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: 4JVGN

Calculation Name: 2GZQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2GZQ

Chain ID: A

ChEMBL ID:

UniProt ID: A5K000

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 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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2258258.493775
FMO2-HF: Nuclear repulsion 2181324.801451
FMO2-HF: Total energy -76933.692325
FMO2-MP2: Total energy -77156.104818


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:GLY)


Summations of interaction energy for fragment #1(A:2: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.
-11.721-13.48112.028-4.755-5.514-0.046
Interaction energy analysis for fragmet #1(A:2:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.033 / q_NPA : -0.029
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].
3A4PRO00.0350.0081.926-4.350-7.3419.472-3.301-3.181-0.046
4A5PRO0-0.052-0.0284.647-0.245-0.198-0.001-0.020-0.0260.000
5A6THR00.0510.0425.833-0.225-0.2250.0000.0000.0000.000
6A7ILE00.0670.0167.9260.3080.3080.0000.0000.0000.000
7A8GLU-1-0.868-0.9449.9310.4050.4050.0000.0000.0000.000
8A9GLU-1-0.783-0.8685.5761.9141.9140.0000.0000.0000.000
9A10LEU0-0.011-0.0159.6770.1420.1420.0000.0000.0000.000
10A11LYS10.8290.90311.7860.1000.1000.0000.0000.0000.000
11A12ARG10.8150.9198.892-0.814-0.8140.0000.0000.0000.000
12A13GLU-1-0.876-0.92911.7000.7510.7510.0000.0000.0000.000
13A14LYS10.8480.91514.576-0.272-0.2720.0000.0000.0000.000
14A15ILE00.0130.01012.044-0.027-0.0270.0000.0000.0000.000
15A16ILE00.0190.06414.188-0.043-0.0430.0000.0000.0000.000
16A17PRO0-0.024-0.03517.0580.0320.0320.0000.0000.0000.000
17A18HIS0-0.061-0.04019.2720.0150.0150.0000.0000.0000.000
18A19VAL0-0.016-0.00516.1490.0060.0060.0000.0000.0000.000
19A20PHE00.0250.00812.635-0.022-0.0220.0000.0000.0000.000
20A21PRO00.012-0.00218.3040.0120.0120.0000.0000.0000.000
21A22ASP-1-0.818-0.90620.027-0.117-0.1170.0000.0000.0000.000
22A23GLU-1-0.837-0.92316.718-0.122-0.1220.0000.0000.0000.000
23A24ASN0-0.068-0.02716.591-0.067-0.0670.0000.0000.0000.000
24A25VAL0-0.025-0.00313.588-0.008-0.0080.0000.0000.0000.000
25A26ASP-1-0.813-0.89114.294-0.655-0.6550.0000.0000.0000.000
26A27LEU0-0.076-0.0399.0500.0260.0260.0000.0000.0000.000
27A28THR00.0550.0199.635-0.236-0.2360.0000.0000.0000.000
28A29VAL0-0.0350.0049.560-0.200-0.2000.0000.0000.0000.000
29A30ASP-1-0.886-0.9533.616-5.051-4.4600.015-0.350-0.256-0.002
30A31MET0-0.039-0.0205.8730.4980.4980.0000.0000.0000.000
31A32TYR0-0.050-0.0317.2910.3770.3770.0000.0000.0000.000
32A33ILE00.020-0.0048.148-0.137-0.1370.0000.0000.0000.000
33A34SER00.0390.02411.0430.1960.1960.0000.0000.0000.000
34A35PHE0-0.008-0.02313.332-0.102-0.1020.0000.0000.0000.000
35A36LYS10.8460.91716.285-0.388-0.3880.0000.0000.0000.000
36A37SER00.0400.03016.1660.0720.0720.0000.0000.0000.000
37A38GLY00.0690.03814.849-0.021-0.0210.0000.0000.0000.000
38A39LYS10.7600.88114.818-0.453-0.4530.0000.0000.0000.000
39A40GLU-1-0.802-0.8839.4780.8370.8370.0000.0000.0000.000
40A41VAL0-0.061-0.0229.6000.0760.0760.0000.0000.0000.000
41A42ASN00.000-0.0124.7741.8541.996-0.001-0.007-0.1340.000
42A43HIS10.8710.9282.030-3.018-2.5672.543-1.077-1.9170.002
43A44GLY0-0.007-0.0017.143-0.251-0.2510.0000.0000.0000.000
44A45ASN00.0290.0089.964-0.205-0.2050.0000.0000.0000.000
45A46ILE0-0.009-0.00811.630-0.187-0.1870.0000.0000.0000.000
46A47LEU00.0050.00913.454-0.032-0.0320.0000.0000.0000.000
47A48ASP-1-0.820-0.89916.4490.3610.3610.0000.0000.0000.000
48A49LEU00.0470.02619.8130.0000.0000.0000.0000.0000.000
49A50ALA00.0190.02822.053-0.024-0.0240.0000.0000.0000.000
50A51GLY00.0300.00121.5060.0360.0360.0000.0000.0000.000
51A52THR0-0.014-0.02618.6000.0040.0040.0000.0000.0000.000
52A53GLY00.0140.01921.165-0.012-0.0120.0000.0000.0000.000
53A54SER0-0.033-0.01222.865-0.020-0.0200.0000.0000.0000.000
54A55VAL00.0320.02919.7760.0320.0320.0000.0000.0000.000
55A56PRO0-0.022-0.00915.6000.0030.0030.0000.0000.0000.000
56A57ARG10.9460.98517.767-0.183-0.1830.0000.0000.0000.000
57A58ASN0-0.013-0.01314.696-0.024-0.0240.0000.0000.0000.000
58A59ILE00.0050.01311.9490.0970.0970.0000.0000.0000.000
59A60LYS10.8220.89810.6550.0560.0560.0000.0000.0000.000
60A61PHE00.0340.0159.978-0.001-0.0010.0000.0000.0000.000
61A62SER00.0280.0168.2190.0150.0150.0000.0000.0000.000
62A63GLU-1-0.965-0.98310.266-0.888-0.8880.0000.0000.0000.000
63A64GLU-1-0.921-0.95413.701-0.277-0.2770.0000.0000.0000.000
64A65PRO0-0.060-0.00216.892-0.037-0.0370.0000.0000.0000.000
65A66PRO00.0390.00618.1570.0150.0150.0000.0000.0000.000
66A67GLU-1-0.914-0.95821.016-0.187-0.1870.0000.0000.0000.000
67A68ASP-1-0.894-0.94724.491-0.165-0.1650.0000.0000.0000.000
68A69TYR0-0.059-0.02021.6510.0170.0170.0000.0000.0000.000
69A70CYS0-0.064-0.00520.9020.0020.0020.0000.0000.0000.000
70A71TYR00.005-0.03514.3500.0020.0020.0000.0000.0000.000
71A72ILE0-0.015-0.00718.4610.0360.0360.0000.0000.0000.000
72A73LEU0-0.031-0.01114.007-0.013-0.0130.0000.0000.0000.000
73A74PHE00.0210.00916.9210.0240.0240.0000.0000.0000.000
74A75MET0-0.049-0.01016.4410.0180.0180.0000.0000.0000.000
75A76ILE00.018-0.00317.401-0.020-0.0200.0000.0000.0000.000
76A77ASP-1-0.773-0.88118.1450.3370.3370.0000.0000.0000.000
77A78PRO00.0410.04417.987-0.033-0.0330.0000.0000.0000.000
78A79ASP-1-0.799-0.87419.8210.2960.2960.0000.0000.0000.000
79A80PHE00.0180.03422.8190.0050.0050.0000.0000.0000.000
80A81PRO00.0250.01225.571-0.013-0.0130.0000.0000.0000.000
81A82SER0-0.063-0.05726.3590.0170.0170.0000.0000.0000.000
82A83ARG10.9420.97118.192-0.393-0.3930.0000.0000.0000.000
83A84ARG10.9190.94924.742-0.206-0.2060.0000.0000.0000.000
84A85ARG10.9911.00127.762-0.143-0.1430.0000.0000.0000.000
85A86PRO00.0120.03325.270-0.001-0.0010.0000.0000.0000.000
86A87ASP-1-0.867-0.95027.2230.1040.1040.0000.0000.0000.000
87A88GLY0-0.059-0.05128.598-0.014-0.0140.0000.0000.0000.000
88A89ARG10.8230.93022.567-0.162-0.1620.0000.0000.0000.000
89A90ASP-1-0.796-0.90721.6720.0970.0970.0000.0000.0000.000
90A91TYR0-0.037-0.03523.546-0.016-0.0160.0000.0000.0000.000
91A92VAL00.0170.01322.1360.0230.0230.0000.0000.0000.000
92A93HIS0-0.064-0.04620.6190.0080.0080.0000.0000.0000.000
93A94TRP0-0.026-0.02416.5030.0100.0100.0000.0000.0000.000
94A95ALA00.0370.02420.8150.0020.0020.0000.0000.0000.000
95A96VAL0-0.034-0.00319.6450.0000.0000.0000.0000.0000.000
96A97SER00.0400.00620.704-0.022-0.0220.0000.0000.0000.000
97A98GLY00.0840.01622.1830.0140.0140.0000.0000.0000.000
98A99ILE0-0.058-0.01617.1740.0000.0000.0000.0000.0000.000
99A100LYS10.9550.96520.1320.1980.1980.0000.0000.0000.000
100A101SER00.0370.03819.191-0.035-0.0350.0000.0000.0000.000
101A102LYS10.9380.96312.9100.6560.6560.0000.0000.0000.000
102A103GLU-1-0.851-0.90714.287-0.112-0.1120.0000.0000.0000.000
103A104LEU0-0.0070.00816.0760.0110.0110.0000.0000.0000.000
104A105VAL00.025-0.00117.2670.0400.0400.0000.0000.0000.000
105A106LYS10.9030.92819.781-0.087-0.0870.0000.0000.0000.000
106A107GLY00.008-0.00119.8410.0000.0000.0000.0000.0000.000
107A108THR00.0160.00220.835-0.013-0.0130.0000.0000.0000.000
108A109ASP-1-0.768-0.87922.868-0.096-0.0960.0000.0000.0000.000
109A110LYS10.9560.97824.8500.0980.0980.0000.0000.0000.000
110A111ASN0-0.058-0.03223.8420.0020.0020.0000.0000.0000.000
111A112CYS0-0.076-0.02022.524-0.007-0.0070.0000.0000.0000.000
112A113ILE00.0520.02824.9970.0120.0120.0000.0000.0000.000
113A114THR0-0.036-0.03025.1530.0040.0040.0000.0000.0000.000
114A115LEU0-0.0020.00924.9610.0050.0050.0000.0000.0000.000
115A116LEU00.0260.00825.0030.0070.0070.0000.0000.0000.000
116A117PRO00.0340.02424.7230.0080.0080.0000.0000.0000.000
117A118TYR00.006-0.02419.1200.0190.0190.0000.0000.0000.000
118A119VAL0-0.0020.01423.877-0.002-0.0020.0000.0000.0000.000
119A120GLY00.0210.01322.4210.0140.0140.0000.0000.0000.000
120A121PRO0-0.007-0.01019.991-0.016-0.0160.0000.0000.0000.000
121A122SER00.0520.03622.783-0.011-0.0110.0000.0000.0000.000
122A123ILE00.0010.00521.321-0.005-0.0050.0000.0000.0000.000
123A124LYS10.9420.97926.009-0.173-0.1730.0000.0000.0000.000
124A125LYS10.9970.99628.097-0.174-0.1740.0000.0000.0000.000
125A126GLY0-0.022-0.01428.718-0.014-0.0140.0000.0000.0000.000
126A127THR0-0.0050.00326.7420.0000.0000.0000.0000.0000.000
127A128GLY00.0260.01524.7350.0020.0020.0000.0000.0000.000
128A129LEU0-0.015-0.00518.517-0.009-0.0090.0000.0000.0000.000
129A130HIS10.7720.85719.968-0.308-0.3080.0000.0000.0000.000
130A131ARG10.7960.86215.432-0.277-0.2770.0000.0000.0000.000
131A132ILE0-0.035-0.00215.986-0.060-0.0600.0000.0000.0000.000
132A133SER00.012-0.01313.3190.1360.1360.0000.0000.0000.000
133A134PHE0-0.019-0.01811.624-0.049-0.0490.0000.0000.0000.000
134A135ILE00.0220.01012.008-0.011-0.0110.0000.0000.0000.000
135A136LEU00.0200.01211.6860.0340.0340.0000.0000.0000.000
136A137SER00.0340.01214.205-0.060-0.0600.0000.0000.0000.000
137A138LEU0-0.0170.00317.0050.0070.0070.0000.0000.0000.000
138A139VAL00.0280.00319.3940.0190.0190.0000.0000.0000.000
139A140LYS10.9080.95122.9970.1190.1190.0000.0000.0000.000
140A141GLU-1-0.790-0.90025.766-0.116-0.1160.0000.0000.0000.000
141A142GLU-1-0.840-0.92226.994-0.103-0.1030.0000.0000.0000.000
142A143ASN00.007-0.01128.0040.0190.0190.0000.0000.0000.000
143A144LYS10.8040.91925.4490.1070.1070.0000.0000.0000.000
144A145GLY0-0.007-0.01226.8150.0090.0090.0000.0000.0000.000
145A146ASN0-0.091-0.04429.3040.0160.0160.0000.0000.0000.000
146A147VAL00.0450.03725.674-0.006-0.0060.0000.0000.0000.000
147A148THR00.0670.02828.6740.0140.0140.0000.0000.0000.000
148A149GLY00.0280.00129.023-0.001-0.0010.0000.0000.0000.000
149A150VAL0-0.068-0.04425.7270.0140.0140.0000.0000.0000.000
150A151PRO00.0020.01129.089-0.006-0.0060.0000.0000.0000.000
151A152LEU00.0490.02730.6120.0050.0050.0000.0000.0000.000
152A153TYR0-0.054-0.05430.1380.0040.0040.0000.0000.0000.000
153A154ARG10.9460.96732.166-0.011-0.0110.0000.0000.0000.000
154A155GLY00.0350.01433.8100.0010.0010.0000.0000.0000.000
155A156GLU-1-0.765-0.85030.7860.0710.0710.0000.0000.0000.000
156A157HIS0-0.033-0.00334.1110.0020.0020.0000.0000.0000.000
157A158TYR0-0.050-0.03035.929-0.003-0.0030.0000.0000.0000.000
158A159ILE0-0.0220.01230.292-0.005-0.0050.0000.0000.0000.000
159A160THR00.0060.00631.5030.0090.0090.0000.0000.0000.000
160A161ARG10.7860.85925.638-0.096-0.0960.0000.0000.0000.000
161A162VAL0-0.023-0.00927.0420.0110.0110.0000.0000.0000.000
162A163LYS10.9490.99027.630-0.080-0.0800.0000.0000.0000.000
163A164PHE00.018-0.00321.484-0.011-0.0110.0000.0000.0000.000
164A165ASN00.0370.01626.677-0.007-0.0070.0000.0000.0000.000
165A166ASN0-0.027-0.01029.923-0.003-0.0030.0000.0000.0000.000
166A167CYS0-0.0080.02428.044-0.010-0.0100.0000.0000.0000.000
167A168GLN0-0.028-0.00728.0760.0010.0010.0000.0000.0000.000
168A169SER00.027-0.00522.8760.0100.0100.0000.0000.0000.000
169A170ALA00.0310.01119.778-0.013-0.0130.0000.0000.0000.000
170A171TYR00.007-0.00619.047-0.015-0.0150.0000.0000.0000.000
171A172ASN0-0.024-0.01721.362-0.027-0.0270.0000.0000.0000.000
172A173VAL00.0190.00523.943-0.010-0.0100.0000.0000.0000.000
173A174ILE00.0140.00418.414-0.007-0.0070.0000.0000.0000.000
174A175GLN0-0.0140.00022.696-0.020-0.0200.0000.0000.0000.000
175A176MET0-0.053-0.01624.5450.0000.0000.0000.0000.0000.000
176A177ASN0-0.107-0.07525.6140.0070.0070.0000.0000.0000.000
177A178ASP-1-0.889-0.92125.739-0.118-0.1180.0000.0000.0000.000
178A179MET0-0.095-0.02721.207-0.012-0.0120.0000.0000.0000.000
179A180LYS10.8700.91716.9890.4330.4330.0000.0000.0000.000
180A181ILE0-0.030-0.01813.849-0.013-0.0130.0000.0000.0000.000
181A182VAL00.015-0.00613.365-0.025-0.0250.0000.0000.0000.000
182A183GLY00.0650.0419.638-0.214-0.2140.0000.0000.0000.000
183A184PHE0-0.002-0.0188.5010.2130.2130.0000.0000.0000.000
184A185ASN0-0.003-0.0036.8100.4640.4640.0000.0000.0000.000
185A186TRP00.0250.0267.552-0.185-0.1850.0000.0000.0000.000
186A187CYS0-0.0240.0199.8940.3050.3050.0000.0000.0000.000
187A188GLN0-0.014-0.01512.576-0.299-0.2990.0000.0000.0000.000
188A189MET00.0020.01915.848-0.004-0.0040.0000.0000.0000.000
189A190ARG10.9690.97018.944-0.384-0.3840.0000.0000.0000.000
190A191ARG10.9350.96022.502-0.224-0.2240.0000.0000.0000.000
191A192LYS10.8730.91522.350-0.430-0.4300.0000.0000.0000.000