FMO DATABASE

FMODB ID: 535RZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1144904.347592
FMO2-HF: Nuclear repulsion	1095339.621362
FMO2-HF: Total energy	-49564.72623
FMO2-MP2: Total energy	-49714.701898

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.
25.751	28.385	4.964	-2.536	-5.061	-0.014

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 : 0.961 / q_NPA : 0.978

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	0.024	0.016	3.886	-4.689	-3.006	-0.009	-0.790	-0.884	0.004
4	A	11	LEU	0	0.020	-0.003	5.913	3.374	3.374	0.000	0.000	0.000	0.000
5	A	12	TRP	0	-0.001	-0.015	8.758	1.704	1.704	0.000	0.000	0.000	0.000
6	A	13	GLU	-1	-0.783	-0.865	7.868	-23.413	-23.413	0.000	0.000	0.000	0.000
7	A	14	LEU	0	-0.063	-0.013	6.270	0.573	0.573	0.000	0.000	0.000	0.000
8	A	15	VAL	0	-0.028	-0.008	9.661	1.574	1.574	0.000	0.000	0.000	0.000
9	A	16	GLY	0	0.021	0.005	12.749	1.345	1.345	0.000	0.000	0.000	0.000
10	A	17	ARG	1	0.773	0.862	11.838	22.824	22.824	0.000	0.000	0.000	0.000
11	A	18	ASN	0	0.058	0.044	15.624	1.069	1.069	0.000	0.000	0.000	0.000
12	A	19	LYS	1	0.944	0.960	17.593	13.033	13.033	0.000	0.000	0.000	0.000
13	A	20	ASP	-1	-0.816	-0.879	19.570	-13.123	-13.123	0.000	0.000	0.000	0.000
14	A	21	ALA	0	0.035	0.017	17.156	-0.127	-0.127	0.000	0.000	0.000	0.000
15	A	22	LEU	0	-0.031	-0.019	13.674	-0.872	-0.872	0.000	0.000	0.000	0.000
16	A	23	ARG	1	0.746	0.835	16.539	12.684	12.684	0.000	0.000	0.000	0.000
17	A	24	ASP	-1	-0.786	-0.879	19.627	-13.652	-13.652	0.000	0.000	0.000	0.000
18	A	25	PHE	0	0.047	0.028	11.185	-0.353	-0.353	0.000	0.000	0.000	0.000
19	A	26	LEU	0	-0.045	-0.028	13.810	-0.788	-0.788	0.000	0.000	0.000	0.000
20	A	27	LYS	1	0.839	0.905	16.629	12.680	12.680	0.000	0.000	0.000	0.000
21	A	28	GLU	-1	-0.905	-0.959	17.435	-16.575	-16.575	0.000	0.000	0.000	0.000
22	A	29	HIS	1	0.823	0.911	14.681	19.345	19.345	0.000	0.000	0.000	0.000
23	A	30	ARG	1	0.840	0.921	16.251	12.360	12.360	0.000	0.000	0.000	0.000
24	A	31	GLY	0	-0.035	-0.012	17.360	0.808	0.808	0.000	0.000	0.000	0.000
25	A	32	THR	0	0.010	0.009	15.461	-0.300	-0.300	0.000	0.000	0.000	0.000
26	A	33	ILE	0	-0.043	-0.009	10.622	-1.750	-1.750	0.000	0.000	0.000	0.000
27	A	34	LEU	0	-0.035	-0.006	10.735	1.720	1.720	0.000	0.000	0.000	0.000
28	A	35	LEU	0	0.025	0.006	8.494	-2.268	-2.268	0.000	0.000	0.000	0.000
29	A	36	ARG	1	0.882	0.943	3.838	45.144	45.315	-0.001	-0.015	-0.155	0.000
30	A	37	ASP	-1	-0.749	-0.853	5.749	-34.345	-34.345	0.000	0.000	0.000	0.000
31	A	38	ILE	0	-0.057	-0.043	2.348	-7.914	-6.965	0.567	-0.434	-1.081	-0.005
32	A	39	ALA	0	0.043	0.035	5.821	0.667	0.667	0.000	0.000	0.000	0.000
33	A	40	SER	0	-0.012	-0.006	9.272	2.342	2.342	0.000	0.000	0.000	0.000
34	A	41	GLU	-1	-0.847	-0.922	9.809	-27.238	-27.238	0.000	0.000	0.000	0.000
35	A	42	HIS	0	0.045	0.015	10.552	-3.086	-3.086	0.000	0.000	0.000	0.000
36	A	43	LYS	1	0.835	0.957	6.047	32.892	32.892	0.000	0.000	0.000	0.000
37	A	44	VAL	0	-0.015	-0.016	7.849	-2.298	-2.298	0.000	0.000	0.000	0.000
38	A	45	VAL	0	-0.021	-0.015	8.163	-2.788	-2.788	0.000	0.000	0.000	0.000
39	A	46	TYR	0	0.025	0.003	10.243	3.044	3.044	0.000	0.000	0.000	0.000
40	A	47	LYS	1	0.930	0.960	12.372	15.450	15.450	0.000	0.000	0.000	0.000
41	A	48	PRO	0	0.029	0.014	13.410	0.885	0.885	0.000	0.000	0.000	0.000
42	A	49	ILE	0	-0.020	-0.001	16.220	0.657	0.657	0.000	0.000	0.000	0.000
43	A	50	PHE	0	-0.025	-0.019	18.258	-0.369	-0.369	0.000	0.000	0.000	0.000
44	A	51	LYS	1	0.913	0.977	22.601	13.439	13.439	0.000	0.000	0.000	0.000
45	A	52	ARG	1	0.942	0.960	25.889	9.965	9.965	0.000	0.000	0.000	0.000
46	A	53	TYR	0	0.020	0.011	28.612	0.141	0.141	0.000	0.000	0.000	0.000
47	A	54	ASN	0	-0.003	0.018	25.453	0.079	0.079	0.000	0.000	0.000	0.000
48	A	55	GLY	0	0.064	0.049	26.926	0.055	0.055	0.000	0.000	0.000	0.000
49	A	56	ASP	-1	-0.798	-0.897	23.943	-12.842	-12.842	0.000	0.000	0.000	0.000
50	A	57	PRO	0	-0.014	-0.005	19.401	0.227	0.227	0.000	0.000	0.000	0.000
51	A	58	ASP	-1	-0.875	-0.969	20.829	-12.345	-12.345	0.000	0.000	0.000	0.000
52	A	59	LEU	0	-0.060	-0.028	18.352	-1.056	-1.056	0.000	0.000	0.000	0.000
53	A	60	ILE	0	0.021	0.027	21.112	0.677	0.677	0.000	0.000	0.000	0.000
54	A	61	GLU	-1	-0.924	-0.983	21.777	-14.283	-14.283	0.000	0.000	0.000	0.000
55	A	62	ASP	-1	-0.877	-0.949	23.867	-11.872	-11.872	0.000	0.000	0.000	0.000
56	A	63	ASN	0	0.014	0.002	25.027	0.376	0.376	0.000	0.000	0.000	0.000
57	A	64	SER	0	0.007	-0.009	23.246	-0.438	-0.438	0.000	0.000	0.000	0.000
58	A	65	ASN	0	-0.003	-0.002	23.241	-0.220	-0.220	0.000	0.000	0.000	0.000
59	A	66	ASP	-1	-0.818	-0.895	22.096	-13.480	-13.480	0.000	0.000	0.000	0.000
60	A	67	VAL	0	-0.053	-0.022	18.092	-0.828	-0.828	0.000	0.000	0.000	0.000
61	A	68	GLU	-1	-0.809	-0.904	19.065	-13.700	-13.700	0.000	0.000	0.000	0.000
62	A	69	HIS	0	0.017	0.019	20.637	-0.354	-0.354	0.000	0.000	0.000	0.000
63	A	70	TRP	0	-0.037	-0.040	16.933	-0.837	-0.837	0.000	0.000	0.000	0.000
64	A	71	TYR	0	-0.015	-0.026	15.034	-1.267	-1.267	0.000	0.000	0.000	0.000
65	A	72	ASP	-1	-0.829	-0.934	16.650	-16.386	-16.386	0.000	0.000	0.000	0.000
66	A	73	TYR	0	-0.044	-0.011	16.855	0.386	0.386	0.000	0.000	0.000	0.000
67	A	74	HIS	1	0.760	0.829	12.152	22.600	22.600	0.000	0.000	0.000	0.000
68	A	75	LEU	0	0.004	0.010	15.514	-0.457	-0.457	0.000	0.000	0.000	0.000
69	A	76	GLU	-1	-0.814	-0.902	17.002	-13.638	-13.638	0.000	0.000	0.000	0.000
70	A	77	ARG	1	0.765	0.874	17.762	15.345	15.345	0.000	0.000	0.000	0.000
71	A	78	TYR	0	-0.034	-0.014	13.454	0.429	0.429	0.000	0.000	0.000	0.000
72	A	79	TRP	0	-0.039	-0.036	9.176	-2.071	-2.071	0.000	0.000	0.000	0.000
73	A	80	ASN	0	-0.024	-0.004	15.742	0.575	0.575	0.000	0.000	0.000	0.000
74	A	81	THR	0	0.026	-0.008	18.882	0.389	0.389	0.000	0.000	0.000	0.000
75	A	82	PRO	0	0.030	0.014	19.390	-0.739	-0.739	0.000	0.000	0.000	0.000
76	A	83	GLU	-1	-0.863	-0.921	18.132	-15.458	-15.458	0.000	0.000	0.000	0.000
77	A	84	LEU	0	0.036	0.032	13.547	-1.218	-1.218	0.000	0.000	0.000	0.000
78	A	85	LYS	1	0.975	1.000	14.757	14.491	14.491	0.000	0.000	0.000	0.000
79	A	86	LYS	1	0.876	0.933	15.438	17.721	17.721	0.000	0.000	0.000	0.000
80	A	87	GLU	-1	-0.896	-0.937	9.483	-30.507	-30.507	0.000	0.000	0.000	0.000
81	A	88	PHE	0	0.027	0.001	11.392	-1.396	-1.396	0.000	0.000	0.000	0.000
82	A	89	TYR	0	0.018	0.006	11.979	-1.009	-1.009	0.000	0.000	0.000	0.000
83	A	90	LYS	1	0.917	0.951	11.459	18.243	18.243	0.000	0.000	0.000	0.000
84	A	91	LYS	1	0.782	0.922	6.432	37.135	37.135	0.000	0.000	0.000	0.000
85	A	92	PHE	0	-0.014	-0.012	7.168	-3.726	-3.726	0.000	0.000	0.000	0.000
86	A	93	GLY	0	0.033	0.044	10.481	0.792	0.792	0.000	0.000	0.000	0.000
87	A	94	PRO	0	0.012	0.009	13.623	-0.347	-0.347	0.000	0.000	0.000	0.000
88	A	95	VAL	0	0.023	0.028	16.265	-0.919	-0.919	0.000	0.000	0.000	0.000
89	A	96	ASP	-1	-0.769	-0.862	16.277	-16.835	-16.835	0.000	0.000	0.000	0.000
90	A	97	LEU	0	0.023	0.000	18.097	-0.409	-0.409	0.000	0.000	0.000	0.000
91	A	98	ASN	0	-0.040	-0.015	19.756	1.046	1.046	0.000	0.000	0.000	0.000
92	A	99	GLN	0	-0.068	-0.041	14.655	-1.292	-1.292	0.000	0.000	0.000	0.000
93	A	100	PRO	0	-0.002	0.012	17.340	0.495	0.495	0.000	0.000	0.000	0.000
94	A	101	ILE	0	0.001	-0.015	17.279	-1.385	-1.385	0.000	0.000	0.000	0.000
95	A	102	ILE	0	-0.008	-0.013	13.112	0.662	0.662	0.000	0.000	0.000	0.000
96	A	103	LEU	0	0.041	0.036	16.766	-0.337	-0.337	0.000	0.000	0.000	0.000
97	A	104	ALA	0	-0.015	-0.013	14.880	-0.464	-0.464	0.000	0.000	0.000	0.000
98	A	105	LYS	1	1.017	1.010	16.847	15.011	15.011	0.000	0.000	0.000	0.000
99	A	106	PRO	0	-0.004	0.010	15.347	-1.183	-1.183	0.000	0.000	0.000	0.000
100	A	107	LEU	0	-0.014	-0.015	13.256	0.847	0.847	0.000	0.000	0.000	0.000
101	A	108	ARG	1	0.887	0.946	17.074	17.165	17.165	0.000	0.000	0.000	0.000
102	A	109	GLN	0	0.047	0.016	19.280	-0.883	-0.883	0.000	0.000	0.000	0.000
103	A	110	HIS	0	-0.008	-0.019	15.926	-0.496	-0.496	0.000	0.000	0.000	0.000
104	A	111	ASN	0	0.020	0.006	19.989	0.038	0.038	0.000	0.000	0.000	0.000
105	A	112	ARG	1	0.924	0.965	18.926	14.988	14.988	0.000	0.000	0.000	0.000
106	A	113	GLY	0	0.054	0.048	21.221	0.325	0.325	0.000	0.000	0.000	0.000
107	A	114	ASP	-1	-0.913	-0.964	20.448	-14.230	-14.230	0.000	0.000	0.000	0.000
108	A	115	LEU	0	-0.039	-0.030	20.187	0.015	0.015	0.000	0.000	0.000	0.000
109	A	116	VAL	0	-0.030	-0.007	14.833	0.043	0.043	0.000	0.000	0.000	0.000
110	A	117	HIS	0	0.046	0.030	17.450	-0.296	-0.296	0.000	0.000	0.000	0.000
111	A	118	LEU	0	-0.047	-0.025	11.321	-0.987	-0.987	0.000	0.000	0.000	0.000
112	A	119	LEU	0	0.049	0.035	13.079	0.749	0.749	0.000	0.000	0.000	0.000
113	A	120	PRO	0	0.044	0.012	11.408	-2.914	-2.914	0.000	0.000	0.000	0.000
114	A	121	GLN	0	-0.035	-0.029	10.051	-2.155	-2.155	0.000	0.000	0.000	0.000
115	A	122	PHE	0	-0.021	-0.008	8.879	-2.296	-2.296	0.000	0.000	0.000	0.000
116	A	123	VAL	0	-0.012	0.007	6.622	-3.819	-3.819	0.000	0.000	0.000	0.000
117	A	124	VAL	0	-0.020	-0.015	1.936	-9.320	-9.591	4.408	-1.295	-2.842	-0.013
118	A	125	PRO	0	0.026	0.015	4.988	3.752	3.752	0.000	0.000	0.000	0.000
119	A	126	VAL	0	-0.063	-0.037	5.122	-6.565	-6.463	-0.001	-0.002	-0.099	0.000
120	A	127	TYR	0	0.051	0.020	7.472	3.249	3.249	0.000	0.000	0.000	0.000
121	A	128	ASN	0	-0.015	-0.003	10.274	1.334	1.334	0.000	0.000	0.000	0.000

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