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

tag_button

FMODB ID: R1J38

Calculation Name: 3C38-A-Xray311

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3C38

Chain ID: A

ChEMBL ID:

UniProt ID: Q9KLK7

Base Structure: X-ray

Registration Date: 2021-09-06

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 222
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2525057.467393
FMO2-HF: Nuclear repulsion 2440402.637377
FMO2-HF: Total energy -84654.830016
FMO2-MP2: Total energy -84905.851921


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:51:ACE )


Summations of interaction energy for fragment #1(A:51: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.
1.6352.961-0.004-0.547-0.773-0.001
Interaction energy analysis for fragmet #1(A:51:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.039 / 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].
3A53SER 00.0620.0273.8440.6671.679-0.006-0.495-0.510-0.001
4A54VAL 00.0420.0067.0370.2520.2520.0000.0000.0000.000
5A55GLN 0-0.035-0.0224.0540.1890.3810.001-0.029-0.1630.000
6A56THR 00.0100.0174.0920.2730.3950.001-0.023-0.1000.000
7A57SER 00.018-0.0406.6380.0800.0800.0000.0000.0000.000
8A58SER 0-0.036-0.0148.9220.0850.0850.0000.0000.0000.000
9A59LEU 00.0130.0207.6820.0470.0470.0000.0000.0000.000
10A60ILE 00.0100.0059.9070.0050.0050.0000.0000.0000.000
11A61GLN 00.0050.00812.205-0.013-0.0130.0000.0000.0000.000
12A62SER 0-0.032-0.01312.8350.0180.0180.0000.0000.0000.000
13A63LEU 0-0.017-0.00812.2860.0000.0000.0000.0000.0000.000
14A64PHE 0-0.021-0.01315.704-0.010-0.0100.0000.0000.0000.000
15A65ASP -1-0.835-0.92717.9320.0160.0160.0000.0000.0000.000
16A66PHE 0-0.073-0.03418.247-0.002-0.0020.0000.0000.0000.000
17A67ARG 10.9740.99220.083-0.070-0.0700.0000.0000.0000.000
18A68LEU 00.0340.01022.341-0.006-0.0060.0000.0000.0000.000
19A69ALA 0-0.044-0.02123.215-0.006-0.0060.0000.0000.0000.000
20A70ALA 00.0190.01324.400-0.004-0.0040.0000.0000.0000.000
21A71LEU 00.0170.01126.263-0.005-0.0050.0000.0000.0000.000
22A72ARG 10.9380.98125.439-0.035-0.0350.0000.0000.0000.000
23A73ILE 0-0.056-0.02726.806-0.004-0.0040.0000.0000.0000.000
24A74HIS 00.0380.02429.561-0.007-0.0070.0000.0000.0000.000
25A75GLN 0-0.0060.01432.261-0.003-0.0030.0000.0000.0000.000
26A76ASP -1-0.800-0.91133.1270.0180.0180.0000.0000.0000.000
27A77SER 0-0.081-0.02634.715-0.003-0.0030.0000.0000.0000.000
28A78THR 0-0.003-0.01136.352-0.001-0.0010.0000.0000.0000.000
29A79ALA 0-0.034-0.00738.020-0.002-0.0020.0000.0000.0000.000
30A80LYS 10.9170.95438.383-0.020-0.0200.0000.0000.0000.000
31A81ASN 00.0450.03541.454-0.001-0.0010.0000.0000.0000.000
32A82ALA 00.0610.01943.157-0.001-0.0010.0000.0000.0000.000
33A83SER 0-0.016-0.00245.423-0.001-0.0010.0000.0000.0000.000
34A84LEU 0-0.0010.02441.598-0.001-0.0010.0000.0000.0000.000
35A85ILE 00.0200.00444.902-0.001-0.0010.0000.0000.0000.000
36A86ASN 00.010-0.02647.495-0.001-0.0010.0000.0000.0000.000
37A87ALA 00.035-0.00648.000-0.001-0.0010.0000.0000.0000.000
38A88LEU 00.0060.00146.367-0.001-0.0010.0000.0000.0000.000
39A89VAL 00.0070.02149.475-0.001-0.0010.0000.0000.0000.000
40A90SER 0-0.076-0.03252.444-0.001-0.0010.0000.0000.0000.000
41A91ARG 10.8500.90951.476-0.009-0.0090.0000.0000.0000.000
42A92ASP -1-0.863-0.90553.0580.0140.0140.0000.0000.0000.000
43A93SER 0-0.019-0.02650.0650.0010.0010.0000.0000.0000.000
44A94SER 00.0560.01349.0910.0010.0010.0000.0000.0000.000
45A95ARG 10.8440.95350.068-0.015-0.0150.0000.0000.0000.000
46A96LEU 0-0.080-0.03445.8650.0010.0010.0000.0000.0000.000
47A97ASP -1-0.814-0.89845.1250.0200.0200.0000.0000.0000.000
48A98GLU -1-0.919-0.95544.4780.0260.0260.0000.0000.0000.000
49A99PHE 0-0.007-0.00941.4600.0020.0020.0000.0000.0000.000
50A100PHE 00.011-0.01939.2190.0020.0020.0000.0000.0000.000
51A101SER 00.0400.03439.6650.0020.0020.0000.0000.0000.000
52A102SER 0-0.003-0.00540.5030.0020.0020.0000.0000.0000.000
53A103VAL 0-0.078-0.03436.3860.0020.0020.0000.0000.0000.000
54A104ASP -1-0.750-0.85535.6220.0400.0400.0000.0000.0000.000
55A105GLU -1-1.001-0.97935.9840.0410.0410.0000.0000.0000.000
56A106LEU 0-0.036-0.02335.4870.0030.0030.0000.0000.0000.000
57A107GLU -1-0.918-0.97930.9740.0680.0680.0000.0000.0000.000
58A108LEU 0-0.021-0.00831.9750.0020.0020.0000.0000.0000.000
59A109SER 0-0.035-0.00527.791-0.002-0.0020.0000.0000.0000.000
60A110ASN 0-0.117-0.06326.8610.0080.0080.0000.0000.0000.000
61A111ALA 00.0380.02728.927-0.004-0.0040.0000.0000.0000.000
62A112PRO 0-0.088-0.05230.2330.0020.0020.0000.0000.0000.000
63A113ASP -1-0.787-0.88329.5220.0380.0380.0000.0000.0000.000
64A114LEU 0-0.056-0.03032.518-0.003-0.0030.0000.0000.0000.000
65A115ARG 10.8010.86835.257-0.032-0.0320.0000.0000.0000.000
66A116PHE 00.0440.02637.904-0.001-0.0010.0000.0000.0000.000
67A117ILE 0-0.008-0.01040.7330.0000.0000.0000.0000.0000.000
68A118SER 0-0.0260.00243.051-0.001-0.0010.0000.0000.0000.000
69A119SER 00.038-0.00344.9300.0010.0010.0000.0000.0000.000
70A120HIS 0-0.003-0.00147.073-0.001-0.0010.0000.0000.0000.000
71A121ASP -1-0.837-0.88846.9830.0000.0000.0000.0000.0000.000
72A122ASN 0-0.021-0.00448.0570.0000.0000.0000.0000.0000.000
73A123ILE 00.0260.00243.9090.0000.0000.0000.0000.0000.000
74A124LEU 0-0.108-0.04947.2960.0000.0000.0000.0000.0000.000
75A125TRP 0-0.012-0.02541.0220.0000.0000.0000.0000.0000.000
76A126ASP -1-0.802-0.91542.0140.0140.0140.0000.0000.0000.000
77A127ASP -1-0.808-0.89338.1930.0230.0230.0000.0000.0000.000
78A128GLY 0-0.0070.00141.8810.0010.0010.0000.0000.0000.000
79A129ASN 0-0.002-0.01836.9250.0000.0000.0000.0000.0000.000
80A130ALA 0-0.015-0.01437.9040.0000.0000.0000.0000.0000.000
81A131SER 0-0.009-0.00538.959-0.001-0.0010.0000.0000.0000.000
82A132PHE 00.0140.02833.906-0.001-0.0010.0000.0000.0000.000
83A133TYR 0-0.007-0.00331.4930.0000.0000.0000.0000.0000.000
84A134GLY 00.0570.03136.623-0.002-0.0020.0000.0000.0000.000
85A135ILE 0-0.073-0.03135.403-0.003-0.0030.0000.0000.0000.000
86A136ALA 00.003-0.00339.6890.0010.0010.0000.0000.0000.000
87A137GLN 00.0490.02143.003-0.001-0.0010.0000.0000.0000.000
88A138GLN 00.012-0.01444.7870.0010.0010.0000.0000.0000.000
89A139GLU -1-0.876-0.95540.397-0.003-0.0030.0000.0000.0000.000
90A140LEU 00.0500.02838.987-0.001-0.0010.0000.0000.0000.000
91A141ASN 0-0.009-0.01641.4240.0000.0000.0000.0000.0000.000
92A142LYS 10.8420.92741.5330.0030.0030.0000.0000.0000.000
93A143LEU 00.015-0.00336.315-0.002-0.0020.0000.0000.0000.000
94A144ILE 0-0.0150.01939.0100.0000.0000.0000.0000.0000.000
95A145ARG 10.7830.85640.9850.0030.0030.0000.0000.0000.000
96A146ARG 10.8240.90336.2460.0050.0050.0000.0000.0000.000
97A147VAL 00.0030.02334.692-0.002-0.0020.0000.0000.0000.000
98A148ALA 0-0.0030.00636.9310.0010.0010.0000.0000.0000.000
99A149ILE 0-0.016-0.01633.7760.0010.0010.0000.0000.0000.000
100A150SER 0-0.021-0.02036.2380.0010.0010.0000.0000.0000.000
101A151GLY 0-0.031-0.01833.225-0.001-0.0010.0000.0000.0000.000
102A152ASN 0-0.0060.00630.2480.0030.0030.0000.0000.0000.000
103A153TRP 0-0.046-0.04426.9030.0000.0000.0000.0000.0000.000
104A154HIS 0-0.021-0.01529.409-0.006-0.0060.0000.0000.0000.000
105A155LEU 0-0.0030.01425.5230.0040.0040.0000.0000.0000.000
106A156VAL 0-0.032-0.01129.105-0.004-0.0040.0000.0000.0000.000
107A157GLN 00.0720.02630.7760.0040.0040.0000.0000.0000.000
108A158THR 0-0.0010.00433.195-0.002-0.0020.0000.0000.0000.000
109A159PRO 0-0.051-0.01835.8620.0000.0000.0000.0000.0000.000
110A160SER 00.0370.02136.5060.0010.0010.0000.0000.0000.000
111A161GLU -1-0.982-0.97638.5100.0090.0090.0000.0000.0000.000
112A162GLY 00.025-0.01437.6700.0000.0000.0000.0000.0000.000
113A163LYS 10.9050.97329.075-0.007-0.0070.0000.0000.0000.000
114A164SER 0-0.019-0.01032.3190.0010.0010.0000.0000.0000.000
115A165VAL 00.0060.00431.6500.0000.0000.0000.0000.0000.000
116A166HIS 00.0370.02927.924-0.003-0.0030.0000.0000.0000.000
117A167ILE 00.004-0.00929.2120.0050.0050.0000.0000.0000.000
118A168LEU 00.0110.03424.195-0.004-0.0040.0000.0000.0000.000
119A169MET 0-0.008-0.01528.8370.0040.0040.0000.0000.0000.000
120A170ARG 10.8490.92229.983-0.020-0.0200.0000.0000.0000.000
121A171ARG 10.9140.98233.040-0.001-0.0010.0000.0000.0000.000
122A172SER 0-0.021-0.03036.037-0.001-0.0010.0000.0000.0000.000
123A173SER 0-0.016-0.03837.7660.0000.0000.0000.0000.0000.000
124A174LEU 00.0370.04541.2890.0010.0010.0000.0000.0000.000
125A175ILE 0-0.048-0.00443.513-0.001-0.0010.0000.0000.0000.000
126A176GLU -1-0.898-0.95146.0930.0120.0120.0000.0000.0000.000
127A177ALA 0-0.004-0.01049.0070.0000.0000.0000.0000.0000.000
128A178GLY 00.0650.05549.463-0.001-0.0010.0000.0000.0000.000
129A179THR 0-0.051-0.04251.069-0.001-0.0010.0000.0000.0000.000
130A180GLY 00.0060.01252.699-0.001-0.0010.0000.0000.0000.000
131A181GLN 0-0.055-0.07047.9260.0000.0000.0000.0000.0000.000
132A182VAL 0-0.048-0.02545.3800.0010.0010.0000.0000.0000.000
133A183VAL 00.0100.01747.549-0.001-0.0010.0000.0000.0000.000
134A184GLY 0-0.002-0.00446.2210.0000.0000.0000.0000.0000.000
135A185TYR 0-0.053-0.01640.6910.0000.0000.0000.0000.0000.000
136A186LEU 00.0520.03937.9210.0000.0000.0000.0000.0000.000
137A187TYR 0-0.027-0.03037.008-0.001-0.0010.0000.0000.0000.000
138A188VAL 00.0100.00732.0300.0010.0010.0000.0000.0000.000
139A189GLY 00.003-0.01531.737-0.003-0.0030.0000.0000.0000.000
140A190ILE 0-0.0120.01025.8260.0040.0040.0000.0000.0000.000
141A191VAL 0-0.039-0.02428.855-0.006-0.0060.0000.0000.0000.000
142A192LEU 00.024-0.00623.7150.0050.0050.0000.0000.0000.000
143A193ASN 0-0.036-0.01925.6820.0020.0020.0000.0000.0000.000
144A194ASP -1-0.875-0.94226.7160.0240.0240.0000.0000.0000.000
145A195ASN 0-0.0140.01024.7400.0130.0130.0000.0000.0000.000
146A196PHE 0-0.001-0.02321.6620.0060.0060.0000.0000.0000.000
147A197ALA 00.0220.01222.0090.0110.0110.0000.0000.0000.000
148A198LEU 00.0090.00720.7090.0130.0130.0000.0000.0000.000
149A199LEU 00.008-0.00316.9700.0120.0120.0000.0000.0000.000
150A200GLU -1-0.767-0.85717.1820.1850.1850.0000.0000.0000.000
151A201ASN 0-0.066-0.02817.2290.0250.0250.0000.0000.0000.000
152A202ILE 00.0490.02713.6390.0270.0270.0000.0000.0000.000
153A203ARG 10.7930.87513.087-0.186-0.1860.0000.0000.0000.000
154A204SER 0-0.043-0.02312.4290.0700.0700.0000.0000.0000.000
155A205GLY 00.0240.02813.0140.0630.0630.0000.0000.0000.000
156A206SER 0-0.055-0.0449.0180.0550.0550.0000.0000.0000.000
157A207ASN 0-0.119-0.0648.3210.0970.0970.0000.0000.0000.000
158A208SER 00.0050.0029.0070.0640.0640.0000.0000.0000.000
159A209GLU -1-0.854-0.9409.9800.1230.1230.0000.0000.0000.000
160A210ASN 0-0.043-0.03912.151-0.019-0.0190.0000.0000.0000.000
161A211LEU 0-0.0050.00811.761-0.010-0.0100.0000.0000.0000.000
162A212VAL 00.0010.00515.1640.0010.0010.0000.0000.0000.000
163A213LEU 0-0.0020.02317.748-0.014-0.0140.0000.0000.0000.000
164A214ALA 00.017-0.00119.8410.0040.0040.0000.0000.0000.000
165A215VAL 0-0.0070.00222.080-0.005-0.0050.0000.0000.0000.000
166A216ASP -1-0.940-0.97323.811-0.050-0.0500.0000.0000.0000.000
167A217THR 00.0650.03723.377-0.008-0.0080.0000.0000.0000.000
168A218THR 0-0.063-0.03125.2870.0060.0060.0000.0000.0000.000
169A219PRO 0-0.018-0.01123.1520.0000.0000.0000.0000.0000.000
170A220LEU 0-0.099-0.05023.5730.0030.0030.0000.0000.0000.000
171A221VAL 00.0580.02621.4350.0040.0040.0000.0000.0000.000
172A222SER 00.0170.00520.144-0.002-0.0020.0000.0000.0000.000
173A223THR 00.0400.02017.2060.0040.0040.0000.0000.0000.000
174A224LEU 0-0.096-0.04117.6920.0100.0100.0000.0000.0000.000
175A225LYS 10.8620.93118.103-0.122-0.1220.0000.0000.0000.000
176A226GLY 0-0.014-0.01322.418-0.006-0.0060.0000.0000.0000.000
177A227ASN 0-0.061-0.03122.211-0.005-0.0050.0000.0000.0000.000
178A228GLU -1-0.760-0.86118.2070.0730.0730.0000.0000.0000.000
179A229PRO 0-0.038-0.02318.562-0.009-0.0090.0000.0000.0000.000
180A230TYR 00.0140.03314.991-0.013-0.0130.0000.0000.0000.000
181A231SER 00.0460.01720.3460.0080.0080.0000.0000.0000.000
182A232LEU 00.0480.00721.087-0.005-0.0050.0000.0000.0000.000
183A233ASP -1-0.916-0.95921.747-0.036-0.0360.0000.0000.0000.000
184A234TYR 00.0090.00616.254-0.009-0.0090.0000.0000.0000.000
185A235VAL 00.0240.00216.286-0.012-0.0120.0000.0000.0000.000
186A236VAL 0-0.0190.02218.410-0.015-0.0150.0000.0000.0000.000
187A237HIS 0-0.078-0.02820.763-0.008-0.0080.0000.0000.0000.000
188A238SER 0-0.057-0.04617.347-0.013-0.0130.0000.0000.0000.000
189A239ALA 0-0.027-0.01518.200-0.005-0.0050.0000.0000.0000.000
190A240LYS 10.9260.94812.0110.3830.3830.0000.0000.0000.000
191A241ASP -1-0.893-0.9439.293-0.729-0.7290.0000.0000.0000.000
192A242ALA 0-0.0230.00911.871-0.036-0.0360.0000.0000.0000.000
193A243MET 0-0.024-0.0248.6490.0050.0050.0000.0000.0000.000
194A244ARG 10.8170.86611.9500.1810.1810.0000.0000.0000.000
195A245ASP -1-0.835-0.87114.994-0.126-0.1260.0000.0000.0000.000
196A246SER 0-0.022-0.01114.021-0.011-0.0110.0000.0000.0000.000
197A247PHE 00.014-0.00913.0440.0210.0210.0000.0000.0000.000
198A248ILE 0-0.0040.0178.516-0.037-0.0370.0000.0000.0000.000
199A249VAL 00.0570.02710.8300.0420.0420.0000.0000.0000.000
200A250GLY 00.0170.0229.976-0.063-0.0630.0000.0000.0000.000
201A251GLN 00.012-0.01410.9150.0580.0580.0000.0000.0000.000
202A252THR 00.0320.05711.789-0.064-0.0640.0000.0000.0000.000
203A253PHE 0-0.039-0.00214.2670.0280.0280.0000.0000.0000.000
204A254LEU 00.0140.01416.306-0.005-0.0050.0000.0000.0000.000
205A255GLU -1-0.938-0.93718.720-0.076-0.0760.0000.0000.0000.000
206A256VAL 00.013-0.00920.8500.0140.0140.0000.0000.0000.000
207A257GLU -1-0.852-0.90423.780-0.001-0.0010.0000.0000.0000.000
208A258SER 0-0.039-0.02521.867-0.001-0.0010.0000.0000.0000.000
209A259VAL 0-0.0120.01122.984-0.009-0.0090.0000.0000.0000.000
210A260PRO 00.0130.00622.2670.0030.0030.0000.0000.0000.000
211A261THR 0-0.031-0.04521.9000.0090.0090.0000.0000.0000.000
212A262TYR 0-0.029-0.05322.581-0.010-0.0100.0000.0000.0000.000
213A263LEU 0-0.029-0.00821.3760.0010.0010.0000.0000.0000.000
214A264CYS 0-0.0260.00317.820-0.014-0.0140.0000.0000.0000.000
215A265VAL 00.031-0.00113.7280.0150.0150.0000.0000.0000.000
216A266TYR 00.018-0.00114.237-0.032-0.0320.0000.0000.0000.000
217A267SER 00.005-0.0108.8710.0220.0220.0000.0000.0000.000
218A268ILE 0-0.013-0.00211.103-0.066-0.0660.0000.0000.0000.000
219A269GLN 00.013-0.0016.2160.1160.1160.0000.0000.0000.000
220A270THR 0-0.039-0.0199.481-0.095-0.0950.0000.0000.0000.000
221A271ASN 0-0.013-0.0149.6940.0260.0260.0000.0000.0000.000
222A272NME 0-0.0120.0099.6490.0490.0490.0000.0000.0000.000