FMO DATABASE

FMODB ID: 94G62

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1024799.45084
FMO2-HF: Nuclear repulsion	975279.658194
FMO2-HF: Total energy	-49519.792646
FMO2-MP2: Total energy	-49662.325444

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.
-58.809	-59.172	26.556	-11.51	-14.682	-0.033

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 : 0.890 / q_NPA : 0.955

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	6	ARG	1	0.836	0.877	2.756	17.078	20.263	0.279	-1.591	-1.872	-0.015
4	A	7	TYR	0	-0.007	-0.044	5.382	0.523	0.609	-0.001	-0.001	-0.083	0.000
5	A	8	GLN	0	-0.043	-0.035	2.377	-13.853	-11.169	4.349	-2.008	-5.026	-0.018
6	A	9	TYR	0	-0.073	-0.055	1.810	-15.381	-21.779	21.930	-7.903	-7.629	0.000
7	A	10	THR	0	-0.064	-0.030	4.588	5.788	5.868	-0.001	-0.007	-0.072	0.000
8	A	11	ARG	1	0.835	0.910	7.244	27.798	27.798	0.000	0.000	0.000	0.000
9	A	12	SER	0	-0.014	-0.032	7.187	-4.267	-4.267	0.000	0.000	0.000	0.000
10	A	13	PHE	0	0.042	0.001	7.305	0.066	0.066	0.000	0.000	0.000	0.000
11	A	14	ALA	0	-0.007	0.004	8.943	1.390	1.390	0.000	0.000	0.000	0.000
12	A	15	GLU	-1	-0.800	-0.878	11.355	-22.005	-22.005	0.000	0.000	0.000	0.000
13	A	16	ARG	1	0.802	0.896	5.121	42.191	42.191	0.000	0.000	0.000	0.000
14	A	17	ALA	0	0.038	0.016	11.635	1.100	1.100	0.000	0.000	0.000	0.000
15	A	18	LYS	1	0.851	0.925	13.573	16.575	16.575	0.000	0.000	0.000	0.000
16	A	19	GLU	-1	-0.773	-0.838	13.545	-20.158	-20.158	0.000	0.000	0.000	0.000
17	A	20	THR	0	-0.033	-0.048	13.128	1.694	1.694	0.000	0.000	0.000	0.000
18	A	21	GLU	-1	-0.833	-0.896	16.451	-14.343	-14.343	0.000	0.000	0.000	0.000
19	A	22	SER	0	-0.049	-0.045	19.163	1.236	1.236	0.000	0.000	0.000	0.000
20	A	23	ALA	0	-0.025	-0.008	18.651	0.780	0.780	0.000	0.000	0.000	0.000
21	A	24	ARG	1	0.892	0.938	18.704	15.675	15.675	0.000	0.000	0.000	0.000
22	A	25	LEU	0	-0.011	0.009	21.522	0.602	0.602	0.000	0.000	0.000	0.000
23	A	26	ARG	1	0.912	0.963	24.304	12.006	12.006	0.000	0.000	0.000	0.000
24	A	27	TYR	0	-0.025	-0.024	22.909	0.558	0.558	0.000	0.000	0.000	0.000
25	A	28	PRO	0	0.054	0.034	22.819	-0.570	-0.570	0.000	0.000	0.000	0.000
26	A	29	LYS	1	0.856	0.924	23.525	10.984	10.984	0.000	0.000	0.000	0.000
27	A	30	HIS	0	-0.012	-0.004	21.339	0.026	0.026	0.000	0.000	0.000	0.000
28	A	31	ILE	0	-0.007	0.004	15.680	-0.439	-0.439	0.000	0.000	0.000	0.000
29	A	32	PRO	0	-0.013	0.010	14.545	0.406	0.406	0.000	0.000	0.000	0.000
30	A	33	ILE	0	0.010	-0.001	12.686	-1.242	-1.242	0.000	0.000	0.000	0.000
31	A	34	LEU	0	-0.025	0.001	8.134	0.997	0.997	0.000	0.000	0.000	0.000
32	A	35	CYS	0	-0.036	-0.019	9.680	-1.113	-1.113	0.000	0.000	0.000	0.000
33	A	36	GLU	-1	-0.745	-0.884	6.906	-37.586	-37.586	0.000	0.000	0.000	0.000
34	A	37	PRO	0	0.031	0.016	10.392	-0.205	-0.205	0.000	0.000	0.000	0.000
35	A	38	THR	0	-0.007	-0.010	9.368	-2.141	-2.141	0.000	0.000	0.000	0.000
36	A	39	SER	0	-0.050	-0.005	9.112	-1.550	-1.550	0.000	0.000	0.000	0.000
37	A	49	VAL	0	0.008	-0.009	12.794	0.268	0.268	0.000	0.000	0.000	0.000
38	A	50	ARG	1	1.011	1.004	16.153	11.867	11.867	0.000	0.000	0.000	0.000
39	A	51	LEU	0	-0.006	0.012	15.410	0.552	0.552	0.000	0.000	0.000	0.000
40	A	52	PHE	0	0.035	0.009	16.232	-1.002	-1.002	0.000	0.000	0.000	0.000
41	A	53	SER	0	0.025	0.006	18.245	0.618	0.618	0.000	0.000	0.000	0.000
42	A	54	THR	0	0.026	0.004	19.400	-0.685	-0.685	0.000	0.000	0.000	0.000
43	A	55	ARG	1	0.993	0.996	21.037	11.650	11.650	0.000	0.000	0.000	0.000
44	A	56	GLN	0	-0.037	-0.013	14.650	-1.135	-1.135	0.000	0.000	0.000	0.000
45	A	57	GLN	0	0.050	0.026	13.258	-2.089	-2.089	0.000	0.000	0.000	0.000
46	A	58	VAL	0	0.056	0.026	15.121	-0.799	-0.799	0.000	0.000	0.000	0.000
47	A	59	GLN	0	0.000	-0.012	17.353	0.316	0.316	0.000	0.000	0.000	0.000
48	A	60	ARG	1	0.974	0.993	11.124	21.122	21.122	0.000	0.000	0.000	0.000
49	A	61	GLU	-1	-0.817	-0.859	12.109	-23.737	-23.737	0.000	0.000	0.000	0.000
50	A	62	LEU	0	-0.015	-0.012	14.062	-0.222	-0.222	0.000	0.000	0.000	0.000
51	A	63	ASP	-1	-0.868	-0.911	13.730	-18.004	-18.004	0.000	0.000	0.000	0.000
52	A	64	CYS	0	-0.095	-0.021	10.327	-0.921	-0.921	0.000	0.000	0.000	0.000
53	A	65	ASN	0	0.002	0.006	13.033	2.018	2.018	0.000	0.000	0.000	0.000
54	A	66	LYS	1	0.853	0.908	12.796	19.901	19.901	0.000	0.000	0.000	0.000
55	A	67	PHE	0	-0.037	-0.030	15.272	1.423	1.423	0.000	0.000	0.000	0.000
56	A	68	LEU	0	0.022	0.011	16.806	-0.743	-0.743	0.000	0.000	0.000	0.000
57	A	69	LEU	0	0.013	0.013	18.935	0.831	0.831	0.000	0.000	0.000	0.000
58	A	70	PRO	0	0.037	0.020	20.951	-0.403	-0.403	0.000	0.000	0.000	0.000
59	A	71	GLU	-1	-0.826	-0.921	21.408	-12.680	-12.680	0.000	0.000	0.000	0.000
60	A	72	THR	0	0.004	-0.015	22.474	-0.232	-0.232	0.000	0.000	0.000	0.000
61	A	73	ALA	0	-0.005	0.022	22.418	0.304	0.304	0.000	0.000	0.000	0.000
62	A	74	THR	0	0.000	-0.040	22.670	-0.474	-0.474	0.000	0.000	0.000	0.000
63	A	75	VAL	0	-0.019	-0.015	18.238	-0.366	-0.366	0.000	0.000	0.000	0.000
64	A	76	MET	0	0.022	0.013	20.549	-0.296	-0.296	0.000	0.000	0.000	0.000
65	A	77	GLU	-1	-0.826	-0.882	23.303	-11.430	-11.430	0.000	0.000	0.000	0.000
66	A	78	PHE	0	0.001	-0.009	14.479	-0.098	-0.098	0.000	0.000	0.000	0.000
67	A	79	MET	0	-0.013	-0.002	18.957	-0.295	-0.295	0.000	0.000	0.000	0.000
68	A	80	MET	0	-0.023	-0.010	20.585	0.113	0.113	0.000	0.000	0.000	0.000
69	A	81	ALA	0	0.023	0.009	21.131	0.177	0.177	0.000	0.000	0.000	0.000
70	A	82	LEU	0	-0.036	-0.022	16.220	-0.028	-0.028	0.000	0.000	0.000	0.000
71	A	83	ARG	1	0.854	0.901	19.956	11.279	11.279	0.000	0.000	0.000	0.000
72	A	84	GLN	0	-0.037	-0.023	22.851	0.256	0.256	0.000	0.000	0.000	0.000
73	A	85	ARG	1	0.846	0.938	18.997	15.107	15.107	0.000	0.000	0.000	0.000
74	A	86	LEU	0	-0.037	-0.023	17.751	-0.129	-0.129	0.000	0.000	0.000	0.000
75	A	87	LEU	0	-0.063	-0.021	21.851	0.280	0.280	0.000	0.000	0.000	0.000
76	A	88	LEU	0	-0.005	0.015	21.348	0.129	0.129	0.000	0.000	0.000	0.000
77	A	89	GLU	-1	-0.884	-0.940	25.603	-9.686	-9.686	0.000	0.000	0.000	0.000
78	A	90	GLU	-1	-0.927	-0.965	28.167	-9.052	-9.052	0.000	0.000	0.000	0.000
79	A	91	GLY	0	-0.022	0.001	29.298	-0.006	-0.006	0.000	0.000	0.000	0.000
80	A	92	GLN	0	-0.037	-0.017	24.205	-0.260	-0.260	0.000	0.000	0.000	0.000
81	A	93	ALA	0	0.002	0.009	23.412	0.154	0.154	0.000	0.000	0.000	0.000
82	A	94	VAL	0	0.003	0.006	17.916	-0.423	-0.423	0.000	0.000	0.000	0.000
83	A	95	PHE	0	0.006	0.011	15.721	0.322	0.322	0.000	0.000	0.000	0.000
84	A	96	VAL	0	-0.005	-0.022	14.409	-0.848	-0.848	0.000	0.000	0.000	0.000
85	A	97	PHE	0	0.009	-0.009	11.010	0.677	0.677	0.000	0.000	0.000	0.000
86	A	98	ILE	0	0.000	-0.015	10.145	-1.258	-1.258	0.000	0.000	0.000	0.000
87	A	99	GLY	0	0.014	0.009	8.045	0.843	0.843	0.000	0.000	0.000	0.000
88	A	100	ASN	0	-0.038	-0.030	8.810	-0.269	-0.269	0.000	0.000	0.000	0.000
89	A	101	GLU	-1	-0.909	-0.934	10.960	-16.461	-16.461	0.000	0.000	0.000	0.000
90	A	102	LEU	0	-0.007	0.005	13.965	-0.770	-0.770	0.000	0.000	0.000	0.000
91	A	103	PRO	0	-0.059	-0.011	15.237	0.651	0.651	0.000	0.000	0.000	0.000
92	A	104	PRO	0	0.068	0.013	17.968	0.461	0.461	0.000	0.000	0.000	0.000
93	A	105	ASN	0	0.071	0.004	21.330	-0.590	-0.590	0.000	0.000	0.000	0.000
94	A	106	SER	0	-0.022	-0.001	23.177	-0.124	-0.124	0.000	0.000	0.000	0.000
95	A	107	ALA	0	-0.001	0.016	20.590	0.201	0.201	0.000	0.000	0.000	0.000
96	A	108	CYS	0	0.029	0.022	22.081	0.063	0.063	0.000	0.000	0.000	0.000
97	A	109	LEU	0	0.004	-0.006	17.399	-0.721	-0.721	0.000	0.000	0.000	0.000
98	A	110	GLY	0	0.018	-0.006	17.897	-0.891	-0.891	0.000	0.000	0.000	0.000
99	A	111	ASP	-1	-0.895	-0.936	19.520	-13.391	-13.391	0.000	0.000	0.000	0.000
100	A	112	ILE	0	-0.069	-0.041	14.265	-0.597	-0.597	0.000	0.000	0.000	0.000
101	A	113	TYR	0	-0.078	-0.055	13.792	-0.580	-0.580	0.000	0.000	0.000	0.000
102	A	114	ALA	0	-0.034	-0.017	14.978	-1.003	-1.003	0.000	0.000	0.000	0.000
103	A	115	ARG	1	0.948	0.973	14.420	18.010	18.010	0.000	0.000	0.000	0.000
104	A	116	ALA	0	-0.041	-0.015	11.202	-0.765	-0.765	0.000	0.000	0.000	0.000
105	A	117	LYS	1	0.905	0.977	10.189	16.751	16.751	0.000	0.000	0.000	0.000
106	A	118	ASP	-1	-0.808	-0.902	6.087	-44.814	-44.814	0.000	0.000	0.000	0.000
107	A	119	PRO	0	-0.009	-0.016	7.532	2.809	2.809	0.000	0.000	0.000	0.000
108	A	120	ASP	-1	-0.771	-0.853	8.370	-32.730	-32.730	0.000	0.000	0.000	0.000
109	A	121	GLY	0	0.026	0.029	10.807	1.977	1.977	0.000	0.000	0.000	0.000
110	A	122	PHE	0	0.001	0.003	9.531	2.210	2.210	0.000	0.000	0.000	0.000
111	A	123	LEU	0	-0.001	-0.001	10.090	-1.361	-1.361	0.000	0.000	0.000	0.000
112	A	124	TYR	0	-0.059	-0.060	6.014	-0.662	-0.662	0.000	0.000	0.000	0.000
113	A	125	VAL	0	0.006	0.002	7.989	0.866	0.866	0.000	0.000	0.000	0.000
114	A	126	SER	0	-0.044	-0.012	8.086	-1.871	-1.871	0.000	0.000	0.000	0.000
115	A	127	TYR	0	-0.018	-0.030	10.152	1.887	1.887	0.000	0.000	0.000	0.000
116	A	128	GLY	0	0.016	0.016	13.361	-0.805	-0.805	0.000	0.000	0.000	0.000
117	A	129	VAL	0	0.005	-0.011	15.560	0.459	0.459	0.000	0.000	0.000	0.000
118	A	130	GLU	-1	-0.896	-0.944	19.138	-13.235	-13.235	0.000	0.000	0.000	0.000
119	A	131	ASN	0	-0.036	-0.019	21.749	0.507	0.507	0.000	0.000	0.000	0.000
120	A	132	THR	0	-0.001	0.010	25.176	0.453	0.453	0.000	0.000	0.000	0.000

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