FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: JLRZ9

Calculation Name: 5U15-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5U15

Chain ID: A

ChEMBL ID:

UniProt ID:

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 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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2101263.01797
FMO2-HF: Nuclear repulsion 2019297.698401
FMO2-HF: Total energy -81965.319568
FMO2-MP2: Total energy -82202.717612


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:GLN)


Summations of interaction energy for fragment #1(A:1:GLN)
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.
-0.0733.2620.434-1.161-2.6070
Interaction energy analysis for fragmet #1(A:1:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.007 / q_NPA : -0.015
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].
3A3GLN00.0170.0072.471-1.9020.5670.428-0.919-1.9780.000
4A4LEU0-0.027-0.0035.0430.9481.031-0.001-0.006-0.0760.000
5A5VAL00.0220.0098.1050.1650.1650.0000.0000.0000.000
6A6GLN0-0.003-0.02910.7860.0920.0920.0000.0000.0000.000
7A7SER00.0080.02314.5640.0200.0200.0000.0000.0000.000
8A8GLY00.0220.00817.696-0.010-0.0100.0000.0000.0000.000
9A9ALA0-0.028-0.01119.5020.0090.0090.0000.0000.0000.000
10A10GLU-1-0.755-0.87022.297-0.325-0.3250.0000.0000.0000.000
11A11VAL0-0.037-0.01525.4450.0150.0150.0000.0000.0000.000
12A12LYS10.8120.89727.9610.3080.3080.0000.0000.0000.000
13A13LYS10.8580.91931.9900.1780.1780.0000.0000.0000.000
14A14PRO00.024-0.00835.034-0.007-0.0070.0000.0000.0000.000
15A15GLY0-0.026-0.00136.6910.0070.0070.0000.0000.0000.000
16A16ALA00.0000.00833.859-0.001-0.0010.0000.0000.0000.000
17A17SER00.018-0.01530.4390.0050.0050.0000.0000.0000.000
18A18VAL0-0.040-0.02025.1180.0040.0040.0000.0000.0000.000
19A19LYS10.8740.91923.3140.3670.3670.0000.0000.0000.000
20A20VAL00.0070.02718.928-0.013-0.0130.0000.0000.0000.000
21A21SER00.0310.00217.3020.0020.0020.0000.0000.0000.000
22A22CYS0-0.022-0.01213.419-0.051-0.0510.0000.0000.0000.000
23A23LYS10.8620.9459.9401.6031.6030.0000.0000.0000.000
24A24ALA00.0250.0159.099-0.332-0.3320.0000.0000.0000.000
25A25SER0-0.043-0.0355.345-0.175-0.1750.0000.0000.0000.000
26A26GLY00.0820.0293.831-1.733-1.3640.009-0.194-0.1830.000
27A27TYR0-0.007-0.0064.5262.2612.524-0.001-0.034-0.2280.000
28A28THR00.0280.0117.358-0.295-0.2950.0000.0000.0000.000
29A29PHE00.0270.01911.1900.0120.0120.0000.0000.0000.000
30A30THR00.005-0.00812.5980.0000.0000.0000.0000.0000.000
31A31GLY00.0260.02113.7970.0550.0550.0000.0000.0000.000
32A32TYR0-0.018-0.01810.3460.0530.0530.0000.0000.0000.000
33A33TYR0-0.044-0.03314.473-0.046-0.0460.0000.0000.0000.000
34A34MET0-0.0350.00012.273-0.069-0.0690.0000.0000.0000.000
35A35HIS00.0320.00816.6640.0880.0880.0000.0000.0000.000
36A36TRP00.000-0.01017.608-0.110-0.1100.0000.0000.0000.000
37A37VAL0-0.002-0.00219.4870.0700.0700.0000.0000.0000.000
38A38ARG10.7890.87620.6460.2720.2720.0000.0000.0000.000
39A39GLN00.0190.01222.006-0.022-0.0220.0000.0000.0000.000
40A40ALA00.0410.03224.473-0.006-0.0060.0000.0000.0000.000
41A41PRO00.004-0.01827.427-0.001-0.0010.0000.0000.0000.000
42A42GLY00.0060.00827.7440.0170.0170.0000.0000.0000.000
43A43GLN0-0.052-0.00428.1850.0190.0190.0000.0000.0000.000
44A44GLY00.0390.01526.318-0.016-0.0160.0000.0000.0000.000
45A45LEU0-0.011-0.00720.304-0.008-0.0080.0000.0000.0000.000
46A46GLU-1-0.775-0.87624.254-0.248-0.2480.0000.0000.0000.000
47A47TRP0-0.012-0.00622.283-0.008-0.0080.0000.0000.0000.000
48A48MET0-0.015-0.00823.7330.0200.0200.0000.0000.0000.000
49A49GLY00.004-0.01323.8120.0310.0310.0000.0000.0000.000
50A50TRP0-0.0020.02120.783-0.051-0.0510.0000.0000.0000.000
51A51ILE0-0.003-0.00619.1290.0420.0420.0000.0000.0000.000
52A52ASN00.0450.03619.440-0.052-0.0520.0000.0000.0000.000
53A53PRO00.010-0.00315.8360.0420.0420.0000.0000.0000.000
54A54ASN00.0320.02218.8250.0060.0060.0000.0000.0000.000
55A55SER00.0070.01320.2670.0070.0070.0000.0000.0000.000
56A56GLY0-0.012-0.00922.7160.0140.0140.0000.0000.0000.000
57A57GLY00.0010.01023.8660.0040.0040.0000.0000.0000.000
58A58THR0-0.016-0.02124.032-0.028-0.0280.0000.0000.0000.000
59A59ASN0-0.028-0.00726.0460.0340.0340.0000.0000.0000.000
60A60TYR00.0320.00125.9910.0020.0020.0000.0000.0000.000
61A61ALA00.0510.04527.7070.0170.0170.0000.0000.0000.000
62A62GLN00.024-0.01329.4200.0010.0010.0000.0000.0000.000
63A63LYS10.8600.93431.0770.2420.2420.0000.0000.0000.000
64A64PHE0-0.027-0.01828.2200.0030.0030.0000.0000.0000.000
65A65GLN00.0810.05431.475-0.018-0.0180.0000.0000.0000.000
66A66GLY00.0390.02832.9410.0140.0140.0000.0000.0000.000
67A67ARG10.7000.80832.1460.2530.2530.0000.0000.0000.000
68A68VAL0-0.0050.00426.435-0.009-0.0090.0000.0000.0000.000
69A69THR0-0.015-0.00226.8470.0240.0240.0000.0000.0000.000
70A70MET0-0.0440.00122.370-0.030-0.0300.0000.0000.0000.000
71A71THR00.0100.00522.2130.0240.0240.0000.0000.0000.000
72A72ARG10.8320.89618.5760.3060.3060.0000.0000.0000.000
73A73ASP-1-0.801-0.87318.302-0.409-0.4090.0000.0000.0000.000
74A74THR00.018-0.00816.669-0.092-0.0920.0000.0000.0000.000
75A75SER0-0.054-0.03016.030-0.044-0.0440.0000.0000.0000.000
76A76ILE00.0540.03314.970-0.023-0.0230.0000.0000.0000.000
77A77SER0-0.052-0.02611.910-0.178-0.1780.0000.0000.0000.000
78A78THR0-0.0160.00012.358-0.285-0.2850.0000.0000.0000.000
79A79ALA00.0050.00514.8490.1410.1410.0000.0000.0000.000
80A80TYR0-0.005-0.02117.091-0.069-0.0690.0000.0000.0000.000
81A81MET0-0.0350.00119.9660.0470.0470.0000.0000.0000.000
82A82GLU-1-0.832-0.90422.542-0.342-0.3420.0000.0000.0000.000
83A83LEU00.0060.00325.9490.0180.0180.0000.0000.0000.000
84A84SER00.0360.00928.6720.0060.0060.0000.0000.0000.000
85A85ARG10.8770.93432.2410.2010.2010.0000.0000.0000.000
86A86LEU0-0.0180.01629.5390.0040.0040.0000.0000.0000.000
87A87ARG10.8650.88533.3630.2260.2260.0000.0000.0000.000
88A88SER00.0630.02533.278-0.013-0.0130.0000.0000.0000.000
89A89ASP-1-0.819-0.87032.914-0.225-0.2250.0000.0000.0000.000
90A90ASP-1-0.728-0.82129.603-0.271-0.2710.0000.0000.0000.000
91A91THR0-0.0140.00828.286-0.027-0.0270.0000.0000.0000.000
92A92ALA00.002-0.00625.2650.0130.0130.0000.0000.0000.000
93A93VAL00.0100.02219.509-0.009-0.0090.0000.0000.0000.000
94A94TYR0-0.021-0.03820.7620.0210.0210.0000.0000.0000.000
95A95TYR00.0240.00215.973-0.052-0.0520.0000.0000.0000.000
96A97ALA00.0570.01113.289-0.127-0.1270.0000.0000.0000.000
97A98ARG10.7630.8697.6811.0391.0390.0000.0000.0000.000
98A99GLY00.0520.02312.8390.0310.0310.0000.0000.0000.000
99A100GLY00.0150.00614.253-0.001-0.0010.0000.0000.0000.000
100A101TRP00.0160.00113.899-0.039-0.0390.0000.0000.0000.000
101A102ILE0-0.063-0.03715.8230.0160.0160.0000.0000.0000.000
102A103SER0-0.016-0.00518.5490.0380.0380.0000.0000.0000.000
103A104LEU00.0130.00721.105-0.013-0.0130.0000.0000.0000.000
104A105TYR0-0.014-0.01024.5690.0050.0050.0000.0000.0000.000
105A106TYR00.0140.01323.7260.0080.0080.0000.0000.0000.000
106A107ASP-1-0.757-0.83923.620-0.258-0.2580.0000.0000.0000.000
107A108SER0-0.015-0.01019.8720.0120.0120.0000.0000.0000.000
108A109SER0-0.083-0.06820.433-0.039-0.0390.0000.0000.0000.000
109A110GLY00.008-0.00421.563-0.036-0.0360.0000.0000.0000.000
110A111TYR0-0.023-0.00818.7320.0100.0100.0000.0000.0000.000
111A112PRO00.0110.01019.431-0.045-0.0450.0000.0000.0000.000
112A113ASN0-0.030-0.01416.040-0.015-0.0150.0000.0000.0000.000
113A114PHE0-0.022-0.02914.830-0.030-0.0300.0000.0000.0000.000
114A115ASP-1-0.744-0.8329.699-1.029-1.0290.0000.0000.0000.000
115A116TYR0-0.016-0.0014.520-0.603-0.452-0.001-0.008-0.1420.000
116A117TRP0-0.008-0.0249.5250.2540.2540.0000.0000.0000.000
117A118GLY00.0270.0159.731-0.342-0.3420.0000.0000.0000.000
118A119GLN0-0.026-0.00811.576-0.030-0.0300.0000.0000.0000.000
119A120GLY00.0030.01212.8640.1520.1520.0000.0000.0000.000
120A121THR0-0.045-0.03516.375-0.030-0.0300.0000.0000.0000.000
121A122LEU0-0.0190.00319.3090.0320.0320.0000.0000.0000.000
122A123VAL0-0.0030.00922.5980.0010.0010.0000.0000.0000.000
123A124THR0-0.003-0.01025.6350.0180.0180.0000.0000.0000.000
124A125VAL0-0.014-0.00129.1650.0070.0070.0000.0000.0000.000
125A126SER00.0400.01132.3780.0120.0120.0000.0000.0000.000
126A127GLY00.0300.00435.8340.0010.0010.0000.0000.0000.000
127A128ALA0-0.0170.01539.2660.0060.0060.0000.0000.0000.000
128A129SER0-0.001-0.00840.043-0.005-0.0050.0000.0000.0000.000
129A130THR00.007-0.00142.261-0.001-0.0010.0000.0000.0000.000
130A131LYS10.8980.96643.5920.1140.1140.0000.0000.0000.000
131A132GLY00.0770.04545.314-0.003-0.0030.0000.0000.0000.000
132A133PRO0-0.041-0.01446.4820.0000.0000.0000.0000.0000.000
133A134SER00.0120.01948.3690.0050.0050.0000.0000.0000.000
134A135VAL0-0.002-0.01850.232-0.003-0.0030.0000.0000.0000.000
135A136PHE0-0.013-0.00552.4320.0040.0040.0000.0000.0000.000
136A137PRO0-0.018-0.00253.334-0.001-0.0010.0000.0000.0000.000
137A138LEU00.0190.01050.1550.0000.0000.0000.0000.0000.000
138A149THR0-0.025-0.01955.0670.0010.0010.0000.0000.0000.000
139A150ALA0-0.042-0.02957.2790.0000.0000.0000.0000.0000.000
140A151ALA00.0180.01052.849-0.001-0.0010.0000.0000.0000.000
141A152LEU0-0.0190.00853.8670.0010.0010.0000.0000.0000.000
142A153GLY00.0560.00851.614-0.002-0.0020.0000.0000.0000.000
143A154CYS0-0.091-0.02650.7220.0010.0010.0000.0000.0000.000
144A155LEU00.0200.03047.999-0.003-0.0030.0000.0000.0000.000
145A156VAL00.001-0.01145.4600.0030.0030.0000.0000.0000.000
146A157LYS10.9070.92346.3330.0900.0900.0000.0000.0000.000
147A158ASP-1-0.799-0.88645.331-0.104-0.1040.0000.0000.0000.000
148A159TYR0-0.053-0.03840.5610.0060.0060.0000.0000.0000.000
149A160PHE00.0270.00936.738-0.009-0.0090.0000.0000.0000.000
150A161PRO00.0090.01737.0150.0060.0060.0000.0000.0000.000
151A162GLU-1-0.714-0.84835.883-0.122-0.1220.0000.0000.0000.000
152A163PRO0-0.033-0.01336.611-0.004-0.0040.0000.0000.0000.000
153A164VAL0-0.011-0.01038.5680.0060.0060.0000.0000.0000.000
154A165THR0-0.059-0.02741.0860.0000.0000.0000.0000.0000.000
155A166VAL00.0220.00343.5200.0020.0020.0000.0000.0000.000
156A167SER0-0.014-0.00145.9750.0020.0020.0000.0000.0000.000
157A168TRP00.0490.02248.7650.0010.0010.0000.0000.0000.000
158A169ASN00.010-0.02052.0220.0000.0000.0000.0000.0000.000
159A170SER0-0.016-0.01252.7490.0010.0010.0000.0000.0000.000
160A171GLY00.0120.01350.3180.0000.0000.0000.0000.0000.000
161A172ALA0-0.029-0.00151.2700.0010.0010.0000.0000.0000.000
162A173LEU0-0.030-0.00852.2820.0020.0020.0000.0000.0000.000
163A174THR00.0270.00147.513-0.002-0.0020.0000.0000.0000.000
164A175SER00.0350.01348.114-0.003-0.0030.0000.0000.0000.000
165A176GLY00.0590.02748.8630.0000.0000.0000.0000.0000.000
166A177VAL0-0.049-0.01546.658-0.002-0.0020.0000.0000.0000.000
167A178HIS00.0040.00840.6480.0010.0010.0000.0000.0000.000
168A179THR00.0080.00741.6460.0030.0030.0000.0000.0000.000
169A180PHE0-0.0110.00541.009-0.003-0.0030.0000.0000.0000.000
170A181PRO00.023-0.00536.0620.0000.0000.0000.0000.0000.000
171A182ALA0-0.0060.00838.1300.0030.0030.0000.0000.0000.000
172A183VAL0-0.0080.00137.467-0.009-0.0090.0000.0000.0000.000
173A184LEU0-0.029-0.01634.2820.0040.0040.0000.0000.0000.000
174A185GLN0-0.045-0.03337.9810.0000.0000.0000.0000.0000.000
175A186SER00.0250.00339.161-0.005-0.0050.0000.0000.0000.000
176A187SER0-0.011-0.00640.233-0.005-0.0050.0000.0000.0000.000
177A188GLY0-0.007-0.00438.4830.0000.0000.0000.0000.0000.000
178A189LEU0-0.068-0.02539.4960.0000.0000.0000.0000.0000.000
179A190TYR00.0390.02134.356-0.003-0.0030.0000.0000.0000.000
180A191SER0-0.005-0.01440.9800.0090.0090.0000.0000.0000.000
181A192LEU00.0070.03041.199-0.005-0.0050.0000.0000.0000.000
182A193SER00.007-0.01443.7140.0060.0060.0000.0000.0000.000
183A194SER00.000-0.00344.973-0.004-0.0040.0000.0000.0000.000
184A195VAL00.004-0.01747.0050.0030.0030.0000.0000.0000.000
185A196VAL0-0.005-0.00448.781-0.001-0.0010.0000.0000.0000.000
186A197THR0-0.0180.00049.9300.0000.0000.0000.0000.0000.000
187A198VAL00.0070.00852.5480.0020.0020.0000.0000.0000.000
188A199PRO00.0500.03056.1760.0000.0000.0000.0000.0000.000
189A200SER00.028-0.00959.5370.0000.0000.0000.0000.0000.000
190A201SER0-0.031-0.01861.8900.0010.0010.0000.0000.0000.000
191A202SER00.0440.02062.5410.0010.0010.0000.0000.0000.000
192A203LEU0-0.011-0.00164.486-0.001-0.0010.0000.0000.0000.000
193A204GLY00.0070.00665.621-0.001-0.0010.0000.0000.0000.000
194A205THR0-0.038-0.01965.9710.0010.0010.0000.0000.0000.000
195A206GLN00.0160.02460.4830.0010.0010.0000.0000.0000.000
196A207THR0-0.036-0.00461.186-0.001-0.0010.0000.0000.0000.000
197A208TYR00.0460.01156.7830.0000.0000.0000.0000.0000.000
198A209ILE0-0.018-0.01755.884-0.001-0.0010.0000.0000.0000.000
199A211ASN00.0480.03050.8440.0000.0000.0000.0000.0000.000
200A212VAL0-0.010-0.00948.053-0.002-0.0020.0000.0000.0000.000
201A213ASN0-0.003-0.01546.2910.0040.0040.0000.0000.0000.000
202A214HIS00.0000.00741.7290.0020.0020.0000.0000.0000.000
203A215LYS10.9710.97541.9960.0880.0880.0000.0000.0000.000
204A216PRO00.0050.01040.2420.0030.0030.0000.0000.0000.000
205A217SER0-0.018-0.03242.7420.0000.0000.0000.0000.0000.000
206A218ASN0-0.024-0.01746.2750.0010.0010.0000.0000.0000.000
207A219THR00.0100.02047.9960.0050.0050.0000.0000.0000.000
208A220LYS10.8320.88848.8180.0600.0600.0000.0000.0000.000
209A221VAL0-0.0070.00051.2100.0020.0020.0000.0000.0000.000
210A222ASP-1-0.813-0.88652.993-0.058-0.0580.0000.0000.0000.000
211A223LYS10.9330.97354.3780.0620.0620.0000.0000.0000.000
212A224ARG10.9620.99455.5080.0500.0500.0000.0000.0000.000