64A64ARG10.9030.97825.5200.0620.0620.0000.0000.0000.000
65A65PHE00.0150.00427.6070.0120.0120.0000.0000.0000.000
66A66GLU-1-0.902-0.95528.995-0.082-0.0820.0000.0000.0000.000
67A67PHE00.034-0.00329.0150.0060.0060.0000.0000.0000.000
68A68PRO0-0.037-0.02032.944-0.005-0.0050.0000.0000.0000.000
69A69SER00.0180.02632.126-0.003-0.0030.0000.0000.0000.000
70A70PHE0-0.028-0.03633.8650.0090.0090.0000.0000.0000.000
71A71LEU00.0040.01434.3670.0050.0050.0000.0000.0000.000
72A72LYS10.8730.94135.2100.0990.0990.0000.0000.0000.000
73A73THR0-0.001-0.00334.196-0.004-0.0040.0000.0000.0000.000
74A74GLU-1-0.953-0.98537.318-0.069-0.0690.0000.0000.0000.000
75A75GLU-1-0.955-0.97438.324-0.085-0.0850.0000.0000.0000.000
76A76TYR00.0050.00834.1180.0020.0020.0000.0000.0000.000
77A77ILE00.025-0.00235.514-0.006-0.0060.0000.0000.0000.000
78A78GLU-1-0.837-0.94332.119-0.070-0.0700.0000.0000.0000.000
79A79ASN00.0240.02530.052-0.012-0.0120.0000.0000.0000.000
80A80ASN0-0.0170.00431.695-0.016-0.0160.0000.0000.0000.000
81A81ILE0-0.030-0.00131.2400.0010.0010.0000.0000.0000.000
82A82VAL00.0200.02327.483-0.006-0.0060.0000.0000.0000.000
83A83TYR00.0170.00126.1790.0140.0140.0000.0000.0000.000
84A84LEU0-0.007-0.00823.969-0.021-0.0210.0000.0000.0000.000
85A85TYR0-0.073-0.06021.4180.0260.0260.0000.0000.0000.000
86A86TYR0-0.006-0.00622.320-0.017-0.0170.0000.0000.0000.000
87A87HIS00.0070.00419.3950.0290.0290.0000.0000.0000.000
88A88PRO0-0.0320.00021.514-0.021-0.0210.0000.0000.0000.000
89A89ALA00.0410.02221.6750.0090.0090.0000.0000.0000.000
90A90LYS10.8650.93323.2220.0510.0510.0000.0000.0000.000
91A91ASP-1-0.941-0.97925.055-0.066-0.0660.0000.0000.0000.000
92A92PRO00.0040.00524.903-0.007-0.0070.0000.0000.0000.000
93A93VAL00.015-0.00723.5800.0110.0110.0000.0000.0000.000
94A94CYS0-0.065-0.01122.970-0.006-0.0060.0000.0000.0000.000
95A95ASN00.004-0.02823.6070.0070.0070.0000.0000.0000.000
96A96ILE00.0050.00017.334-0.016-0.0160.0000.0000.0000.000
97A97LEU0-0.0050.00921.0650.0260.0260.0000.0000.0000.000
98A98LEU0-0.019-0.01614.574-0.037-0.0370.0000.0000.0000.000
99A99LEU00.0090.00618.1700.0440.0440.0000.0000.0000.000
100A100HIS00.010-0.00115.652-0.048-0.0480.0000.0000.0000.000
101A101GLY00.0590.02015.577-0.013-0.0130.0000.0000.0000.000
102A102LEU0-0.024-0.01616.4760.0550.0550.0000.0000.0000.000
103A103TYR0-0.046-0.03417.994-0.010-0.0100.0000.0000.0000.000
104A104ASP-1-0.761-0.78515.131-0.360-0.3600.0000.0000.0000.000
105A105ASP-1-0.859-0.92417.503-0.025-0.0250.0000.0000.0000.000
106A106ASN00.0170.00515.1940.0090.0090.0000.0000.0000.000
107A107MET00.0450.03015.073-0.046-0.0460.0000.0000.0000.000
108A108LEU00.0170.00114.317-0.039-0.0390.0000.0000.0000.000
109A109ASN0-0.070-0.02310.3890.0890.0890.0000.0000.0000.000
110A110TYR0-0.072-0.0979.977-0.143-0.1430.0000.0000.0000.000
111A111GLY0-0.0040.00312.140-0.043-0.0430.0000.0000.0000.000
112A112PHE0-0.034-0.0226.7280.0890.0890.0000.0000.0000.000
113A113LEU00.0720.0239.5620.0130.0130.0000.0000.0000.000
114A114THR00.002-0.00210.9020.0500.0500.0000.0000.0000.000
115A115ARG10.9791.00813.1370.0610.0610.0000.0000.0000.000
116A116MET0-0.006-0.0059.859-0.019-0.0190.0000.0000.0000.000
117A117LEU0-0.0020.01013.5150.0210.0210.0000.0000.0000.000
118A118ASN0-0.062-0.05915.7800.0520.0520.0000.0000.0000.000
119A119GLU-1-0.975-0.99615.032-0.055-0.0550.0000.0000.0000.000
120A120LEU0-0.078-0.02514.5670.0240.0240.0000.0000.0000.000
121A121LYS10.8970.96618.6820.1000.1000.0000.0000.0000.000
122A122PHE00.0780.03118.1790.0030.0030.0000.0000.0000.000
123A123ASN0-0.024-0.00120.6030.0210.0210.0000.0000.0000.000
124A124VAL00.0190.01617.075-0.027-0.0270.0000.0000.0000.000
125A125PHE0-0.011-0.00420.2570.0370.0370.0000.0000.0000.000
126A126LEU0-0.012-0.00416.429-0.032-0.0320.0000.0000.0000.000
127A127MET0-0.022-0.00520.2670.0370.0370.0000.0000.0000.000
128A128GLU-1-0.775-0.88121.320-0.150-0.1500.0000.0000.0000.000
129A129LEU00.0150.00220.2840.0100.0100.0000.0000.0000.000
130A130PRO00.0560.02723.8740.0170.0170.0000.0000.0000.000
131A131PHE0-0.017-0.01425.998-0.010-0.0100.0000.0000.0000.000
132A132HIS0-0.0070.00420.861-0.007-0.0070.0000.0000.0000.000
133A133PHE0-0.028-0.02418.0180.0090.0090.0000.0000.0000.000
134A134ASN0-0.055-0.03324.1870.0230.0230.0000.0000.0000.000
135A135ARG10.7390.88726.6900.1700.1700.0000.0000.0000.000
136A136LYS10.8440.94526.9200.0570.0570.0000.0000.0000.000
137A137PRO00.0230.01128.8430.0080.0080.0000.0000.0000.000
138A138ALA0-0.0030.00031.8760.0020.0020.0000.0000.0000.000
139A139GLU-1-0.963-0.98233.798-0.062-0.0620.0000.0000.0000.000
140A140SER0-0.079-0.03629.289-0.002-0.0020.0000.0000.0000.000
141A141PHE0-0.016-0.01728.2910.0090.0090.0000.0000.0000.000
142A142PHE0-0.056-0.04323.5980.0120.0120.0000.0000.0000.000
143A143SER0-0.026-0.04121.380-0.011-0.0110.0000.0000.0000.000
144A144GLY00.0870.01422.997-0.008-0.0080.0000.0000.0000.000
145A145GLU-1-0.815-0.88024.273-0.097-0.0970.0000.0000.0000.000
146A146TYR0-0.012-0.03026.780-0.005-0.0050.0000.0000.0000.000
147A147PHE0-0.0290.00025.088-0.004-0.0040.0000.0000.0000.000
148A148ILE00.0060.01024.024-0.010-0.0100.0000.0000.0000.000
149A149SER00.0410.04426.7310.0120.0120.0000.0000.0000.000
150A150ALA00.037-0.00129.528-0.008-0.0080.0000.0000.0000.000
151A151ASP-1-0.861-0.92532.536-0.113-0.1130.0000.0000.0000.000
152A152LEU00.013-0.01031.392-0.007-0.0070.0000.0000.0000.000
153A153LEU00.0000.02033.102-0.010-0.0100.0000.0000.0000.000
154A154ARG10.8690.94432.0870.1120.1120.0000.0000.0000.000
155A155ALA0-0.0020.00228.969-0.006-0.0060.0000.0000.0000.000
156A156ARG10.8360.90829.7180.1520.1520.0000.0000.0000.000
157A157ASN0-0.016-0.02931.626-0.012-0.0120.0000.0000.0000.000
158A158ALA00.0330.02628.502-0.001-0.0010.0000.0000.0000.000
159A159PHE00.0370.01024.078-0.012-0.0120.0000.0000.0000.000
160A160ILE00.0210.00428.199-0.010-0.0100.0000.0000.0000.000
161A161GLN00.001-0.00430.223-0.005-0.0050.0000.0000.0000.000
162A162SER00.003-0.01725.424-0.002-0.0020.0000.0000.0000.000
163A163ILE0-0.020-0.00727.267-0.011-0.0110.0000.0000.0000.000
164A164TYR0-0.003-0.01328.828-0.002-0.0020.0000.0000.0000.000
165A165ASP-1-0.715-0.86727.886-0.167-0.1670.0000.0000.0000.000
166A166ILE0-0.0140.00624.2200.0010.0010.0000.0000.0000.000
167A167GLU-1-0.779-0.86327.392-0.186-0.1860.0000.0000.0000.000
168A168ALA00.0210.01630.8600.0070.0070.0000.0000.0000.000
169A169SER00.006-0.02326.7050.0100.0100.0000.0000.0000.000
170A170ARG10.8430.92228.0460.2040.2040.0000.0000.0000.000
171A171ASN00.0360.02029.3010.0110.0110.0000.0000.0000.000
172A172LEU0-0.0060.00530.0310.0080.0080.0000.0000.0000.000
173A173ILE0-0.002-0.01925.6320.0070.0070.0000.0000.0000.000
174A174GLY0-0.047-0.02629.8310.0040.0040.0000.0000.0000.000
175A175ASN0-0.044-0.02632.5770.0160.0160.0000.0000.0000.000
176A176ILE0-0.0510.00029.5530.0080.0080.0000.0000.0000.000
177A177ASN0-0.039-0.00928.1340.0010.0010.0000.0000.0000.000
178A178THR00.0680.03232.469-0.003-0.0030.0000.0000.0000.000
179A179LEU0-0.064-0.01427.348-0.002-0.0020.0000.0000.0000.000
180A180PRO0-0.003-0.00427.088-0.005-0.0050.0000.0000.0000.000
181A181CYS0-0.0180.00025.2290.0010.0010.0000.0000.0000.000
182A182LEU00.0220.00519.6460.0030.0030.0000.0000.0000.000
183A183LEU0-0.0010.02521.5210.0090.0090.0000.0000.0000.000
184A184VAL00.002-0.01515.050-0.043-0.0430.0000.0000.0000.000
185A185GLY00.0470.03417.2600.0470.0470.0000.0000.0000.000
186A186PHE00.003-0.0119.819-0.087-0.0870.0000.0000.0000.000
187A187SER00.001-0.01713.5790.1560.1560.0000.0000.0000.000
188A188MET00.013-0.00415.1070.0230.0230.0000.0000.0000.000
189A189GLY00.0780.04317.7560.0330.0330.0000.0000.0000.000
190A190GLY0-0.033-0.01817.3230.0200.0200.0000.0000.0000.000
191A191CYS0-0.046-0.00918.2310.0370.0370.0000.0000.0000.000
192A192ILE00.0320.00420.9210.0300.0300.0000.0000.0000.000
193A193SER0-0.012-0.01720.6230.0310.0310.0000.0000.0000.000
194A194PHE0-0.026-0.01321.5140.0160.0160.0000.0000.0000.000
195A195ARG10.9090.95223.2180.2800.2800.0000.0000.0000.000
196A196TYR00.0240.00625.8720.0190.0190.0000.0000.0000.000
197A197HIS0-0.0110.00924.9600.0120.0120.0000.0000.0000.000
198A198MET0-0.105-0.03227.0350.0080.0080.0000.0000.0000.000
199A199LEU0-0.054-0.00729.3690.0180.0180.0000.0000.0000.000
200A200ARG10.8350.90930.5400.2040.2040.0000.0000.0000.000
201A201ASP-1-0.940-0.95930.059-0.213-0.2130.0000.0000.0000.000
202A202SER00.021-0.00630.2270.0050.0050.0000.0000.0000.000
203A203PHE0-0.036-0.01824.9340.0060.0060.0000.0000.0000.000
204A204LYS10.9230.97225.5490.2360.2360.0000.0000.0000.000
205A205GLY00.0210.00124.0970.0030.0030.0000.0000.0000.000
206A206THR0-0.025-0.02021.1360.0100.0100.0000.0000.0000.000
207A207PHE00.0000.00813.223-0.011-0.0110.0000.0000.0000.000
208A208LEU0-0.016-0.00516.5650.0070.0070.0000.0000.0000.000
209A209ILE00.000-0.00810.377-0.106-0.1060.0000.0000.0000.000
210A210ASN00.0030.0157.7170.0360.0360.0000.0000.0000.000
211A211PRO0-0.0270.00112.1690.0880.0880.0000.0000.0000.000
212A212VAL00.005-0.00415.770-0.027-0.0270.0000.0000.0000.000
213A213THR0-0.004-0.01617.4720.0280.0280.0000.0000.0000.000
214A214ASP-1-0.845-0.93820.064-0.320-0.3200.0000.0000.0000.000
215A215MET0-0.005-0.00523.444-0.011-0.0110.0000.0000.0000.000
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290A290ALA0-0.0060.00127.0350.0250.0250.0000.0000.0000.000
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301A301GLY00.0360.0243.1682.0321.8100.0260.486-0.289-0.001
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