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: 34NKL

Calculation Name: 2PB9-A-Xray549

Preferred Name:

Target Type:

Ligand Name: phosphate ion

Ligand 3-letter code: PO4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2PB9

Chain ID: A

ChEMBL ID:

UniProt ID: Q8U193

Base Structure: X-ray

Registration Date: 2025-10-12

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 OptH
Protonation MOE:Protonate 3D
Complement ac.sh, 23 2024 Oct
Water No
Procedure Manual calculation
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 184
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2152294.34897
FMO2-HF: Nuclear repulsion 2078897.166233
FMO2-HF: Total energy -73397.182736
FMO2-MP2: Total energy -73615.70382


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:268:GLU)


Summations of interaction energy for fragment #1(A:268:GLU)
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.
20.60825.7611.191-2.159-4.1870.01
Interaction energy analysis for fragmet #1(A:268:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.052 / q_NPA : -0.045
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].
3A270TRP00.0580.0443.662-1.2200.3390.015-0.517-1.058-0.001
4A271ARG10.9850.9963.40421.30922.1270.008-0.258-0.567-0.001
5A272ILE0-0.0170.0013.7483.3133.7770.005-0.086-0.3840.000
36A303LEU0-0.016-0.0012.717-5.062-3.0831.164-1.257-1.8860.012
37A304PRO00.0220.0154.012-2.009-1.8780.000-0.038-0.0940.000
40A307TYR00.009-0.0165.1880.3940.596-0.001-0.003-0.1980.000
6A273TYR00.0200.0086.6372.0462.0460.0000.0000.0000.000
7A274GLU-1-0.854-0.9248.023-4.345-4.3450.0000.0000.0000.000
8A275GLU-1-0.885-0.9418.316-8.207-8.2070.0000.0000.0000.000
9A276LEU00.0080.00210.4420.8960.8960.0000.0000.0000.000
10A277THR0-0.005-0.01412.1940.8620.8620.0000.0000.0000.000
11A278ASN0-0.025-0.01712.0390.9950.9950.0000.0000.0000.000
12A279ALA0-0.0230.00014.5630.3080.3080.0000.0000.0000.000
13A280VAL00.003-0.00116.3460.3250.3250.0000.0000.0000.000
14A281ARG10.9530.96815.6892.7592.7590.0000.0000.0000.000
15A282GLU-1-0.830-0.89719.039-2.073-2.0730.0000.0000.0000.000
16A283PHE00.0090.00420.3710.1610.1610.0000.0000.0000.000
17A284GLU-1-0.857-0.94922.230-0.850-0.8500.0000.0000.0000.000
18A285SER0-0.097-0.05123.6270.0670.0670.0000.0000.0000.000
19A286ILE0-0.008-0.00524.0950.0400.0400.0000.0000.0000.000
20A287ASN00.0000.00826.9120.0800.0800.0000.0000.0000.000
21A288PRO00.0780.05125.6350.0810.0810.0000.0000.0000.000
22A289VAL00.003-0.01028.9670.0630.0630.0000.0000.0000.000
23A290ARG10.8650.92331.6610.5010.5010.0000.0000.0000.000
24A291LEU00.0530.02827.6400.0510.0510.0000.0000.0000.000
25A292ILE0-0.0060.01826.1530.0380.0380.0000.0000.0000.000
26A293PRO0-0.048-0.02727.2350.0140.0140.0000.0000.0000.000
27A294GLU-1-0.863-0.93329.834-0.086-0.0860.0000.0000.0000.000
28A295VAL0-0.074-0.02127.1380.0290.0290.0000.0000.0000.000
29A296GLY00.0280.02326.3440.0490.0490.0000.0000.0000.000
30A297THR0-0.018-0.02822.1940.0670.0670.0000.0000.0000.000
31A298ASN0-0.011-0.01717.887-0.159-0.1590.0000.0000.0000.000
32A299PHE00.0210.00016.048-0.060-0.0600.0000.0000.0000.000
33A300VAL0-0.011-0.01413.4470.0720.0720.0000.0000.0000.000
34A301TYR0-0.073-0.0398.167-0.344-0.3440.0000.0000.0000.000
35A302SER00.0060.0018.7580.6920.6920.0000.0000.0000.000
38A305LEU00.0310.0326.8912.6632.6630.0000.0000.0000.000
39A306PRO00.009-0.0058.328-0.244-0.2440.0000.0000.0000.000
41A308ALA0-0.0170.0067.126-0.018-0.0180.0000.0000.0000.000
42A309ARG10.8790.9469.199-5.937-5.9370.0000.0000.0000.000
43A310SER0-0.029-0.03411.049-1.038-1.0380.0000.0000.0000.000
44A311THR00.0390.00311.8550.4390.4390.0000.0000.0000.000
45A312LYS10.9860.98410.826-3.748-3.7480.0000.0000.0000.000
46A313ASP-1-0.811-0.8707.55210.28210.2820.0000.0000.0000.000
47A314VAL0-0.032-0.0287.797-0.012-0.0120.0000.0000.0000.000
48A315ALA0-0.0150.0148.6730.0690.0690.0000.0000.0000.000
49A316GLY00.0520.00110.478-0.331-0.3310.0000.0000.0000.000
50A317VAL00.0070.01514.2410.0100.0100.0000.0000.0000.000
51A318LYS10.8440.90517.398-0.599-0.5990.0000.0000.0000.000
52A319GLY00.0110.00118.958-0.120-0.1200.0000.0000.0000.000
53A320ARG10.8190.90920.871-0.395-0.3950.0000.0000.0000.000
54A321ILE00.0190.01120.344-0.074-0.0740.0000.0000.0000.000
55A322VAL00.0120.00523.9240.0620.0620.0000.0000.0000.000
56A323LYS10.9340.97627.7350.1550.1550.0000.0000.0000.000
57A324TYR0-0.015-0.02130.4910.0440.0440.0000.0000.0000.000
58A325GLY00.0310.03632.4680.0360.0360.0000.0000.0000.000
59A326ASN0-0.011-0.00935.3010.0130.0130.0000.0000.0000.000
60A327SER00.033-0.00930.864-0.025-0.0250.0000.0000.0000.000
61A328VAL0-0.0060.01326.2250.0630.0630.0000.0000.0000.000
62A329LYS10.9240.97226.3690.3160.3160.0000.0000.0000.000
63A330ALA00.0060.00121.2320.1060.1060.0000.0000.0000.000
64A331VAL0-0.053-0.02123.324-0.003-0.0030.0000.0000.0000.000
65A332GLY00.0170.00721.1260.0700.0700.0000.0000.0000.000
66A333PRO0-0.0170.00116.386-0.160-0.1600.0000.0000.0000.000
67A334VAL0-0.0040.00811.6170.2780.2780.0000.0000.0000.000
68A335GLU-1-0.796-0.90112.6550.8400.8400.0000.0000.0000.000
69A336PHE0-0.008-0.0225.6720.4510.4510.0000.0000.0000.000
70A337GLY0-0.025-0.00711.0470.2500.2500.0000.0000.0000.000
71A338ALA0-0.0250.00313.886-0.199-0.1990.0000.0000.0000.000
72A339SER0-0.038-0.01415.435-0.270-0.2700.0000.0000.0000.000
73A340ASP-1-0.749-0.87416.3231.8101.8100.0000.0000.0000.000
74A341HIS0-0.037-0.03818.697-0.026-0.0260.0000.0000.0000.000
75A342LEU00.0480.02817.8400.0570.0570.0000.0000.0000.000
76A343ALA00.0010.01014.498-0.029-0.0290.0000.0000.0000.000
77A344ARG10.9290.94415.627-1.229-1.2290.0000.0000.0000.000
78A345ALA00.0110.02418.1290.0000.0000.0000.0000.0000.000
79A346VAL00.0180.01213.590-0.016-0.0160.0000.0000.0000.000
80A347LEU00.016-0.00711.681-0.045-0.0450.0000.0000.0000.000
81A348THR0-0.072-0.03115.3240.0830.0830.0000.0000.0000.000
82A349TYR0-0.013-0.03217.598-0.092-0.0920.0000.0000.0000.000
83A350MET0-0.073-0.01610.256-0.097-0.0970.0000.0000.0000.000
84A351ARG10.8190.90215.750-1.221-1.2210.0000.0000.0000.000
85A352PHE0-0.038-0.00418.158-0.018-0.0180.0000.0000.0000.000
86A353TYR00.0470.01117.928-0.127-0.1270.0000.0000.0000.000
87A354PRO00.0250.01113.089-0.132-0.1320.0000.0000.0000.000
88A355GLU-1-0.911-0.96111.940-1.537-1.5370.0000.0000.0000.000
89A356TYR0-0.044-0.03012.511-0.560-0.5600.0000.0000.0000.000
90A357ARG10.9280.9496.0754.1084.1080.0000.0000.0000.000
91A358SER0-0.043-0.03111.5950.0000.0000.0000.0000.0000.000
92A359ALA00.0370.01313.6520.1200.1200.0000.0000.0000.000
93A360ILE0-0.0160.00317.116-0.014-0.0140.0000.0000.0000.000
94A361ASN0-0.026-0.00619.9540.0840.0840.0000.0000.0000.000
95A362ILE00.0140.01223.185-0.053-0.0530.0000.0000.0000.000
96A363ARG10.8790.93526.5380.2960.2960.0000.0000.0000.000
97A364TYR00.0570.02830.209-0.034-0.0340.0000.0000.0000.000
98A365SER0-0.048-0.04532.4730.0080.0080.0000.0000.0000.000
99A366ARG10.9800.99635.6090.1230.1230.0000.0000.0000.000
100A367GLU-1-0.797-0.88237.148-0.314-0.3140.0000.0000.0000.000
101A368ILE0-0.052-0.00930.921-0.031-0.0310.0000.0000.0000.000
102A369ILE0-0.055-0.03231.752-0.025-0.0250.0000.0000.0000.000
103A370GLU-1-0.885-0.94833.893-0.199-0.1990.0000.0000.0000.000
104A371GLU-1-0.786-0.90734.295-0.354-0.3540.0000.0000.0000.000
105A372ILE0-0.068-0.03428.534-0.048-0.0480.0000.0000.0000.000
106A373ILE0-0.066-0.03431.449-0.024-0.0240.0000.0000.0000.000
107A374GLU-1-0.908-0.94633.895-0.451-0.4510.0000.0000.0000.000
108A375ILE00.0240.00729.302-0.036-0.0360.0000.0000.0000.000
109A376ALA0-0.049-0.02929.771-0.052-0.0520.0000.0000.0000.000
110A377GLN0-0.056-0.03330.7660.0190.0190.0000.0000.0000.000
111A378GLU-1-0.928-0.96232.955-0.620-0.6200.0000.0000.0000.000
112A379ARG10.8510.91928.1040.8090.8090.0000.0000.0000.000
113A380GLY0-0.0030.02628.750-0.052-0.0520.0000.0000.0000.000
114A381PHE0-0.063-0.02725.852-0.034-0.0340.0000.0000.0000.000
115A382LYS10.8910.93426.7480.3830.3830.0000.0000.0000.000
116A383VAL00.0200.00626.937-0.023-0.0230.0000.0000.0000.000
117A384SER0-0.051-0.04428.3870.0320.0320.0000.0000.0000.000
118A385PHE00.0150.00429.561-0.011-0.0110.0000.0000.0000.000
119A386TYR0-0.044-0.00326.5250.0530.0530.0000.0000.0000.000
120A387ASP-1-0.752-0.86531.4670.1740.1740.0000.0000.0000.000
121A388ARG10.8410.92228.503-0.360-0.3600.0000.0000.0000.000
122A389ARG10.8400.88834.469-0.146-0.1460.0000.0000.0000.000
123A390GLU-1-0.862-0.92135.7070.2090.2090.0000.0000.0000.000
124A391GLU-1-0.824-0.89631.3510.6020.6020.0000.0000.0000.000
125A392PRO0-0.005-0.01133.514-0.010-0.0100.0000.0000.0000.000
126A393GLU-1-0.810-0.90334.7500.4930.4930.0000.0000.0000.000
127A394GLU-1-0.826-0.91531.9500.8530.8530.0000.0000.0000.000
128A395ILE0-0.039-0.01629.1810.0650.0650.0000.0000.0000.000
129A396LYS10.8260.91330.918-0.380-0.3800.0000.0000.0000.000
130A397ALA0-0.025-0.00232.8150.0140.0140.0000.0000.0000.000
131A398LYS10.7830.90127.403-0.900-0.9000.0000.0000.0000.000
132A399GLU-1-0.883-0.95126.4871.0981.0980.0000.0000.0000.000
133A400GLY0-0.049-0.03924.5270.1010.1010.0000.0000.0000.000
134A401ALA0-0.014-0.00224.3580.0580.0580.0000.0000.0000.000
135A402THR00.004-0.03226.414-0.008-0.0080.0000.0000.0000.000
136A403ILE0-0.083-0.02221.963-0.050-0.0500.0000.0000.0000.000
137A404PRO0-0.007-0.00221.877-0.069-0.0690.0000.0000.0000.000
138A405TRP00.0850.04423.545-0.072-0.0720.0000.0000.0000.000
139A406GLY00.0470.02027.081-0.073-0.0730.0000.0000.0000.000
140A407ILE0-0.037-0.02321.155-0.085-0.0850.0000.0000.0000.000
141A408GLU-1-0.806-0.90324.0750.8900.8900.0000.0000.0000.000
142A409THR0-0.046-0.02025.944-0.067-0.0670.0000.0000.0000.000
143A410ALA0-0.008-0.00426.773-0.055-0.0550.0000.0000.0000.000
144A411ILE0-0.0190.00222.092-0.072-0.0720.0000.0000.0000.000
145A412LYS10.8670.92726.527-0.690-0.6900.0000.0000.0000.000
146A413ARG10.7650.90729.345-0.191-0.1910.0000.0000.0000.000
147A414ILE0-0.010-0.00127.876-0.032-0.0320.0000.0000.0000.000
148A415LYS10.9300.95729.758-0.029-0.0290.0000.0000.0000.000
149A416GLU-1-0.820-0.90327.637-0.190-0.1900.0000.0000.0000.000
150A417ARG10.8150.89020.0310.7020.7020.0000.0000.0000.000
151A418PRO00.0010.01724.177-0.084-0.0840.0000.0000.0000.000
152A419ASP-1-0.798-0.86322.047-0.771-0.7710.0000.0000.0000.000
153A420ILE0-0.0030.00222.846-0.028-0.0280.0000.0000.0000.000
154A421ILE0-0.030-0.01123.1800.0650.0650.0000.0000.0000.000
155A422TYR00.0240.01026.2980.0080.0080.0000.0000.0000.000
156A423HIS0-0.016-0.01728.1360.0730.0730.0000.0000.0000.000
157A424LEU00.0440.02131.403-0.031-0.0310.0000.0000.0000.000
158A425GLY0-0.0020.01233.8510.0310.0310.0000.0000.0000.000
159A426ASP-1-0.809-0.90134.0710.3000.3000.0000.0000.0000.000
160A427VAL00.016-0.00936.708-0.012-0.0120.0000.0000.0000.000
161A428GLY00.0020.01036.6700.0360.0360.0000.0000.0000.000
162A429LYS10.8820.93931.508-0.449-0.4490.0000.0000.0000.000
163A430GLU-1-0.776-0.90031.0930.0830.0830.0000.0000.0000.000
164A431PRO0-0.026-0.01031.5000.0330.0330.0000.0000.0000.000
165A432MET0-0.0030.00226.817-0.053-0.0530.0000.0000.0000.000
166A433ILE00.0170.00826.8050.0270.0270.0000.0000.0000.000
167A434LEU0-0.034-0.01322.320-0.013-0.0130.0000.0000.0000.000
168A435VAL00.0280.01221.678-0.006-0.0060.0000.0000.0000.000
169A436PHE00.007-0.00817.9470.0060.0060.0000.0000.0000.000
170A437GLY00.014-0.00316.687-0.085-0.0850.0000.0000.0000.000
171A438ARG10.8270.89812.8192.5452.5450.0000.0000.0000.000
172A439ASN00.0040.01711.007-0.242-0.2420.0000.0000.0000.000
173A440PRO00.0370.00511.1120.4580.4580.0000.0000.0000.000
174A441ARG10.8510.92813.3893.6643.6640.0000.0000.0000.000
175A442GLU-1-0.725-0.84915.594-2.147-2.1470.0000.0000.0000.000
176A443VAL0-0.042-0.00316.1300.2820.2820.0000.0000.0000.000
177A444LEU0-0.010-0.00318.1430.2130.2130.0000.0000.0000.000
178A445GLU-1-0.914-0.97218.692-2.085-2.0850.0000.0000.0000.000
179A446LYS10.8760.94020.5551.4351.4350.0000.0000.0000.000
180A447ILE0-0.031-0.02022.3990.1050.1050.0000.0000.0000.000
181A448LYS10.8610.91321.5431.7491.7490.0000.0000.0000.000
182A449MET0-0.038-0.00924.5260.0580.0580.0000.0000.0000.000
183A450LEU0-0.053-0.00427.8580.0640.0640.0000.0000.0000.000
184A451ILE-1-0.949-0.96428.237-0.653-0.6530.0000.0000.0000.000