FMO DATABASE

FMODB ID: 852ZY

Calculation Name: 3W1Z-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3W1Z

Chain ID: B

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:

Apendix: None

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	143
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1133346.813749
FMO2-HF: Nuclear repulsion	1078152.146167
FMO2-HF: Total energy	-55194.667582
FMO2-MP2: Total energy	-55358.592294

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(B:1:MET)

Summations of interaction energy for fragment #1(B: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.
-3.011	0.974	1.313	-1.564	-3.733	0

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / q_NPA : 0.001

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].
3	B	3	LEU	0	0.033	0.009	2.317	-2.725	0.576	1.314	-1.422	-3.192
4	B	4	GLN	0	0.010	0.009	3.711	-0.459	0.070	0.000	-0.123	-0.406
5	B	5	PRO	0	-0.027	-0.018	5.239	0.281	0.436	-0.001	-0.019	-0.135
6	B	6	PHE	0	-0.046	-0.007	7.098	0.210	0.210	0.000	0.000	0.000
7	B	7	PHE	0	-0.005	0.003	7.178	0.150	0.150	0.000	0.000	0.000
8	B	8	GLY	0	0.007	-0.008	10.335	-0.122	-0.122	0.000	0.000	0.000
9	B	9	PHE	0	-0.011	0.002	11.062	-0.036	-0.036	0.000	0.000	0.000
10	B	10	PRO	0	0.026	0.016	10.920	0.075	0.075	0.000	0.000	0.000
11	B	11	PRO	0	0.007	-0.002	13.783	-0.053	-0.053	0.000	0.000	0.000
12	B	12	THR	0	0.076	0.035	13.632	-0.027	-0.027	0.000	0.000	0.000
13	B	13	VAL	0	-0.014	-0.002	9.776	-0.059	-0.059	0.000	0.000	0.000
14	B	14	ASN	0	0.000	-0.008	12.622	-0.030	-0.030	0.000	0.000	0.000
15	B	15	ASP	-1	-0.880	-0.936	15.883	-0.399	-0.399	0.000	0.000	0.000
16	B	16	LEU	0	-0.016	0.001	11.092	0.016	0.016	0.000	0.000	0.000
17	B	17	PHE	0	-0.013	-0.023	11.091	-0.003	-0.003	0.000	0.000	0.000
18	B	18	SER	0	0.001	0.008	15.521	0.057	0.057	0.000	0.000	0.000
19	B	19	ASP	-1	-0.815	-0.907	17.747	-0.356	-0.356	0.000	0.000	0.000
20	B	20	PHE	0	-0.087	-0.033	14.691	0.023	0.023	0.000	0.000	0.000
21	B	21	VAL	0	-0.008	-0.011	17.366	0.036	0.036	0.000	0.000	0.000
22	B	22	SER	0	-0.053	-0.015	20.023	0.051	0.051	0.000	0.000	0.000
23	B	23	TYR	0	0.096	0.030	21.232	0.038	0.038	0.000	0.000	0.000
24	B	24	SER	0	-0.071	-0.030	19.048	0.024	0.024	0.000	0.000	0.000
25	B	25	PRO	0	0.054	0.025	21.191	0.006	0.006	0.000	0.000	0.000
26	B	26	ARG	1	0.941	0.948	16.968	0.384	0.384	0.000	0.000	0.000
27	B	27	LEU	0	-0.032	0.002	18.278	-0.004	-0.004	0.000	0.000	0.000
28	B	28	ASN	0	-0.038	-0.028	21.956	0.021	0.021	0.000	0.000	0.000
29	B	29	ASN	0	-0.019	-0.010	25.697	0.010	0.010	0.000	0.000	0.000
30	B	30	GLN	0	-0.013	0.007	25.207	0.003	0.003	0.000	0.000	0.000
31	B	31	ILE	0	0.030	0.038	27.539	0.001	0.001	0.000	0.000	0.000
32	B	32	PRO	0	-0.030	-0.025	26.954	0.005	0.005	0.000	0.000	0.000
33	B	33	GLY	0	-0.037	-0.025	28.944	-0.002	-0.002	0.000	0.000	0.000
34	B	34	GLU	-1	-0.818	-0.887	31.412	-0.101	-0.101	0.000	0.000	0.000
35	B	35	LEU	0	-0.053	-0.022	31.099	-0.009	-0.009	0.000	0.000	0.000
36	B	36	SER	0	0.006	-0.012	27.706	-0.004	-0.004	0.000	0.000	0.000
37	B	37	PRO	0	-0.021	0.002	28.780	-0.007	-0.007	0.000	0.000	0.000
38	B	38	SER	0	-0.022	-0.044	27.451	-0.015	-0.015	0.000	0.000	0.000
39	B	39	ILE	0	-0.063	-0.035	25.475	0.009	0.009	0.000	0.000	0.000
40	B	40	ASP	-1	-0.853	-0.900	25.454	-0.239	-0.239	0.000	0.000	0.000
41	B	41	VAL	0	-0.044	-0.029	24.721	0.012	0.012	0.000	0.000	0.000
42	B	42	HIS	0	-0.028	-0.006	25.405	-0.019	-0.019	0.000	0.000	0.000
43	B	43	GLU	-1	-0.821	-0.899	25.902	-0.223	-0.223	0.000	0.000	0.000
44	B	44	GLY	0	0.022	0.037	27.849	-0.005	-0.005	0.000	0.000	0.000
45	B	45	LYS	1	0.906	0.934	29.174	0.165	0.165	0.000	0.000	0.000
46	B	46	ASP	-1	-0.902	-0.956	31.120	-0.145	-0.145	0.000	0.000	0.000
47	B	47	THR	0	-0.008	-0.011	33.039	0.004	0.004	0.000	0.000	0.000
48	B	48	VAL	0	0.015	0.012	28.288	-0.009	-0.009	0.000	0.000	0.000
49	B	49	SER	0	-0.025	-0.020	30.489	0.010	0.010	0.000	0.000	0.000
50	B	50	VAL	0	-0.001	-0.006	28.887	-0.015	-0.015	0.000	0.000	0.000
51	B	51	ASP	-1	-0.824	-0.879	30.058	-0.140	-0.140	0.000	0.000	0.000
52	B	52	VAL	0	-0.006	-0.014	30.388	-0.010	-0.010	0.000	0.000	0.000
53	B	53	GLU	-1	-0.878	-0.917	30.795	-0.134	-0.134	0.000	0.000	0.000
54	B	54	LEU	0	-0.026	-0.023	33.498	-0.001	-0.001	0.000	0.000	0.000
55	B	55	PRO	0	0.004	0.002	35.763	0.007	0.007	0.000	0.000	0.000
56	B	56	GLY	0	-0.041	-0.027	38.709	0.001	0.001	0.000	0.000	0.000
57	B	57	VAL	0	-0.010	0.004	38.956	0.002	0.002	0.000	0.000	0.000
58	B	58	LYS	1	0.790	0.860	42.203	0.068	0.068	0.000	0.000	0.000
59	B	59	LYS	1	0.948	0.964	44.151	0.073	0.073	0.000	0.000	0.000
60	B	60	GLU	-1	-0.833	-0.907	44.971	-0.070	-0.070	0.000	0.000	0.000
61	B	61	ASP	-1	-0.857	-0.893	43.440	-0.073	-0.073	0.000	0.000	0.000
62	B	62	VAL	0	-0.024	-0.017	38.643	-0.004	-0.004	0.000	0.000	0.000
63	B	63	GLN	0	-0.011	0.007	39.251	0.001	0.001	0.000	0.000	0.000
64	B	64	VAL	0	0.025	-0.003	35.996	-0.006	-0.006	0.000	0.000	0.000
65	B	65	HIS	0	-0.052	-0.021	36.866	0.002	0.002	0.000	0.000	0.000
66	B	66	TYR	0	0.023	-0.006	32.695	-0.011	-0.011	0.000	0.000	0.000
67	B	67	ASP	-1	-0.847	-0.899	35.021	-0.109	-0.109	0.000	0.000	0.000
68	B	68	SER	0	-0.078	-0.059	33.998	-0.012	-0.012	0.000	0.000	0.000
69	B	69	GLY	0	0.019	0.019	30.829	-0.007	-0.007	0.000	0.000	0.000
70	B	70	LYS	1	0.816	0.895	26.416	0.202	0.202	0.000	0.000	0.000
71	B	71	LEU	0	0.019	0.012	30.474	0.013	0.013	0.000	0.000	0.000
72	B	72	THR	0	0.010	0.003	31.050	-0.014	-0.014	0.000	0.000	0.000
73	B	73	ILE	0	0.005	0.017	31.794	0.008	0.008	0.000	0.000	0.000
74	B	74	SER	0	-0.017	-0.013	34.166	-0.004	-0.004	0.000	0.000	0.000
75	B	75	GLY	0	0.061	0.019	36.803	0.004	0.004	0.000	0.000	0.000
76	B	76	GLU	-1	-0.948	-0.972	39.244	-0.076	-0.076	0.000	0.000	0.000
77	B	77	VAL	0	-0.013	0.007	37.025	0.001	0.001	0.000	0.000	0.000
78	B	78	VAL	0	0.075	0.027	40.346	0.002	0.002	0.000	0.000	0.000
79	B	79	ASN	0	-0.016	-0.014	43.046	0.001	0.001	0.000	0.000	0.000
80	B	80	GLU	-1	-0.849	-0.931	44.535	-0.063	-0.063	0.000	0.000	0.000
81	B	81	ARG	1	0.841	0.889	46.655	0.054	0.054	0.000	0.000	0.000
82	B	82	LYS	1	0.931	0.974	46.029	0.051	0.051	0.000	0.000	0.000
83	B	83	ASN	0	-0.045	-0.020	47.767	0.001	0.001	0.000	0.000	0.000
84	B	84	GLU	-1	-0.701	-0.808	50.287	-0.046	-0.046	0.000	0.000	0.000
85	B	85	SER	0	-0.041	-0.040	46.430	0.001	0.001	0.000	0.000	0.000
86	B	86	THR	0	-0.069	-0.037	48.497	0.000	0.000	0.000	0.000	0.000
87	B	87	GLU	-1	-0.890	-0.938	50.210	-0.036	-0.036	0.000	0.000	0.000
88	B	88	GLY	0	0.027	0.033	50.351	0.002	0.002	0.000	0.000	0.000
89	B	89	ASN	0	-0.045	-0.031	51.152	0.002	0.002	0.000	0.000	0.000
90	B	90	GLN	0	-0.018	-0.011	42.881	-0.001	-0.001	0.000	0.000	0.000
91	B	91	ARG	1	0.846	0.910	46.199	0.039	0.039	0.000	0.000	0.000
92	B	92	TRP	0	-0.011	-0.018	37.374	0.004	0.004	0.000	0.000	0.000
93	B	93	SER	0	-0.017	-0.010	40.022	-0.002	-0.002	0.000	0.000	0.000
94	B	94	GLU	-1	-0.844	-0.890	35.888	-0.076	-0.076	0.000	0.000	0.000
95	B	95	ARG	1	0.880	0.943	35.769	0.071	0.071	0.000	0.000	0.000
96	B	96	ARG	1	0.831	0.903	33.553	0.086	0.086	0.000	0.000	0.000
97	B	97	PHE	0	-0.004	-0.011	36.781	-0.001	-0.001	0.000	0.000	0.000
98	B	98	GLY	0	0.029	0.021	38.052	0.000	0.000	0.000	0.000	0.000
99	B	99	SER	0	0.013	-0.019	37.746	0.000	0.000	0.000	0.000	0.000
100	B	100	PHE	0	-0.025	-0.011	34.339	-0.004	-0.004	0.000	0.000	0.000
101	B	101	SER	0	0.035	0.009	33.324	0.002	0.002	0.000	0.000	0.000
102	B	102	ARG	1	0.886	0.953	24.437	0.213	0.213	0.000	0.000	0.000
103	B	103	THR	0	-0.007	-0.009	28.877	0.006	0.006	0.000	0.000	0.000
104	B	104	ILE	0	-0.033	-0.010	25.675	-0.014	-0.014	0.000	0.000	0.000
105	B	105	THR	0	-0.005	0.005	24.658	0.023	0.023	0.000	0.000	0.000
106	B	106	ILE	0	0.011	0.011	26.020	-0.012	-0.012	0.000	0.000	0.000
107	B	107	PRO	0	0.010	0.020	23.380	0.013	0.013	0.000	0.000	0.000
108	B	108	ALA	0	-0.008	-0.010	25.855	0.001	0.001	0.000	0.000	0.000
109	B	109	LYS	1	0.849	0.934	29.105	0.179	0.179	0.000	0.000	0.000
110	B	110	ILE	0	0.041	0.020	32.477	0.000	0.000	0.000	0.000	0.000
111	B	111	ASP	-1	-0.837	-0.897	35.082	-0.097	-0.097	0.000	0.000	0.000
112	B	112	ALA	0	0.048	0.007	38.355	0.000	0.000	0.000	0.000	0.000
113	B	113	ASP	-1	-0.930	-0.958	39.224	-0.091	-0.091	0.000	0.000	0.000
114	B	114	ARG	1	0.781	0.867	41.002	0.097	0.097	0.000	0.000	0.000
115	B	115	ILE	0	-0.024	0.008	36.252	-0.004	-0.004	0.000	0.000	0.000
116	B	116	GLU	-1	-0.964	-0.969	38.878	-0.093	-0.093	0.000	0.000	0.000
117	B	117	ALA	0	0.022	0.001	38.511	-0.007	-0.007	0.000	0.000	0.000
118	B	118	ASN	0	-0.074	-0.031	39.343	0.005	0.005	0.000	0.000	0.000
119	B	119	PHE	0	-0.001	0.000	39.098	-0.004	-0.004	0.000	0.000	0.000
120	B	120	SER	0	-0.021	-0.015	40.640	0.006	0.006	0.000	0.000	0.000
121	B	121	ASN	0	-0.028	-0.025	40.394	-0.001	-0.001	0.000	0.000	0.000
122	B	122	GLY	0	0.018	0.020	39.343	-0.001	-0.001	0.000	0.000	0.000
123	B	123	LEU	0	0.003	0.014	33.548	-0.005	-0.005	0.000	0.000	0.000
124	B	124	LEU	0	-0.038	-0.020	35.839	0.007	0.007	0.000	0.000	0.000
125	B	125	THR	0	0.032	0.012	34.876	-0.006	-0.006	0.000	0.000	0.000
126	B	126	VAL	0	-0.032	-0.020	34.002	0.009	0.009	0.000	0.000	0.000
127	B	127	THR	0	0.028	0.007	34.056	-0.009	-0.009	0.000	0.000	0.000
128	B	128	LEU	0	-0.004	-0.007	32.066	0.007	0.007	0.000	0.000	0.000
129	B	129	PRO	0	0.021	0.018	34.305	-0.008	-0.008	0.000	0.000	0.000
130	B	130	LYS	1	0.749	0.845	28.952	0.192	0.192	0.000	0.000	0.000
131	B	131	VAL	0	-0.024	-0.007	34.612	0.007	0.007	0.000	0.000	0.000
132	B	132	GLU	-1	-0.812	-0.895	33.829	-0.128	-0.128	0.000	0.000	0.000
133	B	133	LYS	1	0.795	0.867	34.546	0.109	0.109	0.000	0.000	0.000
134	B	134	SER	0	0.041	0.020	34.998	0.004	0.004	0.000	0.000	0.000
135	B	135	GLN	0	-0.001	-0.018	36.956	0.001	0.001	0.000	0.000	0.000
136	B	136	THR	0	0.025	0.014	37.526	0.003	0.003	0.000	0.000	0.000
137	B	137	LYS	1	0.913	0.959	35.536	0.108	0.108	0.000	0.000	0.000
138	B	138	LYS	1	0.952	0.983	38.124	0.094	0.094	0.000	0.000	0.000
139	B	139	GLN	0	0.030	0.017	39.674	-0.004	-0.004	0.000	0.000	0.000
140	B	140	ILE	0	0.027	0.008	39.233	0.004	0.004	0.000	0.000	0.000
141	B	141	ALA	0	-0.005	0.002	42.123	0.000	0.000	0.000	0.000	0.000
142	B	142	ILE	0	0.034	0.017	40.311	0.002	0.002	0.000	0.000	0.000
143	B	143	LYS	1	0.939	0.979	43.379	0.060	0.060	0.000	0.000	0.000

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