FMO DATABASE

FMODB ID: Z6QVN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-993147.74879
FMO2-HF: Nuclear repulsion	945540.40296
FMO2-HF: Total energy	-47607.34583
FMO2-MP2: Total energy	-47744.577143

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.
-50.653	-46.652	1.487	-1.987	-3.501	-0.011

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 : 0.999 / q_NPA : 0.993

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	-0.009	-0.027	3.871	2.604	3.616	-0.003	-0.407	-0.603	0.002
4	A	19	PRO	0	0.061	0.011	6.058	1.798	1.798	0.000	0.000	0.000	0.000
5	A	20	ILE	0	-0.007	0.004	8.691	1.650	1.650	0.000	0.000	0.000	0.000
6	A	21	ASP	-1	-0.751	-0.844	8.269	-25.087	-25.087	0.000	0.000	0.000	0.000
7	A	22	LYS	1	0.905	0.964	7.858	22.432	22.432	0.000	0.000	0.000	0.000
8	A	23	ARG	1	0.967	0.987	9.748	17.862	17.862	0.000	0.000	0.000	0.000
9	A	24	LYS	1	0.830	0.928	12.891	20.855	20.855	0.000	0.000	0.000	0.000
10	A	25	CYS	0	0.016	0.030	11.587	1.457	1.457	0.000	0.000	0.000	0.000
11	A	26	GLU	-1	-0.826	-0.927	12.768	-17.096	-17.096	0.000	0.000	0.000	0.000
12	A	27	ARG	1	0.916	0.962	15.241	14.007	14.007	0.000	0.000	0.000	0.000
13	A	28	LEU	0	-0.005	0.000	15.537	0.712	0.712	0.000	0.000	0.000	0.000
14	A	29	LEU	0	0.036	0.021	15.886	0.724	0.724	0.000	0.000	0.000	0.000
15	A	30	LEU	0	-0.025	-0.003	18.702	0.647	0.647	0.000	0.000	0.000	0.000
16	A	31	PHE	0	-0.017	-0.022	21.103	0.542	0.542	0.000	0.000	0.000	0.000
17	A	32	LEU	0	0.008	0.008	20.221	0.448	0.448	0.000	0.000	0.000	0.000
18	A	33	TYR	0	-0.028	-0.033	20.518	0.190	0.190	0.000	0.000	0.000	0.000
19	A	34	CYS	0	-0.096	-0.046	24.509	0.441	0.441	0.000	0.000	0.000	0.000
20	A	35	HIS	0	0.032	0.029	26.705	0.309	0.309	0.000	0.000	0.000	0.000
21	A	36	GLU	-1	-0.804	-0.888	28.540	-8.845	-8.845	0.000	0.000	0.000	0.000
22	A	37	MET	0	-0.034	0.013	30.051	0.180	0.180	0.000	0.000	0.000	0.000
23	A	38	SER	0	0.015	-0.005	25.699	-0.155	-0.155	0.000	0.000	0.000	0.000
24	A	39	LEU	0	0.016	0.004	27.162	-0.190	-0.190	0.000	0.000	0.000	0.000
25	A	40	ALA	0	-0.029	-0.012	29.186	-0.016	-0.016	0.000	0.000	0.000	0.000
26	A	41	PHE	0	-0.002	0.000	24.738	-0.124	-0.124	0.000	0.000	0.000	0.000
27	A	42	GLN	0	-0.035	-0.025	23.935	-0.502	-0.502	0.000	0.000	0.000	0.000
28	A	43	ASP	-1	-0.890	-0.946	23.460	-11.564	-11.564	0.000	0.000	0.000	0.000
29	A	44	PRO	0	-0.061	-0.025	22.833	0.098	0.098	0.000	0.000	0.000	0.000
30	A	45	VAL	0	0.051	0.041	25.093	0.414	0.414	0.000	0.000	0.000	0.000
31	A	46	PRO	0	0.041	0.024	28.182	-0.087	-0.087	0.000	0.000	0.000	0.000
32	A	47	LEU	0	0.000	-0.014	27.738	0.096	0.096	0.000	0.000	0.000	0.000
33	A	48	THR	0	-0.024	-0.008	31.307	0.024	0.024	0.000	0.000	0.000	0.000
34	A	49	VAL	0	-0.012	0.007	32.290	0.273	0.273	0.000	0.000	0.000	0.000
35	A	50	PRO	0	0.018	0.001	34.452	-0.155	-0.155	0.000	0.000	0.000	0.000
36	A	51	ASP	-1	-0.783	-0.900	34.990	-8.345	-8.345	0.000	0.000	0.000	0.000
37	A	52	TYR	0	0.082	0.051	26.420	-0.338	-0.338	0.000	0.000	0.000	0.000
38	A	53	TYR	0	-0.037	-0.039	25.759	-0.406	-0.406	0.000	0.000	0.000	0.000
39	A	54	LYS	1	0.757	0.870	30.036	8.434	8.434	0.000	0.000	0.000	0.000
40	A	55	ILE	0	-0.024	-0.005	31.243	-0.069	-0.069	0.000	0.000	0.000	0.000
41	A	56	ILE	0	0.033	0.029	25.546	-0.209	-0.209	0.000	0.000	0.000	0.000
42	A	57	LYS	1	0.839	0.917	24.898	10.451	10.451	0.000	0.000	0.000	0.000
43	A	58	ASN	0	-0.045	-0.019	20.292	-0.704	-0.704	0.000	0.000	0.000	0.000
44	A	59	PRO	0	0.068	0.053	21.630	-0.244	-0.244	0.000	0.000	0.000	0.000
45	A	60	MET	0	-0.050	-0.015	16.876	-0.679	-0.679	0.000	0.000	0.000	0.000
46	A	61	ASP	-1	-0.696	-0.798	19.972	-12.524	-12.524	0.000	0.000	0.000	0.000
47	A	62	LEU	0	0.047	0.010	19.368	-0.796	-0.796	0.000	0.000	0.000	0.000
48	A	63	SER	0	-0.009	-0.012	18.810	-0.624	-0.624	0.000	0.000	0.000	0.000
49	A	64	THR	0	-0.050	-0.075	16.773	-0.489	-0.489	0.000	0.000	0.000	0.000
50	A	65	ILE	0	0.013	0.023	14.139	-0.900	-0.900	0.000	0.000	0.000	0.000
51	A	66	LYS	1	0.879	0.944	13.834	11.950	11.950	0.000	0.000	0.000	0.000
52	A	67	LYS	1	0.825	0.914	14.066	12.913	12.913	0.000	0.000	0.000	0.000
53	A	68	ARG	1	0.917	0.943	11.170	17.672	17.672	0.000	0.000	0.000	0.000
54	A	69	LEU	0	-0.012	0.005	9.198	-2.029	-2.029	0.000	0.000	0.000	0.000
55	A	70	GLN	0	-0.133	-0.089	9.562	-0.485	-0.485	0.000	0.000	0.000	0.000
56	A	71	GLU	-1	-0.886	-0.941	11.616	-16.688	-16.688	0.000	0.000	0.000	0.000
57	A	72	ASP	-1	-0.941	-0.972	8.005	-24.676	-24.676	0.000	0.000	0.000	0.000
58	A	73	TYR	0	-0.062	-0.029	8.116	-1.396	-1.396	0.000	0.000	0.000	0.000
59	A	74	SER	0	-0.042	-0.021	4.202	-2.318	-2.199	-0.001	-0.008	-0.110	0.000
60	A	75	MET	0	-0.016	0.000	5.547	-2.888	-2.888	0.000	0.000	0.000	0.000
61	A	76	TYR	0	-0.063	-0.052	6.468	0.274	0.274	0.000	0.000	0.000	0.000
62	A	77	SER	0	-0.091	-0.065	2.416	-5.817	-4.574	0.718	-0.593	-1.367	0.000
63	A	78	LYS	1	0.796	0.871	2.632	29.785	31.353	0.774	-0.978	-1.365	-0.013
64	A	79	PRO	0	0.024	0.009	5.376	2.002	2.061	-0.001	-0.001	-0.056	0.000
65	A	80	GLU	-1	-0.738	-0.876	8.666	-26.529	-26.529	0.000	0.000	0.000	0.000
66	A	81	ASP	-1	-0.757	-0.835	6.677	-35.179	-35.179	0.000	0.000	0.000	0.000
67	A	82	PHE	0	0.074	0.029	9.324	1.317	1.317	0.000	0.000	0.000	0.000
68	A	83	VAL	0	-0.040	-0.014	11.941	1.541	1.541	0.000	0.000	0.000	0.000
69	A	84	ALA	0	-0.016	-0.001	13.545	1.226	1.226	0.000	0.000	0.000	0.000
70	A	85	ASP	-1	-0.706	-0.819	13.899	-17.923	-17.923	0.000	0.000	0.000	0.000
71	A	86	PHE	0	-0.008	-0.029	14.853	0.846	0.846	0.000	0.000	0.000	0.000
72	A	87	ARG	1	0.766	0.840	17.965	16.107	16.107	0.000	0.000	0.000	0.000
73	A	88	LEU	0	-0.012	0.009	18.087	0.693	0.693	0.000	0.000	0.000	0.000
74	A	89	ILE	0	-0.038	-0.009	19.774	0.601	0.601	0.000	0.000	0.000	0.000
75	A	90	PHE	0	0.054	0.023	21.867	0.494	0.494	0.000	0.000	0.000	0.000
76	A	91	GLN	0	-0.019	-0.010	21.362	0.000	0.000	0.000	0.000	0.000	0.000
77	A	92	ASN	0	-0.019	-0.028	22.338	0.586	0.586	0.000	0.000	0.000	0.000
78	A	93	CYS	0	-0.085	-0.018	26.078	0.486	0.486	0.000	0.000	0.000	0.000
79	A	94	ALA	0	0.014	-0.007	28.253	0.379	0.379	0.000	0.000	0.000	0.000
80	A	95	GLU	-1	-0.984	-0.981	27.725	-10.730	-10.730	0.000	0.000	0.000	0.000
81	A	96	PHE	0	-0.040	-0.022	30.431	0.291	0.291	0.000	0.000	0.000	0.000
82	A	97	ASN	0	-0.060	-0.029	31.583	0.056	0.056	0.000	0.000	0.000	0.000
83	A	98	GLU	-1	-0.833	-0.920	34.069	-7.991	-7.991	0.000	0.000	0.000	0.000
84	A	99	PRO	0	0.020	0.015	36.149	-0.021	-0.021	0.000	0.000	0.000	0.000
85	A	100	ASP	-1	-0.898	-0.945	37.201	-7.496	-7.496	0.000	0.000	0.000	0.000
86	A	101	SER	0	-0.095	-0.055	36.425	0.041	0.041	0.000	0.000	0.000	0.000
87	A	102	GLU	-1	-0.880	-0.951	36.211	-8.359	-8.359	0.000	0.000	0.000	0.000
88	A	103	VAL	0	-0.025	-0.017	31.600	-0.173	-0.173	0.000	0.000	0.000	0.000
89	A	104	ALA	0	0.073	0.036	32.017	-0.344	-0.344	0.000	0.000	0.000	0.000
90	A	105	ASN	0	-0.044	-0.028	32.307	-0.261	-0.261	0.000	0.000	0.000	0.000
91	A	106	ALA	0	-0.022	-0.017	31.750	-0.161	-0.161	0.000	0.000	0.000	0.000
92	A	107	GLY	0	0.053	0.015	28.414	-0.278	-0.278	0.000	0.000	0.000	0.000
93	A	108	ILE	0	0.006	0.012	28.203	-0.323	-0.323	0.000	0.000	0.000	0.000
94	A	109	LYS	1	0.799	0.878	29.482	8.507	8.507	0.000	0.000	0.000	0.000
95	A	110	LEU	0	-0.043	-0.016	24.621	-0.170	-0.170	0.000	0.000	0.000	0.000
96	A	111	GLU	-1	-0.922	-0.961	24.422	-11.910	-11.910	0.000	0.000	0.000	0.000
97	A	112	ASN	0	-0.048	-0.040	24.654	-0.386	-0.386	0.000	0.000	0.000	0.000
98	A	113	TYR	0	0.029	0.022	25.460	-0.235	-0.235	0.000	0.000	0.000	0.000
99	A	114	PHE	0	0.003	-0.010	17.005	-0.502	-0.502	0.000	0.000	0.000	0.000
100	A	115	GLU	-1	-0.766	-0.858	20.515	-15.050	-15.050	0.000	0.000	0.000	0.000
101	A	116	GLU	-1	-0.930	-0.959	22.186	-10.751	-10.751	0.000	0.000	0.000	0.000
102	A	117	LEU	0	-0.035	-0.008	21.376	-0.283	-0.283	0.000	0.000	0.000	0.000
103	A	118	LEU	0	-0.027	-0.005	15.314	-0.619	-0.619	0.000	0.000	0.000	0.000
104	A	119	LYS	1	0.839	0.914	18.357	12.700	12.700	0.000	0.000	0.000	0.000
105	A	120	ASN	0	-0.050	-0.039	20.783	0.307	0.307	0.000	0.000	0.000	0.000
106	A	121	LEU	0	-0.033	-0.014	16.696	-0.145	-0.145	0.000	0.000	0.000	0.000
107	A	122	TYR	0	-0.103	-0.100	10.978	-1.370	-1.370	0.000	0.000	0.000	0.000
108	A	123	PRO	0	-0.002	0.024	16.799	0.292	0.292	0.000	0.000	0.000	0.000
109	A	124	GLU	-1	-0.861	-0.931	17.311	-14.848	-14.848	0.000	0.000	0.000	0.000
110	A	125	LYS	1	0.784	0.876	9.190	26.571	26.571	0.000	0.000	0.000	0.000
111	A	126	ARG	1	0.991	0.998	15.699	13.660	13.660	0.000	0.000	0.000	0.000
112	A	127	PHE	0	0.046	0.023	11.523	-0.887	-0.887	0.000	0.000	0.000	0.000
113	A	128	PRO	0	0.013	0.022	15.146	0.771	0.771	0.000	0.000	0.000	0.000

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