FMO DATABASE

FMODB ID: 5GV6Z

Calculation Name: 1HFE-S-Xray549

Preferred Name:

Target Type:

Ligand Name: iron/sulfur cluster | carbon monoxide | 1,3-propanedithiol | cyanide ion | fe (ii) ion

Ligand 3-letter code: SF4 | CMO | PDT | CYN | FE2

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1HFE

Chain ID: S

ChEMBL ID:

UniProt ID: P07598

Base Structure: X-ray

Registration Date: 2025-10-11

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	88
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-445729.847895
FMO2-HF: Nuclear repulsion	411035.757584
FMO2-HF: Total energy	-34694.090311
FMO2-MP2: Total energy	-34797.144897

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(S:36:VAL)

Summations of interaction energy for fragment #1(S:36:VAL)

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.
-29.459	-25.373	0.57	-1.81	-2.844	-0.016

Interaction energy analysis for fragmet #1(S:36:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.845 / q_NPA : 0.914

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

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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	S	38	GLN	0	0.061	0.020	2.750	-3.794	0.087	0.572	-1.800	-2.652	-0.016
4	S	39	ILE	0	0.026	0.002	4.934	3.902	3.996	-0.001	-0.007	-0.086	0.000
7	S	42	TYR	0	-0.006	-0.008	4.399	3.090	3.201	-0.001	-0.003	-0.106	0.000
5	S	40	LYS	1	0.917	0.946	8.103	26.291	26.291	0.000	0.000	0.000	0.000
6	S	41	ASP	-1	-0.823	-0.907	6.714	-40.904	-40.904	0.000	0.000	0.000	0.000
8	S	43	MET	0	-0.060	-0.019	9.988	2.015	2.015	0.000	0.000	0.000	0.000
9	S	44	LEU	0	0.028	0.015	12.346	1.719	1.719	0.000	0.000	0.000	0.000
10	S	45	ASP	-1	-0.819	-0.894	10.754	-25.486	-25.486	0.000	0.000	0.000	0.000
11	S	46	ARG	1	0.920	0.960	13.845	20.181	20.181	0.000	0.000	0.000	0.000
12	S	47	ILE	0	0.014	0.015	16.235	1.124	1.124	0.000	0.000	0.000	0.000
13	S	48	ASN	0	0.016	-0.001	15.878	1.702	1.702	0.000	0.000	0.000	0.000
14	S	49	GLY	0	-0.005	0.006	17.966	0.700	0.700	0.000	0.000	0.000	0.000
15	S	50	VAL	0	-0.021	-0.010	19.584	0.799	0.799	0.000	0.000	0.000	0.000
16	S	51	TYR	0	0.026	0.006	21.648	0.526	0.526	0.000	0.000	0.000	0.000
17	S	52	GLY	0	0.005	0.008	22.339	0.498	0.498	0.000	0.000	0.000	0.000
18	S	53	ALA	0	-0.045	-0.027	23.699	0.438	0.438	0.000	0.000	0.000	0.000
19	S	54	ASP	-1	-0.802	-0.884	25.693	-10.333	-10.333	0.000	0.000	0.000	0.000
20	S	55	ALA	0	-0.030	-0.019	27.147	0.462	0.462	0.000	0.000	0.000	0.000
21	S	56	LYS	1	0.906	0.958	24.729	12.616	12.616	0.000	0.000	0.000	0.000
22	S	57	PHE	0	-0.040	-0.008	28.927	0.296	0.296	0.000	0.000	0.000	0.000
23	S	58	PRO	0	-0.021	-0.015	32.391	0.131	0.131	0.000	0.000	0.000	0.000
24	S	59	VAL	0	-0.027	-0.010	35.860	0.223	0.223	0.000	0.000	0.000	0.000
25	S	60	ARG	1	0.859	0.904	30.140	10.073	10.073	0.000	0.000	0.000	0.000
26	S	61	ALA	0	0.028	0.025	34.604	-0.154	-0.154	0.000	0.000	0.000	0.000
27	S	62	SER	0	0.020	-0.002	36.376	0.087	0.087	0.000	0.000	0.000	0.000
28	S	63	GLN	0	0.026	0.016	38.173	0.038	0.038	0.000	0.000	0.000	0.000
29	S	64	ASP	-1	-0.885	-0.955	40.296	-7.328	-7.328	0.000	0.000	0.000	0.000
30	S	65	ASN	0	0.009	0.007	37.567	0.257	0.257	0.000	0.000	0.000	0.000
31	S	66	THR	0	0.031	-0.005	40.672	0.117	0.117	0.000	0.000	0.000	0.000
32	S	67	GLN	0	0.032	0.022	40.235	0.090	0.090	0.000	0.000	0.000	0.000
33	S	68	VAL	0	0.018	0.014	39.700	0.128	0.128	0.000	0.000	0.000	0.000
34	S	69	LYS	1	0.909	0.965	42.922	7.297	7.297	0.000	0.000	0.000	0.000
35	S	70	ALA	0	-0.009	0.000	46.066	0.169	0.169	0.000	0.000	0.000	0.000
36	S	71	LEU	0	0.028	0.035	43.208	0.155	0.155	0.000	0.000	0.000	0.000
37	S	72	TYR	0	-0.014	-0.009	43.185	0.122	0.122	0.000	0.000	0.000	0.000
38	S	73	LYS	1	0.937	0.968	48.418	6.069	6.069	0.000	0.000	0.000	0.000
39	S	74	SER	0	-0.062	-0.045	49.779	0.127	0.127	0.000	0.000	0.000	0.000
40	S	75	TYR	0	0.005	0.001	48.099	0.139	0.139	0.000	0.000	0.000	0.000
41	S	76	LEU	0	0.005	-0.013	45.006	0.071	0.071	0.000	0.000	0.000	0.000
42	S	77	GLU	-1	-0.940	-0.941	49.640	-5.691	-5.691	0.000	0.000	0.000	0.000
43	S	78	LYS	1	0.931	0.950	49.470	5.830	5.830	0.000	0.000	0.000	0.000
44	S	79	PRO	0	0.048	0.018	45.112	-0.014	-0.014	0.000	0.000	0.000	0.000
45	S	80	LEU	0	-0.007	-0.006	45.494	0.107	0.107	0.000	0.000	0.000	0.000
46	S	81	GLY	0	-0.004	0.004	48.452	0.139	0.139	0.000	0.000	0.000	0.000
47	S	82	HIS	0	0.027	0.017	50.385	-0.107	-0.107	0.000	0.000	0.000	0.000
48	S	83	LYS	1	0.978	0.989	49.648	5.870	5.870	0.000	0.000	0.000	0.000
49	S	84	SER	0	-0.018	-0.016	46.362	-0.136	-0.136	0.000	0.000	0.000	0.000
50	S	85	HIS	0	-0.061	-0.037	46.297	-0.182	-0.182	0.000	0.000	0.000	0.000
51	S	86	ASP	-1	-0.848	-0.926	47.513	-6.116	-6.116	0.000	0.000	0.000	0.000
52	S	87	LEU	0	-0.074	-0.034	45.763	-0.034	-0.034	0.000	0.000	0.000	0.000
53	S	88	LEU	0	-0.052	-0.022	41.685	-0.164	-0.164	0.000	0.000	0.000	0.000
54	S	89	HIS	0	-0.052	-0.009	41.988	-0.192	-0.192	0.000	0.000	0.000	0.000
55	S	90	THR	0	0.001	-0.003	40.388	0.115	0.115	0.000	0.000	0.000	0.000
56	S	91	HIS	0	0.008	0.014	43.708	-0.033	-0.033	0.000	0.000	0.000	0.000
57	S	92	TRP	0	-0.008	-0.008	37.493	-0.219	-0.219	0.000	0.000	0.000	0.000
58	S	93	PHE	0	0.011	-0.003	41.555	0.149	0.149	0.000	0.000	0.000	0.000
59	S	94	ASP	-1	-0.804	-0.858	41.411	-7.489	-7.489	0.000	0.000	0.000	0.000
60	S	95	LYS	1	0.971	0.975	38.046	8.028	8.028	0.000	0.000	0.000	0.000
61	S	96	SER	0	-0.055	-0.059	39.319	-0.052	-0.052	0.000	0.000	0.000	0.000
62	S	97	LYS	1	0.925	0.972	40.389	6.553	6.553	0.000	0.000	0.000	0.000
63	S	98	GLY	0	0.044	0.026	39.904	0.036	0.036	0.000	0.000	0.000	0.000
64	S	99	VAL	0	0.054	0.020	35.232	-0.008	-0.008	0.000	0.000	0.000	0.000
65	S	100	LYS	1	0.924	0.975	38.303	7.196	7.196	0.000	0.000	0.000	0.000
66	S	101	GLU	-1	-0.843	-0.922	41.520	-6.699	-6.699	0.000	0.000	0.000	0.000
67	S	102	LEU	0	-0.030	-0.017	36.732	0.038	0.038	0.000	0.000	0.000	0.000
68	S	103	THR	0	-0.032	-0.032	38.146	-0.103	-0.103	0.000	0.000	0.000	0.000
69	S	104	THR	0	-0.048	-0.038	39.695	0.087	0.087	0.000	0.000	0.000	0.000
70	S	105	ALA	0	-0.045	-0.014	42.313	0.120	0.120	0.000	0.000	0.000	0.000
71	S	106	GLY	0	0.014	0.011	40.331	0.014	0.014	0.000	0.000	0.000	0.000
72	S	107	LYS	1	0.891	0.944	37.704	7.353	7.353	0.000	0.000	0.000	0.000
73	S	108	LEU	0	-0.038	-0.002	33.859	-0.291	-0.291	0.000	0.000	0.000	0.000
74	S	109	PRO	0	0.065	0.023	32.322	0.220	0.220	0.000	0.000	0.000	0.000
75	S	110	ASN	0	0.014	-0.004	27.950	0.113	0.113	0.000	0.000	0.000	0.000
76	S	111	PRO	0	0.024	-0.002	30.957	-0.137	-0.137	0.000	0.000	0.000	0.000
77	S	112	ARG	1	0.832	0.881	22.625	12.105	12.105	0.000	0.000	0.000	0.000
78	S	113	ALA	0	-0.022	-0.005	26.694	-0.374	-0.374	0.000	0.000	0.000	0.000
79	S	114	SER	0	0.074	0.033	26.358	-0.217	-0.217	0.000	0.000	0.000	0.000
80	S	115	GLU	-1	-0.858	-0.887	23.525	-12.023	-12.023	0.000	0.000	0.000	0.000
81	S	116	PHE	0	-0.095	-0.053	21.779	-0.560	-0.560	0.000	0.000	0.000	0.000
82	S	117	GLU	-1	-0.958	-0.961	22.412	-10.906	-10.906	0.000	0.000	0.000	0.000
83	S	118	GLY	0	-0.005	-0.009	20.635	0.006	0.006	0.000	0.000	0.000	0.000
84	S	119	PRO	0	-0.020	0.010	16.504	0.254	0.254	0.000	0.000	0.000	0.000
85	S	120	TYR	0	-0.009	-0.016	15.330	0.001	0.001	0.000	0.000	0.000	0.000
86	S	121	PRO	0	-0.018	-0.032	12.199	-0.843	-0.843	0.000	0.000	0.000	0.000
87	S	122	TYR	0	-0.091	-0.039	9.879	-1.990	-1.990	0.000	0.000	0.000	0.000
88	S	123	GLU	-2	-1.701	-1.829	10.679	-42.866	-42.866	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(S:36:VAL)