FMO DATABASE

FMODB ID: MVG9Z

Calculation Name: 1P3F-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1P3F

Chain ID: B

ChEMBL ID:

UniProt ID: P06897

Base Structure: X-ray

Registration Date: 2023-09-20

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	80
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-462572.715816
FMO2-HF: Nuclear repulsion	431363.801793
FMO2-HF: Total energy	-31208.914023
FMO2-MP2: Total energy	-31300.686011

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(B:23:ARG)

Summations of interaction energy for fragment #1(B:23:ARG)

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.
147.547	151.611	4.848	-2.816	-6.097	-0.012

Interaction energy analysis for fragmet #1(B:23:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.979 / q_NPA : 0.993

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	B	25	ASN	0	0.028	-0.009	2.637	-14.194	-11.164	1.769	-2.036	-2.764	-0.009
4	B	26	ILE	0	-0.016	-0.005	4.346	-1.593	-1.441	-0.001	-0.002	-0.148	0.000
5	B	27	GLN	0	-0.013	-0.020	3.292	-1.493	-1.010	0.018	-0.070	-0.432	0.000
6	B	28	GLY	0	-0.032	-0.013	2.367	-8.391	-8.114	2.980	-1.543	-1.714	0.000
7	B	29	ILE	0	-0.005	0.011	3.267	-0.420	-0.847	0.028	1.005	-0.606	-0.002
8	B	30	THR	0	0.000	0.008	3.072	4.570	5.119	0.054	-0.170	-0.433	-0.001
9	B	31	LYS	1	1.042	1.022	5.613	27.709	27.709	0.000	0.000	0.000	0.000
10	B	32	PRO	0	0.003	-0.015	6.987	2.837	2.837	0.000	0.000	0.000	0.000
11	B	33	ALA	0	-0.027	-0.001	7.902	2.513	2.513	0.000	0.000	0.000	0.000
12	B	34	ILE	0	0.058	0.036	9.664	2.487	2.487	0.000	0.000	0.000	0.000
13	B	35	ARG	1	0.914	0.952	11.818	20.400	20.400	0.000	0.000	0.000	0.000
14	B	36	ARG	1	0.965	0.979	8.928	26.922	26.922	0.000	0.000	0.000	0.000
15	B	37	LEU	0	0.005	0.013	12.716	1.257	1.257	0.000	0.000	0.000	0.000
16	B	38	ALA	0	0.040	0.015	15.651	1.149	1.149	0.000	0.000	0.000	0.000
17	B	39	ARG	1	0.819	0.898	17.357	15.790	15.790	0.000	0.000	0.000	0.000
18	B	40	ARG	1	0.951	0.980	18.369	16.265	16.265	0.000	0.000	0.000	0.000
19	B	41	GLY	0	0.017	0.019	20.012	0.567	0.567	0.000	0.000	0.000	0.000
20	B	42	GLY	0	0.026	0.021	21.962	0.434	0.434	0.000	0.000	0.000	0.000
21	B	43	VAL	0	-0.010	0.002	20.441	0.367	0.367	0.000	0.000	0.000	0.000
22	B	44	LYS	1	1.011	1.005	21.210	10.416	10.416	0.000	0.000	0.000	0.000
23	B	45	CYS	0	-0.037	-0.025	21.700	-0.418	-0.418	0.000	0.000	0.000	0.000
24	B	46	ILE	0	0.030	0.015	16.472	-0.007	-0.007	0.000	0.000	0.000	0.000
25	B	47	SER	0	0.065	0.028	18.163	-0.794	-0.794	0.000	0.000	0.000	0.000
26	B	48	GLY	0	0.019	-0.002	16.434	-0.809	-0.809	0.000	0.000	0.000	0.000
27	B	49	LEU	0	0.073	0.032	15.667	-1.320	-1.320	0.000	0.000	0.000	0.000
28	B	50	ILE	0	0.009	0.015	16.405	-0.491	-0.491	0.000	0.000	0.000	0.000
29	B	51	TYR	0	-0.033	-0.016	11.433	-0.436	-0.436	0.000	0.000	0.000	0.000
30	B	52	GLU	-1	-0.746	-0.861	10.076	-28.968	-28.968	0.000	0.000	0.000	0.000
31	B	53	GLU	-1	-0.875	-0.924	12.967	-16.055	-16.055	0.000	0.000	0.000	0.000
32	B	54	THR	0	-0.069	-0.059	13.951	0.477	0.477	0.000	0.000	0.000	0.000
33	B	55	ARG	1	0.748	0.863	6.716	35.894	35.894	0.000	0.000	0.000	0.000
34	B	56	GLY	0	0.054	0.038	12.363	-0.106	-0.106	0.000	0.000	0.000	0.000
35	B	57	VAL	0	0.026	0.007	14.962	0.446	0.446	0.000	0.000	0.000	0.000
36	B	58	LEU	0	-0.035	-0.018	11.395	0.384	0.384	0.000	0.000	0.000	0.000
37	B	59	LYS	1	0.832	0.895	12.200	19.491	19.491	0.000	0.000	0.000	0.000
38	B	60	VAL	0	0.060	0.032	14.266	0.630	0.630	0.000	0.000	0.000	0.000
39	B	61	PHE	0	-0.036	-0.013	17.714	0.920	0.920	0.000	0.000	0.000	0.000
40	B	62	LEU	0	-0.002	-0.014	13.023	0.560	0.560	0.000	0.000	0.000	0.000
41	B	63	GLU	-1	-0.788	-0.883	15.565	-17.443	-17.443	0.000	0.000	0.000	0.000
42	B	64	ASN	0	-0.024	-0.001	17.932	1.189	1.189	0.000	0.000	0.000	0.000
43	B	65	VAL	0	0.002	0.006	20.011	0.569	0.569	0.000	0.000	0.000	0.000
44	B	66	ILE	0	0.008	-0.006	15.620	0.427	0.427	0.000	0.000	0.000	0.000
45	B	67	ARG	1	0.934	0.972	19.999	13.470	13.470	0.000	0.000	0.000	0.000
46	B	68	ASP	-1	-0.791	-0.854	22.377	-11.025	-11.025	0.000	0.000	0.000	0.000
47	B	69	ALA	0	-0.016	-0.006	22.078	0.398	0.398	0.000	0.000	0.000	0.000
48	B	70	VAL	0	0.010	0.007	20.429	0.240	0.240	0.000	0.000	0.000	0.000
49	B	71	THR	0	0.032	0.009	23.644	0.467	0.467	0.000	0.000	0.000	0.000
50	B	72	TYR	0	-0.043	-0.030	27.030	0.419	0.419	0.000	0.000	0.000	0.000
51	B	73	THR	0	-0.029	-0.029	24.416	0.241	0.241	0.000	0.000	0.000	0.000
52	B	74	GLU	-1	-0.911	-0.960	25.768	-11.305	-11.305	0.000	0.000	0.000	0.000
53	B	75	HIS	0	-0.024	0.002	28.496	0.282	0.282	0.000	0.000	0.000	0.000
54	B	76	ALA	0	-0.072	-0.041	30.426	0.346	0.346	0.000	0.000	0.000	0.000
55	B	77	LYS	1	0.921	0.962	30.974	8.626	8.626	0.000	0.000	0.000	0.000
56	B	78	ARG	1	0.797	0.875	26.818	11.064	11.064	0.000	0.000	0.000	0.000
57	B	79	LYS	1	0.989	0.982	24.357	11.363	11.363	0.000	0.000	0.000	0.000
58	B	80	THR	0	0.000	0.003	22.712	-0.542	-0.542	0.000	0.000	0.000	0.000
59	B	81	VAL	0	0.018	0.023	20.838	0.513	0.513	0.000	0.000	0.000	0.000
60	B	82	THR	0	-0.033	-0.048	22.695	-0.167	-0.167	0.000	0.000	0.000	0.000
61	B	83	ALA	0	0.043	0.002	23.266	-0.185	-0.185	0.000	0.000	0.000	0.000
62	B	84	MET	0	0.036	0.022	24.231	-0.030	-0.030	0.000	0.000	0.000	0.000
63	B	85	ASP	-1	-0.746	-0.795	24.809	-11.362	-11.362	0.000	0.000	0.000	0.000
64	B	86	VAL	0	0.029	0.006	20.674	-0.019	-0.019	0.000	0.000	0.000	0.000
65	B	87	VAL	0	-0.013	0.003	23.660	0.025	0.025	0.000	0.000	0.000	0.000
66	B	88	TYR	0	-0.032	-0.024	26.476	0.311	0.311	0.000	0.000	0.000	0.000
67	B	89	ALA	0	0.027	0.017	24.364	0.238	0.238	0.000	0.000	0.000	0.000
68	B	90	LEU	0	-0.013	-0.011	21.700	0.080	0.080	0.000	0.000	0.000	0.000
69	B	91	LYS	1	0.916	0.965	25.592	9.939	9.939	0.000	0.000	0.000	0.000
70	B	92	ARG	1	0.879	0.934	28.755	10.679	10.679	0.000	0.000	0.000	0.000
71	B	93	GLN	0	-0.067	-0.041	24.467	-0.003	-0.003	0.000	0.000	0.000	0.000
72	B	94	GLY	0	0.024	0.025	27.665	-0.096	-0.096	0.000	0.000	0.000	0.000
73	B	95	ARG	1	0.840	0.908	23.736	12.289	12.289	0.000	0.000	0.000	0.000
74	B	96	THR	0	0.020	0.000	25.965	-0.379	-0.379	0.000	0.000	0.000	0.000
75	B	97	LEU	0	0.027	0.037	22.637	-0.048	-0.048	0.000	0.000	0.000	0.000
76	B	98	TYR	0	0.006	0.017	26.823	0.333	0.333	0.000	0.000	0.000	0.000
77	B	99	GLY	0	0.044	0.017	26.470	-0.367	-0.367	0.000	0.000	0.000	0.000
78	B	100	PHE	0	-0.022	-0.009	21.740	-0.193	-0.193	0.000	0.000	0.000	0.000
79	B	101	GLY	0	0.028	0.030	26.793	0.017	0.017	0.000	0.000	0.000	0.000
80	B	102	GLY	0	-0.051	-0.066	28.514	0.196	0.196	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:23:ARG)