Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: YYGM2

Calculation Name: 4LUB-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4LUB

Chain ID: B

ChEMBL ID:

UniProt ID: Q8DUV6

Base Structure: X-ray

Registration Date: 2023-06-19

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 190
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2140964.654777
FMO2-HF: Nuclear repulsion 2066983.095206
FMO2-HF: Total energy -73981.559571
FMO2-MP2: Total energy -74203.114831


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:5:THR)


Summations of interaction energy for fragment #1(B:5:THR)
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.
-6.052-0.6155.816-4.124-7.1280.012
Interaction energy analysis for fragmet #1(B:5:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.059 / q_NPA : 0.005
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].
3B7LYS10.8960.9333.890-2.263-0.561-0.012-0.815-0.8750.002
4B8ILE0-0.0030.0083.3240.6261.1370.027-0.127-0.4110.000
5B9ALA00.0270.0346.484-0.165-0.1650.0000.0000.0000.000
6B10TYR0-0.040-0.03710.0870.0300.0300.0000.0000.0000.000
7B11LEU00.0350.02912.747-0.019-0.0190.0000.0000.0000.000
8B12GLY00.0290.03716.537-0.021-0.0210.0000.0000.0000.000
9B13PRO0-0.002-0.01118.2850.0060.0060.0000.0000.0000.000
10B14SER00.018-0.01217.657-0.003-0.0030.0000.0000.0000.000
11B15GLY00.006-0.00617.7920.0050.0050.0000.0000.0000.000
12B16SER0-0.059-0.02317.6960.0040.0040.0000.0000.0000.000
13B17PHE00.043-0.00317.976-0.008-0.0080.0000.0000.0000.000
14B18THR00.0330.01514.1740.0080.0080.0000.0000.0000.000
15B19HIS00.0630.06812.8840.0530.0530.0000.0000.0000.000
16B20ASN00.003-0.00613.247-0.044-0.0440.0000.0000.0000.000
17B21VAL00.0050.01012.628-0.006-0.0060.0000.0000.0000.000
18B22ALA00.0290.0089.7570.0630.0630.0000.0000.0000.000
19B23LEU0-0.024-0.0148.693-0.049-0.0490.0000.0000.0000.000
20B24HIS0-0.087-0.05110.004-0.037-0.0370.0000.0000.0000.000
21B25ALA0-0.024-0.0058.0670.0380.0380.0000.0000.0000.000
22B26PHE0-0.007-0.0072.770-1.808-0.2030.512-0.664-1.4530.004
23B27PRO00.0030.0085.711-0.611-0.6110.0000.0000.0000.000
24B28ALA0-0.061-0.0316.0400.1060.1060.0000.0000.0000.000
25B29ALA0-0.0130.0033.486-0.719-0.5640.001-0.053-0.1030.000
26B30ASP-1-0.852-0.9125.5940.4780.4780.0000.0000.0000.000
27B31LEU00.0030.0007.2370.1070.1070.0000.0000.0000.000
28B32LEU0-0.024-0.0209.9130.0680.0680.0000.0000.0000.000
29B33PRO0-0.0040.00412.1130.0660.0660.0000.0000.0000.000
30B34PHE0-0.007-0.01512.1740.0160.0160.0000.0000.0000.000
31B35GLU-1-0.906-0.95016.5440.1000.1000.0000.0000.0000.000
32B36ASN0-0.004-0.01019.3260.0050.0050.0000.0000.0000.000
33B37ILE00.0390.01017.2980.0200.0200.0000.0000.0000.000
34B38THR0-0.010-0.02717.0860.0330.0330.0000.0000.0000.000
35B39GLU-1-0.833-0.90917.6990.2230.2230.0000.0000.0000.000
36B40VAL0-0.068-0.02112.6260.0370.0370.0000.0000.0000.000
37B41ILE0-0.018-0.00212.6400.0780.0780.0000.0000.0000.000
38B42LYS10.8610.90213.411-0.142-0.1420.0000.0000.0000.000
39B43ALA00.0160.03511.9480.0230.0230.0000.0000.0000.000
40B44TYR0-0.009-0.0096.8890.0300.0300.0000.0000.0000.000
41B45GLU-1-0.822-0.89910.6090.3540.3540.0000.0000.0000.000
42B46SER0-0.084-0.05313.531-0.051-0.0510.0000.0000.0000.000
43B47LYS10.8730.93010.071-0.485-0.4850.0000.0000.0000.000
44B48GLN0-0.0150.0009.9890.1020.1020.0000.0000.0000.000
45B49VAL0-0.068-0.0347.025-0.082-0.0820.0000.0000.0000.000
46B50CYS0-0.057-0.0152.6031.4441.3862.895-0.876-1.9610.007
47B51PHE00.0180.0162.343-2.259-0.8692.394-1.585-2.199-0.001
48B52ALA00.0150.0115.766-0.177-0.1770.0000.0000.0000.000
49B53ILE0-0.018-0.0028.2820.0150.0150.0000.0000.0000.000
50B54VAL00.0320.00811.471-0.055-0.0550.0000.0000.0000.000
51B55PRO0-0.0060.01115.1620.0090.0090.0000.0000.0000.000
52B56VAL00.0220.00017.5810.0030.0030.0000.0000.0000.000
53B57GLU-1-0.807-0.88720.3320.1080.1080.0000.0000.0000.000
54B58ASN00.0270.02423.171-0.001-0.0010.0000.0000.0000.000
55B59SER00.003-0.00825.871-0.002-0.0020.0000.0000.0000.000
56B60ILE0-0.079-0.02928.711-0.005-0.0050.0000.0000.0000.000
57B61GLU-1-0.956-0.98327.2890.0770.0770.0000.0000.0000.000
58B62GLY00.0210.03228.804-0.001-0.0010.0000.0000.0000.000
59B63SER0-0.007-0.05225.1540.0100.0100.0000.0000.0000.000
60B64VAL0-0.024-0.01421.858-0.008-0.0080.0000.0000.0000.000
61B65HIS00.0190.00523.6000.0090.0090.0000.0000.0000.000
62B66GLU-1-0.806-0.88021.8390.1530.1530.0000.0000.0000.000
63B67THR00.022-0.00217.8320.0030.0030.0000.0000.0000.000
64B68PHE00.0300.01320.1760.0130.0130.0000.0000.0000.000
65B69ASP-1-0.797-0.86122.3960.1090.1090.0000.0000.0000.000
66B70TYR0-0.016-0.03517.682-0.018-0.0180.0000.0000.0000.000
67B71LEU00.0340.00515.9740.0060.0060.0000.0000.0000.000
68B72PHE0-0.0220.01119.6530.0000.0000.0000.0000.0000.000
69B73HIS0-0.059-0.02823.018-0.001-0.0010.0000.0000.0000.000
70B74GLN0-0.093-0.04321.236-0.008-0.0080.0000.0000.0000.000
71B75ALA00.0280.03316.4270.0040.0040.0000.0000.0000.000
72B76LYS10.7800.88312.724-0.313-0.3130.0000.0000.0000.000
73B77ILE0-0.054-0.01410.3810.0280.0280.0000.0000.0000.000
74B78GLU-1-0.867-0.93712.3350.1580.1580.0000.0000.0000.000
75B79ALA0-0.018-0.02112.0750.0730.0730.0000.0000.0000.000
76B80VAL0-0.031-0.0168.642-0.035-0.0350.0000.0000.0000.000
77B81ALA00.001-0.01410.7420.0230.0230.0000.0000.0000.000
78B82GLU-1-0.770-0.84012.5710.1880.1880.0000.0000.0000.000
79B83ILE0-0.022-0.01111.557-0.003-0.0030.0000.0000.0000.000
80B84ILE00.0050.01215.873-0.019-0.0190.0000.0000.0000.000
81B85LEU00.0110.00817.952-0.010-0.0100.0000.0000.0000.000
82B86PRO0-0.0070.00020.589-0.004-0.0040.0000.0000.0000.000
83B87ILE0-0.024-0.00722.428-0.009-0.0090.0000.0000.0000.000
84B88LYS10.9100.95824.499-0.046-0.0460.0000.0000.0000.000
85B173GLU-1-0.839-0.92827.5760.0510.0510.0000.0000.0000.000
86B174ASN0-0.075-0.05527.0580.0100.0100.0000.0000.0000.000
87B175TYR00.0030.00523.5900.0010.0010.0000.0000.0000.000
88B176THR00.0050.01420.822-0.003-0.0030.0000.0000.0000.000
89B177ARG10.7190.82220.038-0.151-0.1510.0000.0000.0000.000
90B178PHE00.026-0.00415.297-0.012-0.0120.0000.0000.0000.000
91B179TRP0-0.018-0.02214.3340.0160.0160.0000.0000.0000.000
92B180VAL0-0.002-0.0067.8270.0000.0000.0000.0000.0000.000
93B181LEU00.004-0.0059.737-0.041-0.0410.0000.0000.0000.000
94B182GLY00.018-0.0127.5990.2100.2100.0000.0000.0000.000
95B183ASP-1-0.799-0.8857.3900.2370.2370.0000.0000.0000.000
96B184GLU-1-0.975-0.9764.841-1.764-1.632-0.001-0.004-0.1260.000
97B185THR00.0290.0017.6420.1710.1710.0000.0000.0000.000
98B186PRO0-0.0290.0075.5800.0230.0230.0000.0000.0000.000
99B187THR0-0.022-0.0226.483-0.457-0.4570.0000.0000.0000.000
100B188ILE00.0110.0057.7660.1640.1640.0000.0000.0000.000
101B189HIS0-0.0060.00510.063-0.085-0.0850.0000.0000.0000.000
102B190LEU00.0000.00112.477-0.063-0.0630.0000.0000.0000.000
103B191LYS10.8150.88915.237-0.109-0.1090.0000.0000.0000.000
104B192GLU-1-0.806-0.87816.2250.2200.2200.0000.0000.0000.000
105B193GLU-1-0.890-0.91918.5810.0800.0800.0000.0000.0000.000
106B194ASP-1-0.792-0.89320.3760.1070.1070.0000.0000.0000.000
107B195GLN0-0.038-0.03516.5680.0290.0290.0000.0000.0000.000
108B196LYS10.8820.96119.259-0.152-0.1520.0000.0000.0000.000
109B197ILE0-0.023-0.01019.2820.0130.0130.0000.0000.0000.000
110B198SER0-0.022-0.01420.096-0.006-0.0060.0000.0000.0000.000
111B199LEU0-0.024-0.01121.3440.0070.0070.0000.0000.0000.000
112B200ALA00.0140.01623.960-0.002-0.0020.0000.0000.0000.000
113B201LEU0-0.023-0.00925.652-0.003-0.0030.0000.0000.0000.000
114B202THR00.011-0.01229.0530.0000.0000.0000.0000.0000.000
115B203LEU0-0.014-0.00731.743-0.002-0.0020.0000.0000.0000.000
116B204PRO00.0440.01235.2440.0000.0000.0000.0000.0000.000
117B205ASP-1-0.922-0.95838.1130.0480.0480.0000.0000.0000.000
118B206ASN0-0.064-0.04734.9770.0020.0020.0000.0000.0000.000
119B207LEU00.0180.01337.4360.0000.0000.0000.0000.0000.000
120B208PRO00.0300.00338.0020.0000.0000.0000.0000.0000.000
121B209GLY0-0.019-0.00139.0640.0000.0000.0000.0000.0000.000
122B210ALA0-0.007-0.01438.456-0.002-0.0020.0000.0000.0000.000
123B211LEU00.0240.02033.7050.0000.0000.0000.0000.0000.000
124B212TYR00.0370.01536.4440.0010.0010.0000.0000.0000.000
125B213LYS10.9250.98238.021-0.045-0.0450.0000.0000.0000.000
126B214ALA00.0570.03732.7870.0000.0000.0000.0000.0000.000
127B215LEU00.0360.01233.1350.0020.0020.0000.0000.0000.000
128B216SER0-0.040-0.04234.747-0.001-0.0010.0000.0000.0000.000
129B217THR0-0.041-0.01532.590-0.002-0.0020.0000.0000.0000.000
130B218PHE00.0300.01427.067-0.001-0.0010.0000.0000.0000.000
131B219ALA00.0180.01332.581-0.001-0.0010.0000.0000.0000.000
132B220TRP0-0.111-0.06635.345-0.003-0.0030.0000.0000.0000.000
133B221ARG10.7220.84131.871-0.055-0.0550.0000.0000.0000.000
134B222GLY0-0.0090.00033.5270.0000.0000.0000.0000.0000.000
135B223ILE0-0.071-0.02627.8480.0020.0020.0000.0000.0000.000
136B224ASP-1-0.829-0.91930.1870.0650.0650.0000.0000.0000.000
137B225LEU0-0.074-0.03228.9740.0070.0070.0000.0000.0000.000
138B226THR0-0.021-0.01726.2240.0010.0010.0000.0000.0000.000
139B227LYS10.8380.89924.366-0.123-0.1230.0000.0000.0000.000
140B228ILE0-0.014-0.01328.5970.0010.0010.0000.0000.0000.000
141B229GLU-1-0.811-0.85127.3360.0900.0900.0000.0000.0000.000
142B230SER0-0.086-0.04129.966-0.001-0.0010.0000.0000.0000.000
143B231ARG10.8410.89026.817-0.104-0.1040.0000.0000.0000.000
144B232PRO00.0160.00130.402-0.002-0.0020.0000.0000.0000.000
145B233LEU00.0050.00330.6780.0070.0070.0000.0000.0000.000
146B234LYS10.7890.88928.840-0.100-0.1000.0000.0000.0000.000
147B235THR0-0.001-0.01933.3200.0000.0000.0000.0000.0000.000
148B236ILE0-0.005-0.01336.394-0.004-0.0040.0000.0000.0000.000
149B237LEU0-0.028-0.01438.2670.0020.0020.0000.0000.0000.000
150B238GLY00.002-0.00538.936-0.003-0.0030.0000.0000.0000.000
151B239GLU-1-0.816-0.84636.2630.0630.0630.0000.0000.0000.000
152B240TYR0-0.044-0.03233.4860.0020.0020.0000.0000.0000.000
153B241PHE00.0180.01125.591-0.001-0.0010.0000.0000.0000.000
154B242PHE0-0.005-0.02529.934-0.001-0.0010.0000.0000.0000.000
155B243ILE0-0.0100.01423.8680.0030.0030.0000.0000.0000.000
156B244ILE0-0.004-0.01625.919-0.007-0.0070.0000.0000.0000.000
157B245ASP-1-0.752-0.83323.3500.1570.1570.0000.0000.0000.000
158B246PHE0-0.020-0.01824.713-0.011-0.0110.0000.0000.0000.000
159B247GLU-1-0.872-0.93624.0510.0940.0940.0000.0000.0000.000
160B248ASN0-0.061-0.07119.444-0.017-0.0170.0000.0000.0000.000
161B249HIS0-0.0040.00122.568-0.002-0.0020.0000.0000.0000.000
162B250ASN0-0.036-0.02224.435-0.008-0.0080.0000.0000.0000.000
163B251GLU-1-0.688-0.80919.8450.1050.1050.0000.0000.0000.000
164B252LYS10.8940.97723.557-0.042-0.0420.0000.0000.0000.000
165B253LEU0-0.007-0.00926.486-0.002-0.0020.0000.0000.0000.000
166B254VAL00.0810.03223.702-0.002-0.0020.0000.0000.0000.000
167B255SER0-0.068-0.04024.6700.0020.0020.0000.0000.0000.000
168B256PHE00.019-0.00726.555-0.002-0.0020.0000.0000.0000.000
169B257ALA00.0170.02329.061-0.003-0.0030.0000.0000.0000.000
170B258LEU00.0050.01024.0290.0000.0000.0000.0000.0000.000
171B259GLU-1-0.905-0.94828.4980.0500.0500.0000.0000.0000.000
172B260GLU-1-0.742-0.84030.6950.0460.0460.0000.0000.0000.000
173B261LEU0-0.0160.00729.014-0.002-0.0020.0000.0000.0000.000
174B262THR0-0.022-0.02829.9500.0000.0000.0000.0000.0000.000
175B263SER0-0.108-0.06032.163-0.003-0.0030.0000.0000.0000.000
176B264ILE0-0.048-0.02135.470-0.003-0.0030.0000.0000.0000.000
177B265GLY0-0.0070.00435.111-0.001-0.0010.0000.0000.0000.000
178B266ILE0-0.082-0.04331.4800.0010.0010.0000.0000.0000.000
179B267HIS00.0350.02629.8870.0050.0050.0000.0000.0000.000
180B268TYR0-0.028-0.02524.7670.0040.0040.0000.0000.0000.000
181B269LYS10.8140.90219.871-0.183-0.1830.0000.0000.0000.000
182B270ILE00.003-0.00318.952-0.003-0.0030.0000.0000.0000.000
183B271LEU0-0.017-0.01618.5520.0080.0080.0000.0000.0000.000
184B272GLY00.0700.03616.2330.0350.0350.0000.0000.0000.000
185B273LYS10.8400.90715.684-0.146-0.1460.0000.0000.0000.000
186B274TYR0-0.059-0.03114.5280.0270.0270.0000.0000.0000.000
187B275ALA00.0660.05714.157-0.035-0.0350.0000.0000.0000.000
188B276VAL0-0.022-0.01315.4330.0370.0370.0000.0000.0000.000
189B277TYR00.000-0.03012.8480.0040.0040.0000.0000.0000.000
190B278ARG10.7700.85817.116-0.116-0.1160.0000.0000.0000.000