FMO DATABASE

FMODB ID: 493JN

Calculation Name: 2Y3V-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2Y3V

Chain ID: A

ChEMBL ID:

UniProt ID: Q7ZVT3

Base Structure: X-ray

Registration Date: 2023-06-21

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	158
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1592203.422243
FMO2-HF: Nuclear repulsion	1528793.373994
FMO2-HF: Total energy	-63410.048249
FMO2-MP2: Total energy	-63596.27289

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:-1:PRO)

Summations of interaction energy for fragment #1(A:-1:PRO)

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.
-2.173	0.585	-0.006	-1.121	-1.631	0.001

Interaction energy analysis for fragmet #1(A:-1:PRO)

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 : -0.027

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	1	MET	0	-0.005	0.002	3.257	-1.208	1.270	-0.006	-1.051	-1.421	0.001
4	A	2	THR	0	-0.020	-0.034	5.654	-0.042	-0.042	0.000	0.000	0.000	0.000
5	A	3	GLU	-1	-0.880	-0.918	9.437	0.124	0.124	0.000	0.000	0.000	0.000
6	A	4	LEU	0	-0.023	-0.015	12.624	-0.025	-0.025	0.000	0.000	0.000	0.000
7	A	5	LEU	0	-0.013	-0.007	15.728	0.013	0.013	0.000	0.000	0.000	0.000
8	A	6	PHE	0	0.011	-0.002	18.721	0.005	0.005	0.000	0.000	0.000	0.000
9	A	7	ASN	0	0.026	0.011	20.238	-0.014	-0.014	0.000	0.000	0.000	0.000
10	A	8	LYS	1	0.826	0.907	22.242	0.012	0.012	0.000	0.000	0.000	0.000
11	A	9	ARG	1	0.803	0.862	24.710	0.015	0.015	0.000	0.000	0.000	0.000
12	A	10	LEU	0	-0.001	0.002	27.699	0.003	0.003	0.000	0.000	0.000	0.000
13	A	11	GLN	0	0.011	0.016	30.878	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	12	VAL	0	-0.020	-0.012	29.852	-0.001	-0.001	0.000	0.000	0.000	0.000
15	A	13	LEU	0	-0.009	-0.006	33.337	0.001	0.001	0.000	0.000	0.000	0.000
16	A	14	VAL	0	-0.014	-0.008	32.247	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	15	LYS	1	0.876	0.934	34.709	0.025	0.025	0.000	0.000	0.000	0.000
18	A	16	SER	0	0.034	0.023	34.875	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	17	LYS	1	0.877	0.944	36.887	0.029	0.029	0.000	0.000	0.000	0.000
20	A	18	ASP	-1	-0.809	-0.885	39.044	-0.026	-0.026	0.000	0.000	0.000	0.000
21	A	19	THR	0	-0.001	0.006	38.510	0.001	0.001	0.000	0.000	0.000	0.000
22	A	20	ASP	-1	-0.875	-0.937	41.099	-0.018	-0.018	0.000	0.000	0.000	0.000
23	A	21	GLU	-1	-0.932	-0.975	38.637	-0.023	-0.023	0.000	0.000	0.000	0.000
24	A	22	ARG	1	0.975	1.004	33.214	0.028	0.028	0.000	0.000	0.000	0.000
25	A	23	ARG	1	0.845	0.906	37.023	0.013	0.013	0.000	0.000	0.000	0.000
26	A	24	SER	0	-0.009	-0.003	33.229	0.001	0.001	0.000	0.000	0.000	0.000
27	A	25	VAL	0	0.002	0.006	31.117	0.000	0.000	0.000	0.000	0.000	0.000
28	A	26	ILE	0	0.037	0.017	27.107	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	27	ARG	1	0.846	0.932	19.265	0.038	0.038	0.000	0.000	0.000	0.000
30	A	28	VAL	0	0.015	-0.002	23.623	-0.006	-0.006	0.000	0.000	0.000	0.000
31	A	29	SER	0	-0.005	-0.015	17.859	0.009	0.009	0.000	0.000	0.000	0.000
32	A	30	ILE	0	-0.010	-0.011	18.554	-0.010	-0.010	0.000	0.000	0.000	0.000
33	A	31	GLU	-1	-0.824	-0.905	13.060	-0.096	-0.096	0.000	0.000	0.000	0.000
34	A	32	LEU	0	0.000	0.010	13.250	-0.012	-0.012	0.000	0.000	0.000	0.000
35	A	33	GLN	0	-0.010	-0.005	8.454	0.001	0.001	0.000	0.000	0.000	0.000
36	A	34	LEU	0	-0.042	-0.028	4.202	-0.195	0.085	0.000	-0.070	-0.210	0.000
37	A	35	PRO	0	-0.004	0.026	7.098	-0.253	-0.253	0.000	0.000	0.000	0.000
38	A	36	SER	0	-0.003	-0.012	6.474	-0.176	-0.176	0.000	0.000	0.000	0.000
39	A	37	SER	0	0.005	0.008	7.524	-0.051	-0.051	0.000	0.000	0.000	0.000
40	A	38	PRO	0	0.006	-0.007	8.099	0.041	0.041	0.000	0.000	0.000	0.000
41	A	39	VAL	0	-0.055	-0.030	9.299	0.061	0.061	0.000	0.000	0.000	0.000
42	A	40	HIS	0	-0.060	-0.016	11.603	-0.013	-0.013	0.000	0.000	0.000	0.000
43	A	41	ARG	1	0.856	0.908	11.825	0.041	0.041	0.000	0.000	0.000	0.000
44	A	42	LYS	1	0.859	0.915	10.173	-0.108	-0.108	0.000	0.000	0.000	0.000
45	A	43	ASP	-1	-0.797	-0.893	10.800	-0.305	-0.305	0.000	0.000	0.000	0.000
46	A	44	LEU	0	-0.044	-0.023	13.034	0.014	0.014	0.000	0.000	0.000	0.000
47	A	45	VAL	0	-0.011	0.000	12.281	-0.015	-0.015	0.000	0.000	0.000	0.000
48	A	46	VAL	0	0.004	0.005	15.646	0.021	0.021	0.000	0.000	0.000	0.000
49	A	47	ARG	1	0.854	0.915	16.080	0.076	0.076	0.000	0.000	0.000	0.000
50	A	48	LEU	0	0.003	-0.004	19.872	0.009	0.009	0.000	0.000	0.000	0.000
51	A	49	THR	0	0.029	-0.003	21.302	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	50	ASP	-1	-0.811	-0.887	24.461	-0.024	-0.024	0.000	0.000	0.000	0.000
53	A	51	ASP	-1	-0.816	-0.871	26.365	-0.024	-0.024	0.000	0.000	0.000	0.000
54	A	52	THR	0	-0.124	-0.074	28.098	0.002	0.002	0.000	0.000	0.000	0.000
55	A	53	ASP	-1	-0.810	-0.918	29.104	-0.031	-0.031	0.000	0.000	0.000	0.000
56	A	54	LEU	0	-0.027	-0.014	24.503	-0.003	-0.003	0.000	0.000	0.000	0.000
57	A	55	TYR	0	-0.062	-0.025	25.060	-0.005	-0.005	0.000	0.000	0.000	0.000
58	A	56	PHE	0	-0.040	0.000	26.640	-0.004	-0.004	0.000	0.000	0.000	0.000
59	A	57	LEU	0	-0.030	-0.021	18.996	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	58	TYR	0	0.008	0.017	22.913	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	59	ASN	0	-0.086	-0.040	17.812	-0.009	-0.009	0.000	0.000	0.000	0.000
62	A	60	LEU	0	0.039	0.016	18.748	0.004	0.004	0.000	0.000	0.000	0.000
63	A	61	ILE	0	-0.002	0.008	12.321	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	62	ILE	0	-0.030	-0.015	16.339	0.009	0.009	0.000	0.000	0.000	0.000
65	A	63	SER	0	0.048	-0.003	14.792	0.008	0.008	0.000	0.000	0.000	0.000
66	A	64	GLU	-1	-0.795	-0.902	15.595	-0.028	-0.028	0.000	0.000	0.000	0.000
67	A	65	GLU	-1	-0.871	-0.945	17.300	-0.106	-0.106	0.000	0.000	0.000	0.000
68	A	66	ASP	-1	-0.819	-0.874	17.645	-0.125	-0.125	0.000	0.000	0.000	0.000
69	A	67	PHE	0	-0.023	-0.017	20.007	0.012	0.012	0.000	0.000	0.000	0.000
70	A	68	GLN	0	0.009	0.008	21.928	0.012	0.012	0.000	0.000	0.000	0.000
71	A	69	SER	0	-0.001	0.004	23.610	0.007	0.007	0.000	0.000	0.000	0.000
72	A	70	LEU	0	-0.016	-0.001	23.752	0.005	0.005	0.000	0.000	0.000	0.000
73	A	71	LYS	1	0.793	0.875	25.826	0.031	0.031	0.000	0.000	0.000	0.000
74	A	72	VAL	0	-0.026	-0.017	27.663	0.004	0.004	0.000	0.000	0.000	0.000
75	A	73	GLN	0	-0.057	-0.028	27.766	0.002	0.002	0.000	0.000	0.000	0.000
76	A	74	GLN	0	-0.017	-0.025	28.815	0.004	0.004	0.000	0.000	0.000	0.000
77	A	75	GLY	0	-0.001	0.025	31.805	0.002	0.002	0.000	0.000	0.000	0.000
78	A	76	LEU	0	0.006	0.013	26.941	0.003	0.003	0.000	0.000	0.000	0.000
79	A	77	LEU	0	0.005	-0.004	30.612	0.000	0.000	0.000	0.000	0.000	0.000
80	A	78	ILE	0	-0.007	0.013	26.474	0.002	0.002	0.000	0.000	0.000	0.000
81	A	79	ASP	-1	-0.801	-0.874	23.447	-0.015	-0.015	0.000	0.000	0.000	0.000
82	A	80	PHE	0	0.028	0.008	15.792	0.006	0.006	0.000	0.000	0.000	0.000
83	A	81	THR	0	-0.063	-0.063	19.708	0.001	0.001	0.000	0.000	0.000	0.000
84	A	82	SER	0	0.004	0.003	21.199	0.003	0.003	0.000	0.000	0.000	0.000
85	A	83	PHE	0	-0.007	-0.006	21.035	0.001	0.001	0.000	0.000	0.000	0.000
86	A	84	PRO	0	0.049	0.022	19.191	0.000	0.000	0.000	0.000	0.000	0.000
87	A	85	GLN	0	-0.013	-0.015	21.919	0.002	0.002	0.000	0.000	0.000	0.000
88	A	86	LYS	1	0.880	0.943	24.725	0.006	0.006	0.000	0.000	0.000	0.000
89	A	87	PHE	0	0.018	0.007	22.441	0.000	0.000	0.000	0.000	0.000	0.000
90	A	88	ILE	0	0.030	0.006	21.712	0.000	0.000	0.000	0.000	0.000	0.000
91	A	89	ASP	-1	-0.832	-0.910	26.194	-0.004	-0.004	0.000	0.000	0.000	0.000
92	A	90	LEU	0	-0.014	-0.005	29.357	0.001	0.001	0.000	0.000	0.000	0.000
93	A	91	LEU	0	0.014	0.011	25.447	0.000	0.000	0.000	0.000	0.000	0.000
94	A	92	GLU	-1	-0.802	-0.884	28.279	-0.006	-0.006	0.000	0.000	0.000	0.000
95	A	93	GLN	0	-0.018	0.002	31.271	0.000	0.000	0.000	0.000	0.000	0.000
96	A	94	CYS	0	-0.043	-0.019	32.287	0.000	0.000	0.000	0.000	0.000	0.000
97	A	95	ILE	0	-0.011	-0.004	29.349	0.001	0.001	0.000	0.000	0.000	0.000
98	A	96	CYS	0	-0.091	-0.052	33.903	0.001	0.001	0.000	0.000	0.000	0.000
99	A	97	GLU	-1	-0.826	-0.896	36.826	-0.008	-0.008	0.000	0.000	0.000	0.000
100	A	98	GLN	0	0.014	0.017	34.248	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	99	ASP	-1	-0.906	-0.952	38.150	-0.010	-0.010	0.000	0.000	0.000	0.000
102	A	100	LYS	1	0.796	0.892	40.869	0.008	0.008	0.000	0.000	0.000	0.000
103	A	101	GLU	-1	-0.899	-0.944	43.717	-0.009	-0.009	0.000	0.000	0.000	0.000
104	A	102	ASN	0	-0.068	-0.045	45.159	0.000	0.000	0.000	0.000	0.000	0.000
105	A	103	PRO	0	-0.013	0.014	39.947	0.000	0.000	0.000	0.000	0.000	0.000
106	A	104	ARG	1	0.865	0.929	40.955	0.009	0.009	0.000	0.000	0.000	0.000
107	A	105	PHE	0	-0.006	-0.003	36.031	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	106	LEU	0	0.004	0.005	36.133	0.001	0.001	0.000	0.000	0.000	0.000
109	A	107	LEU	0	0.017	0.010	28.820	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	108	GLN	0	-0.047	-0.033	32.868	0.000	0.000	0.000	0.000	0.000	0.000
111	A	109	LEU	0	-0.002	0.005	27.952	-0.003	-0.003	0.000	0.000	0.000	0.000
112	A	110	SER	0	0.026	0.002	31.658	0.002	0.002	0.000	0.000	0.000	0.000
113	A	111	SER	0	0.026	0.036	32.182	-0.002	-0.002	0.000	0.000	0.000	0.000
114	A	112	SER	0	-0.049	-0.026	33.390	0.002	0.002	0.000	0.000	0.000	0.000
115	A	113	SER	0	-0.027	-0.032	33.140	0.002	0.002	0.000	0.000	0.000	0.000
116	A	114	SER	0	-0.009	-0.015	35.966	0.001	0.001	0.000	0.000	0.000	0.000
117	A	115	ALA	0	0.003	-0.022	34.778	-0.002	-0.002	0.000	0.000	0.000	0.000
118	A	116	PHE	0	-0.078	-0.026	34.442	-0.001	-0.001	0.000	0.000	0.000	0.000
119	A	117	ASP	-1	-0.865	-0.933	33.172	-0.036	-0.036	0.000	0.000	0.000	0.000
120	A	118	HIS	0	0.002	0.006	24.609	0.003	0.003	0.000	0.000	0.000	0.000
121	A	119	SER	0	-0.026	-0.023	28.755	-0.003	-0.003	0.000	0.000	0.000	0.000
122	A	120	PRO	0	-0.008	-0.031	26.235	0.000	0.000	0.000	0.000	0.000	0.000
123	A	121	SER	0	-0.023	0.002	27.299	0.006	0.006	0.000	0.000	0.000	0.000
124	A	122	ASN	0	-0.038	-0.026	27.747	-0.007	-0.007	0.000	0.000	0.000	0.000
125	A	123	LEU	0	0.012	0.012	25.629	0.003	0.003	0.000	0.000	0.000	0.000
126	A	124	ASN	0	-0.006	0.000	29.008	-0.003	-0.003	0.000	0.000	0.000	0.000
127	A	125	ILE	0	0.044	0.029	28.780	0.001	0.001	0.000	0.000	0.000	0.000
128	A	126	VAL	0	-0.028	-0.026	32.721	0.000	0.000	0.000	0.000	0.000	0.000
129	A	127	GLU	-1	-0.771	-0.851	36.476	-0.012	-0.012	0.000	0.000	0.000	0.000
130	A	128	THR	0	-0.061	-0.058	39.268	0.000	0.000	0.000	0.000	0.000	0.000
131	A	129	ASN	0	0.000	-0.017	42.494	0.001	0.001	0.000	0.000	0.000	0.000
132	A	130	ALA	0	0.018	0.012	45.716	0.000	0.000	0.000	0.000	0.000	0.000
133	A	131	PHE	0	-0.058	-0.017	47.959	0.000	0.000	0.000	0.000	0.000	0.000
134	A	132	LYS	1	0.936	0.943	41.366	0.018	0.018	0.000	0.000	0.000	0.000
135	A	133	HIS	0	0.059	0.043	40.846	0.000	0.000	0.000	0.000	0.000	0.000
136	A	134	LEU	0	-0.029	-0.010	39.812	-0.001	-0.001	0.000	0.000	0.000	0.000
137	A	135	THR	0	0.007	0.001	33.757	0.001	0.001	0.000	0.000	0.000	0.000
138	A	136	HIS	0	-0.050	-0.023	33.283	-0.001	-0.001	0.000	0.000	0.000	0.000
139	A	137	LEU	0	-0.011	-0.002	26.393	-0.001	-0.001	0.000	0.000	0.000	0.000
140	A	138	SER	0	-0.042	-0.023	29.900	0.000	0.000	0.000	0.000	0.000	0.000
141	A	139	LEU	0	0.020	0.023	23.443	-0.003	-0.003	0.000	0.000	0.000	0.000
142	A	140	LYS	1	0.994	0.999	25.571	0.062	0.062	0.000	0.000	0.000	0.000
143	A	141	LEU	0	0.008	0.007	22.823	-0.008	-0.008	0.000	0.000	0.000	0.000
144	A	142	LEU	0	0.015	0.003	20.007	0.007	0.007	0.000	0.000	0.000	0.000
145	A	143	PRO	0	0.026	0.027	22.528	-0.003	-0.003	0.000	0.000	0.000	0.000
146	A	144	GLY	0	-0.031	-0.026	20.465	-0.007	-0.007	0.000	0.000	0.000	0.000
147	A	145	SER	0	-0.007	-0.026	18.357	0.009	0.009	0.000	0.000	0.000	0.000
148	A	146	ASP	-1	-0.828	-0.930	20.678	-0.064	-0.064	0.000	0.000	0.000	0.000
149	A	147	THR	0	-0.060	-0.037	15.050	0.002	0.002	0.000	0.000	0.000	0.000
150	A	148	ASP	-1	-0.839	-0.897	15.476	-0.160	-0.160	0.000	0.000	0.000	0.000
151	A	149	ILE	0	0.081	0.040	17.125	-0.001	-0.001	0.000	0.000	0.000	0.000
152	A	150	LYS	1	0.958	0.988	15.897	0.077	0.077	0.000	0.000	0.000	0.000
153	A	151	LYS	1	0.828	0.904	11.663	0.214	0.214	0.000	0.000	0.000	0.000
154	A	152	TYR	0	0.061	0.024	14.804	0.005	0.005	0.000	0.000	0.000	0.000
155	A	153	LEU	0	0.049	0.025	16.632	0.009	0.009	0.000	0.000	0.000	0.000
156	A	154	ALA	0	-0.057	-0.015	15.124	0.009	0.009	0.000	0.000	0.000	0.000
157	A	155	SER	0	-0.097	-0.050	13.632	0.005	0.005	0.000	0.000	0.000	0.000
158	A	156	CYS	0	-0.067	-0.024	15.352	0.008	0.008	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-1:PRO)