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: M9M3Z

Calculation Name: 1B6D-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1B6D

Chain ID: B

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-09-26

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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2177523.871848
FMO2-HF: Nuclear repulsion 2096721.115839
FMO2-HF: Total energy -80802.756009
FMO2-MP2: Total energy -81038.917899


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(B:1:ASP)


Summations of interaction energy for fragment #1(B:1:ASP)
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.
4.5419.8871.547-2.722-4.170.024
Interaction energy analysis for fragmet #1(B:1:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.929 / q_NPA : -0.970
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].
3B3GLN0-0.028-0.0173.774-3.044-1.2120.004-0.734-1.1020.003
4B4MET00.0110.0175.591-2.960-2.9600.0000.0000.0000.000
5B5THR0-0.002-0.0138.8290.1290.1290.0000.0000.0000.000
6B6GLN0-0.011-0.02211.9320.0930.0930.0000.0000.0000.000
7B7SER0-0.0340.01915.156-0.472-0.4720.0000.0000.0000.000
8B8PRO00.0440.01118.743-0.205-0.2050.0000.0000.0000.000
9B9SER00.0790.03319.1030.2130.2130.0000.0000.0000.000
10B10SER0-0.018-0.02420.0450.0980.0980.0000.0000.0000.000
11B11LEU00.0100.02023.494-0.106-0.1060.0000.0000.0000.000
12B12SER00.0320.01926.602-0.126-0.1260.0000.0000.0000.000
13B13ALA0-0.023-0.02730.184-0.092-0.0920.0000.0000.0000.000
14B14SER00.006-0.00832.1940.0320.0320.0000.0000.0000.000
15B15VAL0-0.003-0.01635.0140.1110.1110.0000.0000.0000.000
16B16GLY00.002-0.00135.467-0.213-0.2130.0000.0000.0000.000
17B17ASP-1-0.846-0.90832.8348.8578.8570.0000.0000.0000.000
18B18ARG10.9440.98530.157-9.645-9.6450.0000.0000.0000.000
19B19VAL0-0.042-0.02725.7800.0580.0580.0000.0000.0000.000
20B20THR0-0.016-0.02323.834-0.094-0.0940.0000.0000.0000.000
21B21ILE0-0.054-0.00118.943-0.009-0.0090.0000.0000.0000.000
22B22THR00.005-0.00818.614-0.016-0.0160.0000.0000.0000.000
23B23CYS0-0.0060.00213.2560.3410.3410.0000.0000.0000.000
24B24GLN00.0490.05213.418-0.132-0.1320.0000.0000.0000.000
25B25ALA00.0200.0119.0351.4831.4830.0000.0000.0000.000
26B26SER0-0.028-0.0105.621-0.492-0.4920.0000.0000.0000.000
27B27GLN0-0.017-0.0155.0691.4161.469-0.001-0.006-0.0460.000
28B28ASP-1-0.879-0.9459.03018.97418.9740.0000.0000.0000.000
29B29ILE00.0020.0038.3131.3241.3240.0000.0000.0000.000
30B30SER0-0.008-0.00311.337-1.011-1.0110.0000.0000.0000.000
31B31SER00.029-0.00215.0570.2150.2150.0000.0000.0000.000
32B32TYR0-0.0160.00511.835-1.152-1.1520.0000.0000.0000.000
33B33LEU00.0350.00011.6531.9071.9070.0000.0000.0000.000
34B34ASN0-0.038-0.00513.645-2.382-2.3820.0000.0000.0000.000
35B35TRP00.0300.00515.1140.9840.9840.0000.0000.0000.000
36B36TYR0-0.031-0.04514.420-1.304-1.3040.0000.0000.0000.000
37B37GLN00.0200.01618.953-0.261-0.2610.0000.0000.0000.000
38B38GLN0-0.005-0.01019.7920.4760.4760.0000.0000.0000.000
39B39LYS10.8680.93622.606-11.065-11.0650.0000.0000.0000.000
40B40PRO00.0600.00925.1800.3080.3080.0000.0000.0000.000
41B41GLY00.0450.02425.472-0.411-0.4110.0000.0000.0000.000
42B42LYS10.8400.93125.285-11.304-11.3040.0000.0000.0000.000
43B43ALA00.0500.03322.0360.5110.5110.0000.0000.0000.000
44B44PRO00.011-0.00717.841-0.547-0.5470.0000.0000.0000.000
45B45LYS10.9210.97620.742-12.246-12.2460.0000.0000.0000.000
46B46LEU00.0020.01117.7980.1370.1370.0000.0000.0000.000
47B47LEU0-0.059-0.03320.831-0.785-0.7850.0000.0000.0000.000
48B48ILE00.0000.00720.277-0.576-0.5760.0000.0000.0000.000
49B49HIS00.0310.01716.8440.6550.6550.0000.0000.0000.000
50B50ALA00.0250.01317.282-0.743-0.7430.0000.0000.0000.000
51B51ALA00.0200.01217.232-0.585-0.5850.0000.0000.0000.000
52B52SER0-0.059-0.04118.502-0.213-0.2130.0000.0000.0000.000
53B53SER0-0.0080.00721.635-0.834-0.8340.0000.0000.0000.000
54B54LEU0-0.052-0.02022.9030.4460.4460.0000.0000.0000.000
55B55GLU-1-0.887-0.94922.38612.74712.7470.0000.0000.0000.000
56B56THR00.004-0.01125.299-0.512-0.5120.0000.0000.0000.000
57B57GLY0-0.006-0.00428.8520.0800.0800.0000.0000.0000.000
58B58VAL0-0.083-0.03125.775-0.144-0.1440.0000.0000.0000.000
59B59PRO00.0310.00528.962-0.150-0.1500.0000.0000.0000.000
60B60SER00.0630.01729.7300.1980.1980.0000.0000.0000.000
61B61ARG10.6920.82630.305-9.684-9.6840.0000.0000.0000.000
62B62PHE00.0050.00825.6810.1180.1180.0000.0000.0000.000
63B63SER00.0260.01025.835-0.262-0.2620.0000.0000.0000.000
64B64GLY00.0230.01321.8390.3270.3270.0000.0000.0000.000
65B65SER0-0.064-0.04221.266-0.738-0.7380.0000.0000.0000.000
66B66GLY00.0580.02018.9720.4570.4570.0000.0000.0000.000
67B67SER0-0.007-0.01417.266-0.149-0.1490.0000.0000.0000.000
68B68GLY0-0.0060.02314.744-0.440-0.4400.0000.0000.0000.000
69B69THR00.001-0.00412.0041.3541.3540.0000.0000.0000.000
70B70ASP-1-0.894-0.92913.97917.34017.3400.0000.0000.0000.000
71B71PHE0-0.0060.00213.140-0.848-0.8480.0000.0000.0000.000
72B72SER0-0.014-0.01717.652-0.071-0.0710.0000.0000.0000.000
73B73PHE0-0.0170.00020.319-0.140-0.1400.0000.0000.0000.000
74B74THR0-0.046-0.04022.147-0.345-0.3450.0000.0000.0000.000
75B75ILE00.0340.04125.879-0.017-0.0170.0000.0000.0000.000
76B76SER0-0.042-0.04828.588-0.197-0.1970.0000.0000.0000.000
77B77SER00.0100.00631.963-0.217-0.2170.0000.0000.0000.000
78B78LEU0-0.042-0.00829.9410.0800.0800.0000.0000.0000.000
79B79GLN00.0400.02632.238-0.498-0.4980.0000.0000.0000.000
80B80PRO00.0550.00532.5860.3080.3080.0000.0000.0000.000
81B81GLU-1-0.826-0.89232.0269.2519.2510.0000.0000.0000.000
82B82ASP-1-0.784-0.87528.71310.54610.5460.0000.0000.0000.000
83B83LEU0-0.0500.01027.8230.3920.3920.0000.0000.0000.000
84B84ALA0-0.039-0.02924.822-0.077-0.0770.0000.0000.0000.000
85B85THR00.0110.01419.351-0.300-0.3000.0000.0000.0000.000
86B86TYR0-0.005-0.01020.005-0.112-0.1120.0000.0000.0000.000
87B87TYR0-0.0110.00114.6010.2000.2000.0000.0000.0000.000
88B89GLN00.0600.03510.228-0.753-0.7530.0000.0000.0000.000
89B90GLN00.0620.0354.622-5.557-5.487-0.001-0.002-0.0660.000
90B91TYR0-0.062-0.0608.6511.6211.6210.0000.0000.0000.000
91B92ASP-1-0.876-0.9298.03526.40226.4020.0000.0000.0000.000
92B93SER00.001-0.0116.441-0.971-0.9710.0000.0000.0000.000
93B94LEU0-0.061-0.0105.9561.3591.3590.0000.0000.0000.000
94B95PRO0-0.0030.0032.573-4.350-1.1871.546-1.951-2.7590.021
95B96LEU0-0.040-0.0235.499-4.535-4.534-0.001-0.0020.0030.000
96B97THR00.0030.0033.908-2.351-2.1240.000-0.027-0.2000.000
97B98PHE0-0.006-0.0066.568-3.778-3.7780.0000.0000.0000.000
98B99GLY00.0270.0159.3901.4371.4370.0000.0000.0000.000
99B100GLY0-0.038-0.02811.316-0.495-0.4950.0000.0000.0000.000
100B101GLY00.0000.00213.479-0.709-0.7090.0000.0000.0000.000
101B102THR0-0.042-0.03616.5980.0130.0130.0000.0000.0000.000
102B103LYS10.8220.90919.938-11.769-11.7690.0000.0000.0000.000
103B104VAL00.0300.01923.055-0.239-0.2390.0000.0000.0000.000
104B105GLU-1-0.825-0.89826.05310.78710.7870.0000.0000.0000.000
105B106ILE00.0620.03829.288-0.068-0.0680.0000.0000.0000.000
106B107LYS10.8560.94632.715-9.184-9.1840.0000.0000.0000.000
107B108ARG10.8650.92934.543-8.912-8.9120.0000.0000.0000.000
108B109THR00.0120.00237.4640.0290.0290.0000.0000.0000.000
109B110VAL0-0.0210.00335.5710.1550.1550.0000.0000.0000.000
110B111ALA00.0020.01136.191-0.231-0.2310.0000.0000.0000.000
111B112ALA00.0280.00335.5500.2930.2930.0000.0000.0000.000
112B113PRO0-0.0050.01932.835-0.116-0.1160.0000.0000.0000.000
113B114SER0-0.019-0.00335.475-0.170-0.1700.0000.0000.0000.000
114B115VAL00.010-0.00733.4920.1360.1360.0000.0000.0000.000
115B116PHE0-0.038-0.02735.072-0.352-0.3520.0000.0000.0000.000
116B117ILE0-0.025-0.01133.7520.2760.2760.0000.0000.0000.000
117B118PHE0-0.017-0.01534.200-0.313-0.3130.0000.0000.0000.000
118B119PRO00.0320.02434.3590.3190.3190.0000.0000.0000.000
119B120PRO0-0.017-0.01033.714-0.023-0.0230.0000.0000.0000.000
120B121SER00.0320.01235.579-0.164-0.1640.0000.0000.0000.000
121B122ASP-1-0.848-0.94237.5518.0078.0070.0000.0000.0000.000
122B123GLU-1-0.815-0.90438.6218.1048.1040.0000.0000.0000.000
123B124GLN0-0.018-0.00331.5660.4310.4310.0000.0000.0000.000
124B125LEU00.011-0.00134.3820.2440.2440.0000.0000.0000.000
125B126LYS10.8170.91036.116-7.976-7.9760.0000.0000.0000.000
126B127SER0-0.045-0.02732.4220.0320.0320.0000.0000.0000.000
127B128GLY0-0.0050.01332.4670.2740.2740.0000.0000.0000.000
128B129THR0-0.060-0.03327.9800.4140.4140.0000.0000.0000.000
129B130ALA00.001-0.00630.218-0.407-0.4070.0000.0000.0000.000
130B131SER00.0210.01928.8260.5310.5310.0000.0000.0000.000
131B132VAL0-0.056-0.01229.906-0.429-0.4290.0000.0000.0000.000
132B133VAL00.0220.01129.6810.3530.3530.0000.0000.0000.000
133B134CYS0-0.041-0.01430.081-0.056-0.0560.0000.0000.0000.000
134B135LEU0-0.0290.00330.1920.2890.2890.0000.0000.0000.000
135B136LEU00.0280.02428.873-0.357-0.3570.0000.0000.0000.000
136B137ASN0-0.009-0.03032.1100.3340.3340.0000.0000.0000.000
137B138ASN00.0340.03234.545-0.104-0.1040.0000.0000.0000.000
138B139PHE00.0080.01428.196-0.219-0.2190.0000.0000.0000.000
139B140TYR00.016-0.00631.3170.2350.2350.0000.0000.0000.000
140B141PRO00.0080.00329.652-0.305-0.3050.0000.0000.0000.000
141B142ARG10.8660.90722.341-12.859-12.8590.0000.0000.0000.000
142B143GLU-1-0.976-0.97225.68611.44311.4430.0000.0000.0000.000
143B144ALA00.0180.00526.038-0.533-0.5330.0000.0000.0000.000
144B145LYS10.9110.96224.677-10.537-10.5370.0000.0000.0000.000
145B146VAL00.0170.01325.769-0.572-0.5720.0000.0000.0000.000
146B147GLN0-0.0030.00225.5260.1930.1930.0000.0000.0000.000
147B148TRP00.0190.00425.857-0.676-0.6760.0000.0000.0000.000
148B149LYS10.8730.90028.575-9.308-9.3080.0000.0000.0000.000
149B150VAL0-0.027-0.00830.315-0.247-0.2470.0000.0000.0000.000
150B151ASP-1-0.827-0.91032.6578.6118.6110.0000.0000.0000.000
151B152ASN0-0.057-0.03734.8560.0370.0370.0000.0000.0000.000
152B153ALA00.0540.05230.5440.0170.0170.0000.0000.0000.000
153B154LEU00.000-0.00325.7780.0220.0220.0000.0000.0000.000
154B155GLN0-0.055-0.01825.7600.3260.3260.0000.0000.0000.000
155B156SER0-0.002-0.01420.6380.2900.2900.0000.0000.0000.000
156B157GLY00.0360.02018.6670.0050.0050.0000.0000.0000.000
157B158ASN00.0160.00719.5380.3630.3630.0000.0000.0000.000
158B159SER00.0150.00421.319-0.502-0.5020.0000.0000.0000.000
159B160GLN0-0.042-0.01917.3701.2111.2110.0000.0000.0000.000
160B161GLU-1-0.790-0.89520.75712.16212.1620.0000.0000.0000.000
161B162SER0-0.025-0.00721.2060.5910.5910.0000.0000.0000.000
162B163VAL0-0.026-0.01223.020-0.607-0.6070.0000.0000.0000.000
163B164THR0-0.0080.00324.9630.2620.2620.0000.0000.0000.000
164B165GLU-1-0.860-0.91424.76412.09712.0970.0000.0000.0000.000
165B166GLN00.036-0.00227.181-0.425-0.4250.0000.0000.0000.000
166B167ASP-1-0.831-0.92729.84410.29310.2930.0000.0000.0000.000
167B168SER0-0.063-0.03531.983-0.273-0.2730.0000.0000.0000.000
168B169LYS10.8350.91229.621-10.381-10.3810.0000.0000.0000.000
169B170ASP-1-0.932-0.95333.4358.2738.2730.0000.0000.0000.000
170B171SER0-0.003-0.00634.004-0.225-0.2250.0000.0000.0000.000
171B172THR0-0.063-0.03333.581-0.014-0.0140.0000.0000.0000.000
172B173TYR0-0.043-0.03427.2250.3200.3200.0000.0000.0000.000
173B174SER00.0440.00729.846-0.390-0.3900.0000.0000.0000.000
174B175LEU0-0.0380.00724.9520.3030.3030.0000.0000.0000.000
175B176SER00.0380.02226.844-0.547-0.5470.0000.0000.0000.000
176B177SER00.004-0.01025.0380.5190.5190.0000.0000.0000.000
177B178THR0-0.030-0.02525.090-0.726-0.7260.0000.0000.0000.000
178B179LEU00.0020.01924.6570.5980.5980.0000.0000.0000.000
179B180THR0-0.011-0.01024.650-0.385-0.3850.0000.0000.0000.000
180B181LEU0-0.025-0.01525.7780.2900.2900.0000.0000.0000.000
181B182SER00.033-0.00228.230-0.297-0.2970.0000.0000.0000.000
182B183LYS10.9200.93129.708-8.808-8.8080.0000.0000.0000.000
183B184ALA00.0370.00932.640-0.209-0.2090.0000.0000.0000.000
184B185ASP-1-0.825-0.88929.16710.64810.6480.0000.0000.0000.000
185B186TYR00.0250.01732.037-0.193-0.1930.0000.0000.0000.000
186B187GLU-1-0.853-0.90133.7668.2828.2820.0000.0000.0000.000
187B188LYS10.8510.93131.555-10.230-10.2300.0000.0000.0000.000
188B189HIS10.8650.92931.551-9.709-9.7090.0000.0000.0000.000
189B190LYS10.9120.94836.455-7.946-7.9460.0000.0000.0000.000
190B191VAL00.0200.01537.474-0.033-0.0330.0000.0000.0000.000
191B192TYR0-0.0060.00532.1180.3780.3780.0000.0000.0000.000
192B193ALA00.015-0.02033.680-0.234-0.2340.0000.0000.0000.000
193B195GLU-1-0.878-0.92531.1819.2729.2720.0000.0000.0000.000
194B196VAL00.0280.01830.4230.3630.3630.0000.0000.0000.000
195B197THR0-0.024-0.02729.619-0.222-0.2220.0000.0000.0000.000
196B198HIS00.0520.00530.3260.0610.0610.0000.0000.0000.000
197B199GLN00.0410.02032.147-0.049-0.0490.0000.0000.0000.000
198B200GLY00.0120.00034.257-0.248-0.2480.0000.0000.0000.000
199B201LEU0-0.090-0.03334.543-0.245-0.2450.0000.0000.0000.000
200B202SER00.0200.01337.1200.0500.0500.0000.0000.0000.000
201B203SER0-0.030-0.02437.836-0.063-0.0630.0000.0000.0000.000
202B204PRO00.0110.00833.557-0.015-0.0150.0000.0000.0000.000
203B205VAL00.0250.02735.315-0.225-0.2250.0000.0000.0000.000
204B206THR0-0.005-0.00835.1870.3390.3390.0000.0000.0000.000
205B207LYS10.9040.96435.503-8.322-8.3220.0000.0000.0000.000
206B208SER00.022-0.00335.7240.2510.2510.0000.0000.0000.000
207B209PHE0-0.0220.00134.837-0.206-0.2060.0000.0000.0000.000
208B210ASN00.0200.00738.6900.2680.2680.0000.0000.0000.000
209B211ARG10.8350.90038.050-8.362-8.3620.0000.0000.0000.000
210B212GLY00.0080.02240.451-0.196-0.1960.0000.0000.0000.000