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: 5JVGZ

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 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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2260460.313445
FMO2-HF: Nuclear repulsion 2183526.350214
FMO2-HF: Total energy -76933.963231
FMO2-MP2: Total energy -77156.467732


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.
-7.984-3.9251.244-2.637-2.667-0.004
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 : -0.013 / q_NPA : -0.004
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].
3A4PRO00.0220.0033.369-2.651-0.5860.071-1.330-0.8060.001
4A5PRO0-0.083-0.0435.743-0.329-0.3290.0000.0000.0000.000
5A6THR00.0400.0266.6250.3750.3750.0000.0000.0000.000
6A7ILE00.0670.0229.1580.2000.2000.0000.0000.0000.000
7A8GLU-1-0.833-0.91011.452-0.333-0.3330.0000.0000.0000.000
8A9GLU-1-0.777-0.8606.348-1.419-1.4190.0000.0000.0000.000
9A10LEU00.002-0.0089.9640.1730.1730.0000.0000.0000.000
10A11LYS10.8380.91012.4960.4660.4660.0000.0000.0000.000
11A12ARG10.7660.8819.2570.3320.3320.0000.0000.0000.000
12A13GLU-1-0.867-0.92211.7550.0550.0550.0000.0000.0000.000
13A14LYS10.8500.91214.7290.1510.1510.0000.0000.0000.000
14A15ILE00.0040.00212.1430.0380.0380.0000.0000.0000.000
15A16ILE00.0250.05114.9680.0010.0010.0000.0000.0000.000
16A17PRO0-0.015-0.02417.6180.0200.0200.0000.0000.0000.000
17A18HIS0-0.055-0.03519.1610.0270.0270.0000.0000.0000.000
18A19VAL0-0.016-0.00616.7520.0320.0320.0000.0000.0000.000
19A20PHE00.0250.01013.2340.0070.0070.0000.0000.0000.000
20A21PRO00.009-0.00518.802-0.009-0.0090.0000.0000.0000.000
21A22ASP-1-0.810-0.87820.539-0.326-0.3260.0000.0000.0000.000
22A23GLU-1-0.808-0.90317.432-0.407-0.4070.0000.0000.0000.000
23A24ASN0-0.058-0.02417.351-0.063-0.0630.0000.0000.0000.000
24A25VAL0-0.022-0.01314.2740.0040.0040.0000.0000.0000.000
25A26ASP-1-0.836-0.91614.446-0.824-0.8240.0000.0000.0000.000
26A27LEU0-0.080-0.04010.2670.0490.0490.0000.0000.0000.000
27A28THR00.0490.02110.649-0.246-0.2460.0000.0000.0000.000
28A29VAL0-0.043-0.01210.156-0.181-0.1810.0000.0000.0000.000
29A30ASP-1-0.870-0.9393.391-6.418-5.3980.017-0.685-0.351-0.005
30A31MET0-0.045-0.0265.9700.6370.6370.0000.0000.0000.000
31A32TYR0-0.032-0.0206.6720.0510.0510.0000.0000.0000.000
32A33ILE00.019-0.0017.492-0.117-0.1170.0000.0000.0000.000
33A34SER00.0390.02110.6020.1550.1550.0000.0000.0000.000
34A35PHE00.019-0.01313.035-0.101-0.1010.0000.0000.0000.000
35A36LYS10.8100.90115.723-0.358-0.3580.0000.0000.0000.000
36A37SER00.0480.03315.6000.0690.0690.0000.0000.0000.000
37A38GLY00.0600.03414.763-0.055-0.0550.0000.0000.0000.000
38A39LYS10.7690.88614.651-0.381-0.3810.0000.0000.0000.000
39A40GLU-1-0.815-0.8899.6061.1941.1940.0000.0000.0000.000
40A41VAL0-0.045-0.0119.3920.0800.0800.0000.0000.0000.000
41A42ASN00.0230.0034.2350.5330.7030.000-0.023-0.1480.000
42A43HIS10.8710.9252.5613.0593.8631.156-0.599-1.3620.000
43A44GLY00.0120.0156.159-0.005-0.0050.0000.0000.0000.000
44A45ASN0-0.015-0.0199.105-0.173-0.1730.0000.0000.0000.000
45A46ILE00.001-0.00510.784-0.151-0.1510.0000.0000.0000.000
46A47LEU00.0050.00412.8760.0520.0520.0000.0000.0000.000
47A48ASP-1-0.808-0.87916.1420.2370.2370.0000.0000.0000.000
48A49LEU00.0330.01419.5070.0110.0110.0000.0000.0000.000
49A50ALA00.0290.03021.815-0.011-0.0110.0000.0000.0000.000
50A51GLY00.0480.01621.1490.0360.0360.0000.0000.0000.000
51A52THR0-0.009-0.01718.0210.0020.0020.0000.0000.0000.000
52A53GLY0-0.0150.00220.504-0.024-0.0240.0000.0000.0000.000
53A54SER0-0.045-0.03021.979-0.013-0.0130.0000.0000.0000.000
54A55VAL00.0500.03919.4640.0220.0220.0000.0000.0000.000
55A56PRO0-0.029-0.01214.9530.0220.0220.0000.0000.0000.000
56A57ARG10.9470.98717.129-0.264-0.2640.0000.0000.0000.000
57A58ASN0-0.017-0.01514.407-0.009-0.0090.0000.0000.0000.000
58A59ILE00.0040.01111.6210.0740.0740.0000.0000.0000.000
59A60LYS10.8000.88510.107-0.217-0.2170.0000.0000.0000.000
60A61PHE00.0330.0199.487-0.043-0.0430.0000.0000.0000.000
61A62SER0-0.007-0.0308.3110.0470.0470.0000.0000.0000.000
62A63GLU-1-0.858-0.90610.105-0.797-0.7970.0000.0000.0000.000
63A64GLU-1-0.867-0.93413.877-0.187-0.1870.0000.0000.0000.000
64A65PRO0-0.054-0.00217.031-0.035-0.0350.0000.0000.0000.000
65A66PRO00.030-0.00318.6870.0330.0330.0000.0000.0000.000
66A67GLU-1-0.910-0.95521.636-0.157-0.1570.0000.0000.0000.000
67A68ASP-1-0.885-0.94025.223-0.162-0.1620.0000.0000.0000.000
68A69TYR0-0.051-0.01422.3070.0030.0030.0000.0000.0000.000
69A70CYS0-0.072-0.01321.3590.0080.0080.0000.0000.0000.000
70A71TYR00.011-0.02614.413-0.031-0.0310.0000.0000.0000.000
71A72ILE0-0.007-0.00318.9270.0460.0460.0000.0000.0000.000
72A73LEU0-0.023-0.00914.383-0.042-0.0420.0000.0000.0000.000
73A74PHE00.0180.00717.3060.0450.0450.0000.0000.0000.000
74A75MET0-0.032-0.00516.617-0.014-0.0140.0000.0000.0000.000
75A76ILE00.010-0.00217.6580.0150.0150.0000.0000.0000.000
76A77ASP-1-0.784-0.88318.2440.0420.0420.0000.0000.0000.000
77A78PRO00.0510.04617.7270.0020.0020.0000.0000.0000.000
78A79ASP-1-0.778-0.86519.373-0.027-0.0270.0000.0000.0000.000
79A80PHE00.0070.02922.4380.0210.0210.0000.0000.0000.000
80A81PRO00.0090.00525.306-0.010-0.0100.0000.0000.0000.000
81A82SER0-0.076-0.06725.8180.0170.0170.0000.0000.0000.000
82A83ARG10.9000.95217.503-0.038-0.0380.0000.0000.0000.000
83A84ARG10.9210.95424.005-0.048-0.0480.0000.0000.0000.000
84A85ARG10.9670.99527.385-0.008-0.0080.0000.0000.0000.000
85A86PRO00.0320.04024.7240.0080.0080.0000.0000.0000.000
86A87ASP-1-0.833-0.93626.693-0.028-0.0280.0000.0000.0000.000
87A88GLY0-0.056-0.05028.359-0.002-0.0020.0000.0000.0000.000
88A89ARG10.8130.91722.4390.0960.0960.0000.0000.0000.000
89A90ASP-1-0.780-0.89921.755-0.140-0.1400.0000.0000.0000.000
90A91TYR0-0.034-0.03223.6290.0070.0070.0000.0000.0000.000
91A92VAL00.0080.01022.3590.0060.0060.0000.0000.0000.000
92A93HIS0-0.056-0.04320.6880.0130.0130.0000.0000.0000.000
93A94TRP0-0.034-0.02316.3580.0210.0210.0000.0000.0000.000
94A95ALA00.0260.01421.023-0.021-0.0210.0000.0000.0000.000
95A96VAL0-0.034-0.00519.6760.0170.0170.0000.0000.0000.000
96A97SER00.024-0.00720.961-0.035-0.0350.0000.0000.0000.000
97A98GLY00.0710.00122.2510.0210.0210.0000.0000.0000.000
98A99ILE0-0.043-0.01217.0830.0120.0120.0000.0000.0000.000
99A100LYS10.8720.92620.3700.1930.1930.0000.0000.0000.000
100A101SER00.0330.01518.755-0.019-0.0190.0000.0000.0000.000
101A102LYS10.9300.96612.0600.3620.3620.0000.0000.0000.000
102A103GLU-1-0.865-0.90913.9620.1230.1230.0000.0000.0000.000
103A104LEU00.0030.03115.709-0.009-0.0090.0000.0000.0000.000
104A105VAL00.018-0.00516.7660.0410.0410.0000.0000.0000.000
105A106LYS10.9050.93319.411-0.118-0.1180.0000.0000.0000.000
106A107GLY0-0.006-0.00219.048-0.009-0.0090.0000.0000.0000.000
107A108THR00.025-0.00220.050-0.026-0.0260.0000.0000.0000.000
108A109ASP-1-0.731-0.86622.102-0.074-0.0740.0000.0000.0000.000
109A110LYS10.9330.96024.0120.0600.0600.0000.0000.0000.000
110A111ASN0-0.035-0.01423.4510.0020.0020.0000.0000.0000.000
111A112CYS0-0.078-0.02322.308-0.016-0.0160.0000.0000.0000.000
112A113ILE00.0550.02924.8650.0150.0150.0000.0000.0000.000
113A114THR0-0.038-0.02624.833-0.007-0.0070.0000.0000.0000.000
114A115LEU00.0070.01425.3120.0090.0090.0000.0000.0000.000
115A116LEU00.0250.00925.2420.0060.0060.0000.0000.0000.000
116A117PRO00.0300.02024.7740.0000.0000.0000.0000.0000.000
117A118TYR00.005-0.01818.8760.0010.0010.0000.0000.0000.000
118A119VAL00.0030.01623.8190.0090.0090.0000.0000.0000.000
119A120GLY00.0180.01522.4750.0010.0010.0000.0000.0000.000
120A121PRO00.0290.01019.752-0.015-0.0150.0000.0000.0000.000
121A122SER00.0400.02822.4900.0120.0120.0000.0000.0000.000
122A123ILE0-0.0100.02220.570-0.007-0.0070.0000.0000.0000.000
123A124LYS10.9450.96525.242-0.045-0.0450.0000.0000.0000.000
124A125LYS10.9700.98327.500-0.082-0.0820.0000.0000.0000.000
125A126GLY00.017-0.00127.791-0.007-0.0070.0000.0000.0000.000
126A127THR0-0.052-0.01426.076-0.003-0.0030.0000.0000.0000.000
127A128GLY00.0450.02724.057-0.011-0.0110.0000.0000.0000.000
128A129LEU0-0.007-0.00417.9570.0080.0080.0000.0000.0000.000
129A130HIS10.7820.86619.394-0.083-0.0830.0000.0000.0000.000
130A131ARG10.8060.87115.1380.1360.1360.0000.0000.0000.000
131A132ILE0-0.049-0.01015.993-0.048-0.0480.0000.0000.0000.000
132A133SER00.018-0.01613.3240.0260.0260.0000.0000.0000.000
133A134PHE0-0.023-0.02111.9860.0620.0620.0000.0000.0000.000
134A135ILE00.0090.00112.495-0.099-0.0990.0000.0000.0000.000
135A136LEU00.0170.01312.0270.0740.0740.0000.0000.0000.000
136A137SER00.0440.01314.757-0.081-0.0810.0000.0000.0000.000
137A138LEU0-0.0190.00017.6350.0270.0270.0000.0000.0000.000
138A139VAL00.0320.00920.0090.0110.0110.0000.0000.0000.000
139A140LYS10.8960.94523.6210.1550.1550.0000.0000.0000.000
140A141GLU-1-0.800-0.91226.343-0.124-0.1240.0000.0000.0000.000
141A142GLU-1-0.834-0.91927.478-0.129-0.1290.0000.0000.0000.000
142A143ASN00.0260.00528.9530.0170.0170.0000.0000.0000.000
143A144LYS10.7670.91425.6470.1190.1190.0000.0000.0000.000
144A145GLY00.008-0.00127.0580.0030.0030.0000.0000.0000.000
145A146ASN0-0.081-0.04429.7870.0170.0170.0000.0000.0000.000
146A147VAL00.0200.02226.047-0.007-0.0070.0000.0000.0000.000
147A148THR00.0670.03429.1100.0160.0160.0000.0000.0000.000
148A149GLY00.027-0.00729.479-0.008-0.0080.0000.0000.0000.000
149A150VAL0-0.076-0.04825.9840.0080.0080.0000.0000.0000.000
150A151PRO00.0370.01629.287-0.002-0.0020.0000.0000.0000.000
151A152LEU00.0420.03030.8080.0020.0020.0000.0000.0000.000
152A153TYR0-0.060-0.06130.0580.0070.0070.0000.0000.0000.000
153A154ARG10.9470.96932.1230.0410.0410.0000.0000.0000.000
154A155GLY00.0370.02333.8620.0040.0040.0000.0000.0000.000
155A156GLU-1-0.782-0.86530.661-0.011-0.0110.0000.0000.0000.000
156A157HIS0-0.019-0.00333.998-0.001-0.0010.0000.0000.0000.000
157A158TYR0-0.051-0.02036.095-0.002-0.0020.0000.0000.0000.000
158A159ILE0-0.0260.01030.543-0.006-0.0060.0000.0000.0000.000
159A160THR0-0.014-0.00631.5650.0080.0080.0000.0000.0000.000
160A161ARG10.7800.85525.5190.0020.0020.0000.0000.0000.000
161A162VAL0-0.022-0.00527.148-0.005-0.0050.0000.0000.0000.000
162A163LYS10.9110.96827.8020.0470.0470.0000.0000.0000.000
163A164PHE00.0190.00221.641-0.005-0.0050.0000.0000.0000.000
164A165ASN00.0460.02026.9220.0020.0020.0000.0000.0000.000
165A166ASN0-0.012-0.00130.1960.0010.0010.0000.0000.0000.000
166A167CYS0-0.0080.03928.592-0.002-0.0020.0000.0000.0000.000
167A168GLN0-0.032-0.01828.348-0.010-0.0100.0000.0000.0000.000
168A169SER00.006-0.01923.0180.0040.0040.0000.0000.0000.000
169A170ALA00.0400.01720.078-0.002-0.0020.0000.0000.0000.000
170A171TYR00.001-0.02519.6360.0030.0030.0000.0000.0000.000
171A172ASN0-0.029-0.01421.826-0.009-0.0090.0000.0000.0000.000
172A173VAL00.0210.00224.4240.0030.0030.0000.0000.0000.000
173A174ILE0-0.008-0.00519.1140.0020.0020.0000.0000.0000.000
174A175GLN0-0.010-0.00623.425-0.002-0.0020.0000.0000.0000.000
175A176MET0-0.063-0.02125.5700.0090.0090.0000.0000.0000.000
176A177ASN0-0.078-0.06126.2870.0250.0250.0000.0000.0000.000
177A178ASP-1-0.879-0.92426.599-0.190-0.1900.0000.0000.0000.000
178A179MET0-0.096-0.02121.773-0.017-0.0170.0000.0000.0000.000
179A180LYS10.8740.93916.9250.5730.5730.0000.0000.0000.000
180A181ILE00.000-0.00414.922-0.014-0.0140.0000.0000.0000.000
181A182VAL00.0040.00114.061-0.011-0.0110.0000.0000.0000.000
182A183GLY00.0650.04310.588-0.184-0.1840.0000.0000.0000.000
183A184PHE0-0.008-0.0239.3580.2410.2410.0000.0000.0000.000
184A185ASN0-0.003-0.0196.711-0.276-0.2760.0000.0000.0000.000
185A186TRP00.0040.0187.2160.1630.1630.0000.0000.0000.000
186A187CYS0-0.0250.0189.3780.1570.1570.0000.0000.0000.000
187A188GLN00.0240.00411.990-0.170-0.1700.0000.0000.0000.000
188A189MET0-0.0040.01815.0900.0430.0430.0000.0000.0000.000
189A190ARG10.9530.94918.246-0.215-0.2150.0000.0000.0000.000
190A191ARG10.9020.95421.906-0.100-0.1000.0000.0000.0000.000
191A192LYS10.8890.92722.051-0.307-0.3070.0000.0000.0000.000