FMO DATABASE

FMODB ID: 2J1NR

Calculation Name: 2YYN-A-Xray372

Preferred Name: Transcription intermediary factor 1-alpha

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2YYN

Chain ID: A

ChEMBL ID: CHEMBL3108638

UniProt ID: O15164

Base Structure: X-ray

Registration Date: 2023-09-20

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	113
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-989211.415097
FMO2-HF: Nuclear repulsion	941605.197783
FMO2-HF: Total energy	-47606.217315
FMO2-MP2: Total energy	-47743.479748

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:16:LYS)

Summations of interaction energy for fragment #1(A:16:LYS)

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.
-48.618	-45.249	1.531	-1.832	-3.068	-0.012

Interaction energy analysis for fragmet #1(A:16:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.951 / q_NPA : 0.963

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	18	THR	0	-0.037	-0.034	3.821	4.924	5.872	-0.008	-0.272	-0.668	0.002
4	A	19	PRO	0	0.070	0.016	5.651	1.720	1.720	0.000	0.000	0.000	0.000
5	A	20	ILE	0	-0.010	0.001	8.461	1.476	1.476	0.000	0.000	0.000	0.000
6	A	21	ASP	-1	-0.759	-0.867	7.942	-25.044	-25.044	0.000	0.000	0.000	0.000
7	A	22	LYS	1	0.947	0.989	8.514	20.568	20.568	0.000	0.000	0.000	0.000
8	A	23	ARG	1	0.999	0.995	10.186	16.888	16.888	0.000	0.000	0.000	0.000
9	A	24	LYS	1	0.834	0.911	13.045	19.096	19.096	0.000	0.000	0.000	0.000
10	A	25	CYS	0	0.019	0.026	11.974	1.289	1.289	0.000	0.000	0.000	0.000
11	A	26	GLU	-1	-0.891	-0.962	13.641	-15.864	-15.864	0.000	0.000	0.000	0.000
12	A	27	ARG	1	0.877	0.956	16.002	13.676	13.676	0.000	0.000	0.000	0.000
13	A	28	LEU	0	0.001	0.008	15.842	0.659	0.659	0.000	0.000	0.000	0.000
14	A	29	LEU	0	0.049	0.020	15.673	0.628	0.628	0.000	0.000	0.000	0.000
15	A	30	LEU	0	-0.029	-0.003	19.167	0.603	0.603	0.000	0.000	0.000	0.000
16	A	31	PHE	0	-0.021	-0.038	21.806	0.454	0.454	0.000	0.000	0.000	0.000
17	A	32	LEU	0	0.016	0.014	20.864	0.421	0.421	0.000	0.000	0.000	0.000
18	A	33	TYR	0	-0.023	-0.003	20.843	0.407	0.407	0.000	0.000	0.000	0.000
19	A	34	CYS	0	-0.087	-0.053	25.270	0.414	0.414	0.000	0.000	0.000	0.000
20	A	35	HIS	0	0.008	0.030	27.309	0.338	0.338	0.000	0.000	0.000	0.000
21	A	36	GLU	-1	-0.904	-0.971	29.134	-8.394	-8.394	0.000	0.000	0.000	0.000
22	A	37	MET	0	-0.062	-0.014	30.735	0.166	0.166	0.000	0.000	0.000	0.000
23	A	38	SER	0	0.041	0.014	26.281	-0.159	-0.159	0.000	0.000	0.000	0.000
24	A	39	LEU	0	0.019	0.007	27.791	-0.190	-0.190	0.000	0.000	0.000	0.000
25	A	40	ALA	0	-0.020	-0.006	29.468	-0.053	-0.053	0.000	0.000	0.000	0.000
26	A	41	PHE	0	-0.020	-0.013	25.286	-0.124	-0.124	0.000	0.000	0.000	0.000
27	A	42	GLN	0	-0.038	-0.018	24.333	-0.564	-0.564	0.000	0.000	0.000	0.000
28	A	43	ASP	-1	-0.901	-0.946	23.783	-10.941	-10.941	0.000	0.000	0.000	0.000
29	A	44	PRO	0	-0.048	-0.015	23.288	0.112	0.112	0.000	0.000	0.000	0.000
30	A	45	VAL	0	0.037	0.031	25.581	0.403	0.403	0.000	0.000	0.000	0.000
31	A	46	PRO	0	0.030	0.008	28.697	-0.089	-0.089	0.000	0.000	0.000	0.000
32	A	47	LEU	0	0.011	-0.011	28.591	0.066	0.066	0.000	0.000	0.000	0.000
33	A	48	THR	0	-0.036	-0.021	31.781	0.023	0.023	0.000	0.000	0.000	0.000
34	A	49	VAL	0	-0.003	0.026	32.523	0.254	0.254	0.000	0.000	0.000	0.000
35	A	50	PRO	0	0.018	-0.008	34.828	-0.183	-0.183	0.000	0.000	0.000	0.000
36	A	51	ASP	-1	-0.877	-0.954	35.745	-8.128	-8.128	0.000	0.000	0.000	0.000
37	A	52	TYR	0	0.157	0.083	27.446	-0.347	-0.347	0.000	0.000	0.000	0.000
38	A	53	TYR	0	-0.015	-0.002	26.168	-0.401	-0.401	0.000	0.000	0.000	0.000
39	A	54	LYS	1	0.696	0.850	30.391	8.486	8.486	0.000	0.000	0.000	0.000
40	A	55	ILE	0	0.001	-0.007	31.233	-0.016	-0.016	0.000	0.000	0.000	0.000
41	A	56	ILE	0	0.031	0.036	25.672	-0.228	-0.228	0.000	0.000	0.000	0.000
42	A	57	LYS	1	0.893	0.937	24.804	10.543	10.543	0.000	0.000	0.000	0.000
43	A	58	ASN	0	-0.032	-0.017	20.474	-0.521	-0.521	0.000	0.000	0.000	0.000
44	A	59	PRO	0	0.043	0.041	22.266	-0.163	-0.163	0.000	0.000	0.000	0.000
45	A	60	MET	0	-0.038	-0.011	17.170	-0.697	-0.697	0.000	0.000	0.000	0.000
46	A	61	ASP	-1	-0.709	-0.833	20.392	-12.152	-12.152	0.000	0.000	0.000	0.000
47	A	62	LEU	0	0.053	0.006	19.796	-0.735	-0.735	0.000	0.000	0.000	0.000
48	A	63	SER	0	-0.090	-0.043	19.042	-0.668	-0.668	0.000	0.000	0.000	0.000
49	A	64	THR	0	-0.050	-0.057	17.152	-0.550	-0.550	0.000	0.000	0.000	0.000
50	A	65	ILE	0	-0.003	0.002	14.409	-0.864	-0.864	0.000	0.000	0.000	0.000
51	A	66	LYS	1	0.896	0.951	14.273	11.839	11.839	0.000	0.000	0.000	0.000
52	A	67	LYS	1	0.944	0.970	14.594	12.623	12.623	0.000	0.000	0.000	0.000
53	A	68	ARG	1	0.936	0.977	11.605	17.408	17.408	0.000	0.000	0.000	0.000
54	A	69	LEU	0	-0.060	-0.012	9.586	-1.611	-1.611	0.000	0.000	0.000	0.000
55	A	70	GLN	0	-0.095	-0.065	9.958	-0.585	-0.585	0.000	0.000	0.000	0.000
56	A	71	GLU	-1	-0.943	-0.955	12.027	-16.544	-16.544	0.000	0.000	0.000	0.000
57	A	72	ASP	-1	-0.972	-0.982	8.494	-24.555	-24.555	0.000	0.000	0.000	0.000
58	A	73	TYR	0	0.012	0.000	9.569	-0.265	-0.265	0.000	0.000	0.000	0.000
59	A	74	SER	0	-0.063	-0.036	4.421	-2.838	-2.742	-0.001	-0.002	-0.093	0.000
60	A	75	MET	0	-0.002	0.003	6.115	-2.706	-2.706	0.000	0.000	0.000	0.000
61	A	76	TYR	0	-0.073	-0.060	6.955	-0.139	-0.139	0.000	0.000	0.000	0.000
62	A	77	SER	0	-0.073	-0.048	2.280	-4.578	-4.089	1.301	-0.442	-1.348	-0.001
63	A	78	LYS	1	0.863	0.924	2.891	28.023	29.795	0.240	-1.115	-0.898	-0.013
64	A	79	PRO	0	-0.002	-0.004	5.355	2.000	2.064	-0.001	-0.001	-0.061	0.000
65	A	80	GLU	-1	-0.837	-0.947	8.641	-25.609	-25.609	0.000	0.000	0.000	0.000
66	A	81	ASP	-1	-0.815	-0.880	6.787	-32.692	-32.692	0.000	0.000	0.000	0.000
67	A	82	PHE	0	0.086	0.023	9.782	1.320	1.320	0.000	0.000	0.000	0.000
68	A	83	VAL	0	-0.046	-0.010	12.098	1.494	1.494	0.000	0.000	0.000	0.000
69	A	84	ALA	0	-0.024	-0.013	13.372	1.220	1.220	0.000	0.000	0.000	0.000
70	A	85	ASP	-1	-0.727	-0.842	14.417	-17.665	-17.665	0.000	0.000	0.000	0.000
71	A	86	PHE	0	-0.010	-0.025	15.230	0.843	0.843	0.000	0.000	0.000	0.000
72	A	87	ARG	1	0.791	0.842	17.851	15.454	15.454	0.000	0.000	0.000	0.000
73	A	88	LEU	0	-0.022	0.017	18.288	0.600	0.600	0.000	0.000	0.000	0.000
74	A	89	ILE	0	-0.040	-0.013	20.447	0.621	0.621	0.000	0.000	0.000	0.000
75	A	90	PHE	0	0.055	0.011	21.463	0.474	0.474	0.000	0.000	0.000	0.000
76	A	91	GLN	0	-0.023	-0.001	21.142	-0.064	-0.064	0.000	0.000	0.000	0.000
77	A	92	ASN	0	0.010	-0.011	23.126	0.488	0.488	0.000	0.000	0.000	0.000
78	A	93	CYS	0	-0.103	-0.013	26.461	0.450	0.450	0.000	0.000	0.000	0.000
79	A	94	ALA	0	0.016	-0.006	28.316	0.365	0.365	0.000	0.000	0.000	0.000
80	A	95	GLU	-1	-1.011	-0.992	28.039	-10.372	-10.372	0.000	0.000	0.000	0.000
81	A	96	PHE	0	-0.038	-0.029	30.411	0.303	0.303	0.000	0.000	0.000	0.000
82	A	97	ASN	0	-0.067	-0.029	31.946	0.002	0.002	0.000	0.000	0.000	0.000
83	A	98	GLU	-1	-0.866	-0.930	34.338	-7.872	-7.872	0.000	0.000	0.000	0.000
84	A	99	PRO	0	0.003	-0.015	35.824	-0.016	-0.016	0.000	0.000	0.000	0.000
85	A	100	ASP	-1	-0.896	-0.930	36.863	-7.325	-7.325	0.000	0.000	0.000	0.000
86	A	101	SER	0	-0.085	-0.054	36.515	-0.015	-0.015	0.000	0.000	0.000	0.000
87	A	102	GLU	-1	-0.859	-0.933	36.578	-8.099	-8.099	0.000	0.000	0.000	0.000
88	A	103	VAL	0	0.001	-0.007	31.809	-0.148	-0.148	0.000	0.000	0.000	0.000
89	A	104	ALA	0	0.072	0.039	32.530	-0.313	-0.313	0.000	0.000	0.000	0.000
90	A	105	ASN	0	0.005	0.006	32.786	-0.265	-0.265	0.000	0.000	0.000	0.000
91	A	106	ALA	0	-0.055	-0.053	32.203	-0.126	-0.126	0.000	0.000	0.000	0.000
92	A	107	GLY	0	0.026	-0.004	28.915	-0.262	-0.262	0.000	0.000	0.000	0.000
93	A	108	ILE	0	0.003	0.012	28.320	-0.321	-0.321	0.000	0.000	0.000	0.000
94	A	109	LYS	1	0.893	0.950	29.450	8.380	8.380	0.000	0.000	0.000	0.000
95	A	110	LEU	0	0.014	-0.002	24.998	-0.227	-0.227	0.000	0.000	0.000	0.000
96	A	111	GLU	-1	-0.920	-0.933	24.240	-11.827	-11.827	0.000	0.000	0.000	0.000
97	A	112	ASN	0	0.003	0.007	24.967	-0.481	-0.481	0.000	0.000	0.000	0.000
98	A	113	TYR	0	-0.031	-0.005	25.856	-0.266	-0.266	0.000	0.000	0.000	0.000
99	A	114	PHE	0	0.010	-0.023	17.251	-0.471	-0.471	0.000	0.000	0.000	0.000
100	A	115	GLU	-1	-0.784	-0.886	21.498	-14.175	-14.175	0.000	0.000	0.000	0.000
101	A	116	GLU	-1	-0.967	-0.971	22.618	-10.403	-10.403	0.000	0.000	0.000	0.000
102	A	117	LEU	0	-0.072	-0.037	21.682	-0.286	-0.286	0.000	0.000	0.000	0.000
103	A	118	LEU	0	-0.020	-0.007	15.673	-0.562	-0.562	0.000	0.000	0.000	0.000
104	A	119	LYS	1	0.905	0.972	18.898	12.037	12.037	0.000	0.000	0.000	0.000
105	A	120	ASN	0	-0.008	-0.020	21.171	-0.121	-0.121	0.000	0.000	0.000	0.000
106	A	121	LEU	0	-0.037	-0.015	17.149	-0.128	-0.128	0.000	0.000	0.000	0.000
107	A	122	TYR	0	-0.118	-0.080	11.474	-1.116	-1.116	0.000	0.000	0.000	0.000
108	A	123	PRO	0	-0.025	0.016	17.487	0.082	0.082	0.000	0.000	0.000	0.000
109	A	124	GLU	-1	-0.839	-0.942	18.155	-13.876	-13.876	0.000	0.000	0.000	0.000
110	A	125	LYS	1	0.880	0.960	10.174	23.900	23.900	0.000	0.000	0.000	0.000
111	A	126	ARG	1	1.008	0.995	16.461	13.973	13.973	0.000	0.000	0.000	0.000
112	A	127	PHE	0	0.017	0.007	11.653	-0.702	-0.702	0.000	0.000	0.000	0.000
113	A	128	PRO	0	0.034	0.038	15.511	0.570	0.570	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:16:LYS)