FMO DATABASE

FMODB ID: 6Y78Z

Calculation Name: 1P78-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1P78

Chain ID: B

ChEMBL ID:

UniProt ID: P05514

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	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	92
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-490489.661246
FMO2-HF: Nuclear repulsion	456057.914531
FMO2-HF: Total energy	-34431.746715
FMO2-MP2: Total energy	-34532.723657

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:1:MET)

Summations of interaction energy for fragment #1(B: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.
-10.555	-5.647	10.532	-5.674	-9.769	-0.045

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.024 / q_NPA : -0.012

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	3	LYS	1	0.946	0.962	2.860	-1.487	0.810	0.407	-1.213	-1.492	-0.003
4	B	4	GLY	0	0.077	0.036	5.263	0.570	0.719	-0.001	-0.005	-0.142	0.000
5	B	5	GLU	-1	-0.814	-0.909	2.141	-7.030	-5.922	7.382	-4.238	-4.253	-0.040
6	B	6	LEU	0	-0.042	-0.029	2.599	-0.891	1.065	2.683	-1.265	-3.375	-0.002
7	B	7	VAL	0	-0.053	-0.024	3.939	0.546	-0.300	0.053	1.095	-0.303	0.000
8	B	8	ASP	-1	-0.913	-0.978	6.038	-0.639	-0.639	0.000	0.000	0.000	0.000
9	B	9	ALA	0	0.022	0.006	3.658	-0.136	0.108	0.008	-0.048	-0.204	0.000
10	B	10	VAL	0	-0.058	-0.033	5.686	0.067	0.067	0.000	0.000	0.000	0.000
11	B	11	ALA	0	-0.047	-0.034	8.095	-0.137	-0.137	0.000	0.000	0.000	0.000
12	B	12	GLU	-1	-0.939	-0.951	9.360	-0.277	-0.277	0.000	0.000	0.000	0.000
13	B	13	LYS	1	0.916	0.955	6.168	-0.816	-0.816	0.000	0.000	0.000	0.000
14	B	14	ALA	0	-0.009	-0.001	10.853	-0.023	-0.023	0.000	0.000	0.000	0.000
15	B	15	SER	0	-0.015	0.010	13.446	-0.050	-0.050	0.000	0.000	0.000	0.000
16	B	16	VAL	0	-0.011	0.001	13.733	-0.007	-0.007	0.000	0.000	0.000	0.000
17	B	17	THR	0	-0.021	-0.018	14.903	-0.033	-0.033	0.000	0.000	0.000	0.000
18	B	18	LYS	1	0.969	0.981	10.144	0.572	0.572	0.000	0.000	0.000	0.000
19	B	19	LYS	1	0.997	0.982	12.953	0.058	0.058	0.000	0.000	0.000	0.000
20	B	20	GLN	0	-0.035	-0.004	15.683	0.018	0.018	0.000	0.000	0.000	0.000
21	B	21	ALA	0	0.091	0.035	11.104	0.002	0.002	0.000	0.000	0.000	0.000
22	B	22	ASP	-1	-0.880	-0.927	10.903	-0.159	-0.159	0.000	0.000	0.000	0.000
23	B	23	ALA	0	0.037	0.019	11.910	0.020	0.020	0.000	0.000	0.000	0.000
24	B	24	VAL	0	-0.030	-0.013	13.955	0.005	0.005	0.000	0.000	0.000	0.000
25	B	25	LEU	0	-0.005	-0.015	7.269	0.009	0.009	0.000	0.000	0.000	0.000
26	B	26	THR	0	-0.010	-0.011	11.685	-0.038	-0.038	0.000	0.000	0.000	0.000
27	B	27	ALA	0	0.072	0.051	13.284	0.001	0.001	0.000	0.000	0.000	0.000
28	B	28	ALA	0	-0.006	0.004	13.417	-0.009	-0.009	0.000	0.000	0.000	0.000
29	B	29	LEU	0	-0.058	-0.032	9.074	-0.007	-0.007	0.000	0.000	0.000	0.000
30	B	30	GLU	-1	-0.912	-0.960	13.777	-0.056	-0.056	0.000	0.000	0.000	0.000
31	B	31	THR	0	0.016	-0.003	17.067	-0.005	-0.005	0.000	0.000	0.000	0.000
32	B	32	ILE	0	-0.060	-0.023	13.829	0.004	0.004	0.000	0.000	0.000	0.000
33	B	33	ILE	0	-0.010	-0.006	15.041	-0.010	-0.010	0.000	0.000	0.000	0.000
34	B	34	GLU	-1	-0.927	-0.965	18.560	0.003	0.003	0.000	0.000	0.000	0.000
35	B	35	ALA	0	0.014	0.014	21.183	-0.003	-0.003	0.000	0.000	0.000	0.000
36	B	36	VAL	0	-0.029	-0.020	19.300	-0.006	-0.006	0.000	0.000	0.000	0.000
37	B	37	SER	0	-0.044	-0.022	22.054	-0.009	-0.009	0.000	0.000	0.000	0.000
38	B	38	SER	0	-0.129	-0.052	24.187	-0.003	-0.003	0.000	0.000	0.000	0.000
39	B	39	GLY	0	-0.024	-0.021	26.024	-0.001	-0.001	0.000	0.000	0.000	0.000
40	B	40	ASP	-1	-0.956	-0.965	24.459	0.100	0.100	0.000	0.000	0.000	0.000
41	B	41	LYS	1	0.920	0.962	23.269	-0.130	-0.130	0.000	0.000	0.000	0.000
42	B	42	VAL	0	0.046	0.036	18.419	0.012	0.012	0.000	0.000	0.000	0.000
43	B	43	THR	0	-0.047	-0.040	19.955	0.016	0.016	0.000	0.000	0.000	0.000
44	B	44	LEU	0	0.021	0.018	14.677	-0.003	-0.003	0.000	0.000	0.000	0.000
45	B	45	VAL	0	0.045	0.000	17.646	0.023	0.023	0.000	0.000	0.000	0.000
46	B	46	GLY	0	-0.017	-0.001	17.135	0.034	0.034	0.000	0.000	0.000	0.000
47	B	47	PHE	0	0.008	0.007	9.791	0.059	0.059	0.000	0.000	0.000	0.000
48	B	48	GLY	0	0.028	0.004	14.879	-0.015	-0.015	0.000	0.000	0.000	0.000
49	B	49	SER	0	-0.099	-0.036	17.109	-0.006	-0.006	0.000	0.000	0.000	0.000
50	B	50	PHE	0	0.054	0.019	12.895	0.000	0.000	0.000	0.000	0.000	0.000
51	B	51	GLU	-1	-0.852	-0.933	19.052	0.094	0.094	0.000	0.000	0.000	0.000
52	B	52	SER	0	0.041	0.044	21.574	-0.008	-0.008	0.000	0.000	0.000	0.000
53	B	53	ARG	1	0.881	0.930	22.453	-0.080	-0.080	0.000	0.000	0.000	0.000
54	B	54	GLU	-1	-0.842	-0.919	25.975	0.020	0.020	0.000	0.000	0.000	0.000
55	B	55	ARG	1	0.843	0.929	23.417	-0.029	-0.029	0.000	0.000	0.000	0.000
56	B	56	LYS	1	0.994	0.981	29.273	-0.027	-0.027	0.000	0.000	0.000	0.000
57	B	57	ALA	0	0.058	0.042	31.357	-0.001	-0.001	0.000	0.000	0.000	0.000
58	B	58	ARG	1	0.933	0.964	25.760	0.001	0.001	0.000	0.000	0.000	0.000
59	B	59	GLU	-1	-0.830	-0.899	33.114	0.005	0.005	0.000	0.000	0.000	0.000
60	B	60	GLY	0	0.004	-0.003	31.646	0.000	0.000	0.000	0.000	0.000	0.000
61	B	61	ARG	1	0.868	0.932	31.733	0.002	0.002	0.000	0.000	0.000	0.000
62	B	62	ASN	0	0.054	0.047	31.813	-0.002	-0.002	0.000	0.000	0.000	0.000
63	B	63	PRO	0	0.007	0.016	29.094	0.001	0.001	0.000	0.000	0.000	0.000
64	B	64	LYS	1	0.905	0.947	30.137	0.022	0.022	0.000	0.000	0.000	0.000
65	B	65	THR	0	0.007	-0.048	34.288	0.001	0.001	0.000	0.000	0.000	0.000
66	B	66	ASN	0	0.002	-0.010	35.876	0.002	0.002	0.000	0.000	0.000	0.000
67	B	67	GLU	-1	-0.848	-0.879	36.918	-0.007	-0.007	0.000	0.000	0.000	0.000
68	B	68	LYS	1	0.833	0.904	36.441	-0.004	-0.004	0.000	0.000	0.000	0.000
69	B	69	MET	0	-0.011	0.002	31.703	0.000	0.000	0.000	0.000	0.000	0.000
70	B	70	GLU	-1	-0.912	-0.957	35.088	0.005	0.005	0.000	0.000	0.000	0.000
71	B	71	ILE	0	-0.066	-0.037	28.533	-0.003	-0.003	0.000	0.000	0.000	0.000
72	B	72	PRO	0	0.057	0.017	31.059	0.003	0.003	0.000	0.000	0.000	0.000
73	B	73	ALA	0	0.000	0.000	30.737	0.000	0.000	0.000	0.000	0.000	0.000
74	B	74	THR	0	-0.009	-0.007	26.459	-0.002	-0.002	0.000	0.000	0.000	0.000
75	B	75	ARG	1	0.982	0.993	26.646	-0.014	-0.014	0.000	0.000	0.000	0.000
76	B	76	VAL	0	-0.050	-0.021	21.790	-0.008	-0.008	0.000	0.000	0.000	0.000
77	B	77	PRO	0	0.061	0.034	18.285	0.012	0.012	0.000	0.000	0.000	0.000
78	B	78	ALA	0	-0.054	-0.027	19.093	-0.008	-0.008	0.000	0.000	0.000	0.000
79	B	79	PHE	0	0.036	0.013	13.145	0.013	0.013	0.000	0.000	0.000	0.000
80	B	80	SER	0	-0.063	-0.029	17.273	-0.015	-0.015	0.000	0.000	0.000	0.000
81	B	81	ALA	0	0.045	0.034	15.046	0.021	0.021	0.000	0.000	0.000	0.000
82	B	82	GLY	0	0.026	-0.007	16.629	-0.048	-0.048	0.000	0.000	0.000	0.000
83	B	83	LYS	1	0.970	0.961	17.966	-0.142	-0.142	0.000	0.000	0.000	0.000
84	B	84	LEU	0	0.067	0.049	15.111	-0.004	-0.004	0.000	0.000	0.000	0.000
85	B	85	PHE	0	0.008	0.007	9.650	0.014	0.014	0.000	0.000	0.000	0.000
86	B	86	ARG	1	0.902	0.929	14.891	-0.196	-0.196	0.000	0.000	0.000	0.000
87	B	87	GLU	-1	-0.922	-0.951	17.184	0.183	0.183	0.000	0.000	0.000	0.000
88	B	88	LYS	1	0.887	0.948	13.149	-0.417	-0.417	0.000	0.000	0.000	0.000
89	B	89	VAL	0	-0.032	-0.015	12.077	-0.009	-0.009	0.000	0.000	0.000	0.000
90	B	90	ALA	0	-0.018	-0.005	14.581	-0.039	-0.039	0.000	0.000	0.000	0.000
91	B	91	PRO	0	-0.014	0.001	17.163	-0.004	-0.004	0.000	0.000	0.000	0.000
92	B	92	PRO	0	-0.012	0.008	19.949	-0.020	-0.020	0.000	0.000	0.000	0.000

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