FMODB

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

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: Z62LN

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 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 211
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2305496.329782
FMO2-HF: Nuclear repulsion 2225965.227291
FMO2-HF: Total energy -79531.102491
FMO2-MP2: Total energy -79765.30261


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.
-109.115-101.34916.816-11.66-12.9220.134
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 : -0.815 / q_NPA : -0.921
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-1-0.805-0.9192.25130.83234.1493.052-2.856-3.5130.027
4A70LEU0-0.016-0.0051.876-29.781-29.78213.073-6.207-6.8650.078
5A71LYS10.9730.9973.852-44.077-43.4230.037-0.291-0.3990.003
6A72ASN0-0.008-0.0015.982-9.138-9.1380.0000.0000.0000.000
7A73ARG10.9430.9872.655-86.590-82.7940.654-2.306-2.1450.026
8A74VAL00.0130.0047.416-4.089-4.0890.0000.0000.0000.000
9A75LEU0-0.025-0.0229.486-3.023-3.0230.0000.0000.0000.000
10A76GLY00.000-0.00210.880-2.277-2.2770.0000.0000.0000.000
11A77MET0-0.041-0.01912.584-2.184-2.1840.0000.0000.0000.000
12A78VAL00.0070.02213.772-1.447-1.4470.0000.0000.0000.000
13A79PRO0-0.028-0.02016.108-0.070-0.0700.0000.0000.0000.000
14A80GLN00.0400.02315.563-1.140-1.1400.0000.0000.0000.000
15A81ALA00.0940.02619.557-0.405-0.4050.0000.0000.0000.000
16A82THR0-0.0680.00423.3560.1880.1880.0000.0000.0000.000
17A83VAL00.0490.03626.352-0.241-0.2410.0000.0000.0000.000
18A84SER0-0.015-0.01929.4390.1260.1260.0000.0000.0000.000
19A85SER00.0160.00431.756-0.314-0.3140.0000.0000.0000.000
20A86THR0-0.033-0.01535.3480.0350.0350.0000.0000.0000.000
21A87GLN0-0.056-0.01637.645-0.155-0.1550.0000.0000.0000.000
22A88ILE0-0.0120.01535.5230.1870.1870.0000.0000.0000.000
23A89LEU00.0450.02633.966-0.204-0.2040.0000.0000.0000.000
24A90THR00.027-0.01336.5980.1730.1730.0000.0000.0000.000
25A91ASP-1-0.943-0.96138.8158.3628.3620.0000.0000.0000.000
26A92TRP00.0250.00530.9940.2340.2340.0000.0000.0000.000
27A93PRO00.020-0.00433.5920.2080.2080.0000.0000.0000.000
28A94GLU-1-0.825-0.89034.6528.5298.5290.0000.0000.0000.000
29A95LEU00.0120.00932.3480.0290.0290.0000.0000.0000.000
30A96VAL0-0.012-0.01429.2450.2040.2040.0000.0000.0000.000
31A97LYS10.8030.88131.253-8.473-8.4730.0000.0000.0000.000
32A98ARG10.8540.93433.584-8.528-8.5280.0000.0000.0000.000
33A99VAL0-0.007-0.00928.377-0.015-0.0150.0000.0000.0000.000
34A100GLU-1-0.919-0.96826.33212.20112.2010.0000.0000.0000.000
35A101ASN0-0.032-0.01828.3330.3240.3240.0000.0000.0000.000
36A102HIS0-0.0230.00228.053-0.470-0.4700.0000.0000.0000.000
37A103PRO00.0370.00927.6870.4200.4200.0000.0000.0000.000
38A104HIS10.8680.89322.335-13.055-13.0550.0000.0000.0000.000
39A105VAL0-0.0150.01922.5750.8140.8140.0000.0000.0000.000
40A106THR0-0.023-0.02719.9920.0820.0820.0000.0000.0000.000
41A107GLY0-0.015-0.00621.6650.3050.3050.0000.0000.0000.000
42A108VAL00.0310.02522.6350.0180.0180.0000.0000.0000.000
43A109ALA00.0040.00224.026-0.061-0.0610.0000.0000.0000.000
44A110PRO0-0.0120.01925.8550.0200.0200.0000.0000.0000.000
45A111PHE0-0.037-0.01525.9440.4740.4740.0000.0000.0000.000
46A112THR00.021-0.00427.927-0.449-0.4490.0000.0000.0000.000
47A113GLN0-0.018-0.00624.3000.2460.2460.0000.0000.0000.000
48A114LEU0-0.0030.00428.502-0.489-0.4890.0000.0000.0000.000
49A115GLN00.0580.01828.2390.7010.7010.0000.0000.0000.000
50A116GLY0-0.029-0.02029.189-0.481-0.4810.0000.0000.0000.000
51A117MET0-0.049-0.01729.7130.1950.1950.0000.0000.0000.000
52A118LEU00.0170.01426.866-0.259-0.2590.0000.0000.0000.000
53A119THR0-0.039-0.03930.597-0.132-0.1320.0000.0000.0000.000
54A120ALA00.028-0.00931.845-0.094-0.0940.0000.0000.0000.000
55A121GLN0-0.009-0.00333.518-0.139-0.1390.0000.0000.0000.000
56A122GLY00.0180.01535.5390.0160.0160.0000.0000.0000.000
57A123GLN0-0.0040.02330.031-0.277-0.2770.0000.0000.0000.000
58A124VAL0-0.001-0.01131.677-0.140-0.1400.0000.0000.0000.000
59A125ALA00.0320.02726.2330.2100.2100.0000.0000.0000.000
60A126GLY0-0.0010.00827.315-0.294-0.2940.0000.0000.0000.000
61A127ILE0-0.013-0.01024.1620.4170.4170.0000.0000.0000.000
62A128MET0-0.0120.00123.322-0.694-0.6940.0000.0000.0000.000
63A129VAL0-0.002-0.01024.1580.4990.4990.0000.0000.0000.000
64A130THR00.0020.00324.087-0.103-0.1030.0000.0000.0000.000
65A131GLY0-0.003-0.00326.1060.1130.1130.0000.0000.0000.000
66A132ILE00.0220.00323.1650.1260.1260.0000.0000.0000.000
67A133ASP-1-0.763-0.87726.95110.50610.5060.0000.0000.0000.000
68A134PRO00.0330.01024.5300.3980.3980.0000.0000.0000.000
69A135LYS10.8040.89224.295-10.182-10.1820.0000.0000.0000.000
70A136TYR00.0340.01125.5200.0050.0050.0000.0000.0000.000
71A137GLU-1-0.816-0.91820.73815.55015.5500.0000.0000.0000.000
72A138LYS10.8450.91219.659-12.893-12.8930.0000.0000.0000.000
73A139ASN0-0.0090.00519.1231.0061.0060.0000.0000.0000.000
74A140VAL0-0.057-0.02019.1000.3500.3500.0000.0000.0000.000
75A141SER0-0.0130.01616.6141.4271.4270.0000.0000.0000.000
76A142ILE00.0190.01911.3220.1650.1650.0000.0000.0000.000
77A143ILE00.0310.02514.2220.8450.8450.0000.0000.0000.000
78A144GLN0-0.009-0.02716.344-0.388-0.3880.0000.0000.0000.000
79A145ASN0-0.076-0.03612.496-1.893-1.8930.0000.0000.0000.000
80A146HIS0-0.033-0.01510.1003.9033.9030.0000.0000.0000.000
81A147ILE0-0.014-0.00514.612-0.463-0.4630.0000.0000.0000.000
82A148VAL0-0.026-0.01016.5340.0410.0410.0000.0000.0000.000
83A149ALA0-0.008-0.01119.110-0.733-0.7330.0000.0000.0000.000
84A150GLY00.0080.00722.8690.1060.1060.0000.0000.0000.000
85A151SER00.014-0.00523.4910.3250.3250.0000.0000.0000.000
86A152LEU00.0600.02720.265-0.442-0.4420.0000.0000.0000.000
87A153ASP-1-0.861-0.93324.33912.52412.5240.0000.0000.0000.000
88A154SER0-0.036-0.01227.288-0.656-0.6560.0000.0000.0000.000
89A155LEU0-0.080-0.01825.656-0.371-0.3710.0000.0000.0000.000
90A156LYS10.8780.92629.521-9.728-9.7280.0000.0000.0000.000
91A157LYS10.8440.90032.949-8.404-8.4040.0000.0000.0000.000
92A158GLY0-0.033-0.02635.694-0.178-0.1780.0000.0000.0000.000
93A159GLU-1-0.882-0.93034.0638.9808.9800.0000.0000.0000.000
94A160PHE0-0.044-0.02533.915-0.048-0.0480.0000.0000.0000.000
95A161GLY00.0360.02530.9100.0080.0080.0000.0000.0000.000
96A162ILE0-0.047-0.03726.6830.0120.0120.0000.0000.0000.000
97A163VAL0-0.039-0.01221.8770.0320.0320.0000.0000.0000.000
98A164LEU00.0210.00122.7720.0350.0350.0000.0000.0000.000
99A165GLY00.0880.05718.8560.4170.4170.0000.0000.0000.000
100A166LYS10.8740.90017.250-16.399-16.3990.0000.0000.0000.000
101A167ASP-1-0.863-0.93117.10717.58117.5810.0000.0000.0000.000
102A168MET0-0.0130.00619.718-1.112-1.1120.0000.0000.0000.000
103A169ALA0-0.017-0.00622.353-0.784-0.7840.0000.0000.0000.000
104A170ASP-1-0.778-0.85321.61913.76013.7600.0000.0000.0000.000
105A171SER0-0.082-0.03923.856-0.683-0.6830.0000.0000.0000.000
106A172LEU0-0.033-0.02325.609-0.574-0.5740.0000.0000.0000.000
107A173GLY0-0.021-0.00327.760-0.411-0.4110.0000.0000.0000.000
108A174LEU0-0.063-0.01427.085-0.328-0.3280.0000.0000.0000.000
109A175ARG10.8090.86424.378-11.888-11.8880.0000.0000.0000.000
110A176LEU00.0230.00526.296-0.129-0.1290.0000.0000.0000.000
111A177ASN00.0120.00628.297-0.463-0.4630.0000.0000.0000.000
112A178ASP-1-0.777-0.86030.5999.7599.7590.0000.0000.0000.000
113A179SER0-0.069-0.04231.926-0.020-0.0200.0000.0000.0000.000
114A180VAL00.0210.01329.4740.0290.0290.0000.0000.0000.000
115A181THR0-0.046-0.01432.727-0.216-0.2160.0000.0000.0000.000
116A182LEU00.0110.01630.2500.2110.2110.0000.0000.0000.000
117A183VAL00.010-0.01033.237-0.413-0.4130.0000.0000.0000.000
118A184LEU00.0240.00832.5140.3170.3170.0000.0000.0000.000
119A185PRO00.006-0.00134.236-0.332-0.3320.0000.0000.0000.000
120A186GLU-1-0.810-0.90837.3128.3448.3440.0000.0000.0000.000
121A187ALA00.0160.01740.124-0.151-0.1510.0000.0000.0000.000
122A188THR0-0.0070.00542.113-0.175-0.1750.0000.0000.0000.000
123A189PRO00.0090.00745.8450.0500.0500.0000.0000.0000.000
124A190SER0-0.041-0.01847.967-0.104-0.1040.0000.0000.0000.000
125A191PRO00.0620.00747.9660.1160.1160.0000.0000.0000.000
126A192ALA0-0.0130.00545.9460.0850.0850.0000.0000.0000.000
127A193GLY00.0140.02243.8500.1650.1650.0000.0000.0000.000
128A194VAL0-0.041-0.04238.9980.1600.1600.0000.0000.0000.000
129A195VAL0-0.014-0.00842.276-0.163-0.1630.0000.0000.0000.000
130A196PRO0-0.033-0.00839.2560.1420.1420.0000.0000.0000.000
131A197ARG10.8610.93538.814-8.249-8.2490.0000.0000.0000.000
132A198PHE00.001-0.00337.4660.2760.2760.0000.0000.0000.000
133A199LYS10.8450.94436.482-8.955-8.9550.0000.0000.0000.000
134A200ARG10.9170.96035.756-8.068-8.0680.0000.0000.0000.000
135A201PHE00.015-0.00831.691-0.154-0.1540.0000.0000.0000.000
136A202LYS10.8570.92732.573-9.386-9.3860.0000.0000.0000.000
137A203VAL00.0340.02226.2900.2080.2080.0000.0000.0000.000
138A204VAL0-0.006-0.00527.440-0.224-0.2240.0000.0000.0000.000
139A205GLY00.015-0.00724.1280.1350.1350.0000.0000.0000.000
140A206ILE0-0.023-0.00119.899-0.257-0.2570.0000.0000.0000.000
141A207PHE0-0.0050.01315.7480.1500.1500.0000.0000.0000.000
142A208SER0-0.053-0.03614.133-0.364-0.3640.0000.0000.0000.000
143A209VAL0-0.043-0.03610.7621.3951.3950.0000.0000.0000.000
144A210GLY00.014-0.0119.7604.2404.2400.0000.0000.0000.000
145A211ALA00.0170.01510.957-2.008-2.0080.0000.0000.0000.000
146A212GLU-1-0.932-0.96313.04820.15620.1560.0000.0000.0000.000
147A213VAL00.0200.00013.167-1.228-1.2280.0000.0000.0000.000
148A214ASP-1-0.748-0.87814.55421.10321.1030.0000.0000.0000.000
149A215SER0-0.018-0.01416.766-1.317-1.3170.0000.0000.0000.000
150A216MET00.0020.01018.238-0.943-0.9430.0000.0000.0000.000
151A217VAL0-0.0100.01118.788-0.760-0.7600.0000.0000.0000.000
152A218GLY00.005-0.00121.3130.2400.2400.0000.0000.0000.000
153A219TYR0-0.0110.00219.2170.0430.0430.0000.0000.0000.000
154A220ILE00.0310.01124.938-0.273-0.2730.0000.0000.0000.000
155A221ALA00.0620.03728.2180.2220.2220.0000.0000.0000.000
156A222LEU00.0160.00629.707-0.196-0.1960.0000.0000.0000.000
157A223TYR00.0330.01331.254-0.113-0.1130.0000.0000.0000.000
158A224ASP-1-0.783-0.87033.1439.0929.0920.0000.0000.0000.000
159A225ALA00.000-0.00731.311-0.159-0.1590.0000.0000.0000.000
160A226SER00.0370.01733.439-0.086-0.0860.0000.0000.0000.000
161A227THR00.007-0.01236.450-0.325-0.3250.0000.0000.0000.000
162A228LEU0-0.049-0.02433.728-0.279-0.2790.0000.0000.0000.000
163A229LEU0-0.029-0.01034.880-0.166-0.1660.0000.0000.0000.000
164A230ARG10.8290.92238.728-8.036-8.0360.0000.0000.0000.000
165A231LEU0-0.0020.01038.186-0.170-0.1700.0000.0000.0000.000
166A232PRO0-0.005-0.00340.8980.0320.0320.0000.0000.0000.000
167A233ASP-1-0.829-0.90138.1748.5598.5590.0000.0000.0000.000
168A234GLY00.0380.00036.412-0.149-0.1490.0000.0000.0000.000
169A235ALA0-0.051-0.01331.5330.1970.1970.0000.0000.0000.000
170A236GLN00.0830.04330.487-0.019-0.0190.0000.0000.0000.000
171A237GLY00.0530.01330.673-0.205-0.2050.0000.0000.0000.000
172A238VAL0-0.044-0.01228.2010.0980.0980.0000.0000.0000.000
173A239ARG10.8580.92717.052-17.088-17.0880.0000.0000.0000.000
174A240LEU00.023-0.00423.434-0.097-0.0970.0000.0000.0000.000
175A241LYS10.8380.92616.492-16.469-16.4690.0000.0000.0000.000
176A242LEU00.0080.00319.134-0.736-0.7360.0000.0000.0000.000
177A243ASP-1-0.856-0.90618.05915.27615.2760.0000.0000.0000.000
178A244ASP-1-0.855-0.93216.80616.85116.8510.0000.0000.0000.000
179A245ILE0-0.0010.00113.164-0.482-0.4820.0000.0000.0000.000
180A246PHE0-0.020-0.01313.569-0.386-0.3860.0000.0000.0000.000
181A247ALA0-0.0020.01018.794-0.736-0.7360.0000.0000.0000.000
182A248ALA0-0.007-0.01420.557-0.574-0.5740.0000.0000.0000.000
183A249PRO0-0.040-0.02621.810-0.459-0.4590.0000.0000.0000.000
184A250GLN00.0690.03423.637-0.202-0.2020.0000.0000.0000.000
185A251VAL00.0130.01624.759-0.407-0.4070.0000.0000.0000.000
186A252ALA00.0260.01326.446-0.384-0.3840.0000.0000.0000.000
187A253ASP-1-0.869-0.93328.28110.00110.0010.0000.0000.0000.000
188A254ASP-1-0.953-0.97430.2769.4779.4770.0000.0000.0000.000
189A255ILE0-0.046-0.02628.762-0.350-0.3500.0000.0000.0000.000
190A256VAL0-0.016-0.01831.987-0.297-0.2970.0000.0000.0000.000
191A257LYS10.8520.92732.808-9.732-9.7320.0000.0000.0000.000
192A258ASN0-0.085-0.02435.755-0.483-0.4830.0000.0000.0000.000
193A259LEU0-0.033-0.00834.544-0.113-0.1130.0000.0000.0000.000
194A260PRO00.0100.00838.583-0.102-0.1020.0000.0000.0000.000
195A261SER00.0670.01939.3530.1460.1460.0000.0000.0000.000
196A262ASN0-0.059-0.02138.646-0.063-0.0630.0000.0000.0000.000
197A263PHE00.036-0.00734.6320.2080.2080.0000.0000.0000.000
198A264TYR0-0.010-0.00130.809-0.177-0.1770.0000.0000.0000.000
199A265ALA00.0420.02528.9590.2140.2140.0000.0000.0000.000
200A266THR0-0.087-0.05325.8820.0490.0490.0000.0000.0000.000
201A267ASN00.0840.04022.8980.5350.5350.0000.0000.0000.000
202A268TRP0-0.019-0.01516.6880.0750.0750.0000.0000.0000.000
203A269THR0-0.080-0.04419.8590.1450.1450.0000.0000.0000.000
204A270TYR0-0.046-0.02221.412-0.454-0.4540.0000.0000.0000.000
205A271THR00.0290.00321.0060.3630.3630.0000.0000.0000.000
206A272HIS0-0.042-0.02623.1850.0980.0980.0000.0000.0000.000
207A273GLY00.0690.02226.730-0.277-0.2770.0000.0000.0000.000
208A274ASN0-0.040-0.01124.399-0.006-0.0060.0000.0000.0000.000
209A275LEU0-0.0080.01926.559-0.121-0.1210.0000.0000.0000.000
210A276PHE00.0200.00830.2320.0210.0210.0000.0000.0000.000
211A277ASN0-0.0210.00032.109-0.066-0.0660.0000.0000.0000.000