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: LNJM9

Calculation Name: 4Z85-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4Z85

Chain ID: A

ChEMBL ID:

UniProt ID: A4UVY1

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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2177021.129925
FMO2-HF: Nuclear repulsion 2096893.848185
FMO2-HF: Total energy -80127.28174
FMO2-MP2: Total energy -80356.491984


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(A:2:THR)


Summations of interaction energy for fragment #1(A:2: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.
-0.0242.0460.351-0.758-1.663-0.001
Interaction energy analysis for fragmet #1(A:2:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.000 / q_NPA : -0.017
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].
3A4ILE00.0170.0022.551-0.9751.0670.352-0.753-1.641-0.001
4A5ALA00.0100.0194.7890.2390.267-0.001-0.005-0.0220.000
5A6MET00.047-0.0038.5670.0230.0230.0000.0000.0000.000
6A7SER0-0.031-0.01611.1010.0280.0280.0000.0000.0000.000
7A8GLY00.0050.01311.4490.0690.0690.0000.0000.0000.000
8A9LEU0-0.0240.0068.8110.0010.0010.0000.0000.0000.000
9A10THR00.0530.01912.8270.0700.0700.0000.0000.0000.000
10A11ASN00.046-0.01515.007-0.090-0.0900.0000.0000.0000.000
11A12MET00.0340.03016.804-0.039-0.0390.0000.0000.0000.000
12A13GLN00.0560.02811.488-0.038-0.0380.0000.0000.0000.000
13A14LYS10.9540.98712.0570.4320.4320.0000.0000.0000.000
14A15TYR00.0220.01913.361-0.050-0.0500.0000.0000.0000.000
15A16TRP00.0210.00912.917-0.016-0.0160.0000.0000.0000.000
16A17LEU00.0030.0067.347-0.055-0.0550.0000.0000.0000.000
17A18ILE00.0060.02810.814-0.051-0.0510.0000.0000.0000.000
18A19THR0-0.070-0.04813.5080.0200.0200.0000.0000.0000.000
19A20GLY00.010-0.00512.6390.0860.0860.0000.0000.0000.000
20A21SER0-0.069-0.04510.059-0.011-0.0110.0000.0000.0000.000
21A22VAL0-0.0180.01312.0060.0740.0740.0000.0000.0000.000
22A23GLY0-0.0040.00115.5130.0290.0290.0000.0000.0000.000
23A24PRO00.0140.00217.819-0.008-0.0080.0000.0000.0000.000
24A25ARG10.7980.88917.6300.5740.5740.0000.0000.0000.000
25A26PRO00.0540.04722.3260.0080.0080.0000.0000.0000.000
26A27ILE0-0.005-0.03026.004-0.019-0.0190.0000.0000.0000.000
27A28ALA00.0280.02128.1200.0170.0170.0000.0000.0000.000
28A29LEU0-0.007-0.00731.090-0.011-0.0110.0000.0000.0000.000
29A30VAL0-0.017-0.00633.0900.0120.0120.0000.0000.0000.000
30A31THR00.0400.02135.601-0.005-0.0050.0000.0000.0000.000
31A32SER0-0.011-0.01638.9570.0020.0020.0000.0000.0000.000
32A33LEU00.0230.00840.9260.0000.0000.0000.0000.0000.000
33A34ASN00.0850.06143.5730.0030.0030.0000.0000.0000.000
34A35SER0-0.008-0.02444.8710.0040.0040.0000.0000.0000.000
35A36GLU-1-0.939-0.96648.040-0.101-0.1010.0000.0000.0000.000
36A37GLY0-0.047-0.01248.4110.0030.0030.0000.0000.0000.000
37A38LEU00.0020.01143.8120.0000.0000.0000.0000.0000.000
38A39CYS00.0000.00342.853-0.005-0.0050.0000.0000.0000.000
39A40ASN0-0.019-0.00438.6380.0030.0030.0000.0000.0000.000
40A41ALA00.037-0.00537.2920.0020.0020.0000.0000.0000.000
41A42ALA0-0.026-0.01032.483-0.005-0.0050.0000.0000.0000.000
42A43PRO0-0.0020.01329.3130.0030.0030.0000.0000.0000.000
43A44TYR00.006-0.01027.440-0.023-0.0230.0000.0000.0000.000
44A45SER00.0100.00323.173-0.010-0.0100.0000.0000.0000.000
45A46ALA0-0.069-0.02822.993-0.025-0.0250.0000.0000.0000.000
46A47PHE0-0.011-0.01024.1460.0210.0210.0000.0000.0000.000
47A48ASN00.0150.00524.3160.0010.0010.0000.0000.0000.000
48A49TYR00.0190.01327.6390.0040.0040.0000.0000.0000.000
49A50MET0-0.096-0.06626.588-0.012-0.0120.0000.0000.0000.000
50A51GLY00.0140.00730.9110.0040.0040.0000.0000.0000.000
51A52GLU-1-0.950-0.98033.798-0.110-0.1100.0000.0000.0000.000
52A53ASP-1-0.968-0.94837.050-0.077-0.0770.0000.0000.0000.000
53A54PRO00.020-0.00438.8190.0020.0020.0000.0000.0000.000
54A55PRO00.0270.01237.501-0.006-0.0060.0000.0000.0000.000
55A56LEU0-0.0130.01535.035-0.004-0.0040.0000.0000.0000.000
56A57PHE00.0180.00031.710-0.009-0.0090.0000.0000.0000.000
57A58VAL0-0.0110.00327.5910.0040.0040.0000.0000.0000.000
58A59ILE00.0300.00328.505-0.016-0.0160.0000.0000.0000.000
59A60ALA0-0.071-0.02525.2140.0090.0090.0000.0000.0000.000
60A61VAL0-0.004-0.00527.304-0.014-0.0140.0000.0000.0000.000
61A62ASP-1-0.849-0.90826.334-0.311-0.3110.0000.0000.0000.000
62A63HIS10.8680.92729.1300.2050.2050.0000.0000.0000.000
63A75LYS10.8700.92132.0860.2090.2090.0000.0000.0000.000
64A76ASP-1-0.828-0.91134.476-0.155-0.1550.0000.0000.0000.000
65A77THR0-0.0100.00534.3640.0010.0010.0000.0000.0000.000
66A78LEU00.0200.00833.3360.0060.0060.0000.0000.0000.000
67A79LYS10.9560.98336.2650.1280.1280.0000.0000.0000.000
68A80ASN00.0410.00839.7070.0100.0100.0000.0000.0000.000
69A81ILE0-0.025-0.00735.9720.0050.0050.0000.0000.0000.000
70A82ILE0-0.072-0.03837.7900.0050.0050.0000.0000.0000.000
71A83GLU-1-0.939-0.97241.138-0.109-0.1090.0000.0000.0000.000
72A84ARG10.9020.94343.7100.1080.1080.0000.0000.0000.000
73A85GLU-1-0.938-0.95742.373-0.097-0.0970.0000.0000.0000.000
74A86GLN00.0230.00142.7240.0000.0000.0000.0000.0000.000
75A87PHE0-0.040-0.03435.687-0.006-0.0060.0000.0000.0000.000
76A88VAL00.0230.02639.1490.0030.0030.0000.0000.0000.000
77A89VAL0-0.032-0.00833.454-0.011-0.0110.0000.0000.0000.000
78A90ASN0-0.007-0.00835.9310.0150.0150.0000.0000.0000.000
79A91MET0-0.014-0.00133.190-0.019-0.0190.0000.0000.0000.000
80A92VAL00.0350.00130.7050.0060.0060.0000.0000.0000.000
81A93ASP-1-0.843-0.93931.576-0.164-0.1640.0000.0000.0000.000
82A94GLU-1-0.945-0.98333.375-0.158-0.1580.0000.0000.0000.000
83A95ARG10.9210.98634.2590.1250.1250.0000.0000.0000.000
84A96ILE00.007-0.00234.6730.0040.0040.0000.0000.0000.000
85A97ALA00.0030.01430.940-0.007-0.0070.0000.0000.0000.000
86A98GLU-1-0.896-0.95132.052-0.223-0.2230.0000.0000.0000.000
87A99ARG10.8730.91033.6340.1360.1360.0000.0000.0000.000
88A100MET0-0.0270.00428.466-0.009-0.0090.0000.0000.0000.000
89A101VAL0-0.006-0.01828.510-0.012-0.0120.0000.0000.0000.000
90A102LEU00.0030.01030.881-0.006-0.0060.0000.0000.0000.000
91A103CYS00.0070.01333.7580.0050.0050.0000.0000.0000.000
92A104GLY0-0.073-0.03230.0530.0010.0010.0000.0000.0000.000
93A105SER0-0.066-0.03130.195-0.016-0.0160.0000.0000.0000.000
94A106ASP-1-0.940-0.98631.324-0.209-0.2090.0000.0000.0000.000
95A107PHE00.0490.01733.1180.0070.0070.0000.0000.0000.000
96A108PRO0-0.0280.02734.5720.0080.0080.0000.0000.0000.000
97A109SER0-0.083-0.05836.6420.0050.0050.0000.0000.0000.000
98A110HIS0-0.047-0.02340.0560.0100.0100.0000.0000.0000.000
99A111ILE00.0090.01339.8780.0070.0070.0000.0000.0000.000
100A112SER0-0.015-0.01240.896-0.005-0.0050.0000.0000.0000.000
101A113GLU-1-0.794-0.90936.332-0.168-0.1680.0000.0000.0000.000
102A114ALA0-0.007-0.01139.579-0.001-0.0010.0000.0000.0000.000
103A115GLU-1-0.885-0.93741.498-0.110-0.1100.0000.0000.0000.000
104A116ALA0-0.061-0.02140.2560.0010.0010.0000.0000.0000.000
105A117VAL0-0.072-0.04037.001-0.002-0.0020.0000.0000.0000.000
106A118GLY00.0100.01640.101-0.001-0.0010.0000.0000.0000.000
107A119PHE0-0.089-0.06536.444-0.002-0.0020.0000.0000.0000.000
108A120ASP-1-0.839-0.90142.367-0.104-0.1040.0000.0000.0000.000
109A121LEU0-0.030-0.02742.928-0.006-0.0060.0000.0000.0000.000
110A122THR0-0.040-0.02645.7430.0070.0070.0000.0000.0000.000
111A123PRO0-0.013-0.01346.677-0.004-0.0040.0000.0000.0000.000
112A124SER0-0.032-0.02645.140-0.001-0.0010.0000.0000.0000.000
113A125THR0-0.052-0.02647.5990.0050.0050.0000.0000.0000.000
114A126THR0-0.085-0.07846.5580.0020.0020.0000.0000.0000.000
115A127ILE0-0.110-0.04543.5380.0000.0000.0000.0000.0000.000
116A128ASP-1-0.871-0.94147.922-0.087-0.0870.0000.0000.0000.000
117A129VAL0-0.104-0.03342.094-0.001-0.0010.0000.0000.0000.000
118A130PRO00.0430.04844.7890.0010.0010.0000.0000.0000.000
119A131ARG10.9380.97841.8710.1020.1020.0000.0000.0000.000
120A132ILE00.011-0.00137.8660.0040.0040.0000.0000.0000.000
121A133THR0-0.002-0.01241.7950.0000.0000.0000.0000.0000.000
122A134ASP-1-0.826-0.90140.722-0.120-0.1200.0000.0000.0000.000
123A135ALA0-0.059-0.02338.396-0.005-0.0050.0000.0000.0000.000
124A136PRO0-0.049-0.01735.6180.0090.0090.0000.0000.0000.000
125A137ILE00.034-0.00336.0340.0070.0070.0000.0000.0000.000
126A138ALA0-0.0100.00037.673-0.009-0.0090.0000.0000.0000.000
127A139TRP00.000-0.00232.7370.0030.0030.0000.0000.0000.000
128A140GLU-1-0.708-0.83239.254-0.104-0.1040.0000.0000.0000.000
129A141CYS0-0.054-0.02238.4200.0000.0000.0000.0000.0000.000
130A142LYS11.0251.01740.9180.0940.0940.0000.0000.0000.000
131A143LEU0-0.042-0.01737.466-0.008-0.0080.0000.0000.0000.000
132A144TYR0-0.0040.01937.5040.0050.0050.0000.0000.0000.000
133A145LYS10.9600.95535.8490.1280.1280.0000.0000.0000.000
134A146ILE00.0160.01733.965-0.010-0.0100.0000.0000.0000.000
135A147ILE0-0.029-0.01030.8400.0090.0090.0000.0000.0000.000
136A148ASP-1-0.879-0.92831.325-0.179-0.1790.0000.0000.0000.000
137A149PHE0-0.062-0.02722.076-0.005-0.0050.0000.0000.0000.000
138A150SER00.018-0.01326.4900.0020.0020.0000.0000.0000.000
139A151LYS10.9740.97228.8080.1660.1660.0000.0000.0000.000
140A152GLN0-0.024-0.01026.3920.0100.0100.0000.0000.0000.000
141A153ARG10.9100.94723.2070.3300.3300.0000.0000.0000.000
142A154SER00.0090.01128.4830.0080.0080.0000.0000.0000.000
143A155MET0-0.035-0.00727.177-0.020-0.0200.0000.0000.0000.000
144A156VAL00.0370.02129.9920.0150.0150.0000.0000.0000.000
145A157PHE00.003-0.00529.989-0.011-0.0110.0000.0000.0000.000
146A158GLY00.0310.01734.2440.0090.0090.0000.0000.0000.000
147A159GLU-1-0.906-0.96536.503-0.106-0.1060.0000.0000.0000.000
148A160ILE0-0.053-0.03535.8330.0000.0000.0000.0000.0000.000
149A161VAL0-0.017-0.01239.9470.0050.0050.0000.0000.0000.000
150A162ALA00.0010.00442.9870.0060.0060.0000.0000.0000.000
151A163MET0-0.042-0.02137.914-0.007-0.0070.0000.0000.0000.000
152A164TYR00.0190.02241.8590.0080.0080.0000.0000.0000.000
153A165PHE00.021-0.01739.096-0.009-0.0090.0000.0000.0000.000
154A166ARG10.8820.93740.9330.1140.1140.0000.0000.0000.000
155A167GLU-1-0.864-0.93643.578-0.076-0.0760.0000.0000.0000.000
156A168GLU-1-0.852-0.90742.409-0.099-0.0990.0000.0000.0000.000
157A169LEU0-0.088-0.05238.190-0.002-0.0020.0000.0000.0000.000
158A170ILE0-0.017-0.00340.589-0.004-0.0040.0000.0000.0000.000
159A171ASP-1-0.940-0.97743.105-0.065-0.0650.0000.0000.0000.000
160A172GLU-1-0.905-0.97145.008-0.070-0.0700.0000.0000.0000.000
161A173GLU-1-0.910-0.94547.421-0.053-0.0530.0000.0000.0000.000
162A174LYS10.8630.94641.7020.0690.0690.0000.0000.0000.000
163A175LEU00.0200.01343.969-0.001-0.0010.0000.0000.0000.000
164A176ARG10.8440.92039.3610.0750.0750.0000.0000.0000.000
165A177VAL00.0730.04736.5290.0010.0010.0000.0000.0000.000
166A178ARG10.9200.96238.6420.0820.0820.0000.0000.0000.000
167A179VAL0-0.008-0.01432.889-0.005-0.0050.0000.0000.0000.000
168A180ASP-1-0.933-0.94734.492-0.109-0.1090.0000.0000.0000.000
169A181LEU0-0.027-0.01235.762-0.004-0.0040.0000.0000.0000.000
170A182PHE00.0340.03232.854-0.006-0.0060.0000.0000.0000.000
171A183GLN0-0.005-0.00532.039-0.009-0.0090.0000.0000.0000.000
172A184PRO00.0010.01929.367-0.006-0.0060.0000.0000.0000.000
173A185TYR00.005-0.00127.368-0.010-0.0100.0000.0000.0000.000
174A186GLY00.0070.01324.0250.0020.0020.0000.0000.0000.000
175A187ARG10.8390.91820.9970.4370.4370.0000.0000.0000.000
176A188LEU00.0330.01117.313-0.026-0.0260.0000.0000.0000.000
177A189GLY00.0400.02215.6320.0110.0110.0000.0000.0000.000
178A190GLY00.0310.01316.6970.0270.0270.0000.0000.0000.000
179A191PRO0-0.032-0.00118.6670.0170.0170.0000.0000.0000.000
180A192ASN0-0.009-0.01118.6260.0690.0690.0000.0000.0000.000
181A193TYR00.0500.01021.696-0.017-0.0170.0000.0000.0000.000
182A194CYS0-0.020-0.00421.6490.0010.0010.0000.0000.0000.000
183A195ARG11.0031.00323.6530.2210.2210.0000.0000.0000.000
184A196THR0-0.004-0.01126.3060.0010.0010.0000.0000.0000.000
185A197THR00.0320.00328.0480.0100.0100.0000.0000.0000.000
186A198ASP-1-0.965-0.95925.279-0.162-0.1620.0000.0000.0000.000
187A199ARG10.7950.85626.1750.1430.1430.0000.0000.0000.000
188A200VAL00.0420.01824.7420.0140.0140.0000.0000.0000.000
189A201ARG10.9460.98027.8310.0650.0650.0000.0000.0000.000
190A202LEU00.016-0.00323.7200.0100.0100.0000.0000.0000.000
191A203THR0-0.027-0.01327.955-0.005-0.0050.0000.0000.0000.000
192A204VAL00.0250.01027.7660.0050.0050.0000.0000.0000.000
193A205PRO0-0.040-0.00428.8150.0010.0010.0000.0000.0000.000
194A206THR00.0420.00531.958-0.001-0.0010.0000.0000.0000.000
195A207PHE0-0.042-0.01633.8740.0040.0040.0000.0000.0000.000
196A208LEU00.0280.01030.725-0.001-0.0010.0000.0000.0000.000
197A209PRO00.0080.01326.9110.0070.0070.0000.0000.0000.000
198A210SER00.024-0.00628.725-0.003-0.0030.0000.0000.0000.000
199A211ALA0-0.034-0.00825.2030.0040.0040.0000.0000.0000.000
200A212GLY00.0050.01426.2320.0100.0100.0000.0000.0000.000