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: 14JJZ

Calculation Name: 4DQZ-B-Xray321

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4DQZ

Chain ID: B

ChEMBL ID:

UniProt ID: A3DJ37

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 178
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -1870730.968369
FMO2-HF: Nuclear repulsion 1801602.931564
FMO2-HF: Total energy -69128.036805
FMO2-MP2: Total energy -69328.601533


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:MET )


Summations of interaction energy for fragment #1(B:1:MET )
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.
-23.954-11.74817.311-10.308-19.21-0.045
Interaction energy analysis for fragmet #1(B:1:MET )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.029 / q_NPA : 0.014
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].
3B3LEU 00.0160.0213.796-0.1612.135-0.015-1.115-1.1670.002
4B4THR 0-0.027-0.0235.522-0.297-0.2970.0000.0000.0000.000
5B5ILE 0-0.016-0.0099.2380.2270.2270.0000.0000.0000.000
6B6THR 0-0.027-0.02112.280-0.093-0.0930.0000.0000.0000.000
7B7TYR 0-0.015-0.01215.7250.0540.0540.0000.0000.0000.000
8B8THR 00.008-0.02219.162-0.030-0.0300.0000.0000.0000.000
9B9GLN 0-0.0020.01822.527-0.013-0.0130.0000.0000.0000.000
10B10PRO 00.0360.00025.3240.0040.0040.0000.0000.0000.000
11B11PRO 0-0.0440.03327.1860.0000.0000.0000.0000.0000.000
12B12ALA 00.0750.03321.9860.0100.0100.0000.0000.0000.000
13B13THR 0-0.015-0.02621.7630.0060.0060.0000.0000.0000.000
14B14ASP -1-0.867-0.95122.7270.0610.0610.0000.0000.0000.000
15B15LEU 0-0.041-0.02215.4290.0250.0250.0000.0000.0000.000
16B16GLY 00.0150.00118.8210.0220.0220.0000.0000.0000.000
17B17TYR 0-0.038-0.02520.1390.0130.0130.0000.0000.0000.000
18B18LEU 00.0020.00019.6050.0250.0250.0000.0000.0000.000
19B19LEU 0-0.031-0.01713.8110.0540.0540.0000.0000.0000.000
20B20HIS 0-0.073-0.02717.169-0.002-0.0020.0000.0000.0000.000
21B21LYS 10.8730.94915.092-0.182-0.1820.0000.0000.0000.000
22B22ASN 00.0100.00718.397-0.029-0.0290.0000.0000.0000.000
23B23PRO 00.0910.03418.762-0.025-0.0250.0000.0000.0000.000
24B24SER 0-0.041-0.02019.653-0.038-0.0380.0000.0000.0000.000
25B25ARG 10.8670.92420.1330.0550.0550.0000.0000.0000.000
26B26PRO 00.0450.03715.4360.0170.0170.0000.0000.0000.000
27B27GLN 0-0.0120.00114.5590.0450.0450.0000.0000.0000.000
28B28THR 00.010-0.00111.527-0.110-0.1100.0000.0000.0000.000
29B29PHE 0-0.069-0.03711.8990.1050.1050.0000.0000.0000.000
30B30GLU -1-0.848-0.92011.631-0.122-0.1220.0000.0000.0000.000
31B31LEU 0-0.065-0.0488.9370.0970.0970.0000.0000.0000.000
32B32ASN 00.006-0.00412.754-0.145-0.1450.0000.0000.0000.000
33B33HIS 0-0.005-0.01111.7280.1860.1860.0000.0000.0000.000
34B34GLY 00.1330.0748.8830.0810.0810.0000.0000.0000.000
35B35LYS 10.8890.9488.3200.3980.3980.0000.0000.0000.000
36B36ALA 00.0300.0227.016-0.115-0.1150.0000.0000.0000.000
37B37HIS 0-0.026-0.0097.5030.1440.1440.0000.0000.0000.000
38B38ILE 00.0000.0028.894-0.136-0.1360.0000.0000.0000.000
39B39PHE 00.001-0.01310.4600.0670.0670.0000.0000.0000.000
40B40TYR 00.0460.01313.351-0.005-0.0050.0000.0000.0000.000
41B41PRO 0-0.046-0.00413.2820.0180.0180.0000.0000.0000.000
42B42GLU -1-0.831-0.91216.367-0.171-0.1710.0000.0000.0000.000
43B43ALA 00.001-0.00918.7260.0290.0290.0000.0000.0000.000
44B44THR 00.0220.01621.3230.0140.0140.0000.0000.0000.000
45B45SER 00.041-0.00724.0580.0130.0130.0000.0000.0000.000
46B46GLU -1-0.887-0.93225.815-0.026-0.0260.0000.0000.0000.000
47B47ARG 10.8750.92818.5660.1470.1470.0000.0000.0000.000
48B48CYS 0-0.086-0.01219.191-0.012-0.0120.0000.0000.0000.000
49B49THR 00.0440.01713.4630.0430.0430.0000.0000.0000.000
50B50VAL 0-0.0300.00711.197-0.053-0.0530.0000.0000.0000.000
51B51ALA 00.007-0.0169.455-0.006-0.0060.0000.0000.0000.000
52B52LEU 0-0.018-0.0206.4410.1650.1650.0000.0000.0000.000
53B53LEU 0-0.009-0.0014.703-0.499-0.4460.000-0.028-0.0240.000
54B54LEU 0-0.048-0.0292.042-0.0721.8632.228-1.501-2.6630.005
55B55ASP -1-0.915-0.9552.930-4.885-3.2370.161-0.923-0.887-0.010
56B56ILE 0-0.036-0.0244.4860.5660.7830.001-0.022-0.1960.000
57B57ASP -1-0.873-0.9327.086-0.237-0.2370.0000.0000.0000.000
58B58NME 0-0.066-0.02610.8100.0470.0470.0000.0000.0000.000
59B86ACE 00.1040.0473.192-0.295-0.1250.031-0.064-0.1380.000
60B87SER 0-0.048-0.0414.058-0.255-0.1580.001-0.010-0.0870.000
61B88PHE 00.0310.0254.8710.1350.1350.0000.0000.0000.000
62B89MET 00.0890.0402.074-1.727-2.9906.147-1.227-3.6580.010
63B90SER 0-0.0030.0024.866-1.221-1.1270.001-0.043-0.0510.000
64B91VAL 0-0.020-0.0098.029-0.599-0.5990.0000.0000.0000.000
65B92ALA 00.0230.0136.690-0.426-0.4260.0000.0000.0000.000
66B93ILE 00.017-0.0036.558-0.450-0.4500.0000.0000.0000.000
67B94SER 0-0.060-0.0239.534-0.372-0.3720.0000.0000.0000.000
68B95ARG 10.8900.95512.074-0.520-0.5200.0000.0000.0000.000
69B96VAL 0-0.085-0.03610.732-0.167-0.1670.0000.0000.0000.000
70B97PHE 00.029-0.0049.462-0.135-0.1350.0000.0000.0000.000
71B98GLY 00.0730.04014.0860.0230.0230.0000.0000.0000.000
72B99THR 0-0.013-0.01816.6730.0010.0010.0000.0000.0000.000
73B100ALA 00.0980.10616.191-0.010-0.0100.0000.0000.0000.000
74B101MET 0-0.032-0.00913.2550.0150.0150.0000.0000.0000.000
75B102SER 0-0.135-0.10417.367-0.035-0.0350.0000.0000.0000.000
76B103GLY 00.0370.00920.516-0.024-0.0240.0000.0000.0000.000
77B104LYS 10.8790.94922.115-0.275-0.2750.0000.0000.0000.000
78B105CYS 00.0410.01822.6500.0040.0040.0000.0000.0000.000
79B106LYS 10.9270.96724.704-0.118-0.1180.0000.0000.0000.000
80B107GLU -1-0.903-0.96225.7750.0970.0970.0000.0000.0000.000
81B108LYS 10.9450.97025.745-0.076-0.0760.0000.0000.0000.000
82B109PRO 0-0.0070.01526.6600.0160.0160.0000.0000.0000.000
83B110GLU -1-0.825-0.93827.8750.1230.1230.0000.0000.0000.000
84B111LEU 0-0.006-0.00424.2460.0100.0100.0000.0000.0000.000
85B112ALA 0-0.0050.00622.8400.0210.0210.0000.0000.0000.000
86B113ALA 0-0.059-0.01723.6490.0310.0310.0000.0000.0000.000
87B114ILE 0-0.0180.00625.5830.0070.0070.0000.0000.0000.000
88B115LYS 10.8950.94623.076-0.168-0.1680.0000.0000.0000.000
89B116LEU 0-0.012-0.00720.891-0.028-0.0280.0000.0000.0000.000
90B117PRO 00.0420.02121.1210.0260.0260.0000.0000.0000.000
91B118LEU 0-0.056-0.02416.280-0.017-0.0170.0000.0000.0000.000
92B119LYS 10.9980.99815.2600.0010.0010.0000.0000.0000.000
93B120ALA 0-0.0070.00010.372-0.015-0.0150.0000.0000.0000.000
94B121LYS 10.9360.9708.5900.5110.5110.0000.0000.0000.000
95B122ILE 00.0440.0213.693-0.4870.0590.276-0.143-0.6790.000
96B123MET 0-0.028-0.0154.293-0.3660.0290.000-0.087-0.3070.000
97B124MET 0-0.002-0.0022.232-4.777-3.8354.868-2.442-3.369-0.028
98B125LEU 00.0310.0182.503-5.760-2.1482.564-2.323-3.853-0.023
99B126PRO 0-0.0180.0022.643-0.2410.1200.781-0.084-1.058-0.001
100B127CYS 00.0340.0295.4200.2400.2400.0000.0000.0000.000
101B128LYS 10.9740.9688.0640.0390.0390.0000.0000.0000.000
102B129GLY 00.0130.00911.318-0.019-0.0190.0000.0000.0000.000
103B130GLY 00.0970.02012.1850.0140.0140.0000.0000.0000.000
104B131GLU -1-0.882-0.96212.2420.0560.0560.0000.0000.0000.000
105B132GLU -1-0.895-0.95213.7560.1580.1580.0000.0000.0000.000
106B133ILE 0-0.052-0.02511.6160.0320.0320.0000.0000.0000.000
107B134ILE 00.010-0.0029.4900.0930.0930.0000.0000.0000.000
108B135TYR 00.0250.00712.2540.0810.0810.0000.0000.0000.000
109B136ARG 10.8610.91015.749-0.229-0.2290.0000.0000.0000.000
110B137LEU 0-0.029-0.00910.9350.0120.0120.0000.0000.0000.000
111B138PHE 0-0.011-0.0128.9310.0640.0640.0000.0000.0000.000
112B139GLU -1-0.851-0.92814.8600.1800.1800.0000.0000.0000.000
113B140PRO 0-0.055-0.02017.720-0.023-0.0230.0000.0000.0000.000
114B141LEU 0-0.076-0.03115.398-0.008-0.0080.0000.0000.0000.000
115B142GLY 0-0.029-0.00718.994-0.005-0.0050.0000.0000.0000.000
116B143TYR 0-0.118-0.07215.020-0.019-0.0190.0000.0000.0000.000
117B144LYS 10.9940.99617.999-0.081-0.0810.0000.0000.0000.000
118B145VAL 0-0.024-0.03113.6120.0290.0290.0000.0000.0000.000
119B146ASP -1-0.970-0.97414.409-0.091-0.0910.0000.0000.0000.000
120B147VAL 0-0.0040.00311.4120.0570.0570.0000.0000.0000.000
121B148GLU -1-0.873-0.92311.363-0.504-0.5040.0000.0000.0000.000
122B149GLY 00.003-0.01110.613-0.051-0.0510.0000.0000.0000.000
123B150TYR 0-0.028-0.0406.992-0.203-0.2030.0000.0000.0000.000
124B151NME 0-0.0750.04910.419-0.023-0.0230.0000.0000.0000.000
125B162ACE 00.001-0.01111.8270.0060.0060.0000.0000.0000.000
126B163ARG 00.0640.04710.2450.0440.0440.0000.0000.0000.000
127B164TYR 0-0.095-0.0414.767-0.0780.0540.000-0.007-0.1240.000
128B165TYR 0-0.069-0.1116.5170.1260.1260.0000.0000.0000.000
129B166THR 0-0.0220.0025.978-0.332-0.3320.0000.0000.0000.000
130B167VAL 00.0410.0427.4940.0650.0650.0000.0000.0000.000
131B168SER 0-0.032-0.0209.2010.0120.0120.0000.0000.0000.000
132B169LEU 0-0.0090.00810.4910.0310.0310.0000.0000.0000.000
133B170GLU -1-0.937-0.98313.9950.0330.0330.0000.0000.0000.000
134B171GLY 00.0500.02517.3070.0070.0070.0000.0000.0000.000
135B172GLU -1-0.941-0.96719.6000.1330.1330.0000.0000.0000.000
136B173VAL 00.0140.01716.9760.0020.0020.0000.0000.0000.000
137B174ARG 10.8780.91820.411-0.342-0.3420.0000.0000.0000.000
138B175VAL 00.0650.02216.2580.0500.0500.0000.0000.0000.000
139B176ARG 10.8840.94216.072-0.239-0.2390.0000.0000.0000.000
140B177ASP -1-0.805-0.88916.5000.4890.4890.0000.0000.0000.000
141B178LEU 00.0220.03612.4580.0740.0740.0000.0000.0000.000
142B179LEU 0-0.031-0.03211.4490.1880.1880.0000.0000.0000.000
143B180ASN 00.0360.01611.5580.3070.3070.0000.0000.0000.000
144B181HIS 00.0990.07612.7630.1340.1340.0000.0000.0000.000
145B182ILE 00.0190.0216.6590.1440.1440.0000.0000.0000.000
146B183TYR 0-0.060-0.0307.9880.4240.4240.0000.0000.0000.000
147B184VAL 00.0040.0019.6600.0790.0790.0000.0000.0000.000
148B185LEU 00.0200.0069.920-0.022-0.0220.0000.0000.0000.000
149B186ILE 0-0.0070.0053.426-0.7090.0580.266-0.219-0.8150.000
150B187PRO 0-0.060-0.0435.566-0.487-0.4870.0000.0000.0000.000
151B188VAL 00.0140.0227.162-0.272-0.2720.0000.0000.0000.000
152B189LEU 0-0.029-0.0056.327-0.141-0.1410.0000.0000.0000.000
153B190ASP -1-0.911-0.9484.153-0.813-0.6090.001-0.070-0.1340.000
154B191NME 0-0.078-0.0477.006-0.085-0.0850.0000.0000.0000.000
155B201ACE 0-0.010-0.01817.5000.0030.0030.0000.0000.0000.000
156B202ILE 00.0260.00818.326-0.004-0.0040.0000.0000.0000.000
157B203ASP -1-0.781-0.89719.7270.4320.4320.0000.0000.0000.000
158B204LYS 10.9050.96412.140-0.972-0.9720.0000.0000.0000.000
159B205LEU 00.0440.02915.7680.0360.0360.0000.0000.0000.000
160B206PHE 0-0.030-0.00417.409-0.025-0.0250.0000.0000.0000.000
161B207GLN 0-0.031-0.03019.1150.0280.0280.0000.0000.0000.000
162B208HIS 10.8360.90815.425-0.746-0.7460.0000.0000.0000.000
163B209GLY 00.0730.04916.9820.0450.0450.0000.0000.0000.000
164B210GLU -1-0.973-0.99318.6270.3180.3180.0000.0000.0000.000
165B211GLY 0-0.028-0.01121.2090.0070.0070.0000.0000.0000.000
166B212TRP 0-0.007-0.02314.9410.0090.0090.0000.0000.0000.000
167B213LEU 00.0020.02517.924-0.014-0.0140.0000.0000.0000.000
168B214VAL 0-0.023-0.02220.425-0.019-0.0190.0000.0000.0000.000
169B215ASP -1-0.913-0.96823.9450.2390.2390.0000.0000.0000.000
170B216HIS 0-0.0040.00216.612-0.034-0.0340.0000.0000.0000.000
171B217PRO 00.0110.00220.806-0.006-0.0060.0000.0000.0000.000
172B218GLU -1-0.785-0.87417.3750.2730.2730.0000.0000.0000.000
173B219LYS 10.8450.92118.188-0.253-0.2530.0000.0000.0000.000
174B220GLU -1-0.972-0.97619.5580.2950.2950.0000.0000.0000.000
175B221LEU 0-0.0200.00614.6560.0000.0000.0000.0000.0000.000
176B222ILE 0-0.062-0.03414.1560.0440.0440.0000.0000.0000.000
177B223THR 0-0.048-0.04715.4760.0510.0510.0000.0000.0000.000
178B224NME 0-0.0180.01017.315-0.019-0.0190.0000.0000.0000.000