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: 53V8Z

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 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 190
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2139423.05772
FMO2-HF: Nuclear repulsion 2065441.9173
FMO2-HF: Total energy -73981.14042
FMO2-MP2: Total energy -74202.687878


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.
-7.305-3.3998.832-5.11-7.6280.012
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 : 0.046 / q_NPA : 0.001
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].
3B7LYS10.9020.9323.849-2.057-0.368-0.017-0.834-0.8380.004
4B8ILE00.0060.0012.6650.6681.2220.270-0.235-0.5890.000
5B9ALA00.0430.0536.428-0.240-0.2400.0000.0000.0000.000
6B10TYR0-0.040-0.0239.8580.0370.0370.0000.0000.0000.000
7B11LEU00.0170.02112.371-0.021-0.0210.0000.0000.0000.000
8B12GLY00.0000.01816.112-0.023-0.0230.0000.0000.0000.000
9B13PRO0-0.007-0.02017.9130.0030.0030.0000.0000.0000.000
10B14SER00.017-0.02617.6740.0050.0050.0000.0000.0000.000
11B15GLY00.002-0.00218.1990.0000.0000.0000.0000.0000.000
12B16SER0-0.0360.00417.7260.0040.0040.0000.0000.0000.000
13B17PHE00.0590.00318.361-0.003-0.0030.0000.0000.0000.000
14B18THR00.0600.02314.0000.0060.0060.0000.0000.0000.000
15B19HIS00.0520.05013.3040.0500.0500.0000.0000.0000.000
16B20ASN0-0.009-0.01513.781-0.026-0.0260.0000.0000.0000.000
17B21VAL00.0040.01012.746-0.002-0.0020.0000.0000.0000.000
18B22ALA00.0150.0029.6480.0580.0580.0000.0000.0000.000
19B23LEU0-0.015-0.0129.052-0.010-0.0100.0000.0000.0000.000
20B24HIS0-0.090-0.04410.092-0.056-0.0560.0000.0000.0000.000
21B25ALA0-0.027-0.0018.1160.0180.0180.0000.0000.0000.000
22B26PHE00.001-0.0083.056-1.580-0.0850.186-0.581-1.0990.003
23B27PRO00.0260.0235.970-0.494-0.4940.0000.0000.0000.000
24B28ALA0-0.069-0.0385.646-0.010-0.0100.0000.0000.0000.000
25B29ALA0-0.0090.0103.843-0.528-0.444-0.001-0.023-0.0610.000
26B30ASP-1-0.861-0.9135.7620.4260.4260.0000.0000.0000.000
27B31LEU00.0200.0117.5690.2060.2060.0000.0000.0000.000
28B32LEU0-0.048-0.0389.7210.0260.0260.0000.0000.0000.000
29B33PRO00.0060.01211.8920.0750.0750.0000.0000.0000.000
30B34PHE00.003-0.01211.9260.0110.0110.0000.0000.0000.000
31B35GLU-1-0.913-0.95816.4710.1280.1280.0000.0000.0000.000
32B36ASN00.003-0.00319.0300.0020.0020.0000.0000.0000.000
33B37ILE00.0430.01517.3550.0270.0270.0000.0000.0000.000
34B38THR0-0.004-0.02416.9340.0370.0370.0000.0000.0000.000
35B39GLU-1-0.822-0.89817.6130.2460.2460.0000.0000.0000.000
36B40VAL0-0.073-0.02212.2850.0450.0450.0000.0000.0000.000
37B41ILE0-0.008-0.00512.6680.0990.0990.0000.0000.0000.000
38B42LYS10.8610.90713.441-0.163-0.1630.0000.0000.0000.000
39B43ALA00.0060.01912.1020.0210.0210.0000.0000.0000.000
40B44TYR0-0.013-0.0186.5080.0360.0360.0000.0000.0000.000
41B45GLU-1-0.820-0.88910.4000.3510.3510.0000.0000.0000.000
42B46SER0-0.091-0.04913.155-0.068-0.0680.0000.0000.0000.000
43B47LYS10.8760.9369.631-0.427-0.4270.0000.0000.0000.000
44B48GLN0-0.029-0.0069.9090.0230.0230.0000.0000.0000.000
45B49VAL0-0.059-0.0357.168-0.023-0.0230.0000.0000.0000.000
46B50CYS0-0.069-0.0222.4190.500-1.0555.352-1.554-2.2430.009
47B51PHE00.0250.0222.224-3.255-1.6163.042-1.883-2.798-0.004
48B52ALA0-0.0050.0025.822-0.111-0.1110.0000.0000.0000.000
49B53ILE0-0.025-0.0047.707-0.036-0.0360.0000.0000.0000.000
50B54VAL00.0230.00011.268-0.059-0.0590.0000.0000.0000.000
51B55PRO0-0.0030.01014.9960.0070.0070.0000.0000.0000.000
52B56VAL00.010-0.00917.213-0.001-0.0010.0000.0000.0000.000
53B57GLU-1-0.789-0.88119.9230.1210.1210.0000.0000.0000.000
54B58ASN00.0170.02422.845-0.001-0.0010.0000.0000.0000.000
55B59SER00.010-0.00625.386-0.003-0.0030.0000.0000.0000.000
56B60ILE0-0.088-0.03728.186-0.007-0.0070.0000.0000.0000.000
57B61GLU-1-0.956-0.98127.2990.0970.0970.0000.0000.0000.000
58B62GLY00.0250.02928.182-0.002-0.0020.0000.0000.0000.000
59B63SER0-0.037-0.05924.7610.0130.0130.0000.0000.0000.000
60B64VAL0-0.009-0.00921.800-0.009-0.0090.0000.0000.0000.000
61B65HIS00.007-0.01123.2760.0090.0090.0000.0000.0000.000
62B66GLU-1-0.817-0.88921.7190.1790.1790.0000.0000.0000.000
63B67THR00.0260.00517.7510.0070.0070.0000.0000.0000.000
64B68PHE00.0300.00920.0690.0120.0120.0000.0000.0000.000
65B69ASP-1-0.803-0.86122.2080.1180.1180.0000.0000.0000.000
66B70TYR0-0.021-0.03717.311-0.022-0.0220.0000.0000.0000.000
67B71LEU00.0390.00815.6240.0040.0040.0000.0000.0000.000
68B72PHE0-0.0270.00619.078-0.005-0.0050.0000.0000.0000.000
69B73HIS0-0.065-0.02822.172-0.005-0.0050.0000.0000.0000.000
70B74GLN0-0.066-0.02920.716-0.008-0.0080.0000.0000.0000.000
71B75ALA00.0530.05215.6790.0050.0050.0000.0000.0000.000
72B76LYS10.8990.95212.831-0.237-0.2370.0000.0000.0000.000
73B77ILE0-0.079-0.02810.0640.0100.0100.0000.0000.0000.000
74B78GLU-1-0.881-0.94211.7790.1320.1320.0000.0000.0000.000
75B79ALA0-0.018-0.01811.5270.0700.0700.0000.0000.0000.000
76B80VAL0-0.032-0.0177.935-0.031-0.0310.0000.0000.0000.000
77B81ALA00.000-0.02010.6050.0270.0270.0000.0000.0000.000
78B82GLU-1-0.772-0.83312.3370.2180.2180.0000.0000.0000.000
79B83ILE0-0.021-0.00511.483-0.005-0.0050.0000.0000.0000.000
80B84ILE00.0060.00315.795-0.018-0.0180.0000.0000.0000.000
81B85LEU0-0.0240.02318.077-0.008-0.0080.0000.0000.0000.000
82B86PRO0-0.002-0.00120.660-0.006-0.0060.0000.0000.0000.000
83B87ILE0-0.040-0.02122.2690.0000.0000.0000.0000.0000.000
84B88LYS10.9560.98225.255-0.071-0.0710.0000.0000.0000.000
85B173GLU-1-0.867-0.94227.2720.0700.0700.0000.0000.0000.000
86B174ASN0-0.062-0.04126.7470.0110.0110.0000.0000.0000.000
87B175TYR00.0290.01923.7720.0030.0030.0000.0000.0000.000
88B176THR00.0120.01620.417-0.005-0.0050.0000.0000.0000.000
89B177ARG10.7140.81919.586-0.165-0.1650.0000.0000.0000.000
90B178PHE00.018-0.00314.871-0.012-0.0120.0000.0000.0000.000
91B179TRP0-0.016-0.02014.0090.0120.0120.0000.0000.0000.000
92B180VAL00.006-0.0047.4400.0230.0230.0000.0000.0000.000
93B181LEU0-0.012-0.0129.980-0.058-0.0580.0000.0000.0000.000
94B182GLY00.022-0.0066.8600.2740.2740.0000.0000.0000.000
95B183ASP-1-0.926-0.9606.4420.0710.0710.0000.0000.0000.000
96B184GLU-1-0.960-0.9705.236-1.816-1.8160.0000.0000.0000.000
97B185THR00.026-0.0017.0360.1630.1630.0000.0000.0000.000
98B186PRO0-0.0210.0145.0540.0300.0300.0000.0000.0000.000
99B187THR0-0.028-0.0276.191-0.484-0.4840.0000.0000.0000.000
100B188ILE00.0080.0047.6320.2050.2050.0000.0000.0000.000
101B189HIS0-0.019-0.00210.106-0.093-0.0930.0000.0000.0000.000
102B190LEU00.0090.01112.438-0.065-0.0650.0000.0000.0000.000
103B191LYS10.9220.95015.267-0.123-0.1230.0000.0000.0000.000
104B192GLU-1-0.839-0.91416.3960.2250.2250.0000.0000.0000.000
105B193GLU-1-0.939-0.94418.6240.1050.1050.0000.0000.0000.000
106B194ASP-1-0.803-0.91020.1900.1130.1130.0000.0000.0000.000
107B195GLN0-0.016-0.01016.7920.0290.0290.0000.0000.0000.000
108B196LYS10.9030.98119.306-0.157-0.1570.0000.0000.0000.000
109B197ILE0-0.024-0.01019.3030.0100.0100.0000.0000.0000.000
110B198SER0-0.017-0.02119.779-0.003-0.0030.0000.0000.0000.000
111B199LEU0-0.032-0.01520.8510.0030.0030.0000.0000.0000.000
112B200ALA00.0010.00223.4170.0000.0000.0000.0000.0000.000
113B201LEU0-0.0090.00124.934-0.005-0.0050.0000.0000.0000.000
114B202THR00.021-0.00128.3660.0000.0000.0000.0000.0000.000
115B203LEU0-0.025-0.00731.001-0.002-0.0020.0000.0000.0000.000
116B204PRO00.0480.01734.4730.0010.0010.0000.0000.0000.000
117B205ASP-1-0.925-0.96237.1150.0440.0440.0000.0000.0000.000
118B206ASN0-0.086-0.05634.4070.0020.0020.0000.0000.0000.000
119B207LEU00.0360.01836.6740.0000.0000.0000.0000.0000.000
120B208PRO00.023-0.00537.2310.0000.0000.0000.0000.0000.000
121B209GLY0-0.0130.00138.2950.0000.0000.0000.0000.0000.000
122B210ALA0-0.018-0.01238.165-0.002-0.0020.0000.0000.0000.000
123B211LEU00.0460.02433.3110.0000.0000.0000.0000.0000.000
124B212TYR00.0430.02035.9630.0010.0010.0000.0000.0000.000
125B213LYS10.9150.98037.657-0.043-0.0430.0000.0000.0000.000
126B214ALA00.0630.03732.411-0.001-0.0010.0000.0000.0000.000
127B215LEU00.029-0.00232.5940.0010.0010.0000.0000.0000.000
128B216SER0-0.029-0.03634.427-0.001-0.0010.0000.0000.0000.000
129B217THR0-0.049-0.00532.325-0.002-0.0020.0000.0000.0000.000
130B218PHE00.0320.01027.127-0.002-0.0020.0000.0000.0000.000
131B219ALA00.0130.01532.553-0.001-0.0010.0000.0000.0000.000
132B220TRP0-0.108-0.05835.440-0.002-0.0020.0000.0000.0000.000
133B221ARG10.7380.84731.896-0.050-0.0500.0000.0000.0000.000
134B222GLY0-0.012-0.00833.6300.0000.0000.0000.0000.0000.000
135B223ILE0-0.067-0.02127.8730.0020.0020.0000.0000.0000.000
136B224ASP-1-0.855-0.92530.2300.0660.0660.0000.0000.0000.000
137B225LEU0-0.075-0.02928.8390.0070.0070.0000.0000.0000.000
138B226THR0-0.014-0.01826.2550.0010.0010.0000.0000.0000.000
139B227LYS10.8310.90523.829-0.140-0.1400.0000.0000.0000.000
140B228ILE0-0.008-0.01228.3660.0000.0000.0000.0000.0000.000
141B229GLU-1-0.854-0.88127.5950.1010.1010.0000.0000.0000.000
142B230SER0-0.0250.01129.1890.0010.0010.0000.0000.0000.000
143B231ARG10.8200.88026.720-0.113-0.1130.0000.0000.0000.000
144B232PRO00.000-0.01530.228-0.003-0.0030.0000.0000.0000.000
145B233LEU00.0030.00930.0380.0080.0080.0000.0000.0000.000
146B234LYS10.8040.89128.703-0.105-0.1050.0000.0000.0000.000
147B235THR00.013-0.02232.9440.0010.0010.0000.0000.0000.000
148B236ILE0-0.022-0.00735.735-0.003-0.0030.0000.0000.0000.000
149B237LEU0-0.014-0.01737.8400.0020.0020.0000.0000.0000.000
150B238GLY0-0.015-0.01038.690-0.003-0.0030.0000.0000.0000.000
151B239GLU-1-0.800-0.83535.7020.0610.0610.0000.0000.0000.000
152B240TYR0-0.043-0.03732.8810.0020.0020.0000.0000.0000.000
153B241PHE00.0080.01125.056-0.002-0.0020.0000.0000.0000.000
154B242PHE0-0.007-0.03129.3370.0000.0000.0000.0000.0000.000
155B243ILE0-0.0100.00223.5890.0030.0030.0000.0000.0000.000
156B244ILE0-0.003-0.00525.745-0.007-0.0070.0000.0000.0000.000
157B245ASP-1-0.752-0.82623.1790.1630.1630.0000.0000.0000.000
158B246PHE0-0.019-0.02824.395-0.012-0.0120.0000.0000.0000.000
159B247GLU-1-0.863-0.93023.9470.1000.1000.0000.0000.0000.000
160B248ASN0-0.108-0.09519.345-0.019-0.0190.0000.0000.0000.000
161B249HIS00.0250.01522.041-0.001-0.0010.0000.0000.0000.000
162B250ASN0-0.032-0.01524.195-0.008-0.0080.0000.0000.0000.000
163B251GLU-1-0.703-0.83019.6310.0900.0900.0000.0000.0000.000
164B252LYS10.8900.96723.686-0.032-0.0320.0000.0000.0000.000
165B253LEU0-0.005-0.01226.387-0.003-0.0030.0000.0000.0000.000
166B254VAL00.0800.03723.856-0.002-0.0020.0000.0000.0000.000
167B255SER0-0.056-0.03924.6800.0000.0000.0000.0000.0000.000
168B256PHE00.001-0.00326.467-0.002-0.0020.0000.0000.0000.000
169B257ALA00.0160.02028.906-0.002-0.0020.0000.0000.0000.000
170B258LEU0-0.002-0.00123.7250.0000.0000.0000.0000.0000.000
171B259GLU-1-0.915-0.95828.2140.0370.0370.0000.0000.0000.000
172B260GLU-1-0.751-0.85530.4060.0420.0420.0000.0000.0000.000
173B261LEU0-0.0080.01228.567-0.001-0.0010.0000.0000.0000.000
174B262THR00.006-0.01029.7300.0000.0000.0000.0000.0000.000
175B263SER0-0.112-0.05431.898-0.003-0.0030.0000.0000.0000.000
176B264ILE0-0.055-0.02634.979-0.002-0.0020.0000.0000.0000.000
177B265GLY0-0.021-0.00334.848-0.001-0.0010.0000.0000.0000.000
178B266ILE0-0.076-0.03930.9100.0020.0020.0000.0000.0000.000
179B267HIS00.0180.01928.8630.0020.0020.0000.0000.0000.000
180B268TYR0-0.016-0.02124.0330.0040.0040.0000.0000.0000.000
181B269LYS10.8090.89419.213-0.177-0.1770.0000.0000.0000.000
182B270ILE00.017-0.00218.1220.0010.0010.0000.0000.0000.000
183B271LEU0-0.015-0.00918.0380.0090.0090.0000.0000.0000.000
184B272GLY00.0770.03815.6280.0360.0360.0000.0000.0000.000
185B273LYS10.8590.93015.408-0.116-0.1160.0000.0000.0000.000
186B274TYR0-0.046-0.02414.3700.0220.0220.0000.0000.0000.000
187B275ALA00.0560.04514.331-0.033-0.0330.0000.0000.0000.000
188B276VAL0-0.018-0.01615.5100.0380.0380.0000.0000.0000.000
189B277TYR00.013-0.00512.7180.0090.0090.0000.0000.0000.000
190B278ARG10.7440.80716.959-0.135-0.1350.0000.0000.0000.000