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: 1NKQZ

Calculation Name: 4JZ5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4JZ5

Chain ID: A

ChEMBL ID:

UniProt ID: B6D7J9

Base Structure: X-ray

Registration Date: 2023-09-23

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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2498843.563875
FMO2-HF: Nuclear repulsion 2417294.239985
FMO2-HF: Total energy -81549.32389
FMO2-MP2: Total energy -81786.60627


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:-3:GLY)


Summations of interaction energy for fragment #1(A:-3:GLY)
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.
-3.704-1.571-0.002-1.151-0.980.004
Interaction energy analysis for fragmet #1(A:-3:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.028 / q_NPA : 0.010
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].
3A-1HIS00.0370.0193.8680.1191.843-0.012-0.957-0.7550.003
4A0MET0-0.0290.0097.0050.6500.6500.0000.0000.0000.000
5A1MET0-0.023-0.0186.022-0.290-0.2900.0000.0000.0000.000
6A2VAL00.0120.0064.802-0.147-0.1470.0000.0000.0000.000
7A3LEU00.0320.0467.2850.2160.2160.0000.0000.0000.000
8A4VAL0-0.010-0.00810.974-0.016-0.0160.0000.0000.0000.000
9A5LEU0-0.010-0.00613.576-0.012-0.0120.0000.0000.0000.000
10A6ASP-1-0.778-0.85517.3180.0860.0860.0000.0000.0000.000
11A7ILE00.0010.00920.698-0.018-0.0180.0000.0000.0000.000
12A8SER00.0300.00423.9600.0150.0150.0000.0000.0000.000
13A9LYS10.8560.94527.717-0.007-0.0070.0000.0000.0000.000
14A10TRP00.0380.00929.073-0.007-0.0070.0000.0000.0000.000
15A11GLN00.0350.02024.7210.0000.0000.0000.0000.0000.000
16A12PRO0-0.0010.00327.984-0.004-0.0040.0000.0000.0000.000
17A13THR0-0.003-0.00529.3760.0020.0020.0000.0000.0000.000
18A14VAL00.0220.01423.254-0.005-0.0050.0000.0000.0000.000
19A15ASN0-0.0120.00724.062-0.002-0.0020.0000.0000.0000.000
20A16TYR00.040-0.01522.093-0.024-0.0240.0000.0000.0000.000
21A17SER00.0230.00920.579-0.010-0.0100.0000.0000.0000.000
22A18GLY0-0.030-0.01319.923-0.036-0.0360.0000.0000.0000.000
23A19LEU0-0.014-0.01517.548-0.014-0.0140.0000.0000.0000.000
24A20LYS10.8080.87715.5870.2470.2470.0000.0000.0000.000
25A21GLU-1-0.968-0.95914.159-0.632-0.6320.0000.0000.0000.000
26A22ASP-1-0.905-0.95211.711-0.881-0.8810.0000.0000.0000.000
27A23VAL0-0.069-0.02611.1540.0020.0020.0000.0000.0000.000
28A24GLY00.0310.01610.422-0.037-0.0370.0000.0000.0000.000
29A25PHE0-0.009-0.01911.3550.0830.0830.0000.0000.0000.000
30A26VAL00.0090.00514.457-0.026-0.0260.0000.0000.0000.000
31A27VAL00.0020.01217.8660.0220.0220.0000.0000.0000.000
32A28ILE0-0.017-0.01320.583-0.019-0.0190.0000.0000.0000.000
33A29ARG10.7940.88524.181-0.014-0.0140.0000.0000.0000.000
34A30SER00.004-0.03727.213-0.009-0.0090.0000.0000.0000.000
35A31SER00.013-0.01029.779-0.004-0.0040.0000.0000.0000.000
36A32ASN0-0.0280.01831.969-0.001-0.0010.0000.0000.0000.000
37A33GLY00.0540.00634.453-0.004-0.0040.0000.0000.0000.000
38A34THR00.016-0.01336.290-0.001-0.0010.0000.0000.0000.000
39A35GLN0-0.0380.00638.782-0.004-0.0040.0000.0000.0000.000
40A36LYS10.8450.91535.986-0.018-0.0180.0000.0000.0000.000
41A37TYR00.0530.01033.7320.0050.0050.0000.0000.0000.000
42A38ASP-1-0.766-0.86830.7980.0010.0010.0000.0000.0000.000
43A39GLU-1-0.781-0.90432.9180.0010.0010.0000.0000.0000.000
44A40ARG10.8520.92130.3160.0340.0340.0000.0000.0000.000
45A41LEU00.0330.03628.553-0.006-0.0060.0000.0000.0000.000
46A42GLU-1-0.785-0.88729.034-0.009-0.0090.0000.0000.0000.000
47A43GLN0-0.058-0.02129.1000.0000.0000.0000.0000.0000.000
48A44HIS00.0350.01825.351-0.018-0.0180.0000.0000.0000.000
49A45ALA00.0190.01425.370-0.009-0.0090.0000.0000.0000.000
50A46LYS10.8880.93725.7610.0170.0170.0000.0000.0000.000
51A47GLY0-0.041-0.01826.304-0.010-0.0100.0000.0000.0000.000
52A48LEU0-0.009-0.02220.163-0.023-0.0230.0000.0000.0000.000
53A49ASP-1-0.855-0.92921.800-0.058-0.0580.0000.0000.0000.000
54A50LYS10.9430.98823.4310.1060.1060.0000.0000.0000.000
55A51VAL0-0.044-0.01720.371-0.014-0.0140.0000.0000.0000.000
56A52GLY00.0720.04119.647-0.037-0.0370.0000.0000.0000.000
57A53MET0-0.082-0.02415.427-0.025-0.0250.0000.0000.0000.000
58A54PRO00.0050.00714.6350.0270.0270.0000.0000.0000.000
59A55PHE00.020-0.01217.196-0.001-0.0010.0000.0000.0000.000
60A56GLY00.0580.03219.5440.0230.0230.0000.0000.0000.000
61A57LEU0-0.043-0.01421.575-0.021-0.0210.0000.0000.0000.000
62A58TYR00.009-0.03023.7910.0200.0200.0000.0000.0000.000
63A59HIS10.7650.89825.847-0.089-0.0890.0000.0000.0000.000
64A60TYR0-0.005-0.00829.4350.0080.0080.0000.0000.0000.000
65A61ALA0-0.032-0.02630.933-0.006-0.0060.0000.0000.0000.000
66A62LEU0-0.081-0.04833.550-0.004-0.0040.0000.0000.0000.000
67A63PHE0-0.0120.01533.867-0.002-0.0020.0000.0000.0000.000
68A64GLU-1-0.792-0.90738.8860.0500.0500.0000.0000.0000.000
69A65GLY00.0340.02140.7310.0010.0010.0000.0000.0000.000
70A66GLY00.0070.00041.729-0.004-0.0040.0000.0000.0000.000
71A67GLN00.0320.00541.8730.0060.0060.0000.0000.0000.000
72A68ASP-1-0.787-0.88941.3780.0550.0550.0000.0000.0000.000
73A69THR0-0.045-0.05136.489-0.002-0.0020.0000.0000.0000.000
74A70ILE00.0270.01236.9180.0040.0040.0000.0000.0000.000
75A71ASN0-0.028-0.00238.4140.0000.0000.0000.0000.0000.000
76A72GLU-1-0.720-0.85635.3180.0660.0660.0000.0000.0000.000
77A73ALA00.0060.01333.6210.0010.0010.0000.0000.0000.000
78A74ASN00.011-0.00633.9690.0020.0020.0000.0000.0000.000
79A75MET0-0.0120.02735.258-0.005-0.0050.0000.0000.0000.000
80A76LEU0-0.024-0.00127.656-0.005-0.0050.0000.0000.0000.000
81A77VAL00.0200.00530.949-0.001-0.0010.0000.0000.0000.000
82A78SER0-0.025-0.02332.727-0.004-0.0040.0000.0000.0000.000
83A79ALA0-0.023-0.01030.673-0.007-0.0070.0000.0000.0000.000
84A80TYR00.0260.01425.944-0.007-0.0070.0000.0000.0000.000
85A81LYS10.9430.97229.837-0.067-0.0670.0000.0000.0000.000
86A82LYS10.8830.93032.888-0.017-0.0170.0000.0000.0000.000
87A83CYS0-0.075-0.03327.671-0.008-0.0080.0000.0000.0000.000
88A84ARG10.8940.91728.362-0.054-0.0540.0000.0000.0000.000
89A85GLN0-0.085-0.03530.490-0.002-0.0020.0000.0000.0000.000
90A86LEU0-0.082-0.04731.005-0.007-0.0070.0000.0000.0000.000
91A87GLY00.0060.01430.093-0.009-0.0090.0000.0000.0000.000
92A88ALA00.0040.01625.7880.0000.0000.0000.0000.0000.000
93A89GLU-1-0.800-0.88123.6180.0590.0590.0000.0000.0000.000
94A90PRO0-0.088-0.03722.4580.0060.0060.0000.0000.0000.000
95A91THR00.008-0.01718.114-0.004-0.0040.0000.0000.0000.000
96A92PHE0-0.050-0.02618.4500.0430.0430.0000.0000.0000.000
97A93LEU0-0.0160.00421.575-0.032-0.0320.0000.0000.0000.000
98A94PHE00.0290.01118.7750.0230.0230.0000.0000.0000.000
99A95LEU0-0.0030.01624.888-0.022-0.0220.0000.0000.0000.000
100A96ASH0-0.076-0.08426.1450.0110.0110.0000.0000.0000.000
101A97TYR00.030-0.00627.711-0.012-0.0120.0000.0000.0000.000
102A98GLU-1-0.822-0.88229.0060.0860.0860.0000.0000.0000.000
103A99GLU-1-0.803-0.87530.8880.0490.0490.0000.0000.0000.000
104A100VAL0-0.021-0.02734.7460.0060.0060.0000.0000.0000.000
105A101LYS10.8800.93637.797-0.054-0.0540.0000.0000.0000.000
106A102LEU0-0.061-0.01738.147-0.002-0.0020.0000.0000.0000.000
107A103LYS10.8620.92941.705-0.050-0.0500.0000.0000.0000.000
108A104SER0-0.037-0.01144.241-0.001-0.0010.0000.0000.0000.000
109A105GLY00.0540.03042.0790.0020.0020.0000.0000.0000.000
110A106ASN0-0.001-0.01137.2360.0040.0040.0000.0000.0000.000
111A107VAL00.0690.02733.3430.0020.0020.0000.0000.0000.000
112A108VAL00.0420.03632.3960.0030.0030.0000.0000.0000.000
113A109ASN00.017-0.00133.8270.0100.0100.0000.0000.0000.000
114A110GLU-1-0.767-0.84436.4200.0860.0860.0000.0000.0000.000
115A111CYS0-0.039-0.02630.830-0.001-0.0010.0000.0000.0000.000
116A112GLN0-0.047-0.02530.4000.0110.0110.0000.0000.0000.000
117A113ARG10.8450.89433.004-0.085-0.0850.0000.0000.0000.000
118A114PHE0-0.0050.00229.712-0.003-0.0030.0000.0000.0000.000
119A115ILE00.021-0.00527.128-0.001-0.0010.0000.0000.0000.000
120A116ASP-1-0.841-0.90830.6680.1490.1490.0000.0000.0000.000
121A117HIS0-0.021-0.01632.8740.0010.0010.0000.0000.0000.000
122A118VAL0-0.021-0.01929.018-0.005-0.0050.0000.0000.0000.000
123A119LYS10.8660.93625.773-0.212-0.2120.0000.0000.0000.000
124A120GLY00.0150.01230.229-0.001-0.0010.0000.0000.0000.000
125A121GLN0-0.034-0.02233.533-0.011-0.0110.0000.0000.0000.000
126A122THR0-0.077-0.05529.112-0.004-0.0040.0000.0000.0000.000
127A123GLY00.0050.01828.800-0.002-0.0020.0000.0000.0000.000
128A124VAL0-0.021-0.00123.6360.0190.0190.0000.0000.0000.000
129A125LYS10.8750.93419.651-0.326-0.3260.0000.0000.0000.000
130A126VAL0-0.001-0.01323.464-0.016-0.0160.0000.0000.0000.000
131A127GLY00.0080.01822.1370.0190.0190.0000.0000.0000.000
132A128LEU0-0.037-0.02522.981-0.030-0.0300.0000.0000.0000.000
133A129TYR0-0.040-0.03121.8630.0240.0240.0000.0000.0000.000
134A130ALA00.0230.01724.213-0.017-0.0170.0000.0000.0000.000
135A131GLY00.0650.04024.2070.0130.0130.0000.0000.0000.000
136A132ASP-1-0.779-0.87023.7740.1780.1780.0000.0000.0000.000
137A133SER00.003-0.01425.4250.0050.0050.0000.0000.0000.000
138A134PHE00.0220.03528.968-0.002-0.0020.0000.0000.0000.000
139A135TRP00.032-0.00723.601-0.003-0.0030.0000.0000.0000.000
140A136LYS10.8900.95227.063-0.166-0.1660.0000.0000.0000.000
141A137THR0-0.040-0.03230.070-0.005-0.0050.0000.0000.0000.000
142A138HIS10.8320.91232.094-0.116-0.1160.0000.0000.0000.000
143A139ASP-1-0.798-0.87732.1320.1460.1460.0000.0000.0000.000
144A140LEU00.0360.01127.9470.0050.0050.0000.0000.0000.000
145A141ASP-1-0.835-0.88525.8110.2510.2510.0000.0000.0000.000
146A142LYS10.8550.91927.920-0.138-0.1380.0000.0000.0000.000
147A143VAL0-0.043-0.00428.371-0.007-0.0070.0000.0000.0000.000
148A144LYS10.8050.89527.546-0.157-0.1570.0000.0000.0000.000
149A145HIS00.0530.01222.667-0.010-0.0100.0000.0000.0000.000
150A146ASP-1-0.761-0.86721.1070.2980.2980.0000.0000.0000.000
151A147LEU0-0.050-0.02315.9750.0530.0530.0000.0000.0000.000
152A148ARG10.7850.86919.399-0.372-0.3720.0000.0000.0000.000
153A149TRP0-0.019-0.00818.5360.0460.0460.0000.0000.0000.000
154A150VAL0-0.005-0.01419.045-0.028-0.0280.0000.0000.0000.000
155A151ALA00.0380.03019.6150.0090.0090.0000.0000.0000.000
156A152ARG10.8400.89420.997-0.140-0.1400.0000.0000.0000.000
157A153TYR00.0310.00420.7110.0080.0080.0000.0000.0000.000
158A154GLY0-0.036-0.00322.416-0.013-0.0130.0000.0000.0000.000
159A155VAL0-0.012-0.01523.247-0.004-0.0040.0000.0000.0000.000
160A156ASP-1-0.761-0.84923.210-0.002-0.0020.0000.0000.0000.000
161A157ASN00.0230.00621.569-0.004-0.0040.0000.0000.0000.000
162A158GLY00.0430.02921.120-0.019-0.0190.0000.0000.0000.000
163A159LYS10.8770.92815.9040.2170.2170.0000.0000.0000.000
164A160PRO00.0250.01713.5650.0260.0260.0000.0000.0000.000
165A161SER00.0520.03416.634-0.015-0.0150.0000.0000.0000.000
166A162THR0-0.035-0.03018.6590.0240.0240.0000.0000.0000.000
167A163LYS10.9710.99412.700-0.500-0.5000.0000.0000.0000.000
168A164PRO0-0.018-0.00818.219-0.024-0.0240.0000.0000.0000.000
169A165SER0-0.085-0.05220.7560.0190.0190.0000.0000.0000.000
170A166ILE00.0170.00721.967-0.008-0.0080.0000.0000.0000.000
171A167PRO00.0440.01419.0940.0180.0180.0000.0000.0000.000
172A168TYR00.0070.00713.006-0.054-0.0540.0000.0000.0000.000
173A169ASP-1-0.775-0.86814.9950.6000.6000.0000.0000.0000.000
174A170LEU0-0.025-0.02313.4840.1020.1020.0000.0000.0000.000
175A171TRP0-0.035-0.02413.901-0.037-0.0370.0000.0000.0000.000
176A172GLN00.0470.02615.613-0.009-0.0090.0000.0000.0000.000
177A173TYR0-0.008-0.02813.412-0.012-0.0120.0000.0000.0000.000
178A174THR0-0.063-0.05318.294-0.026-0.0260.0000.0000.0000.000
179A175SER00.0620.04120.863-0.004-0.0040.0000.0000.0000.000
180A176LYS10.7630.87523.331-0.007-0.0070.0000.0000.0000.000
181A177GLY00.0230.01320.505-0.017-0.0170.0000.0000.0000.000
182A178ARG10.9670.97520.4730.1810.1810.0000.0000.0000.000
183A179ILE00.0450.01617.476-0.028-0.0280.0000.0000.0000.000
184A180LYS10.9750.97720.4970.2560.2560.0000.0000.0000.000
185A181ALA0-0.0150.00721.1560.0140.0140.0000.0000.0000.000
186A182ILE0-0.002-0.00721.8100.0190.0190.0000.0000.0000.000
187A183ALA00.0070.01524.840-0.004-0.0040.0000.0000.0000.000
188A184SER0-0.029-0.02227.3150.0020.0020.0000.0000.0000.000
189A185PRO00.0150.01325.155-0.011-0.0110.0000.0000.0000.000
190A186VAL0-0.012-0.00420.4620.0070.0070.0000.0000.0000.000
191A187ASP-1-0.772-0.86621.0280.0240.0240.0000.0000.0000.000
192A188MET0-0.074-0.01315.561-0.009-0.0090.0000.0000.0000.000
193A189ASN00.003-0.00715.1450.0660.0660.0000.0000.0000.000
194A190THR0-0.029-0.0279.5990.0080.0080.0000.0000.0000.000
195A191CYS0-0.003-0.0089.411-0.078-0.0780.0000.0000.0000.000
196A192SER00.0520.0417.0100.0650.0650.0000.0000.0000.000
197A193SER00.0750.0093.381-2.216-1.8070.010-0.194-0.2250.001
198A194ASP-1-0.914-0.9406.3360.8320.8320.0000.0000.0000.000
199A195ILE00.0160.0029.734-0.340-0.3400.0000.0000.0000.000
200A196LEU0-0.018-0.0057.546-0.243-0.2430.0000.0000.0000.000
201A197ASN0-0.015-0.0129.768-0.249-0.2490.0000.0000.0000.000
202A198LYS10.8860.94811.350-0.708-0.7080.0000.0000.0000.000
203A199LEU0-0.036-0.01912.951-0.096-0.0960.0000.0000.0000.000
204A200LYS10.8370.92510.341-0.045-0.0450.0000.0000.0000.000
205A201GLY00.0430.03015.233-0.045-0.0450.0000.0000.0000.000
206A202SER0-0.075-0.02314.542-0.043-0.0430.0000.0000.0000.000