FMO DATABASE

FMODB ID: 39YLL

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1644262.896693
FMO2-HF: Nuclear repulsion	1577575.215909
FMO2-HF: Total energy	-66687.680784
FMO2-MP2: Total energy	-66880.841588

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.
-203.582	-209.922	42.566	-16.37	-19.857	0.201

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 : -0.760 / q_NPA : -0.886

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	-0.006	-0.007	3.739	7.569	8.985	0.021	-0.574	-0.863	0.002
4	A	21	ALA	0	-0.029	-0.006	2.504	-9.665	-8.534	2.351	-1.889	-1.593	0.019
5	A	22	GLU	-1	-0.876	-0.941	2.847	56.086	58.497	1.469	-0.740	-3.141	0.020
6	A	23	LYS	1	0.848	0.914	1.773	-133.708	-142.568	27.400	-9.196	-9.344	0.106
7	A	24	VAL	0	-0.011	-0.015	1.818	-30.402	-33.434	11.307	-3.798	-4.477	0.052
8	A	25	LEU	0	0.002	-0.005	3.840	-14.065	-13.749	0.020	-0.160	-0.177	0.002
9	A	26	ALA	0	-0.026	-0.001	5.862	-7.223	-7.223	0.000	0.000	0.000	0.000
10	A	27	ARG	1	0.818	0.907	4.647	-53.169	-53.051	-0.001	-0.008	-0.109	0.000
11	A	28	ILE	0	0.002	-0.015	7.981	-4.155	-4.155	0.000	0.000	0.000	0.000
12	A	29	ASN	0	-0.044	-0.039	9.785	-5.150	-5.150	0.000	0.000	0.000	0.000
13	A	30	ARG	1	0.950	1.005	11.488	-24.368	-24.368	0.000	0.000	0.000	0.000
14	A	31	PRO	0	-0.024	-0.008	13.024	-1.673	-1.673	0.000	0.000	0.000	0.000
15	A	32	SER	0	0.028	0.004	16.160	0.168	0.168	0.000	0.000	0.000	0.000
16	A	33	LYS	1	0.838	0.941	18.984	-13.663	-13.663	0.000	0.000	0.000	0.000
17	A	34	ILE	0	0.006	-0.010	14.142	-0.615	-0.615	0.000	0.000	0.000	0.000
18	A	35	VAL	0	0.043	0.029	15.230	0.664	0.664	0.000	0.000	0.000	0.000
19	A	36	SER	0	-0.025	-0.015	11.927	0.107	0.107	0.000	0.000	0.000	0.000
20	A	37	THR	0	-0.020	-0.007	13.947	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	38	SER	0	-0.009	-0.015	14.307	-0.412	-0.412	0.000	0.000	0.000	0.000
22	A	39	SER	0	-0.017	0.002	10.031	1.502	1.502	0.000	0.000	0.000	0.000
23	A	40	CYS	0	-0.040	-0.003	11.732	-0.664	-0.664	0.000	0.000	0.000	0.000
24	A	41	THR	0	0.076	0.035	6.938	-1.569	-1.569	0.000	0.000	0.000	0.000
25	A	42	GLY	0	0.062	0.053	8.785	0.453	0.453	0.000	0.000	0.000	0.000
26	A	43	ARG	1	0.893	0.926	11.406	-16.043	-16.043	0.000	0.000	0.000	0.000
27	A	44	ILE	0	0.042	0.034	14.043	-0.802	-0.802	0.000	0.000	0.000	0.000
28	A	45	THR	0	-0.096	-0.072	16.949	0.138	0.138	0.000	0.000	0.000	0.000
29	A	46	LEU	0	0.029	0.022	20.280	-0.281	-0.281	0.000	0.000	0.000	0.000
30	A	47	ILE	0	-0.044	-0.030	22.558	0.145	0.145	0.000	0.000	0.000	0.000
31	A	48	GLU	-1	-0.896	-0.944	26.234	9.932	9.932	0.000	0.000	0.000	0.000
32	A	49	GLY	0	0.038	0.018	30.028	0.081	0.081	0.000	0.000	0.000	0.000
33	A	50	GLU	-1	-0.841	-0.931	31.885	8.907	8.907	0.000	0.000	0.000	0.000
34	A	51	ALA	0	-0.024	-0.008	31.172	0.079	0.079	0.000	0.000	0.000	0.000
35	A	52	HIS	0	0.078	0.059	25.823	0.692	0.692	0.000	0.000	0.000	0.000
36	A	53	TRP	0	-0.009	-0.015	25.451	0.709	0.709	0.000	0.000	0.000	0.000
37	A	54	LEU	0	0.006	0.004	24.511	0.071	0.071	0.000	0.000	0.000	0.000
38	A	55	ARG	1	0.928	0.955	28.592	-10.145	-10.145	0.000	0.000	0.000	0.000
39	A	56	ASN	0	0.018	0.015	31.430	-0.146	-0.146	0.000	0.000	0.000	0.000
40	A	57	GLY	0	0.027	0.010	30.907	-0.024	-0.024	0.000	0.000	0.000	0.000
41	A	58	ALA	0	0.007	0.031	30.421	0.233	0.233	0.000	0.000	0.000	0.000
42	A	59	ARG	1	0.996	0.980	24.047	-12.040	-12.040	0.000	0.000	0.000	0.000
43	A	60	VAL	0	-0.038	-0.023	21.326	-0.050	-0.050	0.000	0.000	0.000	0.000
44	A	61	ALA	0	0.077	0.069	24.635	0.100	0.100	0.000	0.000	0.000	0.000
45	A	62	TYR	0	-0.033	-0.055	19.164	-0.294	-0.294	0.000	0.000	0.000	0.000
46	A	63	LYS	1	0.874	0.926	15.643	-19.064	-19.064	0.000	0.000	0.000	0.000
47	A	64	THR	0	0.051	0.033	14.725	0.482	0.482	0.000	0.000	0.000	0.000
48	A	65	HIS	0	0.032	0.020	10.621	-1.439	-1.439	0.000	0.000	0.000	0.000
49	A	66	HIS	0	0.038	0.026	8.020	2.638	2.638	0.000	0.000	0.000	0.000
50	A	67	PRO	0	0.030	-0.006	10.505	-0.965	-0.965	0.000	0.000	0.000	0.000
51	A	68	ILE	0	-0.033	0.016	13.729	-0.207	-0.207	0.000	0.000	0.000	0.000
52	A	69	SER	0	0.023	-0.021	17.264	-0.644	-0.644	0.000	0.000	0.000	0.000
53	A	70	ARG	1	0.810	0.840	19.838	-10.457	-10.457	0.000	0.000	0.000	0.000
54	A	71	SER	0	0.004	0.004	22.401	-0.246	-0.246	0.000	0.000	0.000	0.000
55	A	72	GLU	-1	-0.836	-0.862	18.557	15.182	15.182	0.000	0.000	0.000	0.000
56	A	73	VAL	0	0.047	0.015	22.295	-0.195	-0.195	0.000	0.000	0.000	0.000
57	A	74	GLU	-1	-0.839	-0.921	24.536	10.065	10.065	0.000	0.000	0.000	0.000
58	A	75	ARG	1	0.859	0.936	21.651	-13.227	-13.227	0.000	0.000	0.000	0.000
59	A	76	VAL	0	-0.048	-0.026	24.921	-0.179	-0.179	0.000	0.000	0.000	0.000
60	A	77	LEU	0	0.032	0.018	27.924	-0.300	-0.300	0.000	0.000	0.000	0.000
61	A	78	ARG	1	0.934	0.962	28.457	-10.297	-10.297	0.000	0.000	0.000	0.000
62	A	79	ARG	1	0.825	0.915	26.497	-11.169	-11.169	0.000	0.000	0.000	0.000
63	A	80	GLY	0	0.015	0.023	32.808	-0.112	-0.112	0.000	0.000	0.000	0.000
64	A	81	PHE	0	-0.045	-0.022	29.712	-0.060	-0.060	0.000	0.000	0.000	0.000
65	A	82	THR	0	0.045	0.020	33.929	0.051	0.051	0.000	0.000	0.000	0.000
66	A	83	ASN	0	-0.004	0.010	33.747	-0.157	-0.157	0.000	0.000	0.000	0.000
67	A	84	LEU	0	-0.008	-0.005	27.590	0.237	0.237	0.000	0.000	0.000	0.000
68	A	85	TRP	0	-0.012	-0.007	26.615	0.031	0.031	0.000	0.000	0.000	0.000
69	A	86	LEU	0	0.026	0.023	20.901	0.392	0.392	0.000	0.000	0.000	0.000
70	A	87	LYS	1	0.822	0.890	20.989	-13.329	-13.329	0.000	0.000	0.000	0.000
71	A	88	VAL	0	-0.019	0.017	15.851	0.526	0.526	0.000	0.000	0.000	0.000
72	A	89	THR	0	-0.041	-0.034	15.881	-0.961	-0.961	0.000	0.000	0.000	0.000
73	A	90	GLY	0	0.071	0.039	13.016	0.976	0.976	0.000	0.000	0.000	0.000
74	A	91	PRO	0	-0.064	-0.039	9.195	-0.687	-0.687	0.000	0.000	0.000	0.000
75	A	92	ILE	0	-0.009	-0.010	11.626	-1.511	-1.511	0.000	0.000	0.000	0.000
76	A	93	LEU	0	-0.013	-0.010	9.225	1.848	1.848	0.000	0.000	0.000	0.000
77	A	94	HIS	0	-0.034	-0.019	13.297	-0.790	-0.790	0.000	0.000	0.000	0.000
78	A	95	LEU	0	0.011	0.004	12.493	1.191	1.191	0.000	0.000	0.000	0.000
79	A	96	ARG	1	0.859	0.913	16.536	-15.089	-15.089	0.000	0.000	0.000	0.000
80	A	97	VAL	0	0.004	-0.014	18.017	0.730	0.730	0.000	0.000	0.000	0.000
81	A	98	GLU	-1	-0.852	-0.909	20.502	12.419	12.419	0.000	0.000	0.000	0.000
82	A	99	GLY	0	0.046	0.017	23.313	-0.196	-0.196	0.000	0.000	0.000	0.000
83	A	100	TRP	0	0.042	-0.011	24.105	0.624	0.624	0.000	0.000	0.000	0.000
84	A	101	GLN	0	-0.044	-0.017	25.309	0.022	0.022	0.000	0.000	0.000	0.000
85	A	187	CYS	0	-0.010	0.029	18.111	0.240	0.240	0.000	0.000	0.000	0.000
86	A	103	ALA	0	0.042	0.014	20.701	0.586	0.586	0.000	0.000	0.000	0.000
87	A	104	LYS	1	0.843	0.897	21.260	-11.644	-11.644	0.000	0.000	0.000	0.000
88	A	105	SER	0	0.004	-0.007	20.840	0.058	0.058	0.000	0.000	0.000	0.000
89	A	106	LEU	0	0.046	0.025	14.532	0.485	0.485	0.000	0.000	0.000	0.000
90	A	107	LEU	0	-0.030	-0.013	17.242	0.707	0.707	0.000	0.000	0.000	0.000
91	A	108	GLU	-1	-0.915	-0.940	19.632	12.601	12.601	0.000	0.000	0.000	0.000
92	A	109	ALA	0	0.052	0.030	15.790	0.008	0.008	0.000	0.000	0.000	0.000
93	A	110	ALA	0	-0.022	0.001	15.010	0.686	0.686	0.000	0.000	0.000	0.000
94	A	111	ARG	1	0.860	0.930	16.068	-13.568	-13.568	0.000	0.000	0.000	0.000
95	A	112	ARG	1	0.844	0.913	18.231	-15.927	-15.927	0.000	0.000	0.000	0.000
96	A	113	ASN	0	-0.026	-0.001	13.410	0.730	0.730	0.000	0.000	0.000	0.000
97	A	114	GLY	0	0.041	0.030	14.455	0.930	0.930	0.000	0.000	0.000	0.000
98	A	115	PHE	0	-0.044	-0.006	10.827	-0.354	-0.354	0.000	0.000	0.000	0.000
99	A	116	LYS	1	0.941	0.981	16.811	-13.335	-13.335	0.000	0.000	0.000	0.000
100	A	117	HIS	0	-0.051	-0.029	19.777	-1.422	-1.422	0.000	0.000	0.000	0.000
101	A	118	SER	0	0.050	0.008	17.858	0.993	0.993	0.000	0.000	0.000	0.000
102	A	119	GLY	0	-0.004	-0.018	20.003	-0.686	-0.686	0.000	0.000	0.000	0.000
103	A	120	VAL	0	-0.015	-0.004	21.682	0.561	0.561	0.000	0.000	0.000	0.000
104	A	121	ILE	0	-0.012	-0.003	21.601	-0.492	-0.492	0.000	0.000	0.000	0.000
105	A	122	SER	0	-0.027	-0.010	24.826	-0.441	-0.441	0.000	0.000	0.000	0.000
106	A	123	ILE	0	-0.010	-0.012	25.644	0.364	0.364	0.000	0.000	0.000	0.000
107	A	124	ALA	0	-0.002	0.013	25.207	-0.238	-0.238	0.000	0.000	0.000	0.000
108	A	125	GLU	-1	-0.882	-0.944	27.308	10.266	10.266	0.000	0.000	0.000	0.000
109	A	126	ASP	-1	-0.837	-0.888	25.462	12.488	12.488	0.000	0.000	0.000	0.000
110	A	127	SER	0	-0.017	-0.020	28.179	0.024	0.024	0.000	0.000	0.000	0.000
111	A	128	ARG	1	0.776	0.883	22.542	-12.942	-12.942	0.000	0.000	0.000	0.000
112	A	129	LEU	0	0.010	0.012	23.237	-0.162	-0.162	0.000	0.000	0.000	0.000
113	A	130	VAL	0	-0.001	0.003	21.124	0.755	0.755	0.000	0.000	0.000	0.000
114	A	131	ILE	0	-0.028	-0.014	18.722	-0.653	-0.653	0.000	0.000	0.000	0.000
115	A	132	GLU	-1	-0.848	-0.909	17.958	16.090	16.090	0.000	0.000	0.000	0.000
116	A	133	ILE	0	0.007	-0.003	13.858	-0.583	-0.583	0.000	0.000	0.000	0.000
117	A	134	MET	0	0.008	0.002	14.748	1.396	1.396	0.000	0.000	0.000	0.000
118	A	135	SER	0	0.023	0.015	13.922	-1.099	-1.099	0.000	0.000	0.000	0.000
119	A	136	SER	0	-0.080	-0.053	15.895	-1.081	-1.081	0.000	0.000	0.000	0.000
120	A	137	GLN	0	-0.003	-0.010	15.153	-0.132	-0.132	0.000	0.000	0.000	0.000
121	A	138	SER	0	-0.043	-0.030	16.825	0.546	0.546	0.000	0.000	0.000	0.000
122	A	139	MET	0	0.019	0.019	19.184	-0.585	-0.585	0.000	0.000	0.000	0.000
123	A	140	SER	0	-0.058	-0.031	21.811	0.418	0.418	0.000	0.000	0.000	0.000
124	A	141	VAL	0	0.043	0.020	24.611	-0.381	-0.381	0.000	0.000	0.000	0.000
125	A	142	PRO	0	-0.001	0.017	27.205	0.276	0.276	0.000	0.000	0.000	0.000
126	A	143	LEU	0	0.012	-0.010	25.802	-0.097	-0.097	0.000	0.000	0.000	0.000
127	A	144	VAL	0	-0.012	-0.015	30.030	-0.244	-0.244	0.000	0.000	0.000	0.000
128	A	145	MET	0	-0.002	-0.001	33.210	0.197	0.197	0.000	0.000	0.000	0.000
129	A	146	GLU	-1	-0.930	-0.967	35.928	7.445	7.445	0.000	0.000	0.000	0.000
130	A	147	GLY	0	-0.017	-0.005	37.671	-0.210	-0.210	0.000	0.000	0.000	0.000
131	A	148	ALA	0	-0.011	0.009	38.207	0.012	0.012	0.000	0.000	0.000	0.000
132	A	149	ARG	1	0.775	0.862	31.105	-9.012	-9.012	0.000	0.000	0.000	0.000
133	A	150	ILE	0	-0.008	-0.007	33.047	-0.204	-0.204	0.000	0.000	0.000	0.000
134	A	151	VAL	0	-0.016	0.000	29.024	0.059	0.059	0.000	0.000	0.000	0.000
135	A	152	GLY	0	0.070	0.031	32.309	-0.034	-0.034	0.000	0.000	0.000	0.000
136	A	153	ASP	-1	-0.760	-0.873	30.538	9.682	9.682	0.000	0.000	0.000	0.000
137	A	154	ASP	-1	-0.831	-0.913	29.111	9.253	9.253	0.000	0.000	0.000	0.000
138	A	155	ALA	0	-0.028	-0.018	28.281	0.321	0.321	0.000	0.000	0.000	0.000
139	A	156	LEU	0	-0.036	-0.009	25.877	0.403	0.403	0.000	0.000	0.000	0.000
140	A	157	ASP	-1	-0.786	-0.874	24.375	11.397	11.397	0.000	0.000	0.000	0.000
141	A	158	MET	0	0.031	0.019	23.162	0.527	0.527	0.000	0.000	0.000	0.000
142	A	159	LEU	0	-0.027	-0.012	23.004	0.498	0.498	0.000	0.000	0.000	0.000
143	A	160	ILE	0	-0.014	-0.007	19.715	0.654	0.654	0.000	0.000	0.000	0.000
144	A	161	GLU	-1	-0.923	-0.951	18.922	13.553	13.553	0.000	0.000	0.000	0.000
145	A	162	LYS	1	0.945	0.989	18.077	-13.146	-13.146	0.000	0.000	0.000	0.000
146	A	163	ALA	0	0.006	-0.012	18.068	0.679	0.679	0.000	0.000	0.000	0.000
147	A	164	ASN	0	0.026	-0.015	14.660	1.505	1.505	0.000	0.000	0.000	0.000
148	A	165	THR	0	-0.033	-0.020	13.427	1.044	1.044	0.000	0.000	0.000	0.000
149	A	166	ILE	0	0.009	0.009	13.735	1.013	1.013	0.000	0.000	0.000	0.000
150	A	167	LEU	0	-0.056	0.003	10.559	1.114	1.114	0.000	0.000	0.000	0.000
151	A	168	VAL	0	-0.020	-0.008	8.590	2.294	2.294	0.000	0.000	0.000	0.000
152	A	169	GLU	-1	-0.860	-0.936	9.548	18.278	18.278	0.000	0.000	0.000	0.000
153	A	170	SER	0	-0.051	-0.047	11.536	1.409	1.409	0.000	0.000	0.000	0.000
154	A	171	ARG	1	0.780	0.867	6.095	-28.255	-28.255	0.000	0.000	0.000	0.000
155	A	172	ILE	0	0.005	0.013	6.946	3.516	3.516	0.000	0.000	0.000	0.000
156	A	173	GLY	0	0.073	0.045	8.988	0.833	0.833	0.000	0.000	0.000	0.000
157	A	174	LEU	0	0.001	-0.002	5.900	-0.415	-0.415	0.000	0.000	0.000	0.000
158	A	175	ASP	-1	-0.808	-0.857	5.048	47.246	47.406	-0.001	-0.005	-0.153	0.000
159	A	176	THR	0	-0.003	-0.021	6.816	0.106	0.106	0.000	0.000	0.000	0.000
160	A	177	PHE	0	0.007	0.012	10.364	-0.729	-0.729	0.000	0.000	0.000	0.000
161	A	178	SER	0	-0.011	-0.029	6.416	1.500	1.500	0.000	0.000	0.000	0.000
162	A	179	ARG	1	0.818	0.894	6.681	-34.107	-34.107	0.000	0.000	0.000	0.000
163	A	180	GLU	-1	-0.744	-0.852	10.216	16.637	16.637	0.000	0.000	0.000	0.000
164	A	181	VAL	0	-0.035	-0.025	11.270	-1.468	-1.468	0.000	0.000	0.000	0.000
165	A	182	GLU	-1	-0.928	-0.983	10.324	28.781	28.781	0.000	0.000	0.000	0.000
166	A	183	GLU	-1	-0.993	-0.983	13.554	14.980	14.980	0.000	0.000	0.000	0.000
167	A	184	LEU	0	-0.008	0.002	16.166	-1.323	-1.323	0.000	0.000	0.000	0.000
168	A	185	VAL	0	0.042	0.018	18.462	-0.089	-0.089	0.000	0.000	0.000	0.000
169	A	186	GLU	-1	-0.872	-0.920	21.498	11.892	11.892	0.000	0.000	0.000	0.000

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