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: 1Y3JZ

Calculation Name: 4RC5-A-Xray547

Preferred Name:

Target Type:

Ligand Name: hexadecan-1-ol | fe (ii) ion

Ligand 3-letter code: PL3 | FE2

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4RC5

Chain ID: A

ChEMBL ID:

UniProt ID: Q54764

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 221
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2836386.142361
FMO2-HF: Nuclear repulsion 2746082.956261
FMO2-HF: Total energy -90303.186099
FMO2-MP2: Total energy -90561.015408


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:11:ASP)


Summations of interaction energy for fragment #1(A:11: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.
-58.888-53.24510.627-7.291-8.9780.071
Interaction energy analysis for fragmet #1(A:11:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.054 / q_NPA : -0.051
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].
3A13GLN00.0070.0031.899-16.682-14.4619.259-5.576-5.9030.050
4A14SER0-0.0070.0182.696-8.565-5.6311.333-1.406-2.8610.019
5A15GLU-1-0.824-0.9203.8691.6401.9590.036-0.254-0.1010.002
7A17TYR00.0740.0454.363-2.188-2.019-0.001-0.055-0.1130.000
6A16SER0-0.058-0.0306.694-0.568-0.5680.0000.0000.0000.000
8A18LYS10.8360.8966.616-7.116-7.1160.0000.0000.0000.000
9A19ASP-1-0.848-0.8859.241-0.475-0.4750.0000.0000.0000.000
10A20ALA00.0640.0579.301-0.124-0.1240.0000.0000.0000.000
11A21TYR0-0.016-0.0199.3760.4590.4590.0000.0000.0000.000
12A22SER0-0.070-0.05411.3300.2180.2180.0000.0000.0000.000
13A23ARG10.7840.83513.9310.7960.7960.0000.0000.0000.000
14A24ILE00.0370.02712.7880.0510.0510.0000.0000.0000.000
15A25ASN0-0.041-0.04014.0430.3980.3980.0000.0000.0000.000
16A26ALA00.024-0.00115.8030.1240.1240.0000.0000.0000.000
17A27ILE0-0.0070.00718.4100.0750.0750.0000.0000.0000.000
18A28VAL0-0.0060.00516.5200.0460.0460.0000.0000.0000.000
19A29ILE0-0.073-0.04718.7450.1400.1400.0000.0000.0000.000
20A30GLU-1-0.883-0.95721.519-0.237-0.2370.0000.0000.0000.000
21A31GLY00.0490.03623.0610.0410.0410.0000.0000.0000.000
22A32GLU-1-0.797-0.89822.253-0.884-0.8840.0000.0000.0000.000
23A33GLN0-0.092-0.06625.1250.0630.0630.0000.0000.0000.000
24A34GLU-1-0.800-0.90827.568-0.456-0.4560.0000.0000.0000.000
25A35ALA00.0170.02627.7610.0310.0310.0000.0000.0000.000
26A36PHE0-0.078-0.04729.4650.0440.0440.0000.0000.0000.000
27A37ASP-1-0.875-0.93431.308-0.207-0.2070.0000.0000.0000.000
28A38ASN0-0.037-0.02530.9800.0580.0580.0000.0000.0000.000
29A39TYR0-0.041-0.06130.2150.0380.0380.0000.0000.0000.000
30A40ASN0-0.019-0.00935.0290.0220.0220.0000.0000.0000.000
31A41ARG10.8440.89637.2660.2570.2570.0000.0000.0000.000
32A42LEU00.0410.00735.7010.0120.0120.0000.0000.0000.000
33A43ALA0-0.023-0.01039.1310.0100.0100.0000.0000.0000.000
34A44GLU-1-0.991-0.98140.913-0.179-0.1790.0000.0000.0000.000
35A45MET0-0.047-0.00842.0170.0110.0110.0000.0000.0000.000
36A46LEU00.0150.02540.8820.0030.0030.0000.0000.0000.000
37A47PRO0-0.035-0.02844.2360.0000.0000.0000.0000.0000.000
38A48ASP-1-0.894-0.94346.307-0.252-0.2520.0000.0000.0000.000
39A49GLN00.006-0.00241.229-0.013-0.0130.0000.0000.0000.000
40A50ARG10.9070.97941.2110.2040.2040.0000.0000.0000.000
41A51ASP-1-0.870-0.95440.822-0.237-0.2370.0000.0000.0000.000
42A52GLU-1-0.913-0.94937.483-0.424-0.4240.0000.0000.0000.000
43A53LEU00.0130.02836.711-0.021-0.0210.0000.0000.0000.000
44A54HIS0-0.018-0.02635.9500.0050.0050.0000.0000.0000.000
45A55LYS10.7470.86935.5430.3770.3770.0000.0000.0000.000
46A56LEU00.0580.02932.265-0.003-0.0030.0000.0000.0000.000
47A57ALA00.0620.04531.095-0.024-0.0240.0000.0000.0000.000
48A58LYS10.8500.91131.0090.2520.2520.0000.0000.0000.000
49A59MET0-0.073-0.01728.3930.0350.0350.0000.0000.0000.000
50A60GLU-1-0.717-0.86726.520-0.729-0.7290.0000.0000.0000.000
51A61GLN0-0.018-0.01526.1760.0320.0320.0000.0000.0000.000
52A62ARG10.7570.86124.0580.6880.6880.0000.0000.0000.000
53A63HIS10.8000.88222.5820.8100.8100.0000.0000.0000.000
54A64MET00.0420.04021.634-0.004-0.0040.0000.0000.0000.000
55A65LYS10.8910.94021.8840.1530.1530.0000.0000.0000.000
56A66GLY00.0170.01520.6220.1090.1090.0000.0000.0000.000
57A67PHE00.0880.02916.0600.0510.0510.0000.0000.0000.000
58A68MET0-0.0020.01217.3460.0820.0820.0000.0000.0000.000
59A69ALA0-0.055-0.02518.0240.2320.2320.0000.0000.0000.000
60A70CYS0-0.049-0.01013.6620.1710.1710.0000.0000.0000.000
61A71GLY00.0800.05613.1130.1420.1420.0000.0000.0000.000
62A72LYS10.9000.94013.327-0.626-0.6260.0000.0000.0000.000
63A73ASN0-0.046-0.01311.0350.8730.8730.0000.0000.0000.000
64A74LEU0-0.0170.0037.4160.7720.7720.0000.0000.0000.000
65A75SER0-0.068-0.0339.3051.0141.0140.0000.0000.0000.000
66A76VAL0-0.0110.00810.3480.4080.4080.0000.0000.0000.000
67A77THR0-0.085-0.04312.971-0.270-0.2700.0000.0000.0000.000
68A78PRO0-0.0060.00416.4960.0130.0130.0000.0000.0000.000
69A79ASP-1-0.843-0.92518.0470.1260.1260.0000.0000.0000.000
70A80MET0-0.023-0.02619.949-0.149-0.1490.0000.0000.0000.000
71A81GLY0-0.0200.01422.962-0.052-0.0520.0000.0000.0000.000
72A82PHE00.0200.00419.002-0.007-0.0070.0000.0000.0000.000
73A83ALA00.0260.00721.052-0.065-0.0650.0000.0000.0000.000
74A84GLN00.0190.00422.697-0.023-0.0230.0000.0000.0000.000
75A85LYS10.8370.91325.9850.1210.1210.0000.0000.0000.000
76A86PHE00.0090.01921.402-0.035-0.0350.0000.0000.0000.000
77A87PHE00.0370.02522.929-0.072-0.0720.0000.0000.0000.000
78A88GLU-1-0.938-0.95927.392-0.250-0.2500.0000.0000.0000.000
79A89ARG10.9350.95230.4250.4910.4910.0000.0000.0000.000
80A90LEU00.0160.01128.6990.0140.0140.0000.0000.0000.000
81A91HIS0-0.0010.00330.8240.0710.0710.0000.0000.0000.000
82A92GLU-1-0.838-0.93332.611-0.226-0.2260.0000.0000.0000.000
83A93ASN0-0.065-0.02835.0020.0490.0490.0000.0000.0000.000
84A94PHE00.0210.01334.4100.0170.0170.0000.0000.0000.000
85A95LYS10.8090.89535.5660.2730.2730.0000.0000.0000.000
86A96ALA0-0.0270.00138.5320.0230.0230.0000.0000.0000.000
87A97ALA00.0310.01739.3270.0160.0160.0000.0000.0000.000
88A98ALA00.050-0.00139.5490.0140.0140.0000.0000.0000.000
89A99ALA0-0.070-0.01841.5710.0210.0210.0000.0000.0000.000
90A100GLU-1-0.918-0.96144.059-0.281-0.2810.0000.0000.0000.000
91A101GLY0-0.019-0.00245.1970.0030.0030.0000.0000.0000.000
92A102LYS10.8230.92142.9770.3070.3070.0000.0000.0000.000
93A103VAL00.0750.00941.622-0.023-0.0230.0000.0000.0000.000
94A104VAL00.0070.01940.418-0.026-0.0260.0000.0000.0000.000
95A105THR0-0.026-0.04638.545-0.038-0.0380.0000.0000.0000.000
96A106CYS0-0.064-0.01237.013-0.024-0.0240.0000.0000.0000.000
97A107LEU00.0160.00935.666-0.031-0.0310.0000.0000.0000.000
98A108LEU00.0030.01634.857-0.042-0.0420.0000.0000.0000.000
99A109ILE0-0.017-0.00332.117-0.053-0.0530.0000.0000.0000.000
100A110GLN00.0330.01228.432-0.023-0.0230.0000.0000.0000.000
101A111SER0-0.051-0.04430.488-0.047-0.0470.0000.0000.0000.000
102A112LEU00.012-0.00131.593-0.034-0.0340.0000.0000.0000.000
103A113ILE00.0020.00329.331-0.077-0.0770.0000.0000.0000.000
104A114ILE00.0160.00826.077-0.092-0.0920.0000.0000.0000.000
105A115GLU-1-0.744-0.84325.672-0.919-0.9190.0000.0000.0000.000
106A116CYS0-0.065-0.02725.303-0.095-0.0950.0000.0000.0000.000
107A117PHE0-0.0090.00020.864-0.137-0.1370.0000.0000.0000.000
108A118ALA00.0200.02421.241-0.191-0.1910.0000.0000.0000.000
109A119ILE00.0300.00720.428-0.198-0.1980.0000.0000.0000.000
110A120ALA0-0.0080.00720.633-0.177-0.1770.0000.0000.0000.000
111A121ALA00.0190.00317.344-0.289-0.2890.0000.0000.0000.000
112A122TYR0-0.041-0.04615.885-0.494-0.4940.0000.0000.0000.000
113A123ASN0-0.057-0.04916.034-0.277-0.2770.0000.0000.0000.000
114A124ILE00.0060.01713.670-0.334-0.3340.0000.0000.0000.000
115A125TYR00.0410.0089.094-0.805-0.8050.0000.0000.0000.000
116A126ILE0-0.030-0.01211.269-0.745-0.7450.0000.0000.0000.000
117A127PRO0-0.049-0.02712.035-0.215-0.2150.0000.0000.0000.000
118A128VAL0-0.029-0.0097.325-0.612-0.6120.0000.0000.0000.000
119A129ALA00.0040.0246.689-2.427-2.4270.0000.0000.0000.000
120A130ASP-1-0.802-0.9107.448-2.020-2.0200.0000.0000.0000.000
121A131ALA0-0.005-0.0238.5160.5910.5910.0000.0000.0000.000
122A132PHE0-0.051-0.01511.7800.2820.2820.0000.0000.0000.000
123A133ALA00.0640.00311.1680.0350.0350.0000.0000.0000.000
124A134ARG10.8500.9599.4605.0375.0370.0000.0000.0000.000
125A135LYS10.9380.98513.5471.3671.3670.0000.0000.0000.000
126A136ILE0-0.055-0.02716.3960.1790.1790.0000.0000.0000.000
127A137THR00.009-0.01514.8890.0650.0650.0000.0000.0000.000
128A138GLU-1-0.916-0.97316.915-1.709-1.7090.0000.0000.0000.000
129A139GLY0-0.080-0.03219.1990.1450.1450.0000.0000.0000.000
130A140VAL0-0.037-0.01719.7370.1470.1470.0000.0000.0000.000
131A141VAL00.0640.04219.3720.0990.0990.0000.0000.0000.000
132A142ARG10.7610.87622.4010.8930.8930.0000.0000.0000.000
133A143ASP-1-0.761-0.85425.369-0.669-0.6690.0000.0000.0000.000
134A144GLU-1-0.743-0.88622.549-1.284-1.2840.0000.0000.0000.000
135A145TYR0-0.0030.00523.0540.0290.0290.0000.0000.0000.000
136A146LEU0-0.064-0.02628.5090.0560.0560.0000.0000.0000.000
137A147HIS0-0.042-0.01328.6750.0900.0900.0000.0000.0000.000
138A148ARG10.9460.96928.2841.0031.0030.0000.0000.0000.000
139A149ASN0-0.023-0.00531.4510.0040.0040.0000.0000.0000.000
140A150PHE00.0430.01934.0800.0450.0450.0000.0000.0000.000
141A151GLY00.0500.02034.7230.0350.0350.0000.0000.0000.000
142A152GLU-1-0.832-0.93233.086-0.759-0.7590.0000.0000.0000.000
143A153GLU-1-0.989-0.98937.021-0.445-0.4450.0000.0000.0000.000
144A154TRP00.001-0.01039.4800.0240.0240.0000.0000.0000.000
145A155LEU00.014-0.00537.3980.0280.0280.0000.0000.0000.000
146A156LYS10.8460.93240.9890.5550.5550.0000.0000.0000.000
147A157ALA0-0.064-0.02942.6390.0200.0200.0000.0000.0000.000
148A158ASN0-0.056-0.02644.4620.0410.0410.0000.0000.0000.000
149A159PHE00.0430.04441.9280.0110.0110.0000.0000.0000.000
150A160ASP-1-0.927-0.97545.502-0.371-0.3710.0000.0000.0000.000
151A161ALA0-0.077-0.04148.7530.0070.0070.0000.0000.0000.000
152A162SER00.010-0.00943.2710.0060.0060.0000.0000.0000.000
153A163LYS10.8350.92043.9600.4380.4380.0000.0000.0000.000
154A164ALA00.0270.00244.097-0.014-0.0140.0000.0000.0000.000
155A165GLU-1-0.826-0.88842.774-0.369-0.3690.0000.0000.0000.000
156A166LEU00.0240.00638.881-0.016-0.0160.0000.0000.0000.000
157A167GLU-1-0.903-0.96539.670-0.485-0.4850.0000.0000.0000.000
158A168GLU-1-0.884-0.93840.539-0.428-0.4280.0000.0000.0000.000
159A169ALA0-0.0010.00538.548-0.013-0.0130.0000.0000.0000.000
160A170ASN00.0410.02735.295-0.058-0.0580.0000.0000.0000.000
161A171ARG10.8620.94335.7970.4160.4160.0000.0000.0000.000
162A172GLN0-0.063-0.04537.010-0.021-0.0210.0000.0000.0000.000
163A173ASN0-0.016-0.01833.4170.0080.0080.0000.0000.0000.000
164A174LEU0-0.0010.01830.227-0.041-0.0410.0000.0000.0000.000
165A175PRO0-0.010-0.01530.348-0.065-0.0650.0000.0000.0000.000
166A176LEU0-0.035-0.00429.835-0.035-0.0350.0000.0000.0000.000
167A177VAL00.0770.02825.546-0.034-0.0340.0000.0000.0000.000
168A178TRP00.0220.01625.464-0.136-0.1360.0000.0000.0000.000
169A179LEU0-0.064-0.01725.428-0.069-0.0690.0000.0000.0000.000
170A180MET00.0200.02123.582-0.060-0.0600.0000.0000.0000.000
171A181LEU0-0.010-0.00820.440-0.151-0.1510.0000.0000.0000.000
172A182ASN0-0.013-0.02020.296-0.312-0.3120.0000.0000.0000.000
173A183GLU-1-0.959-0.97420.151-0.944-0.9440.0000.0000.0000.000
174A184VAL0-0.012-0.00216.650-0.038-0.0380.0000.0000.0000.000
175A185ALA0-0.037-0.00715.613-0.394-0.3940.0000.0000.0000.000
176A186ASP-1-0.867-0.93914.170-2.637-2.6370.0000.0000.0000.000
177A187ASP-1-0.778-0.87112.018-2.261-2.2610.0000.0000.0000.000
178A188ALA0-0.006-0.01510.870-0.878-0.8780.0000.0000.0000.000
179A189ARG10.8310.91610.6962.1072.1070.0000.0000.0000.000
180A190GLU-1-0.891-0.9227.401-7.256-7.2560.0000.0000.0000.000
181A191LEU0-0.086-0.0505.913-4.131-4.1310.0000.0000.0000.000
182A192GLY0-0.046-0.0167.629-0.955-0.9550.0000.0000.0000.000
183A193MET0-0.069-0.0268.2811.1351.1350.0000.0000.0000.000
184A194GLU-1-0.793-0.89211.947-3.101-3.1010.0000.0000.0000.000
185A195ARG10.9400.96214.7692.0312.0310.0000.0000.0000.000
186A196GLU-1-0.992-0.99517.850-1.910-1.9100.0000.0000.0000.000
187A197SER00.0720.02217.5310.0560.0560.0000.0000.0000.000
188A198LEU00.0050.01217.1130.1540.1540.0000.0000.0000.000
189A199VAL0-0.037-0.01919.5560.2240.2240.0000.0000.0000.000
190A200GLU-1-0.945-0.97122.684-1.699-1.6990.0000.0000.0000.000
191A201ASP-1-0.870-0.94220.338-2.010-2.0100.0000.0000.0000.000
192A202PHE0-0.041-0.01923.3500.1420.1420.0000.0000.0000.000
193A203MET0-0.053-0.03024.8340.1360.1360.0000.0000.0000.000
194A204ILE0-0.0220.00025.5990.1100.1100.0000.0000.0000.000
195A205ALA00.0220.01626.1800.0950.0950.0000.0000.0000.000
196A206TYR0-0.013-0.03728.1680.1070.1070.0000.0000.0000.000
197A207GLY00.005-0.00730.3680.0790.0790.0000.0000.0000.000
198A208GLU-1-0.936-0.97430.328-0.992-0.9920.0000.0000.0000.000
199A209ALA00.0070.01532.0770.0620.0620.0000.0000.0000.000
200A210LEU0-0.044-0.03233.9220.0700.0700.0000.0000.0000.000
201A211GLU-1-0.964-0.99036.293-0.666-0.6660.0000.0000.0000.000
202A212ASN0-0.068-0.03134.6440.0630.0630.0000.0000.0000.000
203A213ILE0-0.053-0.02237.7220.0430.0430.0000.0000.0000.000
204A214GLY00.0140.02040.2670.0350.0350.0000.0000.0000.000
205A215PHE0-0.066-0.02339.3100.0270.0270.0000.0000.0000.000
206A216THR0-0.006-0.02841.336-0.017-0.0170.0000.0000.0000.000
207A217THR00.0830.03139.480-0.001-0.0010.0000.0000.0000.000
208A218ARG10.9100.93740.0690.4730.4730.0000.0000.0000.000
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