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: ZLYRN

Calculation Name: 2X27-X-Xray547

Preferred Name:

Target Type:

Ligand Name: (hydroxyethyloxy)tri(ethyloxy)octane | nickel (ii) ion

Ligand 3-letter code: C8E | NI

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2X27

Chain ID: X

ChEMBL ID:

UniProt ID: Q9HWW1

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 212
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2262191.709671
FMO2-HF: Nuclear repulsion 2180925.318479
FMO2-HF: Total energy -81266.391192
FMO2-MP2: Total energy -81503.390285


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:ASP)


Summations of interaction energy for fragment #1(A:1:ASP)
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.
-17.823-14.8484.486-3.465-3.9960.038
Interaction energy analysis for fragmet #1(A:1:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.047 / q_NPA : -0.042
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].
3A3GLN00.0140.0063.8688.45710.440-0.013-0.889-1.081-0.002
6A6LYS10.8880.9572.028-47.537-46.8894.500-2.550-2.5970.040
161A161GLU-1-0.858-0.9194.88112.33012.439-0.001-0.002-0.1060.000
211A211HIS00.0470.0084.6140.6140.8490.000-0.024-0.2120.000
4A4GLY00.0230.0136.3891.2091.2090.0000.0000.0000.000
5A5HIS0-0.026-0.0257.1842.9802.9800.0000.0000.0000.000
7A7ALA0-0.004-0.0118.4980.2500.2500.0000.0000.0000.000
8A8GLY00.0210.0218.7881.1221.1220.0000.0000.0000.000
9A9ASP-1-0.803-0.9177.27011.93111.9310.0000.0000.0000.000
10A10PHE0-0.022-0.01610.007-1.410-1.4100.0000.0000.0000.000
11A11ILE00.002-0.01211.6910.7510.7510.0000.0000.0000.000
12A12ILE0-0.0190.01114.535-0.506-0.5060.0000.0000.0000.000
13A13ARG10.8090.84716.558-2.079-2.0790.0000.0000.0000.000
14A14GLY00.0090.00819.555-0.120-0.1200.0000.0000.0000.000
15A15GLY0-0.010-0.01322.6480.0500.0500.0000.0000.0000.000
16A16PHE0-0.0280.00325.345-0.035-0.0350.0000.0000.0000.000
17A17ALA00.0470.01828.3300.0280.0280.0000.0000.0000.000
18A18THR0-0.039-0.02930.041-0.019-0.0190.0000.0000.0000.000
19A19VAL0-0.020-0.00333.4080.0100.0100.0000.0000.0000.000
20A20ASP-1-0.865-0.96935.6480.4490.4490.0000.0000.0000.000
21A21PRO0-0.042-0.02038.1330.0020.0020.0000.0000.0000.000
22A22ASP-1-0.928-0.94640.3360.3370.3370.0000.0000.0000.000
23A23ASP-1-0.861-0.91742.1390.3500.3500.0000.0000.0000.000
24A24SER0-0.063-0.03344.974-0.033-0.0330.0000.0000.0000.000
25A25SER00.020-0.01847.8180.0110.0110.0000.0000.0000.000
26A26SER0-0.089-0.04250.526-0.013-0.0130.0000.0000.0000.000
27A27ASP-1-0.820-0.91353.5460.2130.2130.0000.0000.0000.000
28A28ILE00.0060.00955.6940.0050.0050.0000.0000.0000.000
29A29LYS10.8610.93357.443-0.247-0.2470.0000.0000.0000.000
30A30LEU00.0450.02659.5100.0090.0090.0000.0000.0000.000
31A31ASP-1-0.756-0.87862.3740.2130.2130.0000.0000.0000.000
32A32GLY0-0.046-0.01961.031-0.006-0.0060.0000.0000.0000.000
33A33ALA0-0.011-0.01261.831-0.001-0.0010.0000.0000.0000.000
34A34LYS10.9470.97557.206-0.215-0.2150.0000.0000.0000.000
35A35GLN00.0060.00461.019-0.016-0.0160.0000.0000.0000.000
36A36ARG10.8690.94360.686-0.175-0.1750.0000.0000.0000.000
37A37GLY00.0310.01859.072-0.006-0.0060.0000.0000.0000.000
38A38THR0-0.088-0.04258.0350.0010.0010.0000.0000.0000.000
39A39LYS10.9580.97052.030-0.262-0.2620.0000.0000.0000.000
40A40ALA0-0.021-0.01851.171-0.004-0.0040.0000.0000.0000.000
41A41THR0-0.019-0.00948.772-0.013-0.0130.0000.0000.0000.000
42A42VAL0-0.040-0.02943.4870.0010.0010.0000.0000.0000.000
43A43ASP-1-0.809-0.88244.2480.4430.4430.0000.0000.0000.000
44A44SER00.0290.01939.0390.0190.0190.0000.0000.0000.000
45A45ASP-1-0.775-0.86738.2050.6310.6310.0000.0000.0000.000
46A46THR0-0.084-0.04432.9350.0280.0280.0000.0000.0000.000
47A47GLN0-0.0190.02232.8890.0260.0260.0000.0000.0000.000
48A48LEU0-0.043-0.01526.2660.0370.0370.0000.0000.0000.000
49A49GLY00.0460.01327.389-0.021-0.0210.0000.0000.0000.000
50A50LEU0-0.034-0.03723.9160.1070.1070.0000.0000.0000.000
51A51THR00.0100.01120.620-0.085-0.0850.0000.0000.0000.000
52A52PHE0-0.015-0.01319.3240.2310.2310.0000.0000.0000.000
53A53THR00.0300.01615.547-0.253-0.2530.0000.0000.0000.000
54A54TYR0-0.027-0.00713.3950.4470.4470.0000.0000.0000.000
55A55MET0-0.0180.00611.721-0.690-0.6900.0000.0000.0000.000
56A56PHE00.0000.00113.1310.2950.2950.0000.0000.0000.000
57A57ALA0-0.012-0.02013.800-0.247-0.2470.0000.0000.0000.000
58A58ASP-1-0.838-0.9189.6261.9211.9210.0000.0000.0000.000
59A59LYS10.7930.88612.0560.3240.3240.0000.0000.0000.000
60A60TRP0-0.025-0.00815.163-0.195-0.1950.0000.0000.0000.000
61A61GLY00.0670.03415.9360.3340.3340.0000.0000.0000.000
62A62VAL0-0.042-0.01917.374-0.298-0.2980.0000.0000.0000.000
63A63GLU0-0.049-0.06419.2080.3240.3240.0000.0000.0000.000
64A64LEU0-0.0160.01221.430-0.173-0.1730.0000.0000.0000.000
65A65VAL00.0170.00523.4100.1580.1580.0000.0000.0000.000
66A66ALA00.000-0.01225.986-0.085-0.0850.0000.0000.0000.000
67A67ALA00.0320.01328.0500.0390.0390.0000.0000.0000.000
68A68THR0-0.054-0.03730.2750.0140.0140.0000.0000.0000.000
69A69PRO0-0.035-0.03732.812-0.014-0.0140.0000.0000.0000.000
70A70PHE00.0270.02232.385-0.003-0.0030.0000.0000.0000.000
71A71ASN0-0.078-0.05337.638-0.038-0.0380.0000.0000.0000.000
72A72HIS00.0260.01739.3820.0310.0310.0000.0000.0000.000
73A73GLN0-0.025-0.02743.604-0.008-0.0080.0000.0000.0000.000
74A74VAL0-0.0020.00547.208-0.004-0.0040.0000.0000.0000.000
75A75ASP-1-0.797-0.91449.1730.3070.3070.0000.0000.0000.000
76A76VAL0-0.032-0.02252.048-0.001-0.0010.0000.0000.0000.000
77A77LYS10.8440.90353.148-0.281-0.2810.0000.0000.0000.000
78A78GLY00.0360.03957.380-0.001-0.0010.0000.0000.0000.000
79A79LEU0-0.023-0.02260.107-0.001-0.0010.0000.0000.0000.000
80A80GLY00.0340.01762.543-0.004-0.0040.0000.0000.0000.000
81A81PRO0-0.0260.01359.3860.0030.0030.0000.0000.0000.000
82A82GLY00.0230.01861.465-0.009-0.0090.0000.0000.0000.000
83A83LEU0-0.041-0.02761.0400.0040.0040.0000.0000.0000.000
84A84ASP-1-0.773-0.88757.5380.2540.2540.0000.0000.0000.000
85A85GLY0-0.0060.00555.3060.0010.0010.0000.0000.0000.000
86A86LYS10.8460.92150.097-0.376-0.3760.0000.0000.0000.000
87A87LEU0-0.080-0.02752.896-0.016-0.0160.0000.0000.0000.000
88A88ALA0-0.003-0.02950.896-0.008-0.0080.0000.0000.0000.000
89A89ASP-1-0.797-0.85746.8820.4050.4050.0000.0000.0000.000
90A90ILE0-0.027-0.01643.542-0.010-0.0100.0000.0000.0000.000
91A91LYS10.8220.90840.844-0.529-0.5290.0000.0000.0000.000
92A92GLN00.020-0.00336.7180.0110.0110.0000.0000.0000.000
93A93LEU0-0.023-0.00133.6010.0370.0370.0000.0000.0000.000
94A94PRO00.0550.04132.438-0.018-0.0180.0000.0000.0000.000
95A95PRO0-0.045-0.00530.3430.0580.0580.0000.0000.0000.000
96A96THR00.038-0.00228.691-0.079-0.0790.0000.0000.0000.000
97A97LEU0-0.042-0.01524.8220.1160.1160.0000.0000.0000.000
98A98LEU00.0050.00024.205-0.109-0.1090.0000.0000.0000.000
99A99LEU0-0.042-0.00721.5500.1520.1520.0000.0000.0000.000
100A100GLN00.0300.00019.0450.1690.1690.0000.0000.0000.000
101A101TYR0-0.011-0.00919.1890.0180.0180.0000.0000.0000.000
102A102TYR00.0470.00215.1160.0780.0780.0000.0000.0000.000
103A103PRO0-0.007-0.00716.048-0.085-0.0850.0000.0000.0000.000
104A104MET0-0.0250.00514.192-0.325-0.3250.0000.0000.0000.000
105A105GLY00.0830.07611.694-0.051-0.0510.0000.0000.0000.000
106A106GLY00.0270.0108.907-0.646-0.6460.0000.0000.0000.000
107A107THR0-0.101-0.0639.224-1.595-1.5950.0000.0000.0000.000
108A108ASN0-0.006-0.0166.3200.7450.7450.0000.0000.0000.000
109A109SER0-0.051-0.0278.3650.0480.0480.0000.0000.0000.000
110A110ALA00.0830.04011.4090.7720.7720.0000.0000.0000.000
111A111PHE0-0.0310.00212.2140.4530.4530.0000.0000.0000.000
112A112GLN0-0.037-0.02511.543-0.181-0.1810.0000.0000.0000.000
113A113PRO00.0240.00715.3870.1610.1610.0000.0000.0000.000
114A114TYR00.000-0.00818.0550.0690.0690.0000.0000.0000.000
115A115GLY00.0150.01520.093-0.094-0.0940.0000.0000.0000.000
116A116GLY0-0.010-0.00222.5050.0820.0820.0000.0000.0000.000
117A117LEU0-0.017-0.00924.631-0.087-0.0870.0000.0000.0000.000
118A118GLY0-0.001-0.00926.7910.0820.0820.0000.0000.0000.000
119A119VAL0-0.0170.01128.935-0.068-0.0680.0000.0000.0000.000
120A120ASN00.0450.03830.8050.0390.0390.0000.0000.0000.000
121A121TYR0-0.089-0.05733.118-0.029-0.0290.0000.0000.0000.000
122A122THR0-0.003-0.03634.6010.0470.0470.0000.0000.0000.000
123A123THR0-0.057-0.03037.255-0.040-0.0400.0000.0000.0000.000
124A124PHE00.025-0.01439.6940.0170.0170.0000.0000.0000.000
125A125PHE0-0.034-0.01538.541-0.008-0.0080.0000.0000.0000.000
126A126ASP-1-0.836-0.91244.3070.5330.5330.0000.0000.0000.000
127A127GLU-1-0.785-0.88846.3570.4370.4370.0000.0000.0000.000
128A128ASP-1-0.894-0.93148.7400.3590.3590.0000.0000.0000.000
129A129LEU0-0.026-0.01651.051-0.008-0.0080.0000.0000.0000.000
130A130ALA00.0610.02654.203-0.001-0.0010.0000.0000.0000.000
131A131SER00.003-0.01655.479-0.007-0.0070.0000.0000.0000.000
132A132ASN00.0200.00558.451-0.001-0.0010.0000.0000.0000.000
133A133ARG10.7520.87356.803-0.280-0.2800.0000.0000.0000.000
134A134LYS10.8830.93654.408-0.350-0.3500.0000.0000.0000.000
135A135ALA0-0.029-0.01260.442-0.008-0.0080.0000.0000.0000.000
136A136GLN0-0.017-0.01061.881-0.004-0.0040.0000.0000.0000.000
137A137GLY00.0430.02163.494-0.005-0.0050.0000.0000.0000.000
138A138PHE0-0.0050.00058.184-0.001-0.0010.0000.0000.0000.000
139A139SER0-0.023-0.02958.0470.0060.0060.0000.0000.0000.000
140A140SER0-0.026-0.02855.058-0.001-0.0010.0000.0000.0000.000
141A141MET00.0040.02050.143-0.006-0.0060.0000.0000.0000.000
142A142LYS10.8240.90448.747-0.409-0.4090.0000.0000.0000.000
143A143LEU00.0300.01945.233-0.022-0.0220.0000.0000.0000.000
144A144GLN0-0.068-0.02345.535-0.004-0.0040.0000.0000.0000.000
145A145ASP-1-0.772-0.84241.3870.5640.5640.0000.0000.0000.000
146A146SER00.0170.01439.052-0.039-0.0390.0000.0000.0000.000
147A147TRP0-0.063-0.04734.0790.0510.0510.0000.0000.0000.000
148A148GLY00.0550.05236.324-0.038-0.0380.0000.0000.0000.000
149A149LEU0-0.093-0.04232.6410.0480.0480.0000.0000.0000.000
150A150ALA00.0310.01630.213-0.001-0.0010.0000.0000.0000.000
151A151GLY0-0.028-0.02029.122-0.003-0.0030.0000.0000.0000.000
152A152GLU-1-0.747-0.82623.2441.2751.2750.0000.0000.0000.000
153A153LEU0-0.017-0.01324.876-0.049-0.0490.0000.0000.0000.000
154A154GLY00.0480.02522.7620.0190.0190.0000.0000.0000.000
155A155PHE0-0.059-0.02919.063-0.099-0.0990.0000.0000.0000.000
156A156ASP-1-0.704-0.78415.1432.6412.6410.0000.0000.0000.000
157A157TYR0-0.039-0.03115.621-0.258-0.2580.0000.0000.0000.000
158A158MET0-0.058-0.0078.704-0.051-0.0510.0000.0000.0000.000
159A159LEU0-0.015-0.01812.614-0.526-0.5260.0000.0000.0000.000
160A160ASN00.0060.00110.0970.4670.4670.0000.0000.0000.000
162A162HIS10.8160.9075.308-12.351-12.3510.0000.0000.0000.000
163A163ALA00.0410.0299.075-0.626-0.6260.0000.0000.0000.000
164A164LEU0-0.014-0.00912.4010.0430.0430.0000.0000.0000.000
165A165PHE00.0240.00914.643-0.142-0.1420.0000.0000.0000.000
166A166ASN0-0.031-0.04417.7720.0060.0060.0000.0000.0000.000
167A167MET0-0.0060.00020.135-0.155-0.1550.0000.0000.0000.000
168A168ALA0-0.016-0.00522.9330.0310.0310.0000.0000.0000.000
169A169VAL0-0.0030.00225.006-0.040-0.0400.0000.0000.0000.000
170A170TRP0-0.038-0.04624.6410.0240.0240.0000.0000.0000.000
171A171TYR0-0.033-0.00929.947-0.029-0.0290.0000.0000.0000.000
172A172MET0-0.061-0.04730.0020.0490.0490.0000.0000.0000.000
173A173ASP-1-0.806-0.88634.5100.4380.4380.0000.0000.0000.000
174A174ILE0-0.085-0.04935.5140.0370.0370.0000.0000.0000.000
175A175ASP-1-0.779-0.87639.5120.3770.3770.0000.0000.0000.000
176A176THR0-0.090-0.06443.2290.0060.0060.0000.0000.0000.000
177A177LYS10.8300.90745.358-0.356-0.3560.0000.0000.0000.000
178A178ALA00.0460.03848.9400.0120.0120.0000.0000.0000.000
179A179SER0-0.104-0.06250.526-0.023-0.0230.0000.0000.0000.000
180A180ILE00.0470.01453.5180.0110.0110.0000.0000.0000.000
181A181ASN0-0.0110.01056.330-0.017-0.0170.0000.0000.0000.000
182A182GLY00.0300.03159.7590.0040.0040.0000.0000.0000.000
183A183PRO0-0.0180.00361.2520.0030.0030.0000.0000.0000.000
184A184SER00.0490.00163.194-0.004-0.0040.0000.0000.0000.000
185A185ALA0-0.084-0.02266.081-0.007-0.0070.0000.0000.0000.000
186A186LEU0-0.006-0.00165.731-0.006-0.0060.0000.0000.0000.000
187A187GLY0-0.015-0.01268.4760.0020.0020.0000.0000.0000.000
188A188VAL0-0.0100.00862.966-0.003-0.0030.0000.0000.0000.000
189A189ASN0-0.043-0.02464.0820.0100.0100.0000.0000.0000.000
190A190LYS10.8160.89059.205-0.249-0.2490.0000.0000.0000.000
191A191THR00.0520.00856.912-0.011-0.0110.0000.0000.0000.000
192A192LYS10.8770.92455.075-0.270-0.2700.0000.0000.0000.000
193A193VAL0-0.023-0.00651.897-0.015-0.0150.0000.0000.0000.000
194A194ASP-1-0.857-0.90549.7780.3200.3200.0000.0000.0000.000
195A195VAL0-0.011-0.02646.025-0.016-0.0160.0000.0000.0000.000
196A196ASP-1-0.784-0.87144.3150.3480.3480.0000.0000.0000.000
197A197VAL0-0.058-0.05140.539-0.007-0.0070.0000.0000.0000.000
198A198ASP-1-0.758-0.87839.1590.4320.4320.0000.0000.0000.000
199A199PRO0-0.050-0.00635.898-0.006-0.0060.0000.0000.0000.000
200A200TRP00.0100.01433.1730.0350.0350.0000.0000.0000.000
201A201VAL0-0.034-0.02230.7710.0140.0140.0000.0000.0000.000
202A202TYR0-0.015-0.00729.9250.0360.0360.0000.0000.0000.000
203A203MET0-0.0140.00223.364-0.004-0.0040.0000.0000.0000.000
204A204ILE0-0.005-0.00724.872-0.008-0.0080.0000.0000.0000.000
205A205GLY0-0.006-0.00223.197-0.029-0.0290.0000.0000.0000.000
206A206PHE0-0.040-0.01618.640-0.021-0.0210.0000.0000.0000.000
207A207GLY00.0620.02416.810-0.119-0.1190.0000.0000.0000.000
208A208TYR0-0.084-0.04111.1160.1080.1080.0000.0000.0000.000
209A209LYS10.8360.9337.407-8.950-8.9500.0000.0000.0000.000
210A210PHE0-0.069-0.0409.4170.9740.9740.0000.0000.0000.000
212A212ALA-1-0.951-0.9566.7816.6946.6940.0000.0000.0000.000