FMO DATABASE

FMODB ID: LZJ29

Calculation Name: 3W1Y-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3W1Y

Chain ID: A

ChEMBL ID:

UniProt ID: P0A7R5

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	OptH
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	120
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1024494.295121
FMO2-HF: Nuclear repulsion	974975.100037
FMO2-HF: Total energy	-49519.195084
FMO2-MP2: Total energy	-49661.748728

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:4:HIS)

Summations of interaction energy for fragment #1(A:4:HIS)

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.
-51.062	-48.811	19.307	-8.568	-12.988	-0.037

Interaction energy analysis for fragmet #1(A:4:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.885 / q_NPA : 0.942

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

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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	6	ARG	1	0.900	0.928	3.032	18.991	21.811	0.068	-1.357	-1.531	-0.010
4	A	7	TYR	0	-0.006	-0.027	5.768	0.987	0.987	0.000	0.000	0.000	0.000
5	A	8	GLN	0	-0.006	-0.017	1.991	-15.619	-13.745	6.382	-2.718	-5.538	-0.029
6	A	9	TYR	0	-0.083	-0.045	2.036	-10.181	-12.681	12.858	-4.492	-5.865	0.002
7	A	10	THR	0	-0.064	-0.029	5.103	5.232	5.289	-0.001	-0.001	-0.054	0.000
8	A	11	ARG	1	0.845	0.929	7.319	27.305	27.305	0.000	0.000	0.000	0.000
9	A	12	SER	0	-0.007	-0.003	7.394	-3.896	-3.896	0.000	0.000	0.000	0.000
10	A	13	PHE	0	0.044	0.002	7.475	-0.080	-0.080	0.000	0.000	0.000	0.000
11	A	14	ALA	0	-0.013	0.002	8.834	1.331	1.331	0.000	0.000	0.000	0.000
12	A	15	GLU	-1	-0.818	-0.922	11.513	-21.188	-21.188	0.000	0.000	0.000	0.000
13	A	16	ARG	1	0.806	0.889	5.237	40.737	40.737	0.000	0.000	0.000	0.000
14	A	17	ALA	0	0.039	0.020	11.444	1.026	1.026	0.000	0.000	0.000	0.000
15	A	18	LYS	1	0.919	0.976	13.466	16.433	16.433	0.000	0.000	0.000	0.000
16	A	19	GLU	-1	-0.803	-0.896	13.462	-19.462	-19.462	0.000	0.000	0.000	0.000
17	A	20	THR	0	-0.029	-0.048	13.096	1.642	1.642	0.000	0.000	0.000	0.000
18	A	21	GLU	-1	-0.887	-0.934	16.053	-14.355	-14.355	0.000	0.000	0.000	0.000
19	A	22	SER	0	-0.081	-0.055	18.823	1.246	1.246	0.000	0.000	0.000	0.000
20	A	23	ALA	0	-0.017	-0.003	18.555	0.752	0.752	0.000	0.000	0.000	0.000
21	A	24	ARG	1	0.898	0.933	18.522	15.694	15.694	0.000	0.000	0.000	0.000
22	A	25	LEU	0	-0.004	0.013	21.439	0.581	0.581	0.000	0.000	0.000	0.000
23	A	26	ARG	1	0.910	0.962	24.075	11.844	11.844	0.000	0.000	0.000	0.000
24	A	27	TYR	0	-0.031	-0.028	22.786	0.551	0.551	0.000	0.000	0.000	0.000
25	A	28	PRO	0	0.047	0.030	22.755	-0.565	-0.565	0.000	0.000	0.000	0.000
26	A	29	LYS	1	0.943	0.978	23.493	10.314	10.314	0.000	0.000	0.000	0.000
27	A	30	HIS	0	0.007	0.007	21.305	0.038	0.038	0.000	0.000	0.000	0.000
28	A	31	ILE	0	-0.004	0.008	15.693	-0.471	-0.471	0.000	0.000	0.000	0.000
29	A	32	PRO	0	-0.017	0.003	14.556	0.369	0.369	0.000	0.000	0.000	0.000
30	A	33	ILE	0	0.004	0.002	12.648	-1.198	-1.198	0.000	0.000	0.000	0.000
31	A	34	LEU	0	-0.021	0.000	7.986	1.058	1.058	0.000	0.000	0.000	0.000
32	A	35	CYS	0	-0.026	-0.013	9.620	-1.056	-1.056	0.000	0.000	0.000	0.000
33	A	36	GLU	-1	-0.759	-0.889	7.041	-37.151	-37.151	0.000	0.000	0.000	0.000
34	A	37	PRO	0	0.030	0.017	10.319	-0.218	-0.218	0.000	0.000	0.000	0.000
35	A	38	THR	0	-0.011	-0.010	9.376	-2.380	-2.380	0.000	0.000	0.000	0.000
36	A	39	SER	0	-0.050	-0.007	9.089	-1.802	-1.802	0.000	0.000	0.000	0.000
37	A	49	VAL	0	0.020	-0.004	13.065	0.233	0.233	0.000	0.000	0.000	0.000
38	A	50	ARG	1	1.008	1.001	16.132	12.040	12.040	0.000	0.000	0.000	0.000
39	A	51	LEU	0	-0.021	0.008	15.188	0.553	0.553	0.000	0.000	0.000	0.000
40	A	52	PHE	0	0.022	-0.001	16.193	-0.977	-0.977	0.000	0.000	0.000	0.000
41	A	53	SER	0	0.027	0.007	18.196	0.613	0.613	0.000	0.000	0.000	0.000
42	A	54	THR	0	0.024	0.004	19.332	-0.672	-0.672	0.000	0.000	0.000	0.000
43	A	55	ARG	1	0.998	0.999	20.963	11.641	11.641	0.000	0.000	0.000	0.000
44	A	56	GLN	0	-0.032	-0.015	14.725	-0.879	-0.879	0.000	0.000	0.000	0.000
45	A	57	GLN	0	0.010	0.006	14.533	-1.986	-1.986	0.000	0.000	0.000	0.000
46	A	58	VAL	0	0.060	0.032	15.481	-0.781	-0.781	0.000	0.000	0.000	0.000
47	A	59	GLN	0	0.006	-0.015	17.668	0.471	0.471	0.000	0.000	0.000	0.000
48	A	60	ARG	1	0.970	0.993	11.561	21.074	21.074	0.000	0.000	0.000	0.000
49	A	61	GLU	-1	-0.826	-0.890	12.033	-23.476	-23.476	0.000	0.000	0.000	0.000
50	A	62	LEU	0	-0.017	-0.014	14.311	-0.203	-0.203	0.000	0.000	0.000	0.000
51	A	63	ASP	-1	-0.872	-0.906	14.021	-17.729	-17.729	0.000	0.000	0.000	0.000
52	A	64	CYS	0	-0.104	-0.027	10.638	-0.817	-0.817	0.000	0.000	0.000	0.000
53	A	65	ASN	0	0.007	0.009	13.183	1.972	1.972	0.000	0.000	0.000	0.000
54	A	66	LYS	1	0.874	0.932	12.999	19.239	19.239	0.000	0.000	0.000	0.000
55	A	67	PHE	0	-0.039	-0.033	15.155	1.431	1.431	0.000	0.000	0.000	0.000
56	A	68	LEU	0	0.025	0.012	16.722	-0.743	-0.743	0.000	0.000	0.000	0.000
57	A	69	LEU	0	0.006	0.009	19.082	0.803	0.803	0.000	0.000	0.000	0.000
58	A	70	PRO	0	0.034	0.020	20.920	-0.399	-0.399	0.000	0.000	0.000	0.000
59	A	71	GLU	-1	-0.902	-0.968	21.420	-12.729	-12.729	0.000	0.000	0.000	0.000
60	A	72	THR	0	-0.016	-0.023	22.482	-0.218	-0.218	0.000	0.000	0.000	0.000
61	A	73	ALA	0	-0.003	0.028	22.322	0.300	0.300	0.000	0.000	0.000	0.000
62	A	74	THR	0	0.018	-0.010	22.704	-0.459	-0.459	0.000	0.000	0.000	0.000
63	A	75	VAL	0	-0.011	-0.010	18.259	-0.337	-0.337	0.000	0.000	0.000	0.000
64	A	76	MET	0	0.018	0.008	20.605	-0.333	-0.333	0.000	0.000	0.000	0.000
65	A	77	GLU	-1	-0.845	-0.918	23.350	-11.237	-11.237	0.000	0.000	0.000	0.000
66	A	78	PHE	0	-0.008	-0.012	14.549	-0.088	-0.088	0.000	0.000	0.000	0.000
67	A	79	MET	0	-0.010	-0.007	19.091	-0.236	-0.236	0.000	0.000	0.000	0.000
68	A	80	MET	0	-0.029	-0.010	20.600	0.093	0.093	0.000	0.000	0.000	0.000
69	A	81	ALA	0	0.028	0.011	21.112	0.178	0.178	0.000	0.000	0.000	0.000
70	A	82	LEU	0	-0.033	-0.024	16.082	-0.013	-0.013	0.000	0.000	0.000	0.000
71	A	83	ARG	1	0.898	0.951	19.920	11.300	11.300	0.000	0.000	0.000	0.000
72	A	84	GLN	0	-0.047	-0.023	22.825	0.338	0.338	0.000	0.000	0.000	0.000
73	A	85	ARG	1	0.843	0.935	18.373	15.199	15.199	0.000	0.000	0.000	0.000
74	A	86	LEU	0	-0.037	-0.020	17.704	-0.122	-0.122	0.000	0.000	0.000	0.000
75	A	87	LEU	0	-0.062	-0.021	21.782	0.274	0.274	0.000	0.000	0.000	0.000
76	A	88	LEU	0	-0.029	0.000	21.499	0.132	0.132	0.000	0.000	0.000	0.000
77	A	89	GLU	-1	-0.895	-0.961	25.599	-9.603	-9.603	0.000	0.000	0.000	0.000
78	A	90	GLU	-1	-0.928	-0.985	28.165	-8.986	-8.986	0.000	0.000	0.000	0.000
79	A	91	GLY	0	-0.034	0.000	29.300	-0.010	-0.010	0.000	0.000	0.000	0.000
80	A	92	GLN	0	-0.048	-0.019	24.151	-0.181	-0.181	0.000	0.000	0.000	0.000
81	A	93	ALA	0	0.003	0.005	23.342	0.157	0.157	0.000	0.000	0.000	0.000
82	A	94	VAL	0	0.002	0.008	17.876	-0.402	-0.402	0.000	0.000	0.000	0.000
83	A	95	PHE	0	-0.003	0.004	15.790	0.268	0.268	0.000	0.000	0.000	0.000
84	A	96	VAL	0	0.000	-0.018	14.370	-0.820	-0.820	0.000	0.000	0.000	0.000
85	A	97	PHE	0	0.003	-0.011	10.988	0.743	0.743	0.000	0.000	0.000	0.000
86	A	98	ILE	0	-0.002	-0.015	10.265	-1.174	-1.174	0.000	0.000	0.000	0.000
87	A	99	GLY	0	0.007	0.005	7.978	0.815	0.815	0.000	0.000	0.000	0.000
88	A	100	ASN	0	-0.020	-0.021	8.990	-0.306	-0.306	0.000	0.000	0.000	0.000
89	A	101	GLU	-1	-0.916	-0.940	10.939	-16.765	-16.765	0.000	0.000	0.000	0.000
90	A	102	LEU	0	-0.006	0.004	13.935	-0.738	-0.738	0.000	0.000	0.000	0.000
91	A	103	PRO	0	-0.062	-0.013	15.293	0.673	0.673	0.000	0.000	0.000	0.000
92	A	104	PRO	0	0.064	0.016	18.094	0.459	0.459	0.000	0.000	0.000	0.000
93	A	105	ASN	0	0.088	0.013	21.431	-0.622	-0.622	0.000	0.000	0.000	0.000
94	A	106	SER	0	-0.045	-0.009	23.268	-0.114	-0.114	0.000	0.000	0.000	0.000
95	A	107	ALA	0	0.010	0.018	20.677	0.203	0.203	0.000	0.000	0.000	0.000
96	A	108	CYS	0	0.046	0.031	22.153	0.064	0.064	0.000	0.000	0.000	0.000
97	A	109	LEU	0	0.002	-0.011	17.451	-0.699	-0.699	0.000	0.000	0.000	0.000
98	A	110	GLY	0	0.020	-0.004	17.942	-0.882	-0.882	0.000	0.000	0.000	0.000
99	A	111	ASP	-1	-0.894	-0.936	19.575	-13.266	-13.266	0.000	0.000	0.000	0.000
100	A	112	ILE	0	-0.078	-0.041	14.364	-0.587	-0.587	0.000	0.000	0.000	0.000
101	A	113	TYR	0	-0.076	-0.053	13.965	-0.640	-0.640	0.000	0.000	0.000	0.000
102	A	114	ALA	0	-0.030	-0.014	15.036	-0.966	-0.966	0.000	0.000	0.000	0.000
103	A	115	ARG	1	0.949	0.973	14.507	17.949	17.949	0.000	0.000	0.000	0.000
104	A	116	ALA	0	-0.050	-0.017	11.228	-0.740	-0.740	0.000	0.000	0.000	0.000
105	A	117	LYS	1	0.903	0.975	10.272	16.562	16.562	0.000	0.000	0.000	0.000
106	A	118	ASP	-1	-0.820	-0.911	6.160	-42.398	-42.398	0.000	0.000	0.000	0.000
107	A	119	PRO	0	-0.014	-0.017	8.327	2.782	2.782	0.000	0.000	0.000	0.000
108	A	120	ASP	-1	-0.781	-0.858	7.823	-32.463	-32.463	0.000	0.000	0.000	0.000
109	A	121	GLY	0	0.019	0.026	10.860	1.885	1.885	0.000	0.000	0.000	0.000
110	A	122	PHE	0	0.006	0.004	9.348	2.122	2.122	0.000	0.000	0.000	0.000
111	A	123	LEU	0	0.008	0.001	10.065	-1.248	-1.248	0.000	0.000	0.000	0.000
112	A	124	TYR	0	-0.064	-0.052	6.010	-0.443	-0.443	0.000	0.000	0.000	0.000
113	A	125	VAL	0	0.013	0.004	7.983	0.851	0.851	0.000	0.000	0.000	0.000
114	A	126	SER	0	-0.007	0.012	7.562	-1.514	-1.514	0.000	0.000	0.000	0.000
115	A	127	TYR	0	-0.031	-0.030	10.143	1.973	1.973	0.000	0.000	0.000	0.000
116	A	128	GLY	0	0.015	0.016	13.359	-0.824	-0.824	0.000	0.000	0.000	0.000
117	A	129	VAL	0	0.003	-0.010	15.560	0.484	0.484	0.000	0.000	0.000	0.000
118	A	130	GLU	-1	-0.905	-0.954	19.140	-13.626	-13.626	0.000	0.000	0.000	0.000
119	A	131	ASN	0	-0.014	-0.004	21.754	0.566	0.566	0.000	0.000	0.000	0.000
120	A	132	THR	0	0.006	0.015	25.183	0.440	0.440	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:HIS)