FMO DATABASE

FMODB ID: N1K9Q

Calculation Name: 2VVY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2VVY

Chain ID: A

ChEMBL ID:

UniProt ID: P24772

Base Structure: X-ray

Registration Date: 2023-06-19

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	141
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1441451.476432
FMO2-HF: Nuclear repulsion	1381299.193583
FMO2-HF: Total energy	-60152.282849
FMO2-MP2: Total energy	-60321.604717

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:8:HIS)

Summations of interaction energy for fragment #1(A:8:HIS)

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.
-0.932	1.157	-0.02	-0.923	-1.145	0.003

Interaction energy analysis for fragmet #1(A:8:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.018 / q_NPA : -0.024

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	10	PHE	0	0.030	0.019	3.794	-0.612	1.189	-0.029	-0.842	-0.930	0.003
4	A	11	SER	0	0.006	-0.021	6.507	0.527	0.527	0.000	0.000	0.000	0.000
5	A	12	PRO	0	-0.012	0.011	8.035	-0.186	-0.186	0.000	0.000	0.000	0.000
6	A	13	GLN	0	-0.013	0.003	11.832	0.057	0.057	0.000	0.000	0.000	0.000
7	A	14	HIS	0	0.044	0.006	13.982	0.025	0.025	0.000	0.000	0.000	0.000
8	A	15	CYS	0	-0.083	-0.031	11.440	0.139	0.139	0.000	0.000	0.000	0.000
9	A	16	GLY	0	0.017	-0.012	13.871	0.030	0.030	0.000	0.000	0.000	0.000
10	A	17	CYS	0	-0.047	-0.007	15.475	-0.042	-0.042	0.000	0.000	0.000	0.000
11	A	18	ASP	-1	-0.825	-0.916	18.754	0.328	0.328	0.000	0.000	0.000	0.000
12	A	19	ARG	1	0.870	0.929	22.018	-0.182	-0.182	0.000	0.000	0.000	0.000
13	A	20	LEU	0	0.036	0.031	20.985	0.006	0.006	0.000	0.000	0.000	0.000
14	A	21	THR	0	0.000	0.002	24.044	-0.009	-0.009	0.000	0.000	0.000	0.000
15	A	22	SER	0	0.009	0.004	25.585	-0.004	-0.004	0.000	0.000	0.000	0.000
16	A	23	ILE	0	0.011	0.011	26.219	0.014	0.014	0.000	0.000	0.000	0.000
17	A	24	ASP	-1	-0.905	-0.967	26.445	0.030	0.030	0.000	0.000	0.000	0.000
18	A	25	ASP	-1	-0.920	-0.957	21.854	0.057	0.057	0.000	0.000	0.000	0.000
19	A	26	VAL	0	-0.047	-0.017	22.045	0.022	0.022	0.000	0.000	0.000	0.000
20	A	27	ARG	1	0.958	0.984	22.981	-0.040	-0.040	0.000	0.000	0.000	0.000
21	A	28	GLN	0	-0.029	-0.056	15.894	0.003	0.003	0.000	0.000	0.000	0.000
22	A	29	CYS	0	-0.016	0.009	18.401	0.036	0.036	0.000	0.000	0.000	0.000
23	A	30	LEU	0	0.028	0.003	18.467	0.039	0.039	0.000	0.000	0.000	0.000
24	A	31	THR	0	0.014	0.010	17.551	0.020	0.020	0.000	0.000	0.000	0.000
25	A	32	GLU	-1	-0.816	-0.898	14.185	0.174	0.174	0.000	0.000	0.000	0.000
26	A	33	TYR	0	0.014	0.017	14.624	0.081	0.081	0.000	0.000	0.000	0.000
27	A	34	ILE	0	0.033	0.024	16.304	0.060	0.060	0.000	0.000	0.000	0.000
28	A	35	TYR	0	0.010	0.028	10.435	0.012	0.012	0.000	0.000	0.000	0.000
29	A	36	TRP	0	-0.029	-0.017	10.197	-0.042	-0.042	0.000	0.000	0.000	0.000
30	A	37	SER	0	-0.023	-0.037	12.993	0.112	0.112	0.000	0.000	0.000	0.000
31	A	38	SER	0	-0.031	-0.003	13.849	-0.019	-0.019	0.000	0.000	0.000	0.000
32	A	39	TYR	0	-0.028	-0.053	7.830	-0.056	-0.056	0.000	0.000	0.000	0.000
33	A	40	ALA	0	0.004	0.009	8.560	0.174	0.174	0.000	0.000	0.000	0.000
34	A	41	TYR	0	0.053	0.039	9.244	0.416	0.416	0.000	0.000	0.000	0.000
35	A	42	ARG	1	0.870	0.936	10.855	-0.829	-0.829	0.000	0.000	0.000	0.000
36	A	43	ASN	0	-0.071	-0.029	5.982	-0.131	-0.131	0.000	0.000	0.000	0.000
37	A	44	ARG	1	0.858	0.946	3.540	-2.346	-2.058	0.009	-0.081	-0.215	0.000
38	A	45	GLN	0	0.017	0.007	8.394	-0.493	-0.493	0.000	0.000	0.000	0.000
39	A	47	ALA	0	0.002	-0.003	14.010	-0.070	-0.070	0.000	0.000	0.000	0.000
40	A	48	GLY	0	0.037	0.049	16.786	-0.058	-0.058	0.000	0.000	0.000	0.000
41	A	49	GLN	0	-0.031	-0.039	18.795	-0.009	-0.009	0.000	0.000	0.000	0.000
42	A	50	LEU	0	-0.025	0.003	19.084	-0.015	-0.015	0.000	0.000	0.000	0.000
43	A	51	TYR	0	0.079	0.003	14.580	-0.025	-0.025	0.000	0.000	0.000	0.000
44	A	52	SER	0	-0.033	0.008	19.242	0.005	0.005	0.000	0.000	0.000	0.000
45	A	53	THR	0	0.010	0.002	21.915	-0.018	-0.018	0.000	0.000	0.000	0.000
46	A	54	LEU	0	-0.031	-0.006	19.230	-0.012	-0.012	0.000	0.000	0.000	0.000
47	A	55	LEU	0	-0.013	0.000	18.205	-0.007	-0.007	0.000	0.000	0.000	0.000
48	A	56	SER	0	-0.047	-0.020	22.303	-0.017	-0.017	0.000	0.000	0.000	0.000
49	A	57	PHE	0	0.044	0.007	25.129	-0.022	-0.022	0.000	0.000	0.000	0.000
50	A	58	ARG	1	0.920	0.962	24.541	-0.330	-0.330	0.000	0.000	0.000	0.000
51	A	59	ASP	-1	-0.911	-0.952	27.009	0.238	0.238	0.000	0.000	0.000	0.000
52	A	60	ASP	-1	-0.866	-0.940	29.925	0.176	0.176	0.000	0.000	0.000	0.000
53	A	61	ALA	0	-0.025	-0.014	28.692	-0.013	-0.013	0.000	0.000	0.000	0.000
54	A	62	GLU	-1	-0.886	-0.951	30.289	0.214	0.214	0.000	0.000	0.000	0.000
55	A	63	LEU	0	-0.092	-0.030	32.639	-0.013	-0.013	0.000	0.000	0.000	0.000
56	A	64	VAL	0	-0.043	-0.022	34.084	-0.011	-0.011	0.000	0.000	0.000	0.000
57	A	65	PHE	0	-0.025	-0.026	31.116	-0.008	-0.008	0.000	0.000	0.000	0.000
58	A	66	ILE	0	-0.043	-0.018	35.052	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	67	ASP	-1	-0.820	-0.899	32.767	0.201	0.201	0.000	0.000	0.000	0.000
60	A	68	ILE	0	0.018	-0.007	27.630	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	69	ARG	1	0.908	0.968	27.096	-0.257	-0.257	0.000	0.000	0.000	0.000
62	A	70	GLU	-1	-0.817	-0.924	29.517	0.193	0.193	0.000	0.000	0.000	0.000
63	A	71	LEU	0	0.012	0.018	31.823	-0.007	-0.007	0.000	0.000	0.000	0.000
64	A	72	VAL	0	-0.027	-0.014	25.524	-0.004	-0.004	0.000	0.000	0.000	0.000
65	A	73	LYS	1	0.750	0.875	28.432	-0.202	-0.202	0.000	0.000	0.000	0.000
66	A	74	ASN	0	-0.084	-0.040	29.819	-0.010	-0.010	0.000	0.000	0.000	0.000
67	A	75	MET	0	0.004	0.018	29.732	-0.009	-0.009	0.000	0.000	0.000	0.000
68	A	76	PRO	0	0.076	0.052	30.428	0.010	0.010	0.000	0.000	0.000	0.000
69	A	77	TRP	0	-0.008	-0.026	25.959	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	78	ASP	-1	-0.939	-0.960	26.943	0.112	0.112	0.000	0.000	0.000	0.000
71	A	79	ASP	-1	-0.869	-0.941	28.494	0.070	0.070	0.000	0.000	0.000	0.000
72	A	80	VAL	0	-0.004	-0.008	27.018	0.003	0.003	0.000	0.000	0.000	0.000
73	A	81	LYS	1	0.838	0.900	29.879	-0.058	-0.058	0.000	0.000	0.000	0.000
74	A	82	ASP	-1	-0.851	-0.915	33.421	0.091	0.091	0.000	0.000	0.000	0.000
75	A	83	CYS	0	-0.037	-0.010	30.303	0.008	0.008	0.000	0.000	0.000	0.000
76	A	84	ALA	0	-0.038	-0.025	32.229	0.004	0.004	0.000	0.000	0.000	0.000
77	A	85	GLU	-1	-0.898	-0.960	33.367	0.072	0.072	0.000	0.000	0.000	0.000
78	A	86	ILE	0	0.000	0.010	34.588	0.001	0.001	0.000	0.000	0.000	0.000
79	A	87	ILE	0	-0.009	-0.020	30.250	0.003	0.003	0.000	0.000	0.000	0.000
80	A	88	ARG	1	0.905	0.965	34.826	-0.078	-0.078	0.000	0.000	0.000	0.000
81	A	89	CYS	0	-0.045	-0.011	37.797	-0.006	-0.006	0.000	0.000	0.000	0.000
82	A	90	TYR	0	-0.061	-0.031	36.554	0.000	0.000	0.000	0.000	0.000	0.000
83	A	91	ILE	0	-0.056	-0.035	34.112	0.000	0.000	0.000	0.000	0.000	0.000
84	A	92	PRO	0	0.015	0.021	38.002	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	93	ASP	-1	-0.943	-0.967	40.798	0.066	0.066	0.000	0.000	0.000	0.000
86	A	94	GLU	-1	-0.882	-0.953	37.389	0.070	0.070	0.000	0.000	0.000	0.000
87	A	95	GLN	0	-0.121	-0.062	38.108	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	96	LYS	1	0.919	0.976	33.650	-0.086	-0.086	0.000	0.000	0.000	0.000
89	A	97	THR	0	-0.029	-0.028	37.407	0.001	0.001	0.000	0.000	0.000	0.000
90	A	98	ILE	0	0.012	-0.013	32.633	0.006	0.006	0.000	0.000	0.000	0.000
91	A	99	ARG	1	0.962	0.987	32.711	-0.122	-0.122	0.000	0.000	0.000	0.000
92	A	100	GLU	-1	-0.776	-0.883	33.075	0.112	0.112	0.000	0.000	0.000	0.000
93	A	101	ILE	0	0.005	0.004	29.638	0.007	0.007	0.000	0.000	0.000	0.000
94	A	102	SER	0	-0.032	-0.023	28.543	0.011	0.011	0.000	0.000	0.000	0.000
95	A	103	ALA	0	0.037	0.031	28.265	0.017	0.017	0.000	0.000	0.000	0.000
96	A	104	ILE	0	0.025	0.019	28.156	0.013	0.013	0.000	0.000	0.000	0.000
97	A	105	ILE	0	-0.018	-0.018	23.476	0.009	0.009	0.000	0.000	0.000	0.000
98	A	106	GLY	0	0.002	-0.001	24.320	0.023	0.023	0.000	0.000	0.000	0.000
99	A	107	LEU	0	0.004	-0.003	25.127	0.023	0.023	0.000	0.000	0.000	0.000
100	A	108	CYS	0	-0.032	0.002	23.708	0.008	0.008	0.000	0.000	0.000	0.000
101	A	109	ALA	0	0.032	0.007	20.463	0.014	0.014	0.000	0.000	0.000	0.000
102	A	110	TYR	0	-0.017	-0.002	20.712	0.038	0.038	0.000	0.000	0.000	0.000
103	A	111	ALA	0	0.016	0.008	22.451	0.018	0.018	0.000	0.000	0.000	0.000
104	A	112	ALA	0	-0.003	-0.007	18.434	0.003	0.003	0.000	0.000	0.000	0.000
105	A	113	THR	0	-0.024	-0.016	17.511	0.043	0.043	0.000	0.000	0.000	0.000
106	A	114	TYR	0	-0.100	-0.047	18.846	0.020	0.020	0.000	0.000	0.000	0.000
107	A	115	TRP	0	-0.001	-0.008	20.910	0.004	0.004	0.000	0.000	0.000	0.000
108	A	116	GLY	0	-0.019	0.020	16.477	-0.024	-0.024	0.000	0.000	0.000	0.000
109	A	117	GLY	0	-0.024	-0.011	15.019	-0.013	-0.013	0.000	0.000	0.000	0.000
110	A	118	GLU	-1	-0.996	-1.012	10.725	1.239	1.239	0.000	0.000	0.000	0.000
111	A	119	ASP	-1	-0.763	-0.871	8.445	0.799	0.799	0.000	0.000	0.000	0.000
112	A	120	HIS	1	0.773	0.874	9.232	-0.545	-0.545	0.000	0.000	0.000	0.000
113	A	121	PRO	0	0.026	0.016	11.941	0.032	0.032	0.000	0.000	0.000	0.000
114	A	122	THR	0	-0.021	-0.024	14.906	-0.037	-0.037	0.000	0.000	0.000	0.000
115	A	123	SER	0	0.033	-0.003	18.503	-0.005	-0.005	0.000	0.000	0.000	0.000
116	A	124	ASN	0	0.047	0.029	21.292	-0.020	-0.020	0.000	0.000	0.000	0.000
117	A	125	SER	0	0.010	0.014	17.334	-0.007	-0.007	0.000	0.000	0.000	0.000
118	A	126	LEU	0	-0.042	-0.025	16.224	0.002	0.002	0.000	0.000	0.000	0.000
119	A	127	ASN	0	-0.002	-0.024	19.823	-0.015	-0.015	0.000	0.000	0.000	0.000
120	A	128	ALA	0	0.017	0.021	21.677	-0.010	-0.010	0.000	0.000	0.000	0.000
121	A	129	LEU	0	-0.042	-0.019	18.185	-0.002	-0.002	0.000	0.000	0.000	0.000
122	A	130	PHE	0	-0.016	-0.025	20.688	-0.013	-0.013	0.000	0.000	0.000	0.000
123	A	131	VAL	0	0.046	0.037	24.744	-0.011	-0.011	0.000	0.000	0.000	0.000
124	A	132	MET	0	-0.007	-0.008	22.667	-0.010	-0.010	0.000	0.000	0.000	0.000
125	A	133	LEU	0	-0.090	-0.053	22.631	-0.011	-0.011	0.000	0.000	0.000	0.000
126	A	134	GLU	-1	-0.880	-0.917	26.803	0.058	0.058	0.000	0.000	0.000	0.000
127	A	135	MET	0	-0.036	-0.006	29.730	-0.007	-0.007	0.000	0.000	0.000	0.000
128	A	136	LEU	0	-0.062	-0.011	26.989	0.000	0.000	0.000	0.000	0.000	0.000
129	A	137	ASN	0	0.050	0.039	30.403	-0.006	-0.006	0.000	0.000	0.000	0.000
130	A	138	TYR	0	-0.014	-0.048	31.432	0.005	0.005	0.000	0.000	0.000	0.000
131	A	139	VAL	0	0.012	0.006	32.459	0.002	0.002	0.000	0.000	0.000	0.000
132	A	140	ASP	-1	-0.741	-0.877	31.767	0.093	0.093	0.000	0.000	0.000	0.000
133	A	141	TYR	0	0.007	-0.015	25.884	0.004	0.004	0.000	0.000	0.000	0.000
134	A	142	ASN	0	0.037	-0.006	29.772	0.006	0.006	0.000	0.000	0.000	0.000
135	A	143	ILE	0	-0.042	-0.004	32.415	0.003	0.003	0.000	0.000	0.000	0.000
136	A	144	ILE	0	0.023	0.020	27.485	0.004	0.004	0.000	0.000	0.000	0.000
137	A	145	PHE	0	0.045	0.010	26.958	0.012	0.012	0.000	0.000	0.000	0.000
138	A	146	ARG	1	0.848	0.920	29.049	-0.080	-0.080	0.000	0.000	0.000	0.000
139	A	147	ARG	1	0.821	0.904	28.394	-0.185	-0.185	0.000	0.000	0.000	0.000
140	A	148	MET	0	-0.022	0.008	22.660	0.013	0.013	0.000	0.000	0.000	0.000
141	A	149	ASN	0	0.001	0.011	25.927	-0.006	-0.006	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:8:HIS)