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: 136JZ

Calculation Name: 4M5B-A-Xray549

Preferred Name:

Target Type:

Ligand Name: hexane-1,6-diol | nickel (ii) ion

Ligand 3-letter code: HEZ | NI

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4M5B

Chain ID: A

ChEMBL ID:

UniProt ID: Q8R9C0

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 214
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230712
Total energy (hartree)
FMO2-HF: Electronic energy -2261850.528062
FMO2-HF: Nuclear repulsion 2183202.000833
FMO2-HF: Total energy -78648.527228
FMO2-MP2: Total energy -78875.623173


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:1:MET)


Summations of interaction energy for fragment #1(A:1: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.
-168.898-158.85746.562-20.328-36.275-0.212
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.725 / q_NPA : 0.874
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].
3A3ILE00.0380.0153.9030.3341.408-0.005-0.396-0.6720.001
57A57ASN0-0.107-0.0484.618-3.817-3.763-0.001-0.005-0.0470.000
60A60ILE0-0.027-0.0044.0971.1501.299-0.001-0.016-0.1330.000
64A64THR00.006-0.0142.786-2.021-0.5240.481-0.889-1.089-0.009
65A65THR00.0620.0291.945-18.694-17.7935.733-3.276-3.357-0.048
66A66ALA0-0.008-0.0062.208-32.033-30.9766.785-3.731-4.111-0.043
67A67HIS00.0490.0072.106-23.857-24.5009.302-3.842-4.817-0.051
68A68ALA00.0130.0244.303-4.554-4.384-0.001-0.018-0.1520.000
69A69ILE0-0.015-0.0362.462-4.379-3.7200.524-0.175-1.0070.000
112A112ASN0-0.045-0.0393.501-3.026-2.5630.244-0.198-0.5080.000
113A113MET0-0.016-0.0152.782-3.383-7.0709.630-1.259-4.6840.002
114A114ALA0-0.009-0.0034.9700.7580.8360.004-0.055-0.0280.000
117A117ALA00.0030.0114.3190.7740.885-0.001-0.020-0.0910.000
147A147ILE0-0.017-0.0032.443-1.474-1.7832.393-0.300-1.785-0.001
148A148ASN0-0.009-0.0312.471-9.788-8.5991.363-1.022-1.529-0.019
149A149ALA00.0060.0105.182-0.222-0.167-0.001-0.004-0.0490.000
150A150ALA0-0.0010.0032.465-0.416-0.0091.563-0.495-1.4750.002
151A151ALA00.0080.0152.340-2.325-0.7642.282-0.981-2.863-0.006
152A152LEU00.0400.0063.3681.0020.5670.0720.669-0.306-0.001
154A154THR00.040-0.0042.325-4.518-2.6652.014-1.333-2.535-0.012
155A155ALA0-0.013-0.0124.8821.5291.554-0.001-0.011-0.0130.000
186A186MET0-0.0180.0132.109-2.929-2.6342.297-1.055-1.537-0.002
190A190HIS0-0.035-0.0422.825-19.533-16.0161.886-1.916-3.487-0.025
4A4PRO00.0310.0166.4153.6933.6930.0000.0000.0000.000
5A5GLU-1-0.701-0.8569.598-20.873-20.8730.0000.0000.0000.000
6A6GLY0-0.037-0.01413.0860.0780.0780.0000.0000.0000.000
7A7TYR00.0050.0008.325-0.284-0.2840.0000.0000.0000.000
8A8LEU0-0.008-0.0089.1000.4020.4020.0000.0000.0000.000
9A9SER00.0480.03812.9200.4990.4990.0000.0000.0000.000
10A10PRO00.0320.01015.784-0.664-0.6640.0000.0000.0000.000
11A11GLN00.0390.01717.723-0.558-0.5580.0000.0000.0000.000
12A12THR00.0180.01212.2930.0690.0690.0000.0000.0000.000
13A13CYS0-0.052-0.02113.093-0.944-0.9440.0000.0000.0000.000
14A14ALA00.0030.00714.159-0.053-0.0530.0000.0000.0000.000
15A15VAL0-0.011-0.00315.5780.3140.3140.0000.0000.0000.000
16A16MET00.0080.00610.0700.7200.7200.0000.0000.0000.000
17A17GLY00.0160.00413.200-0.294-0.2940.0000.0000.0000.000
18A18ALA0-0.044-0.02714.8230.4470.4470.0000.0000.0000.000
19A19ALA0-0.0010.00713.9700.6360.6360.0000.0000.0000.000
20A20MET0-0.0130.00511.6310.1450.1450.0000.0000.0000.000
21A21VAL00.0350.02314.3880.4520.4520.0000.0000.0000.000
22A22PRO0-0.0020.00517.8300.5520.5520.0000.0000.0000.000
23A23VAL00.0330.02313.6390.5550.5550.0000.0000.0000.000
24A24LEU00.0290.01014.3150.5280.5280.0000.0000.0000.000
25A25THR0-0.037-0.02317.7360.8030.8030.0000.0000.0000.000
26A26VAL0-0.073-0.03820.0120.6660.6660.0000.0000.0000.000
27A27ALA00.0230.00417.4730.4460.4460.0000.0000.0000.000
28A28ALA00.0310.01819.6160.3480.3480.0000.0000.0000.000
29A29LYS10.9280.96522.29511.38211.3820.0000.0000.0000.000
30A30LYS10.8900.95621.57712.03912.0390.0000.0000.0000.000
31A31VAL00.0560.04720.6090.3410.3410.0000.0000.0000.000
32A32ASN0-0.055-0.02223.6770.4950.4950.0000.0000.0000.000
33A33LYS10.9310.96926.8029.9809.9800.0000.0000.0000.000
34A34SER0-0.080-0.06525.0100.1490.1490.0000.0000.0000.000
35A35PHE00.0080.01621.179-0.080-0.0800.0000.0000.0000.000
36A36ASP-1-0.832-0.91826.791-9.428-9.4280.0000.0000.0000.000
37A37LYS10.9380.93928.2308.6758.6750.0000.0000.0000.000
38A38LYS10.8990.95329.1058.9978.9970.0000.0000.0000.000
39A39ASP-1-0.795-0.88324.883-11.019-11.0190.0000.0000.0000.000
40A40VAL0-0.027-0.01923.793-0.577-0.5770.0000.0000.0000.000
41A41PRO00.005-0.00622.897-0.605-0.6050.0000.0000.0000.000
42A42ALA00.0500.03621.557-0.508-0.5080.0000.0000.0000.000
43A43MET0-0.0280.00018.820-0.579-0.5790.0000.0000.0000.000
44A44ALA00.0130.02317.956-1.060-1.0600.0000.0000.0000.000
45A45ILE00.0170.00518.468-0.791-0.7910.0000.0000.0000.000
46A46GLY00.0330.00716.193-0.758-0.7580.0000.0000.0000.000
47A47SER0-0.043-0.03914.007-1.370-1.3700.0000.0000.0000.000
48A48ALA00.0370.01813.822-1.454-1.4540.0000.0000.0000.000
49A49PHE00.0090.01212.689-0.975-0.9750.0000.0000.0000.000
50A50ALA00.0360.0089.966-1.216-1.2160.0000.0000.0000.000
51A51PHE0-0.049-0.0259.655-3.304-3.3040.0000.0000.0000.000
52A52THR00.003-0.01410.457-1.480-1.4800.0000.0000.0000.000
53A53ILE0-0.032-0.0208.750-0.842-0.8420.0000.0000.0000.000
54A54MET0-0.094-0.0245.559-4.605-4.6050.0000.0000.0000.000
55A55MET00.0070.0196.733-3.306-3.3060.0000.0000.0000.000
56A56PHE0-0.049-0.0089.3391.2341.2340.0000.0000.0000.000
58A58VAL00.0400.0245.9395.7095.7090.0000.0000.0000.000
59A59PRO00.0270.0005.707-8.476-8.4760.0000.0000.0000.000
61A61PRO00.0070.0007.5800.4870.4870.0000.0000.0000.000
62A62GLY00.0290.01710.6140.4240.4240.0000.0000.0000.000
63A63GLY0-0.010-0.0226.5140.7600.7600.0000.0000.0000.000
70A70GLY00.0500.0186.6912.8552.8550.0000.0000.0000.000
71A71ALA00.0030.0006.9342.0752.0750.0000.0000.0000.000
72A72THR00.0280.0058.8282.3822.3820.0000.0000.0000.000
73A73LEU00.0100.03810.8711.4741.4740.0000.0000.0000.000
74A74LEU00.0330.04612.4341.4681.4680.0000.0000.0000.000
75A75ALA0-0.005-0.00512.1841.1591.1590.0000.0000.0000.000
76A76THR0-0.122-0.08414.1221.2041.2040.0000.0000.0000.000
77A77THR0-0.059-0.03816.6130.8120.8120.0000.0000.0000.000
78A78LEU0-0.0080.00716.3570.6720.6720.0000.0000.0000.000
79A79GLY00.0430.02917.8320.5890.5890.0000.0000.0000.000
80A80PRO0-0.017-0.02114.265-0.460-0.4600.0000.0000.0000.000
81A81TRP0-0.004-0.00914.838-0.588-0.5880.0000.0000.0000.000
82A82ALA00.0770.04716.899-0.382-0.3820.0000.0000.0000.000
83A83ALA00.0240.01912.923-0.442-0.4420.0000.0000.0000.000
84A84SER0-0.011-0.01412.224-0.905-0.9050.0000.0000.0000.000
85A85ILE00.0030.01313.221-0.816-0.8160.0000.0000.0000.000
86A86SER0-0.012-0.01814.718-0.198-0.1980.0000.0000.0000.000
87A87LEU0-0.0230.0068.628-0.617-0.6170.0000.0000.0000.000
88A88THR00.024-0.01510.510-1.749-1.7490.0000.0000.0000.000
89A89LEU0-0.030-0.00611.811-0.202-0.2020.0000.0000.0000.000
90A90ALA00.0140.01210.6970.1040.1040.0000.0000.0000.000
91A91LEU00.004-0.0055.991-1.104-1.1040.0000.0000.0000.000
92A92PHE0-0.014-0.0059.8520.0450.0450.0000.0000.0000.000
93A93ILE00.0150.00013.2220.6210.6210.0000.0000.0000.000
94A94GLN00.0320.0178.243-1.687-1.6870.0000.0000.0000.000
95A95ALA00.0230.01610.9620.5340.5340.0000.0000.0000.000
96A96LEU0-0.046-0.03512.5191.1151.1150.0000.0000.0000.000
97A97LEU0-0.066-0.02715.5821.1631.1630.0000.0000.0000.000
98A98PHE0-0.031-0.02112.6900.6630.6630.0000.0000.0000.000
99A99GLY00.0020.02712.974-0.213-0.2130.0000.0000.0000.000
100A100ASP-1-0.933-0.9646.566-46.000-46.0000.0000.0000.0000.000
101A101GLY0-0.014-0.0268.278-2.014-2.0140.0000.0000.0000.000
102A102GLY0-0.035-0.0248.8673.0423.0420.0000.0000.0000.000
103A103ILE00.020-0.00411.098-0.757-0.7570.0000.0000.0000.000
104A104LEU0-0.033-0.02713.9270.6270.6270.0000.0000.0000.000
105A105ALA0-0.007-0.0079.3510.0900.0900.0000.0000.0000.000
106A106LEU0-0.0020.0119.063-2.361-2.3610.0000.0000.0000.000
107A107GLY0-0.0050.0169.683-0.590-0.5900.0000.0000.0000.000
108A108ALA00.0340.0188.0160.1570.1570.0000.0000.0000.000
109A109ASN00.0440.0284.849-7.526-7.5260.0000.0000.0000.000
110A110SER00.002-0.0185.449-1.409-1.4090.0000.0000.0000.000
111A111PHE00.027-0.0058.2560.9320.9320.0000.0000.0000.000
115A115PHE0-0.019-0.0078.3032.3272.3270.0000.0000.0000.000
116A116ILE00.0080.0016.6620.8680.8680.0000.0000.0000.000
118A118PRO0-0.0150.0006.2481.4111.4110.0000.0000.0000.000
119A119PHE0-0.016-0.0209.8251.7511.7510.0000.0000.0000.000
120A120VAL0-0.0180.0038.8011.2621.2620.0000.0000.0000.000
121A121GLY00.0590.0409.5940.8730.8730.0000.0000.0000.000
122A122TYR0-0.015-0.01610.6951.5391.5390.0000.0000.0000.000
123A123GLY0-0.002-0.00413.8660.9440.9440.0000.0000.0000.000
124A124ILE00.0050.00812.1440.9340.9340.0000.0000.0000.000
125A125TYR00.0350.01714.5520.9710.9710.0000.0000.0000.000
126A126ARG10.8890.93116.30212.82812.8280.0000.0000.0000.000
127A127LEU00.0240.02817.6980.6370.6370.0000.0000.0000.000
128A128MET00.0090.02217.0880.6270.6270.0000.0000.0000.000
129A129LEU00.0050.00619.8910.5450.5450.0000.0000.0000.000
130A130SER0-0.116-0.06422.3540.6240.6240.0000.0000.0000.000
131A131LEU00.0110.00021.3510.5080.5080.0000.0000.0000.000
132A132LYS10.8600.92824.5729.9849.9840.0000.0000.0000.000
133A133LEU00.0500.04420.0130.1140.1140.0000.0000.0000.000
134A134ASN00.0570.02722.420-0.351-0.3510.0000.0000.0000.000
135A135LYS11.0010.99020.81311.07611.0760.0000.0000.0000.000
136A136VAL00.0730.06319.062-0.631-0.6310.0000.0000.0000.000
137A137LEU00.0430.01317.679-0.879-0.8790.0000.0000.0000.000
138A138SER0-0.028-0.02416.911-0.615-0.6150.0000.0000.0000.000
139A139SER0-0.046-0.02914.945-0.769-0.7690.0000.0000.0000.000
140A140ALA00.0230.01413.118-1.212-1.2120.0000.0000.0000.000
141A141ILE00.014-0.00312.189-1.372-1.3720.0000.0000.0000.000
142A142GLY00.009-0.00211.715-0.770-0.7700.0000.0000.0000.000
143A143GLY00.026-0.0018.912-1.186-1.1860.0000.0000.0000.000
144A144TYR0-0.041-0.0267.368-2.413-2.4130.0000.0000.0000.000
145A145VAL00.0250.0077.504-1.998-1.9980.0000.0000.0000.000
146A146GLY00.0180.0147.077-0.810-0.8100.0000.0000.0000.000
153A153ALA0-0.036-0.0126.1021.3591.3590.0000.0000.0000.000
156A156ILE0-0.005-0.0017.0072.7792.7790.0000.0000.0000.000
157A157GLU-1-0.860-0.9337.885-26.996-26.9960.0000.0000.0000.000
158A158LEU0-0.0030.0035.4791.7651.7650.0000.0000.0000.000
159A159GLY00.0150.0029.3952.0012.0010.0000.0000.0000.000
160A160LEU00.002-0.01011.9371.8161.8160.0000.0000.0000.000
161A161GLN0-0.047-0.02212.2362.3262.3260.0000.0000.0000.000
162A162PRO00.0160.01014.5741.1951.1950.0000.0000.0000.000
163A163LEU0-0.027-0.00117.2110.9490.9490.0000.0000.0000.000
164A164LEU0-0.042-0.02616.9500.9120.9120.0000.0000.0000.000
165A165PHE00.005-0.00116.6040.7650.7650.0000.0000.0000.000
166A166HIS10.8920.94819.66912.47612.4760.0000.0000.0000.000
167A167THR00.0250.00322.3570.4810.4810.0000.0000.0000.000
168A168ALA00.0230.00925.968-0.120-0.1200.0000.0000.0000.000
169A169ASN0-0.014-0.00528.1360.3430.3430.0000.0000.0000.000
170A170GLY00.0170.01825.055-0.046-0.0460.0000.0000.0000.000
171A171THR0-0.011-0.00522.513-0.388-0.3880.0000.0000.0000.000
172A172PRO0-0.009-0.00517.9340.1980.1980.0000.0000.0000.000
173A173LEU0-0.021-0.00519.6620.2700.2700.0000.0000.0000.000
174A174TYR00.0010.00514.9500.3310.3310.0000.0000.0000.000
175A175PHE00.0010.0059.2440.0190.0190.0000.0000.0000.000
176A176PRO0-0.004-0.00913.1280.7420.7420.0000.0000.0000.000
177A177TYR0-0.0140.00111.6951.4721.4720.0000.0000.0000.000
178A178GLY00.0850.03313.025-0.930-0.9300.0000.0000.0000.000
179A179LEU00.0160.00812.157-1.081-1.0810.0000.0000.0000.000
180A180ASN0-0.020-0.01413.262-1.222-1.2220.0000.0000.0000.000
181A181VAL0-0.0330.00112.2260.4240.4240.0000.0000.0000.000
182A182ALA00.0420.0239.112-1.236-1.2360.0000.0000.0000.000
183A183ILE00.002-0.0028.703-3.102-3.1020.0000.0000.0000.000
184A184PRO0-0.011-0.00910.061-1.692-1.6920.0000.0000.0000.000
185A185ALA00.0230.0229.364-0.511-0.5110.0000.0000.0000.000
187A187MET0-0.0050.0106.418-4.027-4.0270.0000.0000.0000.000
188A188PHE00.0450.0328.0810.6700.6700.0000.0000.0000.000
189A189ALA00.0460.0396.8320.8890.8890.0000.0000.0000.000
191A191LEU00.0110.0246.1332.1272.1270.0000.0000.0000.000
192A192THR0-0.042-0.0299.4931.7681.7680.0000.0000.0000.000
193A193VAL00.0220.0149.3211.3501.3500.0000.0000.0000.000
194A194ALA0-0.0030.0005.4151.1241.1240.0000.0000.0000.000
195A195GLY00.0400.0157.0320.5060.5060.0000.0000.0000.000
196A196ILE0-0.0010.0007.7202.3042.3040.0000.0000.0000.000
197A197VAL00.0160.0069.2531.5271.5270.0000.0000.0000.000
198A198GLU-1-0.727-0.8546.630-29.217-29.2170.0000.0000.0000.000
199A199ALA0-0.043-0.0098.7762.0622.0620.0000.0000.0000.000
200A200VAL00.0100.00211.7111.5251.5250.0000.0000.0000.000
201A201ILE00.0200.00510.6721.2411.2410.0000.0000.0000.000
202A202THR0-0.060-0.04510.9131.0791.0790.0000.0000.0000.000
203A203GLY00.009-0.00113.5851.0481.0480.0000.0000.0000.000
204A204LEU00.0020.00516.5080.9290.9290.0000.0000.0000.000
205A205VAL00.0220.00516.3930.7660.7660.0000.0000.0000.000
206A206VAL0-0.031-0.02216.9430.8060.8060.0000.0000.0000.000
207A207TYR0-0.058-0.03319.4010.4420.4420.0000.0000.0000.000
208A208TYR00.0310.02621.4500.4800.4800.0000.0000.0000.000
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210A210LEU0-0.115-0.05422.3490.5440.5440.0000.0000.0000.000
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