FMO DATABASE

FMODB ID: QYVZY

Calculation Name: 1WDV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1WDV

Chain ID: A

ChEMBL ID:

UniProt ID: Q9Y8U3

Base Structure: X-ray

Registration Date: 2023-06-22

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	150
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1345622.744439
FMO2-HF: Nuclear repulsion	1290318.745211
FMO2-HF: Total energy	-55303.999228
FMO2-MP2: Total energy	-55468.658548

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:3:GLU)

Summations of interaction energy for fragment #1(A:3:GLU)

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.
-80.252	-80.974	30.841	-16.035	-14.086	0.069

Interaction energy analysis for fragmet #1(A:3:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.872 / q_NPA : -0.921

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	5	VAL	0	0.005	0.001	3.290	-10.375	-7.988	0.027	-0.939	-1.475	0.006
4	A	6	GLU	-1	-0.876	-0.947	1.907	25.478	24.649	9.358	-4.557	-3.973	-0.050
5	A	7	GLU	-1	-0.956	-0.985	3.658	40.476	41.770	0.023	-0.586	-0.731	-0.002
6	A	8	TRP	0	-0.012	-0.010	5.747	-2.905	-2.905	0.000	0.000	0.000	0.000
7	A	9	ILE	0	-0.016	-0.012	7.382	-2.083	-2.083	0.000	0.000	0.000	0.000
8	A	10	LYS	1	0.964	0.987	8.456	-23.655	-23.655	0.000	0.000	0.000	0.000
9	A	11	ALA	0	-0.041	-0.016	9.851	-1.428	-1.428	0.000	0.000	0.000	0.000
10	A	12	ARG	1	0.830	0.915	11.855	-18.552	-18.552	0.000	0.000	0.000	0.000
11	A	13	GLY	0	0.004	0.014	13.325	-0.953	-0.953	0.000	0.000	0.000	0.000
12	A	14	LEU	0	-0.026	-0.001	13.268	-0.768	-0.768	0.000	0.000	0.000	0.000
13	A	15	THR	0	-0.014	-0.021	13.549	0.601	0.601	0.000	0.000	0.000	0.000
14	A	16	TRP	0	-0.051	-0.034	11.167	0.331	0.331	0.000	0.000	0.000	0.000
15	A	17	ARG	1	0.877	0.916	10.451	-14.809	-14.809	0.000	0.000	0.000	0.000
16	A	18	LEU	0	0.025	0.030	4.250	-0.431	-0.393	-0.001	-0.006	-0.032	0.000
17	A	19	LEU	0	-0.053	-0.019	8.861	-0.713	-0.713	0.000	0.000	0.000	0.000
18	A	20	ILE	0	-0.002	-0.009	7.849	1.011	1.011	0.000	0.000	0.000	0.000
19	A	21	MET	0	0.028	0.027	11.744	-1.332	-1.332	0.000	0.000	0.000	0.000
20	A	22	GLN	0	-0.001	-0.017	13.983	0.124	0.124	0.000	0.000	0.000	0.000
21	A	23	LYS	1	0.908	0.952	15.897	-13.142	-13.142	0.000	0.000	0.000	0.000
22	A	24	PRO	0	0.027	0.015	14.187	-0.242	-0.242	0.000	0.000	0.000	0.000
23	A	25	THR	0	0.011	0.020	15.808	-0.807	-0.807	0.000	0.000	0.000	0.000
24	A	26	ARG	1	0.925	0.942	17.732	-13.251	-13.251	0.000	0.000	0.000	0.000
25	A	27	THR	0	-0.026	-0.012	20.446	-0.407	-0.407	0.000	0.000	0.000	0.000
26	A	28	VAL	0	0.035	0.016	20.591	0.374	0.374	0.000	0.000	0.000	0.000
27	A	29	ALA	0	0.049	0.033	21.652	0.014	0.014	0.000	0.000	0.000	0.000
28	A	30	GLU	-1	-0.882	-0.937	21.203	13.746	13.746	0.000	0.000	0.000	0.000
29	A	31	ALA	0	0.026	0.013	17.860	0.028	0.028	0.000	0.000	0.000	0.000
30	A	32	ALA	0	-0.002	-0.009	19.547	0.009	0.009	0.000	0.000	0.000	0.000
31	A	33	ALA	0	-0.008	-0.001	22.051	-0.199	-0.199	0.000	0.000	0.000	0.000
32	A	34	LEU	0	-0.049	-0.031	19.617	-0.165	-0.165	0.000	0.000	0.000	0.000
33	A	35	LEU	0	-0.029	-0.011	16.121	0.185	0.185	0.000	0.000	0.000	0.000
34	A	36	GLY	0	-0.024	0.007	20.430	-0.205	-0.205	0.000	0.000	0.000	0.000
35	A	37	VAL	0	-0.063	-0.022	20.712	-0.307	-0.307	0.000	0.000	0.000	0.000
36	A	38	SER	0	-0.030	-0.037	23.950	-0.214	-0.214	0.000	0.000	0.000	0.000
37	A	39	GLU	-1	-0.817	-0.951	23.312	11.664	11.664	0.000	0.000	0.000	0.000
38	A	40	SER	0	-0.112	-0.047	22.859	0.377	0.377	0.000	0.000	0.000	0.000
39	A	41	GLU	-1	-0.783	-0.872	21.191	11.206	11.206	0.000	0.000	0.000	0.000
40	A	42	ILE	0	-0.011	0.013	17.516	0.646	0.646	0.000	0.000	0.000	0.000
41	A	43	VAL	0	-0.044	-0.027	16.223	-0.414	-0.414	0.000	0.000	0.000	0.000
42	A	44	LYS	1	0.804	0.898	16.596	-11.875	-11.875	0.000	0.000	0.000	0.000
43	A	45	THR	0	-0.021	-0.014	13.547	-1.150	-1.150	0.000	0.000	0.000	0.000
44	A	46	LEU	0	-0.034	-0.019	16.614	0.510	0.510	0.000	0.000	0.000	0.000
45	A	47	ILE	0	0.052	0.028	15.346	-0.190	-0.190	0.000	0.000	0.000	0.000
46	A	48	VAL	0	-0.034	-0.016	19.352	-0.652	-0.652	0.000	0.000	0.000	0.000
47	A	49	LEU	0	0.007	0.006	20.739	0.388	0.388	0.000	0.000	0.000	0.000
48	A	50	ASP	-1	-0.697	-0.831	24.273	11.296	11.296	0.000	0.000	0.000	0.000
49	A	51	ASN	0	-0.048	-0.042	27.216	0.315	0.315	0.000	0.000	0.000	0.000
50	A	52	ALA	0	-0.038	-0.026	28.475	-0.280	-0.280	0.000	0.000	0.000	0.000
51	A	53	GLY	0	0.006	0.010	25.039	0.047	0.047	0.000	0.000	0.000	0.000
52	A	54	GLY	0	-0.017	0.015	23.399	0.592	0.592	0.000	0.000	0.000	0.000
53	A	55	VAL	0	-0.005	-0.016	18.111	0.000	0.000	0.000	0.000	0.000	0.000
54	A	56	TYR	0	-0.026	-0.029	20.440	0.095	0.095	0.000	0.000	0.000	0.000
55	A	57	ALA	0	0.020	0.014	16.454	0.439	0.439	0.000	0.000	0.000	0.000
56	A	58	VAL	0	0.008	-0.013	18.466	-0.386	-0.386	0.000	0.000	0.000	0.000
57	A	59	VAL	0	0.006	0.007	16.754	0.242	0.242	0.000	0.000	0.000	0.000
58	A	60	ILE	0	-0.022	-0.002	19.474	-0.754	-0.754	0.000	0.000	0.000	0.000
59	A	61	PRO	0	0.051	0.016	20.974	0.532	0.532	0.000	0.000	0.000	0.000
60	A	62	GLY	0	0.076	0.038	22.064	-0.039	-0.039	0.000	0.000	0.000	0.000
61	A	63	ASP	-1	-0.844	-0.918	22.670	10.424	10.424	0.000	0.000	0.000	0.000
62	A	64	LYS	1	0.845	0.933	25.485	-10.513	-10.513	0.000	0.000	0.000	0.000
63	A	65	ARG	1	0.959	0.961	25.652	-10.046	-10.046	0.000	0.000	0.000	0.000
64	A	66	LEU	0	0.054	0.018	24.210	-0.138	-0.138	0.000	0.000	0.000	0.000
65	A	67	ASN	0	0.007	0.018	26.938	-0.233	-0.233	0.000	0.000	0.000	0.000
66	A	68	ILE	0	0.003	-0.024	28.264	0.102	0.102	0.000	0.000	0.000	0.000
67	A	69	ASN	0	-0.033	-0.028	30.606	0.029	0.029	0.000	0.000	0.000	0.000
68	A	70	SER	0	0.061	0.026	30.546	-0.148	-0.148	0.000	0.000	0.000	0.000
69	A	71	MET	0	-0.015	0.000	24.931	0.100	0.100	0.000	0.000	0.000	0.000
70	A	72	LYS	1	0.912	0.967	29.217	-8.804	-8.804	0.000	0.000	0.000	0.000
71	A	73	GLU	-1	-0.923	-0.952	31.909	8.554	8.554	0.000	0.000	0.000	0.000
72	A	74	LEU	0	-0.045	-0.018	26.605	-0.023	-0.023	0.000	0.000	0.000	0.000
73	A	75	ALA	0	-0.022	-0.013	28.097	0.048	0.048	0.000	0.000	0.000	0.000
74	A	76	GLY	0	0.009	0.022	29.590	-0.054	-0.054	0.000	0.000	0.000	0.000
75	A	77	LYS	1	0.832	0.907	28.012	-11.412	-11.412	0.000	0.000	0.000	0.000
76	A	78	PRO	0	-0.069	-0.038	31.664	0.097	0.097	0.000	0.000	0.000	0.000
77	A	79	VAL	0	0.040	0.018	27.544	0.272	0.272	0.000	0.000	0.000	0.000
78	A	80	ARG	1	0.775	0.863	24.728	-13.050	-13.050	0.000	0.000	0.000	0.000
79	A	81	LEU	0	0.026	0.022	23.319	0.351	0.351	0.000	0.000	0.000	0.000
80	A	82	ALA	0	-0.005	0.002	20.391	-0.349	-0.349	0.000	0.000	0.000	0.000
81	A	83	ARG	1	0.861	0.890	22.246	-12.744	-12.744	0.000	0.000	0.000	0.000
82	A	84	ALA	0	0.060	0.015	19.436	0.625	0.625	0.000	0.000	0.000	0.000
83	A	85	ASN	0	0.029	0.004	18.030	0.608	0.608	0.000	0.000	0.000	0.000
84	A	86	GLU	-1	-0.669	-0.770	18.002	14.352	14.352	0.000	0.000	0.000	0.000
85	A	87	VAL	0	-0.007	0.006	14.956	0.685	0.685	0.000	0.000	0.000	0.000
86	A	88	VAL	0	-0.007	0.009	12.510	1.165	1.165	0.000	0.000	0.000	0.000
87	A	89	GLU	-1	-0.970	-0.975	13.048	19.134	19.134	0.000	0.000	0.000	0.000
88	A	90	LEU	0	-0.011	-0.011	14.497	0.720	0.720	0.000	0.000	0.000	0.000
89	A	91	THR	0	-0.057	-0.046	11.608	1.049	1.049	0.000	0.000	0.000	0.000
90	A	92	GLY	0	0.001	0.011	9.288	2.186	2.186	0.000	0.000	0.000	0.000
91	A	93	TYR	0	-0.079	-0.064	4.957	7.631	7.631	0.000	0.000	0.000	0.000
92	A	94	PRO	0	-0.034	-0.009	8.950	-2.740	-2.740	0.000	0.000	0.000	0.000
93	A	95	VAL	0	0.036	0.000	11.922	-0.579	-0.579	0.000	0.000	0.000	0.000
94	A	96	GLY	0	-0.003	0.000	14.543	-0.826	-0.826	0.000	0.000	0.000	0.000
95	A	97	GLY	0	-0.015	-0.013	10.297	-0.310	-0.310	0.000	0.000	0.000	0.000
96	A	98	VAL	0	-0.045	-0.014	9.461	2.457	2.457	0.000	0.000	0.000	0.000
97	A	99	PRO	0	0.013	0.032	7.618	-2.089	-2.089	0.000	0.000	0.000	0.000
98	A	100	PRO	0	0.009	-0.004	10.255	-0.462	-0.462	0.000	0.000	0.000	0.000
99	A	101	VAL	0	0.008	-0.004	8.977	-1.156	-1.156	0.000	0.000	0.000	0.000
100	A	102	ALA	0	-0.010	-0.010	7.260	1.783	1.783	0.000	0.000	0.000	0.000
101	A	103	LEU	0	0.012	0.037	8.269	3.783	3.783	0.000	0.000	0.000	0.000
102	A	104	PRO	0	0.001	-0.002	10.845	-0.456	-0.456	0.000	0.000	0.000	0.000
103	A	105	PRO	0	0.027	-0.003	12.774	-1.034	-1.034	0.000	0.000	0.000	0.000
104	A	106	ASN	0	-0.017	0.005	15.386	-0.108	-0.108	0.000	0.000	0.000	0.000
105	A	107	ILE	0	-0.070	-0.025	14.363	-0.960	-0.960	0.000	0.000	0.000	0.000
106	A	108	VAL	0	0.023	0.018	17.706	0.142	0.142	0.000	0.000	0.000	0.000
107	A	109	LEU	0	-0.022	-0.004	16.062	-0.029	-0.029	0.000	0.000	0.000	0.000
108	A	110	VAL	0	-0.013	-0.009	19.419	-0.700	-0.700	0.000	0.000	0.000	0.000
109	A	111	VAL	0	0.004	-0.005	19.387	0.503	0.503	0.000	0.000	0.000	0.000
110	A	112	ASP	-1	-0.766	-0.873	22.038	10.262	10.262	0.000	0.000	0.000	0.000
111	A	113	ARG	1	0.884	0.897	24.586	-9.504	-9.504	0.000	0.000	0.000	0.000
112	A	114	ILE	0	-0.049	-0.012	26.247	-0.131	-0.131	0.000	0.000	0.000	0.000
113	A	115	LEU	0	-0.014	-0.016	20.661	-0.060	-0.060	0.000	0.000	0.000	0.000
114	A	116	LEU	0	0.032	0.013	23.303	0.126	0.126	0.000	0.000	0.000	0.000
115	A	117	SER	0	-0.065	-0.015	25.219	0.077	0.077	0.000	0.000	0.000	0.000
116	A	118	ARG	1	0.874	0.954	22.899	-10.969	-10.969	0.000	0.000	0.000	0.000
117	A	119	LYS	1	0.980	0.971	22.851	-9.774	-9.774	0.000	0.000	0.000	0.000
118	A	120	LYS	1	0.840	0.920	17.909	-13.107	-13.107	0.000	0.000	0.000	0.000
119	A	121	VAL	0	0.003	0.013	16.896	-0.542	-0.542	0.000	0.000	0.000	0.000
120	A	122	TYR	0	-0.020	-0.028	14.653	0.378	0.378	0.000	0.000	0.000	0.000
121	A	123	GLY	0	0.032	0.022	13.534	-0.560	-0.560	0.000	0.000	0.000	0.000
122	A	124	GLY	0	0.014	0.019	11.269	0.374	0.374	0.000	0.000	0.000	0.000
123	A	125	GLY	0	0.028	-0.008	7.806	0.051	0.051	0.000	0.000	0.000	0.000
124	A	126	GLY	0	-0.004	0.003	5.302	2.791	2.791	0.000	0.000	0.000	0.000
125	A	127	ARG	1	0.825	0.870	1.699	-112.445	-116.057	21.434	-9.947	-7.875	0.115
126	A	128	GLU	-1	-0.809	-0.905	7.888	19.737	19.737	0.000	0.000	0.000	0.000
127	A	129	ASN	0	-0.046	-0.017	9.637	0.188	0.188	0.000	0.000	0.000	0.000
128	A	130	ALA	0	0.002	0.017	7.400	-0.847	-0.847	0.000	0.000	0.000	0.000
129	A	131	LEU	0	0.031	0.015	9.342	0.049	0.049	0.000	0.000	0.000	0.000
130	A	132	LEU	0	0.002	-0.001	8.424	0.329	0.329	0.000	0.000	0.000	0.000
131	A	133	GLU	-1	-0.748	-0.832	10.546	13.514	13.514	0.000	0.000	0.000	0.000
132	A	134	PHE	0	-0.004	-0.024	13.105	0.324	0.324	0.000	0.000	0.000	0.000
133	A	135	SER	0	0.035	0.025	15.029	-0.703	-0.703	0.000	0.000	0.000	0.000
134	A	136	PRO	0	0.021	0.003	18.101	0.369	0.369	0.000	0.000	0.000	0.000
135	A	137	ARG	1	0.911	0.934	19.790	-10.276	-10.276	0.000	0.000	0.000	0.000
136	A	138	GLU	-1	-0.776	-0.875	17.873	13.590	13.590	0.000	0.000	0.000	0.000
137	A	139	LEU	0	-0.016	-0.001	14.499	0.368	0.368	0.000	0.000	0.000	0.000
138	A	140	VAL	0	-0.037	-0.010	17.417	0.235	0.235	0.000	0.000	0.000	0.000
139	A	141	GLU	-1	-0.967	-0.977	20.707	11.733	11.733	0.000	0.000	0.000	0.000
140	A	142	ALA	0	-0.030	-0.006	16.571	0.061	0.061	0.000	0.000	0.000	0.000
141	A	143	THR	0	-0.036	-0.055	15.891	0.417	0.417	0.000	0.000	0.000	0.000
142	A	144	GLY	0	0.019	0.031	18.658	-0.013	-0.013	0.000	0.000	0.000	0.000
143	A	145	ALA	0	-0.056	-0.017	19.677	-0.327	-0.327	0.000	0.000	0.000	0.000
144	A	146	VAL	0	0.032	0.017	21.696	-0.543	-0.543	0.000	0.000	0.000	0.000
145	A	147	VAL	0	0.004	0.001	24.184	0.251	0.251	0.000	0.000	0.000	0.000
146	A	148	ALA	0	-0.027	-0.018	26.050	-0.395	-0.395	0.000	0.000	0.000	0.000
147	A	149	ASP	-1	-0.811	-0.861	27.611	9.649	9.649	0.000	0.000	0.000	0.000
148	A	150	VAL	0	0.015	-0.016	25.107	-0.160	-0.160	0.000	0.000	0.000	0.000
149	A	151	SER	0	-0.047	-0.036	26.295	0.225	0.225	0.000	0.000	0.000	0.000
150	A	152	GLU	-1	-0.913	-0.938	28.290	9.126	9.126	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:GLU)