FMO DATABASE

FMODB ID: 94752

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	OptAll
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	-962663.217829
FMO2-HF: Nuclear repulsion	909154.850693
FMO2-HF: Total energy	-53508.367137
FMO2-MP2: Total energy	-53661.014674

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.
-15.23	-10.404	8.081	-5.446	-7.463	0.015

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 : 0.004 / q_NPA : -0.008

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	-0.004	0.015	3.118	-2.136	0.540	0.152	-1.347	-1.482	0.005
4	A	31	ARG	1	0.904	0.937	2.080	-12.052	-11.114	7.886	-3.689	-5.136	0.013
5	A	32	ILE	0	-0.019	0.002	2.889	-0.501	0.576	0.044	-0.398	-0.723	-0.003
6	A	33	MET	0	-0.011	0.007	5.013	0.637	0.772	-0.001	-0.012	-0.122	0.000
7	A	34	GLU	-1	-0.919	-0.971	6.187	-0.060	-0.060	0.000	0.000	0.000	0.000
8	A	35	GLU	-1	-0.841	-0.916	6.027	0.008	0.008	0.000	0.000	0.000	0.000
9	A	36	LYS	1	0.921	0.976	8.914	0.584	0.584	0.000	0.000	0.000	0.000
10	A	37	ALA	0	0.005	0.005	10.987	0.082	0.082	0.000	0.000	0.000	0.000
11	A	38	LEU	0	0.013	0.008	12.143	0.053	0.053	0.000	0.000	0.000	0.000
12	A	39	GLU	-1	-0.954	-0.978	12.964	-0.153	-0.153	0.000	0.000	0.000	0.000
13	A	40	VAL	0	-0.012	-0.015	14.740	0.032	0.032	0.000	0.000	0.000	0.000
14	A	41	TYR	0	-0.041	-0.062	16.430	0.022	0.022	0.000	0.000	0.000	0.000
15	A	42	ASP	-1	-0.846	-0.926	17.389	-0.028	-0.028	0.000	0.000	0.000	0.000
16	A	43	LEU	0	-0.063	-0.011	18.751	0.015	0.015	0.000	0.000	0.000	0.000
17	A	44	ILE	0	-0.016	-0.016	20.859	0.008	0.008	0.000	0.000	0.000	0.000
18	A	45	ARG	1	0.743	0.851	20.434	0.056	0.056	0.000	0.000	0.000	0.000
19	A	46	THR	0	0.012	-0.010	23.911	0.005	0.005	0.000	0.000	0.000	0.000
20	A	47	ILE	0	-0.030	0.012	25.689	0.007	0.007	0.000	0.000	0.000	0.000
21	A	48	ARG	1	0.832	0.912	28.492	0.033	0.033	0.000	0.000	0.000	0.000
22	A	49	ASP	-1	-0.705	-0.826	32.138	-0.055	-0.055	0.000	0.000	0.000	0.000
23	A	50	PRO	0	0.026	0.001	33.658	0.005	0.005	0.000	0.000	0.000	0.000
24	A	51	GLU	-1	-0.889	-0.929	36.542	-0.037	-0.037	0.000	0.000	0.000	0.000
25	A	52	LYS	1	0.785	0.863	36.250	0.050	0.050	0.000	0.000	0.000	0.000
26	A	53	PRO	0	-0.081	-0.038	36.814	0.000	0.000	0.000	0.000	0.000	0.000
27	A	54	ASN	0	-0.075	-0.049	33.250	0.003	0.003	0.000	0.000	0.000	0.000
28	A	55	THR	0	-0.009	-0.036	28.604	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	56	LEU	0	-0.013	-0.017	26.866	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	57	GLU	-1	-0.765	-0.831	23.041	-0.068	-0.068	0.000	0.000	0.000	0.000
31	A	58	GLU	-1	-0.853	-0.893	26.798	-0.034	-0.034	0.000	0.000	0.000	0.000
32	A	59	LEU	0	-0.075	-0.035	30.124	0.002	0.002	0.000	0.000	0.000	0.000
33	A	60	GLU	-1	-0.969	-0.978	27.697	-0.077	-0.077	0.000	0.000	0.000	0.000
34	A	61	VAL	0	-0.055	-0.005	28.029	-0.006	-0.006	0.000	0.000	0.000	0.000
35	A	62	VAL	0	0.016	-0.010	23.164	-0.010	-0.010	0.000	0.000	0.000	0.000
36	A	63	SER	0	0.043	0.018	21.915	0.003	0.003	0.000	0.000	0.000	0.000
37	A	64	GLU	-1	-0.847	-0.922	14.336	-0.166	-0.166	0.000	0.000	0.000	0.000
38	A	65	SER	0	-0.044	-0.021	17.045	-0.022	-0.022	0.000	0.000	0.000	0.000
39	A	66	CYS	0	-0.082	-0.028	18.106	-0.011	-0.011	0.000	0.000	0.000	0.000
40	A	67	VAL	0	0.025	0.011	15.846	0.003	0.003	0.000	0.000	0.000	0.000
41	A	68	GLU	-1	-0.944	-0.958	13.852	-0.365	-0.365	0.000	0.000	0.000	0.000
42	A	69	VAL	0	-0.017	-0.011	11.936	0.033	0.033	0.000	0.000	0.000	0.000
43	A	70	GLN	0	-0.066	-0.047	12.073	-0.065	-0.065	0.000	0.000	0.000	0.000
44	A	71	GLU	-1	-0.788	-0.889	9.728	-0.663	-0.663	0.000	0.000	0.000	0.000
45	A	72	ILE	0	-0.080	-0.032	12.753	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	73	ASN	0	-0.067	-0.049	15.564	0.032	0.032	0.000	0.000	0.000	0.000
47	A	74	GLU	-1	-0.926	-0.969	12.797	-0.295	-0.295	0.000	0.000	0.000	0.000
48	A	75	GLU	-1	-0.997	-0.987	13.086	-0.021	-0.021	0.000	0.000	0.000	0.000
49	A	76	GLU	-1	-0.967	-0.973	14.360	-0.148	-0.148	0.000	0.000	0.000	0.000
50	A	77	TYR	0	-0.065	-0.068	10.208	-0.043	-0.043	0.000	0.000	0.000	0.000
51	A	78	LEU	0	-0.008	0.016	15.464	0.050	0.050	0.000	0.000	0.000	0.000
52	A	79	VAL	0	0.014	-0.008	15.780	-0.044	-0.044	0.000	0.000	0.000	0.000
53	A	80	ILE	0	-0.032	-0.009	17.747	0.030	0.030	0.000	0.000	0.000	0.000
54	A	81	ILE	0	0.034	0.003	19.097	-0.009	-0.009	0.000	0.000	0.000	0.000
55	A	82	ARG	1	0.810	0.913	17.826	0.226	0.226	0.000	0.000	0.000	0.000
56	A	83	PHE	0	0.031	0.011	23.672	0.004	0.004	0.000	0.000	0.000	0.000
57	A	84	THR	0	-0.005	-0.003	26.295	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	85	PRO	0	-0.013	-0.008	29.491	0.006	0.006	0.000	0.000	0.000	0.000
59	A	86	THR	0	-0.002	-0.007	32.627	0.003	0.003	0.000	0.000	0.000	0.000
60	A	87	VAL	0	-0.005	0.000	35.321	0.001	0.001	0.000	0.000	0.000	0.000
61	A	88	PRO	0	-0.009	-0.012	38.793	0.002	0.002	0.000	0.000	0.000	0.000
62	A	89	HIS	0	-0.013	0.004	41.579	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	90	CYS	0	-0.051	-0.030	43.658	0.002	0.002	0.000	0.000	0.000	0.000
64	A	91	SER	0	0.060	0.055	44.969	0.001	0.001	0.000	0.000	0.000	0.000
65	A	92	LEU	0	0.085	0.027	46.227	0.002	0.002	0.000	0.000	0.000	0.000
66	A	93	ALA	0	0.035	0.015	48.500	0.002	0.002	0.000	0.000	0.000	0.000
67	A	94	THR	0	0.007	-0.001	48.329	0.002	0.002	0.000	0.000	0.000	0.000
68	A	95	LEU	0	0.027	0.003	48.640	0.002	0.002	0.000	0.000	0.000	0.000
69	A	96	ILE	0	0.030	0.023	52.173	0.002	0.002	0.000	0.000	0.000	0.000
70	A	97	GLY	0	0.030	0.016	54.085	0.001	0.001	0.000	0.000	0.000	0.000
71	A	98	LEU	0	-0.014	-0.013	52.795	0.001	0.001	0.000	0.000	0.000	0.000
72	A	99	CYS	0	-0.028	-0.018	55.523	0.002	0.002	0.000	0.000	0.000	0.000
73	A	100	LEU	0	-0.009	-0.003	58.077	0.001	0.001	0.000	0.000	0.000	0.000
74	A	101	ARG	1	0.885	0.930	58.736	0.026	0.026	0.000	0.000	0.000	0.000
75	A	102	VAL	0	-0.011	-0.012	59.279	0.001	0.001	0.000	0.000	0.000	0.000
76	A	103	LYS	1	0.916	0.935	62.049	0.019	0.019	0.000	0.000	0.000	0.000
77	A	104	LEU	0	0.007	-0.007	63.666	0.001	0.001	0.000	0.000	0.000	0.000
78	A	105	GLN	0	0.016	0.005	63.144	0.001	0.001	0.000	0.000	0.000	0.000
79	A	106	ARG	1	0.903	0.951	62.018	0.018	0.018	0.000	0.000	0.000	0.000
80	A	107	CYS	0	-0.051	-0.004	68.189	0.001	0.001	0.000	0.000	0.000	0.000
81	A	108	LEU	0	0.027	0.044	68.506	0.000	0.000	0.000	0.000	0.000	0.000
82	A	109	PRO	0	-0.014	0.003	71.525	0.000	0.000	0.000	0.000	0.000	0.000
83	A	110	PHE	0	0.014	-0.005	72.019	0.000	0.000	0.000	0.000	0.000	0.000
84	A	111	LYS	1	0.965	0.987	73.004	0.014	0.014	0.000	0.000	0.000	0.000
85	A	112	HIS	0	-0.015	-0.008	67.560	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	113	LYS	1	0.939	0.961	66.904	0.019	0.019	0.000	0.000	0.000	0.000
87	A	114	LEU	0	0.038	0.024	62.568	0.000	0.000	0.000	0.000	0.000	0.000
88	A	115	GLU	-1	-0.845	-0.877	61.281	-0.026	-0.026	0.000	0.000	0.000	0.000
89	A	116	ILE	0	-0.043	-0.043	57.067	0.001	0.001	0.000	0.000	0.000	0.000
90	A	117	TYR	0	-0.029	-0.027	55.897	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	118	ILE	0	0.027	0.013	50.548	0.001	0.001	0.000	0.000	0.000	0.000
92	A	119	SER	0	-0.003	-0.002	53.883	0.000	0.000	0.000	0.000	0.000	0.000
93	A	120	GLU	-1	-0.824	-0.905	51.521	-0.042	-0.042	0.000	0.000	0.000	0.000
94	A	121	GLY	0	-0.049	-0.017	54.004	0.000	0.000	0.000	0.000	0.000	0.000
95	A	122	THR	0	-0.088	-0.050	52.785	0.001	0.001	0.000	0.000	0.000	0.000
96	A	123	HIS	0	-0.036	-0.016	48.147	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	124	SER	0	0.014	-0.007	45.423	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	125	THR	0	-0.057	-0.041	40.076	0.001	0.001	0.000	0.000	0.000	0.000
99	A	126	GLU	-1	-0.879	-0.917	38.539	-0.072	-0.072	0.000	0.000	0.000	0.000
100	A	127	GLU	-1	-0.850	-0.921	31.702	-0.099	-0.099	0.000	0.000	0.000	0.000
101	A	128	ASP	-1	-0.824	-0.882	34.749	-0.067	-0.067	0.000	0.000	0.000	0.000
102	A	129	ILE	0	0.025	0.010	33.547	0.001	0.001	0.000	0.000	0.000	0.000
103	A	130	ASN	0	0.053	0.007	29.636	-0.003	-0.003	0.000	0.000	0.000	0.000
104	A	131	LYS	1	0.841	0.925	31.428	0.072	0.072	0.000	0.000	0.000	0.000
105	A	132	GLN	0	-0.105	-0.090	33.566	0.001	0.001	0.000	0.000	0.000	0.000
106	A	133	ILE	0	0.007	0.015	29.293	0.004	0.004	0.000	0.000	0.000	0.000
107	A	134	ASN	0	-0.016	-0.006	26.910	-0.013	-0.013	0.000	0.000	0.000	0.000
108	A	135	ASP	-1	-0.895	-0.933	29.571	-0.076	-0.076	0.000	0.000	0.000	0.000
109	A	136	LYS	1	0.919	0.934	30.906	0.076	0.076	0.000	0.000	0.000	0.000
110	A	137	GLU	-1	-0.838	-0.902	32.408	-0.056	-0.056	0.000	0.000	0.000	0.000
111	A	138	ARG	1	0.747	0.856	35.116	0.067	0.067	0.000	0.000	0.000	0.000
112	A	139	VAL	0	0.059	0.031	30.717	0.004	0.004	0.000	0.000	0.000	0.000
113	A	140	ALA	0	0.006	0.005	33.987	0.004	0.004	0.000	0.000	0.000	0.000
114	A	141	ALA	0	-0.025	-0.023	35.944	0.004	0.004	0.000	0.000	0.000	0.000
115	A	142	ALA	0	-0.039	-0.018	35.980	0.003	0.003	0.000	0.000	0.000	0.000
116	A	143	MET	0	0.007	-0.001	32.945	0.003	0.003	0.000	0.000	0.000	0.000
117	A	144	GLU	-1	-0.923	-0.959	36.981	-0.033	-0.033	0.000	0.000	0.000	0.000
118	A	145	ASN	0	-0.029	0.000	40.248	0.005	0.005	0.000	0.000	0.000	0.000
119	A	146	PRO	0	0.006	-0.004	40.992	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	147	ASN	0	-0.034	-0.025	41.384	0.001	0.001	0.000	0.000	0.000	0.000
121	A	148	LEU	0	-0.044	-0.011	38.445	0.000	0.000	0.000	0.000	0.000	0.000
122	A	149	ARG	1	0.788	0.866	36.637	0.028	0.028	0.000	0.000	0.000	0.000
123	A	150	GLU	-1	-0.831	-0.918	36.795	-0.026	-0.026	0.000	0.000	0.000	0.000
124	A	151	ILE	0	-0.040	-0.013	36.834	0.001	0.001	0.000	0.000	0.000	0.000
125	A	152	VAL	0	0.030	0.011	32.050	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	153	GLU	-1	-0.805	-0.881	32.921	-0.032	-0.032	0.000	0.000	0.000	0.000
127	A	154	GLN	0	-0.063	-0.037	33.445	0.003	0.003	0.000	0.000	0.000	0.000
128	A	155	CYS	0	-0.087	-0.040	32.483	0.002	0.002	0.000	0.000	0.000	0.000
129	A	156	VAL	0	0.008	0.011	28.461	-0.002	-0.002	0.000	0.000	0.000	0.000
130	A	157	LEU	0	-0.063	-0.011	29.297	0.005	0.005	0.000	0.000	0.000	0.000

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