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: JV229

Calculation Name: 2AY4-A-Xray547

Preferred Name:

Target Type:

Ligand Name: pyridoxal-5'-phosphate | 3-(p-tolyl)propionic acid

Ligand 3-letter code: PLP | PPT

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2AY4

Chain ID: A

ChEMBL ID:

UniProt ID: P95468

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 394
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -6425890.830935
FMO2-HF: Nuclear repulsion 6273844.300461
FMO2-HF: Total energy -152046.530474
FMO2-MP2: Total energy -152482.375058


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:5:MET)


Summations of interaction energy for fragment #1(A:5: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.
-8.895-4.5490.041-1.828-2.559-0.006
Interaction energy analysis for fragmet #1(A:5:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.893 / q_NPA : 0.936
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].
3A7GLY00.0410.0293.3457.40810.013-0.011-1.152-1.442-0.003
4A8ASN0-0.017-0.0103.436-2.035-0.5510.053-0.647-0.891-0.003
5A9LEU0-0.036-0.0094.4824.6454.902-0.001-0.029-0.2260.000
6A10LYS10.9810.9937.22426.85926.8590.0000.0000.0000.000
7A11PRO00.0110.01110.7950.0320.0320.0000.0000.0000.000
8A12GLN00.002-0.00111.8562.0292.0290.0000.0000.0000.000
9A13ALA00.0070.00415.2360.1840.1840.0000.0000.0000.000
10A14PRO00.0150.00018.8010.0630.0630.0000.0000.0000.000
11A15ASP-1-0.850-0.91820.344-13.497-13.4970.0000.0000.0000.000
12A16LYS10.9310.98222.75711.54911.5490.0000.0000.0000.000
13A17ILE00.037-0.00525.7610.2950.2950.0000.0000.0000.000
14A18LEU00.009-0.00623.4050.3710.3710.0000.0000.0000.000
15A19ALA0-0.026-0.01226.9300.1730.1730.0000.0000.0000.000
16A20LEU00.0360.02728.5890.2350.2350.0000.0000.0000.000
17A21MET00.0370.01628.6380.3290.3290.0000.0000.0000.000
18A22GLY0-0.051-0.01030.6570.1420.1420.0000.0000.0000.000
19A23GLU-1-0.886-0.94231.503-9.283-9.2830.0000.0000.0000.000
20A24PHE00.0430.03134.3980.1690.1690.0000.0000.0000.000
21A25ARG10.8830.92529.20810.43210.4320.0000.0000.0000.000
22A26ALA0-0.005-0.00134.9140.1700.1700.0000.0000.0000.000
23A27ASP-1-0.757-0.81236.883-7.580-7.5800.0000.0000.0000.000
24A28PRO00.0050.00740.0950.0570.0570.0000.0000.0000.000
25A29ARG10.7410.83442.4807.5847.5840.0000.0000.0000.000
26A30GLN00.012-0.00344.661-0.054-0.0540.0000.0000.0000.000
27A31GLY00.0020.00546.739-0.023-0.0230.0000.0000.0000.000
28A32LYS10.8040.91139.3928.0628.0620.0000.0000.0000.000
29A33ILE00.0210.00543.300-0.009-0.0090.0000.0000.0000.000
30A34ASP-1-0.877-0.94136.632-8.691-8.6910.0000.0000.0000.000
31A35LEU0-0.0110.01739.8370.0640.0640.0000.0000.0000.000
32A36GLY00.021-0.00535.608-0.043-0.0430.0000.0000.0000.000
33A37VAL0-0.041-0.02434.363-0.276-0.2760.0000.0000.0000.000
34A38GLY0-0.004-0.00332.4940.1350.1350.0000.0000.0000.000
35A39VAL0-0.056-0.02232.892-0.093-0.0930.0000.0000.0000.000
36A40TYR00.0980.04235.4970.0590.0590.0000.0000.0000.000
37A41LYS10.8010.90136.8907.9747.9740.0000.0000.0000.000
38A42ASP-1-0.708-0.83141.135-6.874-6.8740.0000.0000.0000.000
39A43ALA00.0300.00344.678-0.070-0.0700.0000.0000.0000.000
40A44THR0-0.077-0.04545.5270.0480.0480.0000.0000.0000.000
41A45GLY00.0250.02442.367-0.082-0.0820.0000.0000.0000.000
42A46HIS0-0.056-0.03740.360-0.414-0.4140.0000.0000.0000.000
43A47THR0-0.034-0.03536.118-0.001-0.0010.0000.0000.0000.000
44A48PRO0-0.0130.00638.482-0.191-0.1910.0000.0000.0000.000
45A49ILE0-0.011-0.00337.599-0.112-0.1120.0000.0000.0000.000
46A50MET0-0.0030.01640.2830.0860.0860.0000.0000.0000.000
47A51ARG10.8360.89042.8246.1936.1930.0000.0000.0000.000
48A52ALA00.0360.01345.068-0.029-0.0290.0000.0000.0000.000
49A53VAL0-0.014-0.00538.667-0.041-0.0410.0000.0000.0000.000
50A54HIS00.0160.00641.543-0.153-0.1530.0000.0000.0000.000
51A55ALA0-0.016-0.00742.7720.0130.0130.0000.0000.0000.000
52A56ALA0-0.005-0.00541.6290.0510.0510.0000.0000.0000.000
53A57GLU-1-0.856-0.93636.938-8.072-8.0720.0000.0000.0000.000
54A58GLN0-0.028-0.00340.735-0.054-0.0540.0000.0000.0000.000
55A59ARG10.9160.95543.8696.2616.2610.0000.0000.0000.000
56A60MET0-0.0410.01036.4180.0350.0350.0000.0000.0000.000
57A61LEU0-0.059-0.01939.250-0.050-0.0500.0000.0000.0000.000
58A62GLU-1-0.961-0.97641.292-6.349-6.3490.0000.0000.0000.000
59A63THR0-0.087-0.06243.1100.0900.0900.0000.0000.0000.000
60A64GLU-1-0.855-0.93237.276-7.510-7.5100.0000.0000.0000.000
61A66THR0-0.001-0.00340.174-0.047-0.0470.0000.0000.0000.000
62A67THR0-0.035-0.02335.826-0.114-0.1140.0000.0000.0000.000
63A68LYS10.9520.97131.5508.7638.7630.0000.0000.0000.000
64A69THR0-0.017-0.00230.999-0.222-0.2220.0000.0000.0000.000
65A70TYR0-0.033-0.01324.2660.0680.0680.0000.0000.0000.000
66A71ALA00.0510.03830.0140.2330.2330.0000.0000.0000.000
67A72GLY00.0180.00330.915-0.140-0.1400.0000.0000.0000.000
68A73LEU0-0.035-0.01825.420-0.179-0.1790.0000.0000.0000.000
69A74SER00.017-0.00527.967-0.319-0.3190.0000.0000.0000.000
70A75GLY00.0300.01630.5010.0710.0710.0000.0000.0000.000
71A76GLU-1-0.798-0.91132.060-8.267-8.2670.0000.0000.0000.000
72A77PRO0-0.008-0.01235.6280.0220.0220.0000.0000.0000.000
73A78GLU-1-0.858-0.90138.481-6.910-6.9100.0000.0000.0000.000
74A79PHE00.0460.00733.2360.0660.0660.0000.0000.0000.000
75A80GLN0-0.005-0.01234.679-0.014-0.0140.0000.0000.0000.000
76A81LYS10.9290.98737.2666.7376.7370.0000.0000.0000.000
77A82ALA0-0.0010.00240.4860.0910.0910.0000.0000.0000.000
78A83MET0-0.018-0.01236.157-0.002-0.0020.0000.0000.0000.000
79A84GLY00.0480.02239.3640.0280.0280.0000.0000.0000.000
80A85GLU-1-0.892-0.96441.009-6.379-6.3790.0000.0000.0000.000
81A86LEU0-0.061-0.01440.6550.1100.1100.0000.0000.0000.000
82A87ILE00.0250.00837.5360.0380.0380.0000.0000.0000.000
83A88LEU0-0.032-0.02041.1720.0560.0560.0000.0000.0000.000
84A89GLY00.0430.04144.3880.1320.1320.0000.0000.0000.000
85A90ASP-1-0.919-0.97447.351-5.842-5.8420.0000.0000.0000.000
86A91GLY0-0.038-0.00747.8400.0500.0500.0000.0000.0000.000
87A95LEU0-0.025-0.01142.062-0.082-0.0820.0000.0000.0000.000
88A96LYS10.9400.97044.2276.3296.3290.0000.0000.0000.000
89A97SER00.0070.00042.435-0.130-0.1300.0000.0000.0000.000
90A98GLU-1-0.904-0.94741.903-6.552-6.5520.0000.0000.0000.000
91A99THR0-0.023-0.01341.512-0.032-0.0320.0000.0000.0000.000
92A100THR0-0.009-0.01138.495-0.123-0.1230.0000.0000.0000.000
93A101ALA00.0130.02134.1900.0140.0140.0000.0000.0000.000
94A102THR0-0.040-0.02234.4240.0170.0170.0000.0000.0000.000
95A103LEU0-0.0040.01326.600-0.083-0.0830.0000.0000.0000.000
96A104ALA00.0260.02330.524-0.010-0.0100.0000.0000.0000.000
97A105THR0-0.002-0.00926.389-0.247-0.2470.0000.0000.0000.000
98A106VAL00.0280.01722.4960.2150.2150.0000.0000.0000.000
99A107GLY0-0.034-0.01725.352-0.258-0.2580.0000.0000.0000.000
100A108GLY00.0530.02027.720-0.072-0.0720.0000.0000.0000.000
101A109THR0-0.012-0.01823.2380.1070.1070.0000.0000.0000.000
102A110GLY00.0080.01723.659-0.338-0.3380.0000.0000.0000.000
103A111ALA00.0040.01724.710-0.099-0.0990.0000.0000.0000.000
104A112LEU00.0190.00026.2280.0140.0140.0000.0000.0000.000
105A113ARG10.8180.90316.42114.07714.0770.0000.0000.0000.000
106A114GLN00.002-0.00722.529-0.297-0.2970.0000.0000.0000.000
107A115ALA00.0240.01225.0070.1340.1340.0000.0000.0000.000
108A116LEU00.018-0.00524.0380.1170.1170.0000.0000.0000.000
109A117GLU-1-0.798-0.88019.394-13.442-13.4420.0000.0000.0000.000
110A118LEU0-0.001-0.00323.6960.0590.0590.0000.0000.0000.000
111A119ALA00.0160.00927.1380.1940.1940.0000.0000.0000.000
112A120ARG10.8350.91018.34213.31813.3180.0000.0000.0000.000
113A121MET0-0.093-0.04724.295-0.082-0.0820.0000.0000.0000.000
114A122ALA0-0.0200.00726.4250.1790.1790.0000.0000.0000.000
115A123ASN0-0.034-0.03129.0460.2060.2060.0000.0000.0000.000
116A124PRO00.002-0.00126.144-0.253-0.2530.0000.0000.0000.000
117A125ASP-1-0.949-0.96926.477-9.994-9.9940.0000.0000.0000.000
118A126LEU0-0.066-0.01826.9200.2060.2060.0000.0000.0000.000
119A129ARG10.7950.88227.9008.2918.2910.0000.0000.0000.000
120A133VAL0-0.009-0.01427.5470.1740.1740.0000.0000.0000.000
121A134PHE0-0.0160.00130.360-0.127-0.1270.0000.0000.0000.000
122A135VAL0-0.027-0.02429.7360.0290.0290.0000.0000.0000.000
123A136SER00.0510.02433.0900.0980.0980.0000.0000.0000.000
124A137ASP-1-0.933-0.94134.442-8.595-8.5950.0000.0000.0000.000
125A138PRO0-0.017-0.01034.3190.2190.2190.0000.0000.0000.000
126A139THR00.0590.01530.3610.2770.2770.0000.0000.0000.000
127A140TRP0-0.007-0.00326.873-0.151-0.1510.0000.0000.0000.000
128A141PRO00.0470.00627.044-0.203-0.2030.0000.0000.0000.000
129A142ASN0-0.012-0.00123.624-0.113-0.1130.0000.0000.0000.000
130A143HIS00.0110.01424.153-0.370-0.3700.0000.0000.0000.000
131A144VAL00.0910.03825.021-0.257-0.2570.0000.0000.0000.000
132A145SER0-0.067-0.03621.129-0.473-0.4730.0000.0000.0000.000
133A146ILE0-0.021-0.01220.322-0.702-0.7020.0000.0000.0000.000
134A147MET00.0080.01320.617-0.318-0.3180.0000.0000.0000.000
135A148ASN00.0250.01020.6460.0060.0060.0000.0000.0000.000
136A149PHE0-0.072-0.02612.839-0.600-0.6000.0000.0000.0000.000
137A150MET0-0.073-0.02716.584-0.553-0.5530.0000.0000.0000.000
138A151GLY0-0.0020.01219.0070.0350.0350.0000.0000.0000.000
139A152LEU0-0.001-0.00520.3490.3080.3080.0000.0000.0000.000
140A154PRO0-0.011-0.01023.871-0.009-0.0090.0000.0000.0000.000
141A155VAL00.0150.01725.7580.3040.3040.0000.0000.0000.000
142A156GLN0-0.030-0.00728.4570.2400.2400.0000.0000.0000.000
143A157THR0-0.025-0.01732.225-0.110-0.1100.0000.0000.0000.000
144A158TYR0-0.039-0.03234.3470.2010.2010.0000.0000.0000.000
145A159ARG10.8410.89037.8986.9726.9720.0000.0000.0000.000
146A160TYR0-0.042-0.05139.0830.0640.0640.0000.0000.0000.000
147A161PHE0-0.010-0.01840.2880.1320.1320.0000.0000.0000.000
148A162ASP-1-0.810-0.88441.947-6.584-6.5840.0000.0000.0000.000
149A163ALA0-0.027-0.03042.8070.0220.0220.0000.0000.0000.000
150A164GLU-1-0.949-0.95244.612-6.246-6.2460.0000.0000.0000.000
151A165THR0-0.004-0.02748.4450.0470.0470.0000.0000.0000.000
152A166ARG10.8170.91445.5386.6186.6180.0000.0000.0000.000
153A167GLY00.0570.03446.204-0.038-0.0380.0000.0000.0000.000
154A168VAL0-0.028-0.03043.665-0.172-0.1720.0000.0000.0000.000
155A169ASP-1-0.799-0.89944.118-6.607-6.6070.0000.0000.0000.000
156A170PHE0-0.004-0.01644.930-0.122-0.1220.0000.0000.0000.000
157A171GLU-1-0.830-0.91146.841-6.047-6.0470.0000.0000.0000.000
158A172GLY0-0.024-0.01744.611-0.037-0.0370.0000.0000.0000.000
159A173MET0-0.0330.00040.419-0.087-0.0870.0000.0000.0000.000
160A174LYS10.7840.88142.7485.9865.9860.0000.0000.0000.000
161A175ALA0-0.057-0.02444.971-0.019-0.0190.0000.0000.0000.000
162A176ASP-1-0.774-0.86039.660-7.456-7.4560.0000.0000.0000.000
163A177LEU0-0.008-0.01338.200-0.171-0.1710.0000.0000.0000.000
164A178ALA0-0.035-0.00440.865-0.018-0.0180.0000.0000.0000.000
165A179ALA0-0.041-0.01339.4880.0530.0530.0000.0000.0000.000
166A180ALA0-0.023-0.00237.646-0.219-0.2190.0000.0000.0000.000
167A181LYS10.9270.94136.8967.5637.5630.0000.0000.0000.000
168A182LYS10.9890.99237.5417.0817.0810.0000.0000.0000.000
169A183GLY0-0.0020.00735.137-0.087-0.0870.0000.0000.0000.000
170A184ASP-1-0.744-0.83432.985-8.835-8.8350.0000.0000.0000.000
171A185MET0-0.022-0.00329.8220.0650.0650.0000.0000.0000.000
172A186VAL00.0030.00233.209-0.091-0.0910.0000.0000.0000.000
173A187LEU0-0.0060.00729.8760.0210.0210.0000.0000.0000.000
174A188LEU0-0.0080.00933.8350.1090.1090.0000.0000.0000.000
175A189HIS0-0.040-0.03233.700-0.073-0.0730.0000.0000.0000.000
176A190GLY00.0210.00437.2170.1720.1720.0000.0000.0000.000
177A191CYS0-0.0290.00939.5060.1360.1360.0000.0000.0000.000
178A192CYS0-0.051-0.02839.373-0.164-0.1640.0000.0000.0000.000
179A193HIS10.8560.93836.6307.7817.7810.0000.0000.0000.000
180A194ASN00.0050.01532.3880.0920.0920.0000.0000.0000.000
181A195PRO0-0.031-0.03934.066-0.120-0.1200.0000.0000.0000.000
182A196THR00.023-0.00736.3670.0680.0680.0000.0000.0000.000
183A197GLY00.0820.07139.8270.1360.1360.0000.0000.0000.000
184A198ALA00.0100.01642.2360.1610.1610.0000.0000.0000.000
185A199ASN0-0.012-0.00742.313-0.315-0.3150.0000.0000.0000.000
186A200LEU00.0410.03643.1960.0930.0930.0000.0000.0000.000
187A201THR00.0560.02146.156-0.008-0.0080.0000.0000.0000.000
188A202LEU00.021-0.00548.611-0.092-0.0920.0000.0000.0000.000
189A203ASP-1-0.891-0.94350.116-5.655-5.6550.0000.0000.0000.000
190A204GLN00.0420.03047.563-0.093-0.0930.0000.0000.0000.000
191A205TRP00.0200.00440.389-0.140-0.1400.0000.0000.0000.000
192A206ALA0-0.0150.00246.730-0.061-0.0610.0000.0000.0000.000
193A207GLU-1-0.850-0.92649.103-5.981-5.9810.0000.0000.0000.000
194A208ILE0-0.008-0.01642.300-0.066-0.0660.0000.0000.0000.000
195A209ALA00.000-0.00444.444-0.105-0.1050.0000.0000.0000.000
196A210SER00.0290.01045.722-0.006-0.0060.0000.0000.0000.000
197A211ILE0-0.041-0.01742.9830.0200.0200.0000.0000.0000.000
198A212LEU0-0.0110.01239.504-0.102-0.1020.0000.0000.0000.000
199A213GLU-1-0.928-0.96842.817-6.218-6.2180.0000.0000.0000.000
200A214LYS10.8860.95045.5906.2466.2460.0000.0000.0000.000
201A215THR0-0.060-0.04441.020-0.038-0.0380.0000.0000.0000.000
202A216GLY0-0.006-0.00141.381-0.085-0.0850.0000.0000.0000.000
203A217ALA0-0.022-0.00737.262-0.179-0.1790.0000.0000.0000.000
204A218LEU00.0160.00532.8840.1300.1300.0000.0000.0000.000
205A219PRO0-0.0030.00535.301-0.216-0.2160.0000.0000.0000.000
206A220LEU0-0.005-0.00429.706-0.086-0.0860.0000.0000.0000.000
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