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: 9MYG2

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 OptH
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 -2177599.491455
FMO2-HF: Nuclear repulsion 2096798.141765
FMO2-HF: Total energy -80801.34969
FMO2-MP2: Total energy -81037.573594


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.
8.03511.8280.57-1.593-2.7690.006
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 : -0.955 / q_NPA : -0.983
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].
3B3GLN0-0.037-0.0323.414-3.201-1.3070.039-0.772-1.1610.002
4B4MET00.0000.0095.344-3.549-3.526-0.001-0.003-0.0180.000
5B5THR00.006-0.0048.5210.3840.3840.0000.0000.0000.000
6B6GLN0-0.004-0.02911.6960.0660.0660.0000.0000.0000.000
7B7SER0-0.0550.01214.894-0.449-0.4490.0000.0000.0000.000
8B8PRO00.0490.01318.497-0.232-0.2320.0000.0000.0000.000
9B9SER00.0830.03218.7750.1920.1920.0000.0000.0000.000
10B10SER0-0.026-0.02819.8720.1030.1030.0000.0000.0000.000
11B11LEU00.0070.01923.304-0.103-0.1030.0000.0000.0000.000
12B12SER00.0340.01726.383-0.141-0.1410.0000.0000.0000.000
13B13ALA0-0.041-0.04229.965-0.093-0.0930.0000.0000.0000.000
14B14SER0-0.013-0.01831.938-0.086-0.0860.0000.0000.0000.000
15B15VAL0-0.004-0.01634.7240.1090.1090.0000.0000.0000.000
16B16GLY00.0000.00035.165-0.214-0.2140.0000.0000.0000.000
17B17ASP-1-0.856-0.91332.6448.8678.8670.0000.0000.0000.000
18B18ARG10.9500.98929.969-9.618-9.6180.0000.0000.0000.000
19B19VAL0-0.042-0.02825.6330.0610.0610.0000.0000.0000.000
20B20THR00.003-0.01023.549-0.126-0.1260.0000.0000.0000.000
21B21ILE0-0.061-0.00118.5530.0160.0160.0000.0000.0000.000
22B22THR0-0.008-0.01418.2220.0140.0140.0000.0000.0000.000
23B23CYS00.0020.00012.9420.2510.2510.0000.0000.0000.000
24B24GLN00.0490.04712.870-0.308-0.3080.0000.0000.0000.000
25B25ALA00.0250.0118.8561.5751.5750.0000.0000.0000.000
26B26SER0-0.031-0.0085.636-0.637-0.6370.0000.0000.0000.000
27B27GLN0-0.007-0.0164.7352.8152.771-0.001-0.0130.0580.000
28B28ASP-1-0.877-0.9459.02818.76018.7600.0000.0000.0000.000
29B29ILE00.0060.0098.5811.2311.2310.0000.0000.0000.000
30B30SER0-0.017-0.00511.325-0.906-0.9060.0000.0000.0000.000
31B31SER00.026-0.00515.0450.2330.2330.0000.0000.0000.000
32B32TYR0-0.030-0.00111.896-1.197-1.1970.0000.0000.0000.000
33B33LEU00.0420.00411.8501.9031.9030.0000.0000.0000.000
34B34ASN0-0.0270.01013.593-2.736-2.7360.0000.0000.0000.000
35B35TRP00.0210.00615.2641.1221.1220.0000.0000.0000.000
36B36TYR0-0.022-0.02414.624-1.285-1.2850.0000.0000.0000.000
37B37GLN0-0.016-0.00418.958-0.155-0.1550.0000.0000.0000.000
38B38GLN0-0.006-0.02319.7470.4160.4160.0000.0000.0000.000
39B39LYS10.8980.96422.363-10.852-10.8520.0000.0000.0000.000
40B40PRO00.0530.00724.9860.3170.3170.0000.0000.0000.000
41B41GLY00.0480.02825.349-0.404-0.4040.0000.0000.0000.000
42B42LYS10.8620.94125.120-11.215-11.2150.0000.0000.0000.000
43B43ALA00.0520.03222.0830.5230.5230.0000.0000.0000.000
44B44PRO00.005-0.00717.828-0.557-0.5570.0000.0000.0000.000
45B45LYS10.9620.99320.733-11.932-11.9320.0000.0000.0000.000
46B46LEU00.0110.00717.8720.1630.1630.0000.0000.0000.000
47B47LEU0-0.070-0.03620.970-0.743-0.7430.0000.0000.0000.000
48B48ILE0-0.0030.00619.846-0.581-0.5810.0000.0000.0000.000
49B49HIS00.0210.00917.0880.6390.6390.0000.0000.0000.000
50B50ALA00.0330.01417.382-0.676-0.6760.0000.0000.0000.000
51B51ALA00.0030.00017.571-0.573-0.5730.0000.0000.0000.000
52B52SER0-0.090-0.05518.630-0.448-0.4480.0000.0000.0000.000
53B53SER00.0130.02121.750-0.782-0.7820.0000.0000.0000.000
54B54LEU0-0.033-0.01923.0170.4390.4390.0000.0000.0000.000
55B55GLU-1-0.902-0.94922.60512.58112.5810.0000.0000.0000.000
56B56THR0-0.029-0.02225.409-0.495-0.4950.0000.0000.0000.000
57B57GLY00.0230.00428.9590.0800.0800.0000.0000.0000.000
58B58VAL0-0.092-0.02325.799-0.161-0.1610.0000.0000.0000.000
59B59PRO00.020-0.00529.113-0.177-0.1770.0000.0000.0000.000
60B60SER00.0750.01929.8540.1960.1960.0000.0000.0000.000
61B61ARG10.7490.88530.205-9.648-9.6480.0000.0000.0000.000
62B62PHE0-0.0060.00525.7120.1080.1080.0000.0000.0000.000
63B63SER0-0.0080.00225.843-0.148-0.1480.0000.0000.0000.000
64B64GLY00.0630.02321.9910.3460.3460.0000.0000.0000.000
65B65SER0-0.053-0.03321.349-0.719-0.7190.0000.0000.0000.000
66B66GLY00.0470.01319.0650.4870.4870.0000.0000.0000.000
67B67SER0-0.049-0.03017.3800.0630.0630.0000.0000.0000.000
68B68GLY00.0550.05014.732-0.379-0.3790.0000.0000.0000.000
69B69THR00.0060.01111.7091.2821.2820.0000.0000.0000.000
70B70ASP-1-0.919-0.94113.97917.14717.1470.0000.0000.0000.000
71B71PHE0-0.009-0.00713.002-0.880-0.8800.0000.0000.0000.000
72B72SER0-0.037-0.03417.524-0.184-0.1840.0000.0000.0000.000
73B73PHE0-0.0060.00720.081-0.133-0.1330.0000.0000.0000.000
74B74THR0-0.005-0.01821.953-0.269-0.2690.0000.0000.0000.000
75B75ILE00.0000.02125.646-0.049-0.0490.0000.0000.0000.000
76B76SER0-0.049-0.05628.337-0.188-0.1880.0000.0000.0000.000
77B77SER00.0070.00431.732-0.210-0.2100.0000.0000.0000.000
78B78LEU0-0.025-0.00729.7640.0760.0760.0000.0000.0000.000
79B79GLN00.0560.03731.922-0.412-0.4120.0000.0000.0000.000
80B80PRO00.0460.00332.2860.3070.3070.0000.0000.0000.000
81B81GLU-1-0.936-0.97032.2409.2739.2730.0000.0000.0000.000
82B82ASP-1-0.759-0.87928.41110.44710.4470.0000.0000.0000.000
83B83LEU0-0.060-0.00327.5370.3930.3930.0000.0000.0000.000
84B84ALA0-0.038-0.03324.780-0.088-0.0880.0000.0000.0000.000
85B85THR00.0100.01719.182-0.290-0.2900.0000.0000.0000.000
86B86TYR00.000-0.00219.717-0.141-0.1410.0000.0000.0000.000
87B87TYR0-0.0110.02114.3000.2700.2700.0000.0000.0000.000
88B89GLN00.0470.01110.237-0.845-0.8450.0000.0000.0000.000
89B90GLN00.0450.0344.817-5.294-5.2940.0000.0000.0000.000
90B91TYR0-0.042-0.0488.7441.4801.4800.0000.0000.0000.000
91B92ASP-1-0.876-0.9347.97924.88124.8810.0000.0000.0000.000
92B93SER00.006-0.0075.787-0.492-0.4920.0000.0000.0000.000
93B94LEU0-0.062-0.0065.9061.3681.3680.0000.0000.0000.000
94B95PRO0-0.001-0.0012.468-0.3411.2900.531-0.757-1.4050.004
95B96LEU0-0.024-0.0185.647-3.530-3.5300.0000.0000.0000.000
96B97THR00.0340.0163.509-3.035-2.7460.002-0.048-0.2430.000
97B98PHE00.0010.0016.570-3.806-3.8060.0000.0000.0000.000
98B99GLY00.0230.0149.1591.6601.6600.0000.0000.0000.000
99B100GLY0-0.027-0.02611.050-0.518-0.5180.0000.0000.0000.000
100B101GLY00.0100.00613.307-0.750-0.7500.0000.0000.0000.000
101B102THR0-0.041-0.03416.3760.0080.0080.0000.0000.0000.000
102B103LYS10.8670.93819.704-11.980-11.9800.0000.0000.0000.000
103B104VAL00.0340.02122.844-0.228-0.2280.0000.0000.0000.000
104B105GLU-1-0.871-0.94325.80810.88310.8830.0000.0000.0000.000
105B106ILE00.0520.03729.068-0.081-0.0810.0000.0000.0000.000
106B107LYS10.8930.96732.730-9.164-9.1640.0000.0000.0000.000
107B108ARG10.8690.91534.468-9.019-9.0190.0000.0000.0000.000
108B109THR00.0110.00337.2790.0180.0180.0000.0000.0000.000
109B110VAL0-0.0140.00435.4950.1620.1620.0000.0000.0000.000
110B111ALA0-0.0070.00636.069-0.236-0.2360.0000.0000.0000.000
111B112ALA00.0300.00135.4690.2990.2990.0000.0000.0000.000
112B113PRO0-0.0040.01933.068-0.116-0.1160.0000.0000.0000.000
113B114SER0-0.0050.00735.452-0.171-0.1710.0000.0000.0000.000
114B115VAL00.020-0.01034.0810.1450.1450.0000.0000.0000.000
115B116PHE0-0.051-0.03135.075-0.356-0.3560.0000.0000.0000.000
116B117ILE0-0.016-0.01233.7310.2870.2870.0000.0000.0000.000
117B118PHE0-0.024-0.01633.893-0.320-0.3200.0000.0000.0000.000
118B119PRO00.0190.01333.9670.3340.3340.0000.0000.0000.000
119B120PRO0-0.012-0.00533.032-0.031-0.0310.0000.0000.0000.000
120B121SER00.0440.02134.929-0.174-0.1740.0000.0000.0000.000
121B122ASP-1-0.857-0.95136.7018.1058.1050.0000.0000.0000.000
122B123GLU-1-0.924-0.96837.6728.2878.2870.0000.0000.0000.000
123B124GLN0-0.0010.00130.9320.4120.4120.0000.0000.0000.000
124B125LEU00.0140.00333.5650.2560.2560.0000.0000.0000.000
125B126LYS10.9390.98435.257-8.065-8.0650.0000.0000.0000.000
126B127SER0-0.046-0.02831.6980.0180.0180.0000.0000.0000.000
127B128GLY0-0.0120.00831.6970.2790.2790.0000.0000.0000.000
128B129THR0-0.051-0.02827.1630.4270.4270.0000.0000.0000.000
129B130ALA00.002-0.00729.432-0.422-0.4220.0000.0000.0000.000
130B131SER00.0040.01928.0280.5280.5280.0000.0000.0000.000
131B132VAL0-0.051-0.01629.438-0.440-0.4400.0000.0000.0000.000
132B133VAL00.0270.01329.4440.3820.3820.0000.0000.0000.000
133B134CYS0-0.048-0.01929.872-0.083-0.0830.0000.0000.0000.000
134B135LEU0-0.0220.00330.1150.3100.3100.0000.0000.0000.000
135B136LEU00.0210.02229.007-0.355-0.3550.0000.0000.0000.000
136B137ASN0-0.003-0.02732.1330.3160.3160.0000.0000.0000.000
137B138ASN00.0360.03634.566-0.072-0.0720.0000.0000.0000.000
138B139PHE0-0.0060.01328.222-0.222-0.2220.0000.0000.0000.000
139B140TYR00.007-0.01131.5490.2420.2420.0000.0000.0000.000
140B141PRO00.0190.00829.560-0.309-0.3090.0000.0000.0000.000
141B142ARG10.9530.97221.297-13.442-13.4420.0000.0000.0000.000
142B143GLU-1-0.979-0.97325.37111.58311.5830.0000.0000.0000.000
143B144ALA00.0170.00525.966-0.546-0.5460.0000.0000.0000.000
144B145LYS10.9090.96125.159-10.993-10.9930.0000.0000.0000.000
145B146VAL00.0290.01925.773-0.562-0.5620.0000.0000.0000.000
146B147GLN00.0250.01825.5720.2420.2420.0000.0000.0000.000
147B148TRP0-0.001-0.01525.990-0.706-0.7060.0000.0000.0000.000
148B149LYS10.9320.95528.704-9.405-9.4050.0000.0000.0000.000
149B150VAL0-0.018-0.00830.214-0.250-0.2500.0000.0000.0000.000
150B151ASP-1-0.825-0.92432.6578.7568.7560.0000.0000.0000.000
151B152ASN0-0.059-0.03534.941-0.045-0.0450.0000.0000.0000.000
152B153ALA00.0390.04130.5130.0200.0200.0000.0000.0000.000
153B154LEU00.007-0.00426.3220.0240.0240.0000.0000.0000.000
154B155GLN0-0.065-0.01425.7110.4440.4440.0000.0000.0000.000
155B156SER00.011-0.01020.5690.2420.2420.0000.0000.0000.000
156B157GLY00.0230.01818.665-0.001-0.0010.0000.0000.0000.000
157B158ASN00.0040.00319.5270.5030.5030.0000.0000.0000.000
158B159SER00.018-0.00221.131-0.606-0.6060.0000.0000.0000.000
159B160GLN0-0.019-0.01216.9350.8110.8110.0000.0000.0000.000
160B161GLU-1-0.883-0.95220.59012.83912.8390.0000.0000.0000.000
161B162SER0-0.0140.00020.9930.6460.6460.0000.0000.0000.000
162B163VAL0-0.036-0.02422.983-0.649-0.6490.0000.0000.0000.000
163B164THR0-0.0230.00024.8310.2270.2270.0000.0000.0000.000
164B165GLU-1-0.945-0.96824.99912.10712.1070.0000.0000.0000.000
165B166GLN00.012-0.02127.120-0.360-0.3600.0000.0000.0000.000
166B167ASP-1-0.899-0.94429.73910.38710.3870.0000.0000.0000.000
167B168SER0-0.066-0.05231.892-0.247-0.2470.0000.0000.0000.000
168B169LYS10.9200.95629.562-10.032-10.0320.0000.0000.0000.000
169B170ASP-1-0.936-0.96033.2928.3138.3130.0000.0000.0000.000
170B171SER00.0330.02833.650-0.172-0.1720.0000.0000.0000.000
171B172THR0-0.091-0.04133.487-0.012-0.0120.0000.0000.0000.000
172B173TYR00.0100.00426.8180.3570.3570.0000.0000.0000.000
173B174SER00.016-0.00529.807-0.471-0.4710.0000.0000.0000.000
174B175LEU0-0.0210.00625.0420.2820.2820.0000.0000.0000.000
175B176SER00.0320.01926.652-0.569-0.5690.0000.0000.0000.000
176B177SER00.0630.05425.0280.5000.5000.0000.0000.0000.000
177B178THR0-0.013-0.01724.637-0.757-0.7570.0000.0000.0000.000
178B179LEU0-0.0050.01824.2970.6260.6260.0000.0000.0000.000
179B180THR0-0.022-0.01624.020-0.520-0.5200.0000.0000.0000.000
180B181LEU0-0.018-0.01125.2520.3080.3080.0000.0000.0000.000
181B182SER00.0410.01627.647-0.312-0.3120.0000.0000.0000.000
182B183LYS10.9500.97629.091-9.064-9.0640.0000.0000.0000.000
183B184ALA00.019-0.00232.488-0.207-0.2070.0000.0000.0000.000
184B185ASP-1-0.857-0.92828.55510.99310.9930.0000.0000.0000.000
185B186TYR00.004-0.00231.846-0.301-0.3010.0000.0000.0000.000
186B187GLU-1-0.916-0.96033.3158.3818.3810.0000.0000.0000.000
187B188LYS10.9000.95631.715-10.337-10.3370.0000.0000.0000.000
188B189HIS10.8550.93531.568-9.871-9.8710.0000.0000.0000.000
189B190LYS10.8910.92836.455-8.198-8.1980.0000.0000.0000.000
190B191VAL00.0280.02337.475-0.032-0.0320.0000.0000.0000.000
191B192TYR0-0.0030.00431.8910.3890.3890.0000.0000.0000.000
192B193ALA00.012-0.02333.756-0.241-0.2410.0000.0000.0000.000
193B195GLU-1-0.948-0.98031.2589.5159.5150.0000.0000.0000.000
194B196VAL00.0270.01730.4620.3800.3800.0000.0000.0000.000
195B197THR00.002-0.00829.562-0.362-0.3620.0000.0000.0000.000
196B198HIS00.021-0.02830.2820.0760.0760.0000.0000.0000.000
197B199GLN00.0360.02132.0750.0180.0180.0000.0000.0000.000
198B200GLY00.005-0.00434.145-0.258-0.2580.0000.0000.0000.000
199B201LEU0-0.088-0.03434.562-0.250-0.2500.0000.0000.0000.000
200B202SER00.0120.00937.0420.0590.0590.0000.0000.0000.000
201B203SER0-0.018-0.01937.825-0.063-0.0630.0000.0000.0000.000
202B204PRO00.0170.01333.695-0.034-0.0340.0000.0000.0000.000
203B205VAL00.0230.02535.302-0.237-0.2370.0000.0000.0000.000
204B206THR00.002-0.00435.2240.3560.3560.0000.0000.0000.000
205B207LYS10.9230.97335.583-8.450-8.4500.0000.0000.0000.000
206B208SER0-0.029-0.02135.8350.2320.2320.0000.0000.0000.000
207B209PHE0-0.0070.00934.546-0.176-0.1760.0000.0000.0000.000
208B210ASN00.0450.01838.5880.3150.3150.0000.0000.0000.000
209B211ARG10.8860.95337.337-8.470-8.4700.0000.0000.0000.000
210B212GLY00.0000.02240.121-0.205-0.2050.0000.0000.0000.000