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

tag_button

FMODB ID: 87MMY

Calculation Name: 6B0B-A-Xray547

Preferred Name:

Target Type:

Ligand Name: zinc ion

Ligand 3-letter code: ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6B0B

Chain ID: A

ChEMBL ID:

UniProt ID: Q6NTF7

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 180
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2104989.003854
FMO2-HF: Nuclear repulsion 2028096.093616
FMO2-HF: Total energy -76892.910238
FMO2-MP2: Total energy -77110.866664


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:3:LEU)


Summations of interaction energy for fragment #1(A:3:LEU)
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.
-76.633-74.9527.266-16.461-12.488-0.165
Interaction energy analysis for fragmet #1(A:3:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.793 / q_NPA : 0.886
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].
3A5THR00.0430.0283.8580.8492.128-0.019-0.634-0.6270.001
44A46TYR0-0.046-0.0302.2573.7544.4911.073-0.439-1.370-0.001
146A148PHE0-0.021-0.0173.840-5.049-4.7020.000-0.071-0.2760.000
147A149VAL0-0.095-0.0452.317-32.661-30.9862.532-2.199-2.008-0.029
148A150ASP-1-0.787-0.8751.805-130.791-133.36023.681-13.000-8.112-0.135
149A151HIS00.0110.0094.0448.4248.638-0.001-0.118-0.095-0.001
4A6ALA00.0900.0366.9761.9551.9550.0000.0000.0000.000
5A7GLU-1-0.886-0.9619.325-18.475-18.4750.0000.0000.0000.000
6A8THR00.026-0.0058.5642.6382.6380.0000.0000.0000.000
7A9PHE00.0830.0528.5891.8171.8170.0000.0000.0000.000
8A10ARG10.9070.96110.11020.82320.8230.0000.0000.0000.000
9A11LEU0-0.063-0.02513.3592.0442.0440.0000.0000.0000.000
10A12GLN0-0.026-0.00411.4872.6292.6290.0000.0000.0000.000
11A13PHE00.0720.0278.6581.5361.5360.0000.0000.0000.000
12A14ASN0-0.070-0.00313.8882.1922.1920.0000.0000.0000.000
13A15ASN0-0.036-0.02616.960-0.203-0.2030.0000.0000.0000.000
14A16LYS10.8400.91619.80013.09613.0960.0000.0000.0000.000
15A17ARG10.9600.97123.24310.56310.5630.0000.0000.0000.000
16A18ARG10.9790.99226.48910.41710.4170.0000.0000.0000.000
17A19LEU00.0230.02022.576-0.228-0.2280.0000.0000.0000.000
18A20ARG10.8360.90021.20714.45914.4590.0000.0000.0000.000
19A21ARG11.0120.99524.08112.15512.1550.0000.0000.0000.000
20A22PRO00.0660.04422.0890.4120.4120.0000.0000.0000.000
21A23TYR00.002-0.00923.886-0.324-0.3240.0000.0000.0000.000
22A24TYR0-0.015-0.02122.966-0.055-0.0550.0000.0000.0000.000
23A25PRO00.0320.03519.373-0.128-0.1280.0000.0000.0000.000
24A26ARG10.8920.95617.07914.03714.0370.0000.0000.0000.000
25A27LYS10.9220.96911.99523.70223.7020.0000.0000.0000.000
26A28ALA0-0.010-0.01114.703-0.610-0.6100.0000.0000.0000.000
27A29LEU0-0.007-0.0108.235-0.478-0.4780.0000.0000.0000.000
28A30LEU00.0130.01810.6881.4661.4660.0000.0000.0000.000
29A31CYS0-0.033-0.0157.432-3.481-3.4810.0000.0000.0000.000
30A32TYR00.0370.0208.4932.2092.2090.0000.0000.0000.000
31A33GLN00.0600.0339.351-5.535-5.5350.0000.0000.0000.000
32A34LEU00.0320.02111.2782.0662.0660.0000.0000.0000.000
33A35THR0-0.033-0.05313.292-0.555-0.5550.0000.0000.0000.000
34A36PRO00.0500.02914.8791.0571.0570.0000.0000.0000.000
35A37GLN0-0.018-0.02218.025-0.039-0.0390.0000.0000.0000.000
36A38ASN0-0.034-0.02019.8610.0030.0030.0000.0000.0000.000
37A39GLY00.0680.03820.7680.6390.6390.0000.0000.0000.000
38A40SER0-0.058-0.02218.646-0.384-0.3840.0000.0000.0000.000
39A41THR0-0.022-0.00414.608-0.467-0.4670.0000.0000.0000.000
40A42PRO0-0.042-0.01611.909-0.220-0.2200.0000.0000.0000.000
41A43THR00.0380.0159.542-1.033-1.0330.0000.0000.0000.000
42A44ARG10.8110.8835.47438.89238.8920.0000.0000.0000.000
43A45GLY00.0380.0314.850-2.916-2.9160.0000.0000.0000.000
45A47PHE00.0570.0396.7060.3440.3440.0000.0000.0000.000
46A48GLU-1-0.858-0.9239.305-25.596-25.5960.0000.0000.0000.000
47A49ASN00.005-0.01310.7870.9080.9080.0000.0000.0000.000
48A50LYS10.8980.94210.86423.13823.1380.0000.0000.0000.000
49A51LYS10.9330.94315.13917.03917.0390.0000.0000.0000.000
50A52GLU-1-0.871-0.92618.503-13.099-13.0990.0000.0000.0000.000
51A53CYS0-0.0140.01517.2450.4250.4250.0000.0000.0000.000
52A54HIS10.8820.92716.67713.78313.7830.0000.0000.0000.000
53A55ALA00.0850.03212.7710.0920.0920.0000.0000.0000.000
54A56GLU-1-0.851-0.94214.203-18.053-18.0530.0000.0000.0000.000
55A57ILE00.0570.02516.7350.1050.1050.0000.0000.0000.000
56A58CYS0-0.082-0.03613.1050.2030.2030.0000.0000.0000.000
57A59PHE00.0100.00512.931-0.131-0.1310.0000.0000.0000.000
58A60ILE00.0110.01214.2050.1090.1090.0000.0000.0000.000
59A61ASN00.007-0.01617.3010.8980.8980.0000.0000.0000.000
60A62GLU-1-0.885-0.9279.815-24.018-24.0180.0000.0000.0000.000
61A63ILE0-0.013-0.01213.5400.3880.3880.0000.0000.0000.000
62A64LYS10.8830.95115.80314.16414.1640.0000.0000.0000.000
63A65SER0-0.048-0.03516.2620.9570.9570.0000.0000.0000.000
64A66MET0-0.068-0.02513.394-0.364-0.3640.0000.0000.0000.000
65A67GLY0-0.0040.01615.3070.2330.2330.0000.0000.0000.000
66A68LEU0-0.024-0.01917.446-0.692-0.6920.0000.0000.0000.000
67A69ASP-1-0.800-0.89819.767-13.702-13.7020.0000.0000.0000.000
68A70GLU-1-0.920-0.97822.416-11.915-11.9150.0000.0000.0000.000
69A71THR0-0.042-0.01224.8460.3740.3740.0000.0000.0000.000
70A72GLN0-0.010-0.01721.951-0.017-0.0170.0000.0000.0000.000
71A73CYS0-0.0170.00223.507-0.156-0.1560.0000.0000.0000.000
72A74TYR0-0.022-0.00817.692-0.454-0.4540.0000.0000.0000.000
73A75GLN00.0160.02119.095-0.040-0.0400.0000.0000.0000.000
74A76VAL0-0.0010.01814.548-1.160-1.1600.0000.0000.0000.000
75A77THR00.0250.00813.3471.3061.3060.0000.0000.0000.000
76A78CYS0-0.026-0.00912.996-2.146-2.1460.0000.0000.0000.000
77A79TYR0-0.048-0.03211.0541.8391.8390.0000.0000.0000.000
78A80LEU00.0320.00511.272-2.256-2.2560.0000.0000.0000.000
79A81THR00.0030.00211.7241.2851.2850.0000.0000.0000.000
80A82TRP0-0.045-0.04314.3352.4992.4990.0000.0000.0000.000
81A83SER00.0310.01017.351-0.379-0.3790.0000.0000.0000.000
82A84PRO00.0450.04818.9360.0350.0350.0000.0000.0000.000
83A85CYS0-0.049-0.02220.3640.7030.7030.0000.0000.0000.000
84A86SER00.0400.00723.537-0.158-0.1580.0000.0000.0000.000
85A87SER00.0320.01625.795-0.139-0.1390.0000.0000.0000.000
86A88CYS0-0.010-0.01020.835-0.030-0.0300.0000.0000.0000.000
87A89ALA00.0290.02622.720-0.319-0.3190.0000.0000.0000.000
88A90TRP00.016-0.00124.0330.1030.1030.0000.0000.0000.000
89A91GLU-1-0.900-0.95123.012-12.429-12.4290.0000.0000.0000.000
90A92LEU0-0.048-0.02418.894-0.198-0.1980.0000.0000.0000.000
91A93VAL00.0020.00122.861-0.092-0.0920.0000.0000.0000.000
92A94ASP-1-0.833-0.91326.098-10.126-10.1260.0000.0000.0000.000
93A95PHE0-0.035-0.02419.3530.1410.1410.0000.0000.0000.000
94A96ILE0-0.029-0.02321.669-0.082-0.0820.0000.0000.0000.000
95A97LYS10.8790.93224.63110.25410.2540.0000.0000.0000.000
96A98ALA0-0.043-0.00226.0890.3560.3560.0000.0000.0000.000
97A99HIS10.7790.89723.67012.47412.4740.0000.0000.0000.000
98A100ASP-1-0.832-0.91325.113-10.719-10.7190.0000.0000.0000.000
99A101HIS0-0.0070.01423.5190.0970.0970.0000.0000.0000.000
100A102LEU0-0.047-0.03018.736-0.729-0.7290.0000.0000.0000.000
101A103ASN00.0120.01321.9960.5750.5750.0000.0000.0000.000
102A104LEU00.0030.00017.490-0.837-0.8370.0000.0000.0000.000
103A105ARG10.9060.96016.74617.88317.8830.0000.0000.0000.000
104A106ILE00.007-0.00317.052-1.184-1.1840.0000.0000.0000.000
105A107PHE00.0410.00816.1990.7020.7020.0000.0000.0000.000
106A108ALA00.0050.01215.775-1.254-1.2540.0000.0000.0000.000
107A109SER0-0.006-0.00915.6570.8500.8500.0000.0000.0000.000
108A110ARG10.8470.92517.59014.40614.4060.0000.0000.0000.000
109A111LEU00.0470.01620.290-0.231-0.2310.0000.0000.0000.000
110A112TYR0-0.078-0.03320.8130.5840.5840.0000.0000.0000.000
111A113TYR00.0890.05022.7040.2900.2900.0000.0000.0000.000
112A114HIS0-0.043-0.02925.5650.3270.3270.0000.0000.0000.000
113A115TRP0-0.011-0.01826.8120.3140.3140.0000.0000.0000.000
114A116CYS00.0040.03130.7290.2540.2540.0000.0000.0000.000
115A117LYS11.0020.98432.0277.8287.8280.0000.0000.0000.000
116A118PRO00.0910.04331.489-0.088-0.0880.0000.0000.0000.000
117A119GLN0-0.003-0.01625.650-0.612-0.6120.0000.0000.0000.000
118A120GLN0-0.035-0.00628.267-0.210-0.2100.0000.0000.0000.000
119A121ASP-1-0.828-0.93630.359-9.806-9.8060.0000.0000.0000.000
120A122GLY0-0.013-0.00328.773-0.125-0.1250.0000.0000.0000.000
121A123LEU0-0.015-0.01024.491-0.369-0.3690.0000.0000.0000.000
122A124ARG10.8100.89626.7759.2459.2450.0000.0000.0000.000
123A125LEU00.0410.03729.4430.0340.0340.0000.0000.0000.000
124A126LEU0-0.0070.02422.9390.0500.0500.0000.0000.0000.000
125A127CYS0-0.065-0.03626.4690.1050.1050.0000.0000.0000.000
126A128GLY00.0230.02027.6770.1850.1850.0000.0000.0000.000
127A129SER0-0.092-0.05929.4330.2100.2100.0000.0000.0000.000
128A130GLN00.0480.01026.4110.0970.0970.0000.0000.0000.000
129A131VAL0-0.031-0.00121.689-0.364-0.3640.0000.0000.0000.000
130A132PRO00.0110.00622.7610.1690.1690.0000.0000.0000.000
131A133VAL00.0020.00521.799-0.775-0.7750.0000.0000.0000.000
132A134GLU-1-0.871-0.94721.432-11.802-11.8020.0000.0000.0000.000
133A135VAL0-0.037-0.02220.439-0.596-0.5960.0000.0000.0000.000
134A136MET0-0.053-0.00816.8430.6600.6600.0000.0000.0000.000
135A137GLY00.019-0.01019.0290.9250.9250.0000.0000.0000.000
136A138PHE00.022-0.00918.556-0.537-0.5370.0000.0000.0000.000
137A139PRO00.0360.02517.534-0.950-0.9500.0000.0000.0000.000
138A140GLU-1-0.766-0.88215.349-17.307-17.3070.0000.0000.0000.000
139A141PHE0-0.043-0.04413.605-1.715-1.7150.0000.0000.0000.000
140A142ALA0-0.030-0.01312.841-1.654-1.6540.0000.0000.0000.000
141A143ASP-1-0.769-0.86812.151-22.324-22.3240.0000.0000.0000.000
142A144CYS0-0.094-0.0499.434-3.878-3.8780.0000.0000.0000.000
143A145TRP0-0.050-0.0287.922-5.470-5.4700.0000.0000.0000.000
144A146GLU-1-0.893-0.9507.474-32.373-32.3730.0000.0000.0000.000
145A147ASN0-0.0270.0017.268-2.883-2.8830.0000.0000.0000.000
150A152GLU-1-0.922-0.9776.453-31.197-31.1970.0000.0000.0000.000
151A153LYS10.9310.9679.05125.94825.9480.0000.0000.0000.000
152A154PRO0-0.0020.01110.4612.4002.4000.0000.0000.0000.000
153A155LEU00.0630.02211.755-1.156-1.1560.0000.0000.0000.000
154A156SER0-0.015-0.00312.5070.8750.8750.0000.0000.0000.000
155A157PHE0-0.028-0.02614.300-0.184-0.1840.0000.0000.0000.000
156A158ASN0-0.039-0.03312.8952.4402.4400.0000.0000.0000.000
157A159PRO00.0400.04414.569-0.935-0.9350.0000.0000.0000.000
158A160TYR00.1160.03916.541-0.227-0.2270.0000.0000.0000.000
159A161LYS10.9010.96118.27714.51914.5190.0000.0000.0000.000
160A162MET00.0300.01214.5811.0961.0960.0000.0000.0000.000
161A163LEU00.0650.04317.7150.2470.2470.0000.0000.0000.000
162A164GLU-1-0.808-0.89520.192-11.593-11.5930.0000.0000.0000.000
163A165GLU-1-0.802-0.89020.054-12.816-12.8160.0000.0000.0000.000
164A166LEU00.0290.04017.1990.2500.2500.0000.0000.0000.000
165A167ASP-1-0.848-0.90220.055-11.912-11.9120.0000.0000.0000.000
166A168LYS10.7150.83023.69612.32512.3250.0000.0000.0000.000
167A169ASN0-0.041-0.03220.1200.1010.1010.0000.0000.0000.000
168A170SER00.0750.04321.6690.5640.5640.0000.0000.0000.000
169A171ARG11.0041.00423.22111.52711.5270.0000.0000.0000.000
170A172ALA0-0.096-0.04526.2060.5770.5770.0000.0000.0000.000
171A173ILE0-0.044-0.02722.0110.5080.5080.0000.0000.0000.000
172A174LYS10.9450.98222.72913.59413.5940.0000.0000.0000.000
173A175ARG10.9340.95425.48710.50710.5070.0000.0000.0000.000
174A176ARG10.8360.91927.58610.59710.5970.0000.0000.0000.000
175A177LEU00.0260.01424.1460.2650.2650.0000.0000.0000.000
176A178ASP-1-0.820-0.92927.301-11.027-11.0270.0000.0000.0000.000
177A179ARG10.8980.94229.7329.3079.3070.0000.0000.0000.000
178A180ILE0-0.071-0.01628.0100.2010.2010.0000.0000.0000.000
179A181LYS10.8730.94226.76511.58811.5880.0000.0000.0000.000
180A182GLN-1-0.881-0.90531.150-8.626-8.6260.0000.0000.0000.000