FMO DATABASE

FMODB ID: 1NVYZ

Calculation Name: 4PEO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4PEO

Chain ID: A

ChEMBL ID:

UniProt ID: Q2FXS9

Base Structure: X-ray

Registration Date: 2023-09-23

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	93
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-643664.940769
FMO2-HF: Nuclear repulsion	607226.668019
FMO2-HF: Total energy	-36438.27275
FMO2-MP2: Total energy	-36543.66434

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:MET)

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

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.
-16.82	-15.76	11.116	-6.325	-5.851	-0.055

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.066 / q_NPA : -0.034

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	THR	0	-0.012	-0.005	3.873	-0.825	0.939	-0.009	-0.865	-0.891	0.003
4	A	4	VAL	0	0.001	-0.013	6.313	0.483	0.483	0.000	0.000	0.000	0.000
5	A	5	ASP	-1	-0.752	-0.836	9.833	-1.226	-1.226	0.000	0.000	0.000	0.000
6	A	6	ILE	0	-0.007	-0.006	12.866	0.078	0.078	0.000	0.000	0.000	0.000
7	A	7	THR	0	-0.010	-0.005	15.859	0.041	0.041	0.000	0.000	0.000	0.000
8	A	8	VAL	0	-0.006	-0.005	19.417	0.016	0.016	0.000	0.000	0.000	0.000
9	A	9	ASN	0	-0.033	-0.024	22.393	-0.001	-0.001	0.000	0.000	0.000	0.000
10	A	10	ASP	-1	-0.888	-0.943	25.940	-0.343	-0.343	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.962	-0.973	28.984	-0.311	-0.311	0.000	0.000	0.000	0.000
12	A	12	GLY	0	-0.044	-0.019	26.463	0.010	0.010	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.848	0.934	25.946	0.312	0.312	0.000	0.000	0.000	0.000
14	A	14	VAL	0	0.029	0.012	20.163	-0.017	-0.017	0.000	0.000	0.000	0.000
15	A	15	THR	0	-0.005	-0.021	22.529	0.030	0.030	0.000	0.000	0.000	0.000
16	A	16	ASP	-1	-0.790	-0.861	19.092	-0.620	-0.620	0.000	0.000	0.000	0.000
17	A	17	VAL	0	-0.008	-0.001	14.374	-0.028	-0.028	0.000	0.000	0.000	0.000
18	A	18	ILE	0	0.003	0.005	12.407	0.104	0.104	0.000	0.000	0.000	0.000
19	A	19	MET	0	-0.030	-0.008	7.784	-0.232	-0.232	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.827	-0.891	7.630	-1.428	-1.428	0.000	0.000	0.000	0.000
21	A	21	GLY	0	-0.016	-0.009	3.414	-2.117	-1.225	0.041	-0.282	-0.651	-0.002
22	A	35	ALA	0	0.027	0.003	6.105	0.036	0.036	0.000	0.000	0.000	0.000
23	A	36	GLY	0	0.027	0.012	8.049	0.036	0.036	0.000	0.000	0.000	0.000
24	A	37	ALA	0	0.086	0.042	7.463	0.111	0.111	0.000	0.000	0.000	0.000
25	A	38	SER	0	0.024	0.006	7.521	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	39	ALA	0	-0.025	-0.006	9.879	0.167	0.167	0.000	0.000	0.000	0.000
27	A	40	VAL	0	0.018	0.021	12.672	0.111	0.111	0.000	0.000	0.000	0.000
28	A	41	LEU	0	0.057	0.025	10.838	0.119	0.119	0.000	0.000	0.000	0.000
29	A	42	PHE	0	-0.001	-0.005	10.861	0.112	0.112	0.000	0.000	0.000	0.000
30	A	43	GLY	0	-0.004	0.007	15.375	0.100	0.100	0.000	0.000	0.000	0.000
31	A	44	SER	0	0.013	-0.013	17.362	0.086	0.086	0.000	0.000	0.000	0.000
32	A	45	VAL	0	0.025	0.013	17.270	0.057	0.057	0.000	0.000	0.000	0.000
33	A	46	ASN	0	-0.071	-0.046	18.689	0.090	0.090	0.000	0.000	0.000	0.000
34	A	47	ALA	0	-0.016	0.000	21.511	0.044	0.044	0.000	0.000	0.000	0.000
35	A	48	ILE	0	0.015	0.006	21.416	0.035	0.035	0.000	0.000	0.000	0.000
36	A	49	ILE	0	-0.008	0.004	22.341	0.039	0.039	0.000	0.000	0.000	0.000
37	A	50	GLY	0	-0.051	-0.019	25.554	0.029	0.029	0.000	0.000	0.000	0.000
38	A	51	LEU	0	-0.093	-0.050	26.290	0.026	0.026	0.000	0.000	0.000	0.000
39	A	52	THR	0	0.021	0.015	27.427	0.004	0.004	0.000	0.000	0.000	0.000
40	A	53	SER	0	-0.020	-0.006	29.877	0.002	0.002	0.000	0.000	0.000	0.000
41	A	54	GLU	-1	-0.723	-0.846	25.930	-0.386	-0.386	0.000	0.000	0.000	0.000
42	A	55	ARG	1	0.756	0.853	26.289	0.299	0.299	0.000	0.000	0.000	0.000
43	A	56	PRO	0	0.008	0.008	21.991	0.013	0.013	0.000	0.000	0.000	0.000
44	A	57	ASP	-1	-0.870	-0.922	22.623	-0.396	-0.396	0.000	0.000	0.000	0.000
45	A	58	ILE	0	-0.085	-0.055	17.682	-0.059	-0.059	0.000	0.000	0.000	0.000
46	A	59	ASN	0	-0.051	-0.016	17.416	0.116	0.116	0.000	0.000	0.000	0.000
47	A	60	TYR	0	-0.044	-0.037	12.118	-0.070	-0.070	0.000	0.000	0.000	0.000
48	A	61	ASP	-1	-0.875	-0.930	13.120	-0.504	-0.504	0.000	0.000	0.000	0.000
49	A	62	ASP	-1	-0.893	-0.957	10.905	-0.417	-0.417	0.000	0.000	0.000	0.000
50	A	63	ASN	0	-0.109	-0.064	10.424	0.001	0.001	0.000	0.000	0.000	0.000
51	A	64	GLY	0	-0.001	-0.002	9.205	0.037	0.037	0.000	0.000	0.000	0.000
52	A	65	GLY	0	-0.049	0.000	6.893	-0.353	-0.353	0.000	0.000	0.000	0.000
53	A	66	HIS	0	-0.031	-0.035	7.976	-0.314	-0.314	0.000	0.000	0.000	0.000
54	A	67	PHE	0	-0.020	-0.024	10.481	0.272	0.272	0.000	0.000	0.000	0.000
55	A	68	HIS	0	-0.026	-0.009	12.463	-0.145	-0.145	0.000	0.000	0.000	0.000
56	A	69	ILE	0	0.002	0.005	15.542	0.114	0.114	0.000	0.000	0.000	0.000
57	A	70	ARG	1	0.851	0.904	18.210	0.505	0.505	0.000	0.000	0.000	0.000
58	A	71	SER	0	-0.039	-0.034	21.658	0.031	0.031	0.000	0.000	0.000	0.000
59	A	72	VAL	0	-0.069	-0.027	24.648	0.010	0.010	0.000	0.000	0.000	0.000
60	A	73	ASP	-1	-0.847	-0.933	27.882	-0.272	-0.272	0.000	0.000	0.000	0.000
61	A	74	THR	0	-0.004	-0.015	26.842	-0.007	-0.007	0.000	0.000	0.000	0.000
62	A	75	ASN	0	-0.052	-0.032	28.999	-0.005	-0.005	0.000	0.000	0.000	0.000
63	A	76	ASN	0	-0.008	-0.007	28.865	0.008	0.008	0.000	0.000	0.000	0.000
64	A	77	ASP	-1	-0.869	-0.944	29.078	-0.331	-0.331	0.000	0.000	0.000	0.000
65	A	78	GLU	-1	-0.961	-0.975	29.048	-0.279	-0.279	0.000	0.000	0.000	0.000
66	A	79	ALA	0	0.044	0.017	25.456	-0.022	-0.022	0.000	0.000	0.000	0.000
67	A	80	GLN	0	-0.005	0.006	24.554	-0.061	-0.061	0.000	0.000	0.000	0.000
68	A	81	LEU	0	0.013	0.017	24.289	-0.034	-0.034	0.000	0.000	0.000	0.000
69	A	82	ILE	0	-0.016	0.008	21.566	-0.028	-0.028	0.000	0.000	0.000	0.000
70	A	83	LEU	0	0.020	0.008	19.837	-0.059	-0.059	0.000	0.000	0.000	0.000
71	A	84	GLN	0	0.035	0.007	19.459	-0.101	-0.101	0.000	0.000	0.000	0.000
72	A	85	THR	0	-0.056	-0.033	19.892	-0.017	-0.017	0.000	0.000	0.000	0.000
73	A	86	MET	0	-0.033	0.013	15.762	-0.037	-0.037	0.000	0.000	0.000	0.000
74	A	87	LEU	0	0.008	0.004	15.359	-0.127	-0.127	0.000	0.000	0.000	0.000
75	A	88	VAL	0	0.031	0.014	15.258	-0.068	-0.068	0.000	0.000	0.000	0.000
76	A	89	SER	0	-0.045	-0.029	15.841	0.032	0.032	0.000	0.000	0.000	0.000
77	A	90	LEU	0	-0.019	-0.017	10.261	-0.051	-0.051	0.000	0.000	0.000	0.000
78	A	91	GLN	0	0.039	0.011	11.147	-0.138	-0.138	0.000	0.000	0.000	0.000
79	A	92	THR	0	-0.045	-0.018	13.020	0.076	0.076	0.000	0.000	0.000	0.000
80	A	93	ILE	0	-0.020	-0.011	8.356	0.059	0.059	0.000	0.000	0.000	0.000
81	A	94	GLU	-1	-0.845	-0.938	8.431	-1.697	-1.697	0.000	0.000	0.000	0.000
82	A	95	GLU	-1	-0.966	-0.972	9.477	-0.338	-0.338	0.000	0.000	0.000	0.000
83	A	96	GLU	-1	-0.954	-0.951	11.620	-0.241	-0.241	0.000	0.000	0.000	0.000
84	A	97	TYR	0	-0.146	-0.101	7.148	0.320	0.320	0.000	0.000	0.000	0.000
85	A	98	ASN	0	0.036	0.015	6.226	-0.373	-0.373	0.000	0.000	0.000	0.000
86	A	99	GLU	-1	-0.907	-0.942	5.346	-0.042	-0.042	0.000	0.000	0.000	0.000
87	A	100	ASN	0	-0.092	-0.049	2.542	0.290	1.298	0.519	-0.412	-1.114	-0.001
88	A	101	ILE	0	0.001	0.015	1.888	-10.653	-13.515	10.566	-4.721	-2.983	-0.055
89	A	102	ARG	1	0.825	0.912	4.186	2.259	2.517	-0.001	-0.045	-0.212	0.000
90	A	103	LEU	0	-0.009	0.004	6.310	-0.317	-0.317	0.000	0.000	0.000	0.000
91	A	104	ASN	0	-0.070	-0.039	9.027	0.301	0.301	0.000	0.000	0.000	0.000
92	A	105	TYR	0	0.004	-0.002	12.238	0.007	0.007	0.000	0.000	0.000	0.000
93	A	106	LYS	1	0.768	0.862	13.119	1.246	1.246	0.000	0.000	0.000	0.000

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