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: YVM12

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 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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2152034.4309
FMO2-HF: Nuclear repulsion 2079238.658749
FMO2-HF: Total energy -72795.772151
FMO2-MP2: Total energy -73012.628201


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.
-6.055-2.20.318-1.66-2.511-0.009
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 : -0.012 / 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].
3A4GLN0-0.0040.0142.822-5.348-2.4160.318-1.514-1.736-0.009
4A5VAL0-0.016-0.0045.3660.8110.831-0.001-0.002-0.0160.000
5A6TYR00.019-0.0148.880-0.140-0.1400.0000.0000.0000.000
6A7ILE0-0.023-0.01711.7490.1430.1430.0000.0000.0000.000
7A8ILE00.0110.00815.011-0.019-0.0190.0000.0000.0000.000
8A9HIS00.0150.02118.3000.0240.0240.0000.0000.0000.000
9A10GLY00.0830.03621.6810.0040.0040.0000.0000.0000.000
10A11TYR00.027-0.00725.244-0.011-0.0110.0000.0000.0000.000
11A12ARG10.8750.95128.6780.1730.1730.0000.0000.0000.000
12A13ALA0-0.0060.00625.0820.0080.0080.0000.0000.0000.000
13A14SER00.0270.01123.350-0.015-0.0150.0000.0000.0000.000
14A15SER00.014-0.03418.6850.0040.0040.0000.0000.0000.000
15A16THR0-0.071-0.04320.058-0.007-0.0070.0000.0000.0000.000
16A17ASN0-0.025-0.01722.5620.0010.0010.0000.0000.0000.000
17A18HIS00.0360.01622.596-0.021-0.0210.0000.0000.0000.000
18A19TRP00.0370.01818.252-0.020-0.0200.0000.0000.0000.000
19A20PHE0-0.0250.00117.848-0.025-0.0250.0000.0000.0000.000
20A21PRO00.0260.00716.888-0.059-0.0590.0000.0000.0000.000
21A22TRP00.0050.00517.195-0.037-0.0370.0000.0000.0000.000
22A23LEU00.0350.01314.2890.0030.0030.0000.0000.0000.000
23A24LYS10.9100.94211.4151.0871.0870.0000.0000.0000.000
24A25LYS10.9360.96112.4170.3120.3120.0000.0000.0000.000
25A26ARG10.7980.90114.4560.1370.1370.0000.0000.0000.000
26A27LEU00.0380.0179.8070.0650.0650.0000.0000.0000.000
27A28LEU00.0240.0249.7720.0240.0240.0000.0000.0000.000
28A29ALA0-0.054-0.02310.9600.0610.0610.0000.0000.0000.000
29A30ASP-1-0.812-0.86310.7870.0220.0220.0000.0000.0000.000
30A31GLY0-0.037-0.0148.0900.1740.1740.0000.0000.0000.000
31A32VAL0-0.093-0.0485.683-0.138-0.1380.0000.0000.0000.000
32A33GLN0-0.027-0.0154.1790.3450.446-0.001-0.007-0.0930.000
33A34ALA00.013-0.0016.011-0.142-0.1420.0000.0000.0000.000
34A35ASP-1-0.858-0.9048.955-1.685-1.6850.0000.0000.0000.000
35A36ILE0-0.024-0.00511.4030.0430.0430.0000.0000.0000.000
36A37LEU0-0.0180.00313.4270.0000.0000.0000.0000.0000.000
37A38ASN00.002-0.00416.7290.1000.1000.0000.0000.0000.000
38A39MET00.0090.01419.004-0.018-0.0180.0000.0000.0000.000
39A40PRO00.0120.01022.8260.0200.0200.0000.0000.0000.000
40A41ASN00.0130.00226.0760.0140.0140.0000.0000.0000.000
41A42PRO00.0640.03726.5340.0150.0150.0000.0000.0000.000
42A43LEU0-0.012-0.02628.4630.0140.0140.0000.0000.0000.000
43A44GLN0-0.057-0.03231.8390.0130.0130.0000.0000.0000.000
44A45PRO0-0.0200.01428.726-0.003-0.0030.0000.0000.0000.000
45A46ARG10.8700.91029.4640.1940.1940.0000.0000.0000.000
46A47LEU00.0180.00826.536-0.023-0.0230.0000.0000.0000.000
47A48GLU-1-0.892-0.96426.644-0.229-0.2290.0000.0000.0000.000
48A49ASP-1-0.855-0.92026.416-0.265-0.2650.0000.0000.0000.000
49A50TRP0-0.056-0.04623.914-0.038-0.0380.0000.0000.0000.000
50A51LEU0-0.006-0.01322.123-0.053-0.0530.0000.0000.0000.000
51A52ASP-1-0.861-0.91821.548-0.344-0.3440.0000.0000.0000.000
52A53THR0-0.068-0.03819.641-0.041-0.0410.0000.0000.0000.000
53A54LEU0-0.026-0.02117.447-0.080-0.0800.0000.0000.0000.000
54A55SER0-0.042-0.02216.645-0.084-0.0840.0000.0000.0000.000
55A56LEU0-0.025-0.01117.356-0.034-0.0340.0000.0000.0000.000
56A57TYR0-0.015-0.01512.004-0.048-0.0480.0000.0000.0000.000
57A58GLN00.0280.03612.209-0.156-0.1560.0000.0000.0000.000
58A59HIS0-0.050-0.03212.121-0.069-0.0690.0000.0000.0000.000
59A60THR0-0.057-0.0297.878-0.127-0.1270.0000.0000.0000.000
60A61LEU0-0.0430.0027.835-0.411-0.4110.0000.0000.0000.000
61A62HIS00.0280.0194.0011.3081.7570.001-0.087-0.3620.000
62A63GLU-1-0.745-0.8526.4670.4850.4850.0000.0000.0000.000
63A64ASN0-0.074-0.0383.868-0.1770.1760.001-0.050-0.3040.000
64A65THR00.0210.0015.921-1.322-1.3220.0000.0000.0000.000
65A66TYR0-0.043-0.0187.4070.4710.4710.0000.0000.0000.000
66A67LEU00.0230.01711.125-0.213-0.2130.0000.0000.0000.000
67A68VAL0-0.0050.00113.7120.1240.1240.0000.0000.0000.000
68A69ALA00.0200.01216.082-0.054-0.0540.0000.0000.0000.000
69A70HIS00.003-0.00619.3380.0200.0200.0000.0000.0000.000
70A71SER00.0200.00122.563-0.010-0.0100.0000.0000.0000.000
71A72LEU0-0.0090.00025.500-0.001-0.0010.0000.0000.0000.000
72A73GLY00.0470.01922.062-0.003-0.0030.0000.0000.0000.000
73A74CYS0-0.094-0.02421.931-0.019-0.0190.0000.0000.0000.000
74A75PRO00.0140.01323.294-0.004-0.0040.0000.0000.0000.000
75A76ALA00.0310.02022.9860.0020.0020.0000.0000.0000.000
76A77ILE00.006-0.00417.972-0.011-0.0110.0000.0000.0000.000
77A78LEU0-0.027-0.00820.4310.0070.0070.0000.0000.0000.000
78A79ARG10.8100.87922.6930.1530.1530.0000.0000.0000.000
79A80PHE0-0.007-0.00215.917-0.002-0.0020.0000.0000.0000.000
80A81LEU0-0.030-0.02615.9920.0000.0000.0000.0000.0000.000
81A82GLU-1-0.789-0.86819.654-0.105-0.1050.0000.0000.0000.000
82A83HIS00.0060.00622.4790.0260.0260.0000.0000.0000.000
83A84LEU0-0.0250.01414.812-0.012-0.0120.0000.0000.0000.000
84A85GLN0-0.011-0.00518.7000.0640.0640.0000.0000.0000.000
85A86LEU0-0.012-0.00413.125-0.048-0.0480.0000.0000.0000.000
86A87ARG10.8150.8639.278-0.230-0.2300.0000.0000.0000.000
87A88ALA0-0.022-0.01811.7750.0860.0860.0000.0000.0000.000
88A89ALA00.0150.02912.980-0.085-0.0850.0000.0000.0000.000
89A90LEU00.0420.01210.6350.0680.0680.0000.0000.0000.000
90A91GLY00.0280.0249.9160.1640.1640.0000.0000.0000.000
91A92GLY0-0.026-0.03510.7650.1020.1020.0000.0000.0000.000
92A93ILE00.0110.00713.758-0.142-0.1420.0000.0000.0000.000
93A94ILE0-0.043-0.01616.0550.0690.0690.0000.0000.0000.000
94A95LEU00.000-0.00818.573-0.053-0.0530.0000.0000.0000.000
95A96VAL00.008-0.00320.5200.0340.0340.0000.0000.0000.000
96A97SER00.018-0.00123.211-0.016-0.0160.0000.0000.0000.000
97A98GLY00.0520.01725.615-0.007-0.0070.0000.0000.0000.000
98A99PHE0-0.021-0.01726.2630.0210.0210.0000.0000.0000.000
99A100ALA00.0490.01328.249-0.015-0.0150.0000.0000.0000.000
100A101LYS10.8390.90930.1540.0730.0730.0000.0000.0000.000
101A102SER0-0.018-0.02833.662-0.004-0.0040.0000.0000.0000.000
102A103LEU00.0500.01931.6120.0080.0080.0000.0000.0000.000
103A104PRO00.002-0.01235.968-0.002-0.0020.0000.0000.0000.000
104A105THR0-0.007-0.00237.3830.0000.0000.0000.0000.0000.000
105A106LEU0-0.038-0.02433.243-0.005-0.0050.0000.0000.0000.000
106A107GLN00.0470.02735.906-0.002-0.0020.0000.0000.0000.000
107A108MET0-0.084-0.02634.5460.0000.0000.0000.0000.0000.000
108A109LEU00.0070.00131.138-0.010-0.0100.0000.0000.0000.000
109A110ASP-1-0.781-0.87632.929-0.116-0.1160.0000.0000.0000.000
110A111GLU-1-0.816-0.88132.120-0.174-0.1740.0000.0000.0000.000
111A112PHE00.005-0.00926.283-0.002-0.0020.0000.0000.0000.000
112A113THR0-0.070-0.02529.4580.0000.0000.0000.0000.0000.000
113A114GLN0-0.0370.00931.7750.0090.0090.0000.0000.0000.000
114A115GLY00.0360.01933.042-0.006-0.0060.0000.0000.0000.000
115A116SER0-0.008-0.01732.658-0.005-0.0050.0000.0000.0000.000
116A117PHE0-0.0020.01326.294-0.008-0.0080.0000.0000.0000.000
117A118ASP-1-0.886-0.93826.568-0.030-0.0300.0000.0000.0000.000
118A119HIS00.017-0.02025.702-0.007-0.0070.0000.0000.0000.000
119A120GLN0-0.041-0.01524.883-0.002-0.0020.0000.0000.0000.000
120A121LYS10.8850.94919.5100.1350.1350.0000.0000.0000.000
121A122ILE0-0.030-0.00720.966-0.007-0.0070.0000.0000.0000.000
122A123ILE0-0.032-0.01519.9890.0010.0010.0000.0000.0000.000
123A124GLU-1-0.929-0.95819.6760.0760.0760.0000.0000.0000.000
124A125SER0-0.026-0.02516.8990.0110.0110.0000.0000.0000.000
125A126ALA0-0.037-0.01614.875-0.052-0.0520.0000.0000.0000.000
126A127LYS10.9260.98112.934-0.694-0.6940.0000.0000.0000.000
127A128HIS0-0.070-0.03613.2160.0600.0600.0000.0000.0000.000
128A129ARG10.8610.93016.719-0.117-0.1170.0000.0000.0000.000
129A130ALA00.0130.00719.4480.0300.0300.0000.0000.0000.000
130A131VAL00.0080.01621.520-0.039-0.0390.0000.0000.0000.000
131A132ILE0-0.0170.00020.9040.0220.0220.0000.0000.0000.000
132A133ALA00.0160.00024.905-0.019-0.0190.0000.0000.0000.000
133A134SER00.0410.03228.2990.0170.0170.0000.0000.0000.000
134A135LYS10.8790.94331.0590.0360.0360.0000.0000.0000.000
135A136ASP-1-0.811-0.90934.556-0.072-0.0720.0000.0000.0000.000
136A137ASP-1-0.719-0.82030.896-0.127-0.1270.0000.0000.0000.000
137A138GLN0-0.082-0.05534.2190.0080.0080.0000.0000.0000.000
138A139ILE0-0.071-0.02932.4350.0000.0000.0000.0000.0000.000
139A140VAL0-0.031-0.01629.6700.0000.0000.0000.0000.0000.000
140A141PRO00.0190.02332.8190.0050.0050.0000.0000.0000.000
141A142PHE00.0730.02430.9590.0020.0020.0000.0000.0000.000
142A143SER0-0.031-0.02732.9870.0000.0000.0000.0000.0000.000
143A144PHE00.011-0.01032.8700.0070.0070.0000.0000.0000.000
144A145SER00.0160.00728.703-0.003-0.0030.0000.0000.0000.000
145A146LYS10.9020.95629.4630.0180.0180.0000.0000.0000.000
146A147ASP-1-0.820-0.87831.264-0.045-0.0450.0000.0000.0000.000
147A148LEU00.0370.02525.7770.0050.0050.0000.0000.0000.000
148A149ALA0-0.018-0.02426.6480.0040.0040.0000.0000.0000.000
149A150GLN0-0.045-0.02527.4970.0090.0090.0000.0000.0000.000
150A151GLN0-0.062-0.03529.1980.0030.0030.0000.0000.0000.000
151A152ILE00.002-0.00322.4680.0020.0020.0000.0000.0000.000
152A153ASP-1-0.908-0.94424.0350.0820.0820.0000.0000.0000.000
153A154ALA0-0.0310.00823.2040.0130.0130.0000.0000.0000.000
154A155ALA0-0.0020.00222.8810.0020.0020.0000.0000.0000.000
155A156LEU0-0.014-0.01024.425-0.021-0.0210.0000.0000.0000.000
156A157TYR0-0.039-0.02722.3470.0170.0170.0000.0000.0000.000
157A158GLU-1-0.887-0.95226.967-0.044-0.0440.0000.0000.0000.000
158A159VAL0-0.016-0.00427.2820.0070.0070.0000.0000.0000.000
159A160GLN0-0.051-0.03030.395-0.001-0.0010.0000.0000.0000.000
160A161HIS0-0.029-0.04633.3980.0060.0060.0000.0000.0000.000
161A162GLY00.0210.00630.431-0.001-0.0010.0000.0000.0000.000
162A163GLY00.0240.04130.403-0.012-0.0120.0000.0000.0000.000
163A164HIS0-0.062-0.07229.231-0.011-0.0110.0000.0000.0000.000
164A165PHE0-0.038-0.02925.616-0.016-0.0160.0000.0000.0000.000
165A166LEU00.0150.00426.213-0.026-0.0260.0000.0000.0000.000
166A167GLU-1-0.770-0.88827.096-0.223-0.2230.0000.0000.0000.000
167A168ASP-1-0.948-0.97128.595-0.146-0.1460.0000.0000.0000.000
168A169GLU-1-0.897-0.93731.098-0.120-0.1200.0000.0000.0000.000
169A170GLY00.0030.00830.5760.0100.0100.0000.0000.0000.000
170A171PHE0-0.036-0.01125.922-0.003-0.0030.0000.0000.0000.000
171A172THR00.017-0.00224.657-0.017-0.0170.0000.0000.0000.000
172A173SER0-0.087-0.04922.053-0.017-0.0170.0000.0000.0000.000
173A174LEU00.0220.00621.2450.0140.0140.0000.0000.0000.000
174A175PRO00.0190.00020.455-0.016-0.0160.0000.0000.0000.000
175A176ILE00.0660.04520.1870.0050.0050.0000.0000.0000.000
176A177VAL00.0330.01816.8110.0150.0150.0000.0000.0000.000
177A178TYR0-0.063-0.05813.432-0.006-0.0060.0000.0000.0000.000
178A179ASP-1-0.877-0.93415.7960.0040.0040.0000.0000.0000.000
179A180VAL0-0.035-0.01817.6430.0510.0510.0000.0000.0000.000
180A181LEU00.0180.01711.4200.0400.0400.0000.0000.0000.000
181A182THR00.021-0.00312.8110.0640.0640.0000.0000.0000.000
182A183SER0-0.053-0.03413.5700.1370.1370.0000.0000.0000.000
183A184TYR0-0.026-0.04112.7960.1050.1050.0000.0000.0000.000
184A185PHE00.0170.0039.4200.1500.1500.0000.0000.0000.000
185A186SER0-0.059-0.00610.7810.2230.2230.0000.0000.0000.000
186A187LYS10.8500.94412.324-0.109-0.1090.0000.0000.0000.000