FMODB

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

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: 64M8Z

Calculation Name: 5DCX-D-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5DCX

Chain ID: D

ChEMBL ID:

UniProt ID: P03132

Base Structure: X-ray

Registration Date: 2025-10-05

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 208
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2493355.963139
FMO2-HF: Nuclear repulsion 2409420.462158
FMO2-HF: Total energy -83935.500981
FMO2-MP2: Total energy -84181.977243


3D Structure Molmil
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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-109.531-105.731.946-2.246-3.502-0.023
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.874 / q_NPA : 0.931
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].
3A3GLY00.0530.0232.377-8.630-6.5391.906-1.696-2.301-0.019
4A4PHE00.0190.0044.3791.6901.894-0.001-0.010-0.1930.000
77A77LEU0-0.0080.0124.1661.9052.043-0.001-0.011-0.1260.000
149A149ASP-1-0.780-0.8734.998-47.856-47.801-0.001-0.003-0.0510.000
150A150GLU-1-0.809-0.8853.505-45.999-44.6860.043-0.526-0.831-0.004
5A5TYR0-0.060-0.0477.5141.3981.3980.0000.0000.0000.000
6A6GLU-1-0.744-0.84211.225-18.722-18.7220.0000.0000.0000.000
7A7ILE0-0.064-0.03213.5700.8800.8800.0000.0000.0000.000
8A8VAL00.0080.01316.870-0.067-0.0670.0000.0000.0000.000
9A9ILE0-0.028-0.01619.7730.4780.4780.0000.0000.0000.000
10A10LYS10.8210.91122.64311.29011.2900.0000.0000.0000.000
11A11VAL0-0.035-0.02225.330-0.012-0.0120.0000.0000.0000.000
12A12PRO0-0.045-0.02227.9570.1810.1810.0000.0000.0000.000
13A13SER0-0.033-0.02331.715-0.075-0.0750.0000.0000.0000.000
14A14ASP-1-0.832-0.90133.684-7.675-7.6750.0000.0000.0000.000
15A15LEU00.001-0.01036.096-0.154-0.1540.0000.0000.0000.000
16A16ASP-1-0.867-0.93038.364-7.244-7.2440.0000.0000.0000.000
17A17GLY0-0.055-0.02938.9200.0450.0450.0000.0000.0000.000
18A18HIS0-0.002-0.01533.859-0.254-0.2540.0000.0000.0000.000
19A19LEU0-0.066-0.02333.175-0.280-0.2800.0000.0000.0000.000
20A20PRO00.0600.03837.0860.1240.1240.0000.0000.0000.000
21A21GLY00.0080.00240.8960.0110.0110.0000.0000.0000.000
22A22ILE0-0.062-0.00635.7350.0090.0090.0000.0000.0000.000
23A23SER00.0280.00440.0830.1040.1040.0000.0000.0000.000
24A24ASP-1-0.796-0.90540.726-7.081-7.0810.0000.0000.0000.000
25A25SER0-0.062-0.01239.748-0.146-0.1460.0000.0000.0000.000
26A26PHE0-0.013-0.02732.748-0.236-0.2360.0000.0000.0000.000
27A27VAL00.0430.02237.416-0.175-0.1750.0000.0000.0000.000
28A28ASN00.002-0.01839.407-0.013-0.0130.0000.0000.0000.000
29A29TRP0-0.074-0.02130.019-0.156-0.1560.0000.0000.0000.000
30A30VAL0-0.030-0.02833.632-0.208-0.2080.0000.0000.0000.000
31A31ALA0-0.037-0.00935.756-0.110-0.1100.0000.0000.0000.000
32A32GLU-1-0.895-0.95338.533-7.453-7.4530.0000.0000.0000.000
33A33LYS10.7710.90430.1129.8179.8170.0000.0000.0000.000
34A34GLU-1-0.921-0.94633.966-8.303-8.3030.0000.0000.0000.000
35A35TRP0-0.070-0.06227.350-0.409-0.4090.0000.0000.0000.000
36A36GLU-1-0.884-0.93830.297-8.895-8.8950.0000.0000.0000.000
37A37LEU0-0.033-0.01825.656-0.400-0.4000.0000.0000.0000.000
38A38PRO0-0.011-0.00122.9180.2390.2390.0000.0000.0000.000
39A39PRO00.021-0.00726.0060.0410.0410.0000.0000.0000.000
40A40ASP-1-0.916-0.94322.667-11.709-11.7090.0000.0000.0000.000
41A41SER0-0.061-0.04323.579-0.301-0.3010.0000.0000.0000.000
42A42ASP-1-0.767-0.86524.514-11.537-11.5370.0000.0000.0000.000
43A43MET0-0.067-0.02123.944-0.022-0.0220.0000.0000.0000.000
44A44ASP-1-0.810-0.90227.388-8.677-8.6770.0000.0000.0000.000
45A45LEU00.0420.01130.513-0.210-0.2100.0000.0000.0000.000
46A46ASN0-0.068-0.04531.8970.1930.1930.0000.0000.0000.000
47A47LEU0-0.067-0.02130.6350.0750.0750.0000.0000.0000.000
48A48ILE0-0.043-0.00927.229-0.334-0.3340.0000.0000.0000.000
49A49GLU-1-0.806-0.89230.136-8.756-8.7560.0000.0000.0000.000
50A50GLN00.0550.01630.879-0.370-0.3700.0000.0000.0000.000
51A51ALA00.0680.04831.806-0.176-0.1760.0000.0000.0000.000
52A52PRO00.019-0.01030.042-0.197-0.1970.0000.0000.0000.000
53A53LEU00.0170.01125.388-0.409-0.4090.0000.0000.0000.000
54A54THR00.0100.02427.364-0.449-0.4490.0000.0000.0000.000
55A55VAL0-0.026-0.01228.453-0.158-0.1580.0000.0000.0000.000
56A56ALA0-0.001-0.00324.337-0.340-0.3400.0000.0000.0000.000
57A57GLU-1-0.719-0.82423.667-12.513-12.5130.0000.0000.0000.000
58A58LYS10.8680.93223.62310.24610.2460.0000.0000.0000.000
59A59LEU0-0.020-0.00723.522-0.284-0.2840.0000.0000.0000.000
60A60GLN0-0.008-0.00618.669-1.049-1.0490.0000.0000.0000.000
61A61ARG10.8240.87119.72511.16611.1660.0000.0000.0000.000
62A62ASP-1-0.818-0.89821.410-11.762-11.7620.0000.0000.0000.000
63A63PHE00.0090.00215.561-0.073-0.0730.0000.0000.0000.000
64A64LEU00.0200.00614.668-0.529-0.5290.0000.0000.0000.000
65A65THR0-0.080-0.03917.904-0.388-0.3880.0000.0000.0000.000
66A66GLU-1-0.870-0.95720.621-12.478-12.4780.0000.0000.0000.000
67A67TRP00.0440.02012.0530.8050.8050.0000.0000.0000.000
68A68ARG10.9230.99814.91717.26217.2620.0000.0000.0000.000
69A69ARG10.8590.93817.42212.45712.4570.0000.0000.0000.000
70A70VAL0-0.059-0.02717.6750.2580.2580.0000.0000.0000.000
71A71SER0-0.036-0.03513.758-0.097-0.0970.0000.0000.0000.000
72A72LYS10.8580.92115.22314.25314.2530.0000.0000.0000.000
73A73ALA00.0420.02811.550-0.080-0.0800.0000.0000.0000.000
74A74PRO0-0.032-0.01613.681-0.356-0.3560.0000.0000.0000.000
75A75GLU-1-0.879-0.96011.646-18.414-18.4140.0000.0000.0000.000
76A76ALA0-0.049-0.0059.411-1.595-1.5950.0000.0000.0000.000
78A78PHE00.004-0.0148.287-0.185-0.1850.0000.0000.0000.000
79A79PHE00.0380.02810.6420.2810.2810.0000.0000.0000.000
80A80VAL0-0.029-0.01212.2820.0850.0850.0000.0000.0000.000
81A81GLN0-0.008-0.00215.9020.1370.1370.0000.0000.0000.000
82A82PHE0-0.025-0.02718.2130.0590.0590.0000.0000.0000.000
83A83GLU-1-0.746-0.87219.937-14.617-14.6170.0000.0000.0000.000
84A84LYS10.8290.90423.9139.5639.5630.0000.0000.0000.000
85A85GLY00.0410.01727.1580.0040.0040.0000.0000.0000.000
86A86GLU-1-0.926-0.97327.737-9.713-9.7130.0000.0000.0000.000
87A87SER0-0.085-0.03930.0600.3030.3030.0000.0000.0000.000
88A88TYR00.010-0.01227.9040.1980.1980.0000.0000.0000.000
89A89PHE00.0710.05327.679-0.331-0.3310.0000.0000.0000.000
90A90HIS0-0.084-0.05022.020-0.325-0.3250.0000.0000.0000.000
91A91MET0-0.0080.01019.881-0.193-0.1930.0000.0000.0000.000
92A92HIS10.8280.91016.20115.65215.6520.0000.0000.0000.000
93A93VAL0-0.001-0.00514.842-0.327-0.3270.0000.0000.0000.000
94A94LEU0-0.0050.0099.934-0.251-0.2510.0000.0000.0000.000
95A95VAL0-0.002-0.01110.2270.3720.3720.0000.0000.0000.000
96A96GLU-1-0.778-0.8975.312-40.801-40.8010.0000.0000.0000.000
97A97THR0-0.079-0.0597.0131.6661.6660.0000.0000.0000.000
98A98THR00.0070.0047.4481.1851.1850.0000.0000.0000.000
99A99GLY00.0220.0199.4552.0862.0860.0000.0000.0000.000
100A100VAL0-0.043-0.00812.3412.0212.0210.0000.0000.0000.000
101A101LYS11.0121.01412.92617.73317.7330.0000.0000.0000.000
102A102SER00.0940.04014.3451.6131.6130.0000.0000.0000.000
103A103MET0-0.018-0.01415.8420.6650.6650.0000.0000.0000.000
104A104VAL0-0.053-0.02818.1120.9680.9680.0000.0000.0000.000
105A105LEU00.0210.03314.6750.7270.7270.0000.0000.0000.000
106A106GLY00.0480.02517.9850.3580.3580.0000.0000.0000.000
107A107ARG10.9450.98121.09613.44113.4410.0000.0000.0000.000
108A108PHE00.0370.00918.0560.4820.4820.0000.0000.0000.000
109A109LEU00.0360.01717.2770.3350.3350.0000.0000.0000.000
110A110SER0-0.015-0.00921.1200.5090.5090.0000.0000.0000.000
111A111GLN0-0.015-0.01624.0640.0550.0550.0000.0000.0000.000
112A112ILE0-0.024-0.00619.2500.3110.3110.0000.0000.0000.000
113A113ARG10.9070.95223.54410.94910.9490.0000.0000.0000.000
114A114GLU-1-0.838-0.91525.590-9.570-9.5700.0000.0000.0000.000
115A115LYS10.8910.95025.47611.62211.6220.0000.0000.0000.000
116A116LEU0-0.024-0.01022.8930.2220.2220.0000.0000.0000.000
117A117ILE00.0290.02227.4560.1630.1630.0000.0000.0000.000
118A118GLN0-0.029-0.02630.8610.4880.4880.0000.0000.0000.000
119A119ARG10.8300.92626.96311.01711.0170.0000.0000.0000.000
120A120ILE0-0.053-0.02226.4540.1200.1200.0000.0000.0000.000
121A121TYR00.0600.01128.1020.2160.2160.0000.0000.0000.000
122A122ARG10.8520.93733.2648.9428.9420.0000.0000.0000.000
123A123GLY00.0290.01834.4720.2480.2480.0000.0000.0000.000
124A124ILE0-0.031-0.00535.8400.0900.0900.0000.0000.0000.000
125A125GLU-1-0.865-0.93232.229-9.743-9.7430.0000.0000.0000.000
126A126PRO0-0.013-0.01329.7910.1960.1960.0000.0000.0000.000
127A127THR0-0.0210.00632.851-0.016-0.0160.0000.0000.0000.000
128A128LEU00.025-0.00229.790-0.004-0.0040.0000.0000.0000.000
129A129PRO00.0040.02031.097-0.210-0.2100.0000.0000.0000.000
130A130ASN0-0.009-0.02626.708-0.211-0.2110.0000.0000.0000.000
131A131TRP00.0290.01326.039-0.660-0.6600.0000.0000.0000.000
132A132PHE00.0380.02621.051-0.408-0.4080.0000.0000.0000.000
133A133ALA0-0.0100.00021.8430.2590.2590.0000.0000.0000.000
134A134VAL0-0.020-0.00315.922-0.485-0.4850.0000.0000.0000.000
135A135THR00.0450.01515.2381.0521.0520.0000.0000.0000.000
136A136LYS10.8150.89816.74114.39514.3950.0000.0000.0000.000
137A137THR00.0270.00915.4110.2000.2000.0000.0000.0000.000
138A138ARG10.8640.92718.30712.91012.9100.0000.0000.0000.000
139A139ASN00.0570.02716.5001.0881.0880.0000.0000.0000.000
140A140GLY00.0230.00819.8390.3180.3180.0000.0000.0000.000
141A141ALA00.0170.01722.7370.5700.5700.0000.0000.0000.000
142A142GLY00.0250.03023.3300.4800.4800.0000.0000.0000.000
143A143GLY00.0240.00523.042-0.141-0.1410.0000.0000.0000.000
144A144GLY00.0040.00919.082-0.080-0.0800.0000.0000.0000.000
145A145ASN0-0.006-0.01915.8030.8420.8420.0000.0000.0000.000
146A146LYS00.008-0.00512.425-0.187-0.1870.0000.0000.0000.000
147A147VAL0-0.038-0.0077.895-0.217-0.2170.0000.0000.0000.000
148A148VAL0-0.030-0.0118.5520.6450.6450.0000.0000.0000.000
151A151SER0-0.019-0.0345.8635.1935.1930.0000.0000.0000.000
152A152TYR0-0.082-0.0708.5672.9192.9190.0000.0000.0000.000
153A153ILE00.0290.0157.8692.2082.2080.0000.0000.0000.000
154A154PRO00.0180.0039.3152.1682.1680.0000.0000.0000.000
155A155ASN00.000-0.00412.2871.8371.8370.0000.0000.0000.000
156A156TYR0-0.037-0.02114.2190.9860.9860.0000.0000.0000.000
157A157LEU0-0.0330.00013.1220.8990.8990.0000.0000.0000.000
158A158LEU00.0250.00812.4050.9930.9930.0000.0000.0000.000
159A159PRO0-0.023-0.01815.9370.8650.8650.0000.0000.0000.000
160A160LYS10.7770.91619.12314.28714.2870.0000.0000.0000.000
161A161THR00.0400.01421.366-0.135-0.1350.0000.0000.0000.000
162A162GLN00.0200.03224.4470.0850.0850.0000.0000.0000.000
163A163PRO00.010-0.00527.3640.1280.1280.0000.0000.0000.000
164A164GLU-1-0.819-0.89024.351-12.508-12.5080.0000.0000.0000.000
165A165LEU0-0.029-0.02420.588-0.232-0.2320.0000.0000.0000.000
166A166GLN0-0.046-0.03223.8430.5970.5970.0000.0000.0000.000
167A167TRP00.0700.00621.7870.2820.2820.0000.0000.0000.000
168A168ALA0-0.020-0.00517.136-0.488-0.4880.0000.0000.0000.000
169A169TRP00.0220.01117.2670.4280.4280.0000.0000.0000.000
170A170THR0-0.004-0.03611.690-1.254-1.2540.0000.0000.0000.000
171A171ASN0-0.009-0.00910.8160.3920.3920.0000.0000.0000.000
172A172MET0-0.053-0.0085.779-0.215-0.2150.0000.0000.0000.000
173A173GLU-1-0.873-0.9528.399-22.928-22.9280.0000.0000.0000.000
174A174GLN00.0260.0094.9534.2014.2010.0000.0000.0000.000
175A175TYR0-0.063-0.0756.7172.2032.2030.0000.0000.0000.000
176A176LEU0-0.0120.00411.8141.2671.2670.0000.0000.0000.000
177A177SER00.0300.01414.5210.9430.9430.0000.0000.0000.000
178A178ALA00.0010.00414.3290.6600.6600.0000.0000.0000.000
179A179CYS0-0.077-0.02915.0410.3310.3310.0000.0000.0000.000
180A180LEU00.0460.02317.4410.3330.3330.0000.0000.0000.000
181A181ASN00.0260.02619.8940.4640.4640.0000.0000.0000.000
182A182LEU00.005-0.01419.943-0.748-0.7480.0000.0000.0000.000
183A183THR0-0.064-0.04721.589-0.168-0.1680.0000.0000.0000.000
184A184GLU-1-0.781-0.85715.579-16.371-16.3710.0000.0000.0000.000
185A185ARG10.7720.88116.74214.41414.4140.0000.0000.0000.000
186A186LYS10.9320.97217.18311.21211.2120.0000.0000.0000.000
187A187ARG10.7760.85413.79816.58016.5800.0000.0000.0000.000
188A188LEU00.0180.00611.670-0.449-0.4490.0000.0000.0000.000
189A189VAL0-0.0040.00213.523-0.959-0.9590.0000.0000.0000.000
190A190ALA00.0030.00315.494-0.290-0.2900.0000.0000.0000.000
191A191GLN00.0130.01512.570-0.082-0.0820.0000.0000.0000.000
192A192HIS0-0.006-0.0038.944-2.289-2.2890.0000.0000.0000.000
193A193LEU0-0.002-0.00612.172-0.336-0.3360.0000.0000.0000.000
194A194THR0-0.019-0.01715.1470.4660.4660.0000.0000.0000.000
195A195HIS00.0010.0059.5771.2621.2620.0000.0000.0000.000
196A196VAL00.0060.00810.461-0.186-0.1860.0000.0000.0000.000
197A197SER0-0.037-0.01212.9020.3090.3090.0000.0000.0000.000
198A198GLN00.0600.01816.5050.7830.7830.0000.0000.0000.000
199A199THR0-0.032-0.02011.7510.0200.0200.0000.0000.0000.000
200A200GLN0-0.029-0.01014.8950.7770.7770.0000.0000.0000.000
201A201GLU-1-0.911-0.94416.505-12.693-12.6930.0000.0000.0000.000
202A202GLN00.015-0.00918.0230.0120.0120.0000.0000.0000.000
203A203ASN0-0.054-0.03213.7720.4670.4670.0000.0000.0000.000
204A204LYS10.7880.88518.25315.19015.1900.0000.0000.0000.000
205A205GLU-1-0.893-0.93121.695-12.151-12.1510.0000.0000.0000.000
206A206ASN0-0.067-0.03319.5100.9190.9190.0000.0000.0000.000
207A207GLN0-0.093-0.04919.603-1.116-1.1160.0000.0000.0000.000
208A208ASN-1-0.957-0.95722.692-11.290-11.2900.0000.0000.0000.000