FMO DATABASE

FMODB ID: 523JZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1595824.709682
FMO2-HF: Nuclear repulsion	1532414.491085
FMO2-HF: Total energy	-63410.218598
FMO2-MP2: Total energy	-63596.484081

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.
-1.438	0.89	-0.001	-0.916	-1.411	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 : -0.013 / q_NPA : -0.029

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	0.002	-0.008	3.469	-0.411	1.610	-0.002	-0.839	-1.180	0.001
4	A	2	THR	0	-0.039	-0.034	5.848	-0.096	-0.096	0.000	0.000	0.000	0.000
5	A	3	GLU	-1	-0.811	-0.890	9.676	0.156	0.156	0.000	0.000	0.000	0.000
6	A	4	LEU	0	-0.034	-0.018	12.957	-0.029	-0.029	0.000	0.000	0.000	0.000
7	A	5	LEU	0	0.010	0.016	16.014	0.014	0.014	0.000	0.000	0.000	0.000
8	A	6	PHE	0	0.012	-0.003	18.999	0.005	0.005	0.000	0.000	0.000	0.000
9	A	7	ASN	0	0.029	0.009	20.256	-0.014	-0.014	0.000	0.000	0.000	0.000
10	A	8	LYS	1	0.812	0.901	22.297	0.014	0.014	0.000	0.000	0.000	0.000
11	A	9	ARG	1	0.800	0.865	25.076	0.012	0.012	0.000	0.000	0.000	0.000
12	A	10	LEU	0	-0.005	-0.002	27.853	0.003	0.003	0.000	0.000	0.000	0.000
13	A	11	GLN	0	-0.013	-0.004	30.977	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	12	VAL	0	-0.016	0.003	29.616	-0.001	-0.001	0.000	0.000	0.000	0.000
15	A	13	LEU	0	0.001	-0.009	33.086	0.001	0.001	0.000	0.000	0.000	0.000
16	A	14	VAL	0	-0.016	-0.002	32.125	-0.003	-0.003	0.000	0.000	0.000	0.000
17	A	15	LYS	1	0.840	0.916	34.653	0.030	0.030	0.000	0.000	0.000	0.000
18	A	16	SER	0	0.049	0.021	35.161	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	17	LYS	1	0.897	0.951	37.220	0.038	0.038	0.000	0.000	0.000	0.000
20	A	18	ASP	-1	-0.814	-0.863	39.475	-0.032	-0.032	0.000	0.000	0.000	0.000
21	A	19	THR	0	-0.014	-0.007	39.192	0.001	0.001	0.000	0.000	0.000	0.000
22	A	20	ASP	-1	-0.859	-0.937	41.362	-0.023	-0.023	0.000	0.000	0.000	0.000
23	A	21	GLU	-1	-0.888	-0.943	38.456	-0.029	-0.029	0.000	0.000	0.000	0.000
24	A	22	ARG	1	0.932	0.981	32.269	0.033	0.033	0.000	0.000	0.000	0.000
25	A	23	ARG	1	0.836	0.905	36.499	0.014	0.014	0.000	0.000	0.000	0.000
26	A	24	SER	0	-0.041	-0.020	33.251	0.001	0.001	0.000	0.000	0.000	0.000
27	A	25	VAL	0	-0.012	-0.004	31.244	0.000	0.000	0.000	0.000	0.000	0.000
28	A	26	ILE	0	0.014	0.003	27.101	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	27	ARG	1	0.861	0.927	18.840	0.036	0.036	0.000	0.000	0.000	0.000
30	A	28	VAL	0	0.022	0.014	24.103	-0.008	-0.008	0.000	0.000	0.000	0.000
31	A	29	SER	0	-0.013	-0.020	18.621	0.010	0.010	0.000	0.000	0.000	0.000
32	A	30	ILE	0	-0.016	-0.013	18.605	-0.012	-0.012	0.000	0.000	0.000	0.000
33	A	31	GLU	-1	-0.797	-0.871	12.880	-0.095	-0.095	0.000	0.000	0.000	0.000
34	A	32	LEU	0	0.003	0.009	13.479	-0.022	-0.022	0.000	0.000	0.000	0.000
35	A	33	GLN	0	-0.022	-0.026	8.744	0.009	0.009	0.000	0.000	0.000	0.000
36	A	34	LEU	0	-0.026	-0.021	4.303	-0.126	0.181	0.001	-0.077	-0.231	0.000
37	A	35	PRO	0	-0.019	0.013	7.152	-0.295	-0.295	0.000	0.000	0.000	0.000
38	A	36	SER	0	-0.022	-0.016	6.951	-0.227	-0.227	0.000	0.000	0.000	0.000
39	A	37	SER	0	0.028	0.015	8.667	0.023	0.023	0.000	0.000	0.000	0.000
40	A	38	PRO	0	-0.026	-0.012	8.147	0.038	0.038	0.000	0.000	0.000	0.000
41	A	39	VAL	0	-0.050	-0.028	9.536	0.078	0.078	0.000	0.000	0.000	0.000
42	A	40	HIS	0	-0.058	-0.018	11.974	-0.009	-0.009	0.000	0.000	0.000	0.000
43	A	41	ARG	1	0.840	0.888	11.937	0.060	0.060	0.000	0.000	0.000	0.000
44	A	42	LYS	1	0.818	0.890	10.371	-0.082	-0.082	0.000	0.000	0.000	0.000
45	A	43	ASP	-1	-0.767	-0.874	11.196	-0.398	-0.398	0.000	0.000	0.000	0.000
46	A	44	LEU	0	-0.039	-0.016	13.338	0.012	0.012	0.000	0.000	0.000	0.000
47	A	45	VAL	0	0.002	-0.003	12.448	-0.023	-0.023	0.000	0.000	0.000	0.000
48	A	46	VAL	0	-0.003	0.007	15.838	0.026	0.026	0.000	0.000	0.000	0.000
49	A	47	ARG	1	0.822	0.883	15.229	0.084	0.084	0.000	0.000	0.000	0.000
50	A	48	LEU	0	-0.005	-0.003	20.205	0.011	0.011	0.000	0.000	0.000	0.000
51	A	49	THR	0	0.010	-0.003	21.638	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	50	ASP	-1	-0.783	-0.869	24.707	-0.025	-0.025	0.000	0.000	0.000	0.000
53	A	51	ASP	-1	-0.800	-0.872	26.351	-0.024	-0.024	0.000	0.000	0.000	0.000
54	A	52	THR	0	-0.111	-0.070	28.355	0.003	0.003	0.000	0.000	0.000	0.000
55	A	53	ASP	-1	-0.831	-0.925	29.484	-0.036	-0.036	0.000	0.000	0.000	0.000
56	A	54	LEU	0	-0.010	-0.010	24.662	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	55	TYR	0	-0.054	-0.018	24.983	-0.005	-0.005	0.000	0.000	0.000	0.000
58	A	56	PHE	0	-0.044	-0.005	26.221	-0.006	-0.006	0.000	0.000	0.000	0.000
59	A	57	LEU	0	-0.014	-0.014	18.959	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	58	TYR	0	0.003	0.000	23.299	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	59	ASN	0	-0.078	-0.045	18.024	-0.014	-0.014	0.000	0.000	0.000	0.000
62	A	60	LEU	0	0.033	0.011	19.189	0.006	0.006	0.000	0.000	0.000	0.000
63	A	61	ILE	0	0.005	0.019	12.481	0.002	0.002	0.000	0.000	0.000	0.000
64	A	62	ILE	0	-0.033	-0.018	16.456	0.018	0.018	0.000	0.000	0.000	0.000
65	A	63	SER	0	0.043	-0.007	15.040	0.008	0.008	0.000	0.000	0.000	0.000
66	A	64	GLU	-1	-0.794	-0.892	15.845	-0.068	-0.068	0.000	0.000	0.000	0.000
67	A	65	GLU	-1	-0.861	-0.931	17.795	-0.144	-0.144	0.000	0.000	0.000	0.000
68	A	66	ASP	-1	-0.816	-0.871	17.910	-0.168	-0.168	0.000	0.000	0.000	0.000
69	A	67	PHE	0	-0.008	-0.006	20.198	0.017	0.017	0.000	0.000	0.000	0.000
70	A	68	GLN	0	-0.004	-0.006	22.003	0.016	0.016	0.000	0.000	0.000	0.000
71	A	69	SER	0	-0.024	-0.008	23.515	0.010	0.010	0.000	0.000	0.000	0.000
72	A	70	LEU	0	-0.015	-0.007	24.276	0.008	0.008	0.000	0.000	0.000	0.000
73	A	71	LYS	1	0.777	0.875	26.051	0.050	0.050	0.000	0.000	0.000	0.000
74	A	72	VAL	0	-0.016	-0.010	27.863	0.006	0.006	0.000	0.000	0.000	0.000
75	A	73	GLN	0	-0.053	-0.028	27.723	0.004	0.004	0.000	0.000	0.000	0.000
76	A	74	GLN	0	-0.024	-0.027	29.180	0.005	0.005	0.000	0.000	0.000	0.000
77	A	75	GLY	0	0.007	0.020	32.172	0.003	0.003	0.000	0.000	0.000	0.000
78	A	76	LEU	0	-0.012	0.013	27.191	0.004	0.004	0.000	0.000	0.000	0.000
79	A	77	LEU	0	0.035	0.010	30.234	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	78	ILE	0	-0.009	0.007	26.928	0.001	0.001	0.000	0.000	0.000	0.000
81	A	79	ASP	-1	-0.770	-0.834	23.388	-0.036	-0.036	0.000	0.000	0.000	0.000
82	A	80	PHE	0	0.016	0.014	15.842	0.007	0.007	0.000	0.000	0.000	0.000
83	A	81	THR	0	-0.069	-0.069	19.378	0.001	0.001	0.000	0.000	0.000	0.000
84	A	82	SER	0	-0.006	-0.032	21.092	0.005	0.005	0.000	0.000	0.000	0.000
85	A	83	PHE	0	0.005	-0.006	21.263	0.003	0.003	0.000	0.000	0.000	0.000
86	A	84	PRO	0	0.027	0.012	19.349	0.001	0.001	0.000	0.000	0.000	0.000
87	A	85	GLN	0	-0.020	-0.012	21.994	0.005	0.005	0.000	0.000	0.000	0.000
88	A	86	LYS	1	0.854	0.919	24.757	0.014	0.014	0.000	0.000	0.000	0.000
89	A	87	PHE	0	0.032	0.015	22.629	0.001	0.001	0.000	0.000	0.000	0.000
90	A	88	ILE	0	0.032	0.017	21.835	0.001	0.001	0.000	0.000	0.000	0.000
91	A	89	ASP	-1	-0.819	-0.904	26.312	-0.009	-0.009	0.000	0.000	0.000	0.000
92	A	90	LEU	0	-0.002	0.005	29.628	0.001	0.001	0.000	0.000	0.000	0.000
93	A	91	LEU	0	0.020	0.016	25.650	0.000	0.000	0.000	0.000	0.000	0.000
94	A	92	GLU	-1	-0.813	-0.890	28.317	-0.007	-0.007	0.000	0.000	0.000	0.000
95	A	93	GLN	0	-0.013	-0.002	31.330	0.000	0.000	0.000	0.000	0.000	0.000
96	A	94	CYS	0	-0.030	-0.006	32.479	0.000	0.000	0.000	0.000	0.000	0.000
97	A	95	ILE	0	-0.010	-0.002	29.420	0.001	0.001	0.000	0.000	0.000	0.000
98	A	96	CYS	0	-0.085	-0.045	33.974	0.002	0.002	0.000	0.000	0.000	0.000
99	A	97	GLU	-1	-0.865	-0.925	37.006	-0.010	-0.010	0.000	0.000	0.000	0.000
100	A	98	GLN	0	0.008	-0.005	34.098	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	99	ASP	-1	-0.859	-0.910	37.821	-0.012	-0.012	0.000	0.000	0.000	0.000
102	A	100	LYS	1	0.823	0.911	40.604	0.010	0.010	0.000	0.000	0.000	0.000
103	A	101	GLU	-1	-0.887	-0.937	43.739	-0.011	-0.011	0.000	0.000	0.000	0.000
104	A	102	ASN	0	-0.097	-0.058	45.291	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	103	PRO	0	-0.005	0.017	39.965	0.000	0.000	0.000	0.000	0.000	0.000
106	A	104	ARG	1	0.860	0.925	41.174	0.013	0.013	0.000	0.000	0.000	0.000
107	A	105	PHE	0	-0.009	-0.012	36.255	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	106	LEU	0	0.010	0.003	36.288	0.001	0.001	0.000	0.000	0.000	0.000
109	A	107	LEU	0	0.036	0.009	29.198	-0.002	-0.002	0.000	0.000	0.000	0.000
110	A	108	GLN	0	-0.047	-0.031	33.467	0.001	0.001	0.000	0.000	0.000	0.000
111	A	109	LEU	0	-0.009	-0.009	28.149	-0.003	-0.003	0.000	0.000	0.000	0.000
112	A	110	SER	0	0.027	0.007	31.753	0.002	0.002	0.000	0.000	0.000	0.000
113	A	111	SER	0	0.038	0.046	32.528	-0.003	-0.003	0.000	0.000	0.000	0.000
114	A	112	SER	0	-0.074	-0.039	33.461	0.002	0.002	0.000	0.000	0.000	0.000
115	A	113	SER	0	-0.043	-0.041	33.523	0.001	0.001	0.000	0.000	0.000	0.000
116	A	114	SER	0	-0.021	-0.032	36.259	0.002	0.002	0.000	0.000	0.000	0.000
117	A	115	ALA	0	-0.003	-0.028	35.293	-0.003	-0.003	0.000	0.000	0.000	0.000
118	A	116	PHE	0	-0.053	-0.019	34.931	-0.001	-0.001	0.000	0.000	0.000	0.000
119	A	117	ASP	-1	-0.857	-0.919	33.389	-0.045	-0.045	0.000	0.000	0.000	0.000
120	A	118	HIS	0	0.018	0.017	24.889	0.004	0.004	0.000	0.000	0.000	0.000
121	A	119	SER	0	-0.016	-0.016	28.993	-0.004	-0.004	0.000	0.000	0.000	0.000
122	A	120	PRO	0	-0.009	-0.026	26.341	0.000	0.000	0.000	0.000	0.000	0.000
123	A	121	SER	0	-0.047	-0.018	27.493	0.008	0.008	0.000	0.000	0.000	0.000
124	A	122	ASN	0	-0.036	-0.016	27.985	-0.009	-0.009	0.000	0.000	0.000	0.000
125	A	123	LEU	0	0.026	0.020	25.691	0.005	0.005	0.000	0.000	0.000	0.000
126	A	124	ASN	0	-0.009	0.002	29.101	-0.004	-0.004	0.000	0.000	0.000	0.000
127	A	125	ILE	0	0.043	0.027	28.888	0.002	0.002	0.000	0.000	0.000	0.000
128	A	126	VAL	0	-0.033	-0.033	32.758	0.000	0.000	0.000	0.000	0.000	0.000
129	A	127	GLU	-1	-0.773	-0.840	36.533	-0.016	-0.016	0.000	0.000	0.000	0.000
130	A	128	THR	0	-0.039	-0.040	39.387	-0.001	-0.001	0.000	0.000	0.000	0.000
131	A	129	ASN	0	0.008	-0.020	42.675	0.001	0.001	0.000	0.000	0.000	0.000
132	A	130	ALA	0	0.027	0.010	45.991	0.000	0.000	0.000	0.000	0.000	0.000
133	A	131	PHE	0	-0.060	-0.012	48.515	0.000	0.000	0.000	0.000	0.000	0.000
134	A	132	LYS	1	0.920	0.937	41.319	0.025	0.025	0.000	0.000	0.000	0.000
135	A	133	HIS	0	0.064	0.050	41.142	0.000	0.000	0.000	0.000	0.000	0.000
136	A	134	LEU	0	-0.049	-0.023	39.809	-0.001	-0.001	0.000	0.000	0.000	0.000
137	A	135	THR	0	0.010	-0.002	33.708	0.001	0.001	0.000	0.000	0.000	0.000
138	A	136	HIS	0	-0.041	-0.019	33.548	-0.002	-0.002	0.000	0.000	0.000	0.000
139	A	137	LEU	0	-0.012	0.003	26.463	-0.002	-0.002	0.000	0.000	0.000	0.000
140	A	138	SER	0	-0.055	-0.032	30.068	0.000	0.000	0.000	0.000	0.000	0.000
141	A	139	LEU	0	0.029	0.023	23.662	-0.005	-0.005	0.000	0.000	0.000	0.000
142	A	140	LYS	1	0.978	0.990	26.081	0.076	0.076	0.000	0.000	0.000	0.000
143	A	141	LEU	0	0.010	0.014	22.702	-0.009	-0.009	0.000	0.000	0.000	0.000
144	A	142	LEU	0	0.015	0.004	20.152	0.009	0.009	0.000	0.000	0.000	0.000
145	A	143	PRO	0	0.036	0.031	22.919	-0.003	-0.003	0.000	0.000	0.000	0.000
146	A	144	GLY	0	-0.041	-0.028	20.577	-0.010	-0.010	0.000	0.000	0.000	0.000
147	A	145	SER	0	-0.013	-0.035	18.589	0.010	0.010	0.000	0.000	0.000	0.000
148	A	146	ASP	-1	-0.833	-0.929	20.608	-0.076	-0.076	0.000	0.000	0.000	0.000
149	A	147	THR	0	-0.060	-0.036	15.327	0.005	0.005	0.000	0.000	0.000	0.000
150	A	148	ASP	-1	-0.822	-0.874	16.010	-0.185	-0.185	0.000	0.000	0.000	0.000
151	A	149	ILE	0	0.073	0.032	17.337	0.002	0.002	0.000	0.000	0.000	0.000
152	A	150	LYS	1	0.947	0.976	16.049	0.092	0.092	0.000	0.000	0.000	0.000
153	A	151	LYS	1	0.835	0.908	11.970	0.252	0.252	0.000	0.000	0.000	0.000
154	A	152	TYR	0	0.062	0.037	14.694	0.006	0.006	0.000	0.000	0.000	0.000
155	A	153	LEU	0	0.045	0.029	16.846	0.012	0.012	0.000	0.000	0.000	0.000
156	A	154	ALA	0	-0.045	-0.016	14.976	0.011	0.011	0.000	0.000	0.000	0.000
157	A	155	SER	0	-0.093	-0.048	13.709	0.006	0.006	0.000	0.000	0.000	0.000
158	A	156	CYS	0	-0.071	-0.031	15.450	0.010	0.010	0.000	0.000	0.000	0.000

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