FMO DATABASE

FMODB ID: ZVR3N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-969020.026828
FMO2-HF: Nuclear repulsion	921659.255682
FMO2-HF: Total energy	-47360.771146
FMO2-MP2: Total energy	-47496.859674

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.
-4.187	-0.173	0.294	-1.779	-2.528	-0.004

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 : 0.012 / q_NPA : 0.000

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	0.054	0.021	3.004	-4.268	-1.526	0.118	-1.345	-1.514	-0.003
4	A	5	HIS	0	0.053	0.023	2.855	-0.421	0.458	0.177	-0.276	-0.780	-0.001
5	A	6	HIS	0	-0.012	-0.006	4.114	0.537	0.930	-0.001	-0.158	-0.234	0.000
6	A	7	CYS	0	-0.051	-0.028	5.970	0.034	0.034	0.000	0.000	0.000	0.000
7	A	8	GLU	-1	-0.833	-0.915	7.673	-0.084	-0.084	0.000	0.000	0.000	0.000
8	A	9	HIS	0	0.003	0.015	8.415	0.012	0.012	0.000	0.000	0.000	0.000
9	A	10	LEU	0	-0.051	-0.029	10.029	0.020	0.020	0.000	0.000	0.000	0.000
10	A	11	LEU	0	0.034	0.032	12.083	-0.005	-0.005	0.000	0.000	0.000	0.000
11	A	12	GLU	-1	-0.755	-0.899	13.265	-0.013	-0.013	0.000	0.000	0.000	0.000
12	A	13	ARG	1	0.827	0.904	13.215	-0.102	-0.102	0.000	0.000	0.000	0.000
13	A	14	LEU	0	-0.007	0.006	15.892	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	15	ASN	0	0.013	0.010	17.634	0.000	0.000	0.000	0.000	0.000	0.000
15	A	16	LYS	1	0.805	0.884	18.482	-0.001	-0.001	0.000	0.000	0.000	0.000
16	A	17	GLN	0	-0.069	-0.037	18.501	-0.003	-0.003	0.000	0.000	0.000	0.000
17	A	18	ARG	1	0.904	0.945	21.963	-0.040	-0.040	0.000	0.000	0.000	0.000
18	A	19	GLU	-1	-0.873	-0.910	22.167	0.005	0.005	0.000	0.000	0.000	0.000
19	A	20	ALA	0	-0.034	-0.006	24.626	-0.003	-0.003	0.000	0.000	0.000	0.000
20	A	21	GLY	0	0.003	0.001	26.433	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	22	PHE	0	-0.021	-0.014	23.123	0.001	0.001	0.000	0.000	0.000	0.000
22	A	23	LEU	0	0.002	-0.016	22.930	0.005	0.005	0.000	0.000	0.000	0.000
23	A	24	CYS	0	-0.064	0.007	25.836	0.005	0.005	0.000	0.000	0.000	0.000
24	A	25	ASP	-1	-0.811	-0.882	27.145	0.071	0.071	0.000	0.000	0.000	0.000
25	A	26	CYS	0	-0.050	0.001	28.748	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	27	THR	0	-0.014	0.000	30.227	-0.003	-0.003	0.000	0.000	0.000	0.000
27	A	28	ILE	0	0.024	0.023	29.112	0.000	0.000	0.000	0.000	0.000	0.000
28	A	29	VAL	0	-0.014	-0.013	33.391	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	30	ILE	0	-0.007	0.000	33.880	0.001	0.001	0.000	0.000	0.000	0.000
30	A	31	GLY	0	0.053	0.027	38.201	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	32	GLU	-1	-0.936	-0.980	40.598	0.021	0.021	0.000	0.000	0.000	0.000
32	A	33	PHE	0	-0.072	-0.016	36.067	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	34	GLN	0	0.040	0.015	35.256	0.003	0.003	0.000	0.000	0.000	0.000
34	A	35	PHE	0	-0.016	-0.005	30.057	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	36	LYS	1	0.865	0.918	28.969	-0.034	-0.034	0.000	0.000	0.000	0.000
36	A	37	ALA	0	0.042	0.016	25.585	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	38	HIS	0	0.031	0.037	22.557	0.001	0.001	0.000	0.000	0.000	0.000
38	A	39	ARG	1	0.810	0.883	24.487	-0.058	-0.058	0.000	0.000	0.000	0.000
39	A	40	ASN	0	0.023	0.003	20.222	-0.009	-0.009	0.000	0.000	0.000	0.000
40	A	41	VAL	0	0.020	0.027	19.371	0.010	0.010	0.000	0.000	0.000	0.000
41	A	42	LEU	0	0.020	0.009	21.543	0.002	0.002	0.000	0.000	0.000	0.000
42	A	43	ALA	0	-0.012	-0.018	24.772	0.000	0.000	0.000	0.000	0.000	0.000
43	A	44	SER	0	-0.095	-0.049	19.640	0.009	0.009	0.000	0.000	0.000	0.000
44	A	45	PHE	0	-0.015	-0.008	17.213	0.008	0.008	0.000	0.000	0.000	0.000
45	A	46	SER	0	-0.049	-0.024	22.923	-0.007	-0.007	0.000	0.000	0.000	0.000
46	A	47	GLU	-1	-0.817	-0.896	26.792	0.079	0.079	0.000	0.000	0.000	0.000
47	A	48	TYR	0	-0.018	0.006	29.340	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	49	PHE	0	0.038	0.000	28.164	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	50	GLY	0	0.035	0.016	28.582	0.000	0.000	0.000	0.000	0.000	0.000
50	A	51	ALA	0	-0.014	0.008	29.145	0.001	0.001	0.000	0.000	0.000	0.000
51	A	52	ILE	0	0.021	0.024	32.857	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	53	TYR	0	0.017	-0.031	27.931	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	54	ARG	1	0.840	0.920	26.740	-0.086	-0.086	0.000	0.000	0.000	0.000
54	A	55	SER	0	-0.044	-0.025	33.120	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	56	THR	0	-0.035	-0.015	35.438	-0.004	-0.004	0.000	0.000	0.000	0.000
56	A	57	SER	0	0.010	0.002	33.998	0.003	0.003	0.000	0.000	0.000	0.000
57	A	58	GLU	-1	-0.836	-0.886	34.777	0.040	0.040	0.000	0.000	0.000	0.000
58	A	59	ASN	0	0.019	0.002	32.907	0.005	0.005	0.000	0.000	0.000	0.000
59	A	60	ASN	0	-0.092	-0.066	33.326	0.001	0.001	0.000	0.000	0.000	0.000
60	A	61	VAL	0	-0.013	-0.014	32.937	0.000	0.000	0.000	0.000	0.000	0.000
61	A	62	PHE	0	0.021	0.002	35.680	0.000	0.000	0.000	0.000	0.000	0.000
62	A	63	LEU	0	-0.005	0.002	33.283	0.001	0.001	0.000	0.000	0.000	0.000
63	A	64	ASP	-1	-0.805	-0.880	37.994	0.027	0.027	0.000	0.000	0.000	0.000
64	A	65	GLN	0	0.031	0.008	39.622	0.001	0.001	0.000	0.000	0.000	0.000
65	A	66	SER	0	-0.108	-0.066	40.745	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	67	GLN	0	-0.067	-0.045	39.085	0.001	0.001	0.000	0.000	0.000	0.000
67	A	68	VAL	0	0.001	0.002	33.979	0.002	0.002	0.000	0.000	0.000	0.000
68	A	69	LYS	1	0.858	0.910	36.514	-0.028	-0.028	0.000	0.000	0.000	0.000
69	A	70	ALA	0	0.026	0.011	34.791	0.002	0.002	0.000	0.000	0.000	0.000
70	A	71	ASP	-1	-0.887	-0.949	32.569	0.022	0.022	0.000	0.000	0.000	0.000
71	A	72	GLY	0	0.031	0.013	31.338	0.001	0.001	0.000	0.000	0.000	0.000
72	A	73	PHE	0	0.031	0.003	29.164	0.003	0.003	0.000	0.000	0.000	0.000
73	A	74	GLN	0	-0.001	0.001	28.793	0.005	0.005	0.000	0.000	0.000	0.000
74	A	75	LYS	1	0.800	0.886	26.793	-0.017	-0.017	0.000	0.000	0.000	0.000
75	A	76	LEU	0	0.007	0.015	25.432	0.002	0.002	0.000	0.000	0.000	0.000
76	A	77	LEU	0	-0.024	-0.008	24.471	0.006	0.006	0.000	0.000	0.000	0.000
77	A	78	GLU	-1	-0.800	-0.910	23.090	0.022	0.022	0.000	0.000	0.000	0.000
78	A	79	PHE	0	-0.009	0.026	19.399	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	80	ILE	0	-0.046	-0.018	19.585	0.004	0.004	0.000	0.000	0.000	0.000
80	A	81	TYR	0	-0.036	-0.044	18.688	0.012	0.012	0.000	0.000	0.000	0.000
81	A	82	THR	0	-0.020	-0.040	16.561	-0.010	-0.010	0.000	0.000	0.000	0.000
82	A	83	GLY	0	0.011	0.018	16.135	-0.010	-0.010	0.000	0.000	0.000	0.000
83	A	84	THR	0	-0.051	-0.020	17.163	-0.003	-0.003	0.000	0.000	0.000	0.000
84	A	85	LEU	0	-0.003	-0.014	19.530	0.003	0.003	0.000	0.000	0.000	0.000
85	A	86	ASN	0	-0.005	0.001	22.956	0.001	0.001	0.000	0.000	0.000	0.000
86	A	87	LEU	0	-0.016	0.009	25.387	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	88	ASP	-1	-0.797	-0.916	28.287	0.014	0.014	0.000	0.000	0.000	0.000
88	A	89	SER	0	-0.019	-0.014	31.587	0.002	0.002	0.000	0.000	0.000	0.000
89	A	90	TRP	0	-0.035	0.002	34.355	0.000	0.000	0.000	0.000	0.000	0.000
90	A	91	ASN	0	0.074	0.036	29.882	0.001	0.001	0.000	0.000	0.000	0.000
91	A	92	VAL	0	0.029	0.013	30.816	0.003	0.003	0.000	0.000	0.000	0.000
92	A	93	LYS	1	0.917	0.939	32.544	-0.026	-0.026	0.000	0.000	0.000	0.000
93	A	94	GLU	-1	-0.828	-0.900	34.268	0.027	0.027	0.000	0.000	0.000	0.000
94	A	95	ILE	0	0.015	0.002	27.893	0.002	0.002	0.000	0.000	0.000	0.000
95	A	96	HIS	0	-0.027	-0.020	30.585	0.003	0.003	0.000	0.000	0.000	0.000
96	A	97	GLN	0	-0.024	0.002	32.181	0.001	0.001	0.000	0.000	0.000	0.000
97	A	98	ALA	0	-0.005	-0.004	31.184	0.001	0.001	0.000	0.000	0.000	0.000
98	A	99	ALA	0	0.009	-0.004	28.398	0.003	0.003	0.000	0.000	0.000	0.000
99	A	100	ASP	-1	-0.917	-0.949	29.951	0.051	0.051	0.000	0.000	0.000	0.000
100	A	101	TYR	0	0.051	0.025	32.820	0.002	0.002	0.000	0.000	0.000	0.000
101	A	102	LEU	0	-0.026	-0.019	30.448	0.001	0.001	0.000	0.000	0.000	0.000
102	A	103	LYS	1	0.801	0.890	29.926	-0.062	-0.062	0.000	0.000	0.000	0.000
103	A	104	VAL	0	0.021	0.014	24.380	0.006	0.006	0.000	0.000	0.000	0.000
104	A	105	GLU	-1	-0.818	-0.921	26.474	0.071	0.071	0.000	0.000	0.000	0.000
105	A	106	GLU	-1	-0.825	-0.905	19.129	0.119	0.119	0.000	0.000	0.000	0.000
106	A	107	VAL	0	0.005	0.017	23.574	-0.004	-0.004	0.000	0.000	0.000	0.000
107	A	108	VAL	0	0.047	0.038	25.596	-0.005	-0.005	0.000	0.000	0.000	0.000
108	A	109	THR	0	-0.044	-0.034	25.744	-0.004	-0.004	0.000	0.000	0.000	0.000
109	A	110	LYS	1	0.844	0.902	20.748	-0.097	-0.097	0.000	0.000	0.000	0.000
110	A	111	CYS	0	-0.034	-0.009	26.531	-0.006	-0.006	0.000	0.000	0.000	0.000
111	A	112	LYS	1	0.897	0.939	29.735	-0.053	-0.053	0.000	0.000	0.000	0.000
112	A	113	ILE	0	0.003	0.004	27.017	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	114	LYS	1	0.817	0.898	28.955	-0.025	-0.025	0.000	0.000	0.000	0.000
114	A	115	MET	0	-0.032	0.007	30.719	-0.004	-0.004	0.000	0.000	0.000	0.000
115	A	116	GLU	-1	-0.974	-0.965	33.092	0.040	0.040	0.000	0.000	0.000	0.000

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