FMO DATABASE

FMODB ID: 49LKN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-320867.673889
FMO2-HF: Nuclear repulsion	295229.55228
FMO2-HF: Total energy	-25638.121609
FMO2-MP2: Total energy	-25713.893775

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.
4.578	8.674	0.714	-1.477	-3.332	0.003

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 : 0.109 / q_NPA : 0.048

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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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	211	LEU	0	0.037	0.018	3.879	-2.624	-1.118	-0.002	-0.650	-0.853	0.003
4	A	212	ILE	0	-0.002	0.007	2.453	-0.956	0.563	0.680	-0.568	-1.631	0.001
5	A	213	GLU	-1	-0.710	-0.821	2.897	-3.140	-2.219	0.037	-0.244	-0.714	-0.001
6	A	214	ARG	1	0.930	0.974	4.763	2.044	2.194	-0.001	-0.015	-0.134	0.000
7	A	215	ARG	1	0.926	0.949	6.186	1.651	1.651	0.000	0.000	0.000	0.000
8	A	216	ARG	1	0.929	0.959	6.993	2.517	2.517	0.000	0.000	0.000	0.000
9	A	217	ARG	1	0.840	0.890	6.418	2.892	2.892	0.000	0.000	0.000	0.000
10	A	218	PHE	0	0.016	0.006	10.383	0.234	0.234	0.000	0.000	0.000	0.000
11	A	219	ASN	0	0.086	0.044	12.745	0.206	0.206	0.000	0.000	0.000	0.000
12	A	220	ILE	0	-0.011	-0.002	11.151	0.100	0.100	0.000	0.000	0.000	0.000
13	A	221	ASN	0	-0.002	-0.008	13.807	0.138	0.138	0.000	0.000	0.000	0.000
14	A	222	ASP	-1	-0.808	-0.895	16.501	-0.495	-0.495	0.000	0.000	0.000	0.000
15	A	223	ARG	1	0.883	0.925	17.905	0.504	0.504	0.000	0.000	0.000	0.000
16	A	224	ILE	0	-0.011	-0.001	17.798	0.040	0.040	0.000	0.000	0.000	0.000
17	A	225	LYS	1	0.844	0.907	18.453	0.521	0.521	0.000	0.000	0.000	0.000
18	A	226	GLU	-1	-0.846	-0.896	22.342	-0.329	-0.329	0.000	0.000	0.000	0.000
19	A	227	LEU	0	0.013	-0.002	22.560	0.025	0.025	0.000	0.000	0.000	0.000
20	A	228	GLY	0	-0.008	-0.017	24.980	0.024	0.024	0.000	0.000	0.000	0.000
21	A	229	THR	0	-0.073	-0.036	26.690	0.020	0.020	0.000	0.000	0.000	0.000
22	A	230	LEU	0	-0.018	-0.004	27.684	0.015	0.015	0.000	0.000	0.000	0.000
23	A	231	ILE	0	-0.056	-0.010	28.572	0.012	0.012	0.000	0.000	0.000	0.000
24	A	232	PRO	0	-0.009	0.008	31.508	0.003	0.003	0.000	0.000	0.000	0.000
25	A	233	LYS	1	0.928	0.955	32.918	0.158	0.158	0.000	0.000	0.000	0.000
26	A	234	SER	0	-0.083	-0.052	35.397	0.003	0.003	0.000	0.000	0.000	0.000
27	A	235	ASN	0	-0.020	-0.029	37.450	0.003	0.003	0.000	0.000	0.000	0.000
28	A	236	ASP	-1	-0.755	-0.856	37.567	-0.120	-0.120	0.000	0.000	0.000	0.000
29	A	237	PRO	0	-0.015	-0.013	38.347	-0.007	-0.007	0.000	0.000	0.000	0.000
30	A	238	ASP	-1	-0.926	-0.955	36.833	-0.119	-0.119	0.000	0.000	0.000	0.000
31	A	239	MET	0	-0.025	0.005	32.376	-0.014	-0.014	0.000	0.000	0.000	0.000
32	A	240	ARG	1	0.939	0.958	25.990	0.186	0.186	0.000	0.000	0.000	0.000
33	A	241	TRP	0	0.016	0.012	27.492	-0.016	-0.016	0.000	0.000	0.000	0.000
34	A	242	ASN	0	-0.003	-0.003	23.930	-0.007	-0.007	0.000	0.000	0.000	0.000
35	A	243	LYS	1	0.907	0.946	15.586	0.685	0.685	0.000	0.000	0.000	0.000
36	A	244	GLY	0	0.041	0.027	22.046	0.000	0.000	0.000	0.000	0.000	0.000
37	A	245	THR	0	0.027	-0.003	23.701	0.002	0.002	0.000	0.000	0.000	0.000
38	A	246	ILE	0	0.040	0.034	24.365	0.012	0.012	0.000	0.000	0.000	0.000
39	A	247	LEU	0	0.007	0.012	20.243	0.005	0.005	0.000	0.000	0.000	0.000
40	A	248	LYS	1	0.894	0.936	24.922	0.177	0.177	0.000	0.000	0.000	0.000
41	A	249	ALA	0	0.023	0.012	28.046	0.012	0.012	0.000	0.000	0.000	0.000
42	A	250	SER	0	0.025	-0.008	26.545	0.007	0.007	0.000	0.000	0.000	0.000
43	A	251	VAL	0	-0.025	-0.008	26.592	0.010	0.010	0.000	0.000	0.000	0.000
44	A	252	ASP	-1	-0.822	-0.901	29.238	-0.151	-0.151	0.000	0.000	0.000	0.000
45	A	253	TYR	0	0.017	0.017	31.927	0.011	0.011	0.000	0.000	0.000	0.000
46	A	254	ILE	0	0.022	0.011	28.164	0.008	0.008	0.000	0.000	0.000	0.000
47	A	255	ARG	1	0.900	0.937	30.930	0.171	0.171	0.000	0.000	0.000	0.000
48	A	256	LYS	1	0.827	0.904	34.855	0.121	0.121	0.000	0.000	0.000	0.000
49	A	257	LEU	0	0.041	0.019	33.692	0.008	0.008	0.000	0.000	0.000	0.000
50	A	258	GLN	0	0.023	0.010	32.859	0.006	0.006	0.000	0.000	0.000	0.000
51	A	259	ARG	1	0.924	0.966	37.437	0.102	0.102	0.000	0.000	0.000	0.000
52	A	260	GLU	-1	-0.866	-0.921	40.289	-0.111	-0.111	0.000	0.000	0.000	0.000
53	A	261	GLN	0	0.014	0.010	37.088	0.002	0.002	0.000	0.000	0.000	0.000
54	A	262	GLN	0	-0.070	-0.036	41.177	0.001	0.001	0.000	0.000	0.000	0.000
55	A	263	ARG	1	0.959	0.969	43.047	0.082	0.082	0.000	0.000	0.000	0.000
56	A	264	ALA	0	0.030	0.008	44.301	0.004	0.004	0.000	0.000	0.000	0.000
57	A	265	LYS	1	0.829	0.895	43.641	0.090	0.090	0.000	0.000	0.000	0.000
58	A	266	ASP	-1	-0.852	-0.890	46.453	-0.078	-0.078	0.000	0.000	0.000	0.000
59	A	267	LEU	0	-0.088	-0.036	49.427	0.003	0.003	0.000	0.000	0.000	0.000
60	A	268	GLU	-1	-0.895	-0.934	48.412	-0.073	-0.073	0.000	0.000	0.000	0.000
61	A	269	ASN	0	-0.090	-0.049	50.616	0.003	0.003	0.000	0.000	0.000	0.000

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