FMO DATABASE

FMODB ID: YVY42

Calculation Name: 1W8I-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1W8I

Chain ID: A

ChEMBL ID:

UniProt ID: O28590

Base Structure: X-ray

Registration Date: 2023-09-21

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	155
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1549419.312913
FMO2-HF: Nuclear repulsion	1488224.12637
FMO2-HF: Total energy	-61195.186543
FMO2-MP2: Total energy	-61377.742575

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:MET)

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

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.
-8.212	-3.784	0.349	-2.316	-2.46	-0.014

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.036 / 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	3	ALA	0	-0.004	0.006	3.866	1.149	2.938	-0.021	-0.971	-0.798	0.000
4	A	4	LEU	0	0.000	0.010	6.640	-0.385	-0.385	0.000	0.000	0.000	0.000
5	A	5	ILE	0	-0.032	-0.024	10.424	0.164	0.164	0.000	0.000	0.000	0.000
6	A	6	ASP	-1	-0.743	-0.860	12.536	0.004	0.004	0.000	0.000	0.000	0.000
7	A	7	THR	0	0.032	-0.017	15.996	-0.007	-0.007	0.000	0.000	0.000	0.000
8	A	8	GLY	0	-0.024	-0.013	19.294	-0.001	-0.001	0.000	0.000	0.000	0.000
9	A	9	ILE	0	-0.031	-0.008	14.271	0.010	0.010	0.000	0.000	0.000	0.000
10	A	10	PHE	0	0.062	0.025	14.576	0.003	0.003	0.000	0.000	0.000	0.000
11	A	11	PHE	0	-0.026	-0.016	19.228	0.000	0.000	0.000	0.000	0.000	0.000
12	A	12	GLY	0	0.028	0.010	21.277	0.001	0.001	0.000	0.000	0.000	0.000
13	A	13	PHE	0	-0.001	-0.005	19.198	0.004	0.004	0.000	0.000	0.000	0.000
14	A	14	TYR	0	0.062	0.020	21.283	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	15	SER	0	-0.022	0.007	24.571	0.000	0.000	0.000	0.000	0.000	0.000
16	A	16	LEU	0	0.051	0.015	26.268	0.009	0.009	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.850	0.916	28.065	-0.028	-0.028	0.000	0.000	0.000	0.000
18	A	18	ASP	-1	-0.827	-0.909	24.300	0.052	0.052	0.000	0.000	0.000	0.000
19	A	19	VAL	0	-0.025	-0.012	25.175	0.004	0.004	0.000	0.000	0.000	0.000
20	A	20	HIS	1	0.856	0.918	20.870	-0.099	-0.099	0.000	0.000	0.000	0.000
21	A	21	HIS	1	0.848	0.955	21.266	-0.019	-0.019	0.000	0.000	0.000	0.000
22	A	22	MET	0	0.014	-0.004	21.553	-0.007	-0.007	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.815	-0.887	18.325	0.149	0.149	0.000	0.000	0.000	0.000
24	A	24	SER	0	0.048	0.026	17.117	0.013	0.013	0.000	0.000	0.000	0.000
25	A	25	VAL	0	-0.018	0.009	17.001	-0.011	-0.011	0.000	0.000	0.000	0.000
26	A	26	ALA	0	-0.010	-0.006	16.583	-0.010	-0.010	0.000	0.000	0.000	0.000
27	A	27	ILE	0	-0.033	-0.011	11.909	0.005	0.005	0.000	0.000	0.000	0.000
28	A	28	VAL	0	0.038	0.017	12.341	-0.026	-0.026	0.000	0.000	0.000	0.000
29	A	29	VAL	0	-0.025	-0.008	13.603	-0.037	-0.037	0.000	0.000	0.000	0.000
30	A	30	HIS	0	0.010	-0.001	10.511	0.024	0.024	0.000	0.000	0.000	0.000
31	A	31	ALA	0	-0.030	-0.012	8.842	-0.045	-0.045	0.000	0.000	0.000	0.000
32	A	32	VAL	0	-0.010	-0.003	9.406	-0.117	-0.117	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.831	-0.877	11.704	0.032	0.032	0.000	0.000	0.000	0.000
34	A	34	GLY	0	0.019	0.014	7.733	0.050	0.050	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.840	0.930	5.993	-0.632	-0.632	0.000	0.000	0.000	0.000
36	A	36	TRP	0	-0.043	-0.040	3.512	-0.163	0.187	0.004	-0.059	-0.296	0.000
37	A	37	GLY	0	-0.018	0.006	2.783	-3.325	-1.652	0.368	-1.197	-0.844	-0.014
38	A	38	ARG	1	0.907	0.955	3.941	2.017	2.345	0.000	-0.052	-0.275	0.000
39	A	39	LEU	0	0.000	0.005	6.277	-0.198	-0.198	0.000	0.000	0.000	0.000
40	A	40	PHE	0	0.026	0.008	5.994	-0.023	-0.023	0.000	0.000	0.000	0.000
41	A	41	VAL	0	0.016	0.018	10.917	0.122	0.122	0.000	0.000	0.000	0.000
42	A	42	THR	0	0.096	0.045	14.309	-0.054	-0.054	0.000	0.000	0.000	0.000
43	A	43	ASN	0	0.054	0.009	16.067	0.006	0.006	0.000	0.000	0.000	0.000
44	A	44	HIS	0	-0.005	-0.013	19.362	0.034	0.034	0.000	0.000	0.000	0.000
45	A	45	ILE	0	0.002	0.008	15.729	0.014	0.014	0.000	0.000	0.000	0.000
46	A	46	LEU	0	-0.035	-0.011	19.047	0.017	0.017	0.000	0.000	0.000	0.000
47	A	47	ASP	-1	-0.886	-0.948	20.525	-0.084	-0.084	0.000	0.000	0.000	0.000
48	A	48	GLU	-1	-0.821	-0.874	22.372	-0.028	-0.028	0.000	0.000	0.000	0.000
49	A	49	THR	0	-0.007	-0.022	20.173	0.019	0.019	0.000	0.000	0.000	0.000
50	A	50	LEU	0	-0.017	-0.002	22.746	0.012	0.012	0.000	0.000	0.000	0.000
51	A	51	THR	0	-0.022	-0.004	25.135	0.012	0.012	0.000	0.000	0.000	0.000
52	A	52	LEU	0	-0.020	-0.002	24.303	0.010	0.010	0.000	0.000	0.000	0.000
53	A	53	LEU	0	-0.008	-0.011	22.686	0.010	0.010	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.997	1.006	27.039	0.067	0.067	0.000	0.000	0.000	0.000
55	A	55	TYR	0	-0.043	-0.021	30.206	0.008	0.008	0.000	0.000	0.000	0.000
56	A	56	LYS	1	0.861	0.927	29.076	0.012	0.012	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.895	0.951	31.397	0.023	0.023	0.000	0.000	0.000	0.000
58	A	58	LEU	0	0.001	0.016	26.679	0.004	0.004	0.000	0.000	0.000	0.000
59	A	59	PRO	0	0.007	0.001	26.555	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	60	ALA	0	0.013	0.008	25.926	-0.006	-0.006	0.000	0.000	0.000	0.000
61	A	61	ASP	-1	-0.818	-0.892	25.816	-0.065	-0.065	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.918	0.935	24.928	0.047	0.047	0.000	0.000	0.000	0.000
63	A	63	PHE	0	-0.056	-0.018	18.391	-0.007	-0.007	0.000	0.000	0.000	0.000
64	A	64	LEU	0	0.020	-0.003	21.388	-0.017	-0.017	0.000	0.000	0.000	0.000
65	A	65	GLU	-1	-0.891	-0.937	22.384	-0.095	-0.095	0.000	0.000	0.000	0.000
66	A	66	GLY	0	0.012	-0.004	21.110	-0.011	-0.011	0.000	0.000	0.000	0.000
67	A	67	PHE	0	-0.065	-0.015	15.485	-0.009	-0.009	0.000	0.000	0.000	0.000
68	A	68	VAL	0	-0.011	-0.006	17.163	-0.039	-0.039	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.936	-0.976	19.449	-0.153	-0.153	0.000	0.000	0.000	0.000
70	A	70	SER	0	-0.064	-0.043	18.350	-0.016	-0.016	0.000	0.000	0.000	0.000
71	A	71	GLY	0	-0.019	-0.003	16.858	-0.007	-0.007	0.000	0.000	0.000	0.000
72	A	72	VAL	0	-0.060	-0.023	13.229	-0.056	-0.056	0.000	0.000	0.000	0.000
73	A	73	LEU	0	-0.040	-0.009	12.404	-0.077	-0.077	0.000	0.000	0.000	0.000
74	A	74	ASN	0	-0.046	-0.028	10.455	-0.129	-0.129	0.000	0.000	0.000	0.000
75	A	75	ILE	0	0.031	0.008	12.993	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	76	ILE	0	-0.023	-0.004	10.271	-0.032	-0.032	0.000	0.000	0.000	0.000
77	A	77	TYR	0	-0.035	-0.032	14.585	0.069	0.069	0.000	0.000	0.000	0.000
78	A	78	THR	0	-0.020	-0.037	16.622	-0.029	-0.029	0.000	0.000	0.000	0.000
79	A	79	ASP	-1	-0.843	-0.911	18.089	-0.283	-0.283	0.000	0.000	0.000	0.000
80	A	80	ASP	-1	-0.908	-0.977	20.742	-0.173	-0.173	0.000	0.000	0.000	0.000
81	A	81	GLU	-1	-0.774	-0.854	20.421	-0.143	-0.143	0.000	0.000	0.000	0.000
82	A	82	VAL	0	-0.014	-0.016	16.451	0.016	0.016	0.000	0.000	0.000	0.000
83	A	83	GLU	-1	-0.736	-0.822	19.379	-0.130	-0.130	0.000	0.000	0.000	0.000
84	A	84	ARG	1	0.727	0.842	22.461	0.145	0.145	0.000	0.000	0.000	0.000
85	A	85	LYS	1	0.814	0.897	17.966	0.248	0.248	0.000	0.000	0.000	0.000
86	A	86	ALA	0	0.008	0.004	20.665	0.022	0.022	0.000	0.000	0.000	0.000
87	A	87	LEU	0	-0.001	0.000	22.190	0.021	0.021	0.000	0.000	0.000	0.000
88	A	88	GLU	-1	-0.910	-0.948	24.729	-0.066	-0.066	0.000	0.000	0.000	0.000
89	A	89	VAL	0	0.006	0.004	20.595	0.014	0.014	0.000	0.000	0.000	0.000
90	A	90	PHE	0	-0.008	-0.016	23.998	0.012	0.012	0.000	0.000	0.000	0.000
91	A	91	LYS	1	0.923	0.958	26.091	0.041	0.041	0.000	0.000	0.000	0.000
92	A	92	ALA	0	-0.062	-0.029	26.289	0.006	0.006	0.000	0.000	0.000	0.000
93	A	93	ARG	1	0.786	0.882	21.710	-0.051	-0.051	0.000	0.000	0.000	0.000
94	A	94	VAL	0	-0.002	0.020	27.865	0.003	0.003	0.000	0.000	0.000	0.000
95	A	95	TYR	0	-0.066	-0.040	30.681	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	96	GLU	-1	-0.862	-0.897	26.762	0.053	0.053	0.000	0.000	0.000	0.000
97	A	97	LYS	1	0.917	0.935	29.201	-0.035	-0.035	0.000	0.000	0.000	0.000
98	A	98	GLY	0	-0.059	-0.039	27.764	0.007	0.007	0.000	0.000	0.000	0.000
99	A	99	PHE	0	0.060	0.060	20.797	0.003	0.003	0.000	0.000	0.000	0.000
100	A	100	SER	0	-0.031	-0.048	23.303	-0.014	-0.014	0.000	0.000	0.000	0.000
101	A	101	TYR	0	-0.025	-0.057	23.718	0.009	0.009	0.000	0.000	0.000	0.000
102	A	102	THR	0	0.032	-0.007	20.060	-0.017	-0.017	0.000	0.000	0.000	0.000
103	A	103	ASP	-1	-0.813	-0.860	19.416	-0.003	-0.003	0.000	0.000	0.000	0.000
104	A	104	ALA	0	0.003	-0.003	18.932	0.007	0.007	0.000	0.000	0.000	0.000
105	A	105	ILE	0	0.001	0.004	17.787	-0.010	-0.010	0.000	0.000	0.000	0.000
106	A	106	SER	0	-0.072	-0.050	15.475	-0.038	-0.038	0.000	0.000	0.000	0.000
107	A	107	GLU	-1	-0.815	-0.893	14.236	0.072	0.072	0.000	0.000	0.000	0.000
108	A	108	VAL	0	0.009	0.013	14.756	0.006	0.006	0.000	0.000	0.000	0.000
109	A	109	VAL	0	0.018	0.007	11.721	-0.042	-0.042	0.000	0.000	0.000	0.000
110	A	110	ALA	0	-0.031	-0.020	10.073	-0.104	-0.104	0.000	0.000	0.000	0.000
111	A	111	GLU	-1	-0.886	-0.944	9.623	-0.027	-0.027	0.000	0.000	0.000	0.000
112	A	112	GLU	-1	-0.808	-0.887	11.238	-0.309	-0.309	0.000	0.000	0.000	0.000
113	A	113	LEU	0	-0.064	-0.033	7.856	-0.129	-0.129	0.000	0.000	0.000	0.000
114	A	114	LYS	1	0.788	0.902	6.201	-0.211	-0.211	0.000	0.000	0.000	0.000
115	A	115	LEU	0	-0.034	0.005	4.900	0.103	0.186	-0.001	-0.012	-0.069	0.000
116	A	116	LYS	1	0.932	0.957	4.512	-4.954	-4.749	-0.001	-0.025	-0.178	0.000
117	A	117	LEU	0	0.056	0.043	7.273	-0.343	-0.343	0.000	0.000	0.000	0.000
118	A	118	ILE	0	-0.033	-0.016	7.800	0.084	0.084	0.000	0.000	0.000	0.000
119	A	119	SER	0	0.061	-0.019	11.768	-0.096	-0.096	0.000	0.000	0.000	0.000
120	A	120	TYR	0	-0.099	-0.073	15.563	0.048	0.048	0.000	0.000	0.000	0.000
121	A	121	ASP	-1	-0.832	-0.919	18.684	0.098	0.098	0.000	0.000	0.000	0.000
122	A	122	SER	0	-0.109	-0.056	19.161	0.019	0.019	0.000	0.000	0.000	0.000
123	A	123	ARG	1	0.895	0.946	21.204	-0.087	-0.087	0.000	0.000	0.000	0.000
124	A	124	PHE	0	0.030	0.030	16.840	-0.007	-0.007	0.000	0.000	0.000	0.000
125	A	125	SER	0	-0.069	-0.048	18.076	0.031	0.031	0.000	0.000	0.000	0.000
126	A	126	LEU	0	-0.018	0.007	12.105	0.030	0.030	0.000	0.000	0.000	0.000
127	A	127	PRO	0	-0.026	-0.014	11.894	-0.011	-0.011	0.000	0.000	0.000	0.000
128	A	128	THR	0	-0.007	0.001	12.797	0.039	0.039	0.000	0.000	0.000	0.000
129	A	129	ILE	0	-0.038	-0.017	8.294	0.045	0.045	0.000	0.000	0.000	0.000
130	A	130	GLY	0	0.074	0.014	12.479	-0.066	-0.066	0.000	0.000	0.000	0.000
131	A	131	ARG	1	0.879	0.932	15.239	-0.287	-0.287	0.000	0.000	0.000	0.000
132	A	132	ASP	-1	-0.916	-0.961	17.941	0.199	0.199	0.000	0.000	0.000	0.000
133	A	133	TYR	0	0.030	0.009	12.028	0.042	0.042	0.000	0.000	0.000	0.000
134	A	134	TRP	0	0.037	0.015	17.219	0.004	0.004	0.000	0.000	0.000	0.000
135	A	135	LYS	1	0.943	0.944	19.815	-0.120	-0.120	0.000	0.000	0.000	0.000
136	A	136	SER	0	-0.053	-0.011	17.204	0.006	0.006	0.000	0.000	0.000	0.000
137	A	137	LEU	0	-0.017	0.006	15.190	0.014	0.014	0.000	0.000	0.000	0.000
138	A	138	ASP	-1	-0.863	-0.930	18.853	0.189	0.189	0.000	0.000	0.000	0.000
139	A	139	GLU	-1	-0.828	-0.912	21.115	0.089	0.089	0.000	0.000	0.000	0.000
140	A	140	SER	0	-0.021	-0.022	22.307	-0.008	-0.008	0.000	0.000	0.000	0.000
141	A	141	GLU	-1	-0.690	-0.804	16.177	0.116	0.116	0.000	0.000	0.000	0.000
142	A	142	ARG	1	0.855	0.932	20.127	-0.152	-0.152	0.000	0.000	0.000	0.000
143	A	143	LYS	1	0.861	0.927	22.015	-0.093	-0.093	0.000	0.000	0.000	0.000
144	A	144	ARG	1	0.731	0.807	15.467	-0.090	-0.090	0.000	0.000	0.000	0.000
145	A	145	ILE	0	0.011	0.005	16.745	-0.012	-0.012	0.000	0.000	0.000	0.000
146	A	146	SER	0	-0.032	-0.038	20.746	-0.011	-0.011	0.000	0.000	0.000	0.000
147	A	147	ALA	0	-0.059	-0.017	24.289	-0.007	-0.007	0.000	0.000	0.000	0.000
148	A	148	ILE	0	0.006	-0.001	19.235	-0.009	-0.009	0.000	0.000	0.000	0.000
149	A	149	LEU	0	-0.032	-0.009	22.948	-0.007	-0.007	0.000	0.000	0.000	0.000
150	A	150	ARG	1	0.820	0.904	24.080	-0.043	-0.043	0.000	0.000	0.000	0.000
151	A	151	GLU	-1	-0.864	-0.930	26.756	0.027	0.027	0.000	0.000	0.000	0.000
152	A	152	LYS	1	0.892	0.936	22.410	-0.010	-0.010	0.000	0.000	0.000	0.000
153	A	153	GLY	0	0.021	0.032	25.753	-0.007	-0.007	0.000	0.000	0.000	0.000
154	A	154	ILE	0	-0.040	-0.005	19.927	-0.006	-0.006	0.000	0.000	0.000	0.000
155	A	155	ASP	-1	-0.847	-0.939	23.035	0.012	0.012	0.000	0.000	0.000	0.000

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