FMO DATABASE

FMODB ID: 5253Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-477224.651673
FMO2-HF: Nuclear repulsion	441673.935741
FMO2-HF: Total energy	-35550.715932
FMO2-MP2: Total energy	-35656.099473

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.
-0.199	1.655	0.004	-0.752	-1.107	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 : 0.034 / q_NPA : 0.006

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	0.027	0.026	3.857	-0.108	1.059	-0.003	-0.534	-0.629	0.000
4	A	4	GLY	0	0.047	0.023	3.507	-0.653	-0.203	0.008	-0.163	-0.296	0.001
5	A	5	SER	0	-0.030	-0.017	3.861	0.005	0.242	-0.001	-0.055	-0.182	0.000
6	A	6	LEU	0	0.029	0.012	5.724	0.502	0.502	0.000	0.000	0.000	0.000
7	A	7	VAL	0	-0.007	-0.012	7.633	0.185	0.185	0.000	0.000	0.000	0.000
8	A	8	ALA	0	-0.005	-0.006	8.013	0.075	0.075	0.000	0.000	0.000	0.000
9	A	9	ILE	0	0.048	0.028	9.710	0.087	0.087	0.000	0.000	0.000	0.000
10	A	10	GLN	0	-0.013	-0.003	11.680	0.101	0.101	0.000	0.000	0.000	0.000
11	A	11	ALA	0	-0.003	-0.001	12.859	0.058	0.058	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.951	-0.978	12.357	-0.520	-0.520	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.024	-0.003	15.807	0.034	0.034	0.000	0.000	0.000	0.000
14	A	14	THR	0	-0.008	-0.006	17.541	0.035	0.035	0.000	0.000	0.000	0.000
15	A	15	LYS	1	1.013	1.012	18.604	0.167	0.167	0.000	0.000	0.000	0.000
16	A	16	SER	0	-0.061	-0.036	19.986	0.012	0.012	0.000	0.000	0.000	0.000
17	A	17	GLN	0	0.010	-0.016	21.615	0.015	0.015	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.940	-0.958	23.316	-0.060	-0.060	0.000	0.000	0.000	0.000
19	A	19	THR	0	-0.074	-0.023	23.705	0.008	0.008	0.000	0.000	0.000	0.000
20	A	20	ILE	0	0.040	0.010	25.887	0.007	0.007	0.000	0.000	0.000	0.000
21	A	21	GLY	0	0.012	0.011	27.902	0.007	0.007	0.000	0.000	0.000	0.000
22	A	22	SER	0	-0.018	-0.013	29.224	0.006	0.006	0.000	0.000	0.000	0.000
23	A	23	LEU	0	0.016	0.002	29.139	0.003	0.003	0.000	0.000	0.000	0.000
24	A	24	ASN	0	-0.023	-0.021	32.252	0.001	0.001	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.930	-0.952	33.743	-0.040	-0.040	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.948	-0.976	34.113	-0.062	-0.062	0.000	0.000	0.000	0.000
27	A	27	ILE	0	-0.034	-0.015	35.139	0.003	0.003	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.891	-0.952	38.414	-0.041	-0.041	0.000	0.000	0.000	0.000
29	A	29	GLN	0	0.012	0.004	38.544	0.005	0.005	0.000	0.000	0.000	0.000
30	A	30	TYR	0	-0.051	-0.042	38.332	0.004	0.004	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.886	0.954	40.828	0.050	0.050	0.000	0.000	0.000	0.000
32	A	32	GLY	0	0.023	0.023	44.332	0.002	0.002	0.000	0.000	0.000	0.000
33	A	33	THR	0	-0.083	-0.042	44.565	0.002	0.002	0.000	0.000	0.000	0.000
34	A	34	VAL	0	0.035	0.020	46.259	0.001	0.001	0.000	0.000	0.000	0.000
35	A	35	SER	0	0.024	0.011	48.531	0.002	0.002	0.000	0.000	0.000	0.000
36	A	36	THR	0	-0.005	-0.004	50.235	0.002	0.002	0.000	0.000	0.000	0.000
37	A	37	LEU	0	-0.002	0.004	49.675	0.001	0.001	0.000	0.000	0.000	0.000
38	A	38	GLU	-1	-0.955	-0.987	51.905	-0.033	-0.033	0.000	0.000	0.000	0.000
39	A	39	ILE	0	-0.034	-0.011	53.632	0.001	0.001	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.977	-0.990	55.639	-0.024	-0.024	0.000	0.000	0.000	0.000
41	A	41	ARG	1	0.956	0.975	55.205	0.030	0.030	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.866	-0.900	58.964	-0.021	-0.021	0.000	0.000	0.000	0.000
43	A	43	PHE	0	-0.026	-0.018	60.824	0.001	0.001	0.000	0.000	0.000	0.000
44	A	44	TYR	0	-0.003	-0.018	57.877	0.001	0.001	0.000	0.000	0.000	0.000
45	A	45	PHE	0	0.041	0.005	61.023	0.000	0.000	0.000	0.000	0.000	0.000
46	A	46	ASN	0	-0.029	-0.032	64.672	0.001	0.001	0.000	0.000	0.000	0.000
47	A	47	LYS	1	0.885	0.959	66.143	0.017	0.017	0.000	0.000	0.000	0.000
48	A	48	LEU	0	0.012	0.006	65.515	0.001	0.001	0.000	0.000	0.000	0.000
49	A	49	ARG	1	0.898	0.952	68.431	0.018	0.018	0.000	0.000	0.000	0.000
50	A	50	ASP	-1	-0.862	-0.919	70.669	-0.016	-0.016	0.000	0.000	0.000	0.000
51	A	51	ILE	0	-0.071	-0.042	71.315	0.001	0.001	0.000	0.000	0.000	0.000
52	A	52	GLU	-1	-0.935	-0.966	72.849	-0.018	-0.018	0.000	0.000	0.000	0.000
53	A	53	ILE	0	0.024	0.017	73.931	0.000	0.000	0.000	0.000	0.000	0.000
54	A	54	LEU	0	-0.042	-0.015	76.972	0.001	0.001	0.000	0.000	0.000	0.000
55	A	55	VAL	0	-0.035	-0.031	77.192	0.001	0.001	0.000	0.000	0.000	0.000
56	A	56	HIS	0	0.051	0.016	76.458	0.000	0.000	0.000	0.000	0.000	0.000
57	A	57	THR	0	0.026	0.026	80.792	0.000	0.000	0.000	0.000	0.000	0.000
58	A	58	THR	0	-0.085	-0.057	82.560	0.000	0.000	0.000	0.000	0.000	0.000
59	A	59	GLN	0	-0.040	-0.052	81.324	0.000	0.000	0.000	0.000	0.000	0.000
60	A	60	ASP	-1	-0.892	-0.924	84.661	-0.013	-0.013	0.000	0.000	0.000	0.000
61	A	61	LEU	0	-0.004	0.001	86.956	0.000	0.000	0.000	0.000	0.000	0.000
62	A	62	ILE	0	-0.112	-0.060	86.432	0.000	0.000	0.000	0.000	0.000	0.000
63	A	63	ASN	0	-0.047	-0.023	86.941	0.000	0.000	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.951	-0.967	89.601	-0.012	-0.012	0.000	0.000	0.000	0.000
65	A	65	GLY	0	-0.018	-0.028	92.740	0.000	0.000	0.000	0.000	0.000	0.000
66	A	66	VAL	0	-0.008	0.027	92.470	0.000	0.000	0.000	0.000	0.000	0.000
67	A	67	TYR	0	0.019	0.006	88.596	0.000	0.000	0.000	0.000	0.000	0.000
68	A	68	LYS	1	0.860	0.932	95.107	0.009	0.009	0.000	0.000	0.000	0.000
69	A	83	GLY	0	0.056	0.019	90.786	0.000	0.000	0.000	0.000	0.000	0.000
70	A	84	ALA	0	-0.033	-0.030	87.808	0.000	0.000	0.000	0.000	0.000	0.000
71	A	85	LEU	0	0.055	0.034	85.032	0.000	0.000	0.000	0.000	0.000	0.000
72	A	86	LEU	0	0.102	0.052	85.033	0.000	0.000	0.000	0.000	0.000	0.000
73	A	87	ARG	1	0.951	0.972	84.678	0.011	0.011	0.000	0.000	0.000	0.000
74	A	88	PHE	0	-0.052	-0.025	78.450	0.000	0.000	0.000	0.000	0.000	0.000
75	A	89	VAL	0	0.082	0.037	80.506	0.000	0.000	0.000	0.000	0.000	0.000
76	A	90	LYS	1	0.911	0.957	80.122	0.014	0.014	0.000	0.000	0.000	0.000
77	A	91	LYS	1	0.900	0.963	78.387	0.013	0.013	0.000	0.000	0.000	0.000
78	A	92	VAL	0	0.015	0.020	75.188	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	93	GLU	-1	-0.766	-0.870	75.118	-0.016	-0.016	0.000	0.000	0.000	0.000
80	A	94	SER	0	-0.066	-0.033	75.370	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	95	ILE	0	-0.029	-0.020	70.734	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	96	LEU	0	0.025	-0.008	70.934	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	97	TYR	0	-0.029	0.000	70.779	0.000	0.000	0.000	0.000	0.000	0.000
84	A	98	ALA	0	0.016	0.000	69.640	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	99	THR	0	-0.128	-0.047	66.723	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	100	ALA	0	0.043	0.027	65.959	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	101	GLU	-1	-0.894	-0.964	66.680	-0.022	-0.022	0.000	0.000	0.000	0.000
88	A	102	GLY	0	-0.057	-0.022	63.985	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	103	PHE	0	-0.050	-0.021	61.167	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	104	GLU	-1	-0.955	-0.967	60.771	-0.029	-0.029	0.000	0.000	0.000	0.000
91	A	105	MET	0	-0.073	-0.029	58.181	-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)