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: 4G73N

Calculation Name: 1V0D-A-Xray549

Preferred Name:

Target Type:

Ligand Name: lead (ii) ion

Ligand 3-letter code: PB

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1V0D

Chain ID: A

ChEMBL ID:

UniProt ID: O54788

Base Structure: X-ray

Registration Date: 2025-10-11

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 244
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -3017351.775814
FMO2-HF: Nuclear repulsion 2917989.161206
FMO2-HF: Total energy -99362.614608
FMO2-MP2: Total energy -99651.438106


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:85:VAL)


Summations of interaction energy for fragment #1(A:85:VAL)
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.
-0.381000000000014.4625.903-5.45-5.296-0.067
Interaction energy analysis for fragmet #1(A:85:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.866 / q_NPA : 0.919
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].
3A87ASP-1-0.806-0.8821.904-89.513-85.0725.905-5.387-4.959-0.067
4A88ILE00.0570.0394.3498.5408.876-0.001-0.062-0.2730.000
6A90ARG10.8830.9234.74247.50147.567-0.001-0.001-0.0640.000
5A89THR00.007-0.0026.5745.9765.9760.0000.0000.0000.000
7A91PHE0-0.0060.0036.9521.7711.7710.0000.0000.0000.000
8A92LEU00.032-0.0019.8142.2712.2710.0000.0000.0000.000
9A93SER0-0.0350.00212.5342.3022.3020.0000.0000.0000.000
10A94VAL00.000-0.00114.1491.3521.3520.0000.0000.0000.000
11A95PHE0-0.017-0.01813.2891.0341.0340.0000.0000.0000.000
12A96ASN0-0.037-0.01615.4341.3411.3410.0000.0000.0000.000
13A97GLU-1-0.841-0.91818.338-13.062-13.0620.0000.0000.0000.000
14A98PRO00.0110.00621.473-0.028-0.0280.0000.0000.0000.000
15A99HIS10.8090.89523.94212.29412.2940.0000.0000.0000.000
16A100ALA00.0710.05023.2630.2190.2190.0000.0000.0000.000
17A101GLY00.004-0.00825.1700.1550.1550.0000.0000.0000.000
18A102VAL00.0380.01619.3380.1540.1540.0000.0000.0000.000
19A103ILE00.0170.01822.339-0.078-0.0780.0000.0000.0000.000
20A104GLN00.051-0.00324.7790.2550.2550.0000.0000.0000.000
21A105ALA0-0.0040.02522.3730.2740.2740.0000.0000.0000.000
22A106ALA00.0320.00821.2860.0330.0330.0000.0000.0000.000
23A107ARG10.9430.96422.78911.15011.1500.0000.0000.0000.000
24A108GLN0-0.040-0.01726.1440.4360.4360.0000.0000.0000.000
25A109GLN0-0.001-0.00719.776-0.244-0.2440.0000.0000.0000.000
26A110LEU0-0.039-0.01923.395-0.174-0.1740.0000.0000.0000.000
27A111SER0-0.054-0.01625.8140.3630.3630.0000.0000.0000.000
28A112ASP-1-0.948-0.96125.406-11.755-11.7550.0000.0000.0000.000
29A113GLU-1-0.921-0.95126.410-10.746-10.7460.0000.0000.0000.000
30A114GLN00.0040.01421.245-1.072-1.0720.0000.0000.0000.000
31A115ALA00.0480.01521.1700.2500.2500.0000.0000.0000.000
32A116PRO00.0540.02521.907-0.494-0.4940.0000.0000.0000.000
33A117LEU00.017-0.00116.885-0.162-0.1620.0000.0000.0000.000
34A118ARG10.8690.91617.17215.11415.1140.0000.0000.0000.000
35A119GLN00.0120.01118.739-0.088-0.0880.0000.0000.0000.000
36A120LYS10.8390.90119.95313.88613.8860.0000.0000.0000.000
37A121LEU00.0070.00613.090-0.048-0.0480.0000.0000.0000.000
38A122LEU00.0060.00717.785-0.248-0.2480.0000.0000.0000.000
39A123ALA00.0300.01819.7270.2990.2990.0000.0000.0000.000
40A124ASP-1-0.810-0.88718.853-14.108-14.1080.0000.0000.0000.000
41A125LEU0-0.029-0.01415.1430.0430.0430.0000.0000.0000.000
42A126LEU0-0.022-0.00219.3980.3360.3360.0000.0000.0000.000
43A127HIS00.0190.01522.8830.5800.5800.0000.0000.0000.000
44A128HIS0-0.059-0.02318.1600.2330.2330.0000.0000.0000.000
45A129VAL0-0.022-0.00720.1730.2470.2470.0000.0000.0000.000
46A130SER0-0.061-0.03922.8370.6150.6150.0000.0000.0000.000
47A131GLN0-0.0040.00023.6310.8010.8010.0000.0000.0000.000
48A132ASN0-0.006-0.01427.016-0.136-0.1360.0000.0000.0000.000
49A133ILE00.0120.00825.1090.3610.3610.0000.0000.0000.000
50A134THR0-0.0060.00329.3920.1900.1900.0000.0000.0000.000
51A135ALA0-0.0260.01731.6830.3160.3160.0000.0000.0000.000
52A136GLU-1-0.703-0.81134.346-8.614-8.6140.0000.0000.0000.000
53A137THR00.021-0.00137.0480.1960.1960.0000.0000.0000.000
54A138ARG10.7750.85039.3967.1777.1770.0000.0000.0000.000
55A139GLU-1-0.925-0.97041.082-7.090-7.0900.0000.0000.0000.000
56A140GLN00.0210.01537.3100.0430.0430.0000.0000.0000.000
57A141ASP-1-0.822-0.91833.580-9.637-9.6370.0000.0000.0000.000
58A142PRO00.0140.01536.764-0.008-0.0080.0000.0000.0000.000
59A143SER0-0.022-0.02234.992-0.006-0.0060.0000.0000.0000.000
60A144TRP00.004-0.00832.3510.2420.2420.0000.0000.0000.000
61A145PHE0-0.011-0.00835.4790.0610.0610.0000.0000.0000.000
62A146GLU-1-0.849-0.90436.983-8.291-8.2910.0000.0000.0000.000
63A147GLY0-0.008-0.00739.105-0.139-0.1390.0000.0000.0000.000
64A148LEU0-0.0450.00338.9330.0970.0970.0000.0000.0000.000
65A149GLU-1-0.774-0.87342.755-6.460-6.4600.0000.0000.0000.000
66A150SER00.019-0.00245.690-0.147-0.1470.0000.0000.0000.000
67A151ARG10.8610.93247.2646.4966.4960.0000.0000.0000.000
68A152PHE0-0.0270.00642.548-0.048-0.0480.0000.0000.0000.000
69A153ARG11.0010.99643.6476.7766.7760.0000.0000.0000.000
70A154ASN00.014-0.00740.140-0.166-0.1660.0000.0000.0000.000
71A155LYS10.7760.89632.7109.4499.4490.0000.0000.0000.000
72A156SER0-0.002-0.02837.421-0.049-0.0490.0000.0000.0000.000
73A157GLY0-0.044-0.02238.4490.1120.1120.0000.0000.0000.000
74A158TYR00.006-0.01137.2350.0530.0530.0000.0000.0000.000
75A159LEU0-0.006-0.00833.4530.0560.0560.0000.0000.0000.000
76A160ARG10.8500.91138.0927.3547.3540.0000.0000.0000.000
77A161TYR00.0680.03140.6230.1390.1390.0000.0000.0000.000
78A162SER0-0.033-0.01037.8060.1040.1040.0000.0000.0000.000
79A163CYS0-0.0220.00837.7420.0260.0260.0000.0000.0000.000
80A164GLU-1-0.903-0.95739.947-6.659-6.6590.0000.0000.0000.000
81A165SER0-0.080-0.05842.5170.1760.1760.0000.0000.0000.000
82A166ARG10.8190.91134.5888.5318.5310.0000.0000.0000.000
83A167ILE00.0490.04340.6490.1210.1210.0000.0000.0000.000
84A168ARG10.9430.96543.9876.4026.4020.0000.0000.0000.000
85A169GLY0-0.032-0.02045.4740.1540.1540.0000.0000.0000.000
86A170TYR00.027-0.00439.0570.1140.1140.0000.0000.0000.000
87A171LEU00.0160.00946.2140.1040.1040.0000.0000.0000.000
88A172ARG10.8790.96146.6346.5646.5640.0000.0000.0000.000
89A173GLU-1-0.829-0.89945.252-6.657-6.6570.0000.0000.0000.000
90A174VAL00.0170.00948.9520.0800.0800.0000.0000.0000.000
91A175SER00.0050.00351.4760.1380.1380.0000.0000.0000.000
92A176ALA0-0.021-0.00452.7820.1070.1070.0000.0000.0000.000
93A177TYR00.020-0.00152.8340.0650.0650.0000.0000.0000.000
94A178THR00.021-0.00154.9070.0460.0460.0000.0000.0000.000
95A179SER0-0.044-0.02457.7290.0680.0680.0000.0000.0000.000
96A180MET0-0.092-0.04054.2120.0240.0240.0000.0000.0000.000
97A181VAL0-0.0130.01057.937-0.048-0.0480.0000.0000.0000.000
98A182ASP-1-0.856-0.92360.251-4.885-4.8850.0000.0000.0000.000
99A183GLU-1-0.905-0.96463.757-4.686-4.6860.0000.0000.0000.000
100A184ALA0-0.062-0.03466.5020.0170.0170.0000.0000.0000.000
101A185ALA00.0220.01562.5070.0150.0150.0000.0000.0000.000
102A186GLN0-0.089-0.04262.039-0.063-0.0630.0000.0000.0000.000
103A187GLU-1-0.885-0.94762.506-4.792-4.7920.0000.0000.0000.000
104A188GLU-1-0.841-0.93862.017-5.050-5.0500.0000.0000.0000.000
105A189TYR0-0.003-0.01554.255-0.117-0.1170.0000.0000.0000.000
106A190LEU00.0230.01658.531-0.121-0.1210.0000.0000.0000.000
107A191ARG10.8760.94959.7415.0485.0480.0000.0000.0000.000
108A192VAL0-0.036-0.01055.807-0.065-0.0650.0000.0000.0000.000
109A193LEU0-0.0180.00254.458-0.112-0.1120.0000.0000.0000.000
110A194GLY00.0250.00155.550-0.085-0.0850.0000.0000.0000.000
111A195SER0-0.037-0.01856.929-0.009-0.0090.0000.0000.0000.000
112A196MET0-0.0100.00851.747-0.129-0.1290.0000.0000.0000.000
113A197CYS0-0.046-0.01052.153-0.087-0.0870.0000.0000.0000.000
114A198GLN0-0.014-0.01353.582-0.072-0.0720.0000.0000.0000.000
115A199LYS10.9711.00049.6046.0766.0760.0000.0000.0000.000
116A200LEU00.0440.03247.097-0.095-0.0950.0000.0000.0000.000
117A201LYS10.8900.94849.5605.4805.4800.0000.0000.0000.000
118A202SER0-0.077-0.04551.539-0.043-0.0430.0000.0000.0000.000
119A203VAL00.0200.02145.629-0.035-0.0350.0000.0000.0000.000
120A204GLN0-0.016-0.01346.385-0.154-0.1540.0000.0000.0000.000
121A205TYR0-0.011-0.03145.836-0.087-0.0870.0000.0000.0000.000
122A206ASN00.0240.01241.879-0.068-0.0680.0000.0000.0000.000
123A207GLY00.0240.01141.231-0.204-0.2040.0000.0000.0000.000
124A208SER0-0.015-0.01939.803-0.166-0.1660.0000.0000.0000.000
125A209TYR00.0700.03136.994-0.198-0.1980.0000.0000.0000.000
126A210PHE00.010-0.00934.747-0.292-0.2920.0000.0000.0000.000
127A211ASP-1-0.797-0.87435.076-7.930-7.9300.0000.0000.0000.000
128A212ARG10.8090.88031.2359.4169.4160.0000.0000.0000.000
129A213GLY0-0.025-0.01635.1970.1500.1500.0000.0000.0000.000
130A214ALA0-0.0030.01937.4380.2230.2230.0000.0000.0000.000
131A215GLU-1-0.842-0.92137.969-7.798-7.7980.0000.0000.0000.000
132A216ALA0-0.048-0.03735.600-0.136-0.1360.0000.0000.0000.000
133A217SER0-0.013-0.00536.032-0.174-0.1740.0000.0000.0000.000
134A218SER0-0.035-0.00738.4120.1340.1340.0000.0000.0000.000
135A219ARG10.8310.91332.7068.9118.9110.0000.0000.0000.000
136A220LEU00.010-0.00532.128-0.129-0.1290.0000.0000.0000.000
137A221CYS0-0.058-0.01229.774-0.280-0.2800.0000.0000.0000.000
138A222THR0-0.003-0.01926.3160.2570.2570.0000.0000.0000.000
139A223PRO00.0130.00729.7580.2040.2040.0000.0000.0000.000
140A224GLU-1-0.788-0.88327.577-10.433-10.4330.0000.0000.0000.000
141A225GLY0-0.002-0.00629.759-0.042-0.0420.0000.0000.0000.000
142A226TRP0-0.035-0.01421.523-0.071-0.0710.0000.0000.0000.000
143A227PHE00.0240.02126.8290.2360.2360.0000.0000.0000.000
144A228SER0-0.005-0.02623.888-0.721-0.7210.0000.0000.0000.000
145A229CYS-1-0.826-0.77923.798-10.998-10.9980.0000.0000.0000.000
146A230GLN00.0340.00924.962-0.190-0.1900.0000.0000.0000.000
147A231GLY00.0280.00626.170-0.016-0.0160.0000.0000.0000.000
148A232PRO0-0.009-0.01326.8460.2690.2690.0000.0000.0000.000
149A233PHE00.0340.00329.792-0.042-0.0420.0000.0000.0000.000
150A234ASP-1-0.783-0.86331.108-9.344-9.3440.0000.0000.0000.000
151A235LEU0-0.032-0.02025.617-0.232-0.2320.0000.0000.0000.000
152A236GLU-1-0.821-0.90928.333-9.346-9.3460.0000.0000.0000.000
153A237SER0-0.057-0.01823.548-0.362-0.3620.0000.0000.0000.000
154A238CYS0-0.0360.00322.312-0.190-0.1900.0000.0000.0000.000
155A239LEU00.0540.02320.043-0.601-0.6010.0000.0000.0000.000
156A240SER0-0.039-0.03517.834-0.511-0.5110.0000.0000.0000.000
157A241LYS10.9290.96315.24616.15016.1500.0000.0000.0000.000
158A242HIS10.8250.86219.15612.40312.4030.0000.0000.0000.000
159A243SER00.0180.01520.3360.3430.3430.0000.0000.0000.000
160A244ILE00.0080.00522.567-0.196-0.1960.0000.0000.0000.000
161A245ASN00.0570.02124.9740.5110.5110.0000.0000.0000.000
162A246PRO00.0060.03126.890-0.061-0.0610.0000.0000.0000.000
163A247TYR00.0310.00430.0230.2820.2820.0000.0000.0000.000
164A248GLY00.0380.02027.8120.1420.1420.0000.0000.0000.000
165A249ASN00.0330.00827.2210.2200.2200.0000.0000.0000.000
166A250ARG10.9961.00729.7848.9038.9030.0000.0000.0000.000
167A251GLU-1-0.935-0.96127.547-10.603-10.6030.0000.0000.0000.000
168A252SER0-0.027-0.03327.417-0.002-0.0020.0000.0000.0000.000
169A253ARG10.8330.90528.7968.5358.5350.0000.0000.0000.000
170A254ILE0-0.024-0.00132.1710.2530.2530.0000.0000.0000.000
171A255LEU00.0580.03126.1540.1580.1580.0000.0000.0000.000
172A256PHE0-0.0130.01529.931-0.024-0.0240.0000.0000.0000.000
173A257SER0-0.045-0.03431.2840.2860.2860.0000.0000.0000.000
174A258THR0-0.092-0.05829.6530.0620.0620.0000.0000.0000.000
175A259TRP00.0070.01124.567-0.132-0.1320.0000.0000.0000.000
176A260ASN0-0.027-0.01131.0110.4090.4090.0000.0000.0000.000
177A261LEU00.0080.00533.021-0.220-0.2200.0000.0000.0000.000
178A262ASP-1-0.756-0.85834.182-8.202-8.2020.0000.0000.0000.000
179A263HIS0-0.024-0.00936.028-0.134-0.1340.0000.0000.0000.000
180A264ILE0-0.012-0.01335.143-0.035-0.0350.0000.0000.0000.000
181A265ILE00.0220.00537.9130.0090.0090.0000.0000.0000.000
182A266GLU-1-0.773-0.89940.119-7.381-7.3810.0000.0000.0000.000
183A267LYS00.0050.00142.2920.2320.2320.0000.0000.0000.000
184A268LYS10.8760.92344.7716.6656.6650.0000.0000.0000.000
185A269ARG10.9070.97244.1736.8296.8290.0000.0000.0000.000
186A270THR00.0380.01045.0110.0580.0580.0000.0000.0000.000
187A271VAL0-0.0110.00745.1030.1390.1390.0000.0000.0000.000
188A272VAL00.004-0.00448.0300.1040.1040.0000.0000.0000.000
189A273PRO00.0130.01849.4980.1140.1140.0000.0000.0000.000
190A274THR00.006-0.01450.1610.1060.1060.0000.0000.0000.000
191A275LEU0-0.064-0.02352.1070.0790.0790.0000.0000.0000.000
192A276ALA00.001-0.00953.9080.0920.0920.0000.0000.0000.000
193A277GLU-1-0.884-0.94655.596-5.223-5.2230.0000.0000.0000.000
194A278ALA0-0.047-0.02455.4920.0860.0860.0000.0000.0000.000
195A279ILE0-0.026-0.03257.3260.0650.0650.0000.0000.0000.000
196A280GLN00.0110.01459.8820.0800.0800.0000.0000.0000.000
197A281ASP-1-0.797-0.84460.269-5.016-5.0160.0000.0000.0000.000
198A282GLY00.0190.01862.2450.0770.0770.0000.0000.0000.000
199A283ARG10.7150.81559.8675.1745.1740.0000.0000.0000.000
200A284GLU-1-0.856-0.92461.122-5.099-5.0990.0000.0000.0000.000
201A285VAL00.0300.01455.681-0.086-0.0860.0000.0000.0000.000
202A286ASN0-0.052-0.03352.2970.0600.0600.0000.0000.0000.000
203A287TRP00.0300.00652.765-0.195-0.1950.0000.0000.0000.000
204A288GLU-1-0.820-0.89651.493-5.746-5.7460.0000.0000.0000.000
205A289TYR00.0290.02345.620-0.155-0.1550.0000.0000.0000.000
206A290PHE00.0630.02547.901-0.158-0.1580.0000.0000.0000.000
207A291TYR00.003-0.01746.984-0.075-0.0750.0000.0000.0000.000
208A292SER0-0.082-0.06744.931-0.072-0.0720.0000.0000.0000.000
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