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: 94M22

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 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 231
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2787747.704051
FMO2-HF: Nuclear repulsion 2696813.041353
FMO2-HF: Total energy -90934.662698
FMO2-MP2: Total energy -91202.165047


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.
-136.462-134.9589.951-5.438-6.0160.061
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 : -0.928 / q_NPA : -0.975
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].
3B5VAL0-0.0060.0061.870-28.505-27.2649.946-5.547-5.6400.059
4B6PHE0-0.034-0.0233.685-0.755-0.4920.0050.109-0.3760.002
5B7TYR0-0.024-0.0175.355-5.172-5.1720.0000.0000.0000.000
6B8ASP-1-0.848-0.9129.56718.78618.7860.0000.0000.0000.000
7B9VAL0-0.065-0.03312.7131.5151.5150.0000.0000.0000.000
8B10ALA0-0.013-0.00115.204-1.215-1.2150.0000.0000.0000.000
9B11SER00.0360.01218.324-0.295-0.2950.0000.0000.0000.000
10B12THR0-0.0170.00221.591-0.503-0.5030.0000.0000.0000.000
11B13GLY00.0320.01423.8490.3350.3350.0000.0000.0000.000
12B14ALA0-0.004-0.00826.502-0.275-0.2750.0000.0000.0000.000
13B15ASN0-0.030-0.02225.578-0.160-0.1600.0000.0000.0000.000
14B16GLY00.0420.01928.645-0.272-0.2720.0000.0000.0000.000
15B17PHE0-0.049-0.03226.792-0.094-0.0940.0000.0000.0000.000
16B18ASP-1-0.759-0.84929.6099.3449.3440.0000.0000.0000.000
17B19PRO00.002-0.00929.381-0.039-0.0390.0000.0000.0000.000
18B20ASP-1-0.775-0.86031.4248.9938.9930.0000.0000.0000.000
19B21ALA0-0.0020.00634.398-0.144-0.1440.0000.0000.0000.000
20B22GLY00.009-0.00231.196-0.048-0.0480.0000.0000.0000.000
21B23TYR0-0.097-0.07632.1690.2340.2340.0000.0000.0000.000
22B24MET00.0200.00733.419-0.193-0.1930.0000.0000.0000.000
23B25ASP-1-0.774-0.86232.3709.8619.8610.0000.0000.0000.000
24B26PHE00.001-0.00729.8080.0210.0210.0000.0000.0000.000
25B27CYS00.0200.00133.0930.0260.0260.0000.0000.0000.000
26B28VAL00.0080.01136.117-0.154-0.1540.0000.0000.0000.000
27B29LYS10.7750.87730.922-10.265-10.2650.0000.0000.0000.000
28B30ASN0-0.052-0.03431.8220.2690.2690.0000.0000.0000.000
29B31ALA0-0.003-0.00635.3250.0180.0180.0000.0000.0000.000
30B32GLU-1-0.912-0.93938.2487.7107.7100.0000.0000.0000.000
31B33SER0-0.040-0.02535.315-0.003-0.0030.0000.0000.0000.000
32B34LEU0-0.066-0.01332.1900.2130.2130.0000.0000.0000.000
33B35ASN00.0470.01334.992-0.206-0.2060.0000.0000.0000.000
34B36LEU00.0920.03734.6980.3720.3720.0000.0000.0000.000
35B37ALA00.0160.01834.1650.2730.2730.0000.0000.0000.000
36B38ALA00.0090.00231.5830.3500.3500.0000.0000.0000.000
37B39VAL00.0170.00929.9420.5360.5360.0000.0000.0000.000
38B40ARG10.8870.94129.439-9.172-9.1720.0000.0000.0000.000
39B41ILE0-0.024-0.00827.3670.4530.4530.0000.0000.0000.000
40B42PHE00.0020.00923.6030.7390.7390.0000.0000.0000.000
41B43PHE00.011-0.00524.5090.7950.7950.0000.0000.0000.000
42B44LEU0-0.0350.00224.6400.4500.4500.0000.0000.0000.000
43B45ASN0-0.064-0.04321.9840.8400.8400.0000.0000.0000.000
44B46ALA00.0490.04020.5340.9040.9040.0000.0000.0000.000
45B47ALA0-0.014-0.02217.1320.9090.9090.0000.0000.0000.000
46B48LYS10.9480.96616.006-13.020-13.0200.0000.0000.0000.000
47B49ALA00.0440.02316.6210.8520.8520.0000.0000.0000.000
48B50LYS10.9290.97514.131-16.960-16.9600.0000.0000.0000.000
49B51ALA00.0190.01611.9881.8111.8110.0000.0000.0000.000
50B52ALA00.0030.01112.2051.8641.8640.0000.0000.0000.000
51B53LEU00.0280.00214.0040.6880.6880.0000.0000.0000.000
52B54SER0-0.074-0.0518.9601.4991.4990.0000.0000.0000.000
53B55ARG10.9130.9449.080-26.372-26.3720.0000.0000.0000.000
54B56LYS10.8650.93611.104-17.748-17.7480.0000.0000.0000.000
55B57PRO00.0380.02512.7590.5210.5210.0000.0000.0000.000
56B58GLU-1-0.811-0.89013.86417.03117.0310.0000.0000.0000.000
57B59ARG10.9480.96116.976-15.856-15.8560.0000.0000.0000.000
58B60LYS10.8190.90818.391-12.582-12.5820.0000.0000.0000.000
59B61ALA0-0.0090.00619.6280.3700.3700.0000.0000.0000.000
60B62ASN00.0350.01421.682-0.012-0.0120.0000.0000.0000.000
61B63PRO0-0.030-0.00322.086-0.119-0.1190.0000.0000.0000.000
62B64LYS10.8490.90324.105-10.554-10.5540.0000.0000.0000.000
63B65PHE0-0.033-0.02223.1020.5630.5630.0000.0000.0000.000
64B66GLY00.0470.01428.291-0.357-0.3570.0000.0000.0000.000
65B67GLU-1-0.850-0.91331.4749.7159.7150.0000.0000.0000.000
66B68TRP00.0520.04028.6230.0070.0070.0000.0000.0000.000
67B69GLN0-0.030-0.02828.0260.3460.3460.0000.0000.0000.000
68B70VAL00.0110.02026.126-0.267-0.2670.0000.0000.0000.000
69B71GLU-1-0.816-0.89625.32512.51312.5130.0000.0000.0000.000
70B72VAL0-0.054-0.02920.6940.0000.0000.0000.0000.0000.000
71B73ILE00.0150.00219.0770.3290.3290.0000.0000.0000.000
72B74ASN0-0.049-0.03714.0251.2251.2250.0000.0000.0000.000
73B75ASN0-0.032-0.02514.212-0.497-0.4970.0000.0000.0000.000
74B76HIS00.0400.01712.2891.4421.4420.0000.0000.0000.000
75B77PHE00.0210.0209.6564.5244.5240.0000.0000.0000.000
76B78PRO0-0.007-0.0065.263-2.070-2.0700.0000.0000.0000.000
77B79GLY00.0680.0357.343-1.722-1.7220.0000.0000.0000.000
78B80ASN0-0.040-0.0309.817-1.882-1.8820.0000.0000.0000.000
79B81ARG10.8690.9486.121-42.816-42.8160.0000.0000.0000.000
80B82ASN00.005-0.00712.677-1.809-1.8090.0000.0000.0000.000
81B83ASN0-0.036-0.01315.627-1.182-1.1820.0000.0000.0000.000
82B84PRO00.0010.00817.8320.0120.0120.0000.0000.0000.000
83B85ILE0-0.037-0.02318.960-0.093-0.0930.0000.0000.0000.000
84B86GLY00.0720.04523.110-0.262-0.2620.0000.0000.0000.000
85B87ASN0-0.067-0.06026.6600.0380.0380.0000.0000.0000.000
86B88ASN00.013-0.00129.1420.0420.0420.0000.0000.0000.000
87B89ASP-1-0.854-0.90524.75912.23912.2390.0000.0000.0000.000
88B90LEU00.0070.01325.0380.0020.0020.0000.0000.0000.000
89B91THR00.0490.01319.9050.4450.4450.0000.0000.0000.000
90B92ILE00.014-0.00218.528-0.412-0.4120.0000.0000.0000.000
91B93HIS0-0.086-0.04719.7560.3910.3910.0000.0000.0000.000
92B94ARG10.8280.90721.599-13.102-13.1020.0000.0000.0000.000
93B95LEU00.0300.02223.612-0.406-0.4060.0000.0000.0000.000
94B96SER0-0.016-0.02323.393-0.408-0.4080.0000.0000.0000.000
95B97GLY00.0290.01725.422-0.384-0.3840.0000.0000.0000.000
96B98TYR0-0.004-0.01627.762-0.318-0.3180.0000.0000.0000.000
97B99LEU00.0190.01027.510-0.409-0.4090.0000.0000.0000.000
98B100ALA0-0.0180.00029.174-0.318-0.3180.0000.0000.0000.000
99B101ARG10.7960.87831.027-9.339-9.3390.0000.0000.0000.000
100B102TRP00.0580.03033.405-0.133-0.1330.0000.0000.0000.000
101B103VAL0-0.009-0.00933.028-0.239-0.2390.0000.0000.0000.000
102B104LEU0-0.024-0.00835.438-0.214-0.2140.0000.0000.0000.000
103B105ASP-1-0.847-0.91137.3088.3428.3420.0000.0000.0000.000
104B106GLN0-0.045-0.04538.397-0.081-0.0810.0000.0000.0000.000
105B107TYR0-0.089-0.05339.437-0.098-0.0980.0000.0000.0000.000
106B108ASN0-0.050-0.03640.788-0.239-0.2390.0000.0000.0000.000
107B109GLU-1-0.870-0.89143.3647.3037.3030.0000.0000.0000.000
108B110ASN0-0.034-0.02845.096-0.307-0.3070.0000.0000.0000.000
109B111ASP-1-0.935-0.95446.8736.6446.6440.0000.0000.0000.000
110B112ASP-1-0.834-0.89148.1996.4526.4520.0000.0000.0000.000
111B113GLU-1-0.780-0.88647.0377.0447.0440.0000.0000.0000.000
112B114SER0-0.072-0.05246.8830.1370.1370.0000.0000.0000.000
113B115GLN00.003-0.00643.5960.0630.0630.0000.0000.0000.000
114B116HIS00.007-0.00142.8790.2710.2710.0000.0000.0000.000
115B117GLU-1-0.841-0.91241.9877.5007.5000.0000.0000.0000.000
116B118LEU0-0.0100.01340.9620.2250.2250.0000.0000.0000.000
117B119ILE0-0.0070.00337.3040.3210.3210.0000.0000.0000.000
118B120ARG10.7500.84537.410-7.061-7.0610.0000.0000.0000.000
119B121THR0-0.043-0.01537.5770.1750.1750.0000.0000.0000.000
120B122THR0-0.091-0.05435.4810.2170.2170.0000.0000.0000.000
121B123ILE0-0.020-0.01132.0460.4170.4170.0000.0000.0000.000
122B124ILE00.0310.02429.811-0.098-0.0980.0000.0000.0000.000
123B125ASN00.028-0.00527.3610.7980.7980.0000.0000.0000.000
124B126PRO00.013-0.00124.710-0.043-0.0430.0000.0000.0000.000
125B127ILE0-0.0370.00322.5310.2030.2030.0000.0000.0000.000
126B128ALA00.0220.03525.6050.0010.0010.0000.0000.0000.000
127B129GLU-1-0.751-0.85429.3429.6359.6350.0000.0000.0000.000
128B130SER0-0.128-0.08125.550-0.053-0.0530.0000.0000.0000.000
129B131ASN0-0.052-0.05625.4140.3240.3240.0000.0000.0000.000
130B132GLY00.0220.02529.270-0.254-0.2540.0000.0000.0000.000
131B133VAL0-0.049-0.01832.032-0.360-0.3600.0000.0000.0000.000
132B134GLY00.1030.03832.8380.2650.2650.0000.0000.0000.000
133B135TRP00.021-0.02135.138-0.103-0.1030.0000.0000.0000.000
134B136ASP-1-0.818-0.87937.5718.0848.0840.0000.0000.0000.000
135B137SER0-0.042-0.02737.141-0.187-0.1870.0000.0000.0000.000
136B138GLY00.0200.02239.270-0.035-0.0350.0000.0000.0000.000
137B139PRO00.0320.02137.2680.3060.3060.0000.0000.0000.000
138B140GLU-1-0.781-0.88935.6718.4538.4530.0000.0000.0000.000
139B141ILE0-0.0100.01434.1640.4130.4130.0000.0000.0000.000
140B142TYR0-0.033-0.02432.6900.4660.4660.0000.0000.0000.000
141B143LEU00.0240.00431.3030.4990.4990.0000.0000.0000.000
142B144SER0-0.022-0.04329.8020.4210.4210.0000.0000.0000.000
143B145PHE0-0.053-0.01527.3820.4750.4750.0000.0000.0000.000
144B146PHE0-0.0390.00625.3520.7330.7330.0000.0000.0000.000
145B147PRO0-0.031-0.00921.111-0.044-0.0440.0000.0000.0000.000
146B148GLY00.0080.00523.748-0.080-0.0800.0000.0000.0000.000
147B149THR00.036-0.00225.334-0.395-0.3950.0000.0000.0000.000
148B150GLU-1-0.795-0.90324.22712.99412.9940.0000.0000.0000.000
149B151MET0-0.110-0.03926.513-0.050-0.0500.0000.0000.0000.000
150B152PHE00.0140.00929.261-0.227-0.2270.0000.0000.0000.000
151B153LEU00.0010.00230.525-0.231-0.2310.0000.0000.0000.000
152B154GLU-1-0.847-0.89033.8297.8307.8300.0000.0000.0000.000
153B155THR00.0170.00735.334-0.098-0.0980.0000.0000.0000.000
154B156PHE00.0070.00932.029-0.034-0.0340.0000.0000.0000.000
155B157LYS10.9040.93835.305-7.733-7.7330.0000.0000.0000.000
156B158PHE00.014-0.01634.212-0.100-0.1000.0000.0000.0000.000
157B159TYR0-0.015-0.01033.1430.2630.2630.0000.0000.0000.000
158B160PRO00.0020.01428.5190.2280.2280.0000.0000.0000.000
159B161LEU0-0.025-0.00928.4130.4450.4450.0000.0000.0000.000
160B162THR00.002-0.01529.8130.3080.3080.0000.0000.0000.000
161B163ILE00.0360.02827.4220.0400.0400.0000.0000.0000.000
162B164GLY0-0.022-0.01326.3320.2990.2990.0000.0000.0000.000
163B165ILE00.001-0.01627.2320.2050.2050.0000.0000.0000.000
164B166HIS00.0240.02629.868-0.102-0.1020.0000.0000.0000.000
165B167ARG10.9300.96024.166-12.724-12.7240.0000.0000.0000.000
166B168VAL0-0.029-0.00824.7670.2170.2170.0000.0000.0000.000
167B169LYS10.8070.88026.920-9.237-9.2370.0000.0000.0000.000
168B170GLN0-0.029-0.00528.851-0.127-0.1270.0000.0000.0000.000
169B171GLY0-0.0020.00825.7560.1390.1390.0000.0000.0000.000
170B172MET0-0.046-0.00424.0700.5920.5920.0000.0000.0000.000
171B173MET0-0.073-0.03520.9270.5220.5220.0000.0000.0000.000
172B174ASP-1-0.745-0.85017.45317.25617.2560.0000.0000.0000.000
173B175PRO00.0470.00220.4730.0430.0430.0000.0000.0000.000
174B176GLN0-0.089-0.05716.152-0.445-0.4450.0000.0000.0000.000
175B177TYR0-0.046-0.02514.2350.1450.1450.0000.0000.0000.000
176B178LEU00.0250.01420.424-0.337-0.3370.0000.0000.0000.000
177B179LYS10.9690.99421.340-15.382-15.3820.0000.0000.0000.000
178B180LYS10.9040.96718.653-16.668-16.6680.0000.0000.0000.000
179B181ALA00.0900.04223.815-0.375-0.3750.0000.0000.0000.000
180B182LEU00.001-0.00926.778-0.404-0.4040.0000.0000.0000.000
181B183ARG10.8640.92423.488-13.449-13.4490.0000.0000.0000.000
182B184GLN0-0.0330.00726.343-0.216-0.2160.0000.0000.0000.000
183B185ARG10.8710.92030.248-9.603-9.6030.0000.0000.0000.000
184B186TYR0-0.061-0.05033.9950.0840.0840.0000.0000.0000.000
185B187GLY00.0880.03636.499-0.262-0.2620.0000.0000.0000.000
186B188THR0-0.003-0.00537.7310.1600.1600.0000.0000.0000.000
187B189LEU0-0.058-0.02138.711-0.067-0.0670.0000.0000.0000.000
188B190THR00.0690.00434.6860.1720.1720.0000.0000.0000.000
189B191ALA00.0430.02632.233-0.174-0.1740.0000.0000.0000.000
190B192ASP-1-0.858-0.94034.3169.2459.2450.0000.0000.0000.000
191B193LYS10.9170.97336.745-8.156-8.1560.0000.0000.0000.000
192B194TRP0-0.022-0.02431.806-0.250-0.2500.0000.0000.0000.000
193B195MET0-0.002-0.01132.881-0.021-0.0210.0000.0000.0000.000
194B196SER0-0.0140.00537.211-0.137-0.1370.0000.0000.0000.000
195B197GLN0-0.036-0.01240.683-0.120-0.1200.0000.0000.0000.000
196B198LYS10.8680.94239.402-7.884-7.8840.0000.0000.0000.000
197B199VAL00.0550.03439.7020.0560.0560.0000.0000.0000.000
198B200ALA00.0350.01640.7120.0820.0820.0000.0000.0000.000
199B201ALA00.0090.00541.275-0.009-0.0090.0000.0000.0000.000
200B202ILE00.0020.00835.5860.1090.1090.0000.0000.0000.000
201B203ALA00.0160.00037.8360.1490.1490.0000.0000.0000.000
202B204LYS10.7980.88039.952-7.631-7.6310.0000.0000.0000.000
203B205SER00.014-0.00236.3990.1220.1220.0000.0000.0000.000
204B206LEU0-0.019-0.02433.7980.1310.1310.0000.0000.0000.000
205B207LYS10.9350.97236.700-7.614-7.6140.0000.0000.0000.000
206B208ASP-1-0.719-0.81338.4887.8587.8580.0000.0000.0000.000
207B209VAL00.008-0.00232.5160.0660.0660.0000.0000.0000.000
208B210GLU-1-0.850-0.91434.9869.2569.2560.0000.0000.0000.000
209B211GLN0-0.040-0.00936.786-0.133-0.1330.0000.0000.0000.000
210B212LEU0-0.0290.00433.636-0.112-0.1120.0000.0000.0000.000
211B213LYS10.8050.88136.834-8.103-8.1030.0000.0000.0000.000
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