FMO DATABASE

FMODB ID: 6YL9Z

Calculation Name: 2VPK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2VPK

Chain ID: A

ChEMBL ID:

UniProt ID: Q9NPC7

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	OptHSide
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	115
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-967862.80282
FMO2-HF: Nuclear repulsion	920502.272745
FMO2-HF: Total energy	-47360.530075
FMO2-MP2: Total energy	-47496.583259

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:2:SER)

Summations of interaction energy for fragment #1(A:2:SER)

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.
-3.915	0.116	1.119	-2.149	-3.001	-0.002

Interaction energy analysis for fragmet #1(A:2:SER)

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 : -0.001

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

Sort

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	4	SER	0	0.073	0.028	3.435	-2.979	-0.460	-0.001	-1.250	-1.268	0.000
4	A	5	HIS	0	0.023	0.015	2.462	-1.443	-0.518	1.118	-0.640	-1.404	-0.002
5	A	6	HIS	0	-0.012	-0.007	3.897	0.413	1.000	0.002	-0.259	-0.329	0.000
6	A	7	CYS	0	-0.064	-0.039	5.655	0.031	0.031	0.000	0.000	0.000	0.000
7	A	8	GLU	-1	-0.823	-0.916	7.342	0.040	0.040	0.000	0.000	0.000	0.000
8	A	9	HIS	0	-0.006	0.009	8.100	-0.004	-0.004	0.000	0.000	0.000	0.000
9	A	10	LEU	0	-0.049	-0.024	9.711	0.015	0.015	0.000	0.000	0.000	0.000
10	A	11	LEU	0	0.027	0.025	11.852	-0.009	-0.009	0.000	0.000	0.000	0.000
11	A	12	GLU	-1	-0.805	-0.915	12.772	0.006	0.006	0.000	0.000	0.000	0.000
12	A	13	ARG	1	0.840	0.914	13.251	-0.096	-0.096	0.000	0.000	0.000	0.000
13	A	14	LEU	0	-0.015	-0.006	15.747	-0.006	-0.006	0.000	0.000	0.000	0.000
14	A	15	ASN	0	0.053	0.014	17.403	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	16	LYS	1	0.819	0.911	18.052	-0.025	-0.025	0.000	0.000	0.000	0.000
16	A	17	GLN	0	-0.042	-0.027	18.285	-0.005	-0.005	0.000	0.000	0.000	0.000
17	A	18	ARG	1	0.889	0.946	21.735	-0.058	-0.058	0.000	0.000	0.000	0.000
18	A	19	GLU	-1	-0.872	-0.915	22.215	0.027	0.027	0.000	0.000	0.000	0.000
19	A	20	ALA	0	-0.042	-0.009	24.351	-0.004	-0.004	0.000	0.000	0.000	0.000
20	A	21	GLY	0	-0.013	0.003	26.063	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	22	PHE	0	-0.052	-0.032	22.354	0.000	0.000	0.000	0.000	0.000	0.000
22	A	23	LEU	0	0.005	-0.015	22.453	0.005	0.005	0.000	0.000	0.000	0.000
23	A	24	CYS	0	-0.071	-0.006	25.464	0.005	0.005	0.000	0.000	0.000	0.000
24	A	25	ASP	-1	-0.775	-0.869	26.937	0.069	0.069	0.000	0.000	0.000	0.000
25	A	26	CYS	0	-0.031	0.007	28.768	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	27	THR	0	-0.027	-0.004	30.033	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	28	ILE	0	0.025	0.019	29.366	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	29	VAL	0	0.004	-0.002	33.361	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	30	ILE	0	0.001	0.008	33.862	0.001	0.001	0.000	0.000	0.000	0.000
30	A	31	GLY	0	0.046	0.016	37.993	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	32	GLU	-1	-0.961	-0.976	41.056	0.025	0.025	0.000	0.000	0.000	0.000
32	A	33	PHE	0	-0.060	-0.022	35.791	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	34	GLN	0	0.039	0.009	35.124	0.003	0.003	0.000	0.000	0.000	0.000
34	A	35	PHE	0	-0.028	-0.011	29.824	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	36	LYS	1	0.886	0.939	28.872	-0.037	-0.037	0.000	0.000	0.000	0.000
36	A	37	ALA	0	0.040	0.010	25.550	0.001	0.001	0.000	0.000	0.000	0.000
37	A	38	HIS	0	0.042	0.039	22.217	0.000	0.000	0.000	0.000	0.000	0.000
38	A	39	ARG	1	0.844	0.914	24.619	-0.057	-0.057	0.000	0.000	0.000	0.000
39	A	40	ASN	0	-0.001	-0.009	20.012	-0.005	-0.005	0.000	0.000	0.000	0.000
40	A	41	VAL	0	0.015	0.024	19.278	0.009	0.009	0.000	0.000	0.000	0.000
41	A	42	LEU	0	0.040	0.007	21.501	0.003	0.003	0.000	0.000	0.000	0.000
42	A	43	ALA	0	-0.019	-0.014	24.571	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	44	SER	0	-0.095	-0.049	19.765	0.005	0.005	0.000	0.000	0.000	0.000
44	A	45	PHE	0	-0.003	-0.002	17.156	0.006	0.006	0.000	0.000	0.000	0.000
45	A	46	SER	0	-0.038	-0.017	23.107	-0.006	-0.006	0.000	0.000	0.000	0.000
46	A	47	GLU	-1	-0.831	-0.908	26.869	0.077	0.077	0.000	0.000	0.000	0.000
47	A	48	TYR	0	-0.022	-0.003	29.288	-0.004	-0.004	0.000	0.000	0.000	0.000
48	A	49	PHE	0	0.037	0.003	28.257	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	50	GLY	0	0.049	0.016	28.494	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	51	ALA	0	-0.067	-0.026	29.054	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	52	ILE	0	0.023	0.016	32.651	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	53	TYR	0	0.006	-0.037	27.595	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	54	ARG	1	0.853	0.938	27.090	-0.079	-0.079	0.000	0.000	0.000	0.000
54	A	55	SER	0	-0.024	-0.003	33.217	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	56	THR	0	-0.017	-0.007	35.344	-0.004	-0.004	0.000	0.000	0.000	0.000
56	A	57	SER	0	0.010	0.002	34.256	0.002	0.002	0.000	0.000	0.000	0.000
57	A	58	GLU	-1	-0.875	-0.913	34.918	0.039	0.039	0.000	0.000	0.000	0.000
58	A	59	ASN	0	-0.004	-0.007	32.938	0.004	0.004	0.000	0.000	0.000	0.000
59	A	60	ASN	0	-0.089	-0.066	33.343	0.002	0.002	0.000	0.000	0.000	0.000
60	A	61	VAL	0	0.009	0.010	33.133	0.000	0.000	0.000	0.000	0.000	0.000
61	A	62	PHE	0	-0.004	-0.009	35.818	0.000	0.000	0.000	0.000	0.000	0.000
62	A	63	LEU	0	0.005	0.001	33.221	0.000	0.000	0.000	0.000	0.000	0.000
63	A	64	ASP	-1	-0.806	-0.880	37.910	0.031	0.031	0.000	0.000	0.000	0.000
64	A	65	GLN	0	0.058	0.016	39.618	0.001	0.001	0.000	0.000	0.000	0.000
65	A	66	SER	0	-0.131	-0.076	40.814	0.000	0.000	0.000	0.000	0.000	0.000
66	A	67	GLN	0	-0.075	-0.039	39.137	0.001	0.001	0.000	0.000	0.000	0.000
67	A	68	VAL	0	0.002	0.003	34.089	0.002	0.002	0.000	0.000	0.000	0.000
68	A	69	LYS	1	0.827	0.902	36.286	-0.035	-0.035	0.000	0.000	0.000	0.000
69	A	70	ALA	0	0.038	0.017	34.775	0.002	0.002	0.000	0.000	0.000	0.000
70	A	71	ASP	-1	-0.903	-0.959	33.109	0.035	0.035	0.000	0.000	0.000	0.000
71	A	72	GLY	0	0.025	0.009	31.648	0.002	0.002	0.000	0.000	0.000	0.000
72	A	73	PHE	0	0.020	-0.001	29.018	0.004	0.004	0.000	0.000	0.000	0.000
73	A	74	GLN	0	0.003	0.001	28.588	0.006	0.006	0.000	0.000	0.000	0.000
74	A	75	LYS	1	0.815	0.898	26.805	-0.035	-0.035	0.000	0.000	0.000	0.000
75	A	76	LEU	0	0.004	0.014	25.335	0.004	0.004	0.000	0.000	0.000	0.000
76	A	77	LEU	0	-0.009	-0.004	24.433	0.007	0.007	0.000	0.000	0.000	0.000
77	A	78	GLU	-1	-0.782	-0.895	22.808	0.046	0.046	0.000	0.000	0.000	0.000
78	A	79	PHE	0	0.007	0.018	19.533	0.002	0.002	0.000	0.000	0.000	0.000
79	A	80	ILE	0	-0.051	-0.013	19.606	0.009	0.009	0.000	0.000	0.000	0.000
80	A	81	TYR	0	-0.022	-0.050	18.717	0.011	0.011	0.000	0.000	0.000	0.000
81	A	82	THR	0	-0.037	-0.037	16.624	-0.004	-0.004	0.000	0.000	0.000	0.000
82	A	83	GLY	0	0.020	0.025	15.701	0.002	0.002	0.000	0.000	0.000	0.000
83	A	84	THR	0	-0.069	-0.030	17.109	0.001	0.001	0.000	0.000	0.000	0.000
84	A	85	LEU	0	-0.010	-0.015	19.583	-0.003	-0.003	0.000	0.000	0.000	0.000
85	A	86	ASN	0	-0.015	0.001	22.870	0.004	0.004	0.000	0.000	0.000	0.000
86	A	87	LEU	0	-0.003	0.011	25.372	-0.004	-0.004	0.000	0.000	0.000	0.000
87	A	88	ASP	-1	-0.820	-0.934	28.485	0.035	0.035	0.000	0.000	0.000	0.000
88	A	89	SER	0	-0.019	-0.026	31.780	0.001	0.001	0.000	0.000	0.000	0.000
89	A	90	TRP	0	-0.016	0.005	34.624	0.000	0.000	0.000	0.000	0.000	0.000
90	A	91	ASN	0	0.068	0.040	29.742	0.001	0.001	0.000	0.000	0.000	0.000
91	A	92	VAL	0	0.043	0.021	31.054	0.002	0.002	0.000	0.000	0.000	0.000
92	A	93	LYS	1	0.970	0.981	32.819	-0.035	-0.035	0.000	0.000	0.000	0.000
93	A	94	GLU	-1	-0.800	-0.886	34.689	0.036	0.036	0.000	0.000	0.000	0.000
94	A	95	ILE	0	-0.017	-0.003	28.302	0.002	0.002	0.000	0.000	0.000	0.000
95	A	96	HIS	0	-0.013	-0.021	31.030	0.004	0.004	0.000	0.000	0.000	0.000
96	A	97	GLN	0	-0.011	0.001	32.348	0.001	0.001	0.000	0.000	0.000	0.000
97	A	98	ALA	0	0.004	-0.005	31.399	0.000	0.000	0.000	0.000	0.000	0.000
98	A	99	ALA	0	-0.009	-0.004	28.549	0.002	0.002	0.000	0.000	0.000	0.000
99	A	100	ASP	-1	-0.906	-0.952	30.181	0.056	0.056	0.000	0.000	0.000	0.000
100	A	101	TYR	0	0.027	0.014	33.005	0.001	0.001	0.000	0.000	0.000	0.000
101	A	102	LEU	0	-0.038	-0.026	30.375	0.000	0.000	0.000	0.000	0.000	0.000
102	A	103	LYS	1	0.849	0.933	29.972	-0.062	-0.062	0.000	0.000	0.000	0.000
103	A	104	VAL	0	0.012	0.013	24.493	0.005	0.005	0.000	0.000	0.000	0.000
104	A	105	GLU	-1	-0.854	-0.955	26.730	0.076	0.076	0.000	0.000	0.000	0.000
105	A	106	GLU	-1	-0.845	-0.922	19.393	0.149	0.149	0.000	0.000	0.000	0.000
106	A	107	VAL	0	-0.007	-0.007	23.914	-0.003	-0.003	0.000	0.000	0.000	0.000
107	A	108	VAL	0	0.059	0.049	25.835	-0.005	-0.005	0.000	0.000	0.000	0.000
108	A	109	THR	0	-0.059	-0.040	26.272	-0.004	-0.004	0.000	0.000	0.000	0.000
109	A	110	LYS	1	0.887	0.937	20.765	-0.124	-0.124	0.000	0.000	0.000	0.000
110	A	111	CYS	0	-0.038	-0.005	26.673	-0.005	-0.005	0.000	0.000	0.000	0.000
111	A	112	LYS	1	0.954	0.973	29.893	-0.068	-0.068	0.000	0.000	0.000	0.000
112	A	113	ILE	0	-0.003	0.008	27.127	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	114	LYS	1	0.856	0.925	29.166	-0.046	-0.046	0.000	0.000	0.000	0.000
114	A	115	MET	0	-0.088	-0.041	30.913	-0.005	-0.005	0.000	0.000	0.000	0.000
115	A	116	GLU	-1	-1.031	-0.993	33.641	0.045	0.045	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:SER)