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: GNL51

Calculation Name: 3PLT-A-Xray318

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3PLT

Chain ID: A

ChEMBL ID:

UniProt ID: Q12230

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 216
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2034826.031202
FMO2-HF: Nuclear repulsion 1950893.276475
FMO2-HF: Total energy -83932.754727
FMO2-MP2: Total energy -84180.745695


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:50:ACE )


Summations of interaction energy for fragment #1(A:50:ACE )
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.
-0.892-0.0872.56-1.86-1.5060
Interaction energy analysis for fragmet #1(A:50:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.012 / q_NPA : -0.020
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].
3A52PRO 00.0290.0073.8540.8361.766-0.006-0.474-0.4510.000
4A53GLU -1-0.836-0.9337.162-0.078-0.0780.0000.0000.0000.000
5A54LEU 0-0.050-0.0198.6560.0170.0170.0000.0000.0000.000
6A55ALA 00.0190.0328.2440.0200.0200.0000.0000.0000.000
7A56ARG 10.9390.9762.083-2.569-2.6942.566-1.386-1.0550.000
8A57LYS 11.0010.9927.7940.0680.0680.0000.0000.0000.000
9A58LEU 00.0980.08210.9980.0340.0340.0000.0000.0000.000
10A59SER 0-0.040-0.0378.308-0.047-0.0470.0000.0000.0000.000
11A60GLN 0-0.043-0.0277.4300.0160.0160.0000.0000.0000.000
12A61LEU 00.0420.03710.7440.0440.0440.0000.0000.0000.000
13A62VAL 00.0300.01413.1990.0150.0150.0000.0000.0000.000
14A63LYS 10.8710.93310.4780.2010.2010.0000.0000.0000.000
15A64THR 00.021-0.00213.5120.0380.0380.0000.0000.0000.000
16A65GLU -1-0.681-0.77415.903-0.095-0.0950.0000.0000.0000.000
17A66LYS 10.8380.92915.8820.2390.2390.0000.0000.0000.000
18A67GLY 0-0.034-0.01117.7330.0120.0120.0000.0000.0000.000
19A68VAL 00.0430.02719.2730.0120.0120.0000.0000.0000.000
20A69LEU 00.0210.02221.7140.0040.0040.0000.0000.0000.000
21A70ARG 10.9540.95918.6030.1180.1180.0000.0000.0000.000
22A71ALA 0-0.0070.00523.4450.0080.0080.0000.0000.0000.000
23A72MET 0-0.028-0.01025.3660.0070.0070.0000.0000.0000.000
24A73GLU -1-0.891-0.94325.417-0.081-0.0810.0000.0000.0000.000
25A74VAL 0-0.024-0.00127.2120.0040.0040.0000.0000.0000.000
26A75VAL 0-0.030-0.00429.7320.0040.0040.0000.0000.0000.000
27A76ALA 00.0110.01331.6810.0030.0030.0000.0000.0000.000
28A77SER 0-0.006-0.01332.4100.0020.0020.0000.0000.0000.000
29A78GLU -1-0.924-0.96733.131-0.019-0.0190.0000.0000.0000.000
30A79ARG 10.8970.95334.8620.0290.0290.0000.0000.0000.000
31A80ARG 10.9040.96834.1480.0440.0440.0000.0000.0000.000
32A81GLU -1-0.935-0.97038.137-0.023-0.0230.0000.0000.0000.000
33A82ALA 0-0.044-0.02339.7030.0020.0020.0000.0000.0000.000
34A83ALA 0-0.0210.00241.5590.0010.0010.0000.0000.0000.000
35A84LYS 10.9660.98140.8900.0270.0270.0000.0000.0000.000
36A85GLN 0-0.011-0.01141.3800.0020.0020.0000.0000.0000.000
37A86LEU 0-0.0200.01045.5780.0010.0010.0000.0000.0000.000
38A87SER 00.0460.00547.4000.0010.0010.0000.0000.0000.000
39A88LEU 0-0.044-0.03947.3840.0010.0010.0000.0000.0000.000
40A89TRP 0-0.047-0.01249.5850.0010.0010.0000.0000.0000.000
41A90GLY 00.0250.00451.2510.0010.0010.0000.0000.0000.000
42A91ALA 0-0.029-0.01553.0520.0000.0000.0000.0000.0000.000
43A92ASP -1-1.008-0.99554.984-0.008-0.0080.0000.0000.0000.000
44A93ASN 0-0.056-0.03355.9010.0010.0010.0000.0000.0000.000
45A94ASP -1-0.884-0.93358.521-0.006-0.0060.0000.0000.0000.000
46A95ASP -1-0.924-0.97359.619-0.009-0.0090.0000.0000.0000.000
47A96ASP -1-0.839-0.92160.115-0.008-0.0080.0000.0000.0000.000
48A97VAL 0-0.028-0.02054.902-0.001-0.0010.0000.0000.0000.000
49A98SER 0-0.020-0.00855.300-0.001-0.0010.0000.0000.0000.000
50A99ASP -1-0.760-0.85755.498-0.014-0.0140.0000.0000.0000.000
51A100VAL 0-0.012-0.01352.952-0.001-0.0010.0000.0000.0000.000
52A101THR 0-0.057-0.02650.217-0.001-0.0010.0000.0000.0000.000
53A102ASP -1-0.896-0.92550.420-0.017-0.0170.0000.0000.0000.000
54A103LYS 10.8670.91550.4610.0140.0140.0000.0000.0000.000
55A104LEU 0-0.029-0.01647.912-0.001-0.0010.0000.0000.0000.000
56A105GLY 00.0110.01046.393-0.001-0.0010.0000.0000.0000.000
57A106VAL 0-0.001-0.00345.742-0.002-0.0020.0000.0000.0000.000
58A107LEU 0-0.007-0.00345.353-0.002-0.0020.0000.0000.0000.000
59A108ILE 0-0.028-0.02341.247-0.002-0.0020.0000.0000.0000.000
60A109TYR 0-0.007-0.00541.130-0.002-0.0020.0000.0000.0000.000
61A110GLU -1-0.852-0.92040.662-0.036-0.0360.0000.0000.0000.000
62A111LEU 0-0.068-0.02438.464-0.003-0.0030.0000.0000.0000.000
63A112GLY 0-0.019-0.00436.559-0.003-0.0030.0000.0000.0000.000
64A113GLU -1-0.855-0.93435.922-0.045-0.0450.0000.0000.0000.000
65A114LEU 0-0.017-0.02236.404-0.004-0.0040.0000.0000.0000.000
66A115GLN 0-0.046-0.03830.971-0.003-0.0030.0000.0000.0000.000
67A116ASP -1-0.851-0.95431.854-0.062-0.0620.0000.0000.0000.000
68A117GLN 00.0030.01331.981-0.006-0.0060.0000.0000.0000.000
69A118PHE 0-0.047-0.02728.328-0.006-0.0060.0000.0000.0000.000
70A119ILE 00.0120.00726.892-0.009-0.0090.0000.0000.0000.000
71A120ASP -1-0.901-0.93127.629-0.092-0.0920.0000.0000.0000.000
72A121LYS 10.9250.95628.2820.0530.0530.0000.0000.0000.000
73A122TYR 0-0.080-0.11022.507-0.008-0.0080.0000.0000.0000.000
74A123ASP -1-0.897-0.95023.064-0.166-0.1660.0000.0000.0000.000
75A124GLN 0-0.009-0.01823.288-0.016-0.0160.0000.0000.0000.000
76A125TYR 0-0.024-0.01921.522-0.017-0.0170.0000.0000.0000.000
77A126ARG 10.9580.98016.3960.1970.1970.0000.0000.0000.000
78A127VAL 0-0.077-0.04819.222-0.044-0.0440.0000.0000.0000.000
79A128THR 00.0300.02519.976-0.027-0.0270.0000.0000.0000.000
80A129LEU 00.0350.01917.800-0.022-0.0220.0000.0000.0000.000
81A130LYS 10.8830.93915.3070.2710.2710.0000.0000.0000.000
82A131SER 0-0.090-0.05316.080-0.049-0.0490.0000.0000.0000.000
83A132ILE 00.0540.02617.279-0.012-0.0120.0000.0000.0000.000
84A133ARG 10.9350.95011.1530.6450.6450.0000.0000.0000.000
85A134ASN 0-0.056-0.02913.533-0.139-0.1390.0000.0000.0000.000
86A135ILE 00.0090.02014.825-0.016-0.0160.0000.0000.0000.000
87A136GLU -1-0.866-0.93613.731-0.311-0.3110.0000.0000.0000.000
88A137ALA 0-0.078-0.03411.300-0.041-0.0410.0000.0000.0000.000
89A138SER 0-0.093-0.05812.5670.0250.0250.0000.0000.0000.000
90A139VAL 00.0690.02915.5960.0320.0320.0000.0000.0000.000
91A140GLN 0-0.015-0.00710.3330.0440.0440.0000.0000.0000.000
92A141PRO 00.0150.02013.1230.0550.0550.0000.0000.0000.000
93A142SER 0-0.062-0.02815.2870.0460.0460.0000.0000.0000.000
94A143ARG 10.9160.95314.7220.1960.1960.0000.0000.0000.000
95A144ASP -1-0.828-0.92912.266-0.234-0.2340.0000.0000.0000.000
96A145ARG 10.9060.95615.4020.1670.1670.0000.0000.0000.000
97A146LYS 10.9760.99818.8000.0920.0920.0000.0000.0000.000
98A147GLU -1-0.940-0.96815.4740.0070.0070.0000.0000.0000.000
99A148LYS 10.9720.99217.3740.0700.0700.0000.0000.0000.000
100A149ILE 00.0170.00719.6230.0110.0110.0000.0000.0000.000
101A150THR 0-0.029-0.01922.0180.0070.0070.0000.0000.0000.000
102A151ASP -1-0.883-0.94919.2730.0250.0250.0000.0000.0000.000
103A152GLU -1-1.001-1.00522.585-0.020-0.0200.0000.0000.0000.000
104A153ILE 0-0.016-0.00424.7430.0050.0050.0000.0000.0000.000
105A154ALA 0-0.0220.00325.0980.0040.0040.0000.0000.0000.000
106A155HIS 0-0.023-0.01125.1010.0090.0090.0000.0000.0000.000
107A156LEU 0-0.054-0.03127.1990.0020.0020.0000.0000.0000.000
108A157LYS 10.8790.90730.1960.0060.0060.0000.0000.0000.000
109A158TYR 0-0.069-0.01529.0910.0030.0030.0000.0000.0000.000
110A159LYS 10.9010.93728.730-0.039-0.0390.0000.0000.0000.000
111A160ASP -1-0.898-0.94932.4730.0060.0060.0000.0000.0000.000
112A161PRO 0-0.0070.00434.610-0.003-0.0030.0000.0000.0000.000
113A162GLN 00.0040.00236.246-0.003-0.0030.0000.0000.0000.000
114A163SER 0-0.0120.01233.949-0.003-0.0030.0000.0000.0000.000
115A164THR 00.0480.01136.565-0.001-0.0010.0000.0000.0000.000
116A165LYS 10.9450.96628.3970.0160.0160.0000.0000.0000.000
117A166ILE 00.0400.02132.148-0.002-0.0020.0000.0000.0000.000
118A167PRO 00.0240.03132.943-0.002-0.0020.0000.0000.0000.000
119A168VAL 0-0.013-0.00832.251-0.003-0.0030.0000.0000.0000.000
120A169LEU 00.0360.01827.262-0.004-0.0040.0000.0000.0000.000
121A170GLU -1-0.838-0.91629.211-0.016-0.0160.0000.0000.0000.000
122A171GLN 0-0.035-0.01531.014-0.002-0.0020.0000.0000.0000.000
123A172GLU -1-0.957-1.01025.986-0.061-0.0610.0000.0000.0000.000
124A173LEU 00.0230.01724.949-0.008-0.0080.0000.0000.0000.000
125A174VAL 0-0.0130.00627.048-0.005-0.0050.0000.0000.0000.000
126A175ARG 10.9330.96428.6900.0570.0570.0000.0000.0000.000
127A176ALA 00.0470.03023.396-0.007-0.0070.0000.0000.0000.000
128A177GLU -1-0.903-0.96924.053-0.062-0.0620.0000.0000.0000.000
129A178ALA 0-0.044-0.01325.484-0.005-0.0050.0000.0000.0000.000
130A179GLU -1-0.971-0.99623.954-0.103-0.1030.0000.0000.0000.000
131A180SER 0-0.0150.00020.317-0.009-0.0090.0000.0000.0000.000
132A181LEU 00.0140.00722.681-0.008-0.0080.0000.0000.0000.000
133A182VAL 0-0.0020.01125.145-0.005-0.0050.0000.0000.0000.000
134A183ALA 0-0.011-0.00220.943-0.007-0.0070.0000.0000.0000.000
135A184GLU -1-0.858-0.93018.927-0.173-0.1730.0000.0000.0000.000
136A185ALA 0-0.020-0.01222.1240.0000.0000.0000.0000.0000.000
137A186GLN 0-0.032-0.03424.1270.0090.0090.0000.0000.0000.000
138A187LEU 00.0310.02517.691-0.003-0.0030.0000.0000.0000.000
139A188SER 0-0.004-0.00621.7300.0000.0000.0000.0000.0000.000
140A189ASN 0-0.027-0.02023.7310.0090.0090.0000.0000.0000.000
141A190ILE 00.0160.02921.8660.0010.0010.0000.0000.0000.000
142A191THR 0-0.025-0.01920.454-0.008-0.0080.0000.0000.0000.000
143A192ARG 10.9510.97722.3700.0950.0950.0000.0000.0000.000
144A193GLU -1-0.923-0.95625.610-0.100-0.1000.0000.0000.0000.000
145A194LYS 10.9500.97722.3770.1770.1770.0000.0000.0000.000
146A195LEU 0-0.0030.00222.0110.0010.0010.0000.0000.0000.000
147A196LYS 10.9520.97224.1190.0780.0780.0000.0000.0000.000
148A197ALA 00.002-0.01827.4380.0060.0060.0000.0000.0000.000
149A198ALA 0-0.012-0.00223.7900.0020.0020.0000.0000.0000.000
150A199TYR 00.004-0.01521.3190.0000.0000.0000.0000.0000.000
151A200SER 0-0.0290.00426.9150.0080.0080.0000.0000.0000.000
152A201TYR 00.0110.02228.4760.0060.0060.0000.0000.0000.000
153A202MET 00.0030.00425.3500.0070.0070.0000.0000.0000.000
154A203PHE 00.010-0.02027.9630.0050.0050.0000.0000.0000.000
155A204ASP -1-0.872-0.91731.315-0.053-0.0530.0000.0000.0000.000
156A205SER 0-0.043-0.02531.2710.0030.0030.0000.0000.0000.000
157A206LEU 0-0.032-0.02229.9830.0030.0030.0000.0000.0000.000
158A207ARG 10.8460.92732.7560.0450.0450.0000.0000.0000.000
159A208GLU -1-0.876-0.93336.031-0.047-0.0470.0000.0000.0000.000
160A209LEU 0-0.050-0.01532.6450.0030.0030.0000.0000.0000.000
161A210SER 0-0.037-0.03334.8620.0040.0040.0000.0000.0000.000
162A211GLU -1-0.879-0.94637.437-0.030-0.0300.0000.0000.0000.000
163A212LYS 10.9770.99139.9560.0420.0420.0000.0000.0000.000
164A213PHE 0-0.027-0.01736.2280.0020.0020.0000.0000.0000.000
165A214ALA 0-0.045-0.01840.7190.0020.0020.0000.0000.0000.000
166A215LEU 0-0.0070.00843.0980.0020.0020.0000.0000.0000.000
167A216ILE 00.0510.03242.4250.0020.0020.0000.0000.0000.000
168A217ALA 0-0.033-0.00243.5770.0020.0020.0000.0000.0000.000
169A218GLY 0-0.022-0.01045.4560.0020.0020.0000.0000.0000.000
170A219TYR 00.0360.00748.5360.0010.0010.0000.0000.0000.000
171A220GLY 00.034-0.00147.9930.0010.0010.0000.0000.0000.000
172A221LYS 10.8780.92849.0190.0110.0110.0000.0000.0000.000
173A222ALA 00.0110.00750.8600.0010.0010.0000.0000.0000.000
174A223LEU 00.0250.00451.0750.0010.0010.0000.0000.0000.000
175A224LEU 0-0.048-0.02449.9480.0010.0010.0000.0000.0000.000
176A225GLU -1-0.986-0.98154.255-0.009-0.0090.0000.0000.0000.000
177A226LEU 0-0.072-0.03256.9960.0000.0000.0000.0000.0000.000
178A227LEU 0-0.048-0.00954.9160.0000.0000.0000.0000.0000.000
179A228ASP -1-0.824-0.89258.512-0.005-0.0050.0000.0000.0000.000
180A229ASP -1-0.949-0.97658.499-0.005-0.0050.0000.0000.0000.000
181A230SER 0-0.069-0.05560.5900.0010.0010.0000.0000.0000.000
182A231PRO 0-0.096-0.05263.4070.0000.0000.0000.0000.0000.000
183A232VAL 00.0680.04365.0960.0000.0000.0000.0000.0000.000
184A233THR 0-0.057-0.02767.5430.0010.0010.0000.0000.0000.000
185A234PRO 0-0.030-0.03068.6860.0000.0000.0000.0000.0000.000
186A235GLY 0-0.015-0.00770.4110.0000.0000.0000.0000.0000.000
187A236GLU -1-0.992-0.98672.624-0.003-0.0030.0000.0000.0000.000
188A237ALA 0-0.013-0.00269.9860.0000.0000.0000.0000.0000.000
189A238ARG 10.9020.94862.0870.0060.0060.0000.0000.0000.000
190A239PRO 0-0.019-0.01667.1270.0000.0000.0000.0000.0000.000
191A240ALA 0-0.0180.00067.9020.0000.0000.0000.0000.0000.000
192A241TYR 0-0.009-0.02559.6220.0000.0000.0000.0000.0000.000
193A242ASP -1-0.948-0.98465.606-0.010-0.0100.0000.0000.0000.000
194A243GLY 00.0300.02361.8080.0000.0000.0000.0000.0000.000
195A244TYR 00.0220.01060.397-0.001-0.0010.0000.0000.0000.000
196A245GLU -1-0.976-0.98960.524-0.013-0.0130.0000.0000.0000.000
197A246ALA 00.0120.00360.562-0.001-0.0010.0000.0000.0000.000
198A247SER 00.0340.02256.521-0.001-0.0010.0000.0000.0000.000
199A248ARG 10.9040.94056.0320.0150.0150.0000.0000.0000.000
200A249GLN 0-0.072-0.04056.547-0.001-0.0010.0000.0000.0000.000
201A250ILE 00.0530.03652.661-0.001-0.0010.0000.0000.0000.000
202A251ILE 0-0.027-0.01051.361-0.001-0.0010.0000.0000.0000.000
203A252MET 00.003-0.00252.024-0.001-0.0010.0000.0000.0000.000
204A253ASP -1-0.846-0.90653.830-0.019-0.0190.0000.0000.0000.000
205A254ALA 0-0.041-0.02548.665-0.001-0.0010.0000.0000.0000.000
206A255GLU -1-0.987-0.99948.738-0.027-0.0270.0000.0000.0000.000
207A256SER 00.0220.02149.600-0.001-0.0010.0000.0000.0000.000
208A257ALA 0-0.038-0.03049.012-0.001-0.0010.0000.0000.0000.000
209A258LEU 0-0.050-0.03843.443-0.002-0.0020.0000.0000.0000.000
210A259GLU -1-0.974-0.97245.450-0.031-0.0310.0000.0000.0000.000
211A260SER 0-0.092-0.04747.411-0.001-0.0010.0000.0000.0000.000
212A261TRP 0-0.032-0.00639.491-0.001-0.0010.0000.0000.0000.000
213A262THR 0-0.020-0.02644.018-0.002-0.0020.0000.0000.0000.000
214A263LEU 0-0.039-0.01837.9920.0010.0010.0000.0000.0000.000
215A264ASP -1-0.910-0.95441.894-0.039-0.0390.0000.0000.0000.000
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