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: 5J73Z

Calculation Name: 1XKR-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1XKR

Chain ID: A

ChEMBL ID:

UniProt ID: Q9X006

Base Structure: X-ray

Registration Date: 2023-09-24

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 OptH
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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2303827.450727
FMO2-HF: Nuclear repulsion 2223737.437742
FMO2-HF: Total energy -80090.012985
FMO2-MP2: Total energy -80319.433223


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:HIS)


Summations of interaction energy for fragment #1(A:0:HIS)
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.
-13.711-9.5212.817-3.185-3.82-0.015
Interaction energy analysis for fragmet #1(A:0:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / q_NPA : 0.009
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].
3A2LYS10.9410.9612.209-10.591-6.6182.817-3.152-3.637-0.015
4A3ILE00.0310.0284.5081.3661.5830.000-0.033-0.1830.000
5A4SER0-0.070-0.0327.3040.3200.3200.0000.0000.0000.000
6A5GLU-1-0.773-0.9149.849-1.623-1.6230.0000.0000.0000.000
7A6ARG10.8920.95912.8330.9220.9220.0000.0000.0000.000
8A7GLN00.016-0.00510.245-0.263-0.2630.0000.0000.0000.000
9A8LYS10.9100.9539.3092.3002.3000.0000.0000.0000.000
10A9ASP-1-0.904-0.95614.176-0.664-0.6640.0000.0000.0000.000
11A10LEU00.0170.01617.0400.0720.0720.0000.0000.0000.000
12A11LEU0-0.022-0.01413.8990.0630.0630.0000.0000.0000.000
13A12LYS10.9540.98817.9280.7110.7110.0000.0000.0000.000
14A13GLU-1-0.953-0.97920.002-0.527-0.5270.0000.0000.0000.000
15A14ILE00.0030.00419.8830.0540.0540.0000.0000.0000.000
16A15GLY00.010-0.00121.8080.0460.0460.0000.0000.0000.000
17A16ASN0-0.045-0.03423.2190.0810.0810.0000.0000.0000.000
18A17ILE0-0.0260.01025.8930.0440.0440.0000.0000.0000.000
19A18GLY00.0200.00326.5100.0330.0330.0000.0000.0000.000
20A19ALA00.0170.00627.1750.0280.0280.0000.0000.0000.000
21A20GLY00.0510.02728.9120.0290.0290.0000.0000.0000.000
22A21ASN0-0.024-0.02130.9970.0430.0430.0000.0000.0000.000
23A22ALA00.0030.00130.9390.0220.0220.0000.0000.0000.000
24A23ALA0-0.006-0.00532.9390.0190.0190.0000.0000.0000.000
25A24THR00.0090.01434.7400.0230.0230.0000.0000.0000.000
26A25ALA00.004-0.00336.1590.0160.0160.0000.0000.0000.000
27A26ILE00.0410.00533.9400.0140.0140.0000.0000.0000.000
28A27SER0-0.037-0.02338.0250.0130.0130.0000.0000.0000.000
29A28TYR0-0.070-0.04140.4440.0150.0150.0000.0000.0000.000
30A29MET0-0.061-0.00639.8720.0050.0050.0000.0000.0000.000
31A30ILE0-0.021-0.01339.5710.0080.0080.0000.0000.0000.000
32A31ASN0-0.057-0.00843.1740.0070.0070.0000.0000.0000.000
33A32LYS10.8220.88642.3940.1750.1750.0000.0000.0000.000
34A33LYS10.8500.93638.8220.2080.2080.0000.0000.0000.000
35A34VAL0-0.015-0.00235.4990.0000.0000.0000.0000.0000.000
36A35GLU-1-0.892-0.93134.213-0.246-0.2460.0000.0000.0000.000
37A36ILE0-0.006-0.00529.027-0.001-0.0010.0000.0000.0000.000
38A37SER0-0.035-0.00527.956-0.009-0.0090.0000.0000.0000.000
39A38VAL00.006-0.00221.736-0.003-0.0030.0000.0000.0000.000
40A39PRO00.0020.01523.088-0.024-0.0240.0000.0000.0000.000
41A40ASN0-0.070-0.06018.435-0.066-0.0660.0000.0000.0000.000
42A41VAL00.0340.02914.7840.0280.0280.0000.0000.0000.000
43A42GLU-1-0.968-0.96713.459-1.062-1.0620.0000.0000.0000.000
44A43ILE0-0.053-0.0349.122-0.022-0.0220.0000.0000.0000.000
45A44VAL00.0190.00910.524-0.226-0.2260.0000.0000.0000.000
46A45PRO00.0180.0149.6540.0380.0380.0000.0000.0000.000
47A46ILE00.0870.02311.6930.1160.1160.0000.0000.0000.000
48A47SER00.0310.02313.9900.0380.0380.0000.0000.0000.000
49A48LYS10.8400.90213.0540.5940.5940.0000.0000.0000.000
50A49VAL00.0600.04215.9430.0180.0180.0000.0000.0000.000
51A50ILE0-0.0160.01218.0500.0360.0360.0000.0000.0000.000
52A51PHE0-0.086-0.05117.8020.0470.0470.0000.0000.0000.000
53A52ILE00.0020.02016.9610.0180.0180.0000.0000.0000.000
54A53ALA0-0.036-0.00420.9890.0240.0240.0000.0000.0000.000
55A54LYS10.9450.96024.4320.3060.3060.0000.0000.0000.000
56A55ASP-1-0.847-0.93027.326-0.189-0.1890.0000.0000.0000.000
57A56PRO0-0.036-0.01925.341-0.011-0.0110.0000.0000.0000.000
58A57GLU-1-0.913-0.99427.054-0.160-0.1600.0000.0000.0000.000
59A58GLU-1-0.840-0.89430.153-0.247-0.2470.0000.0000.0000.000
60A59ILE0-0.049-0.02130.761-0.010-0.0100.0000.0000.0000.000
61A60VAL0-0.029-0.01828.225-0.003-0.0030.0000.0000.0000.000
62A61VAL0-0.009-0.00731.6570.0120.0120.0000.0000.0000.000
63A62GLY00.0260.01328.504-0.024-0.0240.0000.0000.0000.000
64A63VAL0-0.053-0.01928.3330.0240.0240.0000.0000.0000.000
65A64LYS10.9980.99923.3340.3350.3350.0000.0000.0000.000
66A65MET0-0.0210.00225.7560.0260.0260.0000.0000.0000.000
67A66PRO0-0.027-0.01524.340-0.039-0.0390.0000.0000.0000.000
68A67VAL0-0.009-0.01421.6080.0170.0170.0000.0000.0000.000
69A68THR0-0.020-0.02223.2150.0000.0000.0000.0000.0000.000
70A69GLY00.0190.01024.1020.0040.0040.0000.0000.0000.000
71A70ASP-1-0.876-0.94321.877-0.424-0.4240.0000.0000.0000.000
72A71ILE0-0.056-0.03917.533-0.079-0.0790.0000.0000.0000.000
73A72GLU-1-0.834-0.88818.739-0.345-0.3450.0000.0000.0000.000
74A73GLY00.0220.00718.141-0.085-0.0850.0000.0000.0000.000
75A74SER0-0.073-0.02919.6620.0820.0820.0000.0000.0000.000
76A75VAL00.0070.02220.319-0.070-0.0700.0000.0000.0000.000
77A76LEU00.001-0.00422.2040.0580.0580.0000.0000.0000.000
78A77LEU00.0200.00523.685-0.035-0.0350.0000.0000.0000.000
79A78ILE0-0.005-0.00224.4500.0270.0270.0000.0000.0000.000
80A79MET0-0.012-0.01627.195-0.006-0.0060.0000.0000.0000.000
81A80GLY00.0800.04130.4630.0130.0130.0000.0000.0000.000
82A81THR0-0.001-0.03031.6290.0140.0140.0000.0000.0000.000
83A82THR0-0.026-0.02334.5720.0100.0100.0000.0000.0000.000
84A83VAL00.0240.01931.9470.0100.0100.0000.0000.0000.000
85A84VAL00.0160.01134.1460.0090.0090.0000.0000.0000.000
86A85LYS10.8790.93736.5860.1740.1740.0000.0000.0000.000
87A86LYS10.9200.99038.3170.1870.1870.0000.0000.0000.000
88A87ILE00.0080.00135.0440.0070.0070.0000.0000.0000.000
89A88LEU00.004-0.00839.5750.0080.0080.0000.0000.0000.000
90A89GLU-1-0.940-0.94842.079-0.146-0.1460.0000.0000.0000.000
91A90ILE0-0.042-0.02240.9780.0070.0070.0000.0000.0000.000
92A91LEU0-0.040-0.01041.8520.0050.0050.0000.0000.0000.000
93A92THR0-0.048-0.04844.6750.0080.0080.0000.0000.0000.000
94A93GLY0-0.0010.01347.0380.0080.0080.0000.0000.0000.000
95A94ARG10.8900.93347.3460.1300.1300.0000.0000.0000.000
96A95ALA00.0460.03643.203-0.005-0.0050.0000.0000.0000.000
97A96PRO0-0.059-0.01241.8030.0080.0080.0000.0000.0000.000
98A97ASP-1-0.854-0.94143.211-0.127-0.1270.0000.0000.0000.000
99A98ASN0-0.055-0.03441.144-0.008-0.0080.0000.0000.0000.000
100A99LEU00.0560.01035.3000.0020.0020.0000.0000.0000.000
101A100LEU00.0470.01937.888-0.003-0.0030.0000.0000.0000.000
102A101ASN0-0.107-0.05340.3170.0090.0090.0000.0000.0000.000
103A102LEU0-0.0190.01038.3850.0040.0040.0000.0000.0000.000
104A103ASP-1-0.818-0.88742.667-0.142-0.1420.0000.0000.0000.000
105A104GLU-1-0.882-0.96643.287-0.139-0.1390.0000.0000.0000.000
106A105PHE0-0.039-0.01242.976-0.008-0.0080.0000.0000.0000.000
107A106SER00.021-0.01741.927-0.009-0.0090.0000.0000.0000.000
108A107ALA00.0000.01238.971-0.012-0.0120.0000.0000.0000.000
109A108SER0-0.020-0.02038.164-0.014-0.0140.0000.0000.0000.000
110A109ALA00.0000.01038.873-0.010-0.0100.0000.0000.0000.000
111A110LEU00.0300.00335.696-0.012-0.0120.0000.0000.0000.000
112A111ARG10.8610.93234.3190.2030.2030.0000.0000.0000.000
113A112GLU-1-0.879-0.94634.192-0.250-0.2500.0000.0000.0000.000
114A113ILE00.008-0.00533.142-0.012-0.0120.0000.0000.0000.000
115A114GLY00.027-0.00330.979-0.020-0.0200.0000.0000.0000.000
116A115ASN0-0.040-0.02330.367-0.036-0.0360.0000.0000.0000.000
117A116ILE0-0.0150.01031.645-0.016-0.0160.0000.0000.0000.000
118A117MET0-0.0080.00228.508-0.011-0.0110.0000.0000.0000.000
119A118CYS0-0.041-0.01926.644-0.034-0.0340.0000.0000.0000.000
120A119GLY00.0610.03226.987-0.026-0.0260.0000.0000.0000.000
121A120THR0-0.059-0.05429.028-0.014-0.0140.0000.0000.0000.000
122A121TYR00.0060.01119.510-0.028-0.0280.0000.0000.0000.000
123A122VAL00.018-0.00124.162-0.034-0.0340.0000.0000.0000.000
124A123SER0-0.021-0.00625.435-0.013-0.0130.0000.0000.0000.000
125A124ALA00.0230.01825.5560.0030.0030.0000.0000.0000.000
126A125LEU0-0.010-0.01319.048-0.019-0.0190.0000.0000.0000.000
127A126ALA0-0.016-0.01222.995-0.025-0.0250.0000.0000.0000.000
128A127ASP-1-0.894-0.94024.758-0.366-0.3660.0000.0000.0000.000
129A128PHE0-0.071-0.04723.5870.0120.0120.0000.0000.0000.000
130A129LEU0-0.046-0.01018.427-0.027-0.0270.0000.0000.0000.000
131A130GLY0-0.0150.00122.401-0.006-0.0060.0000.0000.0000.000
132A131PHE0-0.089-0.04518.1370.0040.0040.0000.0000.0000.000
133A132LYS10.9160.95224.1270.3250.3250.0000.0000.0000.000
134A133ILE0-0.032-0.01822.252-0.018-0.0180.0000.0000.0000.000
135A134ASP-1-0.898-0.92425.909-0.277-0.2770.0000.0000.0000.000
136A135THR0-0.016-0.03226.804-0.022-0.0220.0000.0000.0000.000
137A136LEU0-0.015-0.00427.8220.0280.0280.0000.0000.0000.000
138A137PRO0-0.027-0.02630.257-0.008-0.0080.0000.0000.0000.000
139A138PRO00.0290.02330.353-0.007-0.0070.0000.0000.0000.000
140A139GLN0-0.010-0.01528.7110.0200.0200.0000.0000.0000.000
141A140LEU0-0.0140.00130.349-0.018-0.0180.0000.0000.0000.000
142A141VAL00.0250.01628.8870.0150.0150.0000.0000.0000.000
143A142ILE0-0.019-0.01632.061-0.012-0.0120.0000.0000.0000.000
144A143ASP-1-0.824-0.90930.441-0.187-0.1870.0000.0000.0000.000
145A144MET0-0.092-0.02029.582-0.011-0.0110.0000.0000.0000.000
146A145ILE00.009-0.00124.843-0.012-0.0120.0000.0000.0000.000
147A146SER00.018-0.01124.893-0.022-0.0220.0000.0000.0000.000
148A147ALA00.0140.01525.032-0.008-0.0080.0000.0000.0000.000
149A148ILE00.0370.02324.402-0.009-0.0090.0000.0000.0000.000
150A149PHE00.000-0.02619.900-0.025-0.0250.0000.0000.0000.000
151A150ALA0-0.0360.01220.832-0.023-0.0230.0000.0000.0000.000
152A151GLU-1-0.930-0.97321.908-0.230-0.2300.0000.0000.0000.000
153A152ALA0-0.016-0.00820.181-0.007-0.0070.0000.0000.0000.000
154A153SER0-0.039-0.05017.378-0.056-0.0560.0000.0000.0000.000
155A154ILE0-0.056-0.02617.4010.0040.0040.0000.0000.0000.000
156A155GLU-1-0.910-0.95319.269-0.277-0.2770.0000.0000.0000.000
157A156GLU-1-0.943-0.97214.684-0.581-0.5810.0000.0000.0000.000
158A157LEU0-0.083-0.04411.907-0.021-0.0210.0000.0000.0000.000
159A158GLU-1-0.980-0.95915.319-0.143-0.1430.0000.0000.0000.000
160A159ASP-1-0.939-0.97617.132-0.099-0.0990.0000.0000.0000.000
161A160ASN0-0.103-0.05912.284-0.059-0.0590.0000.0000.0000.000
162A161SER00.007-0.0119.0640.0710.0710.0000.0000.0000.000
163A162GLU-1-0.956-0.9547.504-1.270-1.2700.0000.0000.0000.000
164A163ASP-1-0.798-0.9108.730-1.139-1.1390.0000.0000.0000.000
165A164GLN0-0.096-0.0406.171-0.286-0.2860.0000.0000.0000.000
166A165ILE00.0230.0269.9890.1150.1150.0000.0000.0000.000
167A166VAL0-0.047-0.02313.103-0.203-0.2030.0000.0000.0000.000
168A167PHE00.017-0.00415.2330.1650.1650.0000.0000.0000.000
169A168VAL00.0340.00117.347-0.047-0.0470.0000.0000.0000.000
170A169GLU-1-0.881-0.92720.215-0.444-0.4440.0000.0000.0000.000
171A170THR0-0.023-0.04123.2440.0000.0000.0000.0000.0000.000
172A171LEU00.0220.01026.4230.0250.0250.0000.0000.0000.000
173A172LEU00.0090.00729.1810.0070.0070.0000.0000.0000.000
174A173LYS10.9150.94432.5720.2250.2250.0000.0000.0000.000
175A174VAL00.0180.01635.4620.0040.0040.0000.0000.0000.000
176A175GLU-1-0.889-0.97339.077-0.176-0.1760.0000.0000.0000.000
177A176GLU-1-0.951-0.94141.415-0.147-0.1470.0000.0000.0000.000
178A177GLU-1-0.894-0.96939.669-0.171-0.1710.0000.0000.0000.000
179A178GLU-1-0.958-0.98739.285-0.188-0.1880.0000.0000.0000.000
180A179GLU-1-0.907-0.94334.964-0.227-0.2270.0000.0000.0000.000
181A180PRO0-0.079-0.03932.1350.0000.0000.0000.0000.0000.000
182A181LEU0-0.012-0.01032.919-0.005-0.0050.0000.0000.0000.000
183A182THR0-0.021-0.00826.924-0.017-0.0170.0000.0000.0000.000
184A183SER0-0.042-0.01528.1340.0260.0260.0000.0000.0000.000
185A184TYR00.0190.01822.823-0.011-0.0110.0000.0000.0000.000
186A185MET0-0.035-0.01022.8520.0450.0450.0000.0000.0000.000
187A186MET0-0.0080.01718.344-0.064-0.0640.0000.0000.0000.000
188A187MET0-0.0240.00617.3430.0510.0510.0000.0000.0000.000
189A188ILE00.028-0.00116.079-0.145-0.1450.0000.0000.0000.000
190A189PRO0-0.032-0.01512.9420.0900.0900.0000.0000.0000.000
191A190LYS10.9800.99414.3830.4390.4390.0000.0000.0000.000
192A191PRO00.0410.00811.807-0.125-0.1250.0000.0000.0000.000
193A192GLY0-0.015-0.01210.8270.1030.1030.0000.0000.0000.000
194A193TYR0-0.010-0.02411.892-0.067-0.0670.0000.0000.0000.000
195A194LEU00.0520.0389.000-0.044-0.0440.0000.0000.0000.000
196A195VAL0-0.009-0.0148.039-0.163-0.1630.0000.0000.0000.000
197A196LYS10.9430.97810.7400.7520.7520.0000.0000.0000.000
198A197ILE00.0400.02414.3400.0900.0900.0000.0000.0000.000
199A198PHE00.001-0.0299.9660.0310.0310.0000.0000.0000.000
200A199GLU-1-0.971-0.97113.499-0.668-0.6680.0000.0000.0000.000
201A200ARG10.8490.93214.7420.7090.7090.0000.0000.0000.000
202A201MET0-0.0300.01615.3170.0330.0330.0000.0000.0000.000
203A202GLY0-0.020-0.00117.3910.0600.0600.0000.0000.0000.000
204A203ILE00.009-0.01015.421-0.095-0.0950.0000.0000.0000.000
205A204GLN0-0.0250.00412.941-0.004-0.0040.0000.0000.0000.000