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: VQ6N1

Calculation Name: 1UXO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1UXO

Chain ID: A

ChEMBL ID:

UniProt ID: P96671

Base Structure: X-ray

Registration Date: 2023-09-23

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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2158197.674185
FMO2-HF: Nuclear repulsion 2085401.641646
FMO2-HF: Total energy -72796.032538
FMO2-MP2: Total energy -73012.889631


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:2:THR)


Summations of interaction energy for fragment #1(A:2:THR)
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.
-4.357-1.0580.216-1.342-2.175-0.005
Interaction energy analysis for fragmet #1(A:2:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.009 / q_NPA : -0.018
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].
3A4GLN0-0.0100.0052.932-3.918-1.3540.220-1.258-1.526-0.005
4A5VAL0-0.022-0.0155.0850.6470.668-0.001-0.002-0.0180.000
5A6TYR00.016-0.0128.728-0.032-0.0320.0000.0000.0000.000
6A7ILE0-0.021-0.01011.6590.1040.1040.0000.0000.0000.000
7A8ILE00.0100.00915.021-0.001-0.0010.0000.0000.0000.000
8A9HIS00.0220.02018.2200.0220.0220.0000.0000.0000.000
9A10GLY00.0690.03221.527-0.006-0.0060.0000.0000.0000.000
10A11TYR00.021-0.01425.112-0.004-0.0040.0000.0000.0000.000
11A12ARG10.8770.94128.5020.1350.1350.0000.0000.0000.000
12A13ALA0-0.0180.01625.0350.0100.0100.0000.0000.0000.000
13A14SER00.0260.00423.254-0.012-0.0120.0000.0000.0000.000
14A15SER0-0.002-0.04818.4010.0070.0070.0000.0000.0000.000
15A16THR0-0.077-0.05019.8450.0060.0060.0000.0000.0000.000
16A17ASN0-0.019-0.00722.4490.0020.0020.0000.0000.0000.000
17A18HIS00.0320.01222.527-0.011-0.0110.0000.0000.0000.000
18A19TRP00.0410.02218.464-0.008-0.0080.0000.0000.0000.000
19A20PHE0-0.0130.00317.750-0.010-0.0100.0000.0000.0000.000
20A21PRO00.0170.00416.959-0.027-0.0270.0000.0000.0000.000
21A22TRP0-0.014-0.00217.8150.0020.0020.0000.0000.0000.000
22A23LEU00.0270.00914.4470.0190.0190.0000.0000.0000.000
23A24LYS10.9110.94811.1740.6330.6330.0000.0000.0000.000
24A25LYS10.9230.96512.6870.1490.1490.0000.0000.0000.000
25A26ARG10.7730.88214.690-0.080-0.0800.0000.0000.0000.000
26A27LEU00.0310.00910.0400.0660.0660.0000.0000.0000.000
27A28LEU00.0180.0179.8060.0730.0730.0000.0000.0000.000
28A29ALA0-0.041-0.02111.0430.1040.1040.0000.0000.0000.000
29A30ASP-1-0.796-0.85011.7040.2810.2810.0000.0000.0000.000
30A31GLY0-0.032-0.0158.5290.1740.1740.0000.0000.0000.000
31A32VAL0-0.105-0.0536.1100.1480.1480.0000.0000.0000.000
32A33GLN0-0.013-0.0124.0320.2210.341-0.001-0.010-0.1090.000
33A34ALA00.0160.0015.958-0.265-0.2650.0000.0000.0000.000
34A35ASP-1-0.863-0.9068.669-1.022-1.0220.0000.0000.0000.000
35A36ILE0-0.015-0.00211.309-0.001-0.0010.0000.0000.0000.000
36A37LEU0-0.0220.00213.1170.0220.0220.0000.0000.0000.000
37A38ASN00.0170.01216.4660.0800.0800.0000.0000.0000.000
38A39MET00.0110.01918.659-0.027-0.0270.0000.0000.0000.000
39A40PRO00.0220.02122.4570.0280.0280.0000.0000.0000.000
40A41ASN00.002-0.00225.7040.0130.0130.0000.0000.0000.000
41A42PRO00.0620.03526.3760.0130.0130.0000.0000.0000.000
42A43LEU0-0.015-0.01628.4140.0100.0100.0000.0000.0000.000
43A44GLN0-0.070-0.04431.7490.0110.0110.0000.0000.0000.000
44A45PRO0-0.0110.02228.414-0.003-0.0030.0000.0000.0000.000
45A46ARG10.8660.90428.9380.1970.1970.0000.0000.0000.000
46A47LEU00.0020.00726.374-0.021-0.0210.0000.0000.0000.000
47A48GLU-1-0.848-0.94326.400-0.267-0.2670.0000.0000.0000.000
48A49ASP-1-0.851-0.92925.971-0.263-0.2630.0000.0000.0000.000
49A50TRP0-0.049-0.04223.379-0.034-0.0340.0000.0000.0000.000
50A51LEU0-0.0060.00021.867-0.049-0.0490.0000.0000.0000.000
51A52ASP-1-0.861-0.92521.281-0.390-0.3900.0000.0000.0000.000
52A53THR0-0.073-0.04819.426-0.038-0.0380.0000.0000.0000.000
53A54LEU0-0.031-0.02117.071-0.067-0.0670.0000.0000.0000.000
54A55SER0-0.040-0.03216.560-0.098-0.0980.0000.0000.0000.000
55A56LEU0-0.021-0.00217.053-0.060-0.0600.0000.0000.0000.000
56A57TYR0-0.0020.00011.731-0.033-0.0330.0000.0000.0000.000
57A58GLN00.0150.02512.112-0.195-0.1950.0000.0000.0000.000
58A59HIS0-0.051-0.03312.005-0.168-0.1680.0000.0000.0000.000
59A60THR0-0.060-0.0347.819-0.205-0.2050.0000.0000.0000.000
60A61LEU0-0.0290.0077.637-0.503-0.5030.0000.0000.0000.000
61A62HIS00.0220.0114.2570.8511.208-0.001-0.048-0.3090.000
62A63GLU-1-0.735-0.8366.625-0.745-0.7450.0000.0000.0000.000
63A64ASN0-0.051-0.0324.2210.5380.775-0.001-0.024-0.2130.000
64A65THR00.0210.0096.148-0.926-0.9260.0000.0000.0000.000
65A66TYR0-0.064-0.0387.2010.4490.4490.0000.0000.0000.000
66A67LEU00.0160.00510.981-0.112-0.1120.0000.0000.0000.000
67A68VAL00.0110.00713.8230.1120.1120.0000.0000.0000.000
68A69ALA00.0080.00716.024-0.042-0.0420.0000.0000.0000.000
69A70HIS00.020-0.00519.2950.0200.0200.0000.0000.0000.000
70A71SER00.0110.00022.644-0.013-0.0130.0000.0000.0000.000
71A72LEU0-0.008-0.00825.396-0.007-0.0070.0000.0000.0000.000
72A73GLY00.0530.02921.908-0.010-0.0100.0000.0000.0000.000
73A74CYS0-0.106-0.02121.724-0.028-0.0280.0000.0000.0000.000
74A75PRO00.0080.01023.083-0.015-0.0150.0000.0000.0000.000
75A76ALA00.0290.02422.653-0.006-0.0060.0000.0000.0000.000
76A77ILE00.004-0.01017.760-0.023-0.0230.0000.0000.0000.000
77A78LEU0-0.036-0.01120.566-0.013-0.0130.0000.0000.0000.000
78A79ARG10.8200.88823.0050.1980.1980.0000.0000.0000.000
79A80PHE00.003-0.00515.958-0.011-0.0110.0000.0000.0000.000
80A81LEU0-0.022-0.02416.373-0.025-0.0250.0000.0000.0000.000
81A82GLU-1-0.805-0.86920.148-0.205-0.2050.0000.0000.0000.000
82A83HIS00.0170.00223.1020.0030.0030.0000.0000.0000.000
83A84LEU0-0.0230.01115.070-0.016-0.0160.0000.0000.0000.000
84A85GLN0-0.0060.00319.1210.0500.0500.0000.0000.0000.000
85A86LEU0-0.019-0.00813.526-0.077-0.0770.0000.0000.0000.000
86A87ARG10.8160.8639.2020.7470.7470.0000.0000.0000.000
87A88ALA0-0.031-0.02011.5010.0780.0780.0000.0000.0000.000
88A89ALA00.0420.03713.459-0.083-0.0830.0000.0000.0000.000
89A90LEU00.0160.00010.934-0.016-0.0160.0000.0000.0000.000
90A91GLY00.0260.0269.7880.1760.1760.0000.0000.0000.000
91A92GLY0-0.024-0.02110.5770.1800.1800.0000.0000.0000.000
92A93ILE00.0200.01213.962-0.126-0.1260.0000.0000.0000.000
93A94ILE0-0.047-0.01016.3930.0700.0700.0000.0000.0000.000
94A95LEU00.0100.00418.703-0.035-0.0350.0000.0000.0000.000
95A96VAL00.007-0.00120.7060.0320.0320.0000.0000.0000.000
96A97SER0-0.010-0.04123.431-0.009-0.0090.0000.0000.0000.000
97A98GLY00.0480.01825.387-0.009-0.0090.0000.0000.0000.000
98A99PHE0-0.039-0.02926.1720.0190.0190.0000.0000.0000.000
99A100ALA00.0490.01427.840-0.016-0.0160.0000.0000.0000.000
100A101LYS10.8450.91429.9590.0980.0980.0000.0000.0000.000
101A102SER0-0.001-0.01633.353-0.001-0.0010.0000.0000.0000.000
102A103LEU00.0390.02031.6450.0060.0060.0000.0000.0000.000
103A104PRO0-0.011-0.02036.0770.0000.0000.0000.0000.0000.000
104A105THR0-0.0080.00236.8390.0010.0010.0000.0000.0000.000
105A106LEU0-0.024-0.01933.117-0.001-0.0010.0000.0000.0000.000
106A107GLN00.0100.00435.680-0.003-0.0030.0000.0000.0000.000
107A108MET0-0.075-0.01934.150-0.001-0.0010.0000.0000.0000.000
108A109LEU00.0080.00530.829-0.009-0.0090.0000.0000.0000.000
109A110ASP-1-0.767-0.87432.477-0.130-0.1300.0000.0000.0000.000
110A111GLU-1-0.820-0.88731.808-0.186-0.1860.0000.0000.0000.000
111A112PHE00.0120.00125.920-0.006-0.0060.0000.0000.0000.000
112A113THR0-0.073-0.03329.347-0.004-0.0040.0000.0000.0000.000
113A114GLN0-0.0200.00931.8030.0100.0100.0000.0000.0000.000
114A115GLY00.0230.01133.496-0.009-0.0090.0000.0000.0000.000
115A116SER0-0.005-0.01333.374-0.002-0.0020.0000.0000.0000.000
116A117PHE00.0050.01526.755-0.010-0.0100.0000.0000.0000.000
117A118ASP-1-0.864-0.92326.500-0.154-0.1540.0000.0000.0000.000
118A119HIS00.014-0.01625.667-0.024-0.0240.0000.0000.0000.000
119A120GLN0-0.064-0.02025.0970.0060.0060.0000.0000.0000.000
120A121LYS10.8580.92019.7550.3330.3330.0000.0000.0000.000
121A122ILE0-0.026-0.00221.185-0.030-0.0300.0000.0000.0000.000
122A123ILE0-0.047-0.02320.202-0.017-0.0170.0000.0000.0000.000
123A124GLU-1-0.895-0.94519.704-0.138-0.1380.0000.0000.0000.000
124A125SER0-0.037-0.03317.058-0.030-0.0300.0000.0000.0000.000
125A126ALA0-0.039-0.01715.012-0.085-0.0850.0000.0000.0000.000
126A127LYS10.8810.95612.426-0.340-0.3400.0000.0000.0000.000
127A128HIS0-0.051-0.03713.0280.1130.1130.0000.0000.0000.000
128A129ARG10.8540.93216.8060.0380.0380.0000.0000.0000.000
129A130ALA00.0250.01419.5430.0380.0380.0000.0000.0000.000
130A131VAL0-0.0170.00121.730-0.034-0.0340.0000.0000.0000.000
131A132ILE00.0010.00320.9780.0230.0230.0000.0000.0000.000
132A133ALA00.0170.00724.971-0.015-0.0150.0000.0000.0000.000
133A134SER00.0270.02828.3590.0160.0160.0000.0000.0000.000
134A135LYS10.8850.94031.0320.0350.0350.0000.0000.0000.000
135A136ASP-1-0.766-0.88334.444-0.050-0.0500.0000.0000.0000.000
136A137ASP-1-0.723-0.80830.933-0.109-0.1090.0000.0000.0000.000
137A138GLN0-0.086-0.05634.2470.0040.0040.0000.0000.0000.000
138A139ILE0-0.059-0.02532.2790.0000.0000.0000.0000.0000.000
139A140VAL0-0.018-0.01729.651-0.005-0.0050.0000.0000.0000.000
140A141PRO00.0310.02432.7870.0050.0050.0000.0000.0000.000
141A142PHE00.0500.02730.942-0.001-0.0010.0000.0000.0000.000
142A143SER0-0.027-0.02233.117-0.003-0.0030.0000.0000.0000.000
143A144PHE0-0.002-0.02132.9770.0020.0020.0000.0000.0000.000
144A145SER00.0310.01028.754-0.005-0.0050.0000.0000.0000.000
145A146LYS10.8240.91529.5000.0340.0340.0000.0000.0000.000
146A147ASP-1-0.793-0.86831.556-0.086-0.0860.0000.0000.0000.000
147A148LEU00.0040.01725.848-0.001-0.0010.0000.0000.0000.000
148A149ALA0-0.009-0.01826.856-0.005-0.0050.0000.0000.0000.000
149A150GLN0-0.055-0.02427.5880.0040.0040.0000.0000.0000.000
150A151GLN0-0.052-0.04329.606-0.006-0.0060.0000.0000.0000.000
151A152ILE00.0010.00122.779-0.006-0.0060.0000.0000.0000.000
152A153ASP-1-0.917-0.95024.070-0.044-0.0440.0000.0000.0000.000
153A154ALA00.0160.01823.232-0.002-0.0020.0000.0000.0000.000
154A155ALA0-0.013-0.00822.6360.0100.0100.0000.0000.0000.000
155A156LEU00.000-0.00224.364-0.016-0.0160.0000.0000.0000.000
156A157TYR0-0.047-0.02922.6730.0160.0160.0000.0000.0000.000
157A158GLU-1-0.832-0.92427.191-0.044-0.0440.0000.0000.0000.000
158A159VAL0-0.0090.00127.6040.0100.0100.0000.0000.0000.000
159A160GLN0-0.069-0.04630.832-0.003-0.0030.0000.0000.0000.000
160A161HIS0-0.030-0.03133.5480.0040.0040.0000.0000.0000.000
161A162GLY0-0.007-0.01230.8840.0030.0030.0000.0000.0000.000
162A163GLY00.0130.03530.819-0.008-0.0080.0000.0000.0000.000
163A164HIS0-0.049-0.05829.304-0.014-0.0140.0000.0000.0000.000
164A165PHE0-0.009-0.01225.878-0.014-0.0140.0000.0000.0000.000
165A166LEU00.001-0.00526.394-0.017-0.0170.0000.0000.0000.000
166A167GLU-1-0.767-0.89127.109-0.137-0.1370.0000.0000.0000.000
167A168ASP-1-0.945-0.96828.774-0.086-0.0860.0000.0000.0000.000
168A169GLU-1-0.883-0.92631.136-0.084-0.0840.0000.0000.0000.000
169A170GLY00.0060.00830.7130.0080.0080.0000.0000.0000.000
170A171PHE0-0.042-0.00725.9010.0030.0030.0000.0000.0000.000
171A172THR00.022-0.00224.989-0.015-0.0150.0000.0000.0000.000
172A173SER0-0.067-0.04322.218-0.005-0.0050.0000.0000.0000.000
173A174LEU00.0210.00821.6490.0060.0060.0000.0000.0000.000
174A175PRO00.0010.00120.762-0.013-0.0130.0000.0000.0000.000
175A176ILE00.0800.04420.1220.0010.0010.0000.0000.0000.000
176A177VAL00.0170.01116.9950.0050.0050.0000.0000.0000.000
177A178TYR0-0.036-0.04114.062-0.033-0.0330.0000.0000.0000.000
178A179ASP-1-0.885-0.93516.1800.0820.0820.0000.0000.0000.000
179A180VAL0-0.008-0.00417.8880.0400.0400.0000.0000.0000.000
180A181LEU00.0190.03511.5610.0180.0180.0000.0000.0000.000
181A182THR00.011-0.01313.1130.0600.0600.0000.0000.0000.000
182A183SER0-0.062-0.05114.0450.1060.1060.0000.0000.0000.000
183A184TYR0-0.018-0.03313.0860.0730.0730.0000.0000.0000.000
184A185PHE00.0220.0079.7460.1360.1360.0000.0000.0000.000
185A186SER0-0.077-0.03311.1590.1800.1800.0000.0000.0000.000
186A187LYS10.8840.96512.491-0.157-0.1570.0000.0000.0000.000