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: NLZJQ

Calculation Name: 2FYF-A-Xray547

Preferred Name:

Target Type:

Ligand Name: pyridoxal-5'-phosphate | tetrachloroplatinate(ii)

Ligand 3-letter code: PLP | PC4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2FYF

Chain ID: A

ChEMBL ID:

UniProt ID: P9WQ73

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 369
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -5744834.948214
FMO2-HF: Nuclear repulsion 5608589.315811
FMO2-HF: Total energy -136245.632402
FMO2-MP2: Total energy -136652.282922


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:8:HIS)


Summations of interaction energy for fragment #1(A:8:HIS)
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.
-179.722-172.0712.121-3.168-6.603-0.015
Interaction energy analysis for fragmet #1(A:8:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.835 / q_NPA : 0.903
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].
3A10GLU-1-0.968-0.9663.120-43.272-39.1250.872-1.502-3.517-0.006
4A11ILE00.0310.0063.8894.2264.5160.017-0.045-0.2620.000
322A329ILE00.0070.0164.471-3.104-2.828-0.001-0.019-0.2560.000
323A330LEU00.0350.0284.337-3.881-3.741-0.001-0.025-0.1140.000
325A332ALA0-0.053-0.0272.492-0.2130.4950.760-0.500-0.9680.002
326A333ASN0-0.072-0.0462.951-10.177-8.1420.475-1.066-1.443-0.011
327A334GLY00.0000.0064.4303.0493.104-0.001-0.011-0.0430.000
5A12PRO00.002-0.0036.9080.6580.6580.0000.0000.0000.000
6A13THR00.019-0.0229.3880.7090.7090.0000.0000.0000.000
7A14ALA0-0.054-0.02310.6020.9920.9920.0000.0000.0000.000
8A15ILE00.0380.03311.6650.9210.9210.0000.0000.0000.000
9A16LYS10.8470.9346.03030.94430.9440.0000.0000.0000.000
10A17PRO0-0.0170.00211.6181.0181.0180.0000.0000.0000.000
11A18ARG10.9130.93913.76412.54312.5430.0000.0000.0000.000
12A19ASP-1-0.813-0.88615.644-14.795-14.7950.0000.0000.0000.000
13A20GLY00.0370.03312.116-0.100-0.1000.0000.0000.0000.000
14A21ARG10.7530.84112.95413.64713.6470.0000.0000.0000.000
15A22PHE00.0680.03213.7430.7900.7900.0000.0000.0000.000
16A23GLY00.0690.04716.9220.3420.3420.0000.0000.0000.000
17A24SER0-0.021-0.02818.4150.5940.5940.0000.0000.0000.000
18A25GLY00.002-0.00221.6750.6500.6500.0000.0000.0000.000
19A26PRO0-0.037-0.04721.0500.1460.1460.0000.0000.0000.000
20A27SER0-0.038-0.01120.233-0.388-0.3880.0000.0000.0000.000
21A28LYS10.8750.95319.18013.22613.2260.0000.0000.0000.000
22A29VAL00.0100.02520.8930.3900.3900.0000.0000.0000.000
23A30ARG10.8480.90522.1329.3469.3460.0000.0000.0000.000
24A31LEU00.0240.01421.6350.1370.1370.0000.0000.0000.000
25A32GLU-1-0.817-0.91624.097-10.353-10.3530.0000.0000.0000.000
26A33GLN0-0.018-0.01626.8630.0200.0200.0000.0000.0000.000
27A34LEU00.0230.01923.0670.2840.2840.0000.0000.0000.000
28A35GLN0-0.0050.00126.938-0.073-0.0730.0000.0000.0000.000
29A36THR0-0.0140.00128.7410.3120.3120.0000.0000.0000.000
30A37LEU0-0.023-0.00828.3990.3120.3120.0000.0000.0000.000
31A38THR0-0.025-0.01229.1250.1740.1740.0000.0000.0000.000
32A39THR0-0.041-0.04632.0270.1910.1910.0000.0000.0000.000
33A40THR0-0.005-0.00134.5490.1320.1320.0000.0000.0000.000
34A41ALA00.0260.00934.3940.2150.2150.0000.0000.0000.000
35A42ALA00.0210.02135.0310.0770.0770.0000.0000.0000.000
36A43ALA0-0.027-0.02536.3140.0670.0670.0000.0000.0000.000
37A44LEU00.0060.00838.3590.1960.1960.0000.0000.0000.000
38A45PHE00.0110.01632.2710.0560.0560.0000.0000.0000.000
39A46GLY0-0.0110.00137.9850.0990.0990.0000.0000.0000.000
40A47THR0-0.066-0.03440.4460.2550.2550.0000.0000.0000.000
41A48SER00.023-0.00142.471-0.048-0.0480.0000.0000.0000.000
42A49HIS00.0750.02642.7010.0260.0260.0000.0000.0000.000
43A50ARG10.8370.90344.5596.3766.3760.0000.0000.0000.000
44A51GLN0-0.025-0.02047.3180.1680.1680.0000.0000.0000.000
45A52ALA00.0310.01147.095-0.097-0.0970.0000.0000.0000.000
46A53PRO00.0190.00944.198-0.052-0.0520.0000.0000.0000.000
47A54VAL00.0420.03040.850-0.103-0.1030.0000.0000.0000.000
48A55LYS10.9260.98242.8115.9195.9190.0000.0000.0000.000
49A56ASN0-0.011-0.00845.1740.0610.0610.0000.0000.0000.000
50A57LEU0-0.0130.01337.074-0.025-0.0250.0000.0000.0000.000
51A58VAL00.001-0.00340.635-0.102-0.1020.0000.0000.0000.000
52A59GLY00.0120.00341.962-0.001-0.0010.0000.0000.0000.000
53A60ARG10.7550.85136.8597.6817.6810.0000.0000.0000.000
54A61VAL0-0.0100.00237.200-0.040-0.0400.0000.0000.0000.000
55A62ARG10.8210.88739.6696.3866.3860.0000.0000.0000.000
56A63SER0-0.015-0.00142.7560.0480.0480.0000.0000.0000.000
57A64GLY00.0660.02340.2780.0310.0310.0000.0000.0000.000
58A65LEU0-0.034-0.02936.642-0.100-0.1000.0000.0000.0000.000
59A66ALA00.0110.00340.485-0.005-0.0050.0000.0000.0000.000
60A67GLU-1-0.919-0.94442.152-6.634-6.6340.0000.0000.0000.000
61A68LEU0-0.058-0.03235.437-0.031-0.0310.0000.0000.0000.000
62A69PHE0-0.055-0.04535.835-0.211-0.2110.0000.0000.0000.000
63A70SER0-0.017-0.00741.4330.0730.0730.0000.0000.0000.000
64A71LEU0-0.044-0.01743.4070.0560.0560.0000.0000.0000.000
65A72PRO00.0180.01846.7620.1050.1050.0000.0000.0000.000
66A73ASP-1-0.888-0.94850.271-5.575-5.5750.0000.0000.0000.000
67A74GLY0-0.045-0.03153.0960.0290.0290.0000.0000.0000.000
68A75TYR0-0.032-0.02646.7200.0230.0230.0000.0000.0000.000
69A76GLU-1-0.860-0.93247.667-6.060-6.0600.0000.0000.0000.000
70A77VAL0-0.0190.00341.461-0.134-0.1340.0000.0000.0000.000
71A78ILE0-0.018-0.01243.4670.0900.0900.0000.0000.0000.000
72A79LEU0-0.012-0.01539.569-0.208-0.2080.0000.0000.0000.000
73A80GLY00.0280.00739.5310.2010.2010.0000.0000.0000.000
74A81ASN0-0.047-0.04437.242-0.342-0.3420.0000.0000.0000.000
75A82GLY00.012-0.00435.3880.1130.1130.0000.0000.0000.000
76A83GLY0-0.030-0.00232.990-0.196-0.1960.0000.0000.0000.000
77A84ALA00.0530.00933.0570.1930.1930.0000.0000.0000.000
78A85THR0-0.033-0.01432.9600.0640.0640.0000.0000.0000.000
79A86ALA00.0130.01135.1630.1530.1530.0000.0000.0000.000
80A87PHE00.0260.01137.6450.2170.2170.0000.0000.0000.000
81A88TRP0-0.024-0.01432.3830.0250.0250.0000.0000.0000.000
82A89ASP-1-0.859-0.93639.585-7.294-7.2940.0000.0000.0000.000
83A90ALA0-0.021-0.01141.7580.1860.1860.0000.0000.0000.000
84A91ALA0-0.018-0.00442.7750.1860.1860.0000.0000.0000.000
85A92ALA0-0.006-0.00943.6850.1450.1450.0000.0000.0000.000
86A93PHE0-0.037-0.01545.3410.1140.1140.0000.0000.0000.000
87A94GLY00.0170.00247.2440.1610.1610.0000.0000.0000.000
88A95LEU0-0.023-0.01845.1800.0530.0530.0000.0000.0000.000
89A96ILE00.0180.02945.6420.0760.0760.0000.0000.0000.000
90A97ASP-1-0.805-0.88249.789-5.397-5.3970.0000.0000.0000.000
91A98LYS10.7870.87153.5725.3935.3930.0000.0000.0000.000
92A99ARG10.8580.90850.5665.9105.9100.0000.0000.0000.000
93A100SER00.0490.01045.3700.0630.0630.0000.0000.0000.000
94A101LEU00.0210.02044.9080.0130.0130.0000.0000.0000.000
95A102HIS0-0.0130.00340.6330.0630.0630.0000.0000.0000.000
96A103LEU00.0210.02439.8670.0060.0060.0000.0000.0000.000
97A104THR0-0.077-0.04737.068-0.137-0.1370.0000.0000.0000.000
98A105TYR00.1020.04033.2980.1370.1370.0000.0000.0000.000
99A106GLY00.014-0.00930.936-0.342-0.3420.0000.0000.0000.000
100A107GLU-1-0.867-0.91328.700-9.627-9.6270.0000.0000.0000.000
101A108PHE0-0.051-0.03926.7340.1270.1270.0000.0000.0000.000
102A109SER00.0290.00632.2370.2670.2670.0000.0000.0000.000
103A110ALA00.0310.00734.4040.2590.2590.0000.0000.0000.000
104A111LYS10.8840.95133.3888.8118.8110.0000.0000.0000.000
105A112PHE00.0490.02135.5920.1630.1630.0000.0000.0000.000
106A113ALA00.0630.03538.2410.1810.1810.0000.0000.0000.000
107A114SER0-0.054-0.03637.9550.1240.1240.0000.0000.0000.000
108A115ALA0-0.031-0.01439.1130.0820.0820.0000.0000.0000.000
109A116VAL00.0200.00340.8900.1440.1440.0000.0000.0000.000
110A117SER0-0.066-0.05043.3080.0930.0930.0000.0000.0000.000
111A118LYS10.8620.93739.2767.6957.6950.0000.0000.0000.000
112A119ASN00.0180.01644.9530.1850.1850.0000.0000.0000.000
113A120PRO0-0.009-0.00446.7510.0750.0750.0000.0000.0000.000
114A121PHE0-0.034-0.02449.5180.1520.1520.0000.0000.0000.000
115A122VAL0-0.029-0.00248.0520.1020.1020.0000.0000.0000.000
116A123GLY00.0060.00351.2230.0040.0040.0000.0000.0000.000
117A124GLU-1-0.864-0.91547.290-6.590-6.5900.0000.0000.0000.000
118A125PRO0-0.0120.01545.0310.1060.1060.0000.0000.0000.000
119A126ILE0-0.030-0.00547.161-0.015-0.0150.0000.0000.0000.000
120A127ILE0-0.025-0.02041.439-0.130-0.1300.0000.0000.0000.000
121A128ILE0-0.0100.00442.9690.0500.0500.0000.0000.0000.000
122A129THR0-0.027-0.02937.753-0.093-0.0930.0000.0000.0000.000
123A130SER0-0.010-0.01336.6220.1730.1730.0000.0000.0000.000
124A131ASP-1-0.889-0.93534.050-8.660-8.6600.0000.0000.0000.000
125A132PRO0-0.033-0.02529.744-0.064-0.0640.0000.0000.0000.000
126A133GLY00.0340.02029.868-0.153-0.1530.0000.0000.0000.000
127A134SER0-0.042-0.03030.5790.1670.1670.0000.0000.0000.000
128A135ALA00.031-0.00634.132-0.144-0.1440.0000.0000.0000.000
129A136PRO0-0.042-0.00736.8370.0960.0960.0000.0000.0000.000
130A137GLU-1-0.865-0.93640.440-7.193-7.1930.0000.0000.0000.000
131A138PRO0-0.052-0.01641.7440.0810.0810.0000.0000.0000.000
132A139GLN0-0.036-0.02444.2410.1980.1980.0000.0000.0000.000
133A140THR0-0.025-0.03147.481-0.075-0.0750.0000.0000.0000.000
134A141ASP-1-0.800-0.88850.177-5.775-5.7750.0000.0000.0000.000
135A142PRO0-0.009-0.01052.8400.0160.0160.0000.0000.0000.000
136A143SER0-0.102-0.05654.0620.0540.0540.0000.0000.0000.000
137A144VAL0-0.054-0.02549.903-0.035-0.0350.0000.0000.0000.000
138A145ASP-1-0.666-0.81652.050-5.830-5.8300.0000.0000.0000.000
139A146VAL0-0.030-0.00746.173-0.014-0.0140.0000.0000.0000.000
140A147ILE00.0090.01146.471-0.025-0.0250.0000.0000.0000.000
141A148ALA00.0040.00241.611-0.046-0.0460.0000.0000.0000.000
142A149TRP0-0.014-0.01438.459-0.006-0.0060.0000.0000.0000.000
143A150ALA0-0.009-0.00333.8890.0160.0160.0000.0000.0000.000
144A151HIS00.0380.04334.966-0.100-0.1000.0000.0000.0000.000
145A152ASN00.0460.01527.890-0.062-0.0620.0000.0000.0000.000
146A153GLU-1-0.717-0.79129.879-9.649-9.6490.0000.0000.0000.000
147A154THR0-0.044-0.04424.814-0.265-0.2650.0000.0000.0000.000
148A155SER0-0.128-0.08825.115-0.500-0.5000.0000.0000.0000.000
149A156THR00.0280.00725.245-0.401-0.4010.0000.0000.0000.000
150A157GLY00.0510.04426.139-0.196-0.1960.0000.0000.0000.000
151A158VAL0-0.0220.01026.8860.0320.0320.0000.0000.0000.000
152A159ALA0-0.033-0.01230.6940.0480.0480.0000.0000.0000.000
153A160VAL00.0320.01032.8210.0950.0950.0000.0000.0000.000
154A161ALA0-0.024-0.01236.6010.0100.0100.0000.0000.0000.000
155A162VAL00.002-0.00138.6750.0420.0420.0000.0000.0000.000
156A163ARG10.9530.96041.3057.0557.0550.0000.0000.0000.000
157A164ARG10.8750.91545.0155.9845.9840.0000.0000.0000.000
158A165PRO0-0.047-0.01946.8930.0710.0710.0000.0000.0000.000
159A166GLU-1-0.924-0.93849.482-5.501-5.5010.0000.0000.0000.000
160A167GLY00.0080.01453.161-0.009-0.0090.0000.0000.0000.000
161A168SER0-0.066-0.06350.208-0.105-0.1050.0000.0000.0000.000
162A169ASP-1-0.897-0.94652.160-5.606-5.6060.0000.0000.0000.000
163A170ASP-1-0.932-0.96155.039-5.394-5.3940.0000.0000.0000.000
164A171ALA0-0.041-0.02651.591-0.058-0.0580.0000.0000.0000.000
165A172LEU0-0.010-0.00249.626-0.076-0.0760.0000.0000.0000.000
166A173VAL00.0400.02644.582-0.123-0.1230.0000.0000.0000.000
167A174VAL0-0.029-0.02242.405-0.044-0.0440.0000.0000.0000.000
168A175ILE0-0.023-0.01238.100-0.120-0.1200.0000.0000.0000.000
169A176ASP-1-0.799-0.86334.194-8.632-8.6320.0000.0000.0000.000
170A177ALA00.0720.02034.776-0.142-0.1420.0000.0000.0000.000
171A178THR0-0.068-0.06229.850-0.202-0.2020.0000.0000.0000.000
172A179SER0-0.062-0.02627.621-0.349-0.3490.0000.0000.0000.000
173A180GLY00.0430.03229.354-0.211-0.2110.0000.0000.0000.000
174A181ALA00.0570.02632.1300.0550.0550.0000.0000.0000.000
175A182GLY00.009-0.00132.172-0.235-0.2350.0000.0000.0000.000
176A183GLY0-0.012-0.01530.256-0.173-0.1730.0000.0000.0000.000
177A184LEU0-0.0200.00831.047-0.145-0.1450.0000.0000.0000.000
178A185PRO00.0240.01133.7290.1120.1120.0000.0000.0000.000
179A186VAL0-0.034-0.03637.475-0.063-0.0630.0000.0000.0000.000
180A187ASP-1-0.830-0.89840.222-6.403-6.4030.0000.0000.0000.000
181A188ILE00.009-0.00141.250-0.038-0.0380.0000.0000.0000.000
182A189ALA00.0480.03544.7760.0500.0500.0000.0000.0000.000
183A190GLU-1-0.888-0.92245.078-6.207-6.2070.0000.0000.0000.000
184A191THR0-0.099-0.06242.330-0.134-0.1340.0000.0000.0000.000
185A192ASP-1-0.724-0.82045.689-5.975-5.9750.0000.0000.0000.000
186A193ALA0-0.006-0.01643.8060.0400.0400.0000.0000.0000.000
187A194TYR00.0400.01436.543-0.159-0.1590.0000.0000.0000.000
188A195TYR00.0080.00436.729-0.083-0.0830.0000.0000.0000.000
189A196PHE00.002-0.00133.374-0.226-0.2260.0000.0000.0000.000
190A197ALA00.007-0.01031.0100.1460.1460.0000.0000.0000.000
191A198PRO00.0190.00930.442-0.142-0.1420.0000.0000.0000.000
192A199GLN00.0030.01925.4900.0800.0800.0000.0000.0000.000
193A200LYS10.8940.95425.01310.04310.0430.0000.0000.0000.000
194A201ASN0-0.001-0.00626.451-0.396-0.3960.0000.0000.0000.000
195A202PHE00.0220.00128.3680.0410.0410.0000.0000.0000.000
196A203ALA0-0.0030.00725.6950.1300.1300.0000.0000.0000.000
197A204SER00.0260.01626.542-0.124-0.1240.0000.0000.0000.000
198A205ASP-1-0.866-0.93926.214-10.922-10.9220.0000.0000.0000.000
199A206GLY0-0.050-0.03127.4650.2230.2230.0000.0000.0000.000
200A207GLY0-0.030-0.02528.9650.1550.1550.0000.0000.0000.000
201A208LEU0-0.012-0.00232.3200.2570.2570.0000.0000.0000.000
202A209TRP0-0.005-0.00233.706-0.233-0.2330.0000.0000.0000.000
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