FMO DATABASE

FMODB ID: V5Y21

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

Total energy (hartree)

FMO2-HF: Electronic energy	-479762.557766
FMO2-HF: Nuclear repulsion	444210.973435
FMO2-HF: Total energy	-35551.584331
FMO2-MP2: Total energy	-35656.993589

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.
-0.424	1.549	0.038	-0.79	-1.22	0.002

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 : 0.041 / q_NPA : 0.009

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	0.037	0.038	3.895	-0.190	0.838	-0.001	-0.454	-0.572	0.001
4	A	4	GLY	0	0.041	0.020	3.132	-0.989	-0.306	0.039	-0.275	-0.448	0.001
5	A	5	SER	0	-0.036	-0.033	4.006	0.242	0.504	0.000	-0.061	-0.200	0.000
6	A	6	LEU	0	0.014	-0.002	6.061	0.495	0.495	0.000	0.000	0.000	0.000
7	A	7	VAL	0	-0.003	-0.012	7.504	0.183	0.183	0.000	0.000	0.000	0.000
8	A	8	ALA	0	-0.023	0.001	7.975	0.081	0.081	0.000	0.000	0.000	0.000
9	A	9	ILE	0	0.061	0.027	9.671	0.123	0.123	0.000	0.000	0.000	0.000
10	A	10	GLN	0	-0.017	-0.001	11.701	0.090	0.090	0.000	0.000	0.000	0.000
11	A	11	ALA	0	0.011	0.007	12.777	0.054	0.054	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.959	-0.984	12.270	-0.564	-0.564	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.023	0.006	15.772	0.039	0.039	0.000	0.000	0.000	0.000
14	A	14	THR	0	0.026	0.019	17.443	0.021	0.021	0.000	0.000	0.000	0.000
15	A	15	LYS	1	1.000	1.014	18.523	0.186	0.186	0.000	0.000	0.000	0.000
16	A	16	SER	0	-0.060	-0.042	19.936	0.016	0.016	0.000	0.000	0.000	0.000
17	A	17	GLN	0	0.007	-0.004	21.407	0.024	0.024	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.908	-0.964	21.259	-0.099	-0.099	0.000	0.000	0.000	0.000
19	A	19	THR	0	-0.077	-0.039	23.996	0.005	0.005	0.000	0.000	0.000	0.000
20	A	20	ILE	0	0.014	0.000	26.046	0.008	0.008	0.000	0.000	0.000	0.000
21	A	21	GLY	0	0.012	0.015	27.671	0.008	0.008	0.000	0.000	0.000	0.000
22	A	22	SER	0	-0.027	-0.025	29.037	0.004	0.004	0.000	0.000	0.000	0.000
23	A	23	LEU	0	0.005	0.000	29.059	0.003	0.003	0.000	0.000	0.000	0.000
24	A	24	ASN	0	-0.014	-0.007	31.738	0.003	0.003	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.922	-0.954	33.635	-0.043	-0.043	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.886	-0.923	33.860	-0.068	-0.068	0.000	0.000	0.000	0.000
27	A	27	ILE	0	-0.025	-0.004	35.107	0.003	0.003	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.791	-0.885	38.286	-0.044	-0.044	0.000	0.000	0.000	0.000
29	A	29	GLN	0	-0.029	-0.020	38.832	0.006	0.006	0.000	0.000	0.000	0.000
30	A	30	TYR	0	-0.091	-0.067	37.510	0.004	0.004	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.783	0.874	40.366	0.049	0.049	0.000	0.000	0.000	0.000
32	A	32	GLY	0	0.033	0.029	44.168	0.002	0.002	0.000	0.000	0.000	0.000
33	A	33	THR	0	-0.041	-0.007	44.671	0.002	0.002	0.000	0.000	0.000	0.000
34	A	34	VAL	0	0.041	0.010	46.166	0.002	0.002	0.000	0.000	0.000	0.000
35	A	35	SER	0	0.005	-0.009	48.318	0.002	0.002	0.000	0.000	0.000	0.000
36	A	36	THR	0	-0.067	-0.034	49.737	0.002	0.002	0.000	0.000	0.000	0.000
37	A	37	LEU	0	0.020	0.012	49.660	0.001	0.001	0.000	0.000	0.000	0.000
38	A	38	GLU	-1	-0.864	-0.918	51.637	-0.031	-0.031	0.000	0.000	0.000	0.000
39	A	39	ILE	0	-0.026	-0.006	53.840	0.001	0.001	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.949	-0.985	54.703	-0.026	-0.026	0.000	0.000	0.000	0.000
41	A	41	ARG	1	0.852	0.915	55.363	0.030	0.030	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.857	-0.913	58.736	-0.022	-0.022	0.000	0.000	0.000	0.000
43	A	43	PHE	0	0.012	0.000	60.481	0.002	0.002	0.000	0.000	0.000	0.000
44	A	44	TYR	0	-0.010	-0.015	57.996	0.001	0.001	0.000	0.000	0.000	0.000
45	A	45	PHE	0	0.054	0.016	60.866	0.001	0.001	0.000	0.000	0.000	0.000
46	A	46	ASN	0	-0.062	-0.033	64.150	0.002	0.002	0.000	0.000	0.000	0.000
47	A	47	LYS	1	0.864	0.947	65.238	0.019	0.019	0.000	0.000	0.000	0.000
48	A	48	LEU	0	0.012	0.012	65.357	0.001	0.001	0.000	0.000	0.000	0.000
49	A	49	ARG	1	0.872	0.910	67.726	0.019	0.019	0.000	0.000	0.000	0.000
50	A	50	ASP	-1	-0.845	-0.903	70.679	-0.016	-0.016	0.000	0.000	0.000	0.000
51	A	51	ILE	0	-0.058	-0.032	70.882	0.001	0.001	0.000	0.000	0.000	0.000
52	A	52	GLU	-1	-0.923	-0.964	72.961	-0.018	-0.018	0.000	0.000	0.000	0.000
53	A	53	ILE	0	0.033	0.016	74.036	0.001	0.001	0.000	0.000	0.000	0.000
54	A	54	LEU	0	-0.027	0.008	76.830	0.001	0.001	0.000	0.000	0.000	0.000
55	A	55	VAL	0	-0.002	0.002	76.761	0.001	0.001	0.000	0.000	0.000	0.000
56	A	56	HIS	0	0.016	-0.002	76.791	0.000	0.000	0.000	0.000	0.000	0.000
57	A	57	THR	0	0.010	-0.002	80.570	0.000	0.000	0.000	0.000	0.000	0.000
58	A	58	THR	0	-0.091	-0.077	81.923	0.000	0.000	0.000	0.000	0.000	0.000
59	A	59	GLN	0	-0.050	-0.027	80.802	0.000	0.000	0.000	0.000	0.000	0.000
60	A	60	ASP	-1	-0.832	-0.905	84.377	-0.013	-0.013	0.000	0.000	0.000	0.000
61	A	61	LEU	0	0.016	0.009	86.882	0.000	0.000	0.000	0.000	0.000	0.000
62	A	62	ILE	0	-0.114	-0.059	86.858	0.000	0.000	0.000	0.000	0.000	0.000
63	A	63	ASN	0	-0.066	-0.034	86.287	0.000	0.000	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.952	-0.969	90.538	-0.011	-0.011	0.000	0.000	0.000	0.000
65	A	65	GLY	0	-0.025	-0.009	92.849	0.000	0.000	0.000	0.000	0.000	0.000
66	A	66	VAL	0	-0.010	0.006	92.138	0.000	0.000	0.000	0.000	0.000	0.000
67	A	67	TYR	0	-0.004	-0.009	87.903	0.000	0.000	0.000	0.000	0.000	0.000
68	A	68	LYS	1	0.858	0.930	94.790	0.010	0.010	0.000	0.000	0.000	0.000
69	A	83	GLY	0	0.058	0.019	90.695	0.000	0.000	0.000	0.000	0.000	0.000
70	A	84	ALA	0	-0.029	-0.024	87.994	0.000	0.000	0.000	0.000	0.000	0.000
71	A	85	LEU	0	0.057	0.037	84.868	0.000	0.000	0.000	0.000	0.000	0.000
72	A	86	LEU	0	0.090	0.047	84.857	0.000	0.000	0.000	0.000	0.000	0.000
73	A	87	ARG	1	0.944	0.970	84.377	0.012	0.012	0.000	0.000	0.000	0.000
74	A	88	PHE	0	-0.036	-0.023	78.301	0.000	0.000	0.000	0.000	0.000	0.000
75	A	89	VAL	0	0.061	0.025	80.449	0.000	0.000	0.000	0.000	0.000	0.000
76	A	90	LYS	1	0.867	0.907	79.741	0.015	0.015	0.000	0.000	0.000	0.000
77	A	91	LYS	1	0.885	0.963	77.966	0.014	0.014	0.000	0.000	0.000	0.000
78	A	92	VAL	0	0.017	0.023	74.918	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	93	GLU	-1	-0.730	-0.837	74.927	-0.016	-0.016	0.000	0.000	0.000	0.000
80	A	94	SER	0	-0.068	-0.041	75.148	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	95	ILE	0	-0.014	-0.009	70.567	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	96	LEU	0	0.024	0.021	70.649	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	97	TYR	0	-0.044	-0.030	70.454	0.000	0.000	0.000	0.000	0.000	0.000
84	A	98	ALA	0	0.009	0.002	69.419	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	99	THR	0	-0.110	-0.070	66.322	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	100	ALA	0	0.008	0.006	65.805	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	101	GLU	-1	-0.890	-0.929	66.710	-0.023	-0.023	0.000	0.000	0.000	0.000
88	A	102	GLY	0	-0.010	-0.012	64.252	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	103	PHE	0	-0.057	-0.021	61.520	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	104	GLU	-1	-0.935	-0.961	60.940	-0.029	-0.029	0.000	0.000	0.000	0.000
91	A	105	MET	0	-0.117	-0.048	58.102	-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)