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: 5Y84Z

Calculation Name: 5DBN-H-Xray547

Preferred Name:

Target Type:

Ligand Name: phosphate ion | di(hydroxyethyl)ether | chloride ion

Ligand 3-letter code: PO4 | PEG | CL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5DBN

Chain ID: H

ChEMBL ID:

UniProt ID: P76459

Base Structure: X-ray

Registration Date: 2025-10-04

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 214
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2295706.318927
FMO2-HF: Nuclear repulsion 2213386.97498
FMO2-HF: Total energy -82319.343947
FMO2-MP2: Total energy -82549.853551


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.
-0.9781.17711.244-6.915-6.482-0.081
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 : 0.816 / q_NPA : 0.895
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].
3A3ALA00.0260.0103.602-8.398-6.873-0.001-0.780-0.744-0.001
5A5GLN00.0630.0361.802-39.140-39.48911.239-5.842-5.048-0.079
6A6ARG10.8580.9453.33451.14951.9580.008-0.282-0.535-0.001
7A7ILE00.0100.0224.8244.6594.754-0.001-0.009-0.0840.000
34A34TYR0-0.064-0.0414.649-5.448-5.373-0.001-0.002-0.0710.000
4A4LYS10.9920.9926.34129.14329.1430.0000.0000.0000.000
8A8ALA00.0180.0057.5712.6732.6730.0000.0000.0000.000
9A9ARG10.9610.9775.65342.56342.5630.0000.0000.0000.000
10A10ARG10.7790.8547.90324.07424.0740.0000.0000.0000.000
11A11VAL00.000-0.00810.1622.5512.5510.0000.0000.0000.000
12A12ALA00.0070.00110.9881.8691.8690.0000.0000.0000.000
13A13GLN0-0.030-0.01810.9730.5750.5750.0000.0000.0000.000
14A14GLU-1-0.775-0.83913.937-15.650-15.6500.0000.0000.0000.000
15A15LEU0-0.052-0.02016.1051.1331.1330.0000.0000.0000.000
16A16ARG10.9420.96118.49313.03913.0390.0000.0000.0000.000
17A17ASP-1-0.837-0.92421.258-13.449-13.4490.0000.0000.0000.000
18A18GLY0-0.0040.00622.8820.5160.5160.0000.0000.0000.000
19A19ASP-1-0.882-0.92221.864-13.637-13.6370.0000.0000.0000.000
20A20ILE0-0.018-0.01723.510-0.395-0.3950.0000.0000.0000.000
21A21VAL0-0.017-0.01718.814-0.135-0.1350.0000.0000.0000.000
22A22ASN0-0.039-0.02822.013-0.137-0.1370.0000.0000.0000.000
23A23LEU0-0.019-0.01415.517-0.683-0.6830.0000.0000.0000.000
24A24GLY00.0640.03518.7710.3640.3640.0000.0000.0000.000
25A25ILE00.023-0.00717.204-1.215-1.2150.0000.0000.0000.000
26A26GLY0-0.023-0.00915.4390.0930.0930.0000.0000.0000.000
27A27LEU0-0.046-0.0279.815-1.021-1.0210.0000.0000.0000.000
28A28PRO00.0280.01411.940-1.647-1.6470.0000.0000.0000.000
29A29THR00.0460.02613.832-0.056-0.0560.0000.0000.0000.000
30A30MET0-0.066-0.0296.656-0.291-0.2910.0000.0000.0000.000
31A31VAL0-0.012-0.00810.160-2.076-2.0760.0000.0000.0000.000
32A32ALA00.0350.01811.933-0.264-0.2640.0000.0000.0000.000
33A33ASN0-0.046-0.0189.4212.3422.3420.0000.0000.0000.000
35A35LEU00.0220.02210.115-0.129-0.1290.0000.0000.0000.000
36A36PRO0-0.020-0.00613.482-0.293-0.2930.0000.0000.0000.000
37A37GLU-1-0.841-0.91514.690-15.285-15.2850.0000.0000.0000.000
38A38GLY0-0.063-0.03717.3830.2440.2440.0000.0000.0000.000
39A39ILE0-0.054-0.02617.5220.7440.7440.0000.0000.0000.000
40A40HIS10.8430.91419.21113.94313.9430.0000.0000.0000.000
41A41ILE00.0460.04117.5750.4150.4150.0000.0000.0000.000
42A42THR0-0.021-0.01121.5750.1040.1040.0000.0000.0000.000
43A43LEU0-0.020-0.00218.165-0.047-0.0470.0000.0000.0000.000
44A44GLN00.016-0.00222.4260.2640.2640.0000.0000.0000.000
45A45SER0-0.005-0.01323.611-0.820-0.8200.0000.0000.0000.000
46A46GLU-1-0.825-0.92324.518-12.346-12.3460.0000.0000.0000.000
47A47ASN0-0.062-0.01627.5830.1590.1590.0000.0000.0000.000
48A48GLY0-0.0070.01029.5780.3620.3620.0000.0000.0000.000
49A49PHE00.022-0.00425.5330.1460.1460.0000.0000.0000.000
50A50LEU00.0080.00426.755-0.423-0.4230.0000.0000.0000.000
51A51GLY00.0420.01625.3420.3410.3410.0000.0000.0000.000
52A52LEU0-0.013-0.00420.8960.0530.0530.0000.0000.0000.000
53A53GLY00.0170.00220.537-0.504-0.5040.0000.0000.0000.000
54A54PRO00.004-0.01017.7380.1950.1950.0000.0000.0000.000
55A55VAL00.0040.02020.3140.5770.5770.0000.0000.0000.000
56A56THR0-0.0070.00722.873-0.221-0.2210.0000.0000.0000.000
57A57THR0-0.037-0.03725.3140.3110.3110.0000.0000.0000.000
58A58ALA0-0.0030.01027.1620.0010.0010.0000.0000.0000.000
59A59HIS00.0060.00128.4970.1740.1740.0000.0000.0000.000
60A60PRO0-0.015-0.01630.583-0.272-0.2720.0000.0000.0000.000
61A61ASP-1-0.878-0.93132.236-8.927-8.9270.0000.0000.0000.000
62A62LEU0-0.066-0.01627.511-0.043-0.0430.0000.0000.0000.000
63A63VAL00.0280.01126.547-0.406-0.4060.0000.0000.0000.000
64A64ASN00.0600.02520.9780.4790.4790.0000.0000.0000.000
65A65ALA00.0370.01823.7720.3360.3360.0000.0000.0000.000
66A66GLY0-0.052-0.02323.1040.1700.1700.0000.0000.0000.000
67A67GLY0-0.021-0.01024.1240.0640.0640.0000.0000.0000.000
68A68GLN0-0.051-0.01921.9510.1680.1680.0000.0000.0000.000
69A69PRO00.0130.01524.431-0.013-0.0130.0000.0000.0000.000
70A70CYS0-0.050-0.03222.824-0.622-0.6220.0000.0000.0000.000
71A71GLY00.0270.01023.3560.4800.4800.0000.0000.0000.000
72A72VAL0-0.024-0.01424.722-0.201-0.2010.0000.0000.0000.000
73A73LEU0-0.0040.00321.6680.0070.0070.0000.0000.0000.000
74A74PRO0-0.002-0.02526.0740.3890.3890.0000.0000.0000.000
75A75GLY00.0050.00628.809-0.174-0.1740.0000.0000.0000.000
76A76ALA0-0.0380.00228.1590.0230.0230.0000.0000.0000.000
77A77ALA0-0.021-0.00529.8650.4100.4100.0000.0000.0000.000
78A78MET00.0110.01230.183-0.277-0.2770.0000.0000.0000.000
79A79PHE0-0.042-0.02229.9980.2550.2550.0000.0000.0000.000
80A80ASP-1-0.793-0.88234.563-8.447-8.4470.0000.0000.0000.000
81A81SER00.0610.00034.158-0.124-0.1240.0000.0000.0000.000
82A82ALA0-0.026-0.00534.991-0.158-0.1580.0000.0000.0000.000
83A83MET00.000-0.00235.326-0.021-0.0210.0000.0000.0000.000
84A84SER0-0.048-0.04330.682-0.255-0.2550.0000.0000.0000.000
85A85PHE00.017-0.00829.748-0.275-0.2750.0000.0000.0000.000
86A86ALA0-0.038-0.00333.353-0.006-0.0060.0000.0000.0000.000
87A87LEU0-0.012-0.00831.109-0.009-0.0090.0000.0000.0000.000
88A88ILE0-0.027-0.01027.965-0.141-0.1410.0000.0000.0000.000
89A89ARG10.8930.92730.3678.8748.8740.0000.0000.0000.000
90A90GLY0-0.027-0.00432.9950.1510.1510.0000.0000.0000.000
91A91GLY00.0170.02230.9390.1500.1500.0000.0000.0000.000
92A92HIS0-0.061-0.03531.003-0.090-0.0900.0000.0000.0000.000
93A93ILE0-0.0040.00824.880-0.211-0.2110.0000.0000.0000.000
94A94ASP-1-0.815-0.90824.580-11.539-11.5390.0000.0000.0000.000
95A95ALA0-0.021-0.01920.408-0.222-0.2220.0000.0000.0000.000
96A96CYS0-0.057-0.01521.522-0.110-0.1100.0000.0000.0000.000
97A97VAL00.0010.00814.926-0.521-0.5210.0000.0000.0000.000
98A98LEU00.0230.00618.3470.0660.0660.0000.0000.0000.000
99A99GLY00.0330.02316.790-0.884-0.8840.0000.0000.0000.000
100A100GLY00.029-0.00517.7001.0151.0150.0000.0000.0000.000
101A101LEU0-0.074-0.02918.891-0.796-0.7960.0000.0000.0000.000
102A102GLN00.0380.00021.6810.3110.3110.0000.0000.0000.000
103A103VAL00.0530.02620.7800.0460.0460.0000.0000.0000.000
104A104ASP-1-0.757-0.85623.398-11.180-11.1800.0000.0000.0000.000
105A105GLU-1-0.705-0.85125.875-10.761-10.7610.0000.0000.0000.000
106A106GLU-1-0.928-0.95627.348-9.640-9.6400.0000.0000.0000.000
107A107ALA00.0340.03325.9380.2710.2710.0000.0000.0000.000
108A108ASN0-0.068-0.04626.9870.2950.2950.0000.0000.0000.000
109A109LEU00.0270.01522.194-0.558-0.5580.0000.0000.0000.000
110A110ALA00.0130.01424.7850.5410.5410.0000.0000.0000.000
111A111ASN0-0.014-0.01721.445-0.016-0.0160.0000.0000.0000.000
112A112TRP00.0210.01323.607-0.233-0.2330.0000.0000.0000.000
113A113VAL00.0290.00826.3540.2600.2600.0000.0000.0000.000
114A114VAL00.004-0.00124.584-0.317-0.3170.0000.0000.0000.000
115A115PRO00.0140.00927.7880.2840.2840.0000.0000.0000.000
116A116GLY00.0260.00530.274-0.209-0.2090.0000.0000.0000.000
117A117LYS10.9020.95624.17612.82612.8260.0000.0000.0000.000
118A118MET00.0210.01329.8400.3190.3190.0000.0000.0000.000
119A119VAL0-0.003-0.00529.608-0.387-0.3870.0000.0000.0000.000
120A120PRO0-0.0340.00026.6260.2690.2690.0000.0000.0000.000
121A121GLY00.0340.02029.6390.2140.2140.0000.0000.0000.000
122A122MET00.006-0.01928.462-0.375-0.3750.0000.0000.0000.000
123A123GLY00.0130.01027.950-0.383-0.3830.0000.0000.0000.000
124A124GLY00.0720.02027.8490.3140.3140.0000.0000.0000.000
125A125ALA0-0.0070.00025.376-0.049-0.0490.0000.0000.0000.000
126A126MET0-0.015-0.00626.613-0.019-0.0190.0000.0000.0000.000
127A127ASP-1-0.817-0.89129.691-9.677-9.6770.0000.0000.0000.000
128A128LEU00.0140.00823.9830.0040.0040.0000.0000.0000.000
129A129VAL0-0.024-0.00224.273-0.277-0.2770.0000.0000.0000.000
130A130THR0-0.054-0.03626.7920.2100.2100.0000.0000.0000.000
131A131GLY0-0.0040.00529.6980.2870.2870.0000.0000.0000.000
132A132SER0-0.060-0.03425.2370.0810.0810.0000.0000.0000.000
133A133ARG10.8480.92826.82410.26810.2680.0000.0000.0000.000
134A134LYS10.8220.91220.23915.00615.0060.0000.0000.0000.000
135A135VAL00.0320.01522.571-0.405-0.4050.0000.0000.0000.000
136A136ILE0-0.016-0.01815.970-0.195-0.1950.0000.0000.0000.000
137A137ILE0-0.024-0.00917.608-0.090-0.0900.0000.0000.0000.000
138A138ALA00.0480.01912.782-0.869-0.8690.0000.0000.0000.000
139A139MET0-0.102-0.04413.7330.4930.4930.0000.0000.0000.000
140A140GLU-1-0.801-0.89811.234-25.786-25.7860.0000.0000.0000.000
141A141HIS00.0590.01713.0380.5600.5600.0000.0000.0000.000
142A142CYS0-0.030-0.00815.3191.2231.2230.0000.0000.0000.000
143A143ALA0-0.015-0.00216.721-0.976-0.9760.0000.0000.0000.000
144A144LYS10.7960.86112.55022.92522.9250.0000.0000.0000.000
145A145ASP-1-0.822-0.88218.016-14.101-14.1010.0000.0000.0000.000
146A146GLY0-0.0100.00218.8720.3910.3910.0000.0000.0000.000
147A147SER0-0.064-0.04319.909-0.006-0.0060.0000.0000.0000.000
148A148ALA00.0570.01520.916-0.893-0.8930.0000.0000.0000.000
149A149LYS10.8100.91216.28419.05119.0510.0000.0000.0000.000
150A150ILE00.0090.01617.6290.2800.2800.0000.0000.0000.000
151A151LEU00.010-0.00122.1100.2520.2520.0000.0000.0000.000
152A152ARG10.9310.95725.89110.42010.4200.0000.0000.0000.000
153A153ARG10.8830.93529.30710.14310.1430.0000.0000.0000.000
154A154CYS0-0.093-0.01926.857-0.223-0.2230.0000.0000.0000.000
155A155THR00.0270.00528.6370.3150.3150.0000.0000.0000.000
156A156MET0-0.039-0.00824.9500.1840.1840.0000.0000.0000.000
157A157PRO0-0.004-0.01229.4880.0530.0530.0000.0000.0000.000
158A158LEU0-0.021-0.00629.049-0.307-0.3070.0000.0000.0000.000
159A159THR0-0.019-0.02925.7610.2920.2920.0000.0000.0000.000
160A160ALA00.0500.01828.2470.2870.2870.0000.0000.0000.000
161A161GLN0-0.001-0.00929.214-0.207-0.2070.0000.0000.0000.000
162A162HIS10.8000.88529.7699.8839.8830.0000.0000.0000.000
163A163ALA00.0620.04727.6570.1420.1420.0000.0000.0000.000
164A164VAL0-0.056-0.01321.724-0.318-0.3180.0000.0000.0000.000
165A165HIS00.1010.05823.091-0.215-0.2150.0000.0000.0000.000
166A166MET0-0.061-0.02415.6850.1370.1370.0000.0000.0000.000
167A167LEU00.0060.00816.6480.0040.0040.0000.0000.0000.000
168A168VAL0-0.0120.00611.146-0.202-0.2020.0000.0000.0000.000
169A169THR00.015-0.00812.159-0.467-0.4670.0000.0000.0000.000
170A170GLU-1-0.872-0.9477.897-28.268-28.2680.0000.0000.0000.000
171A171LEU0-0.031-0.0259.181-2.118-2.1180.0000.0000.0000.000
172A172ALA00.0410.02312.0550.9170.9170.0000.0000.0000.000
173A173VAL0-0.0260.00413.441-0.980-0.9800.0000.0000.0000.000
174A174PHE00.027-0.00315.6440.9060.9060.0000.0000.0000.000
175A175ARG10.8290.88918.07315.66815.6680.0000.0000.0000.000
176A176PHE0-0.028-0.01521.9300.2300.2300.0000.0000.0000.000
177A177ILE0-0.006-0.00425.051-0.043-0.0430.0000.0000.0000.000
178A178ASP-1-0.879-0.93528.303-9.694-9.6940.0000.0000.0000.000
179A179GLY0-0.021-0.00730.8690.2540.2540.0000.0000.0000.000
180A180LYS10.8520.93729.6579.9829.9820.0000.0000.0000.000
181A181MET0-0.0200.01521.702-0.164-0.1640.0000.0000.0000.000
182A182TRP00.0260.01124.2090.1340.1340.0000.0000.0000.000
183A183LEU0-0.046-0.01817.858-0.540-0.5400.0000.0000.0000.000
184A184THR0-0.005-0.02518.6260.6580.6580.0000.0000.0000.000
185A185GLU-1-0.766-0.85714.813-19.658-19.6580.0000.0000.0000.000
186A186ILE0-0.023-0.00914.6530.0600.0600.0000.0000.0000.000
187A187ALA0-0.0170.0039.330-0.478-0.4780.0000.0000.0000.000
188A188ASP-1-0.872-0.9489.371-25.410-25.4100.0000.0000.0000.000
189A189GLY0-0.052-0.0299.730-2.417-2.4170.0000.0000.0000.000
190A190CYS0-0.075-0.01311.7880.9350.9350.0000.0000.0000.000
191A191ASP-1-0.736-0.86114.087-14.959-14.9590.0000.0000.0000.000
192A192LEU00.0520.02017.872-0.256-0.2560.0000.0000.0000.000
193A193ALA0-0.016-0.01220.6790.2920.2920.0000.0000.0000.000
194A194THR0-0.069-0.05616.0740.1260.1260.0000.0000.0000.000
195A195VAL0-0.002-0.00216.386-0.206-0.2060.0000.0000.0000.000
196A196ARG10.8010.91118.83512.78112.7810.0000.0000.0000.000
197A197ALA0-0.0070.00121.2460.3240.3240.0000.0000.0000.000
198A198LYS10.9130.96915.90818.27718.2770.0000.0000.0000.000
199A199THR0-0.044-0.03720.277-0.599-0.5990.0000.0000.0000.000
200A200GLU-1-0.902-0.94622.423-11.536-11.5360.0000.0000.0000.000
201A201ALA0-0.055-0.01924.3820.6000.6000.0000.0000.0000.000
202A202ARG10.8330.88026.1339.6009.6000.0000.0000.0000.000
203A203PHE00.0100.01022.2230.0670.0670.0000.0000.0000.000
204A204GLU-1-0.857-0.92526.147-10.002-10.0020.0000.0000.0000.000
205A205VAL0-0.008-0.02322.927-0.572-0.5720.0000.0000.0000.000
206A206ALA00.0410.02423.0150.5120.5120.0000.0000.0000.000
207A207ALA00.006-0.00724.861-0.206-0.2060.0000.0000.0000.000
208A208ASP-1-0.839-0.88425.030-12.531-12.5310.0000.0000.0000.000
209A209LEU00.0070.01618.922-0.548-0.5480.0000.0000.0000.000
210A210ASN0-0.044-0.02617.742-0.195-0.1950.0000.0000.0000.000
211A211THR0-0.035-0.02019.6950.3040.3040.0000.0000.0000.000
212A212GLN0-0.045-0.02719.962-0.994-0.9940.0000.0000.0000.000
213A213ARG10.8210.88021.69513.55413.5540.0000.0000.0000.000
214A214GLY-1-0.893-0.93122.826-13.644-13.6440.0000.0000.0000.000