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: ZVZGN

Calculation Name: 3C8U-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3C8U

Chain ID: A

ChEMBL ID:

UniProt ID: Q1GJR2

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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2246196.228774
FMO2-HF: Nuclear repulsion 2168031.502533
FMO2-HF: Total energy -78164.726241
FMO2-MP2: Total energy -78393.946344


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:0:GLY)


Summations of interaction energy for fragment #1(A:0: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.
-3.574-2.5364.332-2.546-2.824-0.02
Interaction energy analysis for fragmet #1(A:0:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.002 / q_NPA : -0.007
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].
3A2THR00.0340.0183.8212.4863.358-0.012-0.356-0.5050.000
4A3LEU00.0790.0196.845-0.354-0.3540.0000.0000.0000.000
5A4ALA0-0.022-0.0029.704-0.148-0.1480.0000.0000.0000.000
6A5ALA00.0280.0067.730-0.053-0.0530.0000.0000.0000.000
7A6LEU00.0160.0108.347-0.085-0.0850.0000.0000.0000.000
8A7CYS0-0.007-0.0039.9900.0110.0110.0000.0000.0000.000
9A8GLN0-0.067-0.03412.9210.0360.0360.0000.0000.0000.000
10A9GLY00.0320.01812.3190.0020.0020.0000.0000.0000.000
11A10VAL00.019-0.00113.2040.0210.0210.0000.0000.0000.000
12A11LEU00.006-0.00715.3660.0220.0220.0000.0000.0000.000
13A12GLU-1-0.897-0.93215.151-0.421-0.4210.0000.0000.0000.000
14A13ARG10.8020.88913.6260.4940.4940.0000.0000.0000.000
15A14LEU0-0.0270.02018.8510.0170.0170.0000.0000.0000.000
16A15ASP-1-0.797-0.90021.439-0.116-0.1160.0000.0000.0000.000
17A16PRO0-0.060-0.03724.5220.0140.0140.0000.0000.0000.000
18A17ARG10.8740.93027.0550.0930.0930.0000.0000.0000.000
19A18GLN0-0.011-0.00225.6600.0130.0130.0000.0000.0000.000
20A19PRO0-0.051-0.02729.6280.0050.0050.0000.0000.0000.000
21A20GLY00.0250.02830.940-0.003-0.0030.0000.0000.0000.000
22A21ARG10.7230.84026.6670.0280.0280.0000.0000.0000.000
23A22GLN0-0.032-0.03323.371-0.018-0.0180.0000.0000.0000.000
24A23LEU0-0.015-0.01122.9230.0130.0130.0000.0000.0000.000
25A24VAL00.0060.00016.405-0.021-0.0210.0000.0000.0000.000
26A25ALA00.0100.03018.2100.0270.0270.0000.0000.0000.000
27A26LEU0-0.011-0.00911.897-0.033-0.0330.0000.0000.0000.000
28A27SER00.0330.00214.8060.0390.0390.0000.0000.0000.000
29A28GLY0-0.009-0.00214.007-0.025-0.0250.0000.0000.0000.000
30A29ALA00.0430.02515.344-0.015-0.0150.0000.0000.0000.000
31A30PRO00.0040.00317.3870.0300.0300.0000.0000.0000.000
32A31GLY00.0610.03218.325-0.002-0.0020.0000.0000.0000.000
33A32SER0-0.052-0.04913.4700.0330.0330.0000.0000.0000.000
34A33GLY00.0150.00613.3300.0510.0510.0000.0000.0000.000
35A34LYS10.9270.98613.8710.0130.0130.0000.0000.0000.000
36A35SER0-0.003-0.01914.9510.0120.0120.0000.0000.0000.000
37A36THR0-0.102-0.05714.0300.0230.0230.0000.0000.0000.000
38A37LEU00.0070.0149.3150.0570.0570.0000.0000.0000.000
39A38SER0-0.013-0.04112.924-0.018-0.0180.0000.0000.0000.000
40A39ASN0-0.003-0.01515.664-0.033-0.0330.0000.0000.0000.000
41A40PRO00.000-0.00414.011-0.021-0.0210.0000.0000.0000.000
42A41LEU00.0180.01712.577-0.015-0.0150.0000.0000.0000.000
43A42ALA00.0530.02415.033-0.033-0.0330.0000.0000.0000.000
44A43ALA0-0.023-0.00118.481-0.016-0.0160.0000.0000.0000.000
45A44ALA0-0.029-0.01615.660-0.010-0.0100.0000.0000.0000.000
46A45LEU00.0550.00716.899-0.020-0.0200.0000.0000.0000.000
47A46SER00.0290.00919.140-0.011-0.0110.0000.0000.0000.000
48A47ALA0-0.080-0.02920.376-0.005-0.0050.0000.0000.0000.000
49A48GLN0-0.073-0.03218.652-0.013-0.0130.0000.0000.0000.000
50A49GLY0-0.0070.00321.942-0.014-0.0140.0000.0000.0000.000
51A50LEU0-0.049-0.03221.239-0.007-0.0070.0000.0000.0000.000
52A51PRO0-0.038-0.01422.7900.0040.0040.0000.0000.0000.000
53A52ALA00.0230.01720.958-0.010-0.0100.0000.0000.0000.000
54A53GLU-1-0.853-0.92222.9120.0270.0270.0000.0000.0000.000
55A54VAL0-0.029-0.01419.293-0.013-0.0130.0000.0000.0000.000
56A55VAL0-0.0020.00721.8960.0050.0050.0000.0000.0000.000
57A56PRO0-0.022-0.02222.733-0.009-0.0090.0000.0000.0000.000
58A57MET00.0330.04823.215-0.005-0.0050.0000.0000.0000.000
59A58ASP-1-0.826-0.91023.8780.0300.0300.0000.0000.0000.000
60A59GLY0-0.025-0.00226.5910.0020.0020.0000.0000.0000.000
61A60PHE00.016-0.00728.738-0.001-0.0010.0000.0000.0000.000
62A61HIS0-0.072-0.01426.903-0.004-0.0040.0000.0000.0000.000
63A62LEU0-0.006-0.00231.3770.0010.0010.0000.0000.0000.000
64A63ASP-1-0.773-0.86134.7210.0140.0140.0000.0000.0000.000
65A64ASN00.1080.02736.136-0.004-0.0040.0000.0000.0000.000
66A65ARG10.8240.88738.370-0.010-0.0100.0000.0000.0000.000
67A66LEU0-0.044-0.02438.847-0.002-0.0020.0000.0000.0000.000
68A67LEU0-0.022-0.01634.212-0.002-0.0020.0000.0000.0000.000
69A68GLU-1-0.958-0.97938.4550.0030.0030.0000.0000.0000.000
70A69PRO00.0480.03741.121-0.001-0.0010.0000.0000.0000.000
71A70ARG10.8810.94838.1440.0090.0090.0000.0000.0000.000
72A71GLY00.0200.01340.221-0.002-0.0020.0000.0000.0000.000
73A72LEU0-0.015-0.01634.9470.0000.0000.0000.0000.0000.000
74A73LEU00.0110.02134.9630.0010.0010.0000.0000.0000.000
75A74PRO0-0.027-0.02434.6950.0030.0030.0000.0000.0000.000
76A75ARG10.8200.89029.6650.0170.0170.0000.0000.0000.000
77A76LYS10.8130.90430.607-0.023-0.0230.0000.0000.0000.000
78A77GLY00.0430.03027.4150.0060.0060.0000.0000.0000.000
79A78ALA00.0090.03326.364-0.005-0.0050.0000.0000.0000.000
80A79PRO00.0530.04125.8490.0030.0030.0000.0000.0000.000
81A80GLU-1-0.790-0.87828.136-0.022-0.0220.0000.0000.0000.000
82A81THR0-0.098-0.06630.0790.0050.0050.0000.0000.0000.000
83A82PHE0-0.012-0.01126.0730.0040.0040.0000.0000.0000.000
84A83ASP-1-0.868-0.93631.009-0.023-0.0230.0000.0000.0000.000
85A84PHE00.0120.00728.4420.0000.0000.0000.0000.0000.000
86A85GLU-1-0.845-0.91131.363-0.034-0.0340.0000.0000.0000.000
87A86GLY0-0.040-0.02333.945-0.002-0.0020.0000.0000.0000.000
88A87PHE00.0130.00224.0700.0000.0000.0000.0000.0000.000
89A88GLN00.0300.01629.530-0.005-0.0050.0000.0000.0000.000
90A89ARG10.8700.92130.5520.0260.0260.0000.0000.0000.000
91A90LEU0-0.0160.00728.6830.0000.0000.0000.0000.0000.000
92A91CYS0-0.027-0.02026.854-0.001-0.0010.0000.0000.0000.000
93A92HIS00.002-0.01128.627-0.004-0.0040.0000.0000.0000.000
94A93ALA0-0.041-0.01431.447-0.001-0.0010.0000.0000.0000.000
95A94LEU00.003-0.01026.8900.0020.0020.0000.0000.0000.000
96A95LYS10.8750.97826.6400.0930.0930.0000.0000.0000.000
97A96HIS00.033-0.00330.3370.0030.0030.0000.0000.0000.000
98A97GLN0-0.0530.00033.7570.0020.0020.0000.0000.0000.000
99A98GLU-1-0.875-0.93733.582-0.026-0.0260.0000.0000.0000.000
100A99ARG10.8230.89933.8880.0020.0020.0000.0000.0000.000
101A100VAL0-0.032-0.01632.049-0.001-0.0010.0000.0000.0000.000
102A101ILE00.0150.02032.8490.0030.0030.0000.0000.0000.000
103A102TYR0-0.013-0.01627.316-0.003-0.0030.0000.0000.0000.000
104A103PRO0-0.021-0.00331.4440.0040.0040.0000.0000.0000.000
105A104LEU00.0390.02427.9720.0000.0000.0000.0000.0000.000
106A105PHE0-0.046-0.02728.1850.0000.0000.0000.0000.0000.000
107A106ASP-1-0.785-0.87629.3720.0520.0520.0000.0000.0000.000
108A107ARG10.8560.88724.544-0.056-0.0560.0000.0000.0000.000
109A108ALA0-0.0060.01030.174-0.002-0.0020.0000.0000.0000.000
110A109ARG10.8410.89432.989-0.038-0.0380.0000.0000.0000.000
111A110ASP-1-0.814-0.87432.8090.0230.0230.0000.0000.0000.000
112A111ILE0-0.029-0.01133.996-0.005-0.0050.0000.0000.0000.000
113A112ALA00.0130.02032.7270.0040.0040.0000.0000.0000.000
114A113ILE0-0.039-0.01933.658-0.002-0.0020.0000.0000.0000.000
115A114ALA00.022-0.00234.593-0.001-0.0010.0000.0000.0000.000
116A115GLY00.005-0.00736.0640.0020.0020.0000.0000.0000.000
117A116ALA0-0.038-0.01333.1600.0010.0010.0000.0000.0000.000
118A117ALA00.0110.01130.1800.0050.0050.0000.0000.0000.000
119A118GLU-1-0.841-0.92331.780-0.001-0.0010.0000.0000.0000.000
120A119VAL00.0060.02827.9680.0030.0030.0000.0000.0000.000
121A120GLY00.0650.02830.520-0.003-0.0030.0000.0000.0000.000
122A121PRO0-0.013-0.01531.346-0.002-0.0020.0000.0000.0000.000
123A122GLU-1-0.918-0.95330.673-0.002-0.0020.0000.0000.0000.000
124A123CYS0-0.111-0.04426.495-0.005-0.0050.0000.0000.0000.000
125A124ARG10.9650.98626.0450.0500.0500.0000.0000.0000.000
126A125VAL0-0.010-0.01120.436-0.012-0.0120.0000.0000.0000.000
127A126ALA00.0500.03023.4410.0140.0140.0000.0000.0000.000
128A127ILE0-0.010-0.00616.835-0.016-0.0160.0000.0000.0000.000
129A128ILE00.0050.01220.0950.0210.0210.0000.0000.0000.000
130A129GLU-1-0.717-0.82518.0510.0600.0600.0000.0000.0000.000
131A130GLY0-0.005-0.05718.7680.0110.0110.0000.0000.0000.000
132A131ASN0-0.026-0.02318.628-0.002-0.0020.0000.0000.0000.000
133A132TYR0-0.022-0.03619.859-0.013-0.0130.0000.0000.0000.000
134A133LEU00.0370.01818.8280.0010.0010.0000.0000.0000.000
135A134LEU0-0.0130.01015.500-0.011-0.0110.0000.0000.0000.000
136A135PHE0-0.0030.00319.542-0.008-0.0080.0000.0000.0000.000
137A136ASP-1-0.799-0.88422.213-0.112-0.1120.0000.0000.0000.000
138A137ALA0-0.012-0.01424.4700.0080.0080.0000.0000.0000.000
139A138PRO0-0.010-0.02027.787-0.003-0.0030.0000.0000.0000.000
140A139GLY00.0520.04430.3180.0050.0050.0000.0000.0000.000
141A140TRP00.014-0.02225.373-0.003-0.0030.0000.0000.0000.000
142A141ARG10.8750.92324.9110.0900.0900.0000.0000.0000.000
143A142ASP-1-0.917-0.96325.678-0.092-0.0920.0000.0000.0000.000
144A143LEU0-0.019-0.01924.2590.0010.0010.0000.0000.0000.000
145A144THR0-0.059-0.02621.234-0.005-0.0050.0000.0000.0000.000
146A145ALA0-0.0100.00623.075-0.010-0.0100.0000.0000.0000.000
147A146ILE0-0.069-0.03725.3400.0040.0040.0000.0000.0000.000
148A147TRP0-0.061-0.03920.1170.0120.0120.0000.0000.0000.000
149A148ASP-1-0.763-0.86821.892-0.120-0.1200.0000.0000.0000.000
150A149VAL0-0.016-0.00115.357-0.027-0.0270.0000.0000.0000.000
151A150SER0-0.033-0.04316.1940.0260.0260.0000.0000.0000.000
152A151ILE0-0.014-0.01810.352-0.069-0.0690.0000.0000.0000.000
153A152ARG10.8670.94411.0820.4000.4000.0000.0000.0000.000
154A153LEU0-0.060-0.0268.892-0.117-0.1170.0000.0000.0000.000
155A154GLU-1-0.797-0.8777.833-0.356-0.3560.0000.0000.0000.000
156A155VAL0-0.037-0.0318.5270.0730.0730.0000.0000.0000.000
157A156PRO00.0590.0339.737-0.031-0.0310.0000.0000.0000.000
158A157MET00.0450.00712.8870.0390.0390.0000.0000.0000.000
159A158ALA00.0260.02115.7280.0150.0150.0000.0000.0000.000
160A159ASP-1-0.826-0.90312.4420.3280.3280.0000.0000.0000.000
161A160LEU0-0.063-0.03914.8440.0210.0210.0000.0000.0000.000
162A161GLU-1-0.866-0.92316.9420.0540.0540.0000.0000.0000.000
163A162ALA00.0150.01017.8510.0010.0010.0000.0000.0000.000
164A163ARG10.8480.91310.957-0.345-0.3450.0000.0000.0000.000
165A164LEU0-0.044-0.02519.114-0.004-0.0040.0000.0000.0000.000
166A165VAL0-0.0030.00022.025-0.006-0.0060.0000.0000.0000.000
167A166GLN0-0.012-0.02121.747-0.003-0.0030.0000.0000.0000.000
168A167ARG10.8650.94922.860-0.082-0.0820.0000.0000.0000.000
169A168TRP0-0.058-0.04424.550-0.008-0.0080.0000.0000.0000.000
170A169LEU0-0.007-0.00125.868-0.007-0.0070.0000.0000.0000.000
171A170ASP-1-0.869-0.91724.8800.1370.1370.0000.0000.0000.000
172A171HIS0-0.110-0.04628.386-0.002-0.0020.0000.0000.0000.000
173A172GLY0-0.0030.00230.848-0.007-0.0070.0000.0000.0000.000
174A173LEU0-0.103-0.04131.042-0.007-0.0070.0000.0000.0000.000
175A174ASN00.032-0.00431.9010.0040.0040.0000.0000.0000.000
176A175HIS00.0830.02826.4040.0030.0030.0000.0000.0000.000
177A176ASP-1-0.868-0.93130.0160.0530.0530.0000.0000.0000.000
178A177ALA0-0.003-0.00531.905-0.003-0.0030.0000.0000.0000.000
179A178ALA0-0.024-0.00927.885-0.003-0.0030.0000.0000.0000.000
180A179VAL00.0160.00326.5720.0000.0000.0000.0000.0000.000
181A180ALA00.0020.00928.104-0.005-0.0050.0000.0000.0000.000
182A181ARG10.9040.96129.289-0.046-0.0460.0000.0000.0000.000
183A182ALA0-0.019-0.01024.460-0.005-0.0050.0000.0000.0000.000
184A183GLN0-0.047-0.04525.640-0.010-0.0100.0000.0000.0000.000
185A184GLY0-0.0270.01427.032-0.008-0.0080.0000.0000.0000.000
186A185ASN00.015-0.02627.440-0.009-0.0090.0000.0000.0000.000
187A186ASP-1-0.797-0.89623.2660.0400.0400.0000.0000.0000.000
188A187LEU00.0570.02020.737-0.008-0.0080.0000.0000.0000.000
189A188ALA0-0.040-0.01723.161-0.011-0.0110.0000.0000.0000.000
190A189ASN0-0.022-0.02323.964-0.016-0.0160.0000.0000.0000.000
191A190ALA0-0.010-0.00319.042-0.012-0.0120.0000.0000.0000.000
192A191ARG10.9600.98819.802-0.002-0.0020.0000.0000.0000.000
193A192ALA0-0.006-0.00821.997-0.013-0.0130.0000.0000.0000.000
194A193ILE0-0.025-0.01817.855-0.008-0.0080.0000.0000.0000.000
195A194GLU-1-0.863-0.91015.924-0.214-0.2140.0000.0000.0000.000
196A195ALA0-0.064-0.03318.815-0.018-0.0180.0000.0000.0000.000
197A196ALA0-0.027-0.00321.203-0.001-0.0010.0000.0000.0000.000
198A197ARG10.7390.82812.4080.3090.3090.0000.0000.0000.000
199A198LEU0-0.0060.01719.069-0.004-0.0040.0000.0000.0000.000
200A199PRO00.006-0.00716.354-0.024-0.0240.0000.0000.0000.000
201A200ALA00.0050.00712.7710.0310.0310.0000.0000.0000.000
202A201ASP-1-0.834-0.87814.158-0.360-0.3600.0000.0000.0000.000
203A202LEU0-0.054-0.0279.913-0.114-0.1140.0000.0000.0000.000
204A203THR0-0.009-0.0097.3310.2010.2010.0000.0000.0000.000
205A204TRP00.000-0.0015.130-0.417-0.4170.0000.0000.0000.000
206A205PRO00.0500.0392.113-4.856-4.6904.344-2.190-2.319-0.020