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: LZ8G9

Calculation Name: 1UFO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1UFO

Chain ID: A

ChEMBL ID:

UniProt ID: P83821

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 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 238
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2990204.196437
FMO2-HF: Nuclear repulsion 2900653.592958
FMO2-HF: Total energy -89550.603479
FMO2-MP2: Total energy -89817.722623


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-19.044-9.59718.187-9.366-18.269-0.046
Interaction energy analysis for fragmet #1(A:1:MET)
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 : 0.031
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].
3A3VAL0-0.008-0.0112.735-1.9361.8180.817-1.949-2.622-0.006
4A4ARG10.8390.9264.584-0.116-0.067-0.001-0.014-0.0340.000
5A5THR00.007-0.0118.3150.0070.0070.0000.0000.0000.000
6A6GLU-1-0.857-0.91611.3250.2160.2160.0000.0000.0000.000
7A7ARG10.7980.85514.2640.0940.0940.0000.0000.0000.000
8A8LEU00.0290.02314.3470.0310.0310.0000.0000.0000.000
9A9THR00.0340.01618.523-0.021-0.0210.0000.0000.0000.000
10A10LEU0-0.004-0.00717.3920.0230.0230.0000.0000.0000.000
11A11ALA00.0490.01622.065-0.014-0.0140.0000.0000.0000.000
12A12GLY00.0120.01025.422-0.007-0.0070.0000.0000.0000.000
13A13LEU0-0.0180.00824.006-0.004-0.0040.0000.0000.0000.000
14A14SER0-0.0070.00622.1790.0040.0040.0000.0000.0000.000
15A15VAL0-0.026-0.02117.129-0.016-0.0160.0000.0000.0000.000
16A16LEU0-0.0230.00215.0540.0190.0190.0000.0000.0000.000
17A17ALA00.0260.00712.655-0.014-0.0140.0000.0000.0000.000
18A18ARG10.8430.8877.4731.4451.4450.0000.0000.0000.000
19A19ILE00.0110.0147.504-0.079-0.0790.0000.0000.0000.000
20A20PRO00.002-0.0032.705-0.954-2.7335.709-1.481-2.4490.009
21A21GLU-1-0.798-0.8922.958-1.2291.3791.901-1.583-2.926-0.015
22A22ALA0-0.014-0.0112.316-3.717-4.5945.460-1.571-3.0130.006
23A23PRO0-0.043-0.0212.692-4.481-3.4840.670-0.341-1.326-0.012
24A24LYS10.7830.8745.1880.7710.7710.0000.0000.0000.000
25A25ALA0-0.012-0.0106.7430.0700.0700.0000.0000.0000.000
26A26LEU0-0.0100.0098.6550.0570.0570.0000.0000.0000.000
27A27LEU0-0.028-0.01811.316-0.056-0.0560.0000.0000.0000.000
28A28LEU0-0.0060.01712.808-0.001-0.0010.0000.0000.0000.000
29A29ALA0-0.010-0.01015.117-0.013-0.0130.0000.0000.0000.000
30A30LEU0-0.012-0.00917.1340.0200.0200.0000.0000.0000.000
31A31HIS00.0120.00220.838-0.004-0.0040.0000.0000.0000.000
32A32GLY00.0430.02222.2550.0160.0160.0000.0000.0000.000
33A33LEU0-0.020-0.01425.6050.0000.0000.0000.0000.0000.000
34A34GLN0-0.042-0.03128.424-0.007-0.0070.0000.0000.0000.000
35A35GLY0-0.0380.00624.680-0.006-0.0060.0000.0000.0000.000
36A36SER0-0.005-0.04221.9770.0100.0100.0000.0000.0000.000
37A37LYS10.7680.84518.7540.1450.1450.0000.0000.0000.000
38A38GLU-1-0.773-0.86517.438-0.249-0.2490.0000.0000.0000.000
39A39HIS0-0.0220.00417.346-0.059-0.0590.0000.0000.0000.000
40A40ILE0-0.006-0.01517.249-0.026-0.0260.0000.0000.0000.000
41A41LEU00.0020.00012.507-0.043-0.0430.0000.0000.0000.000
42A42ALA0-0.022-0.00413.203-0.098-0.0980.0000.0000.0000.000
43A43LEU0-0.067-0.02315.201-0.031-0.0310.0000.0000.0000.000
44A44LEU0-0.028-0.00612.2160.0250.0250.0000.0000.0000.000
45A45PRO00.0030.00510.512-0.141-0.1410.0000.0000.0000.000
46A46GLY0-0.005-0.0137.1500.1260.1260.0000.0000.0000.000
47A47TYR0-0.011-0.0346.533-0.312-0.3120.0000.0000.0000.000
48A48ALA00.0360.0215.196-0.340-0.222-0.001-0.013-0.1030.000
49A49GLU-1-0.813-0.8952.388-5.470-3.4811.372-1.295-2.067-0.007
50A50ARG10.8160.9052.683-2.098-0.2771.528-1.048-2.301-0.019
51A51GLY00.0480.0282.537-1.661-0.4910.650-0.663-1.157-0.002
52A52PHE0-0.043-0.0233.0731.7271.3240.0820.592-0.2710.000
53A53LEU00.014-0.0016.7350.0110.0110.0000.0000.0000.000
54A54LEU0-0.015-0.0078.462-0.070-0.0700.0000.0000.0000.000
55A55LEU00.0120.00110.9030.0780.0780.0000.0000.0000.000
56A56ALA00.0400.02814.515-0.028-0.0280.0000.0000.0000.000
57A57PHE00.007-0.01417.4420.0140.0140.0000.0000.0000.000
58A58ASP-1-0.742-0.84620.998-0.172-0.1720.0000.0000.0000.000
59A59ALA00.0320.01824.0900.0160.0160.0000.0000.0000.000
60A60PRO00.013-0.01026.8960.0010.0010.0000.0000.0000.000
61A61ARG10.7720.87330.4210.0730.0730.0000.0000.0000.000
62A62HIS00.000-0.00626.990-0.008-0.0080.0000.0000.0000.000
63A63GLY00.0540.01425.3240.0030.0030.0000.0000.0000.000
64A64GLU-1-0.823-0.86623.322-0.127-0.1270.0000.0000.0000.000
65A65ARG10.6890.80226.5430.0960.0960.0000.0000.0000.000
66A66GLU-1-0.891-0.94429.640-0.073-0.0730.0000.0000.0000.000
67A67GLY00.0050.00533.440-0.001-0.0010.0000.0000.0000.000
68A68PRO00.0070.01334.4340.0040.0040.0000.0000.0000.000
69A69PRO00.0520.02431.1500.0050.0050.0000.0000.0000.000
70A70PRO0-0.0170.00733.1660.0050.0050.0000.0000.0000.000
71A71SER00.0210.01335.441-0.005-0.0050.0000.0000.0000.000
72A72SER0-0.003-0.01737.9390.0050.0050.0000.0000.0000.000
73A73LYS10.9520.96939.5460.0830.0830.0000.0000.0000.000
74A74SER00.0140.01341.5360.0050.0050.0000.0000.0000.000
75A75PRO00.0520.01643.342-0.002-0.0020.0000.0000.0000.000
76A76ARG10.8220.89142.9360.0490.0490.0000.0000.0000.000
77A77TYR00.0080.01335.600-0.004-0.0040.0000.0000.0000.000
78A78VAL00.035-0.00738.191-0.004-0.0040.0000.0000.0000.000
79A79GLU-1-0.735-0.85138.172-0.053-0.0530.0000.0000.0000.000
80A80GLU-1-0.793-0.87237.486-0.072-0.0720.0000.0000.0000.000
81A81VAL0-0.018-0.01532.990-0.003-0.0030.0000.0000.0000.000
82A82TYR00.0270.00732.870-0.004-0.0040.0000.0000.0000.000
83A83ARG10.8930.92534.7310.0540.0540.0000.0000.0000.000
84A84VAL0-0.026-0.01330.4070.0010.0010.0000.0000.0000.000
85A85ALA0-0.002-0.00530.012-0.002-0.0020.0000.0000.0000.000
86A86LEU0-0.018-0.01230.2220.0000.0000.0000.0000.0000.000
87A87GLY0-0.0030.00731.7060.0040.0040.0000.0000.0000.000
88A88PHE00.0210.00423.0320.0030.0030.0000.0000.0000.000
89A89LYS10.8640.92526.3680.0520.0520.0000.0000.0000.000
90A90GLU-1-0.856-0.90426.987-0.036-0.0360.0000.0000.0000.000
91A91GLU-1-0.770-0.85926.215-0.069-0.0690.0000.0000.0000.000
92A92ALA00.003-0.00422.7820.0040.0040.0000.0000.0000.000
93A93ARG10.8270.89822.4950.0390.0390.0000.0000.0000.000
94A94ARG10.8300.88723.6760.0420.0420.0000.0000.0000.000
95A95VAL0-0.036-0.02119.2150.0130.0130.0000.0000.0000.000
96A96ALA00.0040.00018.8570.0110.0110.0000.0000.0000.000
97A97GLU-1-0.815-0.91419.216-0.003-0.0030.0000.0000.0000.000
98A98GLU-1-0.859-0.90620.8690.0750.0750.0000.0000.0000.000
99A99ALA0-0.017-0.00715.6840.0260.0260.0000.0000.0000.000
100A100GLU-1-0.894-0.96616.5380.0040.0040.0000.0000.0000.000
101A101ARG10.8380.91517.823-0.006-0.0060.0000.0000.0000.000
102A102ARG10.7730.88517.536-0.079-0.0790.0000.0000.0000.000
103A103PHE0-0.014-0.02012.7680.0370.0370.0000.0000.0000.000
104A104GLY00.0250.02813.6280.0450.0450.0000.0000.0000.000
105A105LEU0-0.050-0.0119.165-0.009-0.0090.0000.0000.0000.000
106A106PRO00.002-0.01411.483-0.023-0.0230.0000.0000.0000.000
107A107LEU00.0040.03312.674-0.054-0.0540.0000.0000.0000.000
108A108PHE0-0.019-0.01312.293-0.003-0.0030.0000.0000.0000.000
109A109LEU00.015-0.00215.5150.0070.0070.0000.0000.0000.000
110A110ALA00.0190.00716.020-0.024-0.0240.0000.0000.0000.000
111A111GLY00.0250.02417.8990.0150.0150.0000.0000.0000.000
112A112GLY00.0160.01021.320-0.008-0.0080.0000.0000.0000.000
113A113SER0-0.039-0.03123.0040.0170.0170.0000.0000.0000.000
114A114LEU0-0.042-0.02326.8490.0050.0050.0000.0000.0000.000
115A115GLY00.0890.04323.9100.0100.0100.0000.0000.0000.000
116A116ALA0-0.036-0.00823.9670.0010.0010.0000.0000.0000.000
117A117PHE0-0.019-0.01024.8960.0090.0090.0000.0000.0000.000
118A118VAL00.0080.00325.2460.0090.0090.0000.0000.0000.000
119A119ALA00.0300.01622.6660.0080.0080.0000.0000.0000.000
120A120HIS0-0.0280.00624.4370.0170.0170.0000.0000.0000.000
121A121LEU0-0.031-0.02127.5110.0090.0090.0000.0000.0000.000
122A122LEU0-0.013-0.00323.0760.0080.0080.0000.0000.0000.000
123A123LEU0-0.0120.01023.3750.0080.0080.0000.0000.0000.000
124A124ALA00.0090.01027.2120.0080.0080.0000.0000.0000.000
125A125GLU-1-0.848-0.89329.503-0.044-0.0440.0000.0000.0000.000
126A126GLY00.0120.01528.9240.0050.0050.0000.0000.0000.000
127A127PHE0-0.0030.00520.4050.0030.0030.0000.0000.0000.000
128A128ARG10.8250.89223.7670.0420.0420.0000.0000.0000.000
129A129PRO00.0320.04018.4950.0060.0060.0000.0000.0000.000
130A130ARG10.8950.92415.6490.1090.1090.0000.0000.0000.000
131A131GLY00.002-0.00318.082-0.006-0.0060.0000.0000.0000.000
132A132VAL0-0.019-0.01117.990-0.011-0.0110.0000.0000.0000.000
133A133LEU0-0.0250.00915.0360.0010.0010.0000.0000.0000.000
134A134ALA00.004-0.01119.4070.0050.0050.0000.0000.0000.000
135A135PHE00.0320.00116.6850.0110.0110.0000.0000.0000.000
136A136ILE0-0.024-0.01922.8200.0110.0110.0000.0000.0000.000
137A137GLY00.0550.01726.2290.0080.0080.0000.0000.0000.000
138A138SER0-0.079-0.04727.9550.0040.0040.0000.0000.0000.000
139A139GLY00.1110.04029.776-0.003-0.0030.0000.0000.0000.000
140A140PHE0-0.026-0.02431.1170.0090.0090.0000.0000.0000.000
141A141PRO00.0300.04133.874-0.007-0.0070.0000.0000.0000.000
142A142MET0-0.0070.00135.0730.0020.0020.0000.0000.0000.000
143A143LYS10.9270.95836.8650.0890.0890.0000.0000.0000.000
144A144LEU00.0610.03440.352-0.003-0.0030.0000.0000.0000.000
145A145PRO0-0.0070.00040.9470.0020.0020.0000.0000.0000.000
146A146GLN00.0480.01843.9080.0010.0010.0000.0000.0000.000
147A147GLY0-0.001-0.00247.646-0.001-0.0010.0000.0000.0000.000
148A148GLN0-0.087-0.03942.567-0.001-0.0010.0000.0000.0000.000
149A149VAL00.0050.00445.8180.0020.0020.0000.0000.0000.000
150A150VAL0-0.052-0.03842.468-0.003-0.0030.0000.0000.0000.000
151A151GLU-1-0.840-0.90045.044-0.040-0.0400.0000.0000.0000.000
152A152ASP-1-0.789-0.87040.187-0.049-0.0490.0000.0000.0000.000
153A153PRO00.0470.00942.788-0.002-0.0020.0000.0000.0000.000
154A154GLY00.0010.01539.3640.0000.0000.0000.0000.0000.000
155A155VAL0-0.017-0.01537.838-0.003-0.0030.0000.0000.0000.000
156A156LEU0-0.001-0.00339.600-0.002-0.0020.0000.0000.0000.000
157A157ALA00.0090.00840.0230.0000.0000.0000.0000.0000.000
158A158LEU0-0.035-0.01934.361-0.002-0.0020.0000.0000.0000.000
159A159TYR0-0.058-0.05737.964-0.004-0.0040.0000.0000.0000.000
160A160GLN0-0.063-0.01240.5620.0000.0000.0000.0000.0000.000
161A161ALA00.0040.00039.3560.0010.0010.0000.0000.0000.000
162A162PRO0-0.0130.00136.007-0.002-0.0020.0000.0000.0000.000
163A163PRO00.0000.02331.0550.0030.0030.0000.0000.0000.000
164A164ALA00.0210.00132.3290.0010.0010.0000.0000.0000.000
165A165THR0-0.111-0.07633.2310.0030.0030.0000.0000.0000.000
166A166ARG10.8880.95334.2370.0560.0560.0000.0000.0000.000
167A167GLY00.0560.01031.924-0.002-0.0020.0000.0000.0000.000
168A168GLU-1-0.842-0.93331.864-0.050-0.0500.0000.0000.0000.000
169A169ALA0-0.034-0.00532.3250.0020.0020.0000.0000.0000.000
170A170TYR00.010-0.02927.5110.0020.0020.0000.0000.0000.000
171A171GLY0-0.023-0.00827.431-0.003-0.0030.0000.0000.0000.000
172A172GLY00.0200.01427.5300.0030.0030.0000.0000.0000.000
173A173VAL0-0.013-0.00221.769-0.006-0.0060.0000.0000.0000.000
174A174PRO0-0.0020.01419.981-0.003-0.0030.0000.0000.0000.000
175A175LEU0-0.013-0.00121.251-0.013-0.0130.0000.0000.0000.000
176A176LEU00.0030.02019.1250.0090.0090.0000.0000.0000.000
177A177HIS00.0450.02021.931-0.007-0.0070.0000.0000.0000.000
178A178LEU0-0.039-0.01519.302-0.001-0.0010.0000.0000.0000.000
179A179HIS0-0.007-0.01523.472-0.008-0.0080.0000.0000.0000.000
180A180GLY00.0530.04026.500-0.005-0.0050.0000.0000.0000.000
181A181SER0-0.039-0.05828.3460.0050.0050.0000.0000.0000.000
182A182ARG10.9160.96331.4950.1230.1230.0000.0000.0000.000
183A183ASP-1-0.763-0.87029.975-0.144-0.1440.0000.0000.0000.000
184A184HIS00.0190.00032.2210.0110.0110.0000.0000.0000.000
185A185ILE0-0.058-0.01531.4590.0070.0070.0000.0000.0000.000
186A186VAL0-0.070-0.03930.4890.0070.0070.0000.0000.0000.000
187A187PRO0-0.0060.00532.220-0.004-0.0040.0000.0000.0000.000
188A188LEU00.0870.05230.6000.0020.0020.0000.0000.0000.000
189A189ALA00.0580.02533.2230.0000.0000.0000.0000.0000.000
190A190ARG10.8480.91733.6240.0890.0890.0000.0000.0000.000
191A191MET00.0470.05928.2780.0040.0040.0000.0000.0000.000
192A192GLU-1-0.848-0.92331.255-0.100-0.1000.0000.0000.0000.000
193A193LYS10.9120.96433.2250.0730.0730.0000.0000.0000.000
194A194THR0-0.055-0.03329.6730.0040.0040.0000.0000.0000.000
195A195LEU00.0350.01027.7860.0030.0030.0000.0000.0000.000
196A196GLU-1-0.824-0.87031.555-0.060-0.0600.0000.0000.0000.000
197A197ALA0-0.061-0.03234.8630.0050.0050.0000.0000.0000.000
198A198LEU00.0390.02629.0820.0030.0030.0000.0000.0000.000
199A199ARG10.8330.88432.6110.0630.0630.0000.0000.0000.000
200A200PRO0-0.058-0.03433.5990.0020.0020.0000.0000.0000.000
201A201HIS00.0110.02132.8190.0050.0050.0000.0000.0000.000
202A202TYR0-0.088-0.05125.7870.0010.0010.0000.0000.0000.000
203A203PRO00.0040.00331.109-0.003-0.0030.0000.0000.0000.000
204A204GLU-1-0.846-0.89429.163-0.041-0.0410.0000.0000.0000.000
205A205GLY00.0170.01327.900-0.005-0.0050.0000.0000.0000.000
206A206ARG10.8360.88723.7420.0650.0650.0000.0000.0000.000
207A207LEU0-0.0230.00923.663-0.015-0.0150.0000.0000.0000.000
208A208ALA0-0.023-0.01223.5090.0050.0050.0000.0000.0000.000
209A209ARG10.8760.90925.4630.1020.1020.0000.0000.0000.000
210A210PHE00.0180.00922.8370.0010.0010.0000.0000.0000.000
211A211VAL00.000-0.01224.951-0.003-0.0030.0000.0000.0000.000
212A212GLU-1-0.775-0.86123.322-0.241-0.2410.0000.0000.0000.000
213A213GLU-1-0.846-0.90826.833-0.117-0.1170.0000.0000.0000.000
214A214GLY0-0.002-0.00229.921-0.002-0.0020.0000.0000.0000.000
215A215ALA0-0.0050.01226.5250.0000.0000.0000.0000.0000.000
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