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: LZ769

Calculation Name: 4BHH-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4BHH

Chain ID: B

ChEMBL ID:

UniProt ID: P04873

Base Structure: X-ray

Registration Date: 2023-06-22

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 231
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2781087.654913
FMO2-HF: Nuclear repulsion 2690153.810259
FMO2-HF: Total energy -90933.844654
FMO2-MP2: Total energy -91201.415403


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:3:ASP)


Summations of interaction energy for fragment #1(B:3: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.
-129.175-123.8191.714-3.152-3.9170.032
Interaction energy analysis for fragmet #1(B:3:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.962 / q_NPA : -0.993
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].
3B5VAL00.0190.0222.411-22.970-17.8511.714-3.119-3.7130.032
4B6PHE0-0.034-0.0224.1690.4700.7070.000-0.033-0.2040.000
5B7TYR00.007-0.0095.476-5.644-5.6440.0000.0000.0000.000
6B8ASP-1-0.854-0.9159.88218.70618.7060.0000.0000.0000.000
7B9VAL0-0.079-0.05113.0461.3611.3610.0000.0000.0000.000
8B10ALA0-0.0030.01015.662-1.094-1.0940.0000.0000.0000.000
9B11SER00.0400.01618.877-0.258-0.2580.0000.0000.0000.000
10B12THR0-0.028-0.01022.110-0.434-0.4340.0000.0000.0000.000
11B13GLY00.0430.01824.1750.3560.3560.0000.0000.0000.000
12B14ALA0-0.023-0.01926.922-0.308-0.3080.0000.0000.0000.000
13B15ASN0-0.017-0.02226.209-0.209-0.2090.0000.0000.0000.000
14B16GLY00.0700.05129.158-0.319-0.3190.0000.0000.0000.000
15B17PHE0-0.072-0.04826.847-0.066-0.0660.0000.0000.0000.000
16B18ASP-1-0.773-0.86229.7419.4039.4030.0000.0000.0000.000
17B19PRO00.001-0.00429.617-0.068-0.0680.0000.0000.0000.000
18B20ASP-1-0.771-0.87631.6019.0109.0100.0000.0000.0000.000
19B21ALA00.0010.01234.436-0.188-0.1880.0000.0000.0000.000
20B22GLY00.008-0.00931.495-0.081-0.0810.0000.0000.0000.000
21B23TYR0-0.084-0.06232.5210.2200.2200.0000.0000.0000.000
22B24MET00.0250.01933.604-0.187-0.1870.0000.0000.0000.000
23B25ASP-1-0.791-0.86333.0869.7269.7260.0000.0000.0000.000
24B26PHE00.0150.00529.9770.0580.0580.0000.0000.0000.000
25B27CYS00.024-0.00333.5550.0140.0140.0000.0000.0000.000
26B28VAL0-0.0010.00536.405-0.147-0.1470.0000.0000.0000.000
27B29LYS10.7990.88231.427-10.154-10.1540.0000.0000.0000.000
28B30ASN0-0.057-0.03432.1420.2180.2180.0000.0000.0000.000
29B31ALA0-0.012-0.00135.4980.0040.0040.0000.0000.0000.000
30B32GLU-1-0.911-0.95638.0947.8537.8530.0000.0000.0000.000
31B33SER0-0.050-0.02035.0720.0020.0020.0000.0000.0000.000
32B34LEU0-0.072-0.01632.3560.2660.2660.0000.0000.0000.000
33B35ASN00.0730.01735.137-0.161-0.1610.0000.0000.0000.000
34B36LEU00.0640.02734.7460.3640.3640.0000.0000.0000.000
35B37ALA00.0150.01833.9360.2980.2980.0000.0000.0000.000
36B38ALA00.0120.00431.6940.3580.3580.0000.0000.0000.000
37B39VAL00.0240.00830.0000.5080.5080.0000.0000.0000.000
38B40ARG10.9030.93629.217-9.304-9.3040.0000.0000.0000.000
39B41ILE0-0.030-0.00326.9790.4430.4430.0000.0000.0000.000
40B42PHE00.0200.02523.4630.7280.7280.0000.0000.0000.000
41B43PHE0-0.001-0.01324.3460.7340.7340.0000.0000.0000.000
42B44LEU0-0.029-0.00324.5600.4390.4390.0000.0000.0000.000
43B45ASN0-0.112-0.05421.7500.8830.8830.0000.0000.0000.000
44B46ALA00.0830.05420.7070.7360.7360.0000.0000.0000.000
45B47ALA0-0.004-0.02316.8070.8370.8370.0000.0000.0000.000
46B48LYS10.9360.96215.788-13.093-13.0930.0000.0000.0000.000
47B49ALA00.0540.02316.1781.0501.0500.0000.0000.0000.000
48B50LYS10.9120.96514.254-17.201-17.2010.0000.0000.0000.000
49B51ALA00.0380.02111.6101.4471.4470.0000.0000.0000.000
50B52ALA0-0.0040.00611.6412.1222.1220.0000.0000.0000.000
51B53LEU00.0220.00914.0870.1090.1090.0000.0000.0000.000
52B54SER0-0.082-0.0498.9781.3181.3180.0000.0000.0000.000
53B55ARG10.8900.9498.692-27.200-27.2000.0000.0000.0000.000
54B56LYS10.8870.93011.093-16.913-16.9130.0000.0000.0000.000
55B57PRO00.0290.02512.6580.2130.2130.0000.0000.0000.000
56B58GLU-1-0.829-0.90013.94017.25217.2520.0000.0000.0000.000
57B59ARG10.9680.97816.667-15.378-15.3780.0000.0000.0000.000
58B60LYS10.8470.91818.538-12.174-12.1740.0000.0000.0000.000
59B61ALA0-0.007-0.00419.4000.5000.5000.0000.0000.0000.000
60B62ASN00.0290.00821.533-0.145-0.1450.0000.0000.0000.000
61B63PRO0-0.0360.00521.773-0.067-0.0670.0000.0000.0000.000
62B64LYS10.8740.91523.803-10.628-10.6280.0000.0000.0000.000
63B65PHE0-0.028-0.01222.6920.4440.4440.0000.0000.0000.000
64B66GLY00.0450.00727.839-0.350-0.3500.0000.0000.0000.000
65B67GLU-1-0.868-0.92931.0699.6639.6630.0000.0000.0000.000
66B68TRP00.0490.03428.3020.0180.0180.0000.0000.0000.000
67B69GLN0-0.037-0.02227.7280.5630.5630.0000.0000.0000.000
68B70VAL00.0280.01625.947-0.253-0.2530.0000.0000.0000.000
69B71GLU-1-0.814-0.89525.60512.39712.3970.0000.0000.0000.000
70B72VAL0-0.061-0.01920.731-0.025-0.0250.0000.0000.0000.000
71B73ILE0-0.003-0.02319.5860.1780.1780.0000.0000.0000.000
72B74ASN0-0.036-0.02314.3151.1091.1090.0000.0000.0000.000
73B75ASN0-0.010-0.02014.364-0.251-0.2510.0000.0000.0000.000
74B76HIS00.0210.00912.2330.9960.9960.0000.0000.0000.000
75B77PHE00.0170.0129.8134.4094.4090.0000.0000.0000.000
76B78PRO0-0.010-0.0085.651-2.525-2.5250.0000.0000.0000.000
77B79GLY00.0580.0397.930-1.698-1.6980.0000.0000.0000.000
78B80ASN0-0.022-0.01810.323-1.666-1.6660.0000.0000.0000.000
79B81ARG10.8810.9536.787-40.630-40.6300.0000.0000.0000.000
80B82ASN00.0190.00713.342-1.503-1.5030.0000.0000.0000.000
81B83ASN0-0.069-0.03016.304-0.924-0.9240.0000.0000.0000.000
82B84PRO00.0000.00518.3970.0470.0470.0000.0000.0000.000
83B85ILE0-0.038-0.02219.565-0.182-0.1820.0000.0000.0000.000
84B86GLY00.0710.04123.700-0.281-0.2810.0000.0000.0000.000
85B87ASN0-0.089-0.06627.423-0.048-0.0480.0000.0000.0000.000
86B88ASN00.0320.00329.350-0.126-0.1260.0000.0000.0000.000
87B89ASP-1-0.890-0.92225.14712.22412.2240.0000.0000.0000.000
88B90LEU00.0210.01925.0210.0510.0510.0000.0000.0000.000
89B91THR00.0320.01719.6910.4070.4070.0000.0000.0000.000
90B92ILE00.041-0.00118.330-0.407-0.4070.0000.0000.0000.000
91B93HIS0-0.105-0.06219.7910.1600.1600.0000.0000.0000.000
92B94ARG10.8770.93321.562-13.203-13.2030.0000.0000.0000.000
93B95LEU00.0440.04123.881-0.467-0.4670.0000.0000.0000.000
94B96SER0-0.026-0.02823.535-0.434-0.4340.0000.0000.0000.000
95B97GLY00.0310.01225.531-0.365-0.3650.0000.0000.0000.000
96B98TYR00.002-0.01427.790-0.328-0.3280.0000.0000.0000.000
97B99LEU00.0190.00327.546-0.395-0.3950.0000.0000.0000.000
98B100ALA0-0.0190.00529.255-0.318-0.3180.0000.0000.0000.000
99B101ARG10.8170.88731.092-9.327-9.3270.0000.0000.0000.000
100B102TRP00.0420.02633.521-0.122-0.1220.0000.0000.0000.000
101B103VAL0-0.012-0.01433.157-0.241-0.2410.0000.0000.0000.000
102B104LEU0-0.040-0.01535.648-0.217-0.2170.0000.0000.0000.000
103B105ASP-1-0.846-0.91437.5318.2968.2960.0000.0000.0000.000
104B106GLN0-0.047-0.02538.314-0.117-0.1170.0000.0000.0000.000
105B107TYR0-0.042-0.02539.719-0.101-0.1010.0000.0000.0000.000
106B108ASN0-0.026-0.03440.983-0.226-0.2260.0000.0000.0000.000
107B109GLU-1-0.908-0.91943.4377.2507.2500.0000.0000.0000.000
108B110ASN0-0.079-0.05045.348-0.303-0.3030.0000.0000.0000.000
109B111ASP-1-0.899-0.94747.0006.6546.6540.0000.0000.0000.000
110B112ASP-1-0.879-0.91848.1316.3866.3860.0000.0000.0000.000
111B113GLU-1-0.794-0.89547.2077.0127.0120.0000.0000.0000.000
112B114SER0-0.083-0.07147.1500.1600.1600.0000.0000.0000.000
113B115GLN00.0190.01443.4890.0690.0690.0000.0000.0000.000
114B116HIS00.005-0.01042.7060.2580.2580.0000.0000.0000.000
115B117GLU-1-0.864-0.91141.9197.4227.4220.0000.0000.0000.000
116B118LEU0-0.0150.01340.6820.2340.2340.0000.0000.0000.000
117B119ILE0-0.0070.00137.3360.3170.3170.0000.0000.0000.000
118B120ARG10.7850.86137.224-7.084-7.0840.0000.0000.0000.000
119B121THR0-0.039-0.01837.0650.1970.1970.0000.0000.0000.000
120B122THR0-0.087-0.04035.1820.2240.2240.0000.0000.0000.000
121B123ILE0-0.024-0.00831.8540.4050.4050.0000.0000.0000.000
122B124ILE00.0380.01929.716-0.073-0.0730.0000.0000.0000.000
123B125ASN00.016-0.00127.2720.8530.8530.0000.0000.0000.000
124B126PRO00.012-0.00624.528-0.083-0.0830.0000.0000.0000.000
125B127ILE0-0.009-0.00822.4780.0730.0730.0000.0000.0000.000
126B128ALA00.0100.03625.687-0.047-0.0470.0000.0000.0000.000
127B129GLU-1-0.720-0.83129.3429.5759.5750.0000.0000.0000.000
128B130SER0-0.156-0.07425.6250.0210.0210.0000.0000.0000.000
129B131ASN0-0.061-0.07425.8270.3370.3370.0000.0000.0000.000
130B132GLY0-0.0130.00429.470-0.255-0.2550.0000.0000.0000.000
131B133VAL0-0.053-0.02332.027-0.338-0.3380.0000.0000.0000.000
132B134GLY00.0880.04133.0050.2310.2310.0000.0000.0000.000
133B135TRP00.031-0.01034.893-0.108-0.1080.0000.0000.0000.000
134B136ASP-1-0.839-0.91337.4578.1038.1030.0000.0000.0000.000
135B137SER0-0.081-0.03737.005-0.138-0.1380.0000.0000.0000.000
136B138GLY00.0170.01039.161-0.082-0.0820.0000.0000.0000.000
137B139PRO00.0370.02237.4960.2950.2950.0000.0000.0000.000
138B140GLU-1-0.789-0.89035.9358.3688.3680.0000.0000.0000.000
139B141ILE0-0.0080.00934.6750.3830.3830.0000.0000.0000.000
140B142TYR0-0.047-0.03432.4110.4940.4940.0000.0000.0000.000
141B143LEU00.021-0.00331.3770.4860.4860.0000.0000.0000.000
142B144SER00.004-0.02130.1000.3740.3740.0000.0000.0000.000
143B145PHE0-0.051-0.02327.4580.5190.5190.0000.0000.0000.000
144B146PHE0-0.0460.00725.6930.6810.6810.0000.0000.0000.000
145B147PRO0-0.034-0.01621.3770.0810.0810.0000.0000.0000.000
146B148GLY00.0150.00523.943-0.111-0.1110.0000.0000.0000.000
147B149THR00.0400.01025.279-0.343-0.3430.0000.0000.0000.000
148B150GLU-1-0.807-0.90824.14913.00713.0070.0000.0000.0000.000
149B151MET0-0.109-0.03226.812-0.037-0.0370.0000.0000.0000.000
150B152PHE00.0060.00529.557-0.235-0.2350.0000.0000.0000.000
151B153LEU00.0060.00830.695-0.201-0.2010.0000.0000.0000.000
152B154GLU-1-0.867-0.91833.9317.8457.8450.0000.0000.0000.000
153B155THR00.0280.01935.656-0.068-0.0680.0000.0000.0000.000
154B156PHE0-0.0020.00232.278-0.079-0.0790.0000.0000.0000.000
155B157LYS10.9100.93535.671-7.722-7.7220.0000.0000.0000.000
156B158PHE0-0.014-0.03234.676-0.072-0.0720.0000.0000.0000.000
157B159TYR0-0.031-0.01733.6640.2430.2430.0000.0000.0000.000
158B160PRO00.0010.00928.9820.2270.2270.0000.0000.0000.000
159B161LEU0-0.048-0.01628.8560.4530.4530.0000.0000.0000.000
160B162THR00.024-0.00730.2490.3350.3350.0000.0000.0000.000
161B163ILE00.0360.03127.9080.0910.0910.0000.0000.0000.000
162B164GLY0-0.014-0.00826.7680.2770.2770.0000.0000.0000.000
163B165ILE00.012-0.00927.5040.2340.2340.0000.0000.0000.000
164B166HIS0-0.022-0.00630.087-0.037-0.0370.0000.0000.0000.000
165B167ARG10.9420.95823.917-12.855-12.8550.0000.0000.0000.000
166B168VAL0-0.036-0.01024.8290.2520.2520.0000.0000.0000.000
167B169LYS10.8320.89727.043-9.170-9.1700.0000.0000.0000.000
168B170GLN0-0.0160.00928.963-0.243-0.2430.0000.0000.0000.000
169B171GLY0-0.0120.00125.6400.0930.0930.0000.0000.0000.000
170B172MET0-0.061-0.01124.2490.4640.4640.0000.0000.0000.000
171B173MET0-0.078-0.03121.3860.6670.6670.0000.0000.0000.000
172B174ASP-1-0.734-0.85917.59317.24917.2490.0000.0000.0000.000
173B175PRO00.043-0.00520.6710.0820.0820.0000.0000.0000.000
174B176GLN0-0.077-0.03616.194-0.374-0.3740.0000.0000.0000.000
175B177TYR0-0.064-0.03814.4860.0590.0590.0000.0000.0000.000
176B178LEU00.0080.01120.770-0.323-0.3230.0000.0000.0000.000
177B179LYS10.9800.99721.709-15.049-15.0490.0000.0000.0000.000
178B180LYS10.8980.94018.694-16.845-16.8450.0000.0000.0000.000
179B181ALA00.0920.04024.147-0.343-0.3430.0000.0000.0000.000
180B182LEU00.0170.01027.452-0.375-0.3750.0000.0000.0000.000
181B183ARG10.8850.95323.502-13.473-13.4730.0000.0000.0000.000
182B184GLN0-0.0430.00026.531-0.362-0.3620.0000.0000.0000.000
183B185ARG10.8790.93130.691-9.586-9.5860.0000.0000.0000.000
184B186TYR0-0.064-0.04734.3130.1180.1180.0000.0000.0000.000
185B187GLY00.0870.04836.839-0.257-0.2570.0000.0000.0000.000
186B188THR0-0.028-0.01838.5450.1060.1060.0000.0000.0000.000
187B189LEU0-0.056-0.01639.035-0.106-0.1060.0000.0000.0000.000
188B190THR00.0530.00235.1900.1610.1610.0000.0000.0000.000
189B191ALA00.0770.03932.800-0.173-0.1730.0000.0000.0000.000
190B192ASP-1-0.888-0.95634.9179.1469.1460.0000.0000.0000.000
191B193LYS10.9000.96937.142-8.048-8.0480.0000.0000.0000.000
192B194TRP0-0.020-0.02932.416-0.240-0.2400.0000.0000.0000.000
193B195MET0-0.018-0.02133.6690.0340.0340.0000.0000.0000.000
194B196SER0-0.0240.00737.756-0.157-0.1570.0000.0000.0000.000
195B197GLN00.006-0.00441.245-0.064-0.0640.0000.0000.0000.000
196B198LYS10.9120.97340.129-7.775-7.7750.0000.0000.0000.000
197B199VAL00.0620.03040.1510.1570.1570.0000.0000.0000.000
198B200ALA00.0170.00241.1130.0870.0870.0000.0000.0000.000
199B201ALA0-0.008-0.01441.8440.0190.0190.0000.0000.0000.000
200B202ILE00.0290.02636.2290.0920.0920.0000.0000.0000.000
201B203ALA00.0210.00938.4340.1370.1370.0000.0000.0000.000
202B204LYS10.8090.89640.184-7.592-7.5920.0000.0000.0000.000
203B205SER00.0420.02036.8780.1210.1210.0000.0000.0000.000
204B206LEU0-0.030-0.02334.2950.1500.1500.0000.0000.0000.000
205B207LYS10.9560.97737.170-7.531-7.5310.0000.0000.0000.000
206B208ASP-1-0.734-0.83238.9137.8337.8330.0000.0000.0000.000
207B209VAL00.0230.00832.9420.0740.0740.0000.0000.0000.000
208B210GLU-1-0.867-0.92535.4389.1329.1320.0000.0000.0000.000
209B211GLN0-0.068-0.01936.878-0.068-0.0680.0000.0000.0000.000
210B212LEU0-0.0150.01234.038-0.128-0.1280.0000.0000.0000.000
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