FMO DATABASE

FMODB ID: K3VK3

Calculation Name: 3DA5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DA5

Chain ID: A

ChEMBL ID:

UniProt ID: D0VWU1

Base Structure: X-ray

Registration Date: 2023-03-14

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	121
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1143519.39017
FMO2-HF: Nuclear repulsion	1093956.684052
FMO2-HF: Total energy	-49562.706118
FMO2-MP2: Total energy	-49712.805349

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:8:LYS)

Summations of interaction energy for fragment #1(A:8:LYS)

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.
59.439	57.777	13.103	-3.731	-7.707	-0.026

Interaction energy analysis for fragmet #1(A:8:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.930 / q_NPA : 0.946

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	10	THR	0	0.021	0.019	3.884	-5.189	-3.869	-0.010	-0.563	-0.746	0.002
4	A	11	LEU	0	0.038	0.000	5.875	2.848	2.848	0.000	0.000	0.000	0.000
5	A	12	TRP	0	-0.012	-0.009	8.930	1.656	1.656	0.000	0.000	0.000	0.000
6	A	13	GLU	-1	-0.905	-0.962	8.044	-20.837	-20.837	0.000	0.000	0.000	0.000
7	A	14	LEU	0	-0.101	-0.053	6.226	1.286	1.286	0.000	0.000	0.000	0.000
8	A	15	VAL	0	-0.010	0.005	9.938	1.316	1.316	0.000	0.000	0.000	0.000
9	A	16	GLY	0	0.011	0.015	13.048	1.345	1.345	0.000	0.000	0.000	0.000
10	A	17	ARG	1	0.874	0.935	12.023	21.149	21.149	0.000	0.000	0.000	0.000
11	A	18	ASN	0	0.078	0.062	15.807	0.962	0.962	0.000	0.000	0.000	0.000
12	A	19	LYS	1	0.936	0.946	17.893	13.172	13.172	0.000	0.000	0.000	0.000
13	A	20	ASP	-1	-0.824	-0.899	19.668	-12.989	-12.989	0.000	0.000	0.000	0.000
14	A	21	ALA	0	0.027	0.005	17.629	-0.170	-0.170	0.000	0.000	0.000	0.000
15	A	22	LEU	0	-0.041	-0.019	13.602	-0.843	-0.843	0.000	0.000	0.000	0.000
16	A	23	ARG	1	0.874	0.933	16.505	12.566	12.566	0.000	0.000	0.000	0.000
17	A	24	ASP	-1	-0.901	-0.946	19.127	-13.935	-13.935	0.000	0.000	0.000	0.000
18	A	25	PHE	0	0.035	0.020	10.443	-0.615	-0.615	0.000	0.000	0.000	0.000
19	A	26	LEU	0	-0.020	-0.022	12.833	-0.746	-0.746	0.000	0.000	0.000	0.000
20	A	27	LYS	1	0.937	0.964	15.895	12.625	12.625	0.000	0.000	0.000	0.000
21	A	28	GLU	-1	-0.925	-0.959	17.491	-15.681	-15.681	0.000	0.000	0.000	0.000
22	A	29	HIS	1	0.866	0.930	13.735	20.520	20.520	0.000	0.000	0.000	0.000
23	A	30	ARG	1	0.879	0.955	15.520	13.144	13.144	0.000	0.000	0.000	0.000
24	A	31	GLY	0	-0.081	-0.045	16.646	0.700	0.700	0.000	0.000	0.000	0.000
25	A	32	THR	0	0.009	0.007	14.432	-0.340	-0.340	0.000	0.000	0.000	0.000
26	A	33	ILE	0	-0.042	0.004	10.014	-1.774	-1.774	0.000	0.000	0.000	0.000
27	A	34	LEU	0	-0.058	-0.032	9.568	1.883	1.883	0.000	0.000	0.000	0.000
28	A	35	LEU	0	0.038	0.013	7.798	-2.820	-2.820	0.000	0.000	0.000	0.000
29	A	36	ARG	1	0.908	0.960	2.423	56.760	57.724	0.284	-0.315	-0.933	-0.002
30	A	37	ASP	-1	-0.758	-0.875	5.207	-35.711	-35.711	0.000	0.000	0.000	0.000
31	A	38	ILE	0	-0.105	-0.079	2.253	-8.254	-7.897	1.628	-0.547	-1.439	-0.007
32	A	39	ALA	0	0.066	0.032	5.429	0.602	0.602	0.000	0.000	0.000	0.000
33	A	40	SER	0	-0.017	-0.006	8.770	2.605	2.605	0.000	0.000	0.000	0.000
34	A	41	GLU	-1	-0.919	-0.947	9.375	-25.396	-25.396	0.000	0.000	0.000	0.000
35	A	42	HIS	0	-0.014	-0.006	10.263	-3.073	-3.073	0.000	0.000	0.000	0.000
36	A	43	LYS	1	0.961	1.000	4.208	46.216	46.355	-0.001	-0.008	-0.130	0.000
37	A	44	VAL	0	0.007	-0.004	7.105	-2.296	-2.296	0.000	0.000	0.000	0.000
38	A	45	VAL	0	-0.032	-0.018	6.869	-3.159	-3.159	0.000	0.000	0.000	0.000
39	A	46	TYR	0	0.013	0.013	9.143	2.594	2.594	0.000	0.000	0.000	0.000
40	A	47	LYS	1	0.942	0.964	11.548	16.362	16.362	0.000	0.000	0.000	0.000
41	A	48	PRO	0	0.025	0.007	12.998	0.963	0.963	0.000	0.000	0.000	0.000
42	A	49	ILE	0	-0.018	0.011	15.658	0.629	0.629	0.000	0.000	0.000	0.000
43	A	50	PHE	0	-0.012	-0.019	17.820	-0.170	-0.170	0.000	0.000	0.000	0.000
44	A	51	LYS	1	1.003	1.000	21.994	12.371	12.371	0.000	0.000	0.000	0.000
45	A	52	ARG	1	0.942	0.953	25.266	10.186	10.186	0.000	0.000	0.000	0.000
46	A	53	TYR	0	0.027	0.006	27.787	0.151	0.151	0.000	0.000	0.000	0.000
47	A	54	ASN	0	-0.028	0.044	24.637	0.109	0.109	0.000	0.000	0.000	0.000
48	A	55	GLY	0	0.067	0.010	25.652	-0.051	-0.051	0.000	0.000	0.000	0.000
49	A	56	ASP	-1	-0.891	-0.949	23.193	-13.023	-13.023	0.000	0.000	0.000	0.000
50	A	57	PRO	0	-0.042	-0.031	18.630	0.184	0.184	0.000	0.000	0.000	0.000
51	A	58	ASP	-1	-0.921	-0.964	20.712	-12.730	-12.730	0.000	0.000	0.000	0.000
52	A	59	LEU	0	-0.056	-0.027	17.792	-1.016	-1.016	0.000	0.000	0.000	0.000
53	A	60	ILE	0	0.044	0.026	20.674	0.622	0.622	0.000	0.000	0.000	0.000
54	A	61	GLU	-1	-0.954	-1.007	21.602	-13.942	-13.942	0.000	0.000	0.000	0.000
55	A	62	ASP	-1	-0.921	-0.954	23.683	-11.618	-11.618	0.000	0.000	0.000	0.000
56	A	63	ASN	0	-0.010	-0.004	24.626	0.552	0.552	0.000	0.000	0.000	0.000
57	A	64	SER	0	0.054	0.012	22.979	-0.435	-0.435	0.000	0.000	0.000	0.000
58	A	65	ASN	0	0.071	0.042	23.460	-0.418	-0.418	0.000	0.000	0.000	0.000
59	A	66	ASP	-1	-0.864	-0.930	22.021	-13.209	-13.209	0.000	0.000	0.000	0.000
60	A	67	VAL	0	-0.088	-0.045	18.004	-0.840	-0.840	0.000	0.000	0.000	0.000
61	A	68	GLU	-1	-0.918	-0.962	19.047	-13.769	-13.769	0.000	0.000	0.000	0.000
62	A	69	HIS	0	0.012	0.027	20.745	-0.137	-0.137	0.000	0.000	0.000	0.000
63	A	70	TRP	0	-0.006	-0.023	16.418	-0.734	-0.734	0.000	0.000	0.000	0.000
64	A	71	TYR	0	-0.027	-0.042	14.697	-1.247	-1.247	0.000	0.000	0.000	0.000
65	A	72	ASP	-1	-0.850	-0.930	16.849	-15.888	-15.888	0.000	0.000	0.000	0.000
66	A	73	TYR	0	-0.052	-0.019	16.434	0.187	0.187	0.000	0.000	0.000	0.000
67	A	74	HIS	1	0.807	0.894	11.928	22.806	22.806	0.000	0.000	0.000	0.000
68	A	75	LEU	0	-0.006	0.019	15.515	-0.283	-0.283	0.000	0.000	0.000	0.000
69	A	76	GLU	-1	-0.803	-0.899	16.732	-13.877	-13.877	0.000	0.000	0.000	0.000
70	A	77	ARG	1	0.749	0.869	17.389	15.396	15.396	0.000	0.000	0.000	0.000
71	A	78	TYR	0	-0.028	-0.030	13.529	0.041	0.041	0.000	0.000	0.000	0.000
72	A	79	TRP	0	-0.075	-0.042	9.096	-2.205	-2.205	0.000	0.000	0.000	0.000
73	A	80	ASN	0	0.008	0.009	15.984	0.621	0.621	0.000	0.000	0.000	0.000
74	A	81	THR	0	0.054	0.023	19.046	0.452	0.452	0.000	0.000	0.000	0.000
75	A	82	PRO	0	0.046	0.024	19.540	-0.656	-0.656	0.000	0.000	0.000	0.000
76	A	83	GLU	-1	-0.910	-0.963	17.789	-14.653	-14.653	0.000	0.000	0.000	0.000
77	A	84	LEU	0	0.021	0.015	14.171	-1.001	-1.001	0.000	0.000	0.000	0.000
78	A	85	LYS	1	1.021	1.020	14.758	14.102	14.102	0.000	0.000	0.000	0.000
79	A	86	LYS	1	0.913	0.961	14.790	17.040	17.040	0.000	0.000	0.000	0.000
80	A	87	GLU	-1	-0.984	-0.991	10.064	-26.410	-26.410	0.000	0.000	0.000	0.000
81	A	88	PHE	0	0.037	0.012	10.844	-1.679	-1.679	0.000	0.000	0.000	0.000
82	A	89	TYR	0	0.006	0.004	11.366	-1.152	-1.152	0.000	0.000	0.000	0.000
83	A	90	LYS	1	0.901	0.941	10.992	17.087	17.087	0.000	0.000	0.000	0.000
84	A	91	LYS	1	0.802	0.945	5.504	41.549	41.549	0.000	0.000	0.000	0.000
85	A	92	PHE	0	-0.002	-0.023	7.113	-3.583	-3.583	0.000	0.000	0.000	0.000
86	A	93	GLY	0	0.008	0.023	10.038	0.625	0.625	0.000	0.000	0.000	0.000
87	A	94	PRO	0	-0.006	-0.009	13.161	-0.371	-0.371	0.000	0.000	0.000	0.000
88	A	95	VAL	0	0.043	0.035	15.738	-0.885	-0.885	0.000	0.000	0.000	0.000
89	A	96	ASP	-1	-0.829	-0.902	16.152	-15.935	-15.935	0.000	0.000	0.000	0.000
90	A	97	LEU	0	0.050	0.008	17.852	-0.565	-0.565	0.000	0.000	0.000	0.000
91	A	98	ASN	0	0.011	0.009	19.929	0.770	0.770	0.000	0.000	0.000	0.000
92	A	99	GLN	0	-0.063	-0.047	14.340	-1.335	-1.335	0.000	0.000	0.000	0.000
93	A	100	PRO	0	-0.019	0.010	16.900	0.491	0.491	0.000	0.000	0.000	0.000
94	A	101	ILE	0	0.021	-0.005	17.152	-1.431	-1.431	0.000	0.000	0.000	0.000
95	A	102	ILE	0	-0.040	-0.032	12.853	0.546	0.546	0.000	0.000	0.000	0.000
96	A	103	LEU	0	0.059	0.049	16.012	-0.617	-0.617	0.000	0.000	0.000	0.000
97	A	104	ALA	0	-0.027	-0.015	14.043	-0.399	-0.399	0.000	0.000	0.000	0.000
98	A	105	LYS	1	1.005	1.002	15.998	15.895	15.895	0.000	0.000	0.000	0.000
99	A	106	PRO	0	-0.003	0.012	14.667	-1.495	-1.495	0.000	0.000	0.000	0.000
100	A	107	LEU	0	-0.007	-0.015	12.599	0.885	0.885	0.000	0.000	0.000	0.000
101	A	108	ARG	1	0.905	0.958	15.592	18.818	18.818	0.000	0.000	0.000	0.000
102	A	109	GLN	0	0.074	0.036	18.423	-0.908	-0.908	0.000	0.000	0.000	0.000
103	A	110	HIS	0	-0.001	0.003	14.648	-0.763	-0.763	0.000	0.000	0.000	0.000
104	A	111	ASN	0	0.049	0.005	19.120	0.916	0.916	0.000	0.000	0.000	0.000
105	A	112	ARG	1	0.916	0.969	18.005	15.485	15.485	0.000	0.000	0.000	0.000
106	A	113	GLY	0	0.028	0.037	20.288	0.171	0.171	0.000	0.000	0.000	0.000
107	A	114	ASP	-1	-0.878	-0.973	19.672	-15.176	-15.176	0.000	0.000	0.000	0.000
108	A	115	LEU	0	-0.039	-0.032	19.216	-0.080	-0.080	0.000	0.000	0.000	0.000
109	A	116	VAL	0	-0.044	-0.010	13.755	0.150	0.150	0.000	0.000	0.000	0.000
110	A	117	HIS	0	0.044	0.025	16.848	-0.430	-0.430	0.000	0.000	0.000	0.000
111	A	118	LEU	0	-0.047	-0.019	10.574	-0.977	-0.977	0.000	0.000	0.000	0.000
112	A	119	LEU	0	0.048	0.030	12.690	1.019	1.019	0.000	0.000	0.000	0.000
113	A	120	PRO	0	0.040	0.005	11.240	-3.038	-3.038	0.000	0.000	0.000	0.000
114	A	121	GLN	0	-0.037	-0.020	9.769	-2.181	-2.181	0.000	0.000	0.000	0.000
115	A	122	PHE	0	-0.008	0.004	8.885	-2.207	-2.207	0.000	0.000	0.000	0.000
116	A	123	VAL	0	-0.009	0.020	6.332	-4.798	-4.798	0.000	0.000	0.000	0.000
117	A	124	VAL	0	-0.026	-0.014	1.685	-7.311	-12.123	11.204	-2.277	-4.114	-0.019
118	A	125	PRO	0	0.041	0.023	4.446	0.561	0.737	-0.001	-0.012	-0.162	0.000
119	A	126	VAL	0	-0.096	-0.048	4.473	-8.073	-7.879	-0.001	-0.009	-0.183	0.000
120	A	127	TYR	0	0.019	0.004	6.399	4.400	4.400	0.000	0.000	0.000	0.000
121	A	128	ASN	0	0.029	0.017	9.394	0.877	0.877	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:8:LYS)