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: R9468

Calculation Name: 3DMP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DMP

Chain ID: A

ChEMBL ID:

UniProt ID: Q63VS8

Base Structure: X-ray

Registration Date: 2023-06-26

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 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2479471.454702
FMO2-HF: Nuclear repulsion 2396312.149709
FMO2-HF: Total energy -83159.304993
FMO2-MP2: Total energy -83402.877264


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:0:SER)


Summations of interaction energy for fragment #1(A:0:SER)
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.
-8.378-2.6410.085-2.774-3.048-0.007
Interaction energy analysis for fragmet #1(A:0:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.011 / q_NPA : -0.006
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].
3A2LYS10.9370.9993.8502.2525.078-0.027-1.574-1.2250.001
4A3GLN0-0.036-0.0336.7420.1950.1950.0000.0000.0000.000
5A4ASP-1-0.786-0.85010.154-0.734-0.7340.0000.0000.0000.000
6A5SER0-0.013-0.01813.6900.0410.0410.0000.0000.0000.000
7A6ARG10.8450.89516.1970.7500.7500.0000.0000.0000.000
8A7PHE0-0.027-0.01915.5300.0440.0440.0000.0000.0000.000
9A8PRO00.0440.02414.578-0.115-0.1150.0000.0000.0000.000
10A9ASN0-0.018-0.02513.952-0.031-0.0310.0000.0000.0000.000
11A10LEU00.0010.02412.425-0.025-0.0250.0000.0000.0000.000
12A11PHE0-0.027-0.0147.786-0.030-0.0300.0000.0000.0000.000
13A12ILE0-0.012-0.0057.9340.1750.1750.0000.0000.0000.000
14A13LEU0-0.006-0.0024.632-1.558-1.493-0.001-0.028-0.0360.000
15A14ASP-1-0.856-0.9423.632-7.756-7.1900.005-0.303-0.268-0.002
16A15HIS00.0710.0482.993-0.2830.5580.047-0.253-0.635-0.001
17A16PRO00.0570.0113.8960.6550.7790.004-0.028-0.1010.000
18A17LEU0-0.006-0.0127.3620.1860.1860.0000.0000.0000.000
19A18ILE00.0050.0175.2090.2720.2720.0000.0000.0000.000
20A19GLN0-0.002-0.0166.4140.8020.8020.0000.0000.0000.000
21A20HIS00.0040.0149.8830.2370.2370.0000.0000.0000.000
22A21LYS10.8280.87911.8990.6800.6800.0000.0000.0000.000
23A22LEU00.0300.01912.1700.1180.1180.0000.0000.0000.000
24A23THR0-0.031-0.01413.9260.1170.1170.0000.0000.0000.000
25A24HIS0-0.045-0.02716.1320.1420.1420.0000.0000.0000.000
26A25MET0-0.0100.02015.6970.0770.0770.0000.0000.0000.000
27A26ARG10.7820.84514.5761.0131.0130.0000.0000.0000.000
28A27ASP-1-0.895-0.92719.665-0.337-0.3370.0000.0000.0000.000
29A28LYS10.8690.91322.3100.2910.2910.0000.0000.0000.000
30A29ASP-1-0.857-0.90525.622-0.252-0.2520.0000.0000.0000.000
31A30THR0-0.083-0.03721.5010.0370.0370.0000.0000.0000.000
32A31SER00.013-0.00424.632-0.005-0.0050.0000.0000.0000.000
33A32THR00.0890.03025.220-0.016-0.0160.0000.0000.0000.000
34A33ARG10.9150.95725.5390.1740.1740.0000.0000.0000.000
35A34THR00.005-0.00421.1640.0020.0020.0000.0000.0000.000
36A35PHE00.0230.02121.159-0.031-0.0310.0000.0000.0000.000
37A36ARG10.8610.91220.5490.2290.2290.0000.0000.0000.000
38A37GLU-1-0.889-0.92420.551-0.307-0.3070.0000.0000.0000.000
39A38LEU00.013-0.00216.600-0.018-0.0180.0000.0000.0000.000
40A39LEU00.0080.00815.845-0.097-0.0970.0000.0000.0000.000
41A40ARG10.8120.89216.2990.2330.2330.0000.0000.0000.000
42A41GLU-1-0.792-0.88914.502-0.485-0.4850.0000.0000.0000.000
43A42ILE00.0000.00110.460-0.051-0.0510.0000.0000.0000.000
44A43THR00.0120.00210.992-0.163-0.1630.0000.0000.0000.000
45A44LEU00.0090.03112.485-0.034-0.0340.0000.0000.0000.000
46A45LEU0-0.025-0.0258.2660.0510.0510.0000.0000.0000.000
47A46MET0-0.035-0.0167.991-0.174-0.1740.0000.0000.0000.000
48A47GLY00.0500.0098.850-0.028-0.0280.0000.0000.0000.000
49A48TYR0-0.0340.0057.5410.3270.3270.0000.0000.0000.000
50A49GLU-1-0.827-0.8843.268-0.4500.7590.058-0.585-0.681-0.005
51A50ILE0-0.051-0.0126.2710.3480.3480.0000.0000.0000.000
52A51THR0-0.069-0.0638.7640.2370.2370.0000.0000.0000.000
53A52ARG10.8260.8834.279-1.882-1.776-0.001-0.003-0.1020.000
54A53ASN0-0.034-0.0149.4420.2880.2880.0000.0000.0000.000
55A54LEU0-0.0100.00312.327-0.078-0.0780.0000.0000.0000.000
56A55PRO0-0.012-0.00515.2090.0620.0620.0000.0000.0000.000
57A56ILE0-0.0130.00317.552-0.031-0.0310.0000.0000.0000.000
58A57THR0-0.045-0.01920.262-0.004-0.0040.0000.0000.0000.000
59A58THR00.009-0.00623.8480.0170.0170.0000.0000.0000.000
60A59LYS10.9210.97726.555-0.098-0.0980.0000.0000.0000.000
61A60ARG10.8390.89929.009-0.124-0.1240.0000.0000.0000.000
62A61VAL0-0.046-0.03328.622-0.011-0.0110.0000.0000.0000.000
63A62GLU-1-0.927-0.95231.9000.1010.1010.0000.0000.0000.000
64A63THR0-0.043-0.02330.467-0.003-0.0030.0000.0000.0000.000
65A64PRO0-0.001-0.02333.133-0.004-0.0040.0000.0000.0000.000
66A65LEU0-0.045-0.01033.344-0.003-0.0030.0000.0000.0000.000
67A66VAL00.0020.00833.538-0.004-0.0040.0000.0000.0000.000
68A67GLU-1-0.814-0.88734.4640.1180.1180.0000.0000.0000.000
69A68ILE0-0.031-0.02428.4530.0110.0110.0000.0000.0000.000
70A69ASP-1-0.801-0.89229.1040.1560.1560.0000.0000.0000.000
71A70ALA0-0.0050.00125.9760.0250.0250.0000.0000.0000.000
72A71PRO00.0150.00220.945-0.020-0.0200.0000.0000.0000.000
73A72VAL0-0.041-0.02422.052-0.016-0.0160.0000.0000.0000.000
74A73ILE00.0860.03316.7650.0140.0140.0000.0000.0000.000
75A74ALA0-0.023-0.01420.905-0.021-0.0210.0000.0000.0000.000
76A75GLY00.0460.02020.897-0.018-0.0180.0000.0000.0000.000
77A76LYS10.9840.97421.946-0.020-0.0200.0000.0000.0000.000
78A77LYS10.8050.90522.629-0.038-0.0380.0000.0000.0000.000
79A78LEU00.0570.02716.767-0.006-0.0060.0000.0000.0000.000
80A79ALA0-0.034-0.01121.4320.0140.0140.0000.0000.0000.000
81A80ILE00.0300.03418.085-0.031-0.0310.0000.0000.0000.000
82A81VAL0-0.027-0.03421.1350.0380.0380.0000.0000.0000.000
83A82PRO0-0.0020.01622.379-0.037-0.0370.0000.0000.0000.000
84A83VAL00.0150.01422.8010.0430.0430.0000.0000.0000.000
85A84LEU0-0.068-0.01624.903-0.012-0.0120.0000.0000.0000.000
86A85ARG10.9630.95327.6700.2510.2510.0000.0000.0000.000
87A86ALA00.0560.00523.6830.0080.0080.0000.0000.0000.000
88A87GLY00.0640.04121.519-0.027-0.0270.0000.0000.0000.000
89A88VAL0-0.048-0.03121.693-0.011-0.0110.0000.0000.0000.000
90A89GLY00.0400.02121.6810.0110.0110.0000.0000.0000.000
91A90MET0-0.0540.00115.5860.0150.0150.0000.0000.0000.000
92A91SER00.0390.00118.1840.0010.0010.0000.0000.0000.000
93A92ASP-1-0.848-0.89920.542-0.260-0.2600.0000.0000.0000.000
94A93GLY00.0620.04517.0330.0360.0360.0000.0000.0000.000
95A94LEU0-0.022-0.02513.9960.0340.0340.0000.0000.0000.000
96A95LEU0-0.038-0.01417.2530.0560.0560.0000.0000.0000.000
97A96GLU-1-0.948-0.96818.723-0.196-0.1960.0000.0000.0000.000
98A97LEU0-0.053-0.01212.9880.0520.0520.0000.0000.0000.000
99A98ILE0-0.064-0.04215.5650.0750.0750.0000.0000.0000.000
100A99PRO00.0570.03419.263-0.012-0.0120.0000.0000.0000.000
101A100SER0-0.129-0.06522.8150.0010.0010.0000.0000.0000.000
102A101ALA00.0060.01621.1480.0120.0120.0000.0000.0000.000
103A102ARG10.9090.95523.3030.0740.0740.0000.0000.0000.000
104A103VAL00.0520.02824.154-0.018-0.0180.0000.0000.0000.000
105A104GLY0-0.045-0.02025.3600.0230.0230.0000.0000.0000.000
106A105HIS0-0.002-0.01326.126-0.028-0.0280.0000.0000.0000.000
107A106ILE00.0260.01125.5910.0230.0230.0000.0000.0000.000
108A107GLY00.0050.00127.945-0.021-0.0210.0000.0000.0000.000
109A108VAL00.003-0.04729.1120.0190.0190.0000.0000.0000.000
110A109TYR00.0060.00429.486-0.008-0.0080.0000.0000.0000.000
111A110ARG10.9250.99330.9720.1730.1730.0000.0000.0000.000
112A111ALA0-0.100-0.01431.2670.0150.0150.0000.0000.0000.000
113A112ASP-1-0.842-0.93032.174-0.250-0.2500.0000.0000.0000.000
114A113ASP-1-0.900-0.94532.083-0.259-0.2590.0000.0000.0000.000
115A114HIS0-0.009-0.00833.619-0.008-0.0080.0000.0000.0000.000
116A115ARG10.9060.94834.6580.1720.1720.0000.0000.0000.000
117A116PRO00.0940.04831.224-0.007-0.0070.0000.0000.0000.000
118A117VAL0-0.089-0.05333.0220.0190.0190.0000.0000.0000.000
119A118GLU-1-0.689-0.81632.408-0.186-0.1860.0000.0000.0000.000
120A119TYR0-0.040-0.01631.0940.0170.0170.0000.0000.0000.000
121A120LEU0-0.024-0.01132.8280.0130.0130.0000.0000.0000.000
122A121VAL00.0440.04230.616-0.015-0.0150.0000.0000.0000.000
123A122ARG10.8400.91330.9710.1600.1600.0000.0000.0000.000
124A123LEU00.0570.03427.261-0.015-0.0150.0000.0000.0000.000
125A124PRO00.0100.00326.5020.0140.0140.0000.0000.0000.000
126A125ASP-1-0.882-0.93429.624-0.081-0.0810.0000.0000.0000.000
127A126LEU00.0210.00728.293-0.006-0.0060.0000.0000.0000.000
128A127GLU-1-0.904-0.96527.747-0.075-0.0750.0000.0000.0000.000
129A128ASP-1-0.920-0.93225.724-0.001-0.0010.0000.0000.0000.000
130A129ARG10.8300.91723.6530.0980.0980.0000.0000.0000.000
131A130ILE00.0320.02617.494-0.009-0.0090.0000.0000.0000.000
132A131PHE0-0.022-0.02020.8640.0090.0090.0000.0000.0000.000
133A132ILE00.0240.00415.050-0.028-0.0280.0000.0000.0000.000
134A133LEU0-0.0050.00418.4420.0250.0250.0000.0000.0000.000
135A134CYS0-0.055-0.02217.945-0.080-0.0800.0000.0000.0000.000
136A135ASP-1-0.807-0.94318.509-0.424-0.4240.0000.0000.0000.000
137A136PRO00.0250.01317.818-0.077-0.0770.0000.0000.0000.000
138A137MET0-0.016-0.00117.699-0.117-0.1170.0000.0000.0000.000
139A138VAL00.0010.00618.6720.0560.0560.0000.0000.0000.000
140A139ALA00.0390.00820.642-0.034-0.0340.0000.0000.0000.000
141A140THR00.0920.03523.270-0.016-0.0160.0000.0000.0000.000
142A141GLY00.0660.03323.390-0.004-0.0040.0000.0000.0000.000
143A142TYR00.0250.00724.3880.0010.0010.0000.0000.0000.000
144A143SER00.0150.00625.2590.0150.0150.0000.0000.0000.000
145A144ALA00.0130.01021.4330.0150.0150.0000.0000.0000.000
146A145ALA00.0520.02823.5080.0100.0100.0000.0000.0000.000
147A146HIS00.0170.01125.2140.0350.0350.0000.0000.0000.000
148A147ALA0-0.020-0.01624.2950.0250.0250.0000.0000.0000.000
149A148ILE00.0200.01120.5100.0180.0180.0000.0000.0000.000
150A149ASP-1-0.851-0.93224.818-0.225-0.2250.0000.0000.0000.000
151A150VAL0-0.130-0.05528.2090.0270.0270.0000.0000.0000.000
152A151LEU00.0200.00124.1190.0220.0220.0000.0000.0000.000
153A152LYS10.9580.98424.6410.2800.2800.0000.0000.0000.000
154A153ARG10.7980.89128.4090.2080.2080.0000.0000.0000.000
155A154ARG10.7270.83530.7960.1760.1760.0000.0000.0000.000
156A155GLY00.0150.00831.1120.0110.0110.0000.0000.0000.000
157A156VAL0-0.061-0.01825.6750.0100.0100.0000.0000.0000.000
158A157PRO00.0360.01324.700-0.018-0.0180.0000.0000.0000.000
159A158GLY00.0460.02022.352-0.013-0.0130.0000.0000.0000.000
160A159GLU-1-0.859-0.94320.149-0.182-0.1820.0000.0000.0000.000
161A160ARG10.7680.89519.4280.1190.1190.0000.0000.0000.000
162A161LEU0-0.022-0.01219.9020.0020.0020.0000.0000.0000.000
163A162MET0-0.018-0.00214.175-0.057-0.0570.0000.0000.0000.000
164A163PHE00.0120.00816.1200.0660.0660.0000.0000.0000.000
165A164LEU00.0020.00111.760-0.121-0.1210.0000.0000.0000.000
166A165ALA00.0300.00514.2090.1360.1360.0000.0000.0000.000
167A166LEU0-0.042-0.01813.336-0.190-0.1900.0000.0000.0000.000
168A167VAL00.014-0.00813.366-0.201-0.2010.0000.0000.0000.000
169A168ALA00.0040.00915.8900.1010.1010.0000.0000.0000.000
170A169ALA00.0200.02317.560-0.057-0.0570.0000.0000.0000.000
171A170PRO00.004-0.01018.940-0.006-0.0060.0000.0000.0000.000
172A171GLU-1-0.819-0.92020.446-0.479-0.4790.0000.0000.0000.000
173A172GLY00.0550.02622.3370.0330.0330.0000.0000.0000.000
174A173VAL0-0.057-0.03816.9610.0090.0090.0000.0000.0000.000
175A174GLN0-0.050-0.02520.082-0.009-0.0090.0000.0000.0000.000
176A175VAL00.0240.01922.8870.0320.0320.0000.0000.0000.000
177A176PHE0-0.056-0.03318.6270.0210.0210.0000.0000.0000.000
178A177GLN0-0.019-0.02719.376-0.010-0.0100.0000.0000.0000.000
179A178ASP-1-0.879-0.92021.951-0.298-0.2980.0000.0000.0000.000
180A179ALA0-0.055-0.01025.5310.0300.0300.0000.0000.0000.000
181A180HIS0-0.070-0.05222.2340.0450.0450.0000.0000.0000.000
182A181PRO00.0660.05021.286-0.044-0.0440.0000.0000.0000.000
183A182ASP-1-0.935-0.96319.702-0.270-0.2700.0000.0000.0000.000
184A183VAL0-0.071-0.02918.3700.0130.0130.0000.0000.0000.000
185A184LYS10.9300.98012.5660.3290.3290.0000.0000.0000.000
186A185LEU00.0050.01314.4830.0310.0310.0000.0000.0000.000
187A186TYR0-0.009-0.0298.368-0.065-0.0650.0000.0000.0000.000
188A187VAL00.0060.00710.3540.1990.1990.0000.0000.0000.000
189A188ALA00.0240.0048.880-0.577-0.5770.0000.0000.0000.000
190A189SER0-0.093-0.0699.577-0.324-0.3240.0000.0000.0000.000
191A190LEU0-0.0220.00112.0740.1340.1340.0000.0000.0000.000
192A191ASP-1-0.747-0.82214.593-0.999-0.9990.0000.0000.0000.000
193A192SER0-0.024-0.04517.324-0.008-0.0080.0000.0000.0000.000
194A193HIS0-0.0240.00920.191-0.006-0.0060.0000.0000.0000.000
195A194LEU0-0.038-0.00423.446-0.027-0.0270.0000.0000.0000.000
196A195ASP-1-0.853-0.93425.991-0.327-0.3270.0000.0000.0000.000
197A196ASP-1-0.916-0.96528.883-0.265-0.2650.0000.0000.0000.000
198A197HIS0-0.097-0.04331.2000.0160.0160.0000.0000.0000.000
199A198ALA0-0.029-0.00428.485-0.004-0.0040.0000.0000.0000.000
200A199TYR0-0.029-0.03825.988-0.027-0.0270.0000.0000.0000.000
201A200ILE0-0.040-0.03019.585-0.003-0.0030.0000.0000.0000.000
202A201VAL0-0.0080.03822.8150.0090.0090.0000.0000.0000.000
203A202PRO0-0.006-0.03819.026-0.037-0.0370.0000.0000.0000.000
204A203GLY00.0090.01319.3020.0370.0370.0000.0000.0000.000
205A204LEU0-0.006-0.02517.306-0.012-0.0120.0000.0000.0000.000
206A205GLY00.0340.02921.2540.0410.0410.0000.0000.0000.000
207A206ASP-1-0.772-0.86224.455-0.368-0.3680.0000.0000.0000.000
208A207ALA00.020-0.00322.7580.0070.0070.0000.0000.0000.000
209A208GLY0-0.003-0.01024.5080.0130.0130.0000.0000.0000.000
210A209ASP-1-0.843-0.92827.586-0.256-0.2560.0000.0000.0000.000
211A210ARG10.7640.88222.5160.4560.4560.0000.0000.0000.000
212A211LEU0-0.042-0.01922.1880.0090.0090.0000.0000.0000.000
213A212PHE0-0.092-0.05226.1630.0210.0210.0000.0000.0000.000
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