FMO DATABASE

FMODB ID: N95KQ

Calculation Name: 2DVK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2DVK

Chain ID: A

ChEMBL ID:

UniProt ID: Q9YDV3

Base Structure: X-ray

Registration Date: 2023-09-20

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	169
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1641990.984375
FMO2-HF: Nuclear repulsion	1575304.576725
FMO2-HF: Total energy	-66686.40765
FMO2-MP2: Total energy	-66879.665784

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:18:ASP)

Summations of interaction energy for fragment #1(A:18:ASP)

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.
-178.367	-174.006	25.017	-12.645	-16.731	0.173

Interaction energy analysis for fragmet #1(A:18:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.805 / 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	20	GLY	0	0.014	0.008	3.836	3.150	4.484	-0.010	-0.475	-0.848	0.002
4	A	21	ALA	0	-0.043	-0.012	2.392	-9.442	-7.862	2.897	-2.491	-1.986	0.024
5	A	22	GLU	-1	-0.902	-0.951	3.121	43.301	44.226	0.628	0.403	-1.956	0.009
6	A	23	LYS	1	0.903	0.938	1.813	-91.903	-94.391	17.883	-7.606	-7.790	0.091
7	A	24	VAL	0	-0.026	-0.006	2.311	-29.275	-26.690	3.615	-2.341	-3.859	0.046
8	A	25	LEU	0	0.031	-0.005	4.170	-12.995	-12.816	0.006	-0.108	-0.076	0.001
9	A	26	ALA	0	-0.009	0.023	6.290	-7.139	-7.139	0.000	0.000	0.000	0.000
10	A	27	ARG	1	0.823	0.928	4.295	-55.251	-55.146	-0.001	-0.025	-0.079	0.000
11	A	28	ILE	0	-0.007	-0.017	8.340	-3.914	-3.914	0.000	0.000	0.000	0.000
12	A	29	ASN	0	-0.056	-0.058	10.185	-5.126	-5.126	0.000	0.000	0.000	0.000
13	A	30	ARG	1	0.935	1.007	11.866	-23.833	-23.833	0.000	0.000	0.000	0.000
14	A	31	PRO	0	-0.013	-0.009	13.411	-1.680	-1.680	0.000	0.000	0.000	0.000
15	A	32	SER	0	0.034	0.013	16.570	0.114	0.114	0.000	0.000	0.000	0.000
16	A	33	LYS	1	0.919	0.975	19.535	-13.176	-13.176	0.000	0.000	0.000	0.000
17	A	34	ILE	0	0.014	-0.005	14.549	-0.565	-0.565	0.000	0.000	0.000	0.000
18	A	35	VAL	0	0.058	0.042	15.606	0.539	0.539	0.000	0.000	0.000	0.000
19	A	36	SER	0	-0.019	-0.004	12.126	0.224	0.224	0.000	0.000	0.000	0.000
20	A	37	THR	0	-0.042	-0.027	14.246	0.076	0.076	0.000	0.000	0.000	0.000
21	A	38	SER	0	-0.016	-0.009	14.392	-0.319	-0.319	0.000	0.000	0.000	0.000
22	A	39	SER	0	0.019	0.013	10.106	1.529	1.529	0.000	0.000	0.000	0.000
23	A	40	CYS	0	-0.009	0.018	11.770	-0.423	-0.423	0.000	0.000	0.000	0.000
24	A	41	THR	0	0.081	0.035	6.743	-1.806	-1.806	0.000	0.000	0.000	0.000
25	A	42	GLY	0	0.062	0.062	9.251	0.398	0.398	0.000	0.000	0.000	0.000
26	A	43	ARG	1	0.892	0.925	11.899	-16.284	-16.284	0.000	0.000	0.000	0.000
27	A	44	ILE	0	0.077	0.052	14.459	-0.799	-0.799	0.000	0.000	0.000	0.000
28	A	45	THR	0	-0.107	-0.076	17.262	-0.043	-0.043	0.000	0.000	0.000	0.000
29	A	46	LEU	0	0.047	0.029	20.515	-0.255	-0.255	0.000	0.000	0.000	0.000
30	A	47	ILE	0	-0.058	-0.035	23.093	0.106	0.106	0.000	0.000	0.000	0.000
31	A	48	GLU	-1	-0.907	-0.942	26.351	9.891	9.891	0.000	0.000	0.000	0.000
32	A	49	GLY	0	0.032	0.001	30.054	0.056	0.056	0.000	0.000	0.000	0.000
33	A	50	GLU	-1	-0.915	-0.964	31.923	8.581	8.581	0.000	0.000	0.000	0.000
34	A	51	ALA	0	-0.024	-0.004	31.409	0.093	0.093	0.000	0.000	0.000	0.000
35	A	52	HIS	0	0.080	0.059	25.887	0.547	0.547	0.000	0.000	0.000	0.000
36	A	53	TRP	0	-0.021	-0.032	25.955	0.666	0.666	0.000	0.000	0.000	0.000
37	A	54	LEU	0	0.010	-0.001	24.334	0.067	0.067	0.000	0.000	0.000	0.000
38	A	55	ARG	1	0.928	0.956	28.608	-10.068	-10.068	0.000	0.000	0.000	0.000
39	A	56	ASN	0	0.028	0.011	31.485	-0.216	-0.216	0.000	0.000	0.000	0.000
40	A	57	GLY	0	0.006	0.002	32.422	0.164	0.164	0.000	0.000	0.000	0.000
41	A	58	ALA	0	0.041	0.064	31.671	-0.099	-0.099	0.000	0.000	0.000	0.000
42	A	59	ARG	1	0.967	0.960	23.286	-12.336	-12.336	0.000	0.000	0.000	0.000
43	A	60	VAL	0	-0.066	-0.032	21.787	0.070	0.070	0.000	0.000	0.000	0.000
44	A	61	ALA	0	0.060	0.051	25.146	-0.034	-0.034	0.000	0.000	0.000	0.000
45	A	62	TYR	0	-0.062	-0.074	18.386	-0.170	-0.170	0.000	0.000	0.000	0.000
46	A	63	LYS	1	0.939	0.963	17.880	-17.094	-17.094	0.000	0.000	0.000	0.000
47	A	64	THR	0	0.043	0.031	14.793	0.531	0.531	0.000	0.000	0.000	0.000
48	A	65	HIS	0	-0.030	-0.011	10.551	-1.213	-1.213	0.000	0.000	0.000	0.000
49	A	66	HIS	0	0.046	0.034	7.733	2.421	2.421	0.000	0.000	0.000	0.000
50	A	67	PRO	0	0.017	-0.002	10.340	-1.108	-1.108	0.000	0.000	0.000	0.000
51	A	68	ILE	0	-0.032	0.003	13.561	-0.172	-0.172	0.000	0.000	0.000	0.000
52	A	69	SER	0	0.013	-0.016	17.096	-0.638	-0.638	0.000	0.000	0.000	0.000
53	A	70	ARG	1	0.859	0.898	19.666	-10.530	-10.530	0.000	0.000	0.000	0.000
54	A	71	SER	0	0.018	0.011	22.056	-0.244	-0.244	0.000	0.000	0.000	0.000
55	A	72	GLU	-1	-0.830	-0.875	18.048	15.420	15.420	0.000	0.000	0.000	0.000
56	A	73	VAL	0	0.040	0.016	22.064	-0.217	-0.217	0.000	0.000	0.000	0.000
57	A	74	GLU	-1	-0.852	-0.936	24.322	9.998	9.998	0.000	0.000	0.000	0.000
58	A	75	ARG	1	0.893	0.948	22.066	-12.870	-12.870	0.000	0.000	0.000	0.000
59	A	76	VAL	0	-0.030	-0.027	24.689	-0.265	-0.265	0.000	0.000	0.000	0.000
60	A	77	LEU	0	0.015	0.013	27.657	-0.312	-0.312	0.000	0.000	0.000	0.000
61	A	78	ARG	1	0.938	0.969	28.839	-10.234	-10.234	0.000	0.000	0.000	0.000
62	A	79	ARG	1	0.826	0.920	26.759	-11.061	-11.061	0.000	0.000	0.000	0.000
63	A	80	GLY	0	0.025	0.033	32.541	-0.129	-0.129	0.000	0.000	0.000	0.000
64	A	81	PHE	0	-0.025	-0.008	29.653	-0.049	-0.049	0.000	0.000	0.000	0.000
65	A	82	THR	0	0.047	0.022	33.983	-0.035	-0.035	0.000	0.000	0.000	0.000
66	A	83	ASN	0	0.031	0.032	33.628	-0.150	-0.150	0.000	0.000	0.000	0.000
67	A	84	LEU	0	-0.012	-0.008	27.642	0.236	0.236	0.000	0.000	0.000	0.000
68	A	85	TRP	0	-0.008	0.013	26.613	0.090	0.090	0.000	0.000	0.000	0.000
69	A	86	LEU	0	0.025	0.017	21.123	0.352	0.352	0.000	0.000	0.000	0.000
70	A	87	LYS	1	0.838	0.901	20.939	-13.545	-13.545	0.000	0.000	0.000	0.000
71	A	88	VAL	0	-0.007	0.017	16.011	0.519	0.519	0.000	0.000	0.000	0.000
72	A	89	THR	0	-0.045	-0.031	16.030	-0.917	-0.917	0.000	0.000	0.000	0.000
73	A	90	GLY	0	0.078	0.038	13.369	1.002	1.002	0.000	0.000	0.000	0.000
74	A	91	PRO	0	-0.053	-0.041	9.689	-0.700	-0.700	0.000	0.000	0.000	0.000
75	A	92	ILE	0	-0.016	-0.014	11.873	-1.418	-1.418	0.000	0.000	0.000	0.000
76	A	93	LEU	0	-0.028	-0.023	9.387	1.453	1.453	0.000	0.000	0.000	0.000
77	A	94	HIS	0	-0.023	0.008	13.570	-0.770	-0.770	0.000	0.000	0.000	0.000
78	A	95	LEU	0	0.011	-0.005	12.931	1.204	1.204	0.000	0.000	0.000	0.000
79	A	96	ARG	1	0.919	0.969	16.926	-15.245	-15.245	0.000	0.000	0.000	0.000
80	A	97	VAL	0	0.014	-0.011	18.444	0.580	0.580	0.000	0.000	0.000	0.000
81	A	98	GLU	-1	-0.908	-0.944	20.846	12.197	12.197	0.000	0.000	0.000	0.000
82	A	99	GLY	0	0.043	0.011	23.712	-0.023	-0.023	0.000	0.000	0.000	0.000
83	A	100	TRP	0	0.068	-0.001	24.406	0.641	0.641	0.000	0.000	0.000	0.000
84	A	101	GLN	0	-0.010	0.007	25.492	0.453	0.453	0.000	0.000	0.000	0.000
85	A	187	CYS	0	-0.055	0.009	18.503	0.164	0.164	0.000	0.000	0.000	0.000
86	A	103	ALA	0	0.038	0.008	20.786	0.626	0.626	0.000	0.000	0.000	0.000
87	A	104	LYS	1	0.871	0.934	21.468	-11.375	-11.375	0.000	0.000	0.000	0.000
88	A	105	SER	0	0.043	0.016	20.816	0.023	0.023	0.000	0.000	0.000	0.000
89	A	106	LEU	0	0.043	0.032	14.798	0.556	0.556	0.000	0.000	0.000	0.000
90	A	107	LEU	0	-0.032	-0.021	17.655	0.621	0.621	0.000	0.000	0.000	0.000
91	A	108	GLU	-1	-0.956	-0.973	19.880	12.803	12.803	0.000	0.000	0.000	0.000
92	A	109	ALA	0	0.050	0.026	15.985	0.013	0.013	0.000	0.000	0.000	0.000
93	A	110	ALA	0	-0.003	0.004	15.364	0.718	0.718	0.000	0.000	0.000	0.000
94	A	111	ARG	1	0.889	0.941	16.432	-13.225	-13.225	0.000	0.000	0.000	0.000
95	A	112	ARG	1	0.884	0.954	18.236	-16.046	-16.046	0.000	0.000	0.000	0.000
96	A	113	ASN	0	-0.015	0.024	13.367	0.740	0.740	0.000	0.000	0.000	0.000
97	A	114	GLY	0	0.048	0.033	14.352	1.132	1.132	0.000	0.000	0.000	0.000
98	A	115	PHE	0	-0.054	-0.019	11.034	-0.239	-0.239	0.000	0.000	0.000	0.000
99	A	116	LYS	1	0.953	0.976	16.978	-13.481	-13.481	0.000	0.000	0.000	0.000
100	A	117	HIS	0	-0.034	-0.016	19.970	-1.226	-1.226	0.000	0.000	0.000	0.000
101	A	118	SER	0	0.076	0.020	18.258	0.955	0.955	0.000	0.000	0.000	0.000
102	A	119	GLY	0	-0.012	-0.014	20.472	-0.652	-0.652	0.000	0.000	0.000	0.000
103	A	120	VAL	0	-0.011	0.004	22.022	0.556	0.556	0.000	0.000	0.000	0.000
104	A	121	ILE	0	-0.007	-0.004	22.014	-0.488	-0.488	0.000	0.000	0.000	0.000
105	A	122	SER	0	-0.030	-0.013	25.344	-0.509	-0.509	0.000	0.000	0.000	0.000
106	A	123	ILE	0	0.007	0.002	26.019	0.422	0.422	0.000	0.000	0.000	0.000
107	A	124	ALA	0	-0.031	-0.001	25.626	-0.185	-0.185	0.000	0.000	0.000	0.000
108	A	125	GLU	-1	-0.879	-0.938	27.590	9.956	9.956	0.000	0.000	0.000	0.000
109	A	126	ASP	-1	-0.888	-0.949	26.211	12.088	12.088	0.000	0.000	0.000	0.000
110	A	127	SER	0	-0.034	-0.030	28.808	-0.002	-0.002	0.000	0.000	0.000	0.000
111	A	128	ARG	1	0.848	0.935	22.335	-13.112	-13.112	0.000	0.000	0.000	0.000
112	A	129	LEU	0	-0.024	-0.009	23.397	-0.202	-0.202	0.000	0.000	0.000	0.000
113	A	130	VAL	0	-0.006	0.004	21.505	0.804	0.804	0.000	0.000	0.000	0.000
114	A	131	ILE	0	-0.027	-0.018	18.137	-0.589	-0.589	0.000	0.000	0.000	0.000
115	A	132	GLU	-1	-0.888	-0.940	18.085	15.766	15.766	0.000	0.000	0.000	0.000
116	A	133	ILE	0	-0.013	-0.006	14.173	-0.643	-0.643	0.000	0.000	0.000	0.000
117	A	134	MET	0	0.035	0.014	15.253	1.111	1.111	0.000	0.000	0.000	0.000
118	A	135	SER	0	-0.010	0.012	14.097	-1.110	-1.110	0.000	0.000	0.000	0.000
119	A	136	SER	0	-0.104	-0.057	16.061	-1.125	-1.125	0.000	0.000	0.000	0.000
120	A	137	GLN	0	0.038	0.022	14.830	-0.906	-0.906	0.000	0.000	0.000	0.000
121	A	138	SER	0	-0.048	-0.033	17.602	0.338	0.338	0.000	0.000	0.000	0.000
122	A	139	MET	0	0.030	0.027	19.698	-0.571	-0.571	0.000	0.000	0.000	0.000
123	A	140	SER	0	-0.061	-0.034	22.207	0.382	0.382	0.000	0.000	0.000	0.000
124	A	141	VAL	0	0.044	0.013	24.919	-0.392	-0.392	0.000	0.000	0.000	0.000
125	A	142	PRO	0	0.024	0.028	27.269	0.244	0.244	0.000	0.000	0.000	0.000
126	A	143	LEU	0	0.004	-0.006	25.658	-0.027	-0.027	0.000	0.000	0.000	0.000
127	A	144	VAL	0	-0.026	-0.019	29.983	-0.255	-0.255	0.000	0.000	0.000	0.000
128	A	145	MET	0	0.017	0.013	33.108	0.206	0.206	0.000	0.000	0.000	0.000
129	A	146	GLU	-1	-0.914	-0.965	35.858	7.575	7.575	0.000	0.000	0.000	0.000
130	A	147	GLY	0	-0.036	-0.024	37.516	-0.195	-0.195	0.000	0.000	0.000	0.000
131	A	148	ALA	0	-0.005	0.010	38.076	-0.040	-0.040	0.000	0.000	0.000	0.000
132	A	149	ARG	1	0.816	0.895	31.242	-9.102	-9.102	0.000	0.000	0.000	0.000
133	A	150	ILE	0	0.003	-0.009	32.738	-0.185	-0.185	0.000	0.000	0.000	0.000
134	A	151	VAL	0	-0.007	0.009	29.277	0.025	0.025	0.000	0.000	0.000	0.000
135	A	152	GLY	0	0.058	0.029	32.347	-0.029	-0.029	0.000	0.000	0.000	0.000
136	A	153	ASP	-1	-0.808	-0.925	30.588	9.550	9.550	0.000	0.000	0.000	0.000
137	A	154	ASP	-1	-0.839	-0.912	29.297	9.309	9.309	0.000	0.000	0.000	0.000
138	A	155	ALA	0	-0.043	-0.025	28.620	0.317	0.317	0.000	0.000	0.000	0.000
139	A	156	LEU	0	-0.031	-0.017	25.874	0.407	0.407	0.000	0.000	0.000	0.000
140	A	157	ASP	-1	-0.787	-0.887	24.606	11.362	11.362	0.000	0.000	0.000	0.000
141	A	158	MET	0	0.032	0.018	23.410	0.532	0.532	0.000	0.000	0.000	0.000
142	A	159	LEU	0	-0.038	-0.021	23.133	0.550	0.550	0.000	0.000	0.000	0.000
143	A	160	ILE	0	-0.015	-0.007	19.823	0.666	0.666	0.000	0.000	0.000	0.000
144	A	161	GLU	-1	-0.922	-0.952	19.092	13.699	13.699	0.000	0.000	0.000	0.000
145	A	162	LYS	1	0.943	0.974	18.371	-12.498	-12.498	0.000	0.000	0.000	0.000
146	A	163	ALA	0	-0.020	-0.023	18.414	0.682	0.682	0.000	0.000	0.000	0.000
147	A	164	ASN	0	0.043	0.013	14.702	1.461	1.461	0.000	0.000	0.000	0.000
148	A	165	THR	0	0.008	0.016	13.640	1.323	1.323	0.000	0.000	0.000	0.000
149	A	166	ILE	0	0.008	0.004	14.280	0.903	0.903	0.000	0.000	0.000	0.000
150	A	167	LEU	0	-0.061	-0.019	10.936	1.153	1.153	0.000	0.000	0.000	0.000
151	A	168	VAL	0	-0.031	-0.024	8.668	2.210	2.210	0.000	0.000	0.000	0.000
152	A	169	GLU	-1	-0.894	-0.954	9.685	19.496	19.496	0.000	0.000	0.000	0.000
153	A	170	SER	0	-0.108	-0.047	11.799	1.021	1.021	0.000	0.000	0.000	0.000
154	A	171	ARG	1	0.793	0.846	6.370	-28.907	-28.907	0.000	0.000	0.000	0.000
155	A	172	ILE	0	0.023	0.029	7.427	3.798	3.798	0.000	0.000	0.000	0.000
156	A	173	GLY	0	0.049	0.032	9.085	0.958	0.958	0.000	0.000	0.000	0.000
157	A	174	LEU	0	-0.003	-0.007	6.249	-0.638	-0.638	0.000	0.000	0.000	0.000
158	A	175	ASP	-1	-0.836	-0.922	5.338	49.784	49.925	-0.001	-0.002	-0.137	0.000
159	A	176	THR	0	0.008	-0.024	6.850	-0.072	-0.072	0.000	0.000	0.000	0.000
160	A	177	PHE	0	0.011	0.012	10.263	-1.193	-1.193	0.000	0.000	0.000	0.000
161	A	178	SER	0	-0.041	-0.032	6.775	1.245	1.245	0.000	0.000	0.000	0.000
162	A	179	ARG	1	0.839	0.901	5.880	-37.921	-37.921	0.000	0.000	0.000	0.000
163	A	180	GLU	-1	-0.839	-0.914	10.519	16.911	16.911	0.000	0.000	0.000	0.000
164	A	181	VAL	0	-0.022	-0.022	11.679	-1.254	-1.254	0.000	0.000	0.000	0.000
165	A	182	GLU	-1	-0.955	-0.992	10.936	27.860	27.860	0.000	0.000	0.000	0.000
166	A	183	GLU	-1	-0.967	-0.983	13.727	15.829	15.829	0.000	0.000	0.000	0.000
167	A	184	LEU	0	-0.033	0.000	16.433	-1.352	-1.352	0.000	0.000	0.000	0.000
168	A	185	VAL	0	0.036	0.013	18.578	-0.046	-0.046	0.000	0.000	0.000	0.000
169	A	186	GLU	-1	-0.936	-0.959	21.671	11.996	11.996	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:18:ASP)