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: LZ2V9

Calculation Name: 3DEL-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DEL

Chain ID: B

ChEMBL ID:

UniProt ID: O84385

Base Structure: X-ray

Registration Date: 2023-09-20

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 232
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2803392.914777
FMO2-HF: Nuclear repulsion 2713174.099692
FMO2-HF: Total energy -90218.815085
FMO2-MP2: Total energy -90486.729874


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:34:GLU)


Summations of interaction energy for fragment #1(B:34:GLU)
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.
9.9636.13817.491-7.118-6.5480.045
Interaction energy analysis for fragmet #1(B:34:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.862 / q_NPA : -0.913
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].
3B36PHE00.0270.0093.340-4.962-1.8510.053-1.827-1.3380.005
4B37ILE0-0.035-0.0135.162-4.286-4.152-0.001-0.002-0.1300.000
5B38VAL00.0050.0028.383-2.302-2.3020.0000.0000.0000.000
6B39GLY00.0160.01312.181-0.579-0.5790.0000.0000.0000.000
7B40THR0-0.001-0.03814.915-1.089-1.0890.0000.0000.0000.000
8B41ASN00.023-0.00118.342-0.506-0.5060.0000.0000.0000.000
9B42ALA00.0090.02921.772-0.443-0.4430.0000.0000.0000.000
10B43THR0-0.069-0.06623.631-0.592-0.5920.0000.0000.0000.000
11B44TYR0-0.077-0.04426.177-0.477-0.4770.0000.0000.0000.000
12B45PRO00.0370.03427.0850.3660.3660.0000.0000.0000.000
13B46PRO00.0240.01727.997-0.252-0.2520.0000.0000.0000.000
14B47PHE0-0.022-0.00724.0090.4440.4440.0000.0000.0000.000
15B48GLH0-0.059-0.06921.6260.5720.5720.0000.0000.0000.000
16B49PHE0-0.030-0.00723.938-0.544-0.5440.0000.0000.0000.000
17B50VAL00.0540.02823.4070.5960.5960.0000.0000.0000.000
18B51ASP-1-0.777-0.87524.61912.19312.1930.0000.0000.0000.000
19B52LYS10.8890.92726.613-10.418-10.4180.0000.0000.0000.000
20B53ARG10.8380.92322.884-13.454-13.4540.0000.0000.0000.000
21B54GLY0-0.031-0.01724.227-0.022-0.0220.0000.0000.0000.000
22B55GLU-1-0.885-0.93719.45716.33416.3340.0000.0000.0000.000
23B56VAL0-0.008-0.01118.687-0.635-0.6350.0000.0000.0000.000
24B57VAL0-0.047-0.02919.8350.6600.6600.0000.0000.0000.000
25B58GLY00.0560.01622.276-0.404-0.4040.0000.0000.0000.000
26B59PHE00.0110.00521.7940.7090.7090.0000.0000.0000.000
27B60ASP-1-0.699-0.81319.43715.20715.2070.0000.0000.0000.000
28B61ILE0-0.048-0.01217.0981.2461.2460.0000.0000.0000.000
29B62ASP-1-0.758-0.87216.68416.44616.4460.0000.0000.0000.000
30B63LEU00.0120.01717.2290.6030.6030.0000.0000.0000.000
31B64ALA00.002-0.00713.8150.8450.8450.0000.0000.0000.000
32B65ARG10.8680.94512.804-16.677-16.6770.0000.0000.0000.000
33B66GLU-1-0.800-0.87912.54119.06019.0600.0000.0000.0000.000
34B67ILE0-0.014-0.00911.5670.6190.6190.0000.0000.0000.000
35B68SER0-0.100-0.0638.7571.5261.5260.0000.0000.0000.000
36B69ASN0-0.014-0.0238.7783.3943.3940.0000.0000.0000.000
37B70LYS10.7740.86610.392-15.822-15.8220.0000.0000.0000.000
38B71LEU0-0.060-0.0198.162-0.054-0.0540.0000.0000.0000.000
39B72GLY0-0.0060.0167.2942.4452.4450.0000.0000.0000.000
40B73LYS10.7220.8281.848-69.096-76.79217.440-5.072-4.6720.040
41B74THR0-0.0030.0013.769-6.560-5.934-0.001-0.217-0.4080.000
42B75LEU00.0310.0065.9174.5254.5250.0000.0000.0000.000
43B76ASP-1-0.827-0.8817.41338.28038.2800.0000.0000.0000.000
44B77VAL00.0430.0289.481-0.053-0.0530.0000.0000.0000.000
45B78ARG10.8440.8987.491-35.542-35.5420.0000.0000.0000.000
46B79GLU-1-0.823-0.91814.39814.93014.9300.0000.0000.0000.000
47B80PHE0-0.055-0.02514.0190.3890.3890.0000.0000.0000.000
48B81SER00.0350.02419.777-0.335-0.3350.0000.0000.0000.000
49B82PHE00.016-0.00221.9660.5040.5040.0000.0000.0000.000
50B83ASP-1-0.873-0.94422.61813.17613.1760.0000.0000.0000.000
51B84ALA00.0150.00820.4480.2180.2180.0000.0000.0000.000
52B85LEU0-0.0320.00817.5021.0641.0640.0000.0000.0000.000
53B86ILE00.0360.01217.5521.0061.0060.0000.0000.0000.000
54B87LEU00.0120.01518.6700.4980.4980.0000.0000.0000.000
55B88ASN0-0.006-0.02514.7171.2011.2010.0000.0000.0000.000
56B89LEU0-0.0170.01913.4041.4561.4560.0000.0000.0000.000
57B90LYS10.8090.88314.302-13.047-13.0470.0000.0000.0000.000
58B91GLN0-0.037-0.01115.3460.2380.2380.0000.0000.0000.000
59B92HIS0-0.062-0.04510.2572.3332.3330.0000.0000.0000.000
60B93ARG10.8430.9269.588-17.026-17.0260.0000.0000.0000.000
61B94ILE0-0.045-0.02210.0351.4151.4150.0000.0000.0000.000
62B95ASP-1-0.797-0.8856.68941.99341.9930.0000.0000.0000.000
63B96ALA0-0.010-0.01410.075-1.929-1.9290.0000.0000.0000.000
64B97VAL0-0.030-0.01113.2950.5460.5460.0000.0000.0000.000
65B98ILE0-0.0160.00214.672-0.757-0.7570.0000.0000.0000.000
66B99THR0-0.009-0.00818.3420.2320.2320.0000.0000.0000.000
67B100GLY00.1030.05621.513-0.639-0.6390.0000.0000.0000.000
68B101MET0-0.060-0.02521.302-0.534-0.5340.0000.0000.0000.000
69B102SER00.0110.02024.294-0.154-0.1540.0000.0000.0000.000
70B103ILE00.0360.02123.8290.1590.1590.0000.0000.0000.000
71B104THR00.0440.02226.730-0.334-0.3340.0000.0000.0000.000
72B105PRO00.0630.02628.5160.4380.4380.0000.0000.0000.000
73B106SER0-0.0100.01430.2150.1690.1690.0000.0000.0000.000
74B107ARG10.8910.91224.498-11.862-11.8620.0000.0000.0000.000
75B108LEU00.0110.00724.7530.4790.4790.0000.0000.0000.000
76B109LYS10.7870.89926.319-10.122-10.1220.0000.0000.0000.000
77B110GLU-1-0.848-0.90323.86812.89512.8950.0000.0000.0000.000
78B111ILE0-0.077-0.04619.6620.7260.7260.0000.0000.0000.000
79B112LEU00.0210.02517.737-0.645-0.6450.0000.0000.0000.000
80B113MET0-0.046-0.02319.6110.4360.4360.0000.0000.0000.000
81B114ILE0-0.0040.01717.376-0.502-0.5020.0000.0000.0000.000
82B115PRO00.0370.01320.3860.2660.2660.0000.0000.0000.000
83B116TYR0-0.084-0.07120.7000.1220.1220.0000.0000.0000.000
84B117TYR00.004-0.00123.101-0.203-0.2030.0000.0000.0000.000
85B118GLY00.0010.00226.5840.0560.0560.0000.0000.0000.000
86B119GLU-1-0.866-0.93729.9419.5219.5210.0000.0000.0000.000
87B120GLU-1-0.838-0.91831.20010.00710.0070.0000.0000.0000.000
88B121ILE0-0.0120.00733.260-0.308-0.3080.0000.0000.0000.000
89B122LYS10.8030.88332.886-9.359-9.3590.0000.0000.0000.000
90B123HIS0-0.010-0.00437.486-0.250-0.2500.0000.0000.0000.000
91B124LEU0-0.008-0.00240.0370.1710.1710.0000.0000.0000.000
92B125VAL00.0090.00442.933-0.136-0.1360.0000.0000.0000.000
93B126LEU00.0150.01746.1640.0040.0040.0000.0000.0000.000
94B127VAL0-0.005-0.01148.891-0.058-0.0580.0000.0000.0000.000
95B128PHE00.0360.01051.636-0.021-0.0210.0000.0000.0000.000
96B129LYS10.8910.93655.447-5.362-5.3620.0000.0000.0000.000
97B130GLY00.0020.01158.862-0.071-0.0710.0000.0000.0000.000
98B131GLU-1-0.928-0.97459.4665.2475.2470.0000.0000.0000.000
99B132ASN0-0.031-0.02155.757-0.040-0.0400.0000.0000.0000.000
100B133LYS10.9370.96557.784-4.980-4.9800.0000.0000.0000.000
101B134HIS00.0080.01157.3500.0530.0530.0000.0000.0000.000
102B135PRO00.0760.04452.7410.0300.0300.0000.0000.0000.000
103B136LEU00.0060.02949.1390.1030.1030.0000.0000.0000.000
104B137PRO00.0310.00852.048-0.088-0.0880.0000.0000.0000.000
105B138LEU00.0440.00047.488-0.106-0.1060.0000.0000.0000.000
106B139THR00.0230.01251.792-0.027-0.0270.0000.0000.0000.000
107B140GLN0-0.107-0.04153.834-0.199-0.1990.0000.0000.0000.000
108B141TYR0-0.014-0.01053.206-0.163-0.1630.0000.0000.0000.000
109B142ARG10.8600.92056.114-5.400-5.4000.0000.0000.0000.000
110B143SER0-0.022-0.04054.232-0.048-0.0480.0000.0000.0000.000
111B144VAL00.0050.01249.190-0.069-0.0690.0000.0000.0000.000
112B145ALA0-0.0080.00050.2800.0910.0910.0000.0000.0000.000
113B146VAL0-0.011-0.00844.0130.0590.0590.0000.0000.0000.000
114B147GLN00.0440.01942.231-0.112-0.1120.0000.0000.0000.000
115B148THR00.006-0.01541.8720.1000.1000.0000.0000.0000.000
116B149GLY0-0.0010.01938.6190.0840.0840.0000.0000.0000.000
117B150THR0-0.056-0.04537.1310.3010.3010.0000.0000.0000.000
118B151TYR0-0.003-0.03535.1160.0180.0180.0000.0000.0000.000
119B152GLN00.0810.02837.5270.1080.1080.0000.0000.0000.000
120B153GLU-1-0.793-0.88341.0667.4657.4650.0000.0000.0000.000
121B154ALA00.0100.00437.854-0.109-0.1090.0000.0000.0000.000
122B155TYR00.0230.00539.845-0.134-0.1340.0000.0000.0000.000
123B156LEU00.0090.00741.011-0.147-0.1470.0000.0000.0000.000
124B157GLN0-0.020-0.01841.529-0.002-0.0020.0000.0000.0000.000
125B158SER0-0.097-0.04340.668-0.027-0.0270.0000.0000.0000.000
126B159LEU0-0.055-0.01842.617-0.089-0.0890.0000.0000.0000.000
127B160SER00.000-0.03846.177-0.047-0.0470.0000.0000.0000.000
128B161GLU-1-0.937-0.95449.0416.1056.1050.0000.0000.0000.000
129B162VAL0-0.0080.00648.814-0.127-0.1270.0000.0000.0000.000
130B163HIS0-0.0080.00550.2790.1350.1350.0000.0000.0000.000
131B164ILE00.0130.00546.1180.0080.0080.0000.0000.0000.000
132B165ARG10.7730.85850.300-6.142-6.1420.0000.0000.0000.000
133B166SER0-0.017-0.00846.060-0.024-0.0240.0000.0000.0000.000
134B167PHE0-0.023-0.00646.884-0.183-0.1830.0000.0000.0000.000
135B168ASP-1-0.836-0.89944.5017.3827.3820.0000.0000.0000.000
136B169SER0-0.069-0.07443.8750.1590.1590.0000.0000.0000.000
137B170THR00.024-0.02343.827-0.109-0.1090.0000.0000.0000.000
138B171LEU0-0.0070.00546.405-0.130-0.1300.0000.0000.0000.000
139B172GLU-1-0.825-0.88148.7506.5376.5370.0000.0000.0000.000
140B173VAL0-0.0130.00946.760-0.141-0.1410.0000.0000.0000.000
141B174LEU00.0270.02249.031-0.113-0.1130.0000.0000.0000.000
142B175MET0-0.008-0.00852.097-0.163-0.1630.0000.0000.0000.000
143B176GLU-1-0.746-0.83953.4425.7375.7370.0000.0000.0000.000
144B177VAL00.0110.01253.526-0.121-0.1210.0000.0000.0000.000
145B178MET0-0.036-0.01556.054-0.145-0.1450.0000.0000.0000.000
146B179HIS0-0.016-0.00958.112-0.184-0.1840.0000.0000.0000.000
147B180GLY0-0.025-0.00559.471-0.087-0.0870.0000.0000.0000.000
148B181LYS10.8400.93857.765-5.628-5.6280.0000.0000.0000.000
149B182SER00.0320.01554.8190.0160.0160.0000.0000.0000.000
150B183PRO0-0.062-0.01756.566-0.027-0.0270.0000.0000.0000.000
151B184VAL00.0040.00652.534-0.023-0.0230.0000.0000.0000.000
152B185ALA00.0020.00349.6120.0140.0140.0000.0000.0000.000
153B186VAL0-0.0010.00044.539-0.027-0.0270.0000.0000.0000.000
154B187LEU0-0.040-0.01643.9960.0840.0840.0000.0000.0000.000
155B188GLU-1-0.731-0.83437.5958.3458.3450.0000.0000.0000.000
156B189PRO0-0.001-0.00339.521-0.153-0.1530.0000.0000.0000.000
157B190SER0-0.036-0.04438.063-0.155-0.1550.0000.0000.0000.000
158B191ILE00.0270.00038.972-0.171-0.1710.0000.0000.0000.000
159B192ALA0-0.015-0.01641.897-0.195-0.1950.0000.0000.0000.000
160B193GLN0-0.044-0.02542.864-0.193-0.1930.0000.0000.0000.000
161B194VAL0-0.0200.00641.379-0.134-0.1340.0000.0000.0000.000
162B195VAL00.009-0.00844.683-0.145-0.1450.0000.0000.0000.000
163B196LEU00.006-0.00147.400-0.169-0.1690.0000.0000.0000.000
164B197LYS10.8050.90547.432-6.775-6.7750.0000.0000.0000.000
165B198ASP-1-0.860-0.91049.8096.3316.3310.0000.0000.0000.000
166B199PHE0-0.037-0.03150.986-0.121-0.1210.0000.0000.0000.000
167B200PRO00.0380.01154.726-0.009-0.0090.0000.0000.0000.000
168B201ALA0-0.047-0.01557.027-0.081-0.0810.0000.0000.0000.000
169B202LEU0-0.026-0.01253.041-0.051-0.0510.0000.0000.0000.000
170B203SER0-0.061-0.03054.854-0.066-0.0660.0000.0000.0000.000
171B204THR0-0.009-0.01249.9090.0870.0870.0000.0000.0000.000
172B205ALA00.0040.00250.725-0.109-0.1090.0000.0000.0000.000
173B206THR00.0060.00745.2790.0450.0450.0000.0000.0000.000
174B207ILE0-0.026-0.00345.160-0.144-0.1440.0000.0000.0000.000
175B208ASP-1-0.894-0.95643.1617.3627.3620.0000.0000.0000.000
176B209LEU0-0.050-0.00538.457-0.068-0.0680.0000.0000.0000.000
177B210PRO00.0210.00840.4270.0580.0580.0000.0000.0000.000
178B211GLU-1-0.843-0.92334.3289.4249.4240.0000.0000.0000.000
179B212ASP-1-0.912-0.96834.9888.7288.7280.0000.0000.0000.000
180B213GLN0-0.020-0.00835.1670.1950.1950.0000.0000.0000.000
181B214TRP0-0.032-0.01233.8870.2120.2120.0000.0000.0000.000
182B215VAL0-0.052-0.02531.4010.3360.3360.0000.0000.0000.000
183B216LEU0-0.053-0.03228.929-0.242-0.2420.0000.0000.0000.000
184B217GLY00.0860.06028.1000.3800.3800.0000.0000.0000.000
185B218TYR0-0.053-0.03725.099-0.114-0.1140.0000.0000.0000.000
186B219GLY00.0340.00222.0450.0120.0120.0000.0000.0000.000
187B220ILE0-0.038-0.00615.3140.2670.2670.0000.0000.0000.000
188B221GLY00.0270.01618.392-0.245-0.2450.0000.0000.0000.000
189B222VAL0-0.017-0.03013.5801.5011.5010.0000.0000.0000.000
190B223ALA00.0480.02814.106-1.246-1.2460.0000.0000.0000.000
191B224SER00.031-0.00515.9690.4570.4570.0000.0000.0000.000
192B225ASP-1-0.856-0.90615.76319.21719.2170.0000.0000.0000.000
193B226ARG10.8280.9138.043-30.249-30.2490.0000.0000.0000.000
194B227PRO00.0530.02014.0530.8030.8030.0000.0000.0000.000
195B228ALA0-0.004-0.00813.245-0.160-0.1600.0000.0000.0000.000
196B229LEU0-0.043-0.0178.8700.7830.7830.0000.0000.0000.000
197B230ALA00.0570.02412.020-0.197-0.1970.0000.0000.0000.000
198B231LEU00.0220.01215.377-0.479-0.4790.0000.0000.0000.000
199B232LYS10.9360.9688.742-28.134-28.1340.0000.0000.0000.000
200B233ILE00.0170.01411.7980.0860.0860.0000.0000.0000.000
201B234GLU-1-0.800-0.89514.56013.40913.4090.0000.0000.0000.000
202B235ALA0-0.035-0.01216.039-0.575-0.5750.0000.0000.0000.000
203B236ALA00.0050.00313.974-0.477-0.4770.0000.0000.0000.000
204B237VAL00.005-0.00416.136-0.602-0.6020.0000.0000.0000.000
205B238GLN0-0.079-0.06118.925-0.865-0.8650.0000.0000.0000.000
206B239GLU-1-0.825-0.87617.68314.96914.9690.0000.0000.0000.000
207B240ILE00.008-0.01116.202-0.487-0.4870.0000.0000.0000.000
208B241ARG10.8790.95220.511-13.404-13.4040.0000.0000.0000.000
209B242LYS10.7470.85521.153-14.033-14.0330.0000.0000.0000.000
210B243GLU-1-0.802-0.88520.07113.95513.9550.0000.0000.0000.000
211B244GLY0-0.0040.01424.103-0.158-0.1580.0000.0000.0000.000
212B245VAL00.0500.01820.060-0.124-0.1240.0000.0000.0000.000
213B246LEU0-0.047-0.01721.8220.1620.1620.0000.0000.0000.000
214B247ALA00.0870.04323.977-0.107-0.1070.0000.0000.0000.000
215B248GLU-1-0.948-0.97224.80211.49911.4990.0000.0000.0000.000
216B249LEU0-0.055-0.03220.178-0.123-0.1230.0000.0000.0000.000
217B250GLU-1-0.885-0.96724.90011.11411.1140.0000.0000.0000.000
218B251GLN0-0.0120.00027.799-0.434-0.4340.0000.0000.0000.000
219B252LYS10.8050.90422.368-13.489-13.4890.0000.0000.0000.000
220B253TRP0-0.066-0.03822.747-0.217-0.2170.0000.0000.0000.000
221B254GLY00.0300.02028.179-0.085-0.0850.0000.0000.0000.000
222B255LEU00.002-0.00726.198-0.246-0.2460.0000.0000.0000.000
223B256ASN0-0.038-0.01530.660-0.007-0.0070.0000.0000.0000.000
224B257ASN0-0.041-0.01633.959-0.456-0.4560.0000.0000.0000.000
225B258LEU0-0.0320.00030.740-0.001-0.0010.0000.0000.0000.000
226B259GLU-1-0.866-0.92133.9458.5858.5850.0000.0000.0000.000
227B260HIS0-0.020-0.01533.168-0.117-0.1170.0000.0000.0000.000
228B261HIS00.0190.00532.5610.6050.6050.0000.0000.0000.000
229B262HIS10.8590.91829.801-10.509-10.5090.0000.0000.0000.000
230B263HIS00.0700.04929.538-0.241-0.2410.0000.0000.0000.000
231B264HIS10.8360.93225.158-11.876-11.8760.0000.0000.0000.000
232B265HIS00.0620.05228.0670.5040.5040.0000.0000.0000.000