FMO DATABASE

FMODB ID: VQYY1

Calculation Name: 2YYO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YYO

Chain ID: A

ChEMBL ID:

UniProt ID: Q8NCJ5

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	160
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1545737.448245
FMO2-HF: Nuclear repulsion	1484712.509976
FMO2-HF: Total energy	-61024.938269
FMO2-MP2: Total energy	-61201.789302

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:6:SER)

Summations of interaction energy for fragment #1(A:6: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.
-16.418	-10.502	11.017	-7.445	-9.488	-0.043

Interaction energy analysis for fragmet #1(A:6:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.063 / q_NPA : -0.031

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	8	PHE	0	0.014	-0.003	3.787	-3.772	-0.798	-0.046	-1.767	-1.161	0.002
4	A	9	LYS	1	0.833	0.923	6.904	0.346	0.346	0.000	0.000	0.000	0.000
5	A	10	HIS	0	-0.005	-0.025	10.499	-0.143	-0.143	0.000	0.000	0.000	0.000
6	A	11	ILE	0	-0.017	0.000	9.922	-0.050	-0.050	0.000	0.000	0.000	0.000
7	A	12	LEU	0	-0.022	-0.003	10.876	0.062	0.062	0.000	0.000	0.000	0.000
8	A	13	VAL	0	-0.025	-0.025	7.476	-0.120	-0.120	0.000	0.000	0.000	0.000
9	A	14	ASP	-1	-0.908	-0.937	10.773	0.072	0.072	0.000	0.000	0.000	0.000
10	A	15	GLY	0	0.017	0.004	12.122	-0.041	-0.041	0.000	0.000	0.000	0.000
11	A	16	ASP	-1	-0.880	-0.935	10.806	-0.464	-0.464	0.000	0.000	0.000	0.000
12	A	17	THR	0	-0.043	-0.012	12.530	-0.111	-0.111	0.000	0.000	0.000	0.000
13	A	18	LEU	0	-0.026	-0.001	8.846	-0.005	-0.005	0.000	0.000	0.000	0.000
14	A	19	SER	0	0.038	-0.026	12.553	0.000	0.000	0.000	0.000	0.000	0.000
15	A	20	TYR	0	-0.099	-0.053	14.493	0.025	0.025	0.000	0.000	0.000	0.000
16	A	21	HIS	0	-0.039	-0.026	15.307	0.051	0.051	0.000	0.000	0.000	0.000
17	A	22	GLY	0	0.003	0.000	16.659	0.029	0.029	0.000	0.000	0.000	0.000
18	A	23	ASN	0	-0.059	-0.041	18.501	-0.008	-0.008	0.000	0.000	0.000	0.000
19	A	24	SER	0	0.003	-0.020	21.669	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	25	GLY	0	0.008	0.011	21.991	0.009	0.009	0.000	0.000	0.000	0.000
21	A	26	GLU	-1	-0.797	-0.864	17.218	-0.023	-0.023	0.000	0.000	0.000	0.000
22	A	27	VAL	0	-0.032	-0.009	13.594	-0.024	-0.024	0.000	0.000	0.000	0.000
23	A	28	GLY	0	0.035	0.029	12.570	0.046	0.046	0.000	0.000	0.000	0.000
24	A	29	CYS	0	-0.087	-0.040	8.729	-0.171	-0.171	0.000	0.000	0.000	0.000
25	A	30	TYR	0	0.058	0.030	5.641	-0.336	-0.336	0.000	0.000	0.000	0.000
26	A	31	VAL	0	0.010	0.000	2.612	-0.792	0.375	0.420	-0.477	-1.111	0.000
27	A	32	ALA	0	0.041	0.016	2.269	-5.703	-4.597	3.885	-2.517	-2.474	-0.031
28	A	33	SER	0	0.009	-0.014	2.137	-7.874	-6.450	6.709	-3.942	-4.192	-0.015
29	A	34	ARG	1	0.932	0.967	3.025	3.574	2.502	0.052	1.291	-0.270	0.001
30	A	35	PRO	0	-0.011	0.015	6.087	-0.378	-0.378	0.000	0.000	0.000	0.000
31	A	36	LEU	0	-0.026	-0.008	8.216	0.181	0.181	0.000	0.000	0.000	0.000
32	A	37	THR	0	0.001	-0.016	11.546	0.109	0.109	0.000	0.000	0.000	0.000
33	A	38	LYS	1	0.898	0.944	14.455	0.303	0.303	0.000	0.000	0.000	0.000
34	A	39	ASP	-1	-0.914	-0.960	17.732	-0.295	-0.295	0.000	0.000	0.000	0.000
35	A	40	SER	0	0.016	0.026	13.817	-0.035	-0.035	0.000	0.000	0.000	0.000
36	A	41	ASN	0	-0.009	-0.006	13.920	-0.118	-0.118	0.000	0.000	0.000	0.000
37	A	42	TYR	0	-0.020	-0.050	15.622	-0.006	-0.006	0.000	0.000	0.000	0.000
38	A	43	PHE	0	0.017	0.024	11.707	-0.083	-0.083	0.000	0.000	0.000	0.000
39	A	44	GLU	-1	-0.757	-0.828	14.749	-0.384	-0.384	0.000	0.000	0.000	0.000
40	A	45	VAL	0	-0.010	-0.007	13.111	-0.067	-0.067	0.000	0.000	0.000	0.000
41	A	46	SER	0	-0.010	-0.021	15.903	0.063	0.063	0.000	0.000	0.000	0.000
42	A	47	ILE	0	-0.027	-0.012	17.999	-0.019	-0.019	0.000	0.000	0.000	0.000
43	A	48	VAL	0	-0.019	-0.004	18.791	0.030	0.030	0.000	0.000	0.000	0.000
44	A	49	ASP	-1	-0.835	-0.932	20.632	-0.160	-0.160	0.000	0.000	0.000	0.000
45	A	50	SER	0	-0.065	-0.038	20.933	-0.028	-0.028	0.000	0.000	0.000	0.000
46	A	51	GLY	0	0.038	0.022	22.612	-0.008	-0.008	0.000	0.000	0.000	0.000
47	A	52	VAL	0	-0.040	-0.023	23.659	0.010	0.010	0.000	0.000	0.000	0.000
48	A	53	ARG	1	0.844	0.910	21.599	0.210	0.210	0.000	0.000	0.000	0.000
49	A	54	GLY	0	0.061	0.036	21.990	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	55	THR	0	-0.158	-0.080	19.470	-0.006	-0.006	0.000	0.000	0.000	0.000
51	A	56	ILE	0	0.023	0.022	15.603	-0.026	-0.026	0.000	0.000	0.000	0.000
52	A	57	ALA	0	-0.046	-0.025	14.318	0.038	0.038	0.000	0.000	0.000	0.000
53	A	58	VAL	0	0.042	0.022	12.919	-0.111	-0.111	0.000	0.000	0.000	0.000
54	A	59	GLY	0	0.002	-0.018	11.850	0.152	0.152	0.000	0.000	0.000	0.000
55	A	60	LEU	0	0.003	0.022	9.944	-0.210	-0.210	0.000	0.000	0.000	0.000
56	A	61	VAL	0	-0.025	-0.016	5.887	0.356	0.356	0.000	0.000	0.000	0.000
57	A	62	PRO	0	0.066	0.051	7.368	-0.406	-0.406	0.000	0.000	0.000	0.000
58	A	63	GLN	0	0.022	-0.001	4.370	-0.236	-0.171	-0.001	-0.005	-0.059	0.000
59	A	64	TYR	0	-0.020	-0.026	4.268	0.400	0.478	-0.001	-0.002	-0.074	0.000
60	A	65	TYR	0	-0.024	-0.009	5.636	0.096	0.096	0.000	0.000	0.000	0.000
61	A	66	SER	0	0.001	0.001	7.026	0.205	0.205	0.000	0.000	0.000	0.000
62	A	67	LEU	0	0.053	0.009	4.882	-0.196	-0.196	0.000	0.000	0.000	0.000
63	A	68	ASP	-1	-0.811	-0.886	8.994	-0.030	-0.030	0.000	0.000	0.000	0.000
64	A	69	HIS	1	0.827	0.903	11.738	0.213	0.213	0.000	0.000	0.000	0.000
65	A	70	GLN	0	0.092	0.045	11.698	-0.167	-0.167	0.000	0.000	0.000	0.000
66	A	71	PRO	0	0.063	0.062	10.284	0.080	0.080	0.000	0.000	0.000	0.000
67	A	72	GLY	0	0.030	-0.001	12.163	0.079	0.079	0.000	0.000	0.000	0.000
68	A	73	TRP	0	-0.067	-0.043	14.971	0.069	0.069	0.000	0.000	0.000	0.000
69	A	74	LEU	0	-0.007	0.007	12.509	0.077	0.077	0.000	0.000	0.000	0.000
70	A	75	PRO	0	0.000	-0.006	14.492	-0.070	-0.070	0.000	0.000	0.000	0.000
71	A	76	ASP	-1	-0.876	-0.927	13.057	-0.354	-0.354	0.000	0.000	0.000	0.000
72	A	77	SER	0	-0.024	-0.009	11.417	-0.126	-0.126	0.000	0.000	0.000	0.000
73	A	78	VAL	0	-0.035	-0.032	12.871	0.121	0.121	0.000	0.000	0.000	0.000
74	A	79	ALA	0	-0.014	-0.006	14.008	-0.115	-0.115	0.000	0.000	0.000	0.000
75	A	80	TYR	0	-0.006	-0.003	15.881	0.098	0.098	0.000	0.000	0.000	0.000
76	A	81	HIS	1	0.865	0.942	16.577	0.406	0.406	0.000	0.000	0.000	0.000
77	A	82	ALA	0	0.071	0.039	19.335	0.037	0.037	0.000	0.000	0.000	0.000
78	A	83	ASP	-1	-0.804	-0.902	21.130	-0.274	-0.274	0.000	0.000	0.000	0.000
79	A	84	ASP	-1	-0.791	-0.890	23.156	-0.250	-0.250	0.000	0.000	0.000	0.000
80	A	85	GLY	0	0.009	0.025	23.523	0.017	0.017	0.000	0.000	0.000	0.000
81	A	86	LYS	1	0.789	0.897	23.530	0.223	0.223	0.000	0.000	0.000	0.000
82	A	87	LEU	0	0.002	0.012	19.509	-0.030	-0.030	0.000	0.000	0.000	0.000
83	A	88	TYR	0	-0.141	-0.098	18.138	0.046	0.046	0.000	0.000	0.000	0.000
84	A	89	ASN	0	-0.018	-0.037	17.165	-0.044	-0.044	0.000	0.000	0.000	0.000
85	A	90	GLY	0	0.070	0.051	17.045	0.029	0.029	0.000	0.000	0.000	0.000
86	A	91	ARG	1	0.938	0.974	18.000	0.211	0.211	0.000	0.000	0.000	0.000
87	A	92	ALA	0	0.044	0.019	20.008	-0.027	-0.027	0.000	0.000	0.000	0.000
88	A	93	LYS	1	0.915	0.964	21.254	0.193	0.193	0.000	0.000	0.000	0.000
89	A	94	GLY	0	0.051	0.035	22.898	-0.011	-0.011	0.000	0.000	0.000	0.000
90	A	95	ARG	1	0.891	0.939	23.805	0.252	0.252	0.000	0.000	0.000	0.000
91	A	96	GLN	0	0.026	-0.004	25.474	-0.023	-0.023	0.000	0.000	0.000	0.000
92	A	97	PHE	0	-0.007	-0.012	22.302	0.002	0.002	0.000	0.000	0.000	0.000
93	A	98	GLY	0	0.065	0.035	25.515	0.009	0.009	0.000	0.000	0.000	0.000
94	A	99	SER	0	-0.045	-0.012	26.594	0.009	0.009	0.000	0.000	0.000	0.000
95	A	100	LYS	1	0.911	0.947	25.233	0.189	0.189	0.000	0.000	0.000	0.000
96	A	101	CYS	0	-0.092	-0.027	22.306	0.002	0.002	0.000	0.000	0.000	0.000
97	A	102	ASN	0	0.027	0.024	24.124	-0.005	-0.005	0.000	0.000	0.000	0.000
98	A	103	SER	0	0.076	0.020	23.780	-0.024	-0.024	0.000	0.000	0.000	0.000
99	A	104	GLY	0	-0.014	0.008	23.672	0.021	0.021	0.000	0.000	0.000	0.000
100	A	105	ASP	-1	-0.815	-0.884	23.732	-0.259	-0.259	0.000	0.000	0.000	0.000
101	A	106	ARG	1	0.856	0.888	20.248	0.335	0.335	0.000	0.000	0.000	0.000
102	A	107	ILE	0	-0.016	-0.013	17.472	0.037	0.037	0.000	0.000	0.000	0.000
103	A	108	GLY	0	0.051	0.034	17.274	-0.057	-0.057	0.000	0.000	0.000	0.000
104	A	109	CYS	0	-0.094	-0.041	14.528	0.015	0.015	0.000	0.000	0.000	0.000
105	A	110	GLY	0	0.083	0.039	15.628	-0.066	-0.066	0.000	0.000	0.000	0.000
106	A	111	ILE	0	-0.030	-0.003	13.400	0.019	0.019	0.000	0.000	0.000	0.000
107	A	112	GLU	-1	-0.763	-0.855	17.790	-0.313	-0.313	0.000	0.000	0.000	0.000
108	A	113	PRO	0	0.026	0.007	20.503	0.001	0.001	0.000	0.000	0.000	0.000
109	A	114	VAL	0	0.031	0.003	21.512	0.002	0.002	0.000	0.000	0.000	0.000
110	A	115	SER	0	-0.026	-0.005	19.967	-0.002	-0.002	0.000	0.000	0.000	0.000
111	A	116	PHE	0	-0.074	-0.033	14.610	-0.013	-0.013	0.000	0.000	0.000	0.000
112	A	117	ASP	-1	-0.926	-0.955	19.510	-0.210	-0.210	0.000	0.000	0.000	0.000
113	A	118	VAL	0	-0.035	-0.039	17.859	0.021	0.021	0.000	0.000	0.000	0.000
114	A	119	GLN	0	-0.001	0.006	19.713	0.005	0.005	0.000	0.000	0.000	0.000
115	A	120	THR	0	0.007	-0.014	20.082	0.017	0.017	0.000	0.000	0.000	0.000
116	A	121	ALA	0	0.008	0.037	16.588	-0.013	-0.013	0.000	0.000	0.000	0.000
117	A	122	GLN	0	-0.019	-0.009	18.556	0.016	0.016	0.000	0.000	0.000	0.000
118	A	123	ILE	0	0.009	0.005	15.115	-0.019	-0.019	0.000	0.000	0.000	0.000
119	A	124	PHE	0	-0.040	-0.019	18.840	0.055	0.055	0.000	0.000	0.000	0.000
120	A	125	PHE	0	0.041	0.015	15.924	-0.048	-0.048	0.000	0.000	0.000	0.000
121	A	126	THR	0	-0.051	-0.042	20.271	0.047	0.047	0.000	0.000	0.000	0.000
122	A	127	LYS	1	0.880	0.940	21.229	0.235	0.235	0.000	0.000	0.000	0.000
123	A	128	ASN	0	-0.053	-0.055	23.240	0.007	0.007	0.000	0.000	0.000	0.000
124	A	129	GLY	0	0.024	0.016	23.474	0.024	0.024	0.000	0.000	0.000	0.000
125	A	130	LYS	1	0.939	0.988	24.846	0.216	0.216	0.000	0.000	0.000	0.000
126	A	131	ARG	1	0.808	0.873	23.527	0.317	0.317	0.000	0.000	0.000	0.000
127	A	132	VAL	0	-0.055	-0.014	23.880	0.025	0.025	0.000	0.000	0.000	0.000
128	A	133	GLY	0	0.022	0.003	24.259	0.028	0.028	0.000	0.000	0.000	0.000
129	A	134	SER	0	-0.029	-0.031	22.375	-0.025	-0.025	0.000	0.000	0.000	0.000
130	A	135	THR	0	-0.038	-0.025	19.566	0.041	0.041	0.000	0.000	0.000	0.000
131	A	136	ILE	0	0.010	0.017	20.828	-0.030	-0.030	0.000	0.000	0.000	0.000
132	A	137	MET	0	-0.035	-0.003	16.434	0.015	0.015	0.000	0.000	0.000	0.000
133	A	138	PRO	0	0.028	0.004	19.130	0.004	0.004	0.000	0.000	0.000	0.000
134	A	139	MET	0	-0.017	0.014	13.411	0.014	0.014	0.000	0.000	0.000	0.000
135	A	140	SER	0	0.038	0.007	15.743	0.009	0.009	0.000	0.000	0.000	0.000
136	A	141	PRO	0	-0.008	0.003	14.148	-0.077	-0.077	0.000	0.000	0.000	0.000
137	A	142	ASP	-1	-0.923	-0.961	12.471	-0.509	-0.509	0.000	0.000	0.000	0.000
138	A	143	GLY	0	-0.006	0.004	9.613	-0.014	-0.014	0.000	0.000	0.000	0.000
139	A	144	LEU	0	-0.064	-0.042	8.965	-0.113	-0.113	0.000	0.000	0.000	0.000
140	A	145	PHE	0	0.000	-0.016	4.292	-0.128	0.046	-0.001	-0.026	-0.147	0.000
141	A	146	PRO	0	0.014	0.019	6.956	0.141	0.141	0.000	0.000	0.000	0.000
142	A	147	ALA	0	-0.011	-0.006	6.313	-0.839	-0.839	0.000	0.000	0.000	0.000
143	A	148	VAL	0	0.001	-0.006	7.963	0.369	0.369	0.000	0.000	0.000	0.000
144	A	149	GLY	0	-0.016	-0.006	9.738	-0.076	-0.076	0.000	0.000	0.000	0.000
145	A	150	MET	0	-0.028	-0.009	12.279	0.056	0.056	0.000	0.000	0.000	0.000
146	A	151	HIS	0	-0.105	-0.064	15.150	0.005	0.005	0.000	0.000	0.000	0.000
147	A	152	SER	0	-0.072	-0.049	18.011	0.049	0.049	0.000	0.000	0.000	0.000
148	A	153	LEU	0	0.071	0.024	20.150	-0.018	-0.018	0.000	0.000	0.000	0.000
149	A	154	GLY	0	0.035	0.005	21.149	0.002	0.002	0.000	0.000	0.000	0.000
150	A	155	GLU	-1	-0.726	-0.802	18.101	-0.327	-0.327	0.000	0.000	0.000	0.000
151	A	156	GLU	-1	-0.824	-0.895	16.774	-0.235	-0.235	0.000	0.000	0.000	0.000
152	A	157	VAL	0	-0.021	-0.013	13.584	-0.001	-0.001	0.000	0.000	0.000	0.000
153	A	158	ARG	1	0.900	0.945	14.572	0.337	0.337	0.000	0.000	0.000	0.000
154	A	159	LEU	0	-0.011	-0.003	8.444	-0.030	-0.030	0.000	0.000	0.000	0.000
155	A	160	HIS	0	-0.014	-0.011	12.669	0.097	0.097	0.000	0.000	0.000	0.000
156	A	161	LEU	0	0.018	-0.016	8.156	-0.010	-0.010	0.000	0.000	0.000	0.000
157	A	162	ASN	0	-0.013	-0.004	12.858	-0.038	-0.038	0.000	0.000	0.000	0.000
158	A	163	ALA	0	-0.009	0.016	16.206	0.061	0.061	0.000	0.000	0.000	0.000
159	A	164	GLU	-1	-0.899	-0.946	18.479	-0.358	-0.358	0.000	0.000	0.000	0.000
160	A	165	LEU	0	-0.038	-0.021	21.346	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:6:SER)