FMO DATABASE

FMODB ID: 1N99Z

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1546060.465827
FMO2-HF: Nuclear repulsion	1485035.25941
FMO2-HF: Total energy	-61025.206417
FMO2-MP2: Total energy	-61202.07217

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.
-21.451	-30.214	31.333	-8.652	-13.917	-0.027

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 : -0.058 / q_NPA : -0.026

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	0.012	-0.003	3.854	-2.975	-0.939	-0.023	-1.216	-0.796	0.001
4	A	9	LYS	1	0.832	0.912	6.839	0.843	0.843	0.000	0.000	0.000	0.000
5	A	10	HIS	0	-0.002	-0.027	10.596	-0.170	-0.170	0.000	0.000	0.000	0.000
6	A	11	ILE	0	-0.028	0.003	10.174	-0.018	-0.018	0.000	0.000	0.000	0.000
7	A	12	LEU	0	-0.006	0.007	11.193	0.026	0.026	0.000	0.000	0.000	0.000
8	A	13	VAL	0	-0.016	-0.026	7.932	-0.129	-0.129	0.000	0.000	0.000	0.000
9	A	14	ASP	-1	-0.905	-0.941	11.292	0.193	0.193	0.000	0.000	0.000	0.000
10	A	15	GLY	0	0.019	0.013	13.236	-0.059	-0.059	0.000	0.000	0.000	0.000
11	A	16	ASP	-1	-0.861	-0.896	11.127	-0.134	-0.134	0.000	0.000	0.000	0.000
12	A	17	THR	0	0.008	0.002	12.213	-0.149	-0.149	0.000	0.000	0.000	0.000
13	A	18	LEU	0	-0.035	-0.016	8.500	-0.021	-0.021	0.000	0.000	0.000	0.000
14	A	19	SER	0	0.025	-0.036	12.420	-0.008	-0.008	0.000	0.000	0.000	0.000
15	A	20	TYR	0	-0.117	-0.070	14.680	0.011	0.011	0.000	0.000	0.000	0.000
16	A	21	HIS	0	-0.033	-0.023	15.424	0.088	0.088	0.000	0.000	0.000	0.000
17	A	22	GLY	0	-0.006	-0.004	16.655	0.001	0.001	0.000	0.000	0.000	0.000
18	A	23	ASN	0	-0.052	-0.033	18.644	0.026	0.026	0.000	0.000	0.000	0.000
19	A	24	SER	0	-0.022	-0.028	21.776	-0.009	-0.009	0.000	0.000	0.000	0.000
20	A	25	GLY	0	0.035	0.032	21.870	0.010	0.010	0.000	0.000	0.000	0.000
21	A	26	GLU	-1	-0.784	-0.866	17.350	-0.218	-0.218	0.000	0.000	0.000	0.000
22	A	27	VAL	0	-0.030	-0.001	13.709	-0.010	-0.010	0.000	0.000	0.000	0.000
23	A	28	GLY	0	0.033	0.032	12.630	0.018	0.018	0.000	0.000	0.000	0.000
24	A	29	CYS	0	-0.085	-0.046	8.765	-0.157	-0.157	0.000	0.000	0.000	0.000
25	A	30	TYR	0	0.051	0.023	5.507	-0.339	-0.339	0.000	0.000	0.000	0.000
26	A	31	VAL	0	0.010	0.002	2.277	-0.473	0.372	1.485	-0.791	-1.539	-0.001
27	A	32	ALA	0	0.089	0.046	2.032	-9.490	-9.717	7.932	-4.169	-3.537	-0.050
28	A	33	SER	0	-0.046	-0.049	1.810	-15.457	-19.904	21.407	-9.650	-7.310	0.019
29	A	34	ARG	1	0.918	0.950	2.350	8.569	0.976	0.533	7.285	-0.225	0.004
30	A	35	PRO	0	-0.006	0.014	5.930	-0.717	-0.717	0.000	0.000	0.000	0.000
31	A	36	LEU	0	-0.027	-0.005	8.026	0.222	0.222	0.000	0.000	0.000	0.000
32	A	37	THR	0	0.032	-0.003	11.354	0.034	0.034	0.000	0.000	0.000	0.000
33	A	38	LYS	1	0.843	0.901	14.129	0.166	0.166	0.000	0.000	0.000	0.000
34	A	39	ASP	-1	-0.887	-0.930	16.885	-0.125	-0.125	0.000	0.000	0.000	0.000
35	A	40	SER	0	0.013	0.021	12.595	0.038	0.038	0.000	0.000	0.000	0.000
36	A	41	ASN	0	-0.017	-0.012	13.642	-0.092	-0.092	0.000	0.000	0.000	0.000
37	A	42	TYR	0	-0.033	-0.053	15.430	-0.060	-0.060	0.000	0.000	0.000	0.000
38	A	43	PHE	0	0.009	0.014	11.270	-0.055	-0.055	0.000	0.000	0.000	0.000
39	A	44	GLU	-1	-0.768	-0.826	14.333	-0.346	-0.346	0.000	0.000	0.000	0.000
40	A	45	VAL	0	0.011	-0.007	12.620	-0.071	-0.071	0.000	0.000	0.000	0.000
41	A	46	SER	0	-0.007	-0.022	15.324	0.033	0.033	0.000	0.000	0.000	0.000
42	A	47	ILE	0	-0.043	-0.020	17.734	-0.017	-0.017	0.000	0.000	0.000	0.000
43	A	48	VAL	0	-0.009	0.005	18.490	0.035	0.035	0.000	0.000	0.000	0.000
44	A	49	ASP	-1	-0.802	-0.909	20.364	-0.189	-0.189	0.000	0.000	0.000	0.000
45	A	50	SER	0	-0.045	-0.033	20.505	-0.043	-0.043	0.000	0.000	0.000	0.000
46	A	51	GLY	0	0.056	0.026	22.504	-0.017	-0.017	0.000	0.000	0.000	0.000
47	A	52	VAL	0	-0.052	-0.025	23.821	0.010	0.010	0.000	0.000	0.000	0.000
48	A	53	ARG	1	0.828	0.904	21.270	0.331	0.331	0.000	0.000	0.000	0.000
49	A	54	GLY	0	0.048	0.037	22.164	0.000	0.000	0.000	0.000	0.000	0.000
50	A	55	THR	0	-0.152	-0.090	19.060	-0.011	-0.011	0.000	0.000	0.000	0.000
51	A	56	ILE	0	0.005	0.012	15.714	-0.060	-0.060	0.000	0.000	0.000	0.000
52	A	57	ALA	0	-0.038	-0.018	14.106	0.052	0.052	0.000	0.000	0.000	0.000
53	A	58	VAL	0	0.037	0.013	12.808	-0.122	-0.122	0.000	0.000	0.000	0.000
54	A	59	GLY	0	-0.001	-0.024	11.729	0.174	0.174	0.000	0.000	0.000	0.000
55	A	60	LEU	0	0.003	0.022	9.650	-0.202	-0.202	0.000	0.000	0.000	0.000
56	A	61	VAL	0	-0.014	-0.010	5.535	0.357	0.357	0.000	0.000	0.000	0.000
57	A	62	PRO	0	0.063	0.047	7.421	-0.287	-0.287	0.000	0.000	0.000	0.000
58	A	63	GLN	0	0.017	-0.009	3.802	-0.767	-0.668	-0.001	-0.015	-0.083	0.000
59	A	64	TYR	0	-0.026	-0.026	3.729	0.508	0.643	-0.001	-0.013	-0.121	0.000
60	A	65	TYR	0	-0.024	-0.016	5.127	0.433	0.433	0.000	0.000	0.000	0.000
61	A	66	SER	0	-0.005	-0.002	6.333	0.096	0.096	0.000	0.000	0.000	0.000
62	A	67	LEU	0	0.045	0.013	4.330	-0.272	-0.173	-0.001	-0.016	-0.081	0.000
63	A	68	ASP	-1	-0.795	-0.871	8.409	-0.361	-0.361	0.000	0.000	0.000	0.000
64	A	69	HIS	1	0.828	0.899	11.354	0.669	0.669	0.000	0.000	0.000	0.000
65	A	70	GLN	0	0.103	0.052	11.353	-0.261	-0.261	0.000	0.000	0.000	0.000
66	A	71	PRO	0	0.045	0.043	10.048	0.049	0.049	0.000	0.000	0.000	0.000
67	A	72	GLY	0	0.032	0.006	11.870	0.150	0.150	0.000	0.000	0.000	0.000
68	A	73	TRP	0	-0.055	-0.041	14.573	0.101	0.101	0.000	0.000	0.000	0.000
69	A	74	LEU	0	-0.017	0.004	12.118	0.110	0.110	0.000	0.000	0.000	0.000
70	A	75	PRO	0	0.014	-0.007	14.189	-0.072	-0.072	0.000	0.000	0.000	0.000
71	A	76	ASP	-1	-0.872	-0.929	12.441	-0.666	-0.666	0.000	0.000	0.000	0.000
72	A	77	SER	0	-0.027	-0.004	10.867	-0.173	-0.173	0.000	0.000	0.000	0.000
73	A	78	VAL	0	-0.045	-0.038	12.449	0.175	0.175	0.000	0.000	0.000	0.000
74	A	79	ALA	0	0.000	0.006	13.531	-0.126	-0.126	0.000	0.000	0.000	0.000
75	A	80	TYR	0	0.010	0.006	15.416	0.105	0.105	0.000	0.000	0.000	0.000
76	A	81	HIS	1	0.853	0.923	16.162	0.549	0.549	0.000	0.000	0.000	0.000
77	A	82	ALA	0	0.050	0.038	19.285	0.049	0.049	0.000	0.000	0.000	0.000
78	A	83	ASP	-1	-0.790	-0.895	20.602	-0.388	-0.388	0.000	0.000	0.000	0.000
79	A	84	ASP	-1	-0.805	-0.893	22.853	-0.345	-0.345	0.000	0.000	0.000	0.000
80	A	85	GLY	0	0.023	0.029	23.448	0.023	0.023	0.000	0.000	0.000	0.000
81	A	86	LYS	1	0.763	0.878	22.953	0.321	0.321	0.000	0.000	0.000	0.000
82	A	87	LEU	0	-0.003	0.013	19.139	-0.037	-0.037	0.000	0.000	0.000	0.000
83	A	88	TYR	0	-0.089	-0.077	17.703	0.058	0.058	0.000	0.000	0.000	0.000
84	A	89	ASN	0	-0.023	-0.033	17.010	-0.051	-0.051	0.000	0.000	0.000	0.000
85	A	90	GLY	0	0.073	0.049	16.474	0.036	0.036	0.000	0.000	0.000	0.000
86	A	91	ARG	1	0.918	0.962	17.483	0.342	0.342	0.000	0.000	0.000	0.000
87	A	92	ALA	0	0.054	0.028	19.522	-0.023	-0.023	0.000	0.000	0.000	0.000
88	A	93	LYS	1	0.874	0.938	20.546	0.303	0.303	0.000	0.000	0.000	0.000
89	A	94	GLY	0	0.067	0.051	22.447	-0.011	-0.011	0.000	0.000	0.000	0.000
90	A	95	ARG	1	0.870	0.929	23.184	0.332	0.332	0.000	0.000	0.000	0.000
91	A	96	GLN	0	0.043	0.001	24.901	-0.031	-0.031	0.000	0.000	0.000	0.000
92	A	97	PHE	0	-0.015	-0.007	22.018	0.002	0.002	0.000	0.000	0.000	0.000
93	A	98	GLY	0	0.077	0.039	25.872	0.011	0.011	0.000	0.000	0.000	0.000
94	A	99	SER	0	-0.033	-0.002	26.741	0.002	0.002	0.000	0.000	0.000	0.000
95	A	100	LYS	1	0.919	0.958	24.875	0.247	0.247	0.000	0.000	0.000	0.000
96	A	101	CYS	0	-0.098	-0.033	22.338	0.010	0.010	0.000	0.000	0.000	0.000
97	A	102	ASN	0	0.022	0.022	24.486	-0.011	-0.011	0.000	0.000	0.000	0.000
98	A	103	SER	0	0.040	-0.009	23.459	-0.022	-0.022	0.000	0.000	0.000	0.000
99	A	104	GLY	0	-0.004	0.018	23.386	0.023	0.023	0.000	0.000	0.000	0.000
100	A	105	ASP	-1	-0.829	-0.896	23.327	-0.263	-0.263	0.000	0.000	0.000	0.000
101	A	106	ARG	1	0.849	0.889	19.731	0.274	0.274	0.000	0.000	0.000	0.000
102	A	107	ILE	0	-0.021	-0.014	17.562	0.029	0.029	0.000	0.000	0.000	0.000
103	A	108	GLY	0	0.061	0.032	16.774	-0.032	-0.032	0.000	0.000	0.000	0.000
104	A	109	CYS	0	-0.094	-0.031	14.135	-0.016	-0.016	0.000	0.000	0.000	0.000
105	A	110	GLY	0	0.075	0.034	15.496	-0.025	-0.025	0.000	0.000	0.000	0.000
106	A	111	ILE	0	-0.022	-0.001	13.038	-0.014	-0.014	0.000	0.000	0.000	0.000
107	A	112	GLU	-1	-0.733	-0.826	17.390	-0.283	-0.283	0.000	0.000	0.000	0.000
108	A	113	PRO	0	0.019	0.000	20.117	-0.005	-0.005	0.000	0.000	0.000	0.000
109	A	114	VAL	0	0.016	0.005	21.124	0.009	0.009	0.000	0.000	0.000	0.000
110	A	115	SER	0	-0.048	-0.021	19.750	-0.008	-0.008	0.000	0.000	0.000	0.000
111	A	116	PHE	0	-0.023	-0.021	14.182	-0.021	-0.021	0.000	0.000	0.000	0.000
112	A	117	ASP	-1	-0.935	-0.947	19.212	-0.156	-0.156	0.000	0.000	0.000	0.000
113	A	118	VAL	0	-0.030	-0.016	17.978	0.014	0.014	0.000	0.000	0.000	0.000
114	A	119	GLN	0	-0.021	-0.016	20.250	0.000	0.000	0.000	0.000	0.000	0.000
115	A	120	THR	0	-0.026	-0.022	20.193	0.012	0.012	0.000	0.000	0.000	0.000
116	A	121	ALA	0	0.029	0.040	16.600	-0.002	-0.002	0.000	0.000	0.000	0.000
117	A	122	GLN	0	-0.038	-0.025	18.554	0.002	0.002	0.000	0.000	0.000	0.000
118	A	123	ILE	0	-0.006	-0.001	15.277	-0.017	-0.017	0.000	0.000	0.000	0.000
119	A	124	PHE	0	-0.056	-0.035	18.653	0.055	0.055	0.000	0.000	0.000	0.000
120	A	125	PHE	0	0.039	0.010	15.526	-0.057	-0.057	0.000	0.000	0.000	0.000
121	A	126	THR	0	-0.030	-0.030	19.986	0.044	0.044	0.000	0.000	0.000	0.000
122	A	127	LYS	1	0.838	0.911	21.052	0.248	0.248	0.000	0.000	0.000	0.000
123	A	128	ASN	0	-0.040	-0.042	23.165	0.012	0.012	0.000	0.000	0.000	0.000
124	A	129	GLY	0	0.059	0.041	23.406	0.027	0.027	0.000	0.000	0.000	0.000
125	A	130	LYS	1	0.930	0.980	24.380	0.209	0.209	0.000	0.000	0.000	0.000
126	A	131	ARG	1	0.821	0.872	23.083	0.302	0.302	0.000	0.000	0.000	0.000
127	A	132	VAL	0	-0.069	-0.024	23.530	0.027	0.027	0.000	0.000	0.000	0.000
128	A	133	GLY	0	0.018	0.002	23.980	0.025	0.025	0.000	0.000	0.000	0.000
129	A	134	SER	0	-0.013	-0.018	22.493	-0.021	-0.021	0.000	0.000	0.000	0.000
130	A	135	THR	0	-0.049	-0.022	19.681	0.037	0.037	0.000	0.000	0.000	0.000
131	A	136	ILE	0	0.031	0.018	21.257	-0.016	-0.016	0.000	0.000	0.000	0.000
132	A	137	MET	0	-0.022	-0.001	16.408	0.007	0.007	0.000	0.000	0.000	0.000
133	A	138	PRO	0	0.020	0.003	18.846	0.009	0.009	0.000	0.000	0.000	0.000
134	A	139	MET	0	-0.015	0.017	13.366	0.012	0.012	0.000	0.000	0.000	0.000
135	A	140	SER	0	0.035	0.003	15.266	0.032	0.032	0.000	0.000	0.000	0.000
136	A	141	PRO	0	-0.005	0.012	13.939	-0.120	-0.120	0.000	0.000	0.000	0.000
137	A	142	ASP	-1	-0.865	-0.944	11.974	-0.323	-0.323	0.000	0.000	0.000	0.000
138	A	143	GLY	0	-0.042	-0.015	9.812	-0.004	-0.004	0.000	0.000	0.000	0.000
139	A	144	LEU	0	-0.037	-0.033	8.850	-0.242	-0.242	0.000	0.000	0.000	0.000
140	A	145	PHE	0	-0.014	-0.005	3.916	-0.036	0.254	0.002	-0.067	-0.225	0.000
141	A	146	PRO	0	0.004	0.007	6.697	-0.046	-0.046	0.000	0.000	0.000	0.000
142	A	147	ALA	0	-0.013	-0.004	6.147	-1.023	-1.023	0.000	0.000	0.000	0.000
143	A	148	VAL	0	0.008	-0.002	7.746	0.502	0.502	0.000	0.000	0.000	0.000
144	A	149	GLY	0	0.002	0.003	9.474	-0.214	-0.214	0.000	0.000	0.000	0.000
145	A	150	MET	0	-0.030	0.001	12.109	0.111	0.111	0.000	0.000	0.000	0.000
146	A	151	HIS	0	-0.097	-0.061	15.370	-0.014	-0.014	0.000	0.000	0.000	0.000
147	A	152	SER	0	-0.056	-0.049	18.297	0.061	0.061	0.000	0.000	0.000	0.000
148	A	153	LEU	0	0.071	0.032	20.217	-0.019	-0.019	0.000	0.000	0.000	0.000
149	A	154	GLY	0	0.047	0.012	21.193	0.010	0.010	0.000	0.000	0.000	0.000
150	A	155	GLU	-1	-0.753	-0.810	17.960	-0.434	-0.434	0.000	0.000	0.000	0.000
151	A	156	GLU	-1	-0.832	-0.892	16.638	-0.239	-0.239	0.000	0.000	0.000	0.000
152	A	157	VAL	0	-0.033	-0.018	13.288	0.001	0.001	0.000	0.000	0.000	0.000
153	A	158	ARG	1	0.871	0.909	14.285	0.193	0.193	0.000	0.000	0.000	0.000
154	A	159	LEU	0	-0.015	0.008	7.907	-0.055	-0.055	0.000	0.000	0.000	0.000
155	A	160	HIS	0	-0.019	-0.011	12.353	0.129	0.129	0.000	0.000	0.000	0.000
156	A	161	LEU	0	0.002	-0.019	7.483	-0.051	-0.051	0.000	0.000	0.000	0.000
157	A	162	ASN	0	0.005	0.002	12.032	0.017	0.017	0.000	0.000	0.000	0.000
158	A	163	ALA	0	-0.001	0.021	15.398	0.037	0.037	0.000	0.000	0.000	0.000
159	A	164	GLU	-1	-0.893	-0.943	17.853	-0.215	-0.215	0.000	0.000	0.000	0.000
160	A	165	LEU	0	-0.055	-0.029	20.810	-0.021	-0.021	0.000	0.000	0.000	0.000

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