FMO DATABASE

FMODB ID: YZRQ2

Calculation Name: 4E61-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4E61

Chain ID: A

ChEMBL ID:

UniProt ID: P40013

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	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	91
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-477593.489826
FMO2-HF: Nuclear repulsion	442042.218957
FMO2-HF: Total energy	-35551.270869
FMO2-MP2: Total energy	-35656.691812

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:1:GLY)

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

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.
-0.63	1.259	0.004	-0.78	-1.111	0.001

Interaction energy analysis for fragmet #1(A:1:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.033 / q_NPA : 0.007

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	3	LEU	0	0.028	0.028	3.857	-0.134	1.068	-0.003	-0.558	-0.639	0.000
4	A	4	GLY	0	0.051	0.024	3.564	-0.752	-0.299	0.008	-0.168	-0.293	0.001
5	A	5	SER	0	-0.032	-0.018	3.917	-0.186	0.048	-0.001	-0.054	-0.179	0.000
6	A	6	LEU	0	0.025	0.005	5.763	0.460	0.460	0.000	0.000	0.000	0.000
7	A	7	VAL	0	-0.004	-0.010	7.697	0.160	0.160	0.000	0.000	0.000	0.000
8	A	8	ALA	0	-0.008	-0.007	8.063	0.056	0.056	0.000	0.000	0.000	0.000
9	A	9	ILE	0	0.038	0.023	9.752	0.067	0.067	0.000	0.000	0.000	0.000
10	A	10	GLN	0	-0.012	-0.004	11.734	0.078	0.078	0.000	0.000	0.000	0.000
11	A	11	ALA	0	0.000	0.006	12.911	0.048	0.048	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.953	-0.979	12.559	-0.475	-0.475	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.021	0.003	15.853	0.030	0.030	0.000	0.000	0.000	0.000
14	A	14	THR	0	0.044	0.019	17.590	0.020	0.020	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.964	0.996	18.650	0.142	0.142	0.000	0.000	0.000	0.000
16	A	16	SER	0	-0.055	-0.037	20.026	0.010	0.010	0.000	0.000	0.000	0.000
17	A	17	GLN	0	0.022	-0.004	21.552	0.019	0.019	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.912	-0.951	22.849	-0.052	-0.052	0.000	0.000	0.000	0.000
19	A	19	THR	0	-0.085	-0.035	24.100	0.004	0.004	0.000	0.000	0.000	0.000
20	A	20	ILE	0	0.003	0.002	25.935	0.007	0.007	0.000	0.000	0.000	0.000
21	A	21	GLY	0	0.021	0.015	27.946	0.006	0.006	0.000	0.000	0.000	0.000
22	A	22	SER	0	-0.028	-0.027	29.267	0.004	0.004	0.000	0.000	0.000	0.000
23	A	23	LEU	0	0.010	-0.002	28.982	0.002	0.002	0.000	0.000	0.000	0.000
24	A	24	ASN	0	-0.022	-0.019	32.004	0.001	0.001	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.913	-0.945	33.996	-0.033	-0.033	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.896	-0.946	34.297	-0.055	-0.055	0.000	0.000	0.000	0.000
27	A	27	ILE	0	-0.023	-0.004	35.237	0.003	0.003	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.791	-0.884	38.423	-0.039	-0.039	0.000	0.000	0.000	0.000
29	A	29	GLN	0	-0.032	-0.020	38.867	0.005	0.005	0.000	0.000	0.000	0.000
30	A	30	TYR	0	-0.073	-0.051	37.843	0.004	0.004	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.786	0.881	40.442	0.043	0.043	0.000	0.000	0.000	0.000
32	A	32	GLY	0	0.026	0.023	44.372	0.002	0.002	0.000	0.000	0.000	0.000
33	A	33	THR	0	-0.048	-0.023	44.566	0.002	0.002	0.000	0.000	0.000	0.000
34	A	34	VAL	0	0.017	0.008	46.283	0.001	0.001	0.000	0.000	0.000	0.000
35	A	35	SER	0	0.000	0.003	48.569	0.002	0.002	0.000	0.000	0.000	0.000
36	A	36	THR	0	-0.002	-0.014	49.951	0.002	0.002	0.000	0.000	0.000	0.000
37	A	37	LEU	0	0.006	0.009	49.720	0.001	0.001	0.000	0.000	0.000	0.000
38	A	38	GLU	-1	-0.887	-0.933	52.224	-0.029	-0.029	0.000	0.000	0.000	0.000
39	A	39	ILE	0	-0.042	-0.011	53.686	0.001	0.001	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.967	-0.987	55.371	-0.021	-0.021	0.000	0.000	0.000	0.000
41	A	41	ARG	1	0.879	0.923	55.279	0.027	0.027	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.861	-0.911	59.000	-0.019	-0.019	0.000	0.000	0.000	0.000
43	A	43	PHE	0	-0.010	-0.004	60.860	0.001	0.001	0.000	0.000	0.000	0.000
44	A	44	TYR	0	-0.007	-0.019	57.768	0.001	0.001	0.000	0.000	0.000	0.000
45	A	45	PHE	0	0.041	0.006	61.026	0.000	0.000	0.000	0.000	0.000	0.000
46	A	46	ASN	0	-0.034	-0.022	64.486	0.001	0.001	0.000	0.000	0.000	0.000
47	A	47	LYS	1	0.897	0.965	65.853	0.016	0.016	0.000	0.000	0.000	0.000
48	A	48	LEU	0	0.017	0.011	65.607	0.001	0.001	0.000	0.000	0.000	0.000
49	A	49	ARG	1	0.868	0.923	68.175	0.016	0.016	0.000	0.000	0.000	0.000
50	A	50	ASP	-1	-0.858	-0.918	70.701	-0.014	-0.014	0.000	0.000	0.000	0.000
51	A	51	ILE	0	-0.071	-0.037	71.036	0.001	0.001	0.000	0.000	0.000	0.000
52	A	52	GLU	-1	-0.926	-0.965	72.968	-0.016	-0.016	0.000	0.000	0.000	0.000
53	A	53	ILE	0	0.031	0.018	74.087	0.000	0.000	0.000	0.000	0.000	0.000
54	A	54	LEU	0	-0.030	0.009	77.006	0.001	0.001	0.000	0.000	0.000	0.000
55	A	55	VAL	0	-0.024	-0.018	77.034	0.001	0.001	0.000	0.000	0.000	0.000
56	A	56	HIS	0	0.014	-0.013	76.685	0.000	0.000	0.000	0.000	0.000	0.000
57	A	57	THR	0	0.026	0.009	80.665	0.000	0.000	0.000	0.000	0.000	0.000
58	A	58	THR	0	-0.097	-0.070	82.350	0.000	0.000	0.000	0.000	0.000	0.000
59	A	59	GLN	0	-0.005	-0.005	81.166	0.000	0.000	0.000	0.000	0.000	0.000
60	A	60	ASP	-1	-0.877	-0.919	84.478	-0.012	-0.012	0.000	0.000	0.000	0.000
61	A	61	LEU	0	-0.013	-0.004	86.986	0.000	0.000	0.000	0.000	0.000	0.000
62	A	62	ILE	0	-0.105	-0.061	86.588	0.000	0.000	0.000	0.000	0.000	0.000
63	A	63	ASN	0	-0.050	-0.020	86.605	0.000	0.000	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.954	-0.966	90.617	-0.010	-0.010	0.000	0.000	0.000	0.000
65	A	65	GLY	0	-0.018	-0.029	92.769	0.000	0.000	0.000	0.000	0.000	0.000
66	A	66	VAL	0	-0.014	0.022	92.578	0.000	0.000	0.000	0.000	0.000	0.000
67	A	67	TYR	0	0.018	0.008	88.221	0.000	0.000	0.000	0.000	0.000	0.000
68	A	68	LYS	1	0.865	0.934	95.138	0.008	0.008	0.000	0.000	0.000	0.000
69	A	83	GLY	0	0.052	0.017	90.812	0.000	0.000	0.000	0.000	0.000	0.000
70	A	84	ALA	0	-0.029	-0.028	87.893	0.000	0.000	0.000	0.000	0.000	0.000
71	A	85	LEU	0	0.060	0.035	85.116	0.000	0.000	0.000	0.000	0.000	0.000
72	A	86	LEU	0	0.097	0.051	85.060	0.000	0.000	0.000	0.000	0.000	0.000
73	A	87	ARG	1	0.953	0.973	84.703	0.010	0.010	0.000	0.000	0.000	0.000
74	A	88	PHE	0	-0.043	-0.027	78.550	0.000	0.000	0.000	0.000	0.000	0.000
75	A	89	VAL	0	0.062	0.026	80.531	0.000	0.000	0.000	0.000	0.000	0.000
76	A	90	LYS	1	0.855	0.900	80.148	0.013	0.013	0.000	0.000	0.000	0.000
77	A	91	LYS	1	0.895	0.964	78.413	0.012	0.012	0.000	0.000	0.000	0.000
78	A	92	VAL	0	0.021	0.021	75.176	0.000	0.000	0.000	0.000	0.000	0.000
79	A	93	GLU	-1	-0.730	-0.836	75.144	-0.015	-0.015	0.000	0.000	0.000	0.000
80	A	94	SER	0	-0.074	-0.040	75.393	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	95	ILE	0	-0.021	-0.017	70.871	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	96	LEU	0	0.036	0.016	70.957	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	97	TYR	0	-0.053	-0.027	70.803	0.000	0.000	0.000	0.000	0.000	0.000
84	A	98	ALA	0	0.018	0.001	69.725	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	99	THR	0	-0.128	-0.064	66.576	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	100	ALA	0	0.012	0.008	65.981	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	101	GLU	-1	-0.884	-0.935	66.701	-0.020	-0.020	0.000	0.000	0.000	0.000
88	A	102	GLY	0	-0.038	-0.015	64.002	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	103	PHE	0	-0.053	-0.024	61.556	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	104	GLU	-1	-0.952	-0.964	60.799	-0.027	-0.027	0.000	0.000	0.000	0.000
91	A	105	MET	0	-0.069	-0.027	58.198	-0.002	-0.002	0.000	0.000	0.000	0.000

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