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: 6N37Z

Calculation Name: 5UDF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5UDF

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0D5

Base Structure: X-ray

Registration Date: 2023-06-21

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 211
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2305138.589449
FMO2-HF: Nuclear repulsion 2225608.253129
FMO2-HF: Total energy -79530.33632
FMO2-MP2: Total energy -79764.551815


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:67:ASP)


Summations of interaction energy for fragment #1(A:67:ASP)
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.
-55.079-48.0164.378-5.536-5.9040.034
Interaction energy analysis for fragmet #1(A:67:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.882 / q_NPA : -0.958
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].
3A69GLU-1-0.831-0.9373.38232.60036.2900.037-1.841-1.8860.010
4A70LEU00.0060.0062.006-15.410-12.8274.338-3.437-3.4850.022
5A71LYS10.9821.0043.747-36.235-35.9640.002-0.028-0.2440.000
6A72ASN00.0190.0115.693-6.400-6.4000.0000.0000.0000.000
7A73ARG10.9791.0003.755-59.034-58.5150.001-0.230-0.2890.002
8A74VAL00.0130.0087.213-3.032-3.0320.0000.0000.0000.000
9A75LEU0-0.025-0.0229.062-2.429-2.4290.0000.0000.0000.000
10A76GLY0-0.007-0.00410.875-1.869-1.8690.0000.0000.0000.000
11A77MET0-0.045-0.02312.549-1.935-1.9350.0000.0000.0000.000
12A78VAL00.0080.02213.425-1.198-1.1980.0000.0000.0000.000
13A79PRO0-0.026-0.01915.733-0.096-0.0960.0000.0000.0000.000
14A80GLN00.0430.02515.246-0.972-0.9720.0000.0000.0000.000
15A81ALA00.0910.02419.198-0.323-0.3230.0000.0000.0000.000
16A82THR0-0.111-0.05022.9990.0490.0490.0000.0000.0000.000
17A83VAL00.0510.03225.967-0.201-0.2010.0000.0000.0000.000
18A84SER0-0.009-0.01328.8890.0590.0590.0000.0000.0000.000
19A85SER00.009-0.00531.369-0.288-0.2880.0000.0000.0000.000
20A86THR0-0.032-0.01334.9660.0770.0770.0000.0000.0000.000
21A87GLN0-0.044-0.01337.282-0.127-0.1270.0000.0000.0000.000
22A88ILE0-0.0160.01835.5980.1730.1730.0000.0000.0000.000
23A89LEU00.0470.02133.937-0.192-0.1920.0000.0000.0000.000
24A90THR0-0.005-0.02236.7470.2070.2070.0000.0000.0000.000
25A91ASP-1-0.893-0.93739.0398.0258.0250.0000.0000.0000.000
26A92TRP00.0050.00131.6520.2190.2190.0000.0000.0000.000
27A93PRO00.009-0.01234.0270.1970.1970.0000.0000.0000.000
28A94GLU-1-0.816-0.88235.0458.2358.2350.0000.0000.0000.000
29A95LEU00.0050.00332.1380.0270.0270.0000.0000.0000.000
30A96VAL0-0.003-0.01329.7800.1870.1870.0000.0000.0000.000
31A97LYS10.8080.88631.496-8.181-8.1810.0000.0000.0000.000
32A98ARG10.8680.94733.874-8.267-8.2670.0000.0000.0000.000
33A99VAL0-0.010-0.01128.357-0.015-0.0150.0000.0000.0000.000
34A100GLU-1-0.934-0.97427.16811.47411.4740.0000.0000.0000.000
35A101ASN0-0.009-0.00828.5470.4540.4540.0000.0000.0000.000
36A102HIS0-0.037-0.00928.042-0.432-0.4320.0000.0000.0000.000
37A103PRO00.0320.00527.7350.4020.4020.0000.0000.0000.000
38A104HIS10.8690.90621.973-12.546-12.5460.0000.0000.0000.000
39A105VAL0-0.0160.01522.5730.7380.7380.0000.0000.0000.000
40A106THR0-0.044-0.03420.2070.1150.1150.0000.0000.0000.000
41A107GLY00.0030.00522.0790.2360.2360.0000.0000.0000.000
42A108VAL00.0240.02223.0170.0230.0230.0000.0000.0000.000
43A109ALA0-0.006-0.00624.400-0.058-0.0580.0000.0000.0000.000
44A110PRO0-0.0100.01926.2370.0380.0380.0000.0000.0000.000
45A111PHE0-0.041-0.01526.0000.4260.4260.0000.0000.0000.000
46A112THR00.0370.00128.037-0.409-0.4090.0000.0000.0000.000
47A113GLN0-0.041-0.02324.3430.2680.2680.0000.0000.0000.000
48A114LEU00.0000.00328.386-0.439-0.4390.0000.0000.0000.000
49A115GLN00.0580.02028.2570.7200.7200.0000.0000.0000.000
50A116GLY0-0.037-0.02329.436-0.454-0.4540.0000.0000.0000.000
51A117MET0-0.045-0.01630.1140.2090.2090.0000.0000.0000.000
52A118LEU00.0150.01227.797-0.259-0.2590.0000.0000.0000.000
53A119THR0-0.034-0.03831.473-0.117-0.1170.0000.0000.0000.000
54A120ALA00.036-0.00732.780-0.095-0.0950.0000.0000.0000.000
55A121GLN0-0.007-0.00134.361-0.135-0.1350.0000.0000.0000.000
56A122GLY00.0120.01636.2980.0230.0230.0000.0000.0000.000
57A123GLN00.0030.02331.088-0.315-0.3150.0000.0000.0000.000
58A124VAL00.001-0.00732.416-0.144-0.1440.0000.0000.0000.000
59A125ALA00.0310.02627.0330.2120.2120.0000.0000.0000.000
60A126GLY0-0.0040.00627.878-0.300-0.3000.0000.0000.0000.000
61A127ILE0-0.014-0.01024.7510.3990.3990.0000.0000.0000.000
62A128MET0-0.0080.00723.460-0.659-0.6590.0000.0000.0000.000
63A129VAL0-0.001-0.00724.4270.4610.4610.0000.0000.0000.000
64A130THR00.0240.01724.239-0.209-0.2090.0000.0000.0000.000
65A131GLY0-0.014-0.00726.2220.1050.1050.0000.0000.0000.000
66A132ILE00.0200.00423.9670.0900.0900.0000.0000.0000.000
67A133ASP-1-0.765-0.88427.51210.04610.0460.0000.0000.0000.000
68A134PRO00.0360.01525.4930.3740.3740.0000.0000.0000.000
69A135LYS10.7920.89525.290-9.751-9.7510.0000.0000.0000.000
70A136TYR00.0230.00026.5560.0170.0170.0000.0000.0000.000
71A137GLU-1-0.862-0.93721.45914.32314.3230.0000.0000.0000.000
72A138LYS10.9160.95220.708-12.464-12.4640.0000.0000.0000.000
73A139ASN0-0.019-0.00720.1430.9120.9120.0000.0000.0000.000
74A140VAL0-0.053-0.02519.4960.3080.3080.0000.0000.0000.000
75A141SER00.0060.03517.0911.2771.2770.0000.0000.0000.000
76A142ILE00.0140.01111.9930.2330.2330.0000.0000.0000.000
77A143ILE00.006-0.00115.1100.7480.7480.0000.0000.0000.000
78A144GLN0-0.001-0.02917.198-0.269-0.2690.0000.0000.0000.000
79A145ASN0-0.079-0.03213.828-1.433-1.4330.0000.0000.0000.000
80A146HIS0-0.039-0.01410.8783.1923.1920.0000.0000.0000.000
81A147ILE0-0.012-0.00515.208-0.330-0.3300.0000.0000.0000.000
82A148VAL0-0.024-0.01217.1050.0360.0360.0000.0000.0000.000
83A149ALA0-0.012-0.01519.500-0.613-0.6130.0000.0000.0000.000
84A150GLY00.0060.00723.2710.0760.0760.0000.0000.0000.000
85A151SER0-0.006-0.01724.1200.3140.3140.0000.0000.0000.000
86A152LEU00.0750.02921.097-0.376-0.3760.0000.0000.0000.000
87A153ASP-1-0.907-0.94725.10611.83411.8340.0000.0000.0000.000
88A154SER0-0.058-0.03028.086-0.613-0.6130.0000.0000.0000.000
89A155LEU0-0.078-0.01726.380-0.327-0.3270.0000.0000.0000.000
90A156LYS10.9410.97230.316-9.490-9.4900.0000.0000.0000.000
91A157LYS10.8900.92533.785-8.035-8.0350.0000.0000.0000.000
92A158GLY0-0.034-0.02236.558-0.163-0.1630.0000.0000.0000.000
93A159GLU-1-0.930-0.96234.8868.4708.4700.0000.0000.0000.000
94A160PHE0-0.071-0.02834.664-0.047-0.0470.0000.0000.0000.000
95A161GLY00.0330.01831.5760.0220.0220.0000.0000.0000.000
96A162ILE0-0.048-0.03627.4730.0210.0210.0000.0000.0000.000
97A163VAL0-0.031-0.01022.5050.0520.0520.0000.0000.0000.000
98A164LEU00.015-0.00223.7020.0250.0250.0000.0000.0000.000
99A165GLY00.0850.05319.8140.3790.3790.0000.0000.0000.000
100A166LYS10.9450.96118.283-16.191-16.1910.0000.0000.0000.000
101A167ASP-1-0.847-0.91717.52017.21117.2110.0000.0000.0000.000
102A168MET00.0050.01220.539-0.962-0.9620.0000.0000.0000.000
103A169ALA0-0.0390.01123.315-0.734-0.7340.0000.0000.0000.000
104A170ASP-1-0.808-0.89321.98313.64713.6470.0000.0000.0000.000
105A171SER0-0.106-0.07924.618-0.610-0.6100.0000.0000.0000.000
106A172LEU0-0.039-0.02726.339-0.554-0.5540.0000.0000.0000.000
107A173GLY0-0.022-0.00328.546-0.399-0.3990.0000.0000.0000.000
108A174LEU0-0.054-0.01028.067-0.314-0.3140.0000.0000.0000.000
109A175ARG10.7960.86424.899-11.788-11.7880.0000.0000.0000.000
110A176LEU00.0190.00226.650-0.117-0.1170.0000.0000.0000.000
111A177ASN00.0150.00128.957-0.358-0.3580.0000.0000.0000.000
112A178ASP-1-0.804-0.88131.4139.5409.5400.0000.0000.0000.000
113A179SER0-0.065-0.04632.767-0.023-0.0230.0000.0000.0000.000
114A180VAL00.0140.01430.4590.0440.0440.0000.0000.0000.000
115A181THR0-0.048-0.01633.757-0.154-0.1540.0000.0000.0000.000
116A182LEU00.0220.02330.9780.2040.2040.0000.0000.0000.000
117A183VAL00.002-0.01633.883-0.394-0.3940.0000.0000.0000.000
118A184LEU00.0360.01032.9770.3050.3050.0000.0000.0000.000
119A185PRO0-0.012-0.00834.549-0.317-0.3170.0000.0000.0000.000
120A186GLU-1-0.838-0.92637.4248.1578.1570.0000.0000.0000.000
121A187ALA00.0180.01940.131-0.139-0.1390.0000.0000.0000.000
122A188THR0-0.013-0.00441.980-0.169-0.1690.0000.0000.0000.000
123A189PRO00.0150.00845.7440.0510.0510.0000.0000.0000.000
124A190SER0-0.042-0.00847.970-0.115-0.1150.0000.0000.0000.000
125A191PRO00.0680.01047.9540.1170.1170.0000.0000.0000.000
126A192ALA0-0.0120.00446.2050.0880.0880.0000.0000.0000.000
127A193GLY00.0040.01643.8830.1620.1620.0000.0000.0000.000
128A194VAL0-0.043-0.04039.1260.1470.1470.0000.0000.0000.000
129A195VAL0-0.012-0.00842.412-0.154-0.1540.0000.0000.0000.000
130A196PRO0-0.035-0.00839.7260.1310.1310.0000.0000.0000.000
131A197ARG10.9010.95839.228-8.049-8.0490.0000.0000.0000.000
132A198PHE00.0030.00338.0810.2620.2620.0000.0000.0000.000
133A199LYS10.8790.95637.095-8.524-8.5240.0000.0000.0000.000
134A200ARG10.9230.96336.577-7.892-7.8920.0000.0000.0000.000
135A201PHE00.013-0.00432.461-0.140-0.1400.0000.0000.0000.000
136A202LYS10.8640.93433.337-9.135-9.1350.0000.0000.0000.000
137A203VAL00.0250.02027.1450.1940.1940.0000.0000.0000.000
138A204VAL00.0000.00327.923-0.197-0.1970.0000.0000.0000.000
139A205GLY00.016-0.00924.7130.1250.1250.0000.0000.0000.000
140A206ILE0-0.0160.00220.584-0.206-0.2060.0000.0000.0000.000
141A207PHE0-0.0060.00916.7220.1820.1820.0000.0000.0000.000
142A208SER0-0.047-0.02114.828-0.195-0.1950.0000.0000.0000.000
143A209VAL0-0.041-0.02811.5451.1771.1770.0000.0000.0000.000
144A210GLY00.013-0.01710.7753.6403.6400.0000.0000.0000.000
145A211ALA00.0370.02711.815-1.712-1.7120.0000.0000.0000.000
146A212GLU-1-0.941-0.96613.71119.27519.2750.0000.0000.0000.000
147A213VAL00.017-0.00413.895-1.136-1.1360.0000.0000.0000.000
148A214ASP-1-0.781-0.90015.24220.01320.0130.0000.0000.0000.000
149A215SER0-0.023-0.01517.777-1.232-1.2320.0000.0000.0000.000
150A216MET00.0000.00918.972-0.770-0.7700.0000.0000.0000.000
151A217VAL0-0.0120.01019.126-0.689-0.6890.0000.0000.0000.000
152A218GLY00.005-0.00521.8910.2400.2400.0000.0000.0000.000
153A219TYR0-0.026-0.00218.804-0.209-0.2090.0000.0000.0000.000
154A220ILE00.0370.01325.471-0.234-0.2340.0000.0000.0000.000
155A221ALA00.0580.03728.8320.2010.2010.0000.0000.0000.000
156A222LEU00.0170.00330.146-0.178-0.1780.0000.0000.0000.000
157A223TYR00.0300.00631.771-0.110-0.1100.0000.0000.0000.000
158A224ASP-1-0.799-0.89033.7058.7998.7990.0000.0000.0000.000
159A225ALA0-0.011-0.01231.648-0.138-0.1380.0000.0000.0000.000
160A226SER00.0560.02733.714-0.054-0.0540.0000.0000.0000.000
161A227THR00.000-0.00436.650-0.311-0.3110.0000.0000.0000.000
162A228LEU0-0.054-0.03234.295-0.264-0.2640.0000.0000.0000.000
163A229LEU0-0.039-0.01634.587-0.148-0.1480.0000.0000.0000.000
164A230ARG10.8560.93938.730-7.789-7.7890.0000.0000.0000.000
165A231LEU0-0.0110.00337.975-0.165-0.1650.0000.0000.0000.000
166A232PRO0-0.012-0.00741.1390.0310.0310.0000.0000.0000.000
167A233ASP-1-0.831-0.91338.5678.2598.2590.0000.0000.0000.000
168A234GLY00.023-0.00836.707-0.142-0.1420.0000.0000.0000.000
169A235ALA0-0.051-0.01231.5950.1810.1810.0000.0000.0000.000
170A236GLN00.0810.04430.164-0.082-0.0820.0000.0000.0000.000
171A237GLY00.0520.01530.393-0.188-0.1880.0000.0000.0000.000
172A238VAL0-0.042-0.00928.2440.0910.0910.0000.0000.0000.000
173A239ARG10.9110.95117.065-15.947-15.9470.0000.0000.0000.000
174A240LEU00.022-0.00323.249-0.075-0.0750.0000.0000.0000.000
175A241LYS10.9130.97016.540-16.423-16.4230.0000.0000.0000.000
176A242LEU0-0.005-0.00218.867-0.642-0.6420.0000.0000.0000.000
177A243ASP-1-0.848-0.90918.00514.58714.5870.0000.0000.0000.000
178A244ASP-1-0.878-0.94416.81016.28716.2870.0000.0000.0000.000
179A245ILE00.0040.00213.255-0.452-0.4520.0000.0000.0000.000
180A246PHE0-0.018-0.00813.373-0.360-0.3600.0000.0000.0000.000
181A247ALA0-0.0010.01218.794-0.635-0.6350.0000.0000.0000.000
182A248ALA0-0.008-0.01320.442-0.533-0.5330.0000.0000.0000.000
183A249PRO0-0.050-0.02821.775-0.435-0.4350.0000.0000.0000.000
184A250GLN00.0920.04223.892-0.160-0.1600.0000.0000.0000.000
185A251VAL00.0180.02324.643-0.380-0.3800.0000.0000.0000.000
186A252ALA00.0230.01026.150-0.366-0.3660.0000.0000.0000.000
187A253ASP-1-0.866-0.93128.0269.7789.7780.0000.0000.0000.000
188A254ASP-1-0.962-0.98430.2789.2699.2690.0000.0000.0000.000
189A255ILE0-0.064-0.03228.562-0.328-0.3280.0000.0000.0000.000
190A256VAL0-0.005-0.01631.490-0.283-0.2830.0000.0000.0000.000
191A257LYS10.8440.92732.749-9.453-9.4530.0000.0000.0000.000
192A258ASN0-0.054-0.01535.912-0.449-0.4490.0000.0000.0000.000
193A259LEU0-0.058-0.02133.990-0.103-0.1030.0000.0000.0000.000
194A260PRO00.0110.00538.210-0.093-0.0930.0000.0000.0000.000
195A261SER00.0380.00838.9970.1840.1840.0000.0000.0000.000
196A262ASN0-0.026-0.00538.322-0.057-0.0570.0000.0000.0000.000
197A263PHE00.026-0.00934.1190.2010.2010.0000.0000.0000.000
198A264TYR0-0.018-0.00530.572-0.141-0.1410.0000.0000.0000.000
199A265ALA00.0520.03228.5640.1910.1910.0000.0000.0000.000
200A266THR0-0.0470.00825.245-0.039-0.0390.0000.0000.0000.000
201A267ASN00.0940.05822.5710.5230.5230.0000.0000.0000.000
202A268TRP0-0.031-0.02416.6830.0630.0630.0000.0000.0000.000
203A269THR0-0.082-0.06119.6660.1480.1480.0000.0000.0000.000
204A270TYR0-0.042-0.01821.253-0.405-0.4050.0000.0000.0000.000
205A271THR00.0320.00520.8570.3540.3540.0000.0000.0000.000
206A272HIS0-0.040-0.03323.0580.1370.1370.0000.0000.0000.000
207A273GLY00.0470.01326.269-0.358-0.3580.0000.0000.0000.000
208A274ASN0-0.032-0.00224.408-0.014-0.0140.0000.0000.0000.000
209A275LEU0-0.0060.01626.539-0.099-0.0990.0000.0000.0000.000
210A276PHE00.0300.01530.2280.0240.0240.0000.0000.0000.000
211A277ASN0-0.030-0.00632.157-0.109-0.1090.0000.0000.0000.000