FMO DATABASE

FMODB ID: 3QL9L

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1446737.144337
FMO2-HF: Nuclear repulsion	1386583.926745
FMO2-HF: Total energy	-60153.217593
FMO2-MP2: Total energy	-60322.568831

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.
-0.77	0.8	-0.017	-0.684	-0.87	0.002

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 : -0.030 / q_NPA : -0.027

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	0.046	0.024	3.862	0.203	1.638	-0.016	-0.674	-0.746	0.002
4	A	11	SER	0	0.013	-0.009	6.634	0.888	0.888	0.000	0.000	0.000	0.000
5	A	12	PRO	0	-0.012	0.010	8.299	-0.257	-0.257	0.000	0.000	0.000	0.000
6	A	13	GLN	0	-0.026	0.000	12.032	0.107	0.107	0.000	0.000	0.000	0.000
7	A	14	HIS	0	0.060	-0.008	13.844	0.058	0.058	0.000	0.000	0.000	0.000
8	A	15	CYS	0	-0.089	-0.026	11.841	0.243	0.243	0.000	0.000	0.000	0.000
9	A	16	GLY	0	0.026	-0.001	14.148	0.066	0.066	0.000	0.000	0.000	0.000
10	A	17	CYS	0	-0.066	-0.008	15.929	-0.054	-0.054	0.000	0.000	0.000	0.000
11	A	18	ASP	-1	-0.768	-0.879	19.134	0.352	0.352	0.000	0.000	0.000	0.000
12	A	19	ARG	1	0.783	0.885	22.313	-0.222	-0.222	0.000	0.000	0.000	0.000
13	A	20	LEU	0	0.003	0.013	21.106	0.006	0.006	0.000	0.000	0.000	0.000
14	A	21	THR	0	-0.045	-0.024	24.020	-0.006	-0.006	0.000	0.000	0.000	0.000
15	A	22	SER	0	-0.048	-0.059	25.624	-0.009	-0.009	0.000	0.000	0.000	0.000
16	A	23	ILE	0	-0.021	-0.005	26.396	0.015	0.015	0.000	0.000	0.000	0.000
17	A	24	ASP	-1	-0.885	-0.921	25.950	0.007	0.007	0.000	0.000	0.000	0.000
18	A	25	ASP	-1	-0.816	-0.904	22.015	0.058	0.058	0.000	0.000	0.000	0.000
19	A	26	VAL	0	-0.028	-0.008	21.846	0.023	0.023	0.000	0.000	0.000	0.000
20	A	27	ARG	1	0.951	0.986	22.894	-0.005	-0.005	0.000	0.000	0.000	0.000
21	A	28	GLN	0	-0.021	-0.008	16.076	0.001	0.001	0.000	0.000	0.000	0.000
22	A	29	CYS	0	-0.010	0.006	18.111	0.027	0.027	0.000	0.000	0.000	0.000
23	A	30	LEU	0	0.046	0.006	18.370	0.044	0.044	0.000	0.000	0.000	0.000
24	A	31	THR	0	-0.014	-0.020	17.797	0.013	0.013	0.000	0.000	0.000	0.000
25	A	32	GLU	-1	-0.845	-0.928	14.105	0.174	0.174	0.000	0.000	0.000	0.000
26	A	33	TYR	0	0.019	0.013	14.600	0.066	0.066	0.000	0.000	0.000	0.000
27	A	34	ILE	0	0.040	0.040	16.601	0.060	0.060	0.000	0.000	0.000	0.000
28	A	35	TYR	0	0.013	0.015	10.424	0.036	0.036	0.000	0.000	0.000	0.000
29	A	36	TRP	0	-0.032	-0.030	10.468	-0.081	-0.081	0.000	0.000	0.000	0.000
30	A	37	SER	0	0.001	-0.026	13.028	0.117	0.117	0.000	0.000	0.000	0.000
31	A	38	SER	0	-0.009	0.015	14.423	-0.027	-0.027	0.000	0.000	0.000	0.000
32	A	39	TYR	0	-0.052	-0.041	7.820	-0.066	-0.066	0.000	0.000	0.000	0.000
33	A	40	ALA	0	0.022	0.018	8.832	0.136	0.136	0.000	0.000	0.000	0.000
34	A	41	TYR	0	0.035	0.037	9.636	0.450	0.450	0.000	0.000	0.000	0.000
35	A	42	ARG	1	0.791	0.884	10.754	-0.749	-0.749	0.000	0.000	0.000	0.000
36	A	43	ASN	0	-0.021	-0.024	5.999	-0.060	-0.060	0.000	0.000	0.000	0.000
37	A	44	ARG	1	0.804	0.908	4.240	-2.905	-2.770	-0.001	-0.010	-0.124	0.000
38	A	45	GLN	0	-0.001	0.006	8.659	-0.608	-0.608	0.000	0.000	0.000	0.000
39	A	47	ALA	0	0.016	0.004	14.322	-0.094	-0.094	0.000	0.000	0.000	0.000
40	A	48	GLY	0	0.032	0.047	17.385	-0.067	-0.067	0.000	0.000	0.000	0.000
41	A	49	GLN	0	-0.019	-0.047	19.431	-0.013	-0.013	0.000	0.000	0.000	0.000
42	A	50	LEU	0	0.013	0.035	19.892	-0.016	-0.016	0.000	0.000	0.000	0.000
43	A	51	TYR	0	0.060	0.017	15.369	-0.017	-0.017	0.000	0.000	0.000	0.000
44	A	52	SER	0	0.000	0.003	19.699	0.003	0.003	0.000	0.000	0.000	0.000
45	A	53	THR	0	-0.050	-0.032	22.398	-0.028	-0.028	0.000	0.000	0.000	0.000
46	A	54	LEU	0	-0.014	0.006	19.874	-0.021	-0.021	0.000	0.000	0.000	0.000
47	A	55	LEU	0	-0.020	-0.005	18.920	-0.013	-0.013	0.000	0.000	0.000	0.000
48	A	56	SER	0	-0.038	-0.029	22.973	-0.025	-0.025	0.000	0.000	0.000	0.000
49	A	57	PHE	0	0.000	-0.020	25.600	-0.025	-0.025	0.000	0.000	0.000	0.000
50	A	58	ARG	1	0.857	0.918	25.422	-0.302	-0.302	0.000	0.000	0.000	0.000
51	A	59	ASP	-1	-0.895	-0.945	27.439	0.245	0.245	0.000	0.000	0.000	0.000
52	A	60	ASP	-1	-0.795	-0.885	30.654	0.157	0.157	0.000	0.000	0.000	0.000
53	A	61	ALA	0	0.010	0.011	29.141	-0.015	-0.015	0.000	0.000	0.000	0.000
54	A	62	GLU	-1	-0.770	-0.884	29.703	0.215	0.215	0.000	0.000	0.000	0.000
55	A	63	LEU	0	-0.098	-0.039	32.859	-0.012	-0.012	0.000	0.000	0.000	0.000
56	A	64	VAL	0	-0.031	-0.020	34.277	-0.010	-0.010	0.000	0.000	0.000	0.000
57	A	65	PHE	0	0.002	-0.007	31.675	-0.008	-0.008	0.000	0.000	0.000	0.000
58	A	66	ILE	0	-0.046	-0.001	35.375	-0.004	-0.004	0.000	0.000	0.000	0.000
59	A	67	ASP	-1	-0.857	-0.933	32.627	0.187	0.187	0.000	0.000	0.000	0.000
60	A	68	ILE	0	0.007	-0.004	27.213	-0.004	-0.004	0.000	0.000	0.000	0.000
61	A	69	ARG	1	0.872	0.953	27.137	-0.230	-0.230	0.000	0.000	0.000	0.000
62	A	70	GLU	-1	-0.805	-0.910	29.448	0.169	0.169	0.000	0.000	0.000	0.000
63	A	71	LEU	0	0.032	0.031	32.079	-0.008	-0.008	0.000	0.000	0.000	0.000
64	A	72	VAL	0	-0.030	-0.012	25.726	-0.007	-0.007	0.000	0.000	0.000	0.000
65	A	73	LYS	1	0.728	0.843	28.857	-0.172	-0.172	0.000	0.000	0.000	0.000
66	A	74	ASN	0	-0.096	-0.047	30.263	-0.015	-0.015	0.000	0.000	0.000	0.000
67	A	75	MET	0	-0.003	0.012	30.267	-0.011	-0.011	0.000	0.000	0.000	0.000
68	A	76	PRO	0	0.062	0.048	30.742	0.009	0.009	0.000	0.000	0.000	0.000
69	A	77	TRP	0	-0.004	-0.027	26.047	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	78	ASP	-1	-0.930	-0.961	26.917	0.066	0.066	0.000	0.000	0.000	0.000
71	A	79	ASP	-1	-0.867	-0.932	28.599	0.026	0.026	0.000	0.000	0.000	0.000
72	A	80	VAL	0	-0.007	-0.020	26.952	0.007	0.007	0.000	0.000	0.000	0.000
73	A	81	LYS	1	0.799	0.881	29.716	-0.019	-0.019	0.000	0.000	0.000	0.000
74	A	82	ASP	-1	-0.869	-0.938	33.400	0.065	0.065	0.000	0.000	0.000	0.000
75	A	83	CYS	0	-0.013	0.006	30.326	0.009	0.009	0.000	0.000	0.000	0.000
76	A	84	ALA	0	-0.010	-0.006	31.881	0.007	0.007	0.000	0.000	0.000	0.000
77	A	85	GLU	-1	-0.852	-0.918	33.212	0.049	0.049	0.000	0.000	0.000	0.000
78	A	86	ILE	0	0.008	0.011	34.605	0.003	0.003	0.000	0.000	0.000	0.000
79	A	87	ILE	0	-0.012	-0.023	30.229	0.005	0.005	0.000	0.000	0.000	0.000
80	A	88	ARG	1	0.802	0.876	34.118	-0.049	-0.049	0.000	0.000	0.000	0.000
81	A	89	CYS	0	-0.086	-0.039	37.669	-0.004	-0.004	0.000	0.000	0.000	0.000
82	A	90	TYR	0	-0.046	-0.025	36.659	0.002	0.002	0.000	0.000	0.000	0.000
83	A	91	ILE	0	-0.081	-0.031	34.117	0.003	0.003	0.000	0.000	0.000	0.000
84	A	92	PRO	0	0.017	0.009	38.219	-0.003	-0.003	0.000	0.000	0.000	0.000
85	A	93	ASP	-1	-0.944	-0.959	41.045	0.050	0.050	0.000	0.000	0.000	0.000
86	A	94	GLU	-1	-0.784	-0.884	36.627	0.050	0.050	0.000	0.000	0.000	0.000
87	A	95	GLN	0	-0.104	-0.045	37.859	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	96	LYS	1	0.814	0.904	34.192	-0.062	-0.062	0.000	0.000	0.000	0.000
89	A	97	THR	0	-0.038	-0.069	37.246	0.003	0.003	0.000	0.000	0.000	0.000
90	A	98	ILE	0	0.009	-0.014	32.449	0.005	0.005	0.000	0.000	0.000	0.000
91	A	99	ARG	1	0.862	0.947	32.654	-0.128	-0.128	0.000	0.000	0.000	0.000
92	A	100	GLU	-1	-0.721	-0.828	32.982	0.102	0.102	0.000	0.000	0.000	0.000
93	A	101	ILE	0	0.000	0.010	29.711	0.007	0.007	0.000	0.000	0.000	0.000
94	A	102	SER	0	-0.036	-0.039	28.640	0.012	0.012	0.000	0.000	0.000	0.000
95	A	103	ALA	0	0.017	0.016	28.294	0.017	0.017	0.000	0.000	0.000	0.000
96	A	104	ILE	0	0.030	0.020	28.112	0.010	0.010	0.000	0.000	0.000	0.000
97	A	105	ILE	0	-0.001	0.002	23.546	0.009	0.009	0.000	0.000	0.000	0.000
98	A	106	GLY	0	0.016	0.006	24.436	0.021	0.021	0.000	0.000	0.000	0.000
99	A	107	LEU	0	0.008	0.007	25.319	0.022	0.022	0.000	0.000	0.000	0.000
100	A	108	CYS	0	-0.040	-0.014	24.010	0.003	0.003	0.000	0.000	0.000	0.000
101	A	109	ALA	0	-0.009	-0.003	20.997	0.010	0.010	0.000	0.000	0.000	0.000
102	A	110	TYR	0	0.006	-0.002	20.969	0.027	0.027	0.000	0.000	0.000	0.000
103	A	111	ALA	0	0.020	0.011	22.826	0.011	0.011	0.000	0.000	0.000	0.000
104	A	112	ALA	0	-0.027	-0.016	18.525	-0.002	-0.002	0.000	0.000	0.000	0.000
105	A	113	THR	0	-0.036	-0.040	17.844	0.015	0.015	0.000	0.000	0.000	0.000
106	A	114	TYR	0	-0.038	-0.009	19.094	0.016	0.016	0.000	0.000	0.000	0.000
107	A	115	TRP	0	-0.023	-0.011	21.431	-0.005	-0.005	0.000	0.000	0.000	0.000
108	A	116	GLY	0	0.056	0.045	17.126	-0.030	-0.030	0.000	0.000	0.000	0.000
109	A	117	GLY	0	-0.031	-0.014	15.065	-0.038	-0.038	0.000	0.000	0.000	0.000
110	A	118	GLU	-1	-0.901	-0.940	11.232	1.021	1.021	0.000	0.000	0.000	0.000
111	A	119	ASP	-1	-0.822	-0.903	9.113	0.511	0.511	0.000	0.000	0.000	0.000
112	A	120	HIS	1	0.796	0.885	9.554	-0.385	-0.385	0.000	0.000	0.000	0.000
113	A	121	PRO	0	0.026	0.023	12.243	0.062	0.062	0.000	0.000	0.000	0.000
114	A	122	THR	0	-0.019	-0.036	15.116	-0.041	-0.041	0.000	0.000	0.000	0.000
115	A	123	SER	0	0.036	0.003	18.797	-0.006	-0.006	0.000	0.000	0.000	0.000
116	A	124	ASN	0	0.044	0.036	21.645	-0.016	-0.016	0.000	0.000	0.000	0.000
117	A	125	SER	0	-0.010	-0.007	17.260	-0.007	-0.007	0.000	0.000	0.000	0.000
118	A	126	LEU	0	-0.031	-0.019	16.046	0.006	0.006	0.000	0.000	0.000	0.000
119	A	127	ASN	0	-0.004	-0.023	19.899	-0.015	-0.015	0.000	0.000	0.000	0.000
120	A	128	ALA	0	0.023	0.020	21.821	-0.004	-0.004	0.000	0.000	0.000	0.000
121	A	129	LEU	0	-0.032	-0.009	18.381	0.003	0.003	0.000	0.000	0.000	0.000
122	A	130	PHE	0	-0.036	-0.028	20.771	-0.012	-0.012	0.000	0.000	0.000	0.000
123	A	131	VAL	0	0.039	0.026	24.774	-0.008	-0.008	0.000	0.000	0.000	0.000
124	A	132	MET	0	-0.010	0.004	22.436	-0.008	-0.008	0.000	0.000	0.000	0.000
125	A	133	LEU	0	-0.065	-0.043	22.497	-0.009	-0.009	0.000	0.000	0.000	0.000
126	A	134	GLU	-1	-0.807	-0.869	26.672	0.022	0.022	0.000	0.000	0.000	0.000
127	A	135	MET	0	-0.032	-0.003	29.450	-0.006	-0.006	0.000	0.000	0.000	0.000
128	A	136	LEU	0	-0.029	-0.002	27.232	0.005	0.005	0.000	0.000	0.000	0.000
129	A	137	ASN	0	0.009	0.000	30.350	-0.010	-0.010	0.000	0.000	0.000	0.000
130	A	138	TYR	0	-0.005	-0.035	31.506	0.006	0.006	0.000	0.000	0.000	0.000
131	A	139	VAL	0	-0.004	0.000	32.579	0.003	0.003	0.000	0.000	0.000	0.000
132	A	140	ASP	-1	-0.719	-0.853	31.866	0.073	0.073	0.000	0.000	0.000	0.000
133	A	141	TYR	0	0.032	-0.005	25.757	0.004	0.004	0.000	0.000	0.000	0.000
134	A	142	ASN	0	0.017	-0.007	29.965	0.008	0.008	0.000	0.000	0.000	0.000
135	A	143	ILE	0	0.001	0.015	32.491	0.003	0.003	0.000	0.000	0.000	0.000
136	A	144	ILE	0	0.023	0.008	27.398	0.007	0.007	0.000	0.000	0.000	0.000
137	A	145	PHE	0	0.033	0.010	27.284	0.014	0.014	0.000	0.000	0.000	0.000
138	A	146	ARG	1	0.836	0.923	29.113	-0.069	-0.069	0.000	0.000	0.000	0.000
139	A	147	ARG	1	0.803	0.893	28.437	-0.188	-0.188	0.000	0.000	0.000	0.000
140	A	148	MET	0	-0.002	-0.001	22.595	0.015	0.015	0.000	0.000	0.000	0.000
141	A	149	ASN	0	-0.032	-0.006	26.148	-0.004	-0.004	0.000	0.000	0.000	0.000

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