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: YVJ92

Calculation Name: 3BZB-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3BZB

Chain ID: B

ChEMBL ID:

UniProt ID: D0VWS8

Base Structure: X-ray

Registration Date: 2023-09-23

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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2272617.019025
FMO2-HF: Nuclear repulsion 2195178.980362
FMO2-HF: Total energy -77438.038663
FMO2-MP2: Total energy -77665.148893


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:29:ARG)


Summations of interaction energy for fragment #1(B:29:ARG)
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.
-115.228-110.91816.059-9.926-10.443-0.09
Interaction energy analysis for fragmet #1(B:29:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.900 / q_NPA : 0.933
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].
3B31GLU-1-0.850-0.9031.748-106.487-105.31813.546-7.515-7.201-0.082
4B32ARG10.9260.9565.08828.80028.872-0.001-0.004-0.0660.000
5B33TYR0-0.021-0.0568.632-2.503-2.5030.0000.0000.0000.000
6B34GLN00.0220.05611.0190.7290.7290.0000.0000.0000.000
7B35SER00.0720.04914.421-0.561-0.5610.0000.0000.0000.000
8B36PRO0-0.031-0.01616.6320.2500.2500.0000.0000.0000.000
9B37ALA00.0380.01318.3970.7310.7310.0000.0000.0000.000
10B38GLY0-0.021-0.01621.2580.1510.1510.0000.0000.0000.000
11B39ALA0-0.0200.00721.3740.5100.5100.0000.0000.0000.000
12B40PRO0-0.0010.00223.378-0.015-0.0150.0000.0000.0000.000
13B41LEU0-0.0080.01720.5540.2440.2440.0000.0000.0000.000
14B42GLN0-0.078-0.05820.883-1.085-1.0850.0000.0000.0000.000
15B43CYS0-0.037-0.02417.9860.0480.0480.0000.0000.0000.000
16B44SER0-0.027-0.04614.855-0.376-0.3760.0000.0000.0000.000
17B45VAL0-0.0020.01311.3130.5050.5050.0000.0000.0000.000
18B46GLN0-0.036-0.0258.861-2.471-2.4710.0000.0000.0000.000
19B47VAL00.0180.0196.4842.0262.0260.0000.0000.0000.000
20B48GLN00.002-0.0054.566-5.987-5.803-0.001-0.039-0.1440.000
21B49THR0-0.021-0.0132.070-0.7010.7492.452-1.688-2.214-0.002
22B50THR00.0130.0173.085-6.799-5.3640.063-0.680-0.818-0.006
23B62SER0-0.025-0.0217.1130.0490.0490.0000.0000.0000.000
24B63GLY00.1050.0328.6492.1172.1170.0000.0000.0000.000
25B64ALA00.0100.0029.4171.5911.5910.0000.0000.0000.000
26B65ARG10.8230.8935.39041.74241.7420.0000.0000.0000.000
27B66ALA00.0370.04211.0891.5971.5970.0000.0000.0000.000
28B67LEU00.0220.01214.1461.3581.3580.0000.0000.0000.000
29B68ALA00.0320.01313.3841.2141.2140.0000.0000.0000.000
30B69ASP-1-0.779-0.88114.403-19.946-19.9460.0000.0000.0000.000
31B70THR0-0.098-0.05116.6921.2881.2880.0000.0000.0000.000
32B71LEU0-0.006-0.00217.9910.8390.8390.0000.0000.0000.000
33B72CYS0-0.033-0.01717.6220.5600.5600.0000.0000.0000.000
34B73TRP0-0.033-0.02619.9050.8880.8880.0000.0000.0000.000
35B74GLN0-0.072-0.02022.7960.3910.3910.0000.0000.0000.000
36B75PRO00.0870.04924.0120.0080.0080.0000.0000.0000.000
37B76GLU-1-0.838-0.94125.169-11.233-11.2330.0000.0000.0000.000
38B77LEU0-0.088-0.03623.3660.2360.2360.0000.0000.0000.000
39B78ILE0-0.069-0.02821.705-0.027-0.0270.0000.0000.0000.000
40B79ALA00.0200.03625.8800.1940.1940.0000.0000.0000.000
41B80GLY0-0.051-0.03328.0440.3200.3200.0000.0000.0000.000
42B81LYS10.8370.93228.11810.41810.4180.0000.0000.0000.000
43B82THR00.0320.02928.040-0.437-0.4370.0000.0000.0000.000
44B83VAL00.003-0.02122.239-0.041-0.0410.0000.0000.0000.000
45B84CYS0-0.032-0.00222.815-0.089-0.0890.0000.0000.0000.000
46B85GLU-1-0.820-0.88715.319-19.776-19.7760.0000.0000.0000.000
47B86LEU0-0.0080.00719.3950.1570.1570.0000.0000.0000.000
48B87GLY00.002-0.00816.332-0.467-0.4670.0000.0000.0000.000
49B88ALA00.0150.00814.330-1.258-1.2580.0000.0000.0000.000
50B89GLY00.0470.03310.950-1.550-1.5500.0000.0000.0000.000
51B90ALA0-0.036-0.0237.0430.4700.4700.0000.0000.0000.000
52B91GLY00.0670.0269.0851.0221.0220.0000.0000.0000.000
53B92LEU0-0.045-0.0129.4021.0851.0850.0000.0000.0000.000
54B93VAL00.010-0.00512.1971.2731.2730.0000.0000.0000.000
55B94SER00.009-0.03114.9571.5561.5560.0000.0000.0000.000
56B95ILE0-0.043-0.01112.5571.1191.1190.0000.0000.0000.000
57B96VAL0-0.018-0.01715.1770.9070.9070.0000.0000.0000.000
58B97ALA00.044-0.00417.7780.9130.9130.0000.0000.0000.000
59B98PHE0-0.016-0.00619.9240.7640.7640.0000.0000.0000.000
60B99LEU0-0.011-0.00817.8990.6440.6440.0000.0000.0000.000
61B100ALA0-0.022-0.00421.7590.4220.4220.0000.0000.0000.000
62B101GLY0-0.033-0.01223.5980.5540.5540.0000.0000.0000.000
63B102ALA0-0.0190.00424.4000.4900.4900.0000.0000.0000.000
64B103ASP-1-0.971-0.99226.383-10.244-10.2440.0000.0000.0000.000
65B104GLN0-0.011-0.01726.3290.0100.0100.0000.0000.0000.000
66B105VAL00.0030.01420.161-0.114-0.1140.0000.0000.0000.000
67B106VAL0-0.010-0.00822.1320.0350.0350.0000.0000.0000.000
68B107ALA00.0400.03016.555-0.242-0.2420.0000.0000.0000.000
69B108THR0-0.066-0.05218.4360.5550.5550.0000.0000.0000.000
70B109ASP-1-0.776-0.88814.279-21.222-21.2220.0000.0000.0000.000
71B110TYR00.0310.00616.8371.6131.6130.0000.0000.0000.000
72B111PRO0-0.033-0.02817.147-0.407-0.4070.0000.0000.0000.000
73B112ASP-1-0.839-0.92513.336-18.213-18.2130.0000.0000.0000.000
74B113PRO0-0.019-0.00114.895-0.497-0.4970.0000.0000.0000.000
75B114GLU-1-0.903-0.9459.375-19.730-19.7300.0000.0000.0000.000
76B115ILE0-0.039-0.02210.312-1.451-1.4510.0000.0000.0000.000
77B116LEU0-0.019-0.01811.655-0.257-0.2570.0000.0000.0000.000
78B117ASN00.0080.00611.9910.8860.8860.0000.0000.0000.000
79B118SER0-0.020-0.0027.791-0.243-0.2430.0000.0000.0000.000
80B119LEU00.0070.0249.783-0.078-0.0780.0000.0000.0000.000
81B120GLU-1-0.859-0.92412.067-13.988-13.9880.0000.0000.0000.000
82B121SER0-0.029-0.02610.1780.3660.3660.0000.0000.0000.000
83B122ASN0-0.019-0.0107.946-0.035-0.0350.0000.0000.0000.000
84B123ILE00.009-0.00611.6960.5420.5420.0000.0000.0000.000
85B124ARG10.8270.89615.01915.96015.9600.0000.0000.0000.000
86B125GLU-1-1.001-0.99011.300-19.561-19.5610.0000.0000.0000.000
87B126HIS0-0.036-0.00612.280-0.204-0.2040.0000.0000.0000.000
88B138ARG10.9740.97927.9039.3049.3040.0000.0000.0000.000
89B139ALA0-0.018-0.01926.954-0.255-0.2550.0000.0000.0000.000
90B140SER00.0320.02722.094-0.023-0.0230.0000.0000.0000.000
91B141PRO00.002-0.00119.3370.3200.3200.0000.0000.0000.000
92B142LYS10.9020.96820.91011.21311.2130.0000.0000.0000.000
93B143VAL00.0250.01816.312-0.273-0.2730.0000.0000.0000.000
94B144VAL0-0.045-0.03119.4070.6300.6300.0000.0000.0000.000
95B145PRO00.0070.00519.953-0.418-0.4180.0000.0000.0000.000
96B146TYR0-0.043-0.05420.7630.6060.6060.0000.0000.0000.000
97B147ARG10.8400.92121.47511.56611.5660.0000.0000.0000.000
98B148TRP00.052-0.00217.5200.6840.6840.0000.0000.0000.000
99B149GLY0-0.031-0.00924.3040.1100.1100.0000.0000.0000.000
100B150ASP-1-0.811-0.88427.269-10.865-10.8650.0000.0000.0000.000
101B151SER0-0.020-0.00129.0080.0100.0100.0000.0000.0000.000
102B152PRO00.0620.01228.547-0.131-0.1310.0000.0000.0000.000
103B153ASP-1-0.797-0.86729.539-9.060-9.0600.0000.0000.0000.000
104B154SER00.0140.00226.8860.1040.1040.0000.0000.0000.000
105B155LEU00.0650.02724.502-0.016-0.0160.0000.0000.0000.000
106B156GLN0-0.058-0.00527.6090.2180.2180.0000.0000.0000.000
107B157ARG10.8210.87330.9849.3289.3280.0000.0000.0000.000
108B158CYS0-0.079-0.02926.3900.0980.0980.0000.0000.0000.000
109B159THR0-0.061-0.05326.024-0.057-0.0570.0000.0000.0000.000
110B160GLY00.0090.03028.9390.1240.1240.0000.0000.0000.000
111B161LEU0-0.013-0.00728.6070.1910.1910.0000.0000.0000.000
112B162GLN0-0.006-0.00631.229-0.229-0.2290.0000.0000.0000.000
113B163ARG10.8440.92830.8309.1899.1890.0000.0000.0000.000
114B164PHE00.0250.00726.9350.0810.0810.0000.0000.0000.000
115B165GLN0-0.021-0.00729.386-0.036-0.0360.0000.0000.0000.000
116B166VAL00.0160.00823.6910.0250.0250.0000.0000.0000.000
117B167VAL0-0.0030.00323.035-0.087-0.0870.0000.0000.0000.000
118B168LEU0-0.011-0.01418.6430.0320.0320.0000.0000.0000.000
119B169LEU00.016-0.00118.294-0.217-0.2170.0000.0000.0000.000
120B170ALA00.0370.01013.4200.2140.2140.0000.0000.0000.000
121B171ASP-1-0.812-0.90311.316-25.167-25.1670.0000.0000.0000.000
122B172LEU0-0.0090.01613.884-0.426-0.4260.0000.0000.0000.000
123B173LEU0-0.013-0.00916.6140.8150.8150.0000.0000.0000.000
124B174SER0-0.0090.01213.8571.0261.0260.0000.0000.0000.000
125B175PHE00.0320.01416.8180.3310.3310.0000.0000.0000.000
126B176HIS00.0710.00319.2980.1190.1190.0000.0000.0000.000
127B177GLN0-0.0180.00122.8430.5710.5710.0000.0000.0000.000
128B178ALA0-0.0040.00921.3260.3740.3740.0000.0000.0000.000
129B179HIS0-0.041-0.02520.8840.6370.6370.0000.0000.0000.000
130B180ASP-1-0.779-0.88024.516-10.501-10.5010.0000.0000.0000.000
131B181ALA00.0070.00824.8840.2310.2310.0000.0000.0000.000
132B182LEU00.0200.02820.1700.2820.2820.0000.0000.0000.000
133B183LEU00.0030.01024.5450.1310.1310.0000.0000.0000.000
134B184ARG10.8430.90027.64810.86210.8620.0000.0000.0000.000
135B185SER00.011-0.00225.3080.1530.1530.0000.0000.0000.000
136B186VAL00.0230.01224.9220.2290.2290.0000.0000.0000.000
137B187LYS10.7850.87727.3869.7229.7220.0000.0000.0000.000
138B188MET0-0.048-0.02330.2470.4160.4160.0000.0000.0000.000
139B189LEU00.0270.01825.3810.2190.2190.0000.0000.0000.000
140B190LEU00.0180.03327.964-0.004-0.0040.0000.0000.0000.000
141B191ALA0-0.008-0.02530.0460.3970.3970.0000.0000.0000.000
142B192LEU00.0140.00633.0390.0310.0310.0000.0000.0000.000
143B193PRO00.0440.01336.1950.0660.0660.0000.0000.0000.000
144B194ALA0-0.055-0.02638.0260.1090.1090.0000.0000.0000.000
145B195ASN0-0.050-0.02637.4520.2540.2540.0000.0000.0000.000
146B196ASP-1-0.748-0.89233.390-9.409-9.4090.0000.0000.0000.000
147B197PRO0-0.040-0.01035.267-0.183-0.1830.0000.0000.0000.000
148B198THR0-0.075-0.03732.540-0.057-0.0570.0000.0000.0000.000
149B199ALA0-0.0200.01630.827-0.322-0.3220.0000.0000.0000.000
150B200VAL0-0.033-0.02326.4110.0990.0990.0000.0000.0000.000
151B201ALA00.0180.00824.674-0.213-0.2130.0000.0000.0000.000
152B202LEU0-0.012-0.00221.5210.1820.1820.0000.0000.0000.000
153B203VAL0-0.003-0.00719.913-0.584-0.5840.0000.0000.0000.000
154B204THR0-0.0110.00214.9490.2330.2330.0000.0000.0000.000
155B205PHE0-0.018-0.00915.108-0.407-0.4070.0000.0000.0000.000
156B206THR0-0.013-0.02910.7620.3040.3040.0000.0000.0000.000
157B207HIS0-0.065-0.03613.8130.2640.2640.0000.0000.0000.000
158B208HIS00.0310.01110.1090.5080.5080.0000.0000.0000.000
159B209ARG10.8530.88715.46815.53815.5380.0000.0000.0000.000
160B210PRO0-0.0070.00919.229-0.085-0.0850.0000.0000.0000.000
161B211HIS00.0270.01221.5950.1480.1480.0000.0000.0000.000
162B212LEU0-0.043-0.01221.130-0.246-0.2460.0000.0000.0000.000
163B213ALA00.006-0.00123.6580.6040.6040.0000.0000.0000.000
164B214GLU-1-0.832-0.91025.643-10.423-10.4230.0000.0000.0000.000
165B215ARG00.0030.01122.068-0.155-0.1550.0000.0000.0000.000
166B216ASP-1-0.749-0.85421.378-14.589-14.5890.0000.0000.0000.000
167B217LEU00.0320.01822.013-0.351-0.3510.0000.0000.0000.000
168B218ALA0-0.058-0.02424.5970.3850.3850.0000.0000.0000.000
169B219PHE00.0470.02623.0580.3680.3680.0000.0000.0000.000
170B220PHE00.0570.01521.4540.3910.3910.0000.0000.0000.000
171B221ARG10.8200.89826.91911.04911.0490.0000.0000.0000.000
172B222LEU00.0150.01227.7880.3660.3660.0000.0000.0000.000
173B223VAL0-0.043-0.03227.1030.2750.2750.0000.0000.0000.000
174B224ASN0-0.0110.00030.1410.3280.3280.0000.0000.0000.000
175B225ALA0-0.0380.00732.8640.2970.2970.0000.0000.0000.000
176B226ASP-1-0.824-0.89433.218-8.985-8.9850.0000.0000.0000.000
177B227GLY00.0470.02334.978-0.034-0.0340.0000.0000.0000.000
178B228ALA0-0.060-0.03134.541-0.034-0.0340.0000.0000.0000.000
179B229LEU0-0.007-0.00229.5270.0160.0160.0000.0000.0000.000
180B230ILE00.0080.01932.4320.1280.1280.0000.0000.0000.000
181B231ALA0-0.028-0.01927.459-0.317-0.3170.0000.0000.0000.000
182B232GLU-1-0.753-0.84328.065-9.638-9.6380.0000.0000.0000.000
183B233PRO00.0170.00425.754-0.440-0.4400.0000.0000.0000.000
184B234TRP0-0.021-0.00820.6420.2630.2630.0000.0000.0000.000
185B235LEU00.0140.00222.7530.2900.2900.0000.0000.0000.000
186B236SER00.0030.00723.709-0.195-0.1950.0000.0000.0000.000
187B237PRO00.0150.00419.727-0.381-0.3810.0000.0000.0000.000
188B238LEU0-0.0030.01916.4150.3610.3610.0000.0000.0000.000
189B239GLN00.0400.01916.379-0.156-0.1560.0000.0000.0000.000
190B240MET00.0060.02011.285-0.495-0.4950.0000.0000.0000.000
191B256GLN0-0.014-0.01114.4930.5130.5130.0000.0000.0000.000
192B257VAL0-0.072-0.04412.551-0.558-0.5580.0000.0000.0000.000
193B258HIS00.004-0.00215.5491.1881.1880.0000.0000.0000.000
194B259ARG10.9210.93718.31014.32614.3260.0000.0000.0000.000
195B260TRP00.0140.00120.6440.9270.9270.0000.0000.0000.000
196B261ARG10.8590.91923.04910.27010.2700.0000.0000.0000.000
197B262LEU0-0.0020.00325.1310.2930.2930.0000.0000.0000.000
198B263ARG10.8670.91627.9449.4529.4520.0000.0000.0000.000
199B264TRP0-0.0020.00331.1090.1790.1790.0000.0000.0000.000
200B265ARG10.9440.97134.4708.3758.3750.0000.0000.0000.000