FMO DATABASE

FMODB ID: 39Z2L

Calculation Name: 3UX2-A-Xray372

Preferred Name: Cytosolic iron-sulfur assembly component 2A

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3UX2

Chain ID: A

ChEMBL ID: CHEMBL4295943

UniProt ID: Q9H5X1

Base Structure: X-ray

Registration Date: 2023-06-22

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	130
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-962073.184932
FMO2-HF: Nuclear repulsion	908565.784328
FMO2-HF: Total energy	-53507.400604
FMO2-MP2: Total energy	-53660.122241

3D Structure

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:-3:SER)

Summations of interaction energy for fragment #1(A:-3:SER)

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.
-14.484	-7.6	4.284	-4.379	-6.789	0.017

Interaction energy analysis for fragmet #1(A:-3:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.012 / q_NPA : -0.004

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	-1	ALA	0	0.009	0.005	2.838	-1.499	1.539	0.240	-1.549	-1.729	0.005
4	A	31	ARG	1	0.914	0.956	2.218	-9.880	-7.037	4.000	-2.481	-4.363	0.013
5	A	32	ILE	0	-0.015	0.000	3.018	-1.476	-0.473	0.044	-0.349	-0.697	-0.001
6	A	33	MET	0	-0.018	-0.007	5.406	0.437	0.437	0.000	0.000	0.000	0.000
7	A	34	GLU	-1	-0.951	-0.976	6.667	-0.622	-0.622	0.000	0.000	0.000	0.000
8	A	35	GLU	-1	-0.861	-0.928	6.911	-0.082	-0.082	0.000	0.000	0.000	0.000
9	A	36	LYS	1	0.928	0.974	9.251	0.476	0.476	0.000	0.000	0.000	0.000
10	A	37	ALA	0	0.022	0.005	11.570	0.051	0.051	0.000	0.000	0.000	0.000
11	A	38	LEU	0	0.016	0.020	12.611	0.035	0.035	0.000	0.000	0.000	0.000
12	A	39	GLU	-1	-0.949	-0.974	13.292	-0.137	-0.137	0.000	0.000	0.000	0.000
13	A	40	VAL	0	-0.030	-0.016	15.548	0.022	0.022	0.000	0.000	0.000	0.000
14	A	41	TYR	0	-0.033	-0.037	17.157	0.018	0.018	0.000	0.000	0.000	0.000
15	A	42	ASP	-1	-0.841	-0.936	18.024	-0.075	-0.075	0.000	0.000	0.000	0.000
16	A	43	LEU	0	-0.071	-0.019	19.982	0.016	0.016	0.000	0.000	0.000	0.000
17	A	44	ILE	0	-0.029	-0.023	21.392	0.009	0.009	0.000	0.000	0.000	0.000
18	A	45	ARG	1	0.796	0.909	21.464	0.082	0.082	0.000	0.000	0.000	0.000
19	A	46	THR	0	0.010	-0.012	24.426	0.005	0.005	0.000	0.000	0.000	0.000
20	A	47	ILE	0	-0.041	0.013	26.268	0.007	0.007	0.000	0.000	0.000	0.000
21	A	48	ARG	1	0.887	0.947	29.263	0.043	0.043	0.000	0.000	0.000	0.000
22	A	49	ASP	-1	-0.713	-0.838	32.762	-0.066	-0.066	0.000	0.000	0.000	0.000
23	A	50	PRO	0	0.012	-0.018	33.977	0.005	0.005	0.000	0.000	0.000	0.000
24	A	51	GLU	-1	-0.904	-0.955	36.961	-0.046	-0.046	0.000	0.000	0.000	0.000
25	A	52	LYS	1	0.846	0.914	36.707	0.061	0.061	0.000	0.000	0.000	0.000
26	A	53	PRO	0	-0.088	-0.040	36.928	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	54	ASN	0	-0.047	-0.028	33.255	0.003	0.003	0.000	0.000	0.000	0.000
28	A	55	THR	0	0.017	0.013	29.158	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	56	LEU	0	0.018	0.001	27.233	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	57	GLU	-1	-0.797	-0.882	23.464	-0.094	-0.094	0.000	0.000	0.000	0.000
31	A	58	GLU	-1	-0.920	-0.961	26.618	-0.055	-0.055	0.000	0.000	0.000	0.000
32	A	59	LEU	0	-0.098	-0.049	29.745	0.002	0.002	0.000	0.000	0.000	0.000
33	A	60	GLU	-1	-0.962	-0.972	27.119	-0.098	-0.098	0.000	0.000	0.000	0.000
34	A	61	VAL	0	-0.061	-0.016	27.817	-0.005	-0.005	0.000	0.000	0.000	0.000
35	A	62	VAL	0	0.016	-0.011	22.906	-0.009	-0.009	0.000	0.000	0.000	0.000
36	A	63	SER	0	0.014	-0.014	21.549	0.002	0.002	0.000	0.000	0.000	0.000
37	A	64	GLU	-1	-0.820	-0.909	14.261	-0.214	-0.214	0.000	0.000	0.000	0.000
38	A	65	SER	0	-0.070	-0.032	16.286	-0.020	-0.020	0.000	0.000	0.000	0.000
39	A	66	CYS	0	-0.134	-0.048	17.376	-0.011	-0.011	0.000	0.000	0.000	0.000
40	A	67	VAL	0	0.034	0.007	15.707	0.009	0.009	0.000	0.000	0.000	0.000
41	A	68	GLU	-1	-0.928	-0.958	13.168	-0.426	-0.426	0.000	0.000	0.000	0.000
42	A	69	VAL	0	-0.031	-0.017	12.080	0.033	0.033	0.000	0.000	0.000	0.000
43	A	70	GLN	0	-0.037	-0.016	11.559	-0.062	-0.062	0.000	0.000	0.000	0.000
44	A	71	GLU	-1	-0.848	-0.936	9.845	-0.600	-0.600	0.000	0.000	0.000	0.000
45	A	72	ILE	0	-0.073	-0.022	12.679	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	73	ASN	0	-0.054	-0.048	15.793	0.027	0.027	0.000	0.000	0.000	0.000
47	A	74	GLU	-1	-0.936	-0.959	12.061	-0.271	-0.271	0.000	0.000	0.000	0.000
48	A	75	GLU	-1	-1.020	-1.013	12.970	-0.022	-0.022	0.000	0.000	0.000	0.000
49	A	76	GLU	-1	-0.967	-0.968	14.258	-0.132	-0.132	0.000	0.000	0.000	0.000
50	A	77	TYR	0	-0.025	-0.026	10.257	-0.018	-0.018	0.000	0.000	0.000	0.000
51	A	78	LEU	0	-0.022	-0.001	15.290	0.048	0.048	0.000	0.000	0.000	0.000
52	A	79	VAL	0	0.015	-0.004	16.033	-0.038	-0.038	0.000	0.000	0.000	0.000
53	A	80	ILE	0	-0.022	0.003	16.805	0.030	0.030	0.000	0.000	0.000	0.000
54	A	81	ILE	0	0.025	-0.003	18.743	-0.010	-0.010	0.000	0.000	0.000	0.000
55	A	82	ARG	1	0.875	0.954	19.063	0.224	0.224	0.000	0.000	0.000	0.000
56	A	83	PHE	0	0.020	-0.003	23.562	0.000	0.000	0.000	0.000	0.000	0.000
57	A	84	THR	0	-0.002	-0.007	26.218	0.000	0.000	0.000	0.000	0.000	0.000
58	A	85	PRO	0	-0.020	-0.001	29.285	0.005	0.005	0.000	0.000	0.000	0.000
59	A	86	THR	0	-0.013	-0.003	32.223	0.001	0.001	0.000	0.000	0.000	0.000
60	A	87	VAL	0	-0.030	-0.020	34.831	0.001	0.001	0.000	0.000	0.000	0.000
61	A	88	PRO	0	-0.003	-0.019	38.392	0.002	0.002	0.000	0.000	0.000	0.000
62	A	89	HIS	0	-0.022	0.001	41.445	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	90	CYS	0	-0.067	-0.041	43.453	0.002	0.002	0.000	0.000	0.000	0.000
64	A	91	SER	0	0.067	0.047	44.812	0.001	0.001	0.000	0.000	0.000	0.000
65	A	92	LEU	0	0.119	0.037	45.929	0.002	0.002	0.000	0.000	0.000	0.000
66	A	93	ALA	0	0.007	0.018	47.953	0.002	0.002	0.000	0.000	0.000	0.000
67	A	94	THR	0	0.018	0.004	48.896	0.001	0.001	0.000	0.000	0.000	0.000
68	A	95	LEU	0	0.045	0.010	49.070	0.002	0.002	0.000	0.000	0.000	0.000
69	A	96	ILE	0	0.018	0.018	51.897	0.002	0.002	0.000	0.000	0.000	0.000
70	A	97	GLY	0	0.030	0.018	53.600	0.002	0.002	0.000	0.000	0.000	0.000
71	A	98	LEU	0	0.002	-0.014	52.605	0.002	0.002	0.000	0.000	0.000	0.000
72	A	99	CYS	0	-0.038	-0.013	55.606	0.002	0.002	0.000	0.000	0.000	0.000
73	A	100	LEU	0	-0.011	-0.003	57.837	0.002	0.002	0.000	0.000	0.000	0.000
74	A	101	ARG	1	0.917	0.942	58.861	0.031	0.031	0.000	0.000	0.000	0.000
75	A	102	VAL	0	-0.001	-0.005	59.117	0.001	0.001	0.000	0.000	0.000	0.000
76	A	103	LYS	1	0.961	0.981	61.856	0.023	0.023	0.000	0.000	0.000	0.000
77	A	104	LEU	0	0.012	0.002	63.790	0.001	0.001	0.000	0.000	0.000	0.000
78	A	105	GLN	0	-0.026	-0.016	62.363	0.001	0.001	0.000	0.000	0.000	0.000
79	A	106	ARG	1	0.905	0.947	61.958	0.024	0.024	0.000	0.000	0.000	0.000
80	A	107	CYS	0	-0.052	-0.019	67.722	0.001	0.001	0.000	0.000	0.000	0.000
81	A	108	LEU	0	-0.017	0.012	68.499	0.000	0.000	0.000	0.000	0.000	0.000
82	A	109	PRO	0	0.004	0.012	71.116	0.000	0.000	0.000	0.000	0.000	0.000
83	A	110	PHE	0	0.022	0.006	71.439	0.001	0.001	0.000	0.000	0.000	0.000
84	A	111	LYS	1	0.970	0.986	72.591	0.018	0.018	0.000	0.000	0.000	0.000
85	A	112	HIS	0	-0.025	-0.015	67.115	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	113	LYS	1	0.949	0.973	66.216	0.024	0.024	0.000	0.000	0.000	0.000
87	A	114	LEU	0	0.030	0.017	61.826	0.000	0.000	0.000	0.000	0.000	0.000
88	A	115	GLU	-1	-0.899	-0.910	60.968	-0.030	-0.030	0.000	0.000	0.000	0.000
89	A	116	ILE	0	-0.022	-0.018	56.941	0.001	0.001	0.000	0.000	0.000	0.000
90	A	117	TYR	0	-0.035	-0.044	55.992	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	118	ILE	0	0.016	0.012	50.427	0.001	0.001	0.000	0.000	0.000	0.000
92	A	119	SER	0	-0.016	-0.014	53.811	0.000	0.000	0.000	0.000	0.000	0.000
93	A	120	GLU	-1	-0.793	-0.886	51.572	-0.047	-0.047	0.000	0.000	0.000	0.000
94	A	121	GLY	0	-0.071	-0.029	54.173	0.000	0.000	0.000	0.000	0.000	0.000
95	A	122	THR	0	-0.086	-0.049	52.728	0.001	0.001	0.000	0.000	0.000	0.000
96	A	123	HIS	0	-0.040	-0.025	48.241	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	124	SER	0	0.014	-0.002	45.118	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	125	THR	0	-0.049	-0.036	39.742	0.001	0.001	0.000	0.000	0.000	0.000
99	A	126	GLU	-1	-0.894	-0.922	38.556	-0.075	-0.075	0.000	0.000	0.000	0.000
100	A	127	GLU	-1	-0.847	-0.908	31.722	-0.109	-0.109	0.000	0.000	0.000	0.000
101	A	128	ASP	-1	-0.922	-0.982	34.526	-0.073	-0.073	0.000	0.000	0.000	0.000
102	A	129	ILE	0	0.044	0.020	32.984	0.001	0.001	0.000	0.000	0.000	0.000
103	A	130	ASN	0	0.017	-0.006	30.006	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	131	LYS	1	0.935	0.970	31.403	0.070	0.070	0.000	0.000	0.000	0.000
105	A	132	GLN	0	-0.129	-0.083	33.847	0.002	0.002	0.000	0.000	0.000	0.000
106	A	133	ILE	0	0.004	0.014	29.400	0.004	0.004	0.000	0.000	0.000	0.000
107	A	134	ASN	0	-0.028	-0.015	27.219	-0.010	-0.010	0.000	0.000	0.000	0.000
108	A	135	ASP	-1	-0.933	-0.948	29.981	-0.076	-0.076	0.000	0.000	0.000	0.000
109	A	136	LYS	1	0.963	0.965	31.050	0.073	0.073	0.000	0.000	0.000	0.000
110	A	137	GLU	-1	-0.861	-0.939	32.503	-0.055	-0.055	0.000	0.000	0.000	0.000
111	A	138	ARG	1	0.843	0.930	35.579	0.069	0.069	0.000	0.000	0.000	0.000
112	A	139	VAL	0	0.053	0.039	31.155	0.004	0.004	0.000	0.000	0.000	0.000
113	A	140	ALA	0	0.018	0.009	34.352	0.003	0.003	0.000	0.000	0.000	0.000
114	A	141	ALA	0	-0.020	-0.016	36.041	0.004	0.004	0.000	0.000	0.000	0.000
115	A	142	ALA	0	-0.036	-0.021	36.546	0.003	0.003	0.000	0.000	0.000	0.000
116	A	143	MET	0	-0.012	-0.015	33.778	0.002	0.002	0.000	0.000	0.000	0.000
117	A	144	GLU	-1	-0.901	-0.944	37.203	-0.036	-0.036	0.000	0.000	0.000	0.000
118	A	145	ASN	0	-0.066	-0.016	40.553	0.005	0.005	0.000	0.000	0.000	0.000
119	A	146	PRO	0	0.030	-0.002	41.357	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	147	ASN	0	-0.001	-0.008	42.257	0.001	0.001	0.000	0.000	0.000	0.000
121	A	148	LEU	0	-0.034	-0.014	38.901	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	149	ARG	1	0.969	0.997	37.119	0.033	0.033	0.000	0.000	0.000	0.000
123	A	150	GLU	-1	-0.980	-0.983	37.396	-0.031	-0.031	0.000	0.000	0.000	0.000
124	A	151	ILE	0	-0.033	-0.016	37.224	0.000	0.000	0.000	0.000	0.000	0.000
125	A	152	VAL	0	0.023	0.008	32.568	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	153	GLU	-1	-0.910	-0.971	33.532	-0.041	-0.041	0.000	0.000	0.000	0.000
127	A	154	GLN	0	-0.018	0.001	34.158	0.003	0.003	0.000	0.000	0.000	0.000
128	A	155	CYS	0	-0.137	-0.064	33.063	0.001	0.001	0.000	0.000	0.000	0.000
129	A	156	VAL	0	0.007	0.004	29.071	-0.002	-0.002	0.000	0.000	0.000	0.000
130	A	157	LEU	0	-0.057	-0.001	29.781	0.003	0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-3:SER)