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: JLZV9

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 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 232
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2792332.85424
FMO2-HF: Nuclear repulsion 2702115.265344
FMO2-HF: Total energy -90217.588896
FMO2-MP2: Total energy -90485.470421


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.
16.40718.4738-4.254-5.8110.024
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 : -0.911 / q_NPA : -0.986
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].
3B36PHE00.0130.0173.6435.7158.6110.034-1.403-1.5260.000
4B37ILE0-0.005-0.0074.917-6.672-6.525-0.001-0.005-0.1410.000
5B38VAL00.007-0.0058.043-1.726-1.7260.0000.0000.0000.000
6B39GLY0-0.0010.00611.703-0.578-0.5780.0000.0000.0000.000
7B40THR00.006-0.03214.467-1.264-1.2640.0000.0000.0000.000
8B41ASN00.0220.01117.962-0.583-0.5830.0000.0000.0000.000
9B42ALA00.0260.02121.120-0.437-0.4370.0000.0000.0000.000
10B43THR0-0.064-0.05722.776-0.536-0.5360.0000.0000.0000.000
11B44TYR0-0.076-0.04325.604-0.425-0.4250.0000.0000.0000.000
12B45PRO00.0280.02926.6520.3690.3690.0000.0000.0000.000
13B46PRO00.0270.01528.034-0.250-0.2500.0000.0000.0000.000
14B47PHE0-0.029-0.00923.6400.3810.3810.0000.0000.0000.000
15B48GLH0-0.062-0.06121.2610.4590.4590.0000.0000.0000.000
16B49PHE0-0.023-0.01223.311-0.555-0.5550.0000.0000.0000.000
17B50VAL00.0530.03723.2650.4620.4620.0000.0000.0000.000
18B51ASP-1-0.771-0.87924.09712.42112.4210.0000.0000.0000.000
19B52LYS10.9200.92426.526-10.007-10.0070.0000.0000.0000.000
20B53ARG10.8680.93923.778-12.724-12.7240.0000.0000.0000.000
21B54GLY0-0.039-0.00824.2070.1340.1340.0000.0000.0000.000
22B55GLU-1-0.935-0.96218.47817.28917.2890.0000.0000.0000.000
23B56VAL0-0.016-0.00518.660-0.656-0.6560.0000.0000.0000.000
24B57VAL0-0.018-0.01019.7930.6320.6320.0000.0000.0000.000
25B58GLY00.0480.00321.918-0.193-0.1930.0000.0000.0000.000
26B59PHE00.0260.00821.3930.7310.7310.0000.0000.0000.000
27B60ASP-1-0.692-0.83519.34615.49615.4960.0000.0000.0000.000
28B61ILE0-0.066-0.01816.7681.3341.3340.0000.0000.0000.000
29B62ASP-1-0.803-0.90516.40715.69015.6900.0000.0000.0000.000
30B63LEU0-0.0040.00617.0440.5700.5700.0000.0000.0000.000
31B64ALA00.005-0.01113.6610.9030.9030.0000.0000.0000.000
32B65ARG10.9430.97912.310-18.016-18.0160.0000.0000.0000.000
33B66GLU-1-0.862-0.93112.27117.45117.4510.0000.0000.0000.000
34B67ILE0-0.004-0.00611.5730.5600.5600.0000.0000.0000.000
35B68SER0-0.102-0.0588.2601.3811.3810.0000.0000.0000.000
36B69ASN00.0290.0088.3642.9422.9420.0000.0000.0000.000
37B70LYS10.7670.87110.314-16.098-16.0980.0000.0000.0000.000
38B71LEU0-0.083-0.0347.9630.5540.5540.0000.0000.0000.000
39B72GLY0-0.0100.0157.0402.2042.2040.0000.0000.0000.000
40B73LYS10.8270.9141.983-71.020-72.5037.969-2.728-3.7580.024
41B74THR00.0050.0053.801-5.340-4.883-0.001-0.118-0.3380.000
42B75LEU0-0.008-0.0055.5935.0665.0660.0000.0000.0000.000
43B76ASP-1-0.900-0.9537.34335.36335.3630.0000.0000.0000.000
44B77VAL00.0210.0159.3470.6310.6310.0000.0000.0000.000
45B78ARG10.8860.9387.201-35.746-35.7460.0000.0000.0000.000
46B79GLU-1-0.897-0.95113.77715.49515.4950.0000.0000.0000.000
47B80PHE0-0.045-0.02213.5480.3290.3290.0000.0000.0000.000
48B81SER00.0470.01819.149-0.467-0.4670.0000.0000.0000.000
49B82PHE00.023-0.00621.5240.5380.5380.0000.0000.0000.000
50B83ASP-1-0.912-0.96122.28813.42213.4220.0000.0000.0000.000
51B84ALA00.0160.01620.2450.0910.0910.0000.0000.0000.000
52B85LEU0-0.042-0.00317.0661.1061.1060.0000.0000.0000.000
53B86ILE00.0330.00916.8721.1221.1220.0000.0000.0000.000
54B87LEU00.0080.00417.6230.6370.6370.0000.0000.0000.000
55B88ASN0-0.010-0.02914.2401.6791.6790.0000.0000.0000.000
56B89LEU0-0.0230.01412.4001.6681.6680.0000.0000.0000.000
57B90LYS10.8560.91713.232-13.884-13.8840.0000.0000.0000.000
58B91GLN0-0.038-0.01814.4820.4950.4950.0000.0000.0000.000
59B92HIS0-0.081-0.0369.3221.9261.9260.0000.0000.0000.000
60B93ARG10.9210.9778.881-17.693-17.6930.0000.0000.0000.000
61B94ILE0-0.055-0.0139.2621.9461.9460.0000.0000.0000.000
62B95ASP-1-0.803-0.8925.55752.78252.831-0.0010.000-0.0480.000
63B96ALA0-0.011-0.0148.792-2.307-2.3070.0000.0000.0000.000
64B97VAL0-0.0170.00412.1850.2630.2630.0000.0000.0000.000
65B98ILE00.0130.01514.632-0.585-0.5850.0000.0000.0000.000
66B99THR0-0.032-0.02117.5660.1640.1640.0000.0000.0000.000
67B100GLY00.1160.07120.711-0.638-0.6380.0000.0000.0000.000
68B101MET0-0.077-0.03520.863-0.503-0.5030.0000.0000.0000.000
69B102SER00.0190.02523.697-0.108-0.1080.0000.0000.0000.000
70B103ILE00.0500.02123.7700.3630.3630.0000.0000.0000.000
71B104THR00.0340.01726.090-0.357-0.3570.0000.0000.0000.000
72B105PRO00.0920.03427.2830.4990.4990.0000.0000.0000.000
73B106SER0-0.049-0.02428.5350.2590.2590.0000.0000.0000.000
74B107ARG10.9070.93123.570-12.417-12.4170.0000.0000.0000.000
75B108LEU00.0160.00823.3270.5690.5690.0000.0000.0000.000
76B109LYS10.9230.97624.367-10.415-10.4150.0000.0000.0000.000
77B110GLU-1-0.909-0.93822.43413.11913.1190.0000.0000.0000.000
78B111ILE0-0.112-0.05218.4580.8970.8970.0000.0000.0000.000
79B112LEU00.0270.01816.641-0.720-0.7200.0000.0000.0000.000
80B113MET0-0.058-0.02518.5620.5030.5030.0000.0000.0000.000
81B114ILE0-0.0070.02117.206-0.506-0.5060.0000.0000.0000.000
82B115PRO00.0530.01720.2300.3060.3060.0000.0000.0000.000
83B116TYR0-0.101-0.06720.7360.2640.2640.0000.0000.0000.000
84B117TYR00.0320.01922.952-0.220-0.2200.0000.0000.0000.000
85B118GLY0-0.0040.00926.3350.1230.1230.0000.0000.0000.000
86B119GLU-1-0.901-0.94429.7819.5059.5050.0000.0000.0000.000
87B120GLU-1-0.982-0.99430.42410.51510.5150.0000.0000.0000.000
88B121ILE0-0.032-0.01632.883-0.324-0.3240.0000.0000.0000.000
89B122LYS10.9360.95833.842-9.302-9.3020.0000.0000.0000.000
90B123HIS00.0120.00137.333-0.263-0.2630.0000.0000.0000.000
91B124LEU0-0.008-0.00339.5630.1510.1510.0000.0000.0000.000
92B125VAL00.0150.01342.757-0.146-0.1460.0000.0000.0000.000
93B126LEU0-0.005-0.00145.9740.0110.0110.0000.0000.0000.000
94B127VAL00.004-0.00348.718-0.088-0.0880.0000.0000.0000.000
95B128PHE00.0570.01151.439-0.026-0.0260.0000.0000.0000.000
96B129LYS10.9110.96855.210-5.422-5.4220.0000.0000.0000.000
97B130GLY0-0.0150.00258.661-0.056-0.0560.0000.0000.0000.000
98B131GLU-1-0.921-0.96759.2785.2645.2640.0000.0000.0000.000
99B132ASN0-0.036-0.02555.013-0.051-0.0510.0000.0000.0000.000
100B133LYS10.9260.96557.425-5.056-5.0560.0000.0000.0000.000
101B134HIS00.007-0.00156.6360.0700.0700.0000.0000.0000.000
102B135PRO00.0860.05352.0690.0160.0160.0000.0000.0000.000
103B136LEU00.0000.03348.4430.0880.0880.0000.0000.0000.000
104B137PRO00.0290.00351.241-0.098-0.0980.0000.0000.0000.000
105B138LEU00.046-0.00446.848-0.111-0.1110.0000.0000.0000.000
106B139THR00.0200.01250.820-0.029-0.0290.0000.0000.0000.000
107B140GLN0-0.102-0.03852.797-0.212-0.2120.0000.0000.0000.000
108B141TYR0-0.033-0.01352.645-0.160-0.1600.0000.0000.0000.000
109B142ARG10.9230.96055.233-5.465-5.4650.0000.0000.0000.000
110B143SER0-0.036-0.04653.479-0.033-0.0330.0000.0000.0000.000
111B144VAL00.0080.01048.489-0.062-0.0620.0000.0000.0000.000
112B145ALA0-0.0040.00149.6020.0920.0920.0000.0000.0000.000
113B146VAL00.001-0.00443.3970.0610.0610.0000.0000.0000.000
114B147GLN0-0.002-0.00941.624-0.077-0.0770.0000.0000.0000.000
115B148THR00.0460.01241.0480.1260.1260.0000.0000.0000.000
116B149GLY00.0360.02837.9800.0820.0820.0000.0000.0000.000
117B150THR0-0.052-0.02736.5330.3140.3140.0000.0000.0000.000
118B151TYR0-0.033-0.06234.3620.0480.0480.0000.0000.0000.000
119B152GLN00.0740.02136.6800.1110.1110.0000.0000.0000.000
120B153GLU-1-0.858-0.92740.2837.6887.6880.0000.0000.0000.000
121B154ALA00.0280.02037.014-0.115-0.1150.0000.0000.0000.000
122B155TYR00.012-0.00338.953-0.104-0.1040.0000.0000.0000.000
123B156LEU0-0.015-0.00840.080-0.164-0.1640.0000.0000.0000.000
124B157GLN0-0.010-0.01340.3710.0220.0220.0000.0000.0000.000
125B158SER0-0.105-0.04739.723-0.061-0.0610.0000.0000.0000.000
126B159LEU0-0.041-0.01141.709-0.102-0.1020.0000.0000.0000.000
127B160SER00.0130.00345.058-0.069-0.0690.0000.0000.0000.000
128B161GLU-1-0.998-1.00847.9126.0236.0230.0000.0000.0000.000
129B162VAL00.0340.02047.904-0.123-0.1230.0000.0000.0000.000
130B163HIS0-0.035-0.00549.3230.1340.1340.0000.0000.0000.000
131B164ILE00.0440.01845.209-0.044-0.0440.0000.0000.0000.000
132B165ARG10.7650.86249.364-6.152-6.1520.0000.0000.0000.000
133B166SER00.0240.01345.344-0.036-0.0360.0000.0000.0000.000
134B167PHE0-0.050-0.02846.505-0.176-0.1760.0000.0000.0000.000
135B168ASP-1-0.824-0.89244.3607.3777.3770.0000.0000.0000.000
136B169SER0-0.050-0.02943.7610.1510.1510.0000.0000.0000.000
137B170THR00.0600.01144.220-0.071-0.0710.0000.0000.0000.000
138B171LEU00.0020.00546.320-0.138-0.1380.0000.0000.0000.000
139B172GLU-1-0.857-0.94048.5736.5486.5480.0000.0000.0000.000
140B173VAL0-0.0110.00946.269-0.132-0.1320.0000.0000.0000.000
141B174LEU00.0110.00348.754-0.127-0.1270.0000.0000.0000.000
142B175MET0-0.017-0.01551.822-0.160-0.1600.0000.0000.0000.000
143B176GLU-1-0.718-0.81752.9985.8065.8060.0000.0000.0000.000
144B177VAL0-0.0020.00352.936-0.130-0.1300.0000.0000.0000.000
145B178MET0-0.043-0.01755.722-0.149-0.1490.0000.0000.0000.000
146B179HIS0-0.030-0.02557.986-0.177-0.1770.0000.0000.0000.000
147B180GLY0-0.026-0.00259.208-0.095-0.0950.0000.0000.0000.000
148B181LYS10.8420.93057.378-5.677-5.6770.0000.0000.0000.000
149B182SER00.008-0.00154.2470.0270.0270.0000.0000.0000.000
150B183PRO0-0.070-0.02255.727-0.034-0.0340.0000.0000.0000.000
151B184VAL00.0000.01051.732-0.013-0.0130.0000.0000.0000.000
152B185ALA00.0030.00349.0570.0120.0120.0000.0000.0000.000
153B186VAL00.0070.01043.880-0.021-0.0210.0000.0000.0000.000
154B187LEU0-0.045-0.02043.8320.0700.0700.0000.0000.0000.000
155B188GLU-1-0.748-0.84737.4258.5868.5860.0000.0000.0000.000
156B189PRO0-0.018-0.01839.384-0.146-0.1460.0000.0000.0000.000
157B190SER0-0.019-0.03437.808-0.170-0.1700.0000.0000.0000.000
158B191ILE00.0270.01538.990-0.142-0.1420.0000.0000.0000.000
159B192ALA0-0.031-0.02441.814-0.203-0.2030.0000.0000.0000.000
160B193GLN0-0.025-0.02342.646-0.217-0.2170.0000.0000.0000.000
161B194VAL0-0.0060.02341.558-0.127-0.1270.0000.0000.0000.000
162B195VAL0-0.002-0.02344.664-0.181-0.1810.0000.0000.0000.000
163B196LEU00.0220.00347.210-0.168-0.1680.0000.0000.0000.000
164B197LYS10.8670.95147.703-6.766-6.7660.0000.0000.0000.000
165B198ASP-1-0.911-0.94550.3896.2566.2560.0000.0000.0000.000
166B199PHE0-0.072-0.04950.861-0.128-0.1280.0000.0000.0000.000
167B200PRO00.0380.01854.6530.0010.0010.0000.0000.0000.000
168B201ALA0-0.055-0.02757.099-0.051-0.0510.0000.0000.0000.000
169B202LEU0-0.037-0.01752.799-0.049-0.0490.0000.0000.0000.000
170B203SER0-0.0100.00054.821-0.012-0.0120.0000.0000.0000.000
171B204THR0-0.018-0.02449.6680.1020.1020.0000.0000.0000.000
172B205ALA0-0.0010.00350.558-0.113-0.1130.0000.0000.0000.000
173B206THR00.0080.00944.9350.0540.0540.0000.0000.0000.000
174B207ILE0-0.038-0.00544.240-0.140-0.1400.0000.0000.0000.000
175B208ASP-1-0.886-0.95242.9237.5317.5310.0000.0000.0000.000
176B209LEU0-0.064-0.02437.775-0.063-0.0630.0000.0000.0000.000
177B210PRO00.0380.02539.4840.0570.0570.0000.0000.0000.000
178B211GLU-1-0.872-0.94433.9499.5019.5010.0000.0000.0000.000
179B212ASP-1-0.973-0.99434.2148.9748.9740.0000.0000.0000.000
180B213GLN0-0.029-0.01234.6400.1370.1370.0000.0000.0000.000
181B214TRP0-0.0210.01633.3010.1560.1560.0000.0000.0000.000
182B215VAL0-0.045-0.02030.6020.3740.3740.0000.0000.0000.000
183B216LEU0-0.047-0.02928.294-0.291-0.2910.0000.0000.0000.000
184B217GLY00.0990.06428.0340.2960.2960.0000.0000.0000.000
185B218TYR0-0.031-0.02524.439-0.075-0.0750.0000.0000.0000.000
186B219GLY00.0270.00221.8390.0110.0110.0000.0000.0000.000
187B220ILE0-0.046-0.01315.1550.3390.3390.0000.0000.0000.000
188B221GLY0-0.001-0.00117.235-0.327-0.3270.0000.0000.0000.000
189B222VAL00.013-0.01812.7071.8501.8500.0000.0000.0000.000
190B223ALA00.0370.02213.251-1.480-1.4800.0000.0000.0000.000
191B224SER00.0650.00514.9730.2250.2250.0000.0000.0000.000
192B225ASP-1-0.887-0.92314.54720.81520.8150.0000.0000.0000.000
193B226ARG10.8210.9056.538-36.574-36.5740.0000.0000.0000.000
194B227PRO00.0720.02713.5120.6940.6940.0000.0000.0000.000
195B228ALA00.0100.00013.106-0.139-0.1390.0000.0000.0000.000
196B229LEU0-0.067-0.0368.7530.8050.8050.0000.0000.0000.000
197B230ALA00.0730.03311.927-0.086-0.0860.0000.0000.0000.000
198B231LEU00.0070.01515.202-0.681-0.6810.0000.0000.0000.000
199B232LYS10.9440.9698.378-32.286-32.2860.0000.0000.0000.000
200B233ILE00.0140.00711.527-0.098-0.0980.0000.0000.0000.000
201B234GLU-1-0.828-0.90014.40413.77113.7710.0000.0000.0000.000
202B235ALA0-0.033-0.02015.969-0.762-0.7620.0000.0000.0000.000
203B236ALA00.0080.00313.989-0.632-0.6320.0000.0000.0000.000
204B237VAL00.0170.00616.144-0.748-0.7480.0000.0000.0000.000
205B238GLN0-0.093-0.05918.964-1.018-1.0180.0000.0000.0000.000
206B239GLU-1-0.923-0.93717.75015.30615.3060.0000.0000.0000.000
207B240ILE00.0480.01815.906-0.452-0.4520.0000.0000.0000.000
208B241ARG10.9380.97220.172-13.422-13.4220.0000.0000.0000.000
209B242LYS10.9050.94821.799-13.764-13.7640.0000.0000.0000.000
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