FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: MV9QZ

Calculation Name: 4LDS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4LDS

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0H2

Base Structure: X-ray

Registration Date: 2023-06-22

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 421
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -7156884.792994
FMO2-HF: Nuclear repulsion 6999503.070892
FMO2-HF: Total energy -157381.722102
FMO2-MP2: Total energy -157843.09245


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:7:LEU)


Summations of interaction energy for fragment #1(A:7:LEU)
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.
-3.0990.7732.048-1.469-4.4510
Interaction energy analysis for fragmet #1(A:7:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.058 / q_NPA : 0.013
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].
3A9PHE00.0540.0123.887-2.072-0.982-0.003-0.430-0.6570.001
4A10ILE0-0.0020.0112.498-1.673-0.2511.723-0.686-2.4590.000
5A11LEU00.0400.0092.634-0.8210.4490.329-0.348-1.251-0.001
6A12GLY00.0070.0055.0460.2950.385-0.001-0.005-0.0840.000
7A13ALA00.0070.0047.6580.0980.0980.0000.0000.0000.000
8A14LEU0-0.025-0.0176.3850.0730.0730.0000.0000.0000.000
9A15GLY00.0380.0249.0520.0610.0610.0000.0000.0000.000
10A16GLY00.0200.01211.6040.0570.0570.0000.0000.0000.000
11A17LEU0-0.052-0.01511.0950.0280.0280.0000.0000.0000.000
12A18LEU00.005-0.00612.4060.0340.0340.0000.0000.0000.000
13A19TYR0-0.035-0.01114.7780.0320.0320.0000.0000.0000.000
14A20GLY00.017-0.00416.7250.0190.0190.0000.0000.0000.000
15A21TYR00.007-0.01016.2810.0190.0190.0000.0000.0000.000
16A22ASP-1-0.725-0.88518.227-0.116-0.1160.0000.0000.0000.000
17A23ASN0-0.005-0.01121.1090.0130.0130.0000.0000.0000.000
18A24GLY00.0130.00821.5670.0090.0090.0000.0000.0000.000
19A25VAL0-0.012-0.01221.0200.0050.0050.0000.0000.0000.000
20A26ILE0-0.001-0.01023.4360.0060.0060.0000.0000.0000.000
21A27SER0-0.0150.00825.4190.0090.0090.0000.0000.0000.000
22A28GLY00.0280.00825.7750.0050.0050.0000.0000.0000.000
23A29ALA00.0130.01427.1320.0030.0030.0000.0000.0000.000
24A30LEU0-0.026-0.02929.2500.0060.0060.0000.0000.0000.000
25A31LEU0-0.0450.00829.5110.0060.0060.0000.0000.0000.000
26A32PHE00.0410.00828.4980.0050.0050.0000.0000.0000.000
27A33ILE0-0.0160.00133.0830.0020.0020.0000.0000.0000.000
28A34HIS0-0.015-0.01634.727-0.002-0.0020.0000.0000.0000.000
29A35LYS10.7990.89534.6250.0830.0830.0000.0000.0000.000
30A36ASP-1-0.821-0.91031.871-0.093-0.0930.0000.0000.0000.000
31A37ILE0-0.068-0.02335.5360.0010.0010.0000.0000.0000.000
32A38PRO00.0270.02736.9780.0020.0020.0000.0000.0000.000
33A39LEU0-0.046-0.02138.7430.0030.0030.0000.0000.0000.000
34A40ASN00.024-0.00741.537-0.001-0.0010.0000.0000.0000.000
35A41SER00.042-0.02138.805-0.001-0.0010.0000.0000.0000.000
36A42THR0-0.024-0.01639.1510.0000.0000.0000.0000.0000.000
37A43THR0-0.029-0.02538.9420.0000.0000.0000.0000.0000.000
38A44GLU-1-0.749-0.85235.167-0.058-0.0580.0000.0000.0000.000
39A45GLY00.0580.03634.540-0.003-0.0030.0000.0000.0000.000
40A46ILE0-0.0130.00735.2100.0000.0000.0000.0000.0000.000
41A47VAL00.0340.02131.695-0.001-0.0010.0000.0000.0000.000
42A48VAL00.0080.00929.242-0.005-0.0050.0000.0000.0000.000
43A49SER0-0.002-0.02230.6540.0010.0010.0000.0000.0000.000
44A50SER0-0.025-0.02732.1500.0030.0030.0000.0000.0000.000
45A51MET0-0.038-0.00225.3120.0000.0000.0000.0000.0000.000
46A52LEU00.0090.00027.090-0.001-0.0010.0000.0000.0000.000
47A53ILE0-0.003-0.00429.3500.0050.0050.0000.0000.0000.000
48A54GLY00.0160.01328.2120.0030.0030.0000.0000.0000.000
49A55ALA0-0.008-0.00225.6030.0010.0010.0000.0000.0000.000
50A56ILE0-0.001-0.00426.5720.0060.0060.0000.0000.0000.000
51A57VAL0-0.022-0.00929.2550.0050.0050.0000.0000.0000.000
52A58GLY00.0290.01825.5700.0040.0040.0000.0000.0000.000
53A59ALA00.0050.02524.5080.0040.0040.0000.0000.0000.000
54A60GLY0-0.024-0.00125.5450.0100.0100.0000.0000.0000.000
55A61SER0-0.029-0.02528.1150.0070.0070.0000.0000.0000.000
56A62SER00.004-0.01623.032-0.002-0.0020.0000.0000.0000.000
57A63GLY00.0160.01524.8540.0040.0040.0000.0000.0000.000
58A64PRO00.0450.00826.0290.0040.0040.0000.0000.0000.000
59A65LEU0-0.0160.00026.2410.0020.0020.0000.0000.0000.000
60A66ALA0-0.003-0.00422.6680.0000.0000.0000.0000.0000.000
61A67ASP-1-0.873-0.92724.3510.0570.0570.0000.0000.0000.000
62A68LYS10.8940.96527.1190.0040.0040.0000.0000.0000.000
63A69LEU0-0.060-0.03825.710-0.001-0.0010.0000.0000.0000.000
64A70GLY00.0710.05122.906-0.006-0.0060.0000.0000.0000.000
65A71ARG10.8580.89118.983-0.104-0.1040.0000.0000.0000.000
66A72ARG10.8550.91814.856-0.001-0.0010.0000.0000.0000.000
67A73ARG10.8960.92717.060-0.016-0.0160.0000.0000.0000.000
68A74LEU00.0100.02519.620-0.020-0.0200.0000.0000.0000.000
69A75VAL00.0360.00814.125-0.014-0.0140.0000.0000.0000.000
70A76MET0-0.0060.00614.512-0.048-0.0480.0000.0000.0000.000
71A77LEU0-0.0160.00316.471-0.020-0.0200.0000.0000.0000.000
72A78ILE0-0.010-0.00117.424-0.010-0.0100.0000.0000.0000.000
73A79ALA00.0070.00014.429-0.010-0.0100.0000.0000.0000.000
74A80ILE00.017-0.00116.331-0.017-0.0170.0000.0000.0000.000
75A81VAL0-0.038-0.02619.0880.0030.0030.0000.0000.0000.000
76A82PHE00.0150.00316.7300.0000.0000.0000.0000.0000.000
77A83ILE00.0050.02518.1900.0030.0030.0000.0000.0000.000
78A84ILE0-0.021-0.01219.7760.0100.0100.0000.0000.0000.000
79A85GLY00.029-0.00122.9330.0080.0080.0000.0000.0000.000
80A86ALA0-0.008-0.00820.4270.0080.0080.0000.0000.0000.000
81A87LEU00.013-0.01021.8380.0040.0040.0000.0000.0000.000
82A88ILE0-0.065-0.01823.8570.0100.0100.0000.0000.0000.000
83A89LEU0-0.028-0.01624.9620.0090.0090.0000.0000.0000.000
84A90ALA00.0130.01824.2800.0010.0010.0000.0000.0000.000
85A91ALA0-0.041-0.01626.2600.0020.0020.0000.0000.0000.000
86A92SER00.013-0.02530.0910.0010.0010.0000.0000.0000.000
87A93THR0-0.019-0.01333.2810.0010.0010.0000.0000.0000.000
88A94ASN00.0340.01136.9020.0040.0040.0000.0000.0000.000
89A95LEU00.0760.03036.464-0.003-0.0030.0000.0000.0000.000
90A96ALA0-0.0020.01236.006-0.001-0.0010.0000.0000.0000.000
91A97LEU00.0010.00532.1050.0000.0000.0000.0000.0000.000
92A98LEU00.0470.03430.855-0.005-0.0050.0000.0000.0000.000
93A99ILE00.0050.00431.378-0.002-0.0020.0000.0000.0000.000
94A100ILE00.004-0.01131.315-0.001-0.0010.0000.0000.0000.000
95A101GLY00.0520.02328.519-0.003-0.0030.0000.0000.0000.000
96A102ARG10.8240.91224.4690.0980.0980.0000.0000.0000.000
97A103LEU0-0.010-0.00127.366-0.001-0.0010.0000.0000.0000.000
98A104ILE0-0.024-0.00924.8240.0010.0010.0000.0000.0000.000
99A105ILE00.0220.00820.445-0.005-0.0050.0000.0000.0000.000
100A106GLY00.0320.02122.699-0.005-0.0050.0000.0000.0000.000
101A107LEU0-0.078-0.03324.3120.0040.0040.0000.0000.0000.000
102A108ALA0-0.0180.00519.6070.0080.0080.0000.0000.0000.000
103A109VAL00.0040.00319.839-0.002-0.0020.0000.0000.0000.000
104A110GLY00.001-0.01020.7320.0070.0070.0000.0000.0000.000
105A111GLY00.0240.00821.1400.0120.0120.0000.0000.0000.000
106A112SER0-0.032-0.01615.7140.0180.0180.0000.0000.0000.000
107A113MET0-0.0140.00917.9780.0220.0220.0000.0000.0000.000
108A114SER0-0.040-0.03120.0240.0190.0190.0000.0000.0000.000
109A115THR0-0.041-0.02318.5840.0220.0220.0000.0000.0000.000
110A116VAL0-0.0100.00412.5610.0270.0270.0000.0000.0000.000
111A117PRO00.0310.00614.5490.0420.0420.0000.0000.0000.000
112A118VAL0-0.006-0.00116.2100.0490.0490.0000.0000.0000.000
113A119TYR00.031-0.00612.1980.0420.0420.0000.0000.0000.000
114A120LEU0-0.002-0.00310.3470.0520.0520.0000.0000.0000.000
115A121SER0-0.046-0.02113.2580.0790.0790.0000.0000.0000.000
116A122GLU-1-0.818-0.88115.8090.1370.1370.0000.0000.0000.000
117A123MET0-0.009-0.02710.347-0.005-0.0050.0000.0000.0000.000
118A124ALA0-0.0020.02011.3750.1750.1750.0000.0000.0000.000
119A125PRO00.0120.00613.211-0.096-0.0960.0000.0000.0000.000
120A126THR0-0.056-0.06116.166-0.002-0.0020.0000.0000.0000.000
121A127GLU-1-0.848-0.91416.9630.3500.3500.0000.0000.0000.000
122A128TYR0-0.0140.00410.955-0.002-0.0020.0000.0000.0000.000
123A129ARG10.8730.93414.456-0.288-0.2880.0000.0000.0000.000
124A130GLY00.0610.04015.404-0.052-0.0520.0000.0000.0000.000
125A131SER00.0540.01416.793-0.013-0.0130.0000.0000.0000.000
126A132LEU00.0110.03210.631-0.029-0.0290.0000.0000.0000.000
127A133GLY00.0500.02412.369-0.019-0.0190.0000.0000.0000.000
128A134SER0-0.055-0.04614.577-0.061-0.0610.0000.0000.0000.000
129A135LEU00.0410.0209.335-0.026-0.0260.0000.0000.0000.000
130A136ASN0-0.022-0.02811.329-0.111-0.1110.0000.0000.0000.000
131A137GLN0-0.011-0.00112.422-0.042-0.0420.0000.0000.0000.000
132A138LEU00.0230.00813.728-0.025-0.0250.0000.0000.0000.000
133A139MET0-0.0040.0077.766-0.047-0.0470.0000.0000.0000.000
134A140ILE00.0070.01512.590-0.042-0.0420.0000.0000.0000.000
135A141THR0-0.0070.00215.209-0.021-0.0210.0000.0000.0000.000
136A142ILE00.0090.00012.157-0.006-0.0060.0000.0000.0000.000
137A143GLY00.021-0.00414.916-0.024-0.0240.0000.0000.0000.000
138A144ILE0-0.057-0.01815.380-0.001-0.0010.0000.0000.0000.000
139A145LEU0-0.039-0.00318.233-0.001-0.0010.0000.0000.0000.000
140A146ALA00.015-0.00815.7430.0010.0010.0000.0000.0000.000
141A147ALA0-0.0090.01617.669-0.005-0.0050.0000.0000.0000.000
142A148TYR0-0.026-0.03819.0600.0020.0020.0000.0000.0000.000
143A149LEU0-0.038-0.00619.0640.0070.0070.0000.0000.0000.000
144A150VAL00.007-0.01117.1840.0030.0030.0000.0000.0000.000
145A151ASN0-0.072-0.02920.6240.0080.0080.0000.0000.0000.000
146A152TYR00.0230.00823.4010.0070.0070.0000.0000.0000.000
147A153ALA0-0.0150.00922.3120.0060.0060.0000.0000.0000.000
148A154PHE0-0.072-0.03520.3950.0010.0010.0000.0000.0000.000
149A155ALA00.0100.00025.4980.0070.0070.0000.0000.0000.000
150A156ASP-1-0.796-0.87528.820-0.081-0.0810.0000.0000.0000.000
151A157ILE00.0040.00828.887-0.010-0.0100.0000.0000.0000.000
152A158GLU-1-0.803-0.88128.965-0.106-0.1060.0000.0000.0000.000
153A159GLY0-0.015-0.00526.225-0.009-0.0090.0000.0000.0000.000
154A160TRP00.0380.00824.575-0.017-0.0170.0000.0000.0000.000
155A161ARG10.7880.86724.4600.0970.0970.0000.0000.0000.000
156A162TRP0-0.016-0.00621.291-0.005-0.0050.0000.0000.0000.000
157A163MET0-0.054-0.02719.804-0.027-0.0270.0000.0000.0000.000
158A164LEU00.0090.01420.122-0.017-0.0170.0000.0000.0000.000
159A165GLY00.0500.02620.714-0.009-0.0090.0000.0000.0000.000
160A166LEU0-0.082-0.05716.593-0.028-0.0280.0000.0000.0000.000
161A167ALA00.0190.02216.550-0.022-0.0220.0000.0000.0000.000
162A168VAL0-0.014-0.00716.718-0.019-0.0190.0000.0000.0000.000
163A169VAL0-0.0050.02312.283-0.032-0.0320.0000.0000.0000.000
164A170PRO00.0190.00711.393-0.066-0.0660.0000.0000.0000.000
165A171SER0-0.039-0.03311.740-0.038-0.0380.0000.0000.0000.000
166A172VAL00.045-0.00112.676-0.006-0.0060.0000.0000.0000.000
167A173ILE0-0.0030.0117.307-0.045-0.0450.0000.0000.0000.000
168A174LEU0-0.0040.0158.108-0.146-0.1460.0000.0000.0000.000
169A175LEU0-0.016-0.0099.8680.0200.0200.0000.0000.0000.000
170A176VAL00.007-0.0027.0550.0310.0310.0000.0000.0000.000
171A177GLY0-0.029-0.0196.159-0.064-0.0640.0000.0000.0000.000
172A178ILE0-0.037-0.0337.0980.1640.1640.0000.0000.0000.000
173A179TYR0-0.018-0.01310.4230.0760.0760.0000.0000.0000.000
174A180PHE0-0.015-0.0015.0190.0690.0690.0000.0000.0000.000
175A181MET0-0.0670.0057.9270.1150.1150.0000.0000.0000.000
176A182PRO00.0310.01411.426-0.047-0.0470.0000.0000.0000.000
177A183GLU-1-0.855-0.92914.7610.0280.0280.0000.0000.0000.000
178A184SER0-0.036-0.00116.8010.0240.0240.0000.0000.0000.000
179A185PRO00.0660.02815.168-0.018-0.0180.0000.0000.0000.000
180A186ARG10.8950.91916.923-0.310-0.3100.0000.0000.0000.000
181A187TRP0-0.002-0.00420.779-0.015-0.0150.0000.0000.0000.000
182A188LEU0-0.052-0.01819.358-0.012-0.0120.0000.0000.0000.000
183A189LEU0-0.018-0.02122.374-0.007-0.0070.0000.0000.0000.000
184A190GLU-1-0.916-0.92824.4170.0870.0870.0000.0000.0000.000
185A191ASN0-0.038-0.03326.347-0.011-0.0110.0000.0000.0000.000
186A192ARG10.9440.97727.490-0.073-0.0730.0000.0000.0000.000
187A193ASN0-0.0040.01725.165-0.004-0.0040.0000.0000.0000.000
188A194GLU-1-0.859-0.95724.2200.1700.1700.0000.0000.0000.000
189A195GLU-1-0.918-0.94223.4740.1170.1170.0000.0000.0000.000
190A196ALA00.008-0.00819.7530.0180.0180.0000.0000.0000.000
191A197ALA00.0020.00619.1200.0330.0330.0000.0000.0000.000
192A198ARG10.9140.96119.272-0.134-0.1340.0000.0000.0000.000
193A199GLN00.0210.00519.7160.0240.0240.0000.0000.0000.000
194A200VAL00.0240.01313.7810.0370.0370.0000.0000.0000.000
195A201MET00.0030.00314.9730.0970.0970.0000.0000.0000.000
196A202LYS10.7490.85816.496-0.208-0.2080.0000.0000.0000.000
197A203ILE0-0.051-0.02012.4060.0290.0290.0000.0000.0000.000
198A204THR0-0.079-0.04310.7350.1000.1000.0000.0000.0000.000
199A205TYR0-0.022-0.0329.5050.2380.2380.0000.0000.0000.000
200A206ASP-1-0.896-0.93214.3910.3870.3870.0000.0000.0000.000
201A207ASP-1-0.730-0.84917.0680.2210.2210.0000.0000.0000.000
202A208SER0-0.075-0.04320.278-0.035-0.0350.0000.0000.0000.000
203A209GLU-1-0.844-0.92720.1160.2520.2520.0000.0000.0000.000
204A210ILE0-0.081-0.02518.092-0.016-0.0160.0000.0000.0000.000
205A211ASP-1-0.792-0.87621.1950.1610.1610.0000.0000.0000.000
206A212LYS10.8050.90422.451-0.293-0.2930.0000.0000.0000.000
207A213GLU-1-0.751-0.86419.5270.2880.2880.0000.0000.0000.000
208A214LEU0-0.048-0.02322.601-0.016-0.0160.0000.0000.0000.000
209A215LYS10.7970.87624.212-0.192-0.1920.0000.0000.0000.000
210A216GLU-1-0.841-0.91724.7760.1930.1930.0000.0000.0000.000
211A217MET0-0.0180.01321.496-0.003-0.0030.0000.0000.0000.000
212A218LYS10.8620.92924.973-0.126-0.1260.0000.0000.0000.000
213A219GLU-1-0.823-0.89827.7630.1030.1030.0000.0000.0000.000
214A220ILE0-0.005-0.01224.512-0.013-0.0130.0000.0000.0000.000
215A221ASN0-0.063-0.03825.4040.0000.0000.0000.0000.0000.000
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