FMO DATABASE

FMODB ID: 6NQYZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-990497.431113
FMO2-HF: Nuclear repulsion	942890.40322
FMO2-HF: Total energy	-47607.027893
FMO2-MP2: Total energy	-47744.271247

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.
-47.903	-44.042	1.022	-1.82	-3.063	-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 : 0.981 / q_NPA : 0.986

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	-0.043	-0.052	3.821	4.053	5.146	-0.007	-0.378	-0.709	0.002
4	A	19	PRO	0	0.084	0.022	5.658	1.632	1.632	0.000	0.000	0.000	0.000
5	A	20	ILE	0	-0.009	0.002	8.450	1.631	1.631	0.000	0.000	0.000	0.000
6	A	21	ASP	-1	-0.765	-0.838	7.959	-25.772	-25.772	0.000	0.000	0.000	0.000
7	A	22	LYS	1	0.920	0.968	7.840	23.387	23.387	0.000	0.000	0.000	0.000
8	A	23	ARG	1	0.993	0.993	9.742	17.644	17.644	0.000	0.000	0.000	0.000
9	A	24	LYS	1	0.830	0.911	13.033	20.022	20.022	0.000	0.000	0.000	0.000
10	A	25	CYS	0	0.005	0.021	11.940	1.445	1.445	0.000	0.000	0.000	0.000
11	A	26	GLU	-1	-0.860	-0.943	13.265	-16.622	-16.622	0.000	0.000	0.000	0.000
12	A	27	ARG	1	0.897	0.958	15.603	14.030	14.030	0.000	0.000	0.000	0.000
13	A	28	LEU	0	0.003	0.009	15.766	0.708	0.708	0.000	0.000	0.000	0.000
14	A	29	LEU	0	0.038	0.022	15.944	0.704	0.704	0.000	0.000	0.000	0.000
15	A	30	LEU	0	-0.016	-0.001	19.048	0.635	0.635	0.000	0.000	0.000	0.000
16	A	31	PHE	0	-0.025	-0.032	21.520	0.537	0.537	0.000	0.000	0.000	0.000
17	A	32	LEU	0	0.011	0.012	20.656	0.454	0.454	0.000	0.000	0.000	0.000
18	A	33	TYR	0	-0.006	-0.003	21.003	0.157	0.157	0.000	0.000	0.000	0.000
19	A	34	CYS	0	-0.095	-0.056	25.153	0.423	0.423	0.000	0.000	0.000	0.000
20	A	35	HIS	0	0.016	0.029	27.192	0.319	0.319	0.000	0.000	0.000	0.000
21	A	36	GLU	-1	-0.835	-0.936	29.017	-8.693	-8.693	0.000	0.000	0.000	0.000
22	A	37	MET	0	-0.052	0.000	30.650	0.192	0.192	0.000	0.000	0.000	0.000
23	A	38	SER	0	0.055	0.024	26.211	-0.179	-0.179	0.000	0.000	0.000	0.000
24	A	39	LEU	0	0.008	0.011	27.690	-0.196	-0.196	0.000	0.000	0.000	0.000
25	A	40	ALA	0	-0.018	-0.008	29.369	-0.054	-0.054	0.000	0.000	0.000	0.000
26	A	41	PHE	0	-0.018	-0.013	25.234	-0.146	-0.146	0.000	0.000	0.000	0.000
27	A	42	GLN	0	-0.033	-0.026	24.241	-0.535	-0.535	0.000	0.000	0.000	0.000
28	A	43	ASP	-1	-0.902	-0.949	23.688	-11.358	-11.358	0.000	0.000	0.000	0.000
29	A	44	PRO	0	-0.045	-0.018	23.192	0.089	0.089	0.000	0.000	0.000	0.000
30	A	45	VAL	0	0.041	0.037	25.510	0.421	0.421	0.000	0.000	0.000	0.000
31	A	46	PRO	0	0.039	0.024	28.629	-0.098	-0.098	0.000	0.000	0.000	0.000
32	A	47	LEU	0	0.004	-0.012	28.358	0.068	0.068	0.000	0.000	0.000	0.000
33	A	48	THR	0	-0.028	-0.017	31.732	0.018	0.018	0.000	0.000	0.000	0.000
34	A	49	VAL	0	-0.013	0.018	32.772	0.255	0.255	0.000	0.000	0.000	0.000
35	A	50	PRO	0	0.035	0.000	34.779	-0.183	-0.183	0.000	0.000	0.000	0.000
36	A	51	ASP	-1	-0.831	-0.911	35.632	-8.238	-8.238	0.000	0.000	0.000	0.000
37	A	52	TYR	0	0.157	0.077	27.378	-0.352	-0.352	0.000	0.000	0.000	0.000
38	A	53	TYR	0	0.003	0.001	26.071	-0.405	-0.405	0.000	0.000	0.000	0.000
39	A	54	LYS	1	0.657	0.812	30.357	8.525	8.525	0.000	0.000	0.000	0.000
40	A	55	ILE	0	0.009	0.000	31.615	-0.024	-0.024	0.000	0.000	0.000	0.000
41	A	56	ILE	0	0.027	0.035	25.924	-0.205	-0.205	0.000	0.000	0.000	0.000
42	A	57	LYS	1	0.839	0.906	24.801	10.465	10.465	0.000	0.000	0.000	0.000
43	A	58	ASN	0	-0.038	-0.017	20.626	-0.638	-0.638	0.000	0.000	0.000	0.000
44	A	59	PRO	0	0.058	0.050	22.449	-0.171	-0.171	0.000	0.000	0.000	0.000
45	A	60	MET	0	-0.044	-0.015	17.390	-0.723	-0.723	0.000	0.000	0.000	0.000
46	A	61	ASP	-1	-0.697	-0.810	20.296	-12.464	-12.464	0.000	0.000	0.000	0.000
47	A	62	LEU	0	0.048	0.006	19.705	-0.765	-0.765	0.000	0.000	0.000	0.000
48	A	63	SER	0	-0.024	-0.016	18.942	-0.701	-0.701	0.000	0.000	0.000	0.000
49	A	64	THR	0	-0.102	-0.105	17.249	-0.560	-0.560	0.000	0.000	0.000	0.000
50	A	65	ILE	0	-0.005	0.008	14.467	-0.882	-0.882	0.000	0.000	0.000	0.000
51	A	66	LYS	1	0.882	0.946	14.175	12.052	12.052	0.000	0.000	0.000	0.000
52	A	67	LYS	1	0.893	0.951	14.454	12.744	12.744	0.000	0.000	0.000	0.000
53	A	68	ARG	1	0.921	0.950	11.553	17.799	17.799	0.000	0.000	0.000	0.000
54	A	69	LEU	0	-0.044	-0.006	9.351	-1.887	-1.887	0.000	0.000	0.000	0.000
55	A	70	GLN	0	-0.123	-0.083	9.577	-0.879	-0.879	0.000	0.000	0.000	0.000
56	A	71	GLU	-1	-0.903	-0.935	11.760	-17.073	-17.073	0.000	0.000	0.000	0.000
57	A	72	ASP	-1	-0.972	-0.987	7.787	-25.598	-25.598	0.000	0.000	0.000	0.000
58	A	73	TYR	0	-0.005	-0.003	9.540	-0.149	-0.149	0.000	0.000	0.000	0.000
59	A	74	SER	0	-0.056	-0.032	4.382	-2.626	-2.527	-0.001	-0.003	-0.095	0.000
60	A	75	MET	0	0.003	0.012	6.088	-2.527	-2.527	0.000	0.000	0.000	0.000
61	A	76	TYR	0	-0.075	-0.063	6.890	-0.387	-0.387	0.000	0.000	0.000	0.000
62	A	77	SER	0	-0.068	-0.047	2.595	-5.513	-4.616	0.691	-0.385	-1.203	-0.001
63	A	78	LYS	1	0.800	0.867	2.818	30.770	32.482	0.340	-1.052	-1.000	-0.013
64	A	79	PRO	0	0.033	0.006	5.254	1.924	1.984	-0.001	-0.002	-0.056	0.000
65	A	80	GLU	-1	-0.771	-0.893	8.646	-25.723	-25.723	0.000	0.000	0.000	0.000
66	A	81	ASP	-1	-0.768	-0.834	6.611	-34.699	-34.699	0.000	0.000	0.000	0.000
67	A	82	PHE	0	0.098	0.035	9.591	1.315	1.315	0.000	0.000	0.000	0.000
68	A	83	VAL	0	-0.039	-0.010	12.168	1.554	1.554	0.000	0.000	0.000	0.000
69	A	84	ALA	0	-0.019	-0.009	13.409	1.271	1.271	0.000	0.000	0.000	0.000
70	A	85	ASP	-1	-0.709	-0.820	14.419	-18.078	-18.078	0.000	0.000	0.000	0.000
71	A	86	PHE	0	-0.016	-0.027	15.218	0.844	0.844	0.000	0.000	0.000	0.000
72	A	87	ARG	1	0.786	0.834	18.038	15.795	15.795	0.000	0.000	0.000	0.000
73	A	88	LEU	0	-0.023	0.013	18.790	0.621	0.621	0.000	0.000	0.000	0.000
74	A	89	ILE	0	-0.043	-0.018	20.236	0.635	0.635	0.000	0.000	0.000	0.000
75	A	90	PHE	0	0.052	0.012	21.780	0.486	0.486	0.000	0.000	0.000	0.000
76	A	91	GLN	0	-0.022	0.001	21.334	0.009	0.009	0.000	0.000	0.000	0.000
77	A	92	ASN	0	0.013	-0.007	23.130	0.537	0.537	0.000	0.000	0.000	0.000
78	A	93	CYS	0	-0.108	-0.023	26.615	0.489	0.489	0.000	0.000	0.000	0.000
79	A	94	ALA	0	0.025	-0.003	28.416	0.381	0.381	0.000	0.000	0.000	0.000
80	A	95	GLU	-1	-1.009	-0.987	28.062	-10.611	-10.611	0.000	0.000	0.000	0.000
81	A	96	PHE	0	-0.041	-0.032	30.563	0.311	0.311	0.000	0.000	0.000	0.000
82	A	97	ASN	0	-0.059	-0.027	32.151	0.055	0.055	0.000	0.000	0.000	0.000
83	A	98	GLU	-1	-0.854	-0.922	34.476	-7.999	-7.999	0.000	0.000	0.000	0.000
84	A	99	PRO	0	0.013	-0.009	35.877	-0.016	-0.016	0.000	0.000	0.000	0.000
85	A	100	ASP	-1	-0.913	-0.944	36.931	-7.440	-7.440	0.000	0.000	0.000	0.000
86	A	101	SER	0	-0.068	-0.048	36.696	-0.020	-0.020	0.000	0.000	0.000	0.000
87	A	102	GLU	-1	-0.849	-0.930	36.643	-8.288	-8.288	0.000	0.000	0.000	0.000
88	A	103	VAL	0	0.002	-0.004	31.947	-0.157	-0.157	0.000	0.000	0.000	0.000
89	A	104	ALA	0	0.076	0.043	32.608	-0.319	-0.319	0.000	0.000	0.000	0.000
90	A	105	ASN	0	-0.042	-0.023	32.833	-0.233	-0.233	0.000	0.000	0.000	0.000
91	A	106	ALA	0	-0.049	-0.033	32.257	-0.140	-0.140	0.000	0.000	0.000	0.000
92	A	107	GLY	0	0.022	-0.008	28.968	-0.282	-0.282	0.000	0.000	0.000	0.000
93	A	108	ILE	0	0.015	0.017	28.339	-0.342	-0.342	0.000	0.000	0.000	0.000
94	A	109	LYS	1	0.839	0.931	29.420	8.484	8.484	0.000	0.000	0.000	0.000
95	A	110	LEU	0	0.007	-0.007	24.937	-0.250	-0.250	0.000	0.000	0.000	0.000
96	A	111	GLU	-1	-0.915	-0.935	24.293	-12.051	-12.051	0.000	0.000	0.000	0.000
97	A	112	ASN	0	-0.039	-0.028	24.900	-0.340	-0.340	0.000	0.000	0.000	0.000
98	A	113	TYR	0	-0.005	0.005	26.048	-0.205	-0.205	0.000	0.000	0.000	0.000
99	A	114	PHE	0	-0.005	-0.026	17.184	-0.510	-0.510	0.000	0.000	0.000	0.000
100	A	115	GLU	-1	-0.775	-0.874	20.955	-14.687	-14.687	0.000	0.000	0.000	0.000
101	A	116	GLU	-1	-0.944	-0.958	22.453	-10.649	-10.649	0.000	0.000	0.000	0.000
102	A	117	LEU	0	-0.054	-0.025	21.630	-0.305	-0.305	0.000	0.000	0.000	0.000
103	A	118	LEU	0	-0.027	-0.012	15.542	-0.610	-0.610	0.000	0.000	0.000	0.000
104	A	119	LYS	1	0.878	0.939	18.674	12.451	12.451	0.000	0.000	0.000	0.000
105	A	120	ASN	0	-0.050	-0.043	20.899	0.014	0.014	0.000	0.000	0.000	0.000
106	A	121	LEU	0	-0.041	-0.009	17.017	-0.125	-0.125	0.000	0.000	0.000	0.000
107	A	122	TYR	0	-0.101	-0.091	11.142	-1.057	-1.057	0.000	0.000	0.000	0.000
108	A	123	PRO	0	0.003	0.028	17.194	0.094	0.094	0.000	0.000	0.000	0.000
109	A	124	GLU	-1	-0.859	-0.932	17.959	-14.290	-14.290	0.000	0.000	0.000	0.000
110	A	125	LYS	1	0.800	0.900	9.389	25.792	25.792	0.000	0.000	0.000	0.000
111	A	126	ARG	1	0.990	0.987	16.148	14.143	14.143	0.000	0.000	0.000	0.000
112	A	127	PHE	0	0.035	0.013	11.515	-0.827	-0.827	0.000	0.000	0.000	0.000
113	A	128	PRO	0	0.028	0.037	15.374	0.569	0.569	0.000	0.000	0.000	0.000

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