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: 9QYJ2

Calculation Name: 1FRF-L-Xray547

Preferred Name:

Target Type:

Ligand Name: iron/sulfur cluster | fe3-s4 cluster | fe (iii) ion | magnesium ion | nickel (ii) ion

Ligand 3-letter code: SF4 | F3S | FE | MG | NI

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1FRF

Chain ID: L

ChEMBL ID:

UniProt ID: P18188

Base Structure: X-ray

Registration Date: 2025-10-06

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 541
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -11472360.905202
FMO2-HF: Nuclear repulsion 11263643.483679
FMO2-HF: Total energy -208717.421523
FMO2-MP2: Total energy -209323.823198


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(L:7:THR)


Summations of interaction energy for fragment #1(L:7:THR)
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.
-0.0309999999999284.297000000000111.165-8.082-7.41-0.092
Interaction energy analysis for fragmet #1(L:7:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.811 / q_NPA : 0.899
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].
3L9GLN0-0.009-0.0093.601-8.200-7.0940.011-0.380-0.7380.001
186L192TYR0-0.053-0.0592.184-11.523-8.7092.342-2.512-2.644-0.033
273L279ASP-1-0.788-0.8781.976-105.036-104.8598.815-5.166-3.825-0.060
274L280TRP00.0300.0004.5704.4724.549-0.001-0.001-0.0740.000
277L283ILE0-0.035-0.0144.226-0.085-0.035-0.001-0.005-0.0440.000
516L523PRO0-0.051-0.0143.8702.4582.562-0.001-0.018-0.0850.000
4L10SER0-0.049-0.0196.4403.0713.0710.0000.0000.0000.000
5L11THR00.0480.00110.200-0.859-0.8590.0000.0000.0000.000
6L12PHE0-0.010-0.00112.9511.3221.3220.0000.0000.0000.000
7L13THR0-0.006-0.02514.365-0.791-0.7910.0000.0000.0000.000
8L14GLY00.0470.03117.1290.8570.8570.0000.0000.0000.000
9L15PRO0-0.005-0.00517.978-0.953-0.9530.0000.0000.0000.000
10L16ILE0-0.036-0.01614.456-0.267-0.2670.0000.0000.0000.000
11L17VAL0-0.007-0.00618.5800.0990.0990.0000.0000.0000.000
12L18VAL0-0.036-0.01717.285-0.264-0.2640.0000.0000.0000.000
13L19ASP-1-0.797-0.87820.634-11.662-11.6620.0000.0000.0000.000
14L20PRO00.0220.01624.2020.2300.2300.0000.0000.0000.000
15L21ILE0-0.015-0.01518.596-0.691-0.6910.0000.0000.0000.000
16L22THR00.0130.01121.3010.3840.3840.0000.0000.0000.000
17L23ARG10.8240.87816.54216.66116.6610.0000.0000.0000.000
18L24ILE0-0.0010.00521.545-0.691-0.6910.0000.0000.0000.000
19L25GLU-1-0.759-0.88423.961-10.072-10.0720.0000.0000.0000.000
20L26GLY00.0330.02327.385-0.126-0.1260.0000.0000.0000.000
21L27HIS00.0040.00027.397-0.550-0.5500.0000.0000.0000.000
22L28LEU00.0020.00621.5450.1980.1980.0000.0000.0000.000
23L29ARG10.8190.88623.82911.49511.4950.0000.0000.0000.000
24L30ILE0-0.020-0.00917.620-0.025-0.0250.0000.0000.0000.000
25L31MET0-0.0010.00220.6690.0220.0220.0000.0000.0000.000
26L32VAL0-0.016-0.01315.138-0.230-0.2300.0000.0000.0000.000
27L33GLU-1-0.831-0.90018.133-13.623-13.6230.0000.0000.0000.000
28L34VAL0-0.042-0.02512.622-1.071-1.0710.0000.0000.0000.000
29L35GLU-1-0.806-0.88614.132-17.132-17.1320.0000.0000.0000.000
30L36ASN0-0.042-0.02012.650-1.770-1.7700.0000.0000.0000.000
31L37GLY00.0220.02810.273-2.385-2.3850.0000.0000.0000.000
32L38LYS10.9020.9406.60633.27433.2740.0000.0000.0000.000
33L39VAL0-0.0090.01210.5102.3782.3780.0000.0000.0000.000
34L40LYS10.9370.97013.12615.59215.5920.0000.0000.0000.000
35L41ASP-1-0.858-0.95115.964-13.364-13.3640.0000.0000.0000.000
36L42ALA0-0.0130.00617.091-0.606-0.6060.0000.0000.0000.000
37L43TRP0-0.018-0.00419.1840.4520.4520.0000.0000.0000.000
38L44SER0-0.050-0.04921.911-0.560-0.5600.0000.0000.0000.000
39L45SER0-0.028-0.02223.3590.5870.5870.0000.0000.0000.000
40L46SER00.000-0.00826.275-0.150-0.1500.0000.0000.0000.000
41L47GLN00.045-0.00128.1700.5230.5230.0000.0000.0000.000
42L48LEU0-0.053-0.01730.6340.2860.2860.0000.0000.0000.000
43L49PHE00.0520.02833.406-0.100-0.1000.0000.0000.0000.000
44L50ARG10.7540.87135.7328.9218.9210.0000.0000.0000.000
45L51GLY00.0640.03139.0140.2310.2310.0000.0000.0000.000
46L52LEU0-0.031-0.02638.8610.2310.2310.0000.0000.0000.000
47L53GLU-1-0.780-0.85638.798-8.098-8.0980.0000.0000.0000.000
48L54ILE0-0.0040.00742.7720.1730.1730.0000.0000.0000.000
49L55ILE0-0.027-0.00843.5150.2070.2070.0000.0000.0000.000
50L56LEU0-0.0090.00343.6490.1760.1760.0000.0000.0000.000
51L57LYS10.8600.93347.4936.4576.4570.0000.0000.0000.000
52L58GLY00.0080.00249.8560.0650.0650.0000.0000.0000.000
53L59ARG10.8630.93149.2076.5586.5580.0000.0000.0000.000
54L60ASP-1-0.797-0.88352.558-5.830-5.8300.0000.0000.0000.000
55L61PRO00.0620.02150.392-0.141-0.1410.0000.0000.0000.000
56L62ARG10.8380.90049.8305.6115.6110.0000.0000.0000.000
57L63ASP-1-0.885-0.94550.034-6.273-6.2730.0000.0000.0000.000
58L64ALA00.0200.01346.128-0.156-0.1560.0000.0000.0000.000
59L65GLN00.0130.02144.095-0.338-0.3380.0000.0000.0000.000
60L66HIS0-0.0210.00043.666-0.300-0.3000.0000.0000.0000.000
61L67PHE00.0420.01444.045-0.146-0.1460.0000.0000.0000.000
62L68THR00.023-0.00140.480-0.216-0.2160.0000.0000.0000.000
63L69GLN00.0060.00139.308-0.392-0.3920.0000.0000.0000.000
64L70ARG10.8720.93338.4567.2457.2450.0000.0000.0000.000
65L71ALA00.0450.03836.032-0.082-0.0820.0000.0000.0000.000
66L72CYS0-0.0720.00731.624-0.290-0.2900.0000.0000.0000.000
67L73GLY00.0020.00534.4410.1930.1930.0000.0000.0000.000
68L74VAL00.0350.00428.3320.0400.0400.0000.0000.0000.000
69L75CYS0-0.020-0.03930.3450.1790.1790.0000.0000.0000.000
70L76THR00.006-0.01132.6640.2830.2830.0000.0000.0000.000
71L77TYR00.006-0.00935.899-0.053-0.0530.0000.0000.0000.000
72L78VAL0-0.008-0.01033.5390.1590.1590.0000.0000.0000.000
73L79HIS00.005-0.00834.867-0.060-0.0600.0000.0000.0000.000
74L80ALA0-0.0100.00238.5000.1790.1790.0000.0000.0000.000
75L81LEU0-0.0030.01538.2680.2160.2160.0000.0000.0000.000
76L82ALA00.0300.01738.3040.1610.1610.0000.0000.0000.000
77L83SER0-0.004-0.02940.4560.1380.1380.0000.0000.0000.000
78L84SER0-0.020-0.00943.4390.2330.2330.0000.0000.0000.000
79L85ARG10.7810.85538.4998.1908.1900.0000.0000.0000.000
80L86CYS0-0.0500.00843.3240.1200.1200.0000.0000.0000.000
81L87VAL0-0.022-0.01645.2380.1370.1370.0000.0000.0000.000
82L88ASP-1-0.713-0.86047.898-6.514-6.5140.0000.0000.0000.000
83L89ASP-1-0.803-0.88946.966-6.614-6.6140.0000.0000.0000.000
84L90ALA0-0.057-0.03748.9470.1150.1150.0000.0000.0000.000
85L91VAL0-0.045-0.02750.7810.1320.1320.0000.0000.0000.000
86L92LYS10.8290.93250.1076.5166.5160.0000.0000.0000.000
87L93VAL0-0.0180.00851.9920.1070.1070.0000.0000.0000.000
88L94SER0-0.006-0.00351.331-0.191-0.1910.0000.0000.0000.000
89L95ILE0-0.024-0.00846.6060.0990.0990.0000.0000.0000.000
90L96PRO00.0250.01851.213-0.019-0.0190.0000.0000.0000.000
91L97ALA00.013-0.00649.700-0.136-0.1360.0000.0000.0000.000
92L98ASN00.0600.02048.500-0.238-0.2380.0000.0000.0000.000
93L99ALA00.0320.01648.210-0.129-0.1290.0000.0000.0000.000
94L100ARG10.9090.97244.3716.7976.7970.0000.0000.0000.000
95L101MET0-0.0460.00143.960-0.184-0.1840.0000.0000.0000.000
96L102MET00.0470.01743.395-0.197-0.1970.0000.0000.0000.000
97L103ARG10.7630.86342.8106.7746.7740.0000.0000.0000.000
98L104ASN0-0.015-0.00339.681-0.284-0.2840.0000.0000.0000.000
99L105LEU00.0360.01138.635-0.286-0.2860.0000.0000.0000.000
100L106VAL0-0.017-0.00438.744-0.212-0.2120.0000.0000.0000.000
101L107MET0-0.0200.01034.796-0.307-0.3070.0000.0000.0000.000
102L108ALA00.0140.01234.628-0.350-0.3500.0000.0000.0000.000
103L109SER00.0250.00234.043-0.273-0.2730.0000.0000.0000.000
104L110GLN00.0150.01931.5740.0590.0590.0000.0000.0000.000
105L111TYR0-0.050-0.06229.231-0.469-0.4690.0000.0000.0000.000
106L112LEU0-0.019-0.01529.184-0.457-0.4570.0000.0000.0000.000
107L113HIS0-0.038-0.01829.622-0.353-0.3530.0000.0000.0000.000
108L114ASP-1-0.769-0.86228.152-11.558-11.5580.0000.0000.0000.000
109L115HIS10.7960.88324.91511.86511.8650.0000.0000.0000.000
110L116LEU00.0400.03124.100-0.618-0.6180.0000.0000.0000.000
111L117VAL00.0140.00724.790-0.414-0.4140.0000.0000.0000.000
112L118HIS0-0.064-0.03118.974-0.292-0.2920.0000.0000.0000.000
113L119PHE00.0190.00316.864-0.727-0.7270.0000.0000.0000.000
114L120TYR0-0.039-0.05519.693-0.609-0.6090.0000.0000.0000.000
115L121HIS0-0.022-0.03021.297-0.380-0.3800.0000.0000.0000.000
116L122LEU0-0.0380.00221.5070.0360.0360.0000.0000.0000.000
117L123HIS0-0.035-0.01114.148-0.942-0.9420.0000.0000.0000.000
118L124ALA00.0710.03916.100-1.313-1.3130.0000.0000.0000.000
119L125LEU00.0300.00915.617-1.193-1.1930.0000.0000.0000.000
120L126ASP-1-0.776-0.82912.695-20.311-20.3110.0000.0000.0000.000
121L127TRP0-0.014-0.0118.195-3.866-3.8660.0000.0000.0000.000
122L128VAL00.0000.01312.134-1.061-1.0610.0000.0000.0000.000
123L129ASP-1-0.821-0.89714.063-18.950-18.9500.0000.0000.0000.000
124L130VAL00.0270.00015.8200.5750.5750.0000.0000.0000.000
125L131THR00.002-0.02018.3080.8180.8180.0000.0000.0000.000
126L132ALA0-0.102-0.05416.2730.4450.4450.0000.0000.0000.000
127L133ALA00.0270.02818.3590.2710.2710.0000.0000.0000.000
128L134LEU0-0.012-0.01021.1430.6120.6120.0000.0000.0000.000
129L135LYS10.9080.95616.48917.61017.6100.0000.0000.0000.000
130L136ALA0-0.0010.02421.051-0.080-0.0800.0000.0000.0000.000
131L137ASP-1-0.752-0.85822.210-10.809-10.8090.0000.0000.0000.000
132L138PRO0-0.006-0.01224.926-0.225-0.2250.0000.0000.0000.000
133L139ASN00.000-0.00326.9200.2860.2860.0000.0000.0000.000
134L140LYS10.9060.96019.25815.00515.0050.0000.0000.0000.000
135L141ALA0-0.005-0.01922.806-0.416-0.4160.0000.0000.0000.000
136L142ALA00.0360.02323.843-0.245-0.2450.0000.0000.0000.000
137L143LYS10.9330.96825.72411.35311.3530.0000.0000.0000.000
138L144LEU0-0.040-0.00518.228-0.141-0.1410.0000.0000.0000.000
139L145ALA00.0750.03222.830-0.134-0.1340.0000.0000.0000.000
140L146ALA0-0.033-0.01724.2180.0340.0340.0000.0000.0000.000
141L147SER0-0.098-0.05922.9950.1270.1270.0000.0000.0000.000
142L148ILE0-0.071-0.03419.303-0.360-0.3600.0000.0000.0000.000
143L149ASP-1-0.812-0.89622.611-13.726-13.7260.0000.0000.0000.000
144L150THR00.007-0.00425.2460.2150.2150.0000.0000.0000.000
145L151ALA0-0.0010.00128.934-0.129-0.1290.0000.0000.0000.000
146L152ARG10.8090.88528.11011.26311.2630.0000.0000.0000.000
147L153THR00.0220.00331.469-0.234-0.2340.0000.0000.0000.000
148L154GLY00.0270.01131.0640.0040.0040.0000.0000.0000.000
149L155ASN0-0.021-0.00326.088-0.254-0.2540.0000.0000.0000.000
150L156SER0-0.001-0.00528.616-0.109-0.1090.0000.0000.0000.000
151L157GLU-1-0.850-0.93429.658-9.853-9.8530.0000.0000.0000.000
152L158LYS10.9700.97430.6578.3498.3490.0000.0000.0000.000
153L159ALA0-0.0260.00831.1200.0750.0750.0000.0000.0000.000
154L160LEU00.0450.01425.194-0.169-0.1690.0000.0000.0000.000
155L161LYS10.8900.93228.0969.9049.9040.0000.0000.0000.000
156L162ALA00.0310.01730.1390.0210.0210.0000.0000.0000.000
157L163VAL0-0.056-0.01826.2440.1230.1230.0000.0000.0000.000
158L164GLN0-0.029-0.03024.5270.3870.3870.0000.0000.0000.000
159L165ASP-1-0.837-0.91727.734-10.090-10.0900.0000.0000.0000.000
160L166LYS10.8780.94430.72810.01410.0140.0000.0000.0000.000
161L167LEU00.0070.00923.7640.1050.1050.0000.0000.0000.000
162L168LYS10.9780.98327.91810.15610.1560.0000.0000.0000.000
163L169ALA0-0.022-0.01428.8760.0650.0650.0000.0000.0000.000
164L170PHE0-0.0150.00627.0410.1130.1130.0000.0000.0000.000
165L171VAL0-0.025-0.00125.096-0.013-0.0130.0000.0000.0000.000
166L172GLU-1-0.917-0.96828.262-10.780-10.7800.0000.0000.0000.000
167L173SER0-0.068-0.03630.8980.3650.3650.0000.0000.0000.000
168L174GLY00.0120.00830.2860.2440.2440.0000.0000.0000.000
169L175GLN0-0.043-0.02430.502-0.130-0.1300.0000.0000.0000.000
170L176LEU00.0290.00824.377-0.073-0.0730.0000.0000.0000.000
171L177GLY00.0270.01926.805-0.323-0.3230.0000.0000.0000.000
172L178ILE0-0.010-0.00725.082-0.172-0.1720.0000.0000.0000.000
173L179PHE0-0.008-0.00621.497-0.644-0.6440.0000.0000.0000.000
174L180THR00.004-0.01122.671-0.424-0.4240.0000.0000.0000.000
175L181ASN0-0.035-0.02622.045-0.149-0.1490.0000.0000.0000.000
176L182ALA00.0290.03018.746-0.657-0.6570.0000.0000.0000.000
177L183TYR00.010-0.01114.1050.0550.0550.0000.0000.0000.000
178L184PHE00.0380.01714.256-0.946-0.9460.0000.0000.0000.000
179L185LEU0-0.0170.00715.2030.1670.1670.0000.0000.0000.000
180L186GLY0-0.005-0.01117.352-0.295-0.2950.0000.0000.0000.000
181L187GLY00.0050.02113.837-0.228-0.2280.0000.0000.0000.000
182L188HIS0-0.027-0.0269.113-1.549-1.5490.0000.0000.0000.000
183L189LYS10.9980.9915.61328.76028.7600.0000.0000.0000.000
184L190ALA00.0310.0255.442-5.498-5.4980.0000.0000.0000.000
185L191TYR0-0.061-0.0346.525-1.551-1.5510.0000.0000.0000.000
187L193LEU0-0.0220.0118.4401.4611.4610.0000.0000.0000.000
188L194PRO00.0280.02112.0520.7630.7630.0000.0000.0000.000
189L195PRO00.024-0.00314.3490.4250.4250.0000.0000.0000.000
190L196GLU-1-0.831-0.93417.764-15.171-15.1710.0000.0000.0000.000
191L197VAL00.0080.00815.6820.5980.5980.0000.0000.0000.000
192L198ASN00.0320.02114.676-0.227-0.2270.0000.0000.0000.000
193L199LEU0-0.0160.00918.0670.5870.5870.0000.0000.0000.000
194L200ILE0-0.0190.00520.6020.6170.6170.0000.0000.0000.000
195L201ALA00.0250.01718.5720.5130.5130.0000.0000.0000.000
196L202THR0-0.028-0.04020.5930.4160.4160.0000.0000.0000.000
197L203ALA0-0.023-0.01122.6410.5710.5710.0000.0000.0000.000
198L204HIS10.8230.87522.65113.71813.7180.0000.0000.0000.000
199L205TYR00.0300.01921.8940.3040.3040.0000.0000.0000.000
200L206LEU00.0120.00124.5260.4340.4340.0000.0000.0000.000
201L207GLU-1-0.822-0.89327.968-10.502-10.5020.0000.0000.0000.000
202L208ALA00.0160.01826.3110.4030.4030.0000.0000.0000.000
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