FMO DATABASE

FMODB ID: LZG59

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	OptHSide
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	-961802.201316
FMO2-HF: Nuclear repulsion	908294.179981
FMO2-HF: Total energy	-53508.021334
FMO2-MP2: Total energy	-53660.694611

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.
-14.573	-7.699	4.635	-4.599	-6.909	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 : -0.002 / q_NPA : -0.003

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	0.014	0.010	2.867	-2.533	0.786	0.686	-1.815	-2.190	0.009
4	A	31	ARG	1	0.886	0.936	2.194	-9.021	-6.277	3.928	-2.507	-4.165	0.006
5	A	32	ILE	0	-0.017	0.002	3.390	-1.301	-0.490	0.021	-0.277	-0.554	0.000
6	A	33	MET	0	-0.031	-0.008	5.567	0.353	0.353	0.000	0.000	0.000	0.000
7	A	34	GLU	-1	-0.934	-0.974	6.130	-0.160	-0.160	0.000	0.000	0.000	0.000
8	A	35	GLU	-1	-0.836	-0.912	6.572	-0.605	-0.605	0.000	0.000	0.000	0.000
9	A	36	LYS	1	0.909	0.973	9.434	0.582	0.582	0.000	0.000	0.000	0.000
10	A	37	ALA	0	0.022	0.008	11.571	0.045	0.045	0.000	0.000	0.000	0.000
11	A	38	LEU	0	0.005	0.015	12.515	0.024	0.024	0.000	0.000	0.000	0.000
12	A	39	GLU	-1	-0.945	-0.977	13.646	-0.230	-0.230	0.000	0.000	0.000	0.000
13	A	40	VAL	0	-0.014	-0.011	15.507	0.022	0.022	0.000	0.000	0.000	0.000
14	A	41	TYR	0	-0.049	-0.067	17.038	0.018	0.018	0.000	0.000	0.000	0.000
15	A	42	ASP	-1	-0.831	-0.919	17.888	-0.074	-0.074	0.000	0.000	0.000	0.000
16	A	43	LEU	0	-0.056	-0.006	19.734	0.012	0.012	0.000	0.000	0.000	0.000
17	A	44	ILE	0	-0.030	-0.024	21.282	0.009	0.009	0.000	0.000	0.000	0.000
18	A	45	ARG	1	0.737	0.856	20.980	0.078	0.078	0.000	0.000	0.000	0.000
19	A	46	THR	0	0.022	-0.009	24.380	0.005	0.005	0.000	0.000	0.000	0.000
20	A	47	ILE	0	-0.032	0.012	26.274	0.005	0.005	0.000	0.000	0.000	0.000
21	A	48	ARG	1	0.865	0.929	29.100	0.038	0.038	0.000	0.000	0.000	0.000
22	A	49	ASP	-1	-0.707	-0.831	32.619	-0.046	-0.046	0.000	0.000	0.000	0.000
23	A	50	PRO	0	0.028	0.001	33.982	0.003	0.003	0.000	0.000	0.000	0.000
24	A	51	GLU	-1	-0.882	-0.933	36.967	-0.032	-0.032	0.000	0.000	0.000	0.000
25	A	52	LYS	1	0.768	0.850	36.611	0.041	0.041	0.000	0.000	0.000	0.000
26	A	53	PRO	0	-0.077	-0.038	36.978	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	54	ASN	0	-0.046	-0.027	33.445	0.003	0.003	0.000	0.000	0.000	0.000
28	A	55	THR	0	-0.005	-0.020	29.027	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	56	LEU	0	0.014	-0.003	27.304	0.001	0.001	0.000	0.000	0.000	0.000
30	A	57	GLU	-1	-0.765	-0.830	23.326	-0.069	-0.069	0.000	0.000	0.000	0.000
31	A	58	GLU	-1	-0.895	-0.920	26.672	-0.040	-0.040	0.000	0.000	0.000	0.000
32	A	59	LEU	0	-0.101	-0.050	29.802	0.002	0.002	0.000	0.000	0.000	0.000
33	A	60	GLU	-1	-0.965	-0.972	27.125	-0.056	-0.056	0.000	0.000	0.000	0.000
34	A	61	VAL	0	-0.062	-0.019	27.908	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	62	VAL	0	0.014	-0.011	22.873	-0.004	-0.004	0.000	0.000	0.000	0.000
36	A	63	SER	0	0.033	-0.004	21.427	0.002	0.002	0.000	0.000	0.000	0.000
37	A	64	GLU	-1	-0.826	-0.913	14.378	-0.131	-0.131	0.000	0.000	0.000	0.000
38	A	65	SER	0	-0.069	-0.026	16.236	-0.008	-0.008	0.000	0.000	0.000	0.000
39	A	66	CYS	0	-0.116	-0.037	17.327	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	67	VAL	0	0.037	0.007	15.821	0.003	0.003	0.000	0.000	0.000	0.000
41	A	68	GLU	-1	-0.912	-0.934	13.110	-0.160	-0.160	0.000	0.000	0.000	0.000
42	A	69	VAL	0	-0.019	-0.012	12.009	0.001	0.001	0.000	0.000	0.000	0.000
43	A	70	GLN	0	-0.067	-0.050	11.362	-0.006	-0.006	0.000	0.000	0.000	0.000
44	A	71	GLU	-1	-0.775	-0.883	9.764	-0.714	-0.714	0.000	0.000	0.000	0.000
45	A	72	ILE	0	-0.073	-0.025	12.679	0.023	0.023	0.000	0.000	0.000	0.000
46	A	73	ASN	0	-0.060	-0.043	15.798	0.034	0.034	0.000	0.000	0.000	0.000
47	A	74	GLU	-1	-0.941	-0.969	12.379	-0.352	-0.352	0.000	0.000	0.000	0.000
48	A	75	GLU	-1	-1.011	-1.008	12.876	-0.197	-0.197	0.000	0.000	0.000	0.000
49	A	76	GLU	-1	-0.967	-0.967	14.330	-0.122	-0.122	0.000	0.000	0.000	0.000
50	A	77	TYR	0	-0.056	-0.066	10.369	-0.032	-0.032	0.000	0.000	0.000	0.000
51	A	78	LEU	0	-0.019	0.001	15.524	0.035	0.035	0.000	0.000	0.000	0.000
52	A	79	VAL	0	0.013	-0.006	15.855	-0.017	-0.017	0.000	0.000	0.000	0.000
53	A	80	ILE	0	-0.033	-0.004	17.129	0.018	0.018	0.000	0.000	0.000	0.000
54	A	81	ILE	0	0.027	-0.004	18.596	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	82	ARG	1	0.846	0.937	18.028	0.119	0.119	0.000	0.000	0.000	0.000
56	A	83	PHE	0	0.022	-0.002	23.415	0.000	0.000	0.000	0.000	0.000	0.000
57	A	84	THR	0	0.000	-0.002	26.114	0.002	0.002	0.000	0.000	0.000	0.000
58	A	85	PRO	0	-0.020	-0.004	29.187	0.002	0.002	0.000	0.000	0.000	0.000
59	A	86	THR	0	0.001	-0.009	32.141	0.002	0.002	0.000	0.000	0.000	0.000
60	A	87	VAL	0	-0.021	-0.015	34.777	0.000	0.000	0.000	0.000	0.000	0.000
61	A	88	PRO	0	-0.002	0.005	38.323	0.001	0.001	0.000	0.000	0.000	0.000
62	A	89	HIS	0	-0.005	0.013	41.394	0.000	0.000	0.000	0.000	0.000	0.000
63	A	90	CYS	0	-0.071	-0.041	43.422	0.002	0.002	0.000	0.000	0.000	0.000
64	A	91	SER	0	0.043	0.035	44.803	0.000	0.000	0.000	0.000	0.000	0.000
65	A	92	LEU	0	0.105	0.029	45.850	0.001	0.001	0.000	0.000	0.000	0.000
66	A	93	ALA	0	0.035	0.027	47.847	0.001	0.001	0.000	0.000	0.000	0.000
67	A	94	THR	0	0.015	0.007	48.465	0.001	0.001	0.000	0.000	0.000	0.000
68	A	95	LEU	0	0.040	0.009	48.734	0.001	0.001	0.000	0.000	0.000	0.000
69	A	96	ILE	0	0.034	0.024	51.704	0.001	0.001	0.000	0.000	0.000	0.000
70	A	97	GLY	0	0.028	0.020	53.504	0.001	0.001	0.000	0.000	0.000	0.000
71	A	98	LEU	0	-0.001	-0.014	52.535	0.001	0.001	0.000	0.000	0.000	0.000
72	A	99	CYS	0	-0.043	-0.020	55.476	0.001	0.001	0.000	0.000	0.000	0.000
73	A	100	LEU	0	-0.005	-0.002	57.638	0.001	0.001	0.000	0.000	0.000	0.000
74	A	101	ARG	1	0.890	0.933	58.767	0.019	0.019	0.000	0.000	0.000	0.000
75	A	102	VAL	0	0.004	-0.002	59.160	0.001	0.001	0.000	0.000	0.000	0.000
76	A	103	LYS	1	0.912	0.942	61.800	0.016	0.016	0.000	0.000	0.000	0.000
77	A	104	LEU	0	0.008	-0.005	63.631	0.001	0.001	0.000	0.000	0.000	0.000
78	A	105	GLN	0	-0.015	-0.004	62.682	0.001	0.001	0.000	0.000	0.000	0.000
79	A	106	ARG	1	0.897	0.943	61.740	0.016	0.016	0.000	0.000	0.000	0.000
80	A	107	CYS	0	-0.014	0.010	67.676	0.000	0.000	0.000	0.000	0.000	0.000
81	A	108	LEU	0	-0.009	0.020	68.380	0.000	0.000	0.000	0.000	0.000	0.000
82	A	109	PRO	0	0.006	0.012	71.038	0.000	0.000	0.000	0.000	0.000	0.000
83	A	110	PHE	0	0.019	0.006	71.406	0.000	0.000	0.000	0.000	0.000	0.000
84	A	111	LYS	1	0.968	0.984	72.507	0.011	0.011	0.000	0.000	0.000	0.000
85	A	112	HIS	0	-0.021	-0.014	66.992	0.000	0.000	0.000	0.000	0.000	0.000
86	A	113	LYS	1	0.952	0.977	66.144	0.014	0.014	0.000	0.000	0.000	0.000
87	A	114	LEU	0	0.040	0.015	62.094	0.000	0.000	0.000	0.000	0.000	0.000
88	A	115	GLU	-1	-0.882	-0.903	60.868	-0.018	-0.018	0.000	0.000	0.000	0.000
89	A	116	ILE	0	-0.027	-0.021	57.032	0.000	0.000	0.000	0.000	0.000	0.000
90	A	117	TYR	0	-0.029	-0.039	55.828	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	118	ILE	0	0.013	0.009	50.275	0.000	0.000	0.000	0.000	0.000	0.000
92	A	119	SER	0	-0.013	-0.009	53.655	0.000	0.000	0.000	0.000	0.000	0.000
93	A	120	GLU	-1	-0.802	-0.895	51.410	-0.027	-0.027	0.000	0.000	0.000	0.000
94	A	121	GLY	0	-0.069	-0.026	53.971	0.000	0.000	0.000	0.000	0.000	0.000
95	A	122	THR	0	-0.082	-0.048	52.709	0.000	0.000	0.000	0.000	0.000	0.000
96	A	123	HIS	0	-0.033	-0.017	48.157	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	124	SER	0	0.017	-0.002	45.112	0.000	0.000	0.000	0.000	0.000	0.000
98	A	125	THR	0	-0.053	-0.038	39.729	0.000	0.000	0.000	0.000	0.000	0.000
99	A	126	GLU	-1	-0.876	-0.918	38.327	-0.044	-0.044	0.000	0.000	0.000	0.000
100	A	127	GLU	-1	-0.857	-0.911	31.372	-0.063	-0.063	0.000	0.000	0.000	0.000
101	A	128	ASP	-1	-0.894	-0.954	34.288	-0.048	-0.048	0.000	0.000	0.000	0.000
102	A	129	ILE	0	0.035	0.016	33.085	0.000	0.000	0.000	0.000	0.000	0.000
103	A	130	ASN	0	0.038	0.000	29.509	-0.004	-0.004	0.000	0.000	0.000	0.000
104	A	131	LYS	1	0.914	0.969	31.213	0.048	0.048	0.000	0.000	0.000	0.000
105	A	132	GLN	0	-0.115	-0.081	33.645	0.000	0.000	0.000	0.000	0.000	0.000
106	A	133	ILE	0	0.000	0.009	29.313	0.001	0.001	0.000	0.000	0.000	0.000
107	A	134	ASN	0	-0.035	-0.019	26.945	-0.009	-0.009	0.000	0.000	0.000	0.000
108	A	135	ASP	-1	-0.937	-0.964	29.810	-0.058	-0.058	0.000	0.000	0.000	0.000
109	A	136	LYS	1	0.933	0.939	31.254	0.060	0.060	0.000	0.000	0.000	0.000
110	A	137	GLU	-1	-0.850	-0.915	32.804	-0.050	-0.050	0.000	0.000	0.000	0.000
111	A	138	ARG	1	0.835	0.923	35.408	0.049	0.049	0.000	0.000	0.000	0.000
112	A	139	VAL	0	0.046	0.032	31.281	0.003	0.003	0.000	0.000	0.000	0.000
113	A	140	ALA	0	0.018	0.012	34.619	0.002	0.002	0.000	0.000	0.000	0.000
114	A	141	ALA	0	-0.018	-0.013	36.358	0.003	0.003	0.000	0.000	0.000	0.000
115	A	142	ALA	0	-0.034	-0.021	36.760	0.002	0.002	0.000	0.000	0.000	0.000
116	A	143	MET	0	-0.008	-0.015	34.119	0.002	0.002	0.000	0.000	0.000	0.000
117	A	144	GLU	-1	-0.918	-0.950	37.505	-0.038	-0.038	0.000	0.000	0.000	0.000
118	A	145	ASN	0	-0.056	-0.011	40.881	0.004	0.004	0.000	0.000	0.000	0.000
119	A	146	PRO	0	0.037	0.005	41.607	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	147	ASN	0	-0.018	-0.018	42.474	0.001	0.001	0.000	0.000	0.000	0.000
121	A	148	LEU	0	-0.032	-0.013	39.041	0.000	0.000	0.000	0.000	0.000	0.000
122	A	149	ARG	1	0.866	0.913	37.315	0.037	0.037	0.000	0.000	0.000	0.000
123	A	150	GLU	-1	-0.972	-0.980	37.589	-0.032	-0.032	0.000	0.000	0.000	0.000
124	A	151	ILE	0	-0.034	-0.016	37.328	0.000	0.000	0.000	0.000	0.000	0.000
125	A	152	VAL	0	0.031	0.014	32.673	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	153	GLU	-1	-0.802	-0.886	33.621	-0.045	-0.045	0.000	0.000	0.000	0.000
127	A	154	GLN	0	-0.049	-0.017	34.287	0.002	0.002	0.000	0.000	0.000	0.000
128	A	155	CYS	0	-0.118	-0.057	33.098	0.001	0.001	0.000	0.000	0.000	0.000
129	A	156	VAL	0	0.009	0.004	29.150	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	157	LEU	0	-0.053	0.002	29.845	-0.001	-0.001	0.000	0.000	0.000	0.000

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