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: ZNNGN

Calculation Name: 5EY6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5EY6

Chain ID: A

ChEMBL ID:

UniProt ID: B9GQ64

Base Structure: X-ray

Registration Date: 2023-09-27

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 215
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2611760.94076
FMO2-HF: Nuclear repulsion 2527019.92301
FMO2-HF: Total energy -84741.01775
FMO2-MP2: Total energy -84990.785346


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:4:PRO)


Summations of interaction energy for fragment #1(A:4:PRO)
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.
-6.762-1.822.841-2.396-5.388-0.02
Interaction energy analysis for fragmet #1(A:4:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.021 / q_NPA : -0.023
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].
3A6LYS10.9010.9553.283-2.541-0.7220.065-0.884-1.0000.000
4A7VAL00.0240.0015.4050.0250.0250.0000.0000.0000.000
5A8TYR0-0.033-0.0318.2550.1120.1120.0000.0000.0000.000
6A9GLY00.0570.00011.001-0.026-0.0260.0000.0000.0000.000
7A10PRO0-0.0220.00312.790-0.008-0.0080.0000.0000.0000.000
8A11PRO00.0910.01612.833-0.009-0.0090.0000.0000.0000.000
9A12LEU00.0100.03315.256-0.007-0.0070.0000.0000.0000.000
10A13SER00.0170.01917.408-0.002-0.0020.0000.0000.0000.000
11A14THR00.0580.03518.053-0.014-0.0140.0000.0000.0000.000
12A15ALA00.0540.02118.545-0.014-0.0140.0000.0000.0000.000
13A16VAL0-0.016-0.01412.765-0.021-0.0210.0000.0000.0000.000
14A17SER00.009-0.00413.976-0.030-0.0300.0000.0000.0000.000
15A18ARG10.8600.92215.3790.0890.0890.0000.0000.0000.000
16A19VAL00.0220.02010.521-0.018-0.0180.0000.0000.0000.000
17A20LEU0-0.044-0.0159.659-0.054-0.0540.0000.0000.0000.000
18A21VAL00.0630.02111.374-0.041-0.0410.0000.0000.0000.000
19A22THR00.0140.00013.252-0.001-0.0010.0000.0000.0000.000
20A23LEU0-0.002-0.0057.145-0.014-0.0140.0000.0000.0000.000
21A24LEU0-0.076-0.0309.540-0.042-0.0420.0000.0000.0000.000
22A25GLU-1-0.745-0.80811.255-0.186-0.1860.0000.0000.0000.000
23A26LYS10.7750.90211.6480.2940.2940.0000.0000.0000.000
24A27ASP-1-0.879-0.91810.152-0.462-0.4620.0000.0000.0000.000
25A28VAL00.0010.0115.603-0.036-0.0360.0000.0000.0000.000
26A29PRO00.001-0.0083.483-0.562-0.0680.010-0.151-0.3530.000
27A30PHE0-0.003-0.0062.622-3.038-0.9271.689-1.668-2.132-0.016
28A31GLN00.006-0.0022.5100.0200.5201.0680.284-1.852-0.004
29A32ILE00.0150.0083.697-0.066-0.0480.0090.023-0.0510.000
30A33ILE0-0.034-0.0096.8210.1350.1350.0000.0000.0000.000
31A34PRO00.0030.0029.459-0.060-0.0600.0000.0000.0000.000
32A35VAL00.0410.00713.2320.0200.0200.0000.0000.0000.000
33A36ASP-1-0.773-0.84415.9620.0320.0320.0000.0000.0000.000
34A37MET0-0.013-0.01819.1650.0000.0000.0000.0000.0000.000
35A38SER0-0.081-0.06521.761-0.001-0.0010.0000.0000.0000.000
36A39LYS10.8440.89822.007-0.058-0.0580.0000.0000.0000.000
37A40GLY00.0160.01623.6960.0060.0060.0000.0000.0000.000
38A41GLU-1-0.804-0.87317.5310.1290.1290.0000.0000.0000.000
39A42HIS00.0060.00219.0850.0140.0140.0000.0000.0000.000
40A43LYS10.8900.95420.071-0.030-0.0300.0000.0000.0000.000
41A44LYS10.9070.94418.342-0.128-0.1280.0000.0000.0000.000
42A45PRO00.0370.00620.821-0.001-0.0010.0000.0000.0000.000
43A46ASP-1-0.858-0.90417.8300.1420.1420.0000.0000.0000.000
44A47TYR0-0.014-0.02014.0470.0020.0020.0000.0000.0000.000
45A48LEU00.002-0.00717.428-0.015-0.0150.0000.0000.0000.000
46A49LYS10.7850.87318.152-0.126-0.1260.0000.0000.0000.000
47A50ILE0-0.0160.00212.680-0.004-0.0040.0000.0000.0000.000
48A51GLN0-0.004-0.01816.629-0.020-0.0200.0000.0000.0000.000
49A52PRO00.0390.04018.4620.0080.0080.0000.0000.0000.000
50A53PHE0-0.014-0.00421.9620.0030.0030.0000.0000.0000.000
51A54GLY0-0.007-0.01520.9640.0010.0010.0000.0000.0000.000
52A55GLN0-0.061-0.02920.307-0.006-0.0060.0000.0000.0000.000
53A56VAL00.0120.02716.0580.0080.0080.0000.0000.0000.000
54A57PRO00.0050.00013.1890.0010.0010.0000.0000.0000.000
55A58ALA00.0030.00013.1360.0130.0130.0000.0000.0000.000
56A59PHE00.0070.0028.034-0.009-0.0090.0000.0000.0000.000
57A60GLN00.0230.0168.4180.2270.2270.0000.0000.0000.000
58A61ASP-1-0.725-0.8466.255-0.812-0.8120.0000.0000.0000.000
59A62GLU-1-0.843-0.8756.364-0.226-0.2260.0000.0000.0000.000
60A63SER0-0.039-0.0307.9700.0830.0830.0000.0000.0000.000
61A64ILE0-0.052-0.01010.8930.0410.0410.0000.0000.0000.000
62A65SER0-0.019-0.01811.0780.0100.0100.0000.0000.0000.000
63A66LEU0-0.027-0.00613.2110.0030.0030.0000.0000.0000.000
64A67PHE00.036-0.00114.3690.0050.0050.0000.0000.0000.000
65A68GLU-1-0.758-0.86316.888-0.102-0.1020.0000.0000.0000.000
66A69SER0-0.021-0.00816.003-0.017-0.0170.0000.0000.0000.000
67A70ARG10.8460.87016.7680.0580.0580.0000.0000.0000.000
68A71SER0-0.0150.00518.423-0.005-0.0050.0000.0000.0000.000
69A72ILE0-0.030-0.00812.136-0.014-0.0140.0000.0000.0000.000
70A73CYS0-0.043-0.01513.852-0.043-0.0430.0000.0000.0000.000
71A74ARG10.8200.89915.4380.0910.0910.0000.0000.0000.000
72A75TYR0-0.010-0.02510.4280.0260.0260.0000.0000.0000.000
73A76VAL0-0.032-0.0199.904-0.027-0.0270.0000.0000.0000.000
74A77CYS0-0.047-0.03112.341-0.017-0.0170.0000.0000.0000.000
75A78GLU-1-0.877-0.91415.212-0.134-0.1340.0000.0000.0000.000
76A79LYS10.7850.8698.9450.4880.4880.0000.0000.0000.000
77A80TYR0-0.006-0.0117.290-0.067-0.0670.0000.0000.0000.000
78A81ALA00.0390.02312.3330.0040.0040.0000.0000.0000.000
79A82ASP-1-0.936-0.97114.052-0.275-0.2750.0000.0000.0000.000
80A83ARG10.8360.9039.7270.4590.4590.0000.0000.0000.000
81A84GLY00.012-0.00313.8140.0120.0120.0000.0000.0000.000
82A85ASP-1-0.806-0.89514.890-0.142-0.1420.0000.0000.0000.000
83A86LYS10.8530.92017.2730.1810.1810.0000.0000.0000.000
84A87GLY00.0770.06119.3000.0060.0060.0000.0000.0000.000
85A88LEU0-0.028-0.01416.5490.0050.0050.0000.0000.0000.000
86A89TYR0-0.015-0.06618.7150.0030.0030.0000.0000.0000.000
87A90GLY00.0350.01321.1960.0070.0070.0000.0000.0000.000
88A91THR0-0.033-0.04122.351-0.007-0.0070.0000.0000.0000.000
89A92ASN0-0.057-0.03524.0460.0060.0060.0000.0000.0000.000
90A93PRO00.045-0.00126.218-0.002-0.0020.0000.0000.0000.000
91A94LEU00.0230.02527.5180.0020.0020.0000.0000.0000.000
92A95GLU-1-0.751-0.82526.410-0.099-0.0990.0000.0000.0000.000
93A96ARG10.7910.89721.4120.1370.1370.0000.0000.0000.000
94A97ALA00.010-0.00725.396-0.001-0.0010.0000.0000.0000.000
95A98SER0-0.032-0.03528.4860.0050.0050.0000.0000.0000.000
96A99ILE0-0.0030.01123.3970.0020.0020.0000.0000.0000.000
97A100ASP-1-0.808-0.88324.247-0.100-0.1000.0000.0000.0000.000
98A101GLN0-0.026-0.00826.3850.0050.0050.0000.0000.0000.000
99A102TRP00.0290.00628.3220.0050.0050.0000.0000.0000.000
100A103VAL0-0.0250.00022.9620.0000.0000.0000.0000.0000.000
101A104GLU-1-0.804-0.88625.795-0.075-0.0750.0000.0000.0000.000
102A105ALA00.0100.01828.4290.0050.0050.0000.0000.0000.000
103A106GLU-1-0.712-0.82124.252-0.082-0.0820.0000.0000.0000.000
104A107GLY0-0.020-0.02026.5690.0050.0050.0000.0000.0000.000
105A108GLN0-0.049-0.02927.2720.0090.0090.0000.0000.0000.000
106A109SER0-0.072-0.03630.8140.0060.0060.0000.0000.0000.000
107A110PHE00.0540.04027.0210.0030.0030.0000.0000.0000.000
108A111GLY00.0110.03727.5550.0020.0020.0000.0000.0000.000
109A112PRO0-0.022-0.01928.1980.0030.0030.0000.0000.0000.000
110A113SER0-0.040-0.01330.7340.0030.0030.0000.0000.0000.000
111A114SER00.053-0.00629.0630.0010.0010.0000.0000.0000.000
112A115GLY00.0270.01528.0810.0010.0010.0000.0000.0000.000
113A116ALA0-0.038-0.01528.8800.0030.0030.0000.0000.0000.000
114A117LEU0-0.0070.00332.1820.0030.0030.0000.0000.0000.000
115A118VAL00.0390.01326.0730.0020.0020.0000.0000.0000.000
116A119PHE0-0.027-0.01629.0950.0030.0030.0000.0000.0000.000
117A120GLN00.0420.00830.1760.0040.0040.0000.0000.0000.000
118A121LEU0-0.0230.00732.6490.0020.0020.0000.0000.0000.000
119A122ALA00.0400.03228.4880.0010.0010.0000.0000.0000.000
120A123PHE0-0.105-0.05623.2500.0020.0020.0000.0000.0000.000
121A124ALA00.0090.01429.1660.0030.0030.0000.0000.0000.000
122A125PRO00.0430.02332.2300.0030.0030.0000.0000.0000.000
123A126ARG10.8990.95027.5990.0190.0190.0000.0000.0000.000
124A127MET0-0.038-0.02530.9320.0000.0000.0000.0000.0000.000
125A128ASN0-0.050-0.02932.8570.0010.0010.0000.0000.0000.000
126A129ILE00.0170.02532.5510.0010.0010.0000.0000.0000.000
127A130PRO0-0.030-0.01736.355-0.001-0.0010.0000.0000.0000.000
128A131GLN00.0170.01836.6970.0000.0000.0000.0000.0000.000
129A132ASP-1-0.829-0.91138.312-0.012-0.0120.0000.0000.0000.000
130A133GLN00.029-0.00639.640-0.003-0.0030.0000.0000.0000.000
131A134GLY0-0.0300.00342.292-0.001-0.0010.0000.0000.0000.000
132A135VAL0-0.040-0.04736.048-0.002-0.0020.0000.0000.0000.000
133A136ILE00.0200.01437.181-0.002-0.0020.0000.0000.0000.000
134A137LYS10.8400.90738.7330.0180.0180.0000.0000.0000.000
135A138GLN00.0430.02040.147-0.003-0.0030.0000.0000.0000.000
136A139ASN0-0.039-0.02935.410-0.002-0.0020.0000.0000.0000.000
137A140GLU-1-0.766-0.87636.684-0.028-0.0280.0000.0000.0000.000
138A141GLU-1-0.831-0.88938.367-0.023-0.0230.0000.0000.0000.000
139A142LYS10.7940.88837.4820.0250.0250.0000.0000.0000.000
140A143LEU00.0310.02132.452-0.002-0.0020.0000.0000.0000.000
141A144GLY00.0260.01236.055-0.002-0.0020.0000.0000.0000.000
142A145LYS10.8570.91638.8880.0280.0280.0000.0000.0000.000
143A146VAL0-0.012-0.00133.134-0.001-0.0010.0000.0000.0000.000
144A147LEU00.011-0.00232.620-0.002-0.0020.0000.0000.0000.000
145A148ASP-1-0.797-0.87936.289-0.033-0.0330.0000.0000.0000.000
146A149ILE0-0.043-0.01637.0090.0000.0000.0000.0000.0000.000
147A150TYR0-0.019-0.04830.1260.0000.0000.0000.0000.0000.000
148A151GLU-1-0.764-0.85735.707-0.045-0.0450.0000.0000.0000.000
149A152GLN0-0.062-0.03738.1110.0010.0010.0000.0000.0000.000
150A153ARG10.8130.90833.2960.0590.0590.0000.0000.0000.000
151A154LEU0-0.028-0.01431.491-0.002-0.0020.0000.0000.0000.000
152A155GLY00.0260.02435.545-0.001-0.0010.0000.0000.0000.000
153A156GLU-1-0.919-0.93937.989-0.045-0.0450.0000.0000.0000.000
154A157SER0-0.052-0.02332.799-0.001-0.0010.0000.0000.0000.000
155A158ARG10.8120.89529.7680.0770.0770.0000.0000.0000.000
156A159PHE00.002-0.00726.914-0.002-0.0020.0000.0000.0000.000
157A160LEU00.0040.00728.0510.0040.0040.0000.0000.0000.000
158A161ALA00.007-0.00127.8100.0050.0050.0000.0000.0000.000
159A162GLY0-0.0030.00629.8340.0020.0020.0000.0000.0000.000
160A163ASP-1-0.839-0.92330.903-0.065-0.0650.0000.0000.0000.000
161A164GLU-1-0.972-0.98925.004-0.117-0.1170.0000.0000.0000.000
162A165PHE0-0.022-0.00419.6220.0020.0020.0000.0000.0000.000
163A166THR0-0.003-0.02222.551-0.009-0.0090.0000.0000.0000.000
164A167PHE00.028-0.01917.539-0.001-0.0010.0000.0000.0000.000
165A168ALA00.0330.01921.1090.0030.0030.0000.0000.0000.000
166A169ASP-1-0.754-0.84224.208-0.090-0.0900.0000.0000.0000.000
167A170LEU00.0110.01116.6570.0040.0040.0000.0000.0000.000
168A171SER0-0.049-0.03921.036-0.002-0.0020.0000.0000.0000.000
169A172HIS00.0230.01721.9990.0140.0140.0000.0000.0000.000
170A173LEU0-0.0090.01120.2150.0070.0070.0000.0000.0000.000
171A174PRO0-0.050-0.02219.6180.0080.0080.0000.0000.0000.000
172A175ASN0-0.038-0.03322.1200.0040.0040.0000.0000.0000.000
173A176GLY00.0530.02725.7620.0060.0060.0000.0000.0000.000
174A177ASP-1-0.772-0.88323.364-0.069-0.0690.0000.0000.0000.000
175A178TYR0-0.063-0.05721.3960.0060.0060.0000.0000.0000.000
176A179LEU0-0.023-0.01026.9290.0050.0050.0000.0000.0000.000
177A180VAL0-0.0030.00629.1460.0040.0040.0000.0000.0000.000
178A181ASN0-0.039-0.01825.7840.0060.0060.0000.0000.0000.000
179A182ALA0-0.071-0.03428.1850.0030.0030.0000.0000.0000.000
180A183THR0-0.085-0.04830.2140.0030.0030.0000.0000.0000.000
181A184ASP-1-0.792-0.90233.377-0.026-0.0260.0000.0000.0000.000
182A185LYS10.8170.89534.3890.0240.0240.0000.0000.0000.000
183A186GLY00.0700.04933.465-0.002-0.0020.0000.0000.0000.000
184A187HIS00.0000.00534.376-0.001-0.0010.0000.0000.0000.000
185A188LEU0-0.072-0.01735.4410.0000.0000.0000.0000.0000.000
186A189PHE00.0220.00330.414-0.001-0.0010.0000.0000.0000.000
187A190THR00.0150.00034.8160.0000.0000.0000.0000.0000.000
188A191SER0-0.093-0.05737.0170.0010.0010.0000.0000.0000.000
189A192ARG10.7770.88237.5040.0380.0380.0000.0000.0000.000
190A193GLU-1-0.891-0.93337.406-0.040-0.0400.0000.0000.0000.000
191A194ASN0-0.016-0.03936.512-0.004-0.0040.0000.0000.0000.000
192A195VAL0-0.010-0.01433.053-0.004-0.0040.0000.0000.0000.000
193A196GLY00.0240.01232.625-0.004-0.0040.0000.0000.0000.000
194A197ARG10.7450.87432.7190.0570.0570.0000.0000.0000.000
195A198TRP0-0.014-0.01927.700-0.002-0.0020.0000.0000.0000.000
196A199TRP00.0380.01325.136-0.008-0.0080.0000.0000.0000.000
197A200ASN0-0.0140.00227.682-0.005-0.0050.0000.0000.0000.000
198A201GLU-1-0.816-0.88727.414-0.077-0.0770.0000.0000.0000.000
199A202ILE0-0.057-0.02424.145-0.009-0.0090.0000.0000.0000.000
200A203SER0-0.100-0.06622.916-0.009-0.0090.0000.0000.0000.000
201A204ASP-1-0.846-0.91523.254-0.087-0.0870.0000.0000.0000.000
202A205ARG10.8150.87618.6670.1530.1530.0000.0000.0000.000
203A206GLU-1-0.833-0.93418.043-0.118-0.1180.0000.0000.0000.000
204A207SER0-0.106-0.06815.145-0.002-0.0020.0000.0000.0000.000
205A208TRP00.0310.00215.695-0.013-0.0130.0000.0000.0000.000
206A209LYS10.8160.90118.2940.1040.1040.0000.0000.0000.000
207A210LYS10.9620.97911.3650.2700.2700.0000.0000.0000.000
208A211VAL00.0110.00413.7880.0040.0040.0000.0000.0000.000
209A212ILE0-0.026-0.00715.7390.0170.0170.0000.0000.0000.000
210A213GLU-1-0.794-0.88417.124-0.054-0.0540.0000.0000.0000.000
211A214MET0-0.069-0.03710.4510.0020.0020.0000.0000.0000.000
212A215ARG10.7810.88815.2010.0960.0960.0000.0000.0000.000
213A216LYS10.7850.89317.7960.0710.0710.0000.0000.0000.000
214A217SER0-0.047-0.01615.5830.0110.0110.0000.0000.0000.000
215A218GLY0-0.030-0.00815.5120.0150.0150.0000.0000.0000.000