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

tag_button

FMODB ID: 3974L

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 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 231
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2778380.351272
FMO2-HF: Nuclear repulsion 2687448.146032
FMO2-HF: Total energy -90932.20524
FMO2-MP2: Total energy -91199.735562


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.
-128.512-123.5550.436-2.51-2.8840.02
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 : -0.944 / q_NPA : -0.982
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].
3B5VAL00.0150.0182.773-20.037-15.2510.437-2.497-2.7270.020
4B6PHE0-0.032-0.0224.6931.1371.308-0.001-0.013-0.1570.000
5B7TYR00.010-0.0145.494-4.980-4.9800.0000.0000.0000.000
6B8ASP-1-0.842-0.90510.29518.33718.3370.0000.0000.0000.000
7B9VAL0-0.102-0.06913.3381.3791.3790.0000.0000.0000.000
8B10ALA00.0050.02115.909-1.031-1.0310.0000.0000.0000.000
9B11SER00.0360.01119.119-0.254-0.2540.0000.0000.0000.000
10B12THR0-0.023-0.01022.344-0.434-0.4340.0000.0000.0000.000
11B13GLY00.0320.01924.3570.3500.3500.0000.0000.0000.000
12B14ALA0-0.017-0.01927.087-0.294-0.2940.0000.0000.0000.000
13B15ASN0-0.037-0.02726.839-0.083-0.0830.0000.0000.0000.000
14B16GLY00.0640.04229.324-0.301-0.3010.0000.0000.0000.000
15B17PHE0-0.099-0.05427.296-0.069-0.0690.0000.0000.0000.000
16B18ASP-1-0.848-0.91629.8019.3949.3940.0000.0000.0000.000
17B19PRO0-0.035-0.01829.8500.0000.0000.0000.0000.0000.000
18B20ASP-1-0.834-0.94331.6449.1049.1040.0000.0000.0000.000
19B21ALA00.0080.00934.351-0.183-0.1830.0000.0000.0000.000
20B22GLY00.013-0.00331.529-0.071-0.0710.0000.0000.0000.000
21B23TYR0-0.081-0.05532.5680.2250.2250.0000.0000.0000.000
22B24MET00.0150.01933.681-0.181-0.1810.0000.0000.0000.000
23B25ASP-1-0.864-0.93133.1609.5959.5950.0000.0000.0000.000
24B26PHE0-0.027-0.01330.1600.0590.0590.0000.0000.0000.000
25B27CYS00.033-0.00433.467-0.060-0.0600.0000.0000.0000.000
26B28VAL0-0.013-0.00236.321-0.149-0.1490.0000.0000.0000.000
27B29LYS10.8630.93431.016-10.244-10.2440.0000.0000.0000.000
28B30ASN0-0.048-0.03132.1030.2250.2250.0000.0000.0000.000
29B31ALA0-0.0040.00935.2610.0120.0120.0000.0000.0000.000
30B32GLU-1-0.918-0.96237.9077.9787.9780.0000.0000.0000.000
31B33SER0-0.034-0.01134.6240.0050.0050.0000.0000.0000.000
32B34LEU0-0.079-0.01932.3830.2720.2720.0000.0000.0000.000
33B35ASN00.0760.01934.908-0.136-0.1360.0000.0000.0000.000
34B36LEU00.0650.02934.5290.3620.3620.0000.0000.0000.000
35B37ALA00.0160.02233.7510.3020.3020.0000.0000.0000.000
36B38ALA00.0170.00531.3750.3720.3720.0000.0000.0000.000
37B39VAL00.0300.01029.7390.5230.5230.0000.0000.0000.000
38B40ARG10.9030.94629.065-9.443-9.4430.0000.0000.0000.000
39B41ILE0-0.0400.00926.6010.4480.4480.0000.0000.0000.000
40B42PHE00.0170.02323.3410.7450.7450.0000.0000.0000.000
41B43PHE0-0.002-0.01424.1960.7620.7620.0000.0000.0000.000
42B44LEU0-0.029-0.00124.5420.4450.4450.0000.0000.0000.000
43B45ASN0-0.117-0.06621.5160.9290.9290.0000.0000.0000.000
44B46ALA00.0790.05420.4600.7560.7560.0000.0000.0000.000
45B47ALA0-0.012-0.02516.7780.8510.8510.0000.0000.0000.000
46B48LYS10.9510.97415.645-13.283-13.2830.0000.0000.0000.000
47B49ALA00.0470.02015.8161.1311.1310.0000.0000.0000.000
48B50LYS10.9080.96314.112-17.644-17.6440.0000.0000.0000.000
49B51ALA00.0470.02711.3581.4081.4080.0000.0000.0000.000
50B52ALA0-0.0170.00011.1652.2512.2510.0000.0000.0000.000
51B53LEU00.0130.00513.4380.1590.1590.0000.0000.0000.000
52B54SER0-0.063-0.0458.5120.6980.6980.0000.0000.0000.000
53B55ARG10.8940.9548.416-27.726-27.7260.0000.0000.0000.000
54B56LYS10.9600.97710.319-17.496-17.4960.0000.0000.0000.000
55B57PRO00.0440.03212.4580.3880.3880.0000.0000.0000.000
56B58GLU-1-0.910-0.95013.63917.44617.4460.0000.0000.0000.000
57B59ARG10.9670.97316.498-15.143-15.1430.0000.0000.0000.000
58B60LYS10.9550.98318.643-12.332-12.3320.0000.0000.0000.000
59B61ALA00.001-0.00118.8870.5320.5320.0000.0000.0000.000
60B62ASN00.0470.01521.001-0.145-0.1450.0000.0000.0000.000
61B63PRO0-0.0420.00821.304-0.036-0.0360.0000.0000.0000.000
62B64LYS10.9800.97723.284-10.868-10.8680.0000.0000.0000.000
63B65PHE0-0.019-0.00522.6230.4620.4620.0000.0000.0000.000
64B66GLY00.053-0.00127.426-0.360-0.3600.0000.0000.0000.000
65B67GLU-1-0.988-1.00430.6309.1259.1250.0000.0000.0000.000
66B68TRP00.0290.03028.1450.0180.0180.0000.0000.0000.000
67B69GLN0-0.050-0.03527.1410.7820.7820.0000.0000.0000.000
68B70VAL00.0250.01525.574-0.273-0.2730.0000.0000.0000.000
69B71GLU-1-0.910-0.95425.33912.34612.3460.0000.0000.0000.000
70B72VAL0-0.068-0.01720.317-0.042-0.0420.0000.0000.0000.000
71B73ILE0-0.017-0.02919.5940.1550.1550.0000.0000.0000.000
72B74ASN0-0.055-0.02913.8831.0691.0690.0000.0000.0000.000
73B75ASN00.015-0.00814.534-0.409-0.4090.0000.0000.0000.000
74B76HIS0-0.011-0.00611.9780.8340.8340.0000.0000.0000.000
75B77PHE00.0020.0089.3364.2544.2540.0000.0000.0000.000
76B78PRO0-0.022-0.0085.957-2.440-2.4400.0000.0000.0000.000
77B79GLY00.0560.0348.230-1.979-1.9790.0000.0000.0000.000
78B80ASN0-0.026-0.01410.804-1.827-1.8270.0000.0000.0000.000
79B81ARG10.9290.9716.808-40.541-40.5410.0000.0000.0000.000
80B82ASN00.0250.00713.578-1.731-1.7310.0000.0000.0000.000
81B83ASN0-0.061-0.02816.613-0.883-0.8830.0000.0000.0000.000
82B84PRO0-0.0020.01218.7340.0630.0630.0000.0000.0000.000
83B85ILE0-0.024-0.02119.935-0.144-0.1440.0000.0000.0000.000
84B86GLY00.0580.03623.914-0.282-0.2820.0000.0000.0000.000
85B87ASN0-0.113-0.08627.573-0.143-0.1430.0000.0000.0000.000
86B88ASN00.1060.05629.473-0.184-0.1840.0000.0000.0000.000
87B89ASP-1-0.905-0.93325.31312.19012.1900.0000.0000.0000.000
88B90LEU00.0160.00524.9310.0700.0700.0000.0000.0000.000
89B91THR00.0280.01819.7370.4080.4080.0000.0000.0000.000
90B92ILE00.0490.00118.195-0.394-0.3940.0000.0000.0000.000
91B93HIS0-0.092-0.04920.0820.1500.1500.0000.0000.0000.000
92B94ARG10.9290.96021.711-13.352-13.3520.0000.0000.0000.000
93B95LEU00.0550.04923.893-0.456-0.4560.0000.0000.0000.000
94B96SER0-0.020-0.01823.574-0.414-0.4140.0000.0000.0000.000
95B97GLY00.0210.00925.620-0.369-0.3690.0000.0000.0000.000
96B98TYR00.003-0.01127.980-0.305-0.3050.0000.0000.0000.000
97B99LEU00.0220.00127.406-0.393-0.3930.0000.0000.0000.000
98B100ALA0-0.0090.00529.438-0.319-0.3190.0000.0000.0000.000
99B101ARG10.8960.96031.226-9.291-9.2910.0000.0000.0000.000
100B102TRP00.0350.02333.595-0.148-0.1480.0000.0000.0000.000
101B103VAL0-0.012-0.01633.159-0.238-0.2380.0000.0000.0000.000
102B104LEU0-0.044-0.01635.775-0.209-0.2090.0000.0000.0000.000
103B105ASP-1-0.857-0.92837.6848.2988.2980.0000.0000.0000.000
104B106GLN0-0.016-0.00837.968-0.254-0.2540.0000.0000.0000.000
105B107TYR0-0.031-0.02139.881-0.120-0.1200.0000.0000.0000.000
106B108ASN0-0.023-0.03441.392-0.243-0.2430.0000.0000.0000.000
107B109GLU-1-1.004-0.96843.5307.2717.2710.0000.0000.0000.000
108B110ASN0-0.025-0.01045.421-0.246-0.2460.0000.0000.0000.000
109B111ASP-1-0.897-0.94547.1156.6926.6920.0000.0000.0000.000
110B112ASP-1-0.941-0.97648.2176.4036.4030.0000.0000.0000.000
111B113GLU-1-0.925-0.96647.3936.7896.7890.0000.0000.0000.000
112B114SER0-0.024-0.02147.1870.1790.1790.0000.0000.0000.000
113B115GLN00.0490.01743.4380.1230.1230.0000.0000.0000.000
114B116HIS00.001-0.00442.7690.2720.2720.0000.0000.0000.000
115B117GLU-1-0.961-0.96941.9677.3517.3510.0000.0000.0000.000
116B118LEU00.0080.04840.6780.2400.2400.0000.0000.0000.000
117B119ILE00.0140.00637.3030.3200.3200.0000.0000.0000.000
118B120ARG10.9450.96637.231-7.247-7.2470.0000.0000.0000.000
119B121THR0-0.053-0.04637.1080.1860.1860.0000.0000.0000.000
120B122THR0-0.084-0.04634.9720.2210.2210.0000.0000.0000.000
121B123ILE0-0.019-0.01331.8600.4130.4130.0000.0000.0000.000
122B124ILE00.0300.01629.757-0.072-0.0720.0000.0000.0000.000
123B125ASN00.014-0.00427.3350.8750.8750.0000.0000.0000.000
124B126PRO00.001-0.00824.667-0.103-0.1030.0000.0000.0000.000
125B127ILE00.002-0.00222.7210.0790.0790.0000.0000.0000.000
126B128ALA00.0030.04125.986-0.054-0.0540.0000.0000.0000.000
127B129GLU-1-0.734-0.86229.5609.6039.6030.0000.0000.0000.000
128B130SER0-0.154-0.07826.0420.0350.0350.0000.0000.0000.000
129B131ASN0-0.079-0.08026.4590.3230.3230.0000.0000.0000.000
130B132GLY0-0.024-0.00429.830-0.263-0.2630.0000.0000.0000.000
131B133VAL0-0.049-0.01832.389-0.325-0.3250.0000.0000.0000.000
132B134GLY00.0930.03733.3040.2500.2500.0000.0000.0000.000
133B135TRP00.022-0.01334.904-0.126-0.1260.0000.0000.0000.000
134B136ASP-1-0.923-0.95337.6958.1588.1580.0000.0000.0000.000
135B137SER0-0.057-0.02537.432-0.082-0.0820.0000.0000.0000.000
136B138GLY00.003-0.00139.539-0.089-0.0890.0000.0000.0000.000
137B139PRO00.0410.02137.8170.2950.2950.0000.0000.0000.000
138B140GLU-1-0.864-0.94536.2268.4228.4220.0000.0000.0000.000
139B141ILE00.0040.01335.0480.3820.3820.0000.0000.0000.000
140B142TYR0-0.037-0.00332.5910.4990.4990.0000.0000.0000.000
141B143LEU00.020-0.00631.6260.4960.4960.0000.0000.0000.000
142B144SER00.005-0.01730.3980.3740.3740.0000.0000.0000.000
143B145PHE0-0.032-0.01527.7660.5060.5060.0000.0000.0000.000
144B146PHE0-0.0610.00225.7100.6920.6920.0000.0000.0000.000
145B147PRO0-0.035-0.02221.6570.0700.0700.0000.0000.0000.000
146B148GLY00.0240.00324.282-0.108-0.1080.0000.0000.0000.000
147B149THR00.0350.00925.587-0.391-0.3910.0000.0000.0000.000
148B150GLU-1-0.825-0.92524.67112.85712.8570.0000.0000.0000.000
149B151MET0-0.117-0.03727.167-0.037-0.0370.0000.0000.0000.000
150B152PHE0-0.0030.00229.752-0.243-0.2430.0000.0000.0000.000
151B153LEU00.0070.00530.899-0.202-0.2020.0000.0000.0000.000
152B154GLU-1-0.937-0.96334.2097.8727.8720.0000.0000.0000.000
153B155THR00.0330.01836.005-0.162-0.1620.0000.0000.0000.000
154B156PHE0-0.0100.00633.276-0.077-0.0770.0000.0000.0000.000
155B157LYS10.9830.98836.078-7.722-7.7220.0000.0000.0000.000
156B158PHE0-0.025-0.03435.100-0.074-0.0740.0000.0000.0000.000
157B159TYR0-0.050-0.01234.0790.2490.2490.0000.0000.0000.000
158B160PRO00.0030.01029.5660.2290.2290.0000.0000.0000.000
159B161LEU0-0.045-0.01729.3110.4430.4430.0000.0000.0000.000
160B162THR00.015-0.00730.6220.3380.3380.0000.0000.0000.000
161B163ILE00.0460.04028.2910.1100.1100.0000.0000.0000.000
162B164GLY0-0.014-0.01327.0660.2790.2790.0000.0000.0000.000
163B165ILE00.000-0.01127.6120.2310.2310.0000.0000.0000.000
164B166HIS0-0.0050.00330.047-0.056-0.0560.0000.0000.0000.000
165B167ARG10.9470.94823.854-13.101-13.1010.0000.0000.0000.000
166B168VAL0-0.038-0.00924.9230.2470.2470.0000.0000.0000.000
167B169LYS10.9500.96926.996-9.290-9.2900.0000.0000.0000.000
168B170GLN0-0.0050.01928.793-0.301-0.3010.0000.0000.0000.000
169B171GLY0-0.016-0.00425.5870.0930.0930.0000.0000.0000.000
170B172MET0-0.083-0.02824.2400.4360.4360.0000.0000.0000.000
171B173MET0-0.086-0.02921.5190.6620.6620.0000.0000.0000.000
172B174ASP-1-0.785-0.90417.60016.93616.9360.0000.0000.0000.000
173B175PRO00.034-0.00420.6130.1070.1070.0000.0000.0000.000
174B176GLN0-0.0120.00917.3830.2520.2520.0000.0000.0000.000
175B177TYR0-0.066-0.03914.5410.1080.1080.0000.0000.0000.000
176B178LEU00.0260.01620.982-0.299-0.2990.0000.0000.0000.000
177B179LYS10.9520.98721.809-14.707-14.7070.0000.0000.0000.000
178B180LYS10.8800.93218.578-17.084-17.0840.0000.0000.0000.000
179B181ALA00.0980.04424.145-0.327-0.3270.0000.0000.0000.000
180B182LEU00.0210.01127.243-0.370-0.3700.0000.0000.0000.000
181B183ARG10.8900.95122.752-13.494-13.4940.0000.0000.0000.000
182B184GLN0-0.0190.00826.523-0.420-0.4200.0000.0000.0000.000
183B185ARG10.9971.00630.624-9.489-9.4890.0000.0000.0000.000
184B186TYR0-0.0020.00334.3570.1380.1380.0000.0000.0000.000
185B187GLY00.1000.05336.928-0.260-0.2600.0000.0000.0000.000
186B188THR0-0.012-0.00738.5200.1010.1010.0000.0000.0000.000
187B189LEU0-0.067-0.02138.935-0.106-0.1060.0000.0000.0000.000
188B190THR00.031-0.00335.2080.1800.1800.0000.0000.0000.000
189B191ALA00.0900.03732.642-0.166-0.1660.0000.0000.0000.000
190B192ASP-1-0.890-0.95434.7498.9628.9620.0000.0000.0000.000
191B193LYS10.8870.95736.985-7.951-7.9510.0000.0000.0000.000
192B194TRP0-0.015-0.02032.498-0.250-0.2500.0000.0000.0000.000
193B195MET0-0.012-0.01833.5410.0260.0260.0000.0000.0000.000
194B196SER0-0.0040.01237.684-0.147-0.1470.0000.0000.0000.000
195B197GLN0-0.002-0.00341.113-0.098-0.0980.0000.0000.0000.000
196B198LYS10.9190.97140.194-7.639-7.6390.0000.0000.0000.000
197B199VAL00.0640.03040.0610.1550.1550.0000.0000.0000.000
198B200ALA00.0190.00441.3280.0850.0850.0000.0000.0000.000
199B201ALA0-0.024-0.02142.0280.0150.0150.0000.0000.0000.000
200B202ILE00.0280.02636.5000.0880.0880.0000.0000.0000.000
201B203ALA00.0270.01138.7690.1350.1350.0000.0000.0000.000
202B204LYS10.9500.98040.391-7.308-7.3080.0000.0000.0000.000
203B205SER00.0340.01637.4200.1160.1160.0000.0000.0000.000
204B206LEU0-0.023-0.02134.6160.1650.1650.0000.0000.0000.000
205B207LYS10.9540.97537.430-7.430-7.4300.0000.0000.0000.000
206B208ASP-1-0.817-0.89639.5367.8437.8430.0000.0000.0000.000
207B209VAL0-0.002-0.01033.1580.0940.0940.0000.0000.0000.000
208B210GLU-1-0.971-0.99935.6618.9898.9890.0000.0000.0000.000
209B211GLN0-0.075-0.02337.001-0.033-0.0330.0000.0000.0000.000
210B212LEU0-0.0130.01034.438-0.123-0.1230.0000.0000.0000.000
211B213LYS10.9610.97037.162-7.865-7.8650.0000.0000.0000.000
212B214TRP0-0.020-0.01228.7460.4460.4460.0000.0000.0000.000
213B215GLY0-0.0130.00433.244-0.046-0.0460.0000.0000.0000.000
214B216LYS10.9320.93824.412-12.367-12.3670.0000.0000.0000.000
215B217GLY0-0.0330.02429.2230.0810.0810.0000.0000.0000.000
216B218GLY00.0240.00629.764-0.304-0.3040.0000.0000.0000.000
217B219LEU00.008-0.01832.9690.0200.0200.0000.0000.0000.000
218B220SER0-0.0150.00335.861-0.214-0.2140.0000.0000.0000.000
219B221ASP-1-0.790-0.91238.3398.0018.0010.0000.0000.0000.000
220B222THR0-0.005-0.01641.489-0.144-0.1440.0000.0000.0000.000
221B223ALA0-0.0100.00139.734-0.144-0.1440.0000.0000.0000.000
222B224LYS10.9580.99237.950-8.516-8.5160.0000.0000.0000.000
223B225THR00.0560.02442.719-0.128-0.1280.0000.0000.0000.000
224B226PHE0-0.031-0.00943.592-0.190-0.1900.0000.0000.0000.000
225B227LEU00.0380.01340.149-0.139-0.1390.0000.0000.0000.000
226B228GLN0-0.036-0.00444.7010.0760.0760.0000.0000.0000.000
227B229LYS10.8980.93747.146-6.574-6.5740.0000.0000.0000.000
228B230PHE0-0.047-0.01946.606-0.136-0.1360.0000.0000.0000.000
229B231GLY0-0.0090.01647.8910.0160.0160.0000.0000.0000.000
230B232ILE0-0.005-0.01141.5950.1010.1010.0000.0000.0000.000
231B233ARG10.9680.99140.110-6.912-6.9120.0000.0000.0000.000