FMO DATABASE

FMODB ID: 7KVMK

Calculation Name: 4AAY-F-Xray547

Preferred Name:

Target Type:

Ligand Name: 2-amino-5,6-dimercapto-7-methyl-3,7,8a,9-tetrahydro-8-oxa-1,3,9,10-tetraaza-anthracen-4-one guanosine dinucleotide | fe3-s4 cluster | fe2/s2 (inorganic) cluster | molybdenum(iv) ion | oxygen atom

Ligand 3-letter code: MGD | F3S | FES | 4MO | O

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4AAY

Chain ID: F

ChEMBL ID:

UniProt ID: Q6VAL9

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	132
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1067488.384088
FMO2-HF: Nuclear repulsion	1018456.46084
FMO2-HF: Total energy	-49031.923248
FMO2-MP2: Total energy	-49176.591563

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:44:ALA)

Summations of interaction energy for fragment #1(A:44: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.
-249.267	-243.522	7.5	-7.535	-5.708	-0.082

Interaction energy analysis for fragmet #1(A:44:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.832 / q_NPA : 0.910

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	46	GLY	0	0.045	0.029	3.883	9.564	11.210	-0.006	-0.812	-0.828	-0.002
4	A	47	VAL	0	0.002	-0.002	3.699	-13.653	-13.295	0.002	-0.213	-0.146	-0.001
5	A	48	GLU	-1	-0.914	-0.965	2.089	-114.251	-110.510	7.504	-6.510	-4.734	-0.079
6	A	49	TYR	0	0.030	0.020	5.650	3.377	3.377	0.000	0.000	0.000	0.000
7	A	50	PRO	0	0.002	0.024	9.479	-0.555	-0.555	0.000	0.000	0.000	0.000
8	A	51	ALA	0	0.032	0.016	11.813	1.175	1.175	0.000	0.000	0.000	0.000
9	A	52	ASN	0	0.004	0.004	14.824	0.215	0.215	0.000	0.000	0.000	0.000
10	A	53	ARG	1	0.839	0.924	17.596	12.410	12.410	0.000	0.000	0.000	0.000
11	A	54	LEU	0	-0.030	-0.012	19.971	-0.114	-0.114	0.000	0.000	0.000	0.000
12	A	55	ALA	0	0.042	0.025	23.210	0.403	0.403	0.000	0.000	0.000	0.000
13	A	56	ASN	0	-0.031	-0.017	26.490	0.043	0.043	0.000	0.000	0.000	0.000
14	A	57	ILE	0	0.010	-0.003	29.115	0.174	0.174	0.000	0.000	0.000	0.000
15	A	58	SER	0	-0.107	-0.073	30.808	0.269	0.269	0.000	0.000	0.000	0.000
16	A	59	GLU	-1	-0.855	-0.927	29.991	-10.576	-10.576	0.000	0.000	0.000	0.000
17	A	60	LEU	0	-0.011	0.005	29.032	0.021	0.021	0.000	0.000	0.000	0.000
18	A	61	THR	0	-0.018	-0.011	33.497	0.158	0.158	0.000	0.000	0.000	0.000
19	A	62	LEU	0	-0.072	-0.033	35.567	-0.191	-0.191	0.000	0.000	0.000	0.000
20	A	63	ASN	0	-0.044	-0.040	36.084	-0.018	-0.018	0.000	0.000	0.000	0.000
21	A	64	GLU	-1	-0.896	-0.932	35.968	-8.176	-8.176	0.000	0.000	0.000	0.000
22	A	65	PRO	0	-0.065	-0.026	31.469	-0.190	-0.190	0.000	0.000	0.000	0.000
23	A	66	LEU	0	0.012	0.006	29.318	0.223	0.223	0.000	0.000	0.000	0.000
24	A	67	ASP	-1	-0.913	-0.961	28.214	-10.926	-10.926	0.000	0.000	0.000	0.000
25	A	68	VAL	0	-0.061	-0.032	23.445	-0.075	-0.075	0.000	0.000	0.000	0.000
26	A	69	ALA	0	-0.003	0.004	21.495	0.187	0.187	0.000	0.000	0.000	0.000
27	A	70	TYR	0	-0.053	-0.020	13.758	-0.522	-0.522	0.000	0.000	0.000	0.000
28	A	71	PRO	0	-0.026	-0.025	13.119	0.227	0.227	0.000	0.000	0.000	0.000
29	A	72	ASP	-1	-0.801	-0.884	15.356	-19.566	-19.566	0.000	0.000	0.000	0.000
30	A	73	GLU	-1	-0.926	-0.971	17.201	-13.138	-13.138	0.000	0.000	0.000	0.000
31	A	74	ASP	-1	-0.908	-0.949	19.848	-14.159	-14.159	0.000	0.000	0.000	0.000
32	A	75	ALA	0	-0.092	-0.034	18.005	0.413	0.413	0.000	0.000	0.000	0.000
33	A	76	ALA	0	0.005	-0.004	20.124	0.018	0.018	0.000	0.000	0.000	0.000
34	A	77	GLY	0	0.029	-0.006	23.611	-0.118	-0.118	0.000	0.000	0.000	0.000
35	A	78	VAL	0	-0.027	-0.001	24.501	0.407	0.407	0.000	0.000	0.000	0.000
36	A	79	LEU	0	0.008	0.001	24.015	-0.427	-0.427	0.000	0.000	0.000	0.000
37	A	80	LEU	0	0.008	0.001	27.357	0.419	0.419	0.000	0.000	0.000	0.000
38	A	81	LYS	1	0.822	0.900	30.168	9.020	9.020	0.000	0.000	0.000	0.000
39	A	82	LEU	0	0.047	0.009	31.112	0.350	0.350	0.000	0.000	0.000	0.000
40	A	83	GLY	0	-0.016	-0.019	34.600	0.298	0.298	0.000	0.000	0.000	0.000
41	A	84	THR	0	-0.068	-0.043	35.450	0.234	0.234	0.000	0.000	0.000	0.000
42	A	85	ARG	1	0.878	0.949	31.389	9.622	9.622	0.000	0.000	0.000	0.000
43	A	86	VAL	0	-0.006	0.006	29.156	0.179	0.179	0.000	0.000	0.000	0.000
44	A	87	GLU	-1	-0.941	-0.974	26.594	-12.023	-12.023	0.000	0.000	0.000	0.000
45	A	88	GLY	0	0.031	0.008	23.994	-0.133	-0.133	0.000	0.000	0.000	0.000
46	A	89	GLY	0	-0.002	0.019	24.649	-0.213	-0.213	0.000	0.000	0.000	0.000
47	A	90	VAL	0	-0.064	-0.032	23.848	0.091	0.091	0.000	0.000	0.000	0.000
48	A	91	GLY	0	0.056	0.019	27.297	0.371	0.371	0.000	0.000	0.000	0.000
49	A	92	PRO	0	-0.036	-0.020	29.876	-0.042	-0.042	0.000	0.000	0.000	0.000
50	A	93	ASP	-1	-0.849	-0.919	33.055	-8.860	-8.860	0.000	0.000	0.000	0.000
51	A	94	GLY	0	-0.055	-0.028	30.132	0.104	0.104	0.000	0.000	0.000	0.000
52	A	95	ASP	-1	-0.778	-0.875	30.711	-9.624	-9.624	0.000	0.000	0.000	0.000
53	A	96	ILE	0	0.006	0.017	27.191	0.121	0.121	0.000	0.000	0.000	0.000
54	A	97	VAL	0	0.044	0.026	26.048	-0.402	-0.402	0.000	0.000	0.000	0.000
55	A	98	GLY	0	0.006	-0.006	23.650	0.243	0.243	0.000	0.000	0.000	0.000
56	A	99	PHE	0	-0.008	0.011	23.114	-0.345	-0.345	0.000	0.000	0.000	0.000
57	A	100	SER	0	0.027	0.029	21.482	0.059	0.059	0.000	0.000	0.000	0.000
58	A	101	THR	0	0.031	0.006	23.197	0.436	0.436	0.000	0.000	0.000	0.000
59	A	102	ILE	0	-0.025	0.005	23.119	0.603	0.603	0.000	0.000	0.000	0.000
60	A	103	CYS	0	-0.036	-0.002	24.903	-0.275	-0.275	0.000	0.000	0.000	0.000
61	A	104	PRO	0	0.057	0.015	23.385	0.069	0.069	0.000	0.000	0.000	0.000
62	A	105	HIS	0	-0.048	-0.013	24.887	-0.077	-0.077	0.000	0.000	0.000	0.000
63	A	106	LYS	1	0.889	0.912	27.247	11.044	11.044	0.000	0.000	0.000	0.000
64	A	107	GLY	0	0.068	0.034	26.215	0.186	0.186	0.000	0.000	0.000	0.000
65	A	108	PHE	0	-0.035	-0.019	27.027	0.168	0.168	0.000	0.000	0.000	0.000
66	A	109	PRO	0	0.019	0.005	29.295	-0.210	-0.210	0.000	0.000	0.000	0.000
67	A	110	LEU	0	-0.053	-0.014	27.940	0.441	0.441	0.000	0.000	0.000	0.000
68	A	111	SER	0	-0.039	-0.019	31.393	0.115	0.115	0.000	0.000	0.000	0.000
69	A	112	TYR	0	0.035	-0.008	33.394	-0.208	-0.208	0.000	0.000	0.000	0.000
70	A	113	SER	0	-0.043	-0.014	35.163	0.296	0.296	0.000	0.000	0.000	0.000
71	A	114	ALA	0	0.062	0.019	38.145	-0.071	-0.071	0.000	0.000	0.000	0.000
72	A	115	ASP	-1	-0.935	-0.961	39.255	-7.359	-7.359	0.000	0.000	0.000	0.000
73	A	116	ASN	0	-0.093	-0.055	39.467	0.095	0.095	0.000	0.000	0.000	0.000
74	A	117	LYS	1	0.889	0.968	35.746	8.451	8.451	0.000	0.000	0.000	0.000
75	A	118	THR	0	-0.019	-0.014	34.616	-0.182	-0.182	0.000	0.000	0.000	0.000
76	A	119	PHE	0	0.039	0.020	29.932	0.097	0.097	0.000	0.000	0.000	0.000
77	A	120	ASN	0	-0.003	-0.001	32.934	0.032	0.032	0.000	0.000	0.000	0.000
78	A	121	CYS	0	0.005	0.009	31.633	0.003	0.003	0.000	0.000	0.000	0.000
79	A	122	PRO	0	-0.012	-0.004	33.738	0.232	0.232	0.000	0.000	0.000	0.000
80	A	123	GLY	0	-0.001	0.004	34.566	0.207	0.207	0.000	0.000	0.000	0.000
81	A	124	HIS	0	-0.011	-0.031	32.854	-0.022	-0.022	0.000	0.000	0.000	0.000
82	A	125	PHE	0	0.004	-0.006	35.819	-0.048	-0.048	0.000	0.000	0.000	0.000
83	A	126	SER	0	-0.007	0.015	32.309	-0.011	-0.011	0.000	0.000	0.000	0.000
84	A	127	VAL	0	-0.027	-0.010	34.006	0.018	0.018	0.000	0.000	0.000	0.000
85	A	128	PHE	0	0.005	-0.009	27.994	-0.105	-0.105	0.000	0.000	0.000	0.000
86	A	129	ASP	-1	-0.804	-0.911	31.036	-9.357	-9.357	0.000	0.000	0.000	0.000
87	A	130	PRO	0	-0.019	0.001	29.194	-0.364	-0.364	0.000	0.000	0.000	0.000
88	A	131	GLU	-1	-0.853	-0.932	30.046	-8.971	-8.971	0.000	0.000	0.000	0.000
89	A	132	LYS	1	0.823	0.910	30.885	9.470	9.470	0.000	0.000	0.000	0.000
90	A	133	GLY	0	0.100	0.061	26.436	-0.058	-0.058	0.000	0.000	0.000	0.000
91	A	134	GLY	0	0.025	0.020	25.815	-0.404	-0.404	0.000	0.000	0.000	0.000
92	A	135	GLN	0	-0.067	-0.032	27.279	0.213	0.213	0.000	0.000	0.000	0.000
93	A	136	GLN	0	0.016	-0.005	29.163	0.301	0.301	0.000	0.000	0.000	0.000
94	A	137	VAL	0	-0.020	0.000	30.761	0.147	0.147	0.000	0.000	0.000	0.000
95	A	138	TRP	0	-0.009	-0.016	34.486	0.232	0.232	0.000	0.000	0.000	0.000
96	A	139	GLY	0	-0.006	-0.017	32.884	-0.080	-0.080	0.000	0.000	0.000	0.000
97	A	140	GLN	0	-0.041	-0.006	31.961	0.052	0.052	0.000	0.000	0.000	0.000
98	A	141	ALA	0	-0.015	0.010	26.475	-0.195	-0.195	0.000	0.000	0.000	0.000
99	A	142	THR	0	-0.043	-0.022	24.061	0.326	0.326	0.000	0.000	0.000	0.000
100	A	143	GLN	0	-0.083	-0.050	20.031	0.181	0.181	0.000	0.000	0.000	0.000
101	A	144	ASN	0	0.029	0.012	24.127	0.973	0.973	0.000	0.000	0.000	0.000
102	A	145	LEU	0	-0.025	-0.019	23.764	-0.425	-0.425	0.000	0.000	0.000	0.000
103	A	146	PRO	0	-0.005	-0.004	19.157	0.111	0.111	0.000	0.000	0.000	0.000
104	A	147	GLN	0	0.015	0.009	20.783	0.547	0.547	0.000	0.000	0.000	0.000
105	A	148	TYR	0	-0.032	-0.028	18.515	-0.767	-0.767	0.000	0.000	0.000	0.000
106	A	149	VAL	0	-0.018	-0.013	15.814	0.783	0.783	0.000	0.000	0.000	0.000
107	A	150	LEU	0	0.001	0.001	18.031	-0.550	-0.550	0.000	0.000	0.000	0.000
108	A	151	ARG	1	0.871	0.926	18.945	15.882	15.882	0.000	0.000	0.000	0.000
109	A	152	VAL	0	-0.023	-0.012	21.610	0.105	0.105	0.000	0.000	0.000	0.000
110	A	153	ALA	0	-0.041	-0.022	23.316	-0.075	-0.075	0.000	0.000	0.000	0.000
111	A	154	ASP	-1	-0.915	-0.981	24.623	-12.610	-12.610	0.000	0.000	0.000	0.000
112	A	155	ASN	0	-0.068	-0.029	27.335	0.228	0.228	0.000	0.000	0.000	0.000
113	A	156	GLY	0	0.040	0.017	28.213	0.476	0.476	0.000	0.000	0.000	0.000
114	A	157	ASP	-1	-0.847	-0.897	24.969	-11.628	-11.628	0.000	0.000	0.000	0.000
115	A	158	ILE	0	-0.011	0.002	23.268	-0.316	-0.316	0.000	0.000	0.000	0.000
116	A	159	PHE	0	-0.012	-0.018	18.590	-0.028	-0.028	0.000	0.000	0.000	0.000
117	A	160	ALA	0	0.015	0.012	17.904	0.407	0.407	0.000	0.000	0.000	0.000
118	A	161	GLU	-1	-0.899	-0.951	14.295	-19.146	-19.146	0.000	0.000	0.000	0.000
119	A	162	GLY	0	0.013	0.001	12.813	-2.161	-2.161	0.000	0.000	0.000	0.000
120	A	163	VAL	0	-0.052	-0.018	13.643	1.601	1.601	0.000	0.000	0.000	0.000
121	A	164	ASP	-1	-0.840	-0.914	14.452	-17.551	-17.551	0.000	0.000	0.000	0.000
122	A	165	GLU	-1	-0.838	-0.891	17.030	-16.206	-16.206	0.000	0.000	0.000	0.000
123	A	166	LEU	0	-0.090	-0.041	14.479	-0.687	-0.687	0.000	0.000	0.000	0.000
124	A	167	ILE	0	0.044	0.013	16.294	1.215	1.215	0.000	0.000	0.000	0.000
125	A	168	TYR	0	-0.005	0.005	18.564	-0.176	-0.176	0.000	0.000	0.000	0.000
126	A	169	GLY	0	-0.026	-0.014	20.619	-0.119	-0.119	0.000	0.000	0.000	0.000
127	A	170	ARG	1	0.775	0.859	14.932	19.036	19.036	0.000	0.000	0.000	0.000
128	A	171	LEU	0	-0.016	-0.017	14.362	0.080	0.080	0.000	0.000	0.000	0.000
129	A	172	SER	0	-0.044	-0.031	9.780	-1.890	-1.890	0.000	0.000	0.000	0.000
130	A	173	ASN	0	0.040	0.001	11.880	1.903	1.903	0.000	0.000	0.000	0.000
131	A	174	VAL	0	-0.017	0.001	8.900	1.622	1.622	0.000	0.000	0.000	0.000
132	A	175	LEU	-1	-0.909	-0.928	10.638	-27.417	-27.417	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:44:ALA)