FMO DATABASE

FMODB ID: JL3Z9

Calculation Name: 3W1Z-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3W1Z

Chain ID: A

ChEMBL ID:

UniProt ID: O14368

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	134
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1030459.758827
FMO2-HF: Nuclear repulsion	979078.94464
FMO2-HF: Total energy	-51380.814188
FMO2-MP2: Total energy	-51534.043422

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:10:PRO)

Summations of interaction energy for fragment #1(A:10: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.
-2.972	-1.062	-0.015	-0.651	-1.245	0.003

Interaction energy analysis for fragmet #1(A:10:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.000 / 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	12	THR	0	0.020	0.010	3.837	-1.037	0.256	-0.016	-0.511	-0.765	0.002
4	A	13	VAL	0	-0.012	0.003	6.308	0.389	0.389	0.000	0.000	0.000	0.000
5	A	14	ASN	0	-0.020	-0.028	9.961	-0.162	-0.162	0.000	0.000	0.000	0.000
6	A	15	ASP	-1	-0.808	-0.898	12.188	-0.304	-0.304	0.000	0.000	0.000	0.000
7	A	16	LEU	0	-0.024	-0.008	11.799	0.040	0.040	0.000	0.000	0.000	0.000
8	A	17	PHE	0	-0.027	-0.029	15.192	0.032	0.032	0.000	0.000	0.000	0.000
9	A	18	SER	0	0.019	0.017	17.146	0.027	0.027	0.000	0.000	0.000	0.000
10	A	19	ASP	-1	-0.805	-0.894	19.067	-0.057	-0.057	0.000	0.000	0.000	0.000
11	A	20	PHE	0	-0.058	-0.021	21.251	0.020	0.020	0.000	0.000	0.000	0.000
12	A	21	VAL	0	-0.026	-0.020	16.741	0.027	0.027	0.000	0.000	0.000	0.000
13	A	22	SER	0	0.029	0.018	16.914	-0.021	-0.021	0.000	0.000	0.000	0.000
14	A	23	TYR	0	0.006	0.003	8.183	0.036	0.036	0.000	0.000	0.000	0.000
15	A	24	SER	0	-0.014	-0.022	12.749	0.033	0.033	0.000	0.000	0.000	0.000
16	A	25	PRO	0	-0.002	0.010	11.825	0.002	0.002	0.000	0.000	0.000	0.000
17	A	26	ARG	1	0.939	0.979	12.767	-0.158	-0.158	0.000	0.000	0.000	0.000
18	A	27	LEU	0	0.002	-0.007	13.235	0.063	0.063	0.000	0.000	0.000	0.000
19	A	28	ASN	0	0.030	0.014	9.200	-0.188	-0.188	0.000	0.000	0.000	0.000
20	A	29	ASN	0	-0.023	-0.024	9.955	-0.019	-0.019	0.000	0.000	0.000	0.000
21	A	30	GLN	0	-0.006	-0.010	3.699	-1.271	-0.920	0.000	-0.097	-0.255	0.001
22	A	31	ILE	0	0.030	0.022	7.581	-0.218	-0.218	0.000	0.000	0.000	0.000
23	A	32	PRO	0	0.009	0.003	3.611	-0.428	-0.162	0.001	-0.043	-0.225	0.000
24	A	33	GLY	0	-0.005	-0.002	5.657	0.253	0.253	0.000	0.000	0.000	0.000
25	A	34	GLU	-1	-0.899	-0.938	7.701	-0.371	-0.371	0.000	0.000	0.000	0.000
26	A	35	LEU	0	-0.045	-0.019	9.524	-0.292	-0.292	0.000	0.000	0.000	0.000
27	A	36	SER	0	0.003	-0.006	8.431	0.003	0.003	0.000	0.000	0.000	0.000
28	A	37	PRO	0	-0.002	0.009	9.856	-0.145	-0.145	0.000	0.000	0.000	0.000
29	A	38	SER	0	-0.003	-0.019	9.935	-0.089	-0.089	0.000	0.000	0.000	0.000
30	A	39	ILE	0	-0.040	-0.023	10.680	0.129	0.129	0.000	0.000	0.000	0.000
31	A	40	ASP	-1	-0.858	-0.899	11.919	-0.537	-0.537	0.000	0.000	0.000	0.000
32	A	41	VAL	0	-0.042	-0.031	14.348	0.041	0.041	0.000	0.000	0.000	0.000
33	A	42	HIS	0	-0.056	-0.025	16.624	0.052	0.052	0.000	0.000	0.000	0.000
34	A	43	GLU	-1	-0.821	-0.899	19.974	-0.105	-0.105	0.000	0.000	0.000	0.000
35	A	44	GLY	0	-0.059	-0.025	23.136	0.010	0.010	0.000	0.000	0.000	0.000
36	A	45	LYS	1	0.717	0.847	26.289	0.082	0.082	0.000	0.000	0.000	0.000
37	A	46	ASP	-1	-0.776	-0.900	29.848	-0.083	-0.083	0.000	0.000	0.000	0.000
38	A	47	THR	0	-0.023	-0.012	26.000	0.001	0.001	0.000	0.000	0.000	0.000
39	A	48	VAL	0	0.050	0.037	21.961	0.001	0.001	0.000	0.000	0.000	0.000
40	A	49	SER	0	0.002	0.011	21.709	0.009	0.009	0.000	0.000	0.000	0.000
41	A	50	VAL	0	-0.012	-0.012	17.456	-0.015	-0.015	0.000	0.000	0.000	0.000
42	A	51	ASP	-1	-0.838	-0.892	17.092	-0.289	-0.289	0.000	0.000	0.000	0.000
43	A	52	VAL	0	0.005	-0.013	14.933	-0.058	-0.058	0.000	0.000	0.000	0.000
44	A	53	GLU	-1	-0.895	-0.918	12.157	-0.701	-0.701	0.000	0.000	0.000	0.000
45	A	54	LEU	0	-0.037	-0.034	15.115	-0.046	-0.046	0.000	0.000	0.000	0.000
46	A	55	PRO	0	0.044	0.017	15.847	0.057	0.057	0.000	0.000	0.000	0.000
47	A	56	GLY	0	-0.057	-0.045	18.821	-0.009	-0.009	0.000	0.000	0.000	0.000
48	A	57	VAL	0	-0.012	0.005	19.587	0.011	0.011	0.000	0.000	0.000	0.000
49	A	58	LYS	1	0.860	0.929	22.592	0.216	0.216	0.000	0.000	0.000	0.000
50	A	59	LYS	1	0.893	0.927	25.389	0.159	0.159	0.000	0.000	0.000	0.000
51	A	60	GLU	-1	-0.828	-0.914	26.541	-0.169	-0.169	0.000	0.000	0.000	0.000
52	A	61	ASP	-1	-0.893	-0.945	24.711	-0.200	-0.200	0.000	0.000	0.000	0.000
53	A	62	VAL	0	-0.092	-0.035	21.432	-0.015	-0.015	0.000	0.000	0.000	0.000
54	A	63	GLN	0	-0.012	0.015	23.860	0.011	0.011	0.000	0.000	0.000	0.000
55	A	64	VAL	0	0.007	-0.007	22.967	-0.021	-0.021	0.000	0.000	0.000	0.000
56	A	65	HIS	0	0.010	0.010	24.649	0.024	0.024	0.000	0.000	0.000	0.000
57	A	66	TYR	0	0.013	-0.004	25.241	-0.006	-0.006	0.000	0.000	0.000	0.000
58	A	67	ASP	-1	-0.828	-0.902	26.710	-0.089	-0.089	0.000	0.000	0.000	0.000
59	A	68	SER	0	-0.053	-0.041	27.350	0.000	0.000	0.000	0.000	0.000	0.000
60	A	69	GLY	0	-0.045	-0.017	26.864	0.006	0.006	0.000	0.000	0.000	0.000
61	A	70	LYS	1	0.818	0.901	22.859	0.094	0.094	0.000	0.000	0.000	0.000
62	A	71	LEU	0	0.008	0.013	20.771	0.008	0.008	0.000	0.000	0.000	0.000
63	A	72	THR	0	0.017	0.002	20.690	-0.016	-0.016	0.000	0.000	0.000	0.000
64	A	73	ILE	0	-0.018	-0.006	18.643	0.017	0.017	0.000	0.000	0.000	0.000
65	A	74	SER	0	-0.022	-0.034	18.997	-0.030	-0.030	0.000	0.000	0.000	0.000
66	A	75	GLY	0	0.044	0.017	20.649	0.018	0.018	0.000	0.000	0.000	0.000
67	A	76	GLU	-1	-0.837	-0.892	20.749	-0.288	-0.288	0.000	0.000	0.000	0.000
68	A	77	VAL	0	-0.020	0.005	17.044	0.011	0.011	0.000	0.000	0.000	0.000
69	A	78	VAL	0	0.045	0.020	20.142	-0.004	-0.004	0.000	0.000	0.000	0.000
70	A	79	ASN	0	-0.040	-0.027	21.197	0.001	0.001	0.000	0.000	0.000	0.000
71	A	80	GLU	-1	-0.802	-0.915	22.690	-0.185	-0.185	0.000	0.000	0.000	0.000
72	A	81	ARG	1	0.880	0.948	24.596	0.200	0.200	0.000	0.000	0.000	0.000
73	A	82	LYS	1	0.959	0.989	24.925	0.160	0.160	0.000	0.000	0.000	0.000
74	A	83	ASN	0	-0.064	-0.041	26.854	0.001	0.001	0.000	0.000	0.000	0.000
75	A	84	GLU	-1	-0.791	-0.869	30.017	-0.084	-0.084	0.000	0.000	0.000	0.000
76	A	85	SER	0	-0.074	-0.038	29.781	-0.009	-0.009	0.000	0.000	0.000	0.000
77	A	86	THR	0	-0.105	-0.080	30.821	0.005	0.005	0.000	0.000	0.000	0.000
78	A	87	GLU	-1	-0.951	-0.959	31.820	-0.112	-0.112	0.000	0.000	0.000	0.000
79	A	88	GLY	0	0.030	0.034	31.037	-0.006	-0.006	0.000	0.000	0.000	0.000
80	A	89	ASN	0	-0.015	-0.025	27.156	0.000	0.000	0.000	0.000	0.000	0.000
81	A	90	GLN	0	0.034	0.032	21.029	-0.010	-0.010	0.000	0.000	0.000	0.000
82	A	91	ARG	1	0.933	0.960	23.743	0.120	0.120	0.000	0.000	0.000	0.000
83	A	92	TRP	0	-0.049	-0.045	15.858	0.031	0.031	0.000	0.000	0.000	0.000
84	A	93	SER	0	-0.025	-0.038	17.091	-0.004	-0.004	0.000	0.000	0.000	0.000
85	A	94	GLU	-1	-0.848	-0.895	12.948	-0.450	-0.450	0.000	0.000	0.000	0.000
86	A	95	ARG	1	0.892	0.958	12.736	0.303	0.303	0.000	0.000	0.000	0.000
87	A	96	ARG	1	0.896	0.953	5.975	1.687	1.687	0.000	0.000	0.000	0.000
88	A	97	PHE	0	-0.026	-0.027	14.105	0.001	0.001	0.000	0.000	0.000	0.000
89	A	98	GLY	0	0.026	0.022	16.503	-0.030	-0.030	0.000	0.000	0.000	0.000
90	A	99	SER	0	-0.001	-0.032	18.887	-0.011	-0.011	0.000	0.000	0.000	0.000
91	A	100	PHE	0	-0.030	-0.016	15.719	-0.057	-0.057	0.000	0.000	0.000	0.000
92	A	101	SER	0	0.031	-0.001	16.915	0.049	0.049	0.000	0.000	0.000	0.000
93	A	102	ARG	1	0.818	0.925	9.589	0.853	0.853	0.000	0.000	0.000	0.000
94	A	103	THR	0	0.007	0.010	16.596	0.035	0.035	0.000	0.000	0.000	0.000
95	A	104	ILE	0	-0.014	-0.005	16.380	-0.022	-0.022	0.000	0.000	0.000	0.000
96	A	105	THR	0	-0.008	-0.003	18.536	0.027	0.027	0.000	0.000	0.000	0.000
97	A	106	ILE	0	-0.017	-0.015	20.828	-0.003	-0.003	0.000	0.000	0.000	0.000
98	A	107	PRO	0	-0.005	0.017	20.701	0.018	0.018	0.000	0.000	0.000	0.000
99	A	108	ALA	0	0.013	-0.007	23.370	0.010	0.010	0.000	0.000	0.000	0.000
100	A	109	LYS	1	0.939	0.978	26.921	0.067	0.067	0.000	0.000	0.000	0.000
101	A	110	ILE	0	0.015	-0.005	26.792	0.001	0.001	0.000	0.000	0.000	0.000
102	A	111	ASP	-1	-0.853	-0.901	30.269	-0.081	-0.081	0.000	0.000	0.000	0.000
103	A	112	ALA	0	0.033	-0.007	31.207	-0.006	-0.006	0.000	0.000	0.000	0.000
104	A	113	ASP	-1	-0.889	-0.933	32.258	-0.089	-0.089	0.000	0.000	0.000	0.000
105	A	114	ARG	1	0.748	0.845	33.709	0.091	0.091	0.000	0.000	0.000	0.000
106	A	115	ILE	0	-0.054	-0.001	27.363	-0.005	-0.005	0.000	0.000	0.000	0.000
107	A	116	GLU	-1	-0.939	-0.955	28.751	-0.134	-0.134	0.000	0.000	0.000	0.000
108	A	117	ALA	0	-0.004	-0.011	25.593	-0.014	-0.014	0.000	0.000	0.000	0.000
109	A	118	ASN	0	-0.031	-0.008	25.477	0.018	0.018	0.000	0.000	0.000	0.000
110	A	119	PHE	0	0.011	0.006	21.215	-0.014	-0.014	0.000	0.000	0.000	0.000
111	A	120	SER	0	-0.005	-0.007	23.834	0.017	0.017	0.000	0.000	0.000	0.000
112	A	121	ASN	0	-0.009	-0.010	22.989	-0.009	-0.009	0.000	0.000	0.000	0.000
113	A	122	GLY	0	-0.005	0.005	20.550	-0.020	-0.020	0.000	0.000	0.000	0.000
114	A	123	LEU	0	0.007	0.020	17.388	-0.045	-0.045	0.000	0.000	0.000	0.000
115	A	124	LEU	0	-0.023	-0.007	19.386	0.038	0.038	0.000	0.000	0.000	0.000
116	A	125	THR	0	0.008	-0.014	19.926	-0.021	-0.021	0.000	0.000	0.000	0.000
117	A	126	VAL	0	-0.034	-0.024	21.830	0.023	0.023	0.000	0.000	0.000	0.000
118	A	127	THR	0	-0.003	-0.004	23.344	-0.012	-0.012	0.000	0.000	0.000	0.000
119	A	128	LEU	0	0.003	-0.007	23.497	0.011	0.011	0.000	0.000	0.000	0.000
120	A	129	PRO	0	0.014	0.018	27.227	0.003	0.003	0.000	0.000	0.000	0.000
121	A	130	LYS	1	0.828	0.888	27.228	0.104	0.104	0.000	0.000	0.000	0.000
122	A	131	VAL	0	-0.046	-0.027	30.714	0.005	0.005	0.000	0.000	0.000	0.000
123	A	132	GLU	-1	-0.927	-0.957	33.023	-0.051	-0.051	0.000	0.000	0.000	0.000
124	A	133	LYS	1	0.983	0.990	32.844	0.066	0.066	0.000	0.000	0.000	0.000
125	A	134	SER	0	-0.005	-0.001	34.634	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	135	GLN	0	0.014	-0.002	32.490	-0.006	-0.006	0.000	0.000	0.000	0.000
127	A	136	THR	0	0.031	0.009	31.704	0.003	0.003	0.000	0.000	0.000	0.000
128	A	137	LYS	1	0.937	0.974	25.865	0.103	0.103	0.000	0.000	0.000	0.000
129	A	138	LYS	1	0.948	0.965	30.390	0.036	0.036	0.000	0.000	0.000	0.000
130	A	139	GLN	0	0.020	0.024	29.029	-0.003	-0.003	0.000	0.000	0.000	0.000
131	A	140	ILE	0	-0.004	-0.005	29.546	0.004	0.004	0.000	0.000	0.000	0.000
132	A	141	ALA	0	0.001	0.004	30.254	-0.002	-0.002	0.000	0.000	0.000	0.000
133	A	142	ILE	0	0.013	0.002	27.857	0.005	0.005	0.000	0.000	0.000	0.000
134	A	143	LYS	1	0.993	1.006	31.286	-0.013	-0.013	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:10:PRO)