FMO DATABASE

FMODB ID: QYN4Y

Calculation Name: 4ATI-A-Xray372

Preferred Name: Microphthalmia-associated transcription factor

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4ATI

Chain ID: A

ChEMBL ID: CHEMBL1075142

UniProt ID: Q08874

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	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	61
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-321613.154835
FMO2-HF: Nuclear repulsion	295976.204751
FMO2-HF: Total energy	-25636.950084
FMO2-MP2: Total energy	-25712.8069

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:209:HIS)

Summations of interaction energy for fragment #1(A:209:HIS)

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.
2.205	4.569	2.697	-0.987	-4.074	0.004

Interaction energy analysis for fragmet #1(A:209:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.112 / q_NPA : 0.037

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

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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	211	LEU	0	-0.005	0.001	3.065	0.100	0.974	-0.004	0.176	-1.046	0.003
4	A	212	ILE	0	0.027	0.008	2.062	-1.118	-0.456	2.699	-1.021	-2.340	0.001
5	A	213	GLU	-1	-0.781	-0.896	4.233	1.526	2.354	0.002	-0.142	-0.688	0.000
6	A	214	ARG	1	0.879	0.968	6.076	0.847	0.847	0.000	0.000	0.000	0.000
7	A	215	ARG	1	0.932	0.955	7.262	0.570	0.570	0.000	0.000	0.000	0.000
8	A	216	ARG	1	1.024	1.019	7.610	-0.286	-0.286	0.000	0.000	0.000	0.000
9	A	217	ARG	1	0.856	0.919	5.655	0.374	0.374	0.000	0.000	0.000	0.000
10	A	218	PHE	0	0.041	0.006	11.580	0.036	0.036	0.000	0.000	0.000	0.000
11	A	219	ASN	0	0.071	0.054	13.093	0.039	0.039	0.000	0.000	0.000	0.000
12	A	220	ILE	0	0.013	0.011	12.789	0.030	0.030	0.000	0.000	0.000	0.000
13	A	221	ASN	0	-0.070	-0.067	13.968	0.045	0.045	0.000	0.000	0.000	0.000
14	A	222	ASP	-1	-0.862	-0.933	17.369	-0.122	-0.122	0.000	0.000	0.000	0.000
15	A	223	ARG	1	0.864	0.930	18.601	0.056	0.056	0.000	0.000	0.000	0.000
16	A	224	ILE	0	-0.047	-0.013	18.391	0.007	0.007	0.000	0.000	0.000	0.000
17	A	225	LYS	1	0.940	0.957	19.986	0.108	0.108	0.000	0.000	0.000	0.000
18	A	226	GLU	-1	-0.827	-0.890	22.917	-0.039	-0.039	0.000	0.000	0.000	0.000
19	A	227	LEU	0	-0.027	-0.021	23.634	0.005	0.005	0.000	0.000	0.000	0.000
20	A	228	GLY	0	-0.026	-0.015	26.064	0.004	0.004	0.000	0.000	0.000	0.000
21	A	229	THR	0	-0.031	-0.008	27.948	0.000	0.000	0.000	0.000	0.000	0.000
22	A	230	LEU	0	-0.020	-0.014	28.854	0.001	0.001	0.000	0.000	0.000	0.000
23	A	231	ILE	0	-0.056	-0.005	29.088	0.003	0.003	0.000	0.000	0.000	0.000
24	A	232	PRO	0	0.002	0.022	32.472	-0.002	-0.002	0.000	0.000	0.000	0.000
25	A	233	LYS	1	0.965	0.960	34.278	0.020	0.020	0.000	0.000	0.000	0.000
26	A	234	SER	0	-0.063	-0.022	35.988	0.001	0.001	0.000	0.000	0.000	0.000
27	A	235	ASN	0	-0.033	-0.033	37.631	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	236	ASP	-1	-0.778	-0.886	37.435	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	237	PRO	0	-0.039	-0.026	38.689	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	238	ASP	-1	-0.933	-0.962	37.032	-0.007	-0.007	0.000	0.000	0.000	0.000
31	A	239	MET	0	-0.032	0.007	31.945	0.001	0.001	0.000	0.000	0.000	0.000
32	A	240	ARG	1	0.960	0.990	27.761	0.014	0.014	0.000	0.000	0.000	0.000
33	A	241	TRP	0	0.022	0.023	27.805	0.002	0.002	0.000	0.000	0.000	0.000
34	A	242	ASN	0	0.024	-0.007	24.149	-0.010	-0.010	0.000	0.000	0.000	0.000
35	A	243	LYS	1	0.972	0.978	16.077	0.050	0.050	0.000	0.000	0.000	0.000
36	A	244	GLY	0	0.015	-0.001	22.123	0.008	0.008	0.000	0.000	0.000	0.000
37	A	245	THR	0	0.006	-0.023	23.761	0.004	0.004	0.000	0.000	0.000	0.000
38	A	246	ILE	0	0.052	0.039	24.498	0.002	0.002	0.000	0.000	0.000	0.000
39	A	247	LEU	0	-0.021	-0.005	20.707	0.004	0.004	0.000	0.000	0.000	0.000
40	A	248	LYS	1	0.946	0.973	25.335	-0.017	-0.017	0.000	0.000	0.000	0.000
41	A	249	ALA	0	0.013	0.016	28.444	0.001	0.001	0.000	0.000	0.000	0.000
42	A	250	SER	0	0.038	0.003	26.677	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	251	VAL	0	-0.013	-0.001	27.075	0.001	0.001	0.000	0.000	0.000	0.000
44	A	252	ASP	-1	-0.874	-0.960	29.670	0.024	0.024	0.000	0.000	0.000	0.000
45	A	253	TYR	0	0.012	0.018	32.369	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	254	ILE	0	0.010	0.005	28.650	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	255	ARG	1	0.931	0.965	31.035	-0.037	-0.037	0.000	0.000	0.000	0.000
48	A	256	LYS	1	0.942	0.975	35.086	-0.010	-0.010	0.000	0.000	0.000	0.000
49	A	257	LEU	0	0.054	0.024	35.297	0.000	0.000	0.000	0.000	0.000	0.000
50	A	258	GLN	0	0.024	0.011	32.720	0.001	0.001	0.000	0.000	0.000	0.000
51	A	259	ARG	1	0.920	0.962	37.820	-0.015	-0.015	0.000	0.000	0.000	0.000
52	A	260	GLU	-1	-0.988	-0.990	40.831	0.003	0.003	0.000	0.000	0.000	0.000
53	A	261	GLN	0	0.028	0.012	38.012	0.001	0.001	0.000	0.000	0.000	0.000
54	A	262	GLN	0	-0.025	-0.003	41.621	0.000	0.000	0.000	0.000	0.000	0.000
55	A	263	ARG	1	0.927	0.959	43.272	-0.009	-0.009	0.000	0.000	0.000	0.000
56	A	264	ALA	0	0.025	0.012	44.473	0.000	0.000	0.000	0.000	0.000	0.000
57	A	265	LYS	1	0.844	0.913	42.376	-0.011	-0.011	0.000	0.000	0.000	0.000
58	A	266	ASP	-1	-0.906	-0.953	46.481	0.009	0.009	0.000	0.000	0.000	0.000
59	A	267	LEU	0	-0.053	-0.015	49.612	0.000	0.000	0.000	0.000	0.000	0.000
60	A	268	GLU	-1	-0.912	-0.938	48.519	0.001	0.001	0.000	0.000	0.000	0.000
61	A	269	ASN	0	-0.087	-0.049	50.782	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:209:HIS)