FMO DATABASE

FMODB ID: JV3Z9

Calculation Name: 1SJ1-A-Xray547

Preferred Name:

Target Type:

Ligand Name: cobalt hexammine(iii) | fe3-s4 cluster

Ligand 3-letter code: NCO | F3S

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1SJ1

Chain ID: A

ChEMBL ID:

UniProt ID: P29603

Base Structure: X-ray

Registration Date: 2025-10-05

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	65
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-362821.209859
FMO2-HF: Nuclear repulsion	335974.147924
FMO2-HF: Total energy	-26847.061935
FMO2-MP2: Total energy	-26919.491359

3D Structure Molmil

Snapshot

Ligand structure

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/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:1:ALA)

Summations of interaction energy for fragment #1(A:1:ALA)

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.
-381.677	-377.235	17.944	-11.834	-10.556	-0.129

Interaction energy analysis for fragmet #1(A:1:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.775 / 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 ES EX CT+mix DI(MP2)

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].
3	A	3	LYS	1	0.845	0.930	2.738	55.635	57.346	0.113	-0.678	-1.147	0.000
39	A	39	VAL	0	-0.079	-0.050	2.299	-4.419	-4.660	1.593	-0.383	-0.970	-0.001
40	A	40	ILE	0	0.009	0.017	3.701	3.955	4.173	0.000	-0.062	-0.157	0.000
41	A	41	GLU	-1	-0.957	-0.998	2.319	-88.134	-83.461	3.060	-3.966	-3.768	-0.046
42	A	42	ASP	-1	-0.840	-0.929	4.033	-24.365	-24.341	0.000	-0.026	0.002	0.000
65	A	66	ALA	-1	-0.904	-0.941	1.797	-105.425	-107.368	13.178	-6.719	-4.516	-0.082
4	A	4	VAL	0	0.040	0.021	6.268	1.519	1.519	0.000	0.000	0.000	0.000
5	A	5	SER	0	-0.025	-0.017	9.703	1.066	1.066	0.000	0.000	0.000	0.000
6	A	6	VAL	0	0.011	0.001	13.079	0.115	0.115	0.000	0.000	0.000	0.000
7	A	7	ASP	-1	-0.838	-0.891	16.696	-14.128	-14.128	0.000	0.000	0.000	0.000
8	A	8	GLN	0	0.000	-0.027	18.832	1.040	1.040	0.000	0.000	0.000	0.000
9	A	9	ASP	-1	-0.943	-0.960	22.072	-11.650	-11.650	0.000	0.000	0.000	0.000
10	A	10	THR	0	-0.110	-0.073	22.613	0.585	0.585	0.000	0.000	0.000	0.000
11	A	11	CYS	-1	-0.833	-0.843	21.654	-13.207	-13.207	0.000	0.000	0.000	0.000
12	A	12	ILE	0	-0.043	-0.026	23.714	0.552	0.552	0.000	0.000	0.000	0.000
13	A	13	GLY	0	0.030	-0.016	24.952	0.397	0.397	0.000	0.000	0.000	0.000
14	A	14	ASP	-1	-0.976	-0.998	24.791	-11.823	-11.823	0.000	0.000	0.000	0.000
15	A	15	ALA	0	0.018	0.003	22.652	0.131	0.131	0.000	0.000	0.000	0.000
16	A	16	ILE	0	-0.010	0.005	21.882	-0.298	-0.298	0.000	0.000	0.000	0.000
17	A	17	CYS	0	-0.001	-0.001	17.628	0.011	0.011	0.000	0.000	0.000	0.000
18	A	18	ALA	0	0.036	0.012	18.316	-0.612	-0.612	0.000	0.000	0.000	0.000
19	A	19	SER	0	-0.088	-0.042	19.885	0.124	0.124	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.014	-0.005	18.812	0.159	0.159	0.000	0.000	0.000	0.000
21	A	21	CYS	0	-0.010	0.015	12.225	-0.181	-0.181	0.000	0.000	0.000	0.000
22	A	22	PRO	0	0.047	0.025	15.984	-0.695	-0.695	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.945	-0.972	14.052	-17.411	-17.411	0.000	0.000	0.000	0.000
24	A	24	VAL	0	-0.039	-0.020	10.728	-1.125	-1.125	0.000	0.000	0.000	0.000
25	A	25	PHE	0	-0.021	-0.013	12.990	-0.538	-0.538	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.876	-0.931	16.039	-15.080	-15.080	0.000	0.000	0.000	0.000
27	A	27	MET	0	-0.059	-0.022	19.018	-0.388	-0.388	0.000	0.000	0.000	0.000
28	A	28	ASN	0	0.018	0.010	20.682	0.580	0.580	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.916	-0.961	23.074	-10.900	-10.900	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-1.013	-1.010	24.398	-11.513	-11.513	0.000	0.000	0.000	0.000
31	A	31	GLY	0	-0.061	-0.029	26.355	0.196	0.196	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.826	0.897	22.564	12.063	12.063	0.000	0.000	0.000	0.000
33	A	33	ALA	0	0.026	-0.022	18.905	-0.118	-0.118	0.000	0.000	0.000	0.000
34	A	34	GLN	0	-0.044	-0.030	16.798	0.086	0.086	0.000	0.000	0.000	0.000
35	A	35	PRO	0	0.013	-0.004	11.386	0.259	0.259	0.000	0.000	0.000	0.000
36	A	36	LYS	1	0.871	0.949	13.464	18.155	18.155	0.000	0.000	0.000	0.000
37	A	37	VAL	0	-0.031	-0.013	8.793	0.255	0.255	0.000	0.000	0.000	0.000
38	A	38	GLU	-1	-0.917	-0.953	8.316	-24.641	-24.641	0.000	0.000	0.000	0.000
43	A	43	GLU	-1	-0.920	-0.965	7.504	-27.164	-27.164	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.974	-0.977	9.172	-17.509	-17.509	0.000	0.000	0.000	0.000
45	A	45	LEU	0	0.026	0.002	9.310	0.408	0.408	0.000	0.000	0.000	0.000
46	A	46	TYR	0	-0.010	0.002	6.749	1.034	1.034	0.000	0.000	0.000	0.000
47	A	47	ASN	0	-0.035	-0.025	8.775	1.053	1.053	0.000	0.000	0.000	0.000
48	A	49	ALA	0	0.051	0.020	10.381	1.154	1.154	0.000	0.000	0.000	0.000
49	A	50	LYS	1	0.902	0.944	11.689	23.293	23.293	0.000	0.000	0.000	0.000
50	A	51	GLU	-1	-0.958	-0.976	13.297	-14.946	-14.946	0.000	0.000	0.000	0.000
51	A	52	ALA	0	0.003	-0.002	15.565	1.071	1.071	0.000	0.000	0.000	0.000
52	A	53	MET	0	-0.072	-0.026	13.379	0.341	0.341	0.000	0.000	0.000	0.000
53	A	54	GLU	-1	-0.998	-0.993	16.702	-14.761	-14.761	0.000	0.000	0.000	0.000
54	A	55	ALA	0	-0.020	-0.010	19.193	0.884	0.884	0.000	0.000	0.000	0.000
55	A	56	CYS	0	-0.032	0.013	19.951	0.830	0.830	0.000	0.000	0.000	0.000
56	A	57	PRO	0	0.001	0.005	21.898	0.045	0.045	0.000	0.000	0.000	0.000
57	A	58	VAL	0	-0.046	-0.034	23.610	0.428	0.428	0.000	0.000	0.000	0.000
58	A	59	SER	0	-0.049	-0.029	21.226	-0.080	-0.080	0.000	0.000	0.000	0.000
59	A	60	ALA	0	0.038	0.020	20.513	-0.377	-0.377	0.000	0.000	0.000	0.000
60	A	61	ILE	0	-0.037	-0.005	14.770	-0.547	-0.547	0.000	0.000	0.000	0.000
61	A	62	THR	0	-0.007	-0.012	13.739	-0.139	-0.139	0.000	0.000	0.000	0.000
62	A	63	ILE	0	-0.018	-0.024	8.044	-0.887	-0.887	0.000	0.000	0.000	0.000
63	A	64	GLU	-1	-0.895	-0.931	7.539	-33.571	-33.571	0.000	0.000	0.000	0.000
64	A	65	GLU	-1	-0.957	-0.994	4.868	-42.469	-42.469	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1:ALA)