FMO DATABASE

FMODB ID: LZ879

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

Total energy (hartree)

FMO2-HF: Electronic energy	-464210.105898
FMO2-HF: Nuclear repulsion	433002.831987
FMO2-HF: Total energy	-31207.273911
FMO2-MP2: Total energy	-31299.326218

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.
156.45	144.277	25.967	-4.856	-8.941	-0.019

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 : 0.980 / q_NPA : 0.988

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	0.044	-0.008	2.504	-14.894	-14.207	5.341	-1.956	-4.073	-0.020
4	B	26	ILE	0	0.046	0.040	4.192	-2.747	-2.540	-0.001	-0.009	-0.197	0.000
5	B	27	GLN	0	-0.049	-0.039	2.864	-0.393	0.290	0.088	-0.126	-0.645	-0.001
6	B	28	GLY	0	-0.077	-0.045	1.423	-13.322	-20.275	20.274	-10.361	-2.961	0.007
7	B	29	ILE	0	-0.023	0.017	2.444	11.388	3.934	0.067	7.823	-0.437	-0.004
8	B	30	THR	0	0.065	0.029	2.558	4.873	5.490	0.199	-0.225	-0.591	-0.001
9	B	31	LYS	1	1.022	1.017	5.160	27.628	27.668	-0.001	-0.002	-0.037	0.000
10	B	32	PRO	0	0.013	-0.009	6.758	3.423	3.423	0.000	0.000	0.000	0.000
11	B	33	ALA	0	0.003	0.013	8.022	2.652	2.652	0.000	0.000	0.000	0.000
12	B	34	ILE	0	0.070	0.038	9.253	2.437	2.437	0.000	0.000	0.000	0.000
13	B	35	ARG	1	0.855	0.936	11.236	21.008	21.008	0.000	0.000	0.000	0.000
14	B	36	ARG	1	0.967	0.951	9.133	26.061	26.061	0.000	0.000	0.000	0.000
15	B	37	LEU	0	-0.001	0.014	12.205	1.251	1.251	0.000	0.000	0.000	0.000
16	B	38	ALA	0	0.068	0.025	15.390	1.212	1.212	0.000	0.000	0.000	0.000
17	B	39	ARG	1	0.830	0.925	17.017	16.356	16.356	0.000	0.000	0.000	0.000
18	B	40	ARG	1	0.970	0.996	18.182	15.982	15.982	0.000	0.000	0.000	0.000
19	B	41	GLY	0	-0.030	-0.009	19.721	0.598	0.598	0.000	0.000	0.000	0.000
20	B	42	GLY	0	0.027	0.024	21.676	0.430	0.430	0.000	0.000	0.000	0.000
21	B	43	VAL	0	0.025	0.023	20.031	0.375	0.375	0.000	0.000	0.000	0.000
22	B	44	LYS	1	0.968	0.964	20.875	10.522	10.522	0.000	0.000	0.000	0.000
23	B	45	CYS	0	-0.032	-0.023	21.357	-0.341	-0.341	0.000	0.000	0.000	0.000
24	B	46	ILE	0	0.004	-0.002	15.842	0.028	0.028	0.000	0.000	0.000	0.000
25	B	47	SER	0	0.070	0.042	18.021	-0.801	-0.801	0.000	0.000	0.000	0.000
26	B	48	GLY	0	0.012	-0.011	15.887	-0.808	-0.808	0.000	0.000	0.000	0.000
27	B	49	LEU	0	0.068	0.016	15.072	-1.352	-1.352	0.000	0.000	0.000	0.000
28	B	50	ILE	0	0.020	0.037	14.463	-0.297	-0.297	0.000	0.000	0.000	0.000
29	B	51	TYR	0	-0.001	-0.007	10.437	-0.559	-0.559	0.000	0.000	0.000	0.000
30	B	52	GLU	-1	-0.773	-0.873	9.694	-29.238	-29.238	0.000	0.000	0.000	0.000
31	B	53	GLU	-1	-0.864	-0.938	12.751	-16.230	-16.230	0.000	0.000	0.000	0.000
32	B	54	THR	0	-0.089	-0.053	12.895	0.549	0.549	0.000	0.000	0.000	0.000
33	B	55	ARG	1	0.781	0.889	6.731	35.285	35.285	0.000	0.000	0.000	0.000
34	B	56	GLY	0	0.065	0.042	11.885	0.053	0.053	0.000	0.000	0.000	0.000
35	B	57	VAL	0	0.065	0.046	14.407	0.783	0.783	0.000	0.000	0.000	0.000
36	B	58	LEU	0	-0.045	-0.043	10.481	0.341	0.341	0.000	0.000	0.000	0.000
37	B	59	LYS	1	0.882	0.944	12.265	20.411	20.411	0.000	0.000	0.000	0.000
38	B	60	VAL	0	0.048	0.021	13.731	0.633	0.633	0.000	0.000	0.000	0.000
39	B	61	PHE	0	-0.079	-0.024	16.717	0.924	0.924	0.000	0.000	0.000	0.000
40	B	62	LEU	0	0.011	-0.018	12.693	0.597	0.597	0.000	0.000	0.000	0.000
41	B	63	GLU	-1	-0.869	-0.943	15.672	-17.269	-17.269	0.000	0.000	0.000	0.000
42	B	64	ASN	0	-0.015	-0.013	17.912	0.950	0.950	0.000	0.000	0.000	0.000
43	B	65	VAL	0	-0.014	0.004	19.689	0.540	0.540	0.000	0.000	0.000	0.000
44	B	66	ILE	0	0.011	0.002	15.461	0.537	0.537	0.000	0.000	0.000	0.000
45	B	67	ARG	1	0.987	1.021	20.026	13.884	13.884	0.000	0.000	0.000	0.000
46	B	68	ASP	-1	-0.812	-0.888	22.101	-11.251	-11.251	0.000	0.000	0.000	0.000
47	B	69	ALA	0	-0.022	-0.023	22.134	0.359	0.359	0.000	0.000	0.000	0.000
48	B	70	VAL	0	0.006	-0.019	20.358	0.271	0.271	0.000	0.000	0.000	0.000
49	B	71	THR	0	0.046	0.036	23.550	0.426	0.426	0.000	0.000	0.000	0.000
50	B	72	TYR	0	-0.066	-0.032	26.709	0.435	0.435	0.000	0.000	0.000	0.000
51	B	73	THR	0	-0.045	-0.052	24.653	0.108	0.108	0.000	0.000	0.000	0.000
52	B	74	GLU	-1	-0.928	-0.948	25.957	-11.119	-11.119	0.000	0.000	0.000	0.000
53	B	75	HIS	0	-0.008	0.030	28.484	0.290	0.290	0.000	0.000	0.000	0.000
54	B	76	ALA	0	-0.055	-0.038	30.646	0.353	0.353	0.000	0.000	0.000	0.000
55	B	77	LYS	1	0.874	0.930	30.989	8.596	8.596	0.000	0.000	0.000	0.000
56	B	78	ARG	1	0.856	0.921	26.785	10.994	10.994	0.000	0.000	0.000	0.000
57	B	79	LYS	1	0.985	0.975	24.158	11.870	11.870	0.000	0.000	0.000	0.000
58	B	80	THR	0	-0.002	-0.007	22.676	-0.500	-0.500	0.000	0.000	0.000	0.000
59	B	81	VAL	0	0.033	0.037	20.382	0.442	0.442	0.000	0.000	0.000	0.000
60	B	82	THR	0	-0.038	-0.026	22.771	-0.059	-0.059	0.000	0.000	0.000	0.000
61	B	83	ALA	0	0.032	0.012	23.587	-0.085	-0.085	0.000	0.000	0.000	0.000
62	B	84	MET	0	0.054	0.021	24.638	-0.180	-0.180	0.000	0.000	0.000	0.000
63	B	85	ASP	-1	-0.744	-0.826	25.053	-11.326	-11.326	0.000	0.000	0.000	0.000
64	B	86	VAL	0	0.011	-0.007	20.608	-0.105	-0.105	0.000	0.000	0.000	0.000
65	B	87	VAL	0	-0.043	-0.016	23.785	0.115	0.115	0.000	0.000	0.000	0.000
66	B	88	TYR	0	0.001	-0.001	26.459	0.315	0.315	0.000	0.000	0.000	0.000
67	B	89	ALA	0	0.017	0.015	24.214	0.230	0.230	0.000	0.000	0.000	0.000
68	B	90	LEU	0	0.007	-0.013	21.605	0.099	0.099	0.000	0.000	0.000	0.000
69	B	91	LYS	1	0.947	0.978	25.531	9.973	9.973	0.000	0.000	0.000	0.000
70	B	92	ARG	1	0.887	0.941	28.512	10.677	10.677	0.000	0.000	0.000	0.000
71	B	93	GLN	0	-0.077	-0.034	23.888	0.017	0.017	0.000	0.000	0.000	0.000
72	B	94	GLY	0	0.026	0.023	27.333	0.019	0.019	0.000	0.000	0.000	0.000
73	B	95	ARG	1	0.849	0.921	23.344	12.549	12.549	0.000	0.000	0.000	0.000
74	B	96	THR	0	0.004	-0.016	25.923	-0.338	-0.338	0.000	0.000	0.000	0.000
75	B	97	LEU	0	-0.017	0.005	22.755	-0.085	-0.085	0.000	0.000	0.000	0.000
76	B	98	TYR	0	0.014	-0.004	26.655	0.257	0.257	0.000	0.000	0.000	0.000
77	B	99	GLY	0	0.022	0.003	26.839	-0.327	-0.327	0.000	0.000	0.000	0.000
78	B	100	PHE	0	-0.030	-0.010	22.017	-0.275	-0.275	0.000	0.000	0.000	0.000
79	B	101	GLY	0	0.033	0.050	27.096	-0.012	-0.012	0.000	0.000	0.000	0.000
80	B	102	GLY	0	0.006	-0.022	26.911	0.257	0.257	0.000	0.000	0.000	0.000

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