FMO DATABASE

FMODB ID: 6YGZZ

Calculation Name: 2DBB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2DBB

Chain ID: A

ChEMBL ID:

UniProt ID: O57802

Base Structure: X-ray

Registration Date: 2023-09-22

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	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	146
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1281014.22155
FMO2-HF: Nuclear repulsion	1222863.602066
FMO2-HF: Total energy	-58150.619483
FMO2-MP2: Total energy	-58323.822152

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:6:LYS)

Summations of interaction energy for fragment #1(A:6: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.
60.329	59.899	14.528	-6.765	-7.333	-0.076

Interaction energy analysis for fragmet #1(A:6:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.975 / q_NPA : 0.982

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	8	ASP	-1	-0.740	-0.836	1.760	-82.517	-84.080	13.208	-6.048	-5.598	-0.068
4	A	9	ARG	1	1.007	0.986	4.010	27.687	28.030	0.000	-0.081	-0.262	0.000
5	A	10	VAL	0	0.012	0.004	5.090	2.588	2.650	-0.001	-0.001	-0.060	0.000
6	A	11	ASP	-1	-0.773	-0.866	5.366	-35.676	-35.676	0.000	0.000	0.000	0.000
7	A	12	MET	0	-0.022	-0.009	3.001	-7.224	-6.546	1.322	-0.635	-1.365	-0.008
8	A	13	GLN	0	0.026	0.016	5.369	3.676	3.726	-0.001	0.000	-0.048	0.000
9	A	14	LEU	0	0.002	0.001	8.269	3.167	3.167	0.000	0.000	0.000	0.000
10	A	15	VAL	0	0.017	0.003	8.175	2.546	2.546	0.000	0.000	0.000	0.000
11	A	16	LYS	1	0.915	0.973	8.706	26.799	26.799	0.000	0.000	0.000	0.000
12	A	17	ILE	0	0.009	0.009	10.947	2.032	2.032	0.000	0.000	0.000	0.000
13	A	18	LEU	0	-0.036	-0.029	13.535	1.560	1.560	0.000	0.000	0.000	0.000
14	A	19	SER	0	-0.069	-0.050	12.488	0.631	0.631	0.000	0.000	0.000	0.000
15	A	20	GLU	-1	-0.961	-0.949	14.963	-16.225	-16.225	0.000	0.000	0.000	0.000
16	A	21	ASN	0	0.035	-0.003	17.488	1.290	1.290	0.000	0.000	0.000	0.000
17	A	22	SER	0	-0.026	-0.010	18.463	-0.236	-0.236	0.000	0.000	0.000	0.000
18	A	23	ARG	1	0.929	0.951	19.433	12.484	12.484	0.000	0.000	0.000	0.000
19	A	24	LEU	0	-0.007	0.026	17.988	0.498	0.498	0.000	0.000	0.000	0.000
20	A	25	THR	0	-0.012	-0.047	20.720	-0.406	-0.406	0.000	0.000	0.000	0.000
21	A	26	TYR	0	0.014	-0.036	19.645	-0.738	-0.738	0.000	0.000	0.000	0.000
22	A	27	ARG	1	0.822	0.893	20.319	12.017	12.017	0.000	0.000	0.000	0.000
23	A	28	GLU	-1	-0.717	-0.817	21.216	-13.901	-13.901	0.000	0.000	0.000	0.000
24	A	29	LEU	0	0.011	0.007	15.675	-0.727	-0.727	0.000	0.000	0.000	0.000
25	A	30	ALA	0	-0.057	-0.033	16.480	-1.138	-1.138	0.000	0.000	0.000	0.000
26	A	31	ASP	-1	-0.809	-0.885	18.332	-14.138	-14.138	0.000	0.000	0.000	0.000
27	A	32	ILE	0	0.014	0.009	14.894	-0.393	-0.393	0.000	0.000	0.000	0.000
28	A	33	LEU	0	-0.078	-0.045	11.334	-1.118	-1.118	0.000	0.000	0.000	0.000
29	A	34	ASN	0	-0.044	-0.007	14.613	-0.050	-0.050	0.000	0.000	0.000	0.000
30	A	35	THR	0	0.004	0.000	15.006	-0.129	-0.129	0.000	0.000	0.000	0.000
31	A	36	THR	0	0.047	0.015	17.766	0.614	0.614	0.000	0.000	0.000	0.000
32	A	37	ARG	1	1.018	0.990	18.689	11.808	11.808	0.000	0.000	0.000	0.000
33	A	38	GLN	0	0.017	0.018	19.973	-0.556	-0.556	0.000	0.000	0.000	0.000
34	A	39	ARG	1	0.965	0.983	15.525	17.280	17.280	0.000	0.000	0.000	0.000
35	A	40	ILE	0	0.009	0.027	14.813	-1.343	-1.343	0.000	0.000	0.000	0.000
36	A	41	ALA	0	0.024	0.019	15.909	-0.681	-0.681	0.000	0.000	0.000	0.000
37	A	42	ARG	1	0.832	0.898	15.858	16.942	16.942	0.000	0.000	0.000	0.000
38	A	43	ARG	1	0.811	0.877	8.354	31.631	31.631	0.000	0.000	0.000	0.000
39	A	44	ILE	0	0.076	0.034	12.856	-1.039	-1.039	0.000	0.000	0.000	0.000
40	A	45	ASP	-1	-0.848	-0.898	14.938	-16.293	-16.293	0.000	0.000	0.000	0.000
41	A	46	LYS	1	0.875	0.920	7.942	33.640	33.640	0.000	0.000	0.000	0.000
42	A	47	LEU	0	0.003	-0.008	8.244	-0.421	-0.421	0.000	0.000	0.000	0.000
43	A	48	LYS	1	0.933	0.983	11.142	16.802	16.802	0.000	0.000	0.000	0.000
44	A	49	LYS	1	0.872	0.920	13.616	16.256	16.256	0.000	0.000	0.000	0.000
45	A	50	LEU	0	-0.023	-0.007	6.642	0.279	0.279	0.000	0.000	0.000	0.000
46	A	51	GLY	0	0.021	0.020	10.074	-0.483	-0.483	0.000	0.000	0.000	0.000
47	A	52	ILE	0	-0.055	-0.024	6.265	-0.389	-0.389	0.000	0.000	0.000	0.000
48	A	53	ILE	0	-0.037	-0.021	10.056	0.138	0.138	0.000	0.000	0.000	0.000
49	A	54	ARG	1	0.983	0.984	13.419	19.186	19.186	0.000	0.000	0.000	0.000
50	A	55	LYS	1	0.960	0.975	15.953	14.319	14.319	0.000	0.000	0.000	0.000
51	A	56	PHE	0	-0.009	0.014	16.940	-0.952	-0.952	0.000	0.000	0.000	0.000
52	A	57	THR	0	0.013	-0.005	20.004	0.942	0.942	0.000	0.000	0.000	0.000
53	A	58	ILE	0	0.013	0.009	21.954	-0.389	-0.389	0.000	0.000	0.000	0.000
54	A	59	ILE	0	0.015	0.004	20.750	-0.160	-0.160	0.000	0.000	0.000	0.000
55	A	60	PRO	0	-0.006	0.011	24.700	0.213	0.213	0.000	0.000	0.000	0.000
56	A	61	ASP	-1	-0.782	-0.890	28.550	-9.815	-9.815	0.000	0.000	0.000	0.000
57	A	62	ILE	0	-0.008	-0.012	28.764	0.308	0.308	0.000	0.000	0.000	0.000
58	A	63	ASP	-1	-0.796	-0.874	32.107	-8.314	-8.314	0.000	0.000	0.000	0.000
59	A	64	LYS	1	0.851	0.904	33.961	9.524	9.524	0.000	0.000	0.000	0.000
60	A	65	LEU	0	-0.067	-0.023	32.165	0.158	0.158	0.000	0.000	0.000	0.000
61	A	66	GLY	0	0.014	0.023	36.175	0.134	0.134	0.000	0.000	0.000	0.000
62	A	67	TYR	0	-0.026	-0.014	34.438	0.139	0.139	0.000	0.000	0.000	0.000
63	A	68	MET	0	0.004	-0.004	34.332	0.032	0.032	0.000	0.000	0.000	0.000
64	A	69	TYR	0	-0.018	-0.020	26.472	-0.188	-0.188	0.000	0.000	0.000	0.000
65	A	70	ALA	0	0.020	0.017	32.168	0.279	0.279	0.000	0.000	0.000	0.000
66	A	71	ILE	0	-0.037	-0.021	27.504	-0.405	-0.405	0.000	0.000	0.000	0.000
67	A	72	VAL	0	0.017	0.014	30.663	0.362	0.362	0.000	0.000	0.000	0.000
68	A	73	LEU	0	-0.032	-0.009	29.077	-0.465	-0.465	0.000	0.000	0.000	0.000
69	A	74	ILE	0	0.043	0.022	30.325	0.367	0.367	0.000	0.000	0.000	0.000
70	A	75	LYS	1	0.885	0.952	30.477	8.880	8.880	0.000	0.000	0.000	0.000
71	A	76	SER	0	0.069	0.022	31.193	0.184	0.184	0.000	0.000	0.000	0.000
72	A	77	LYS	1	0.854	0.930	33.175	7.621	7.621	0.000	0.000	0.000	0.000
73	A	78	VAL	0	-0.005	-0.004	33.755	-0.032	-0.032	0.000	0.000	0.000	0.000
74	A	79	PRO	0	0.017	-0.009	28.167	-0.086	-0.086	0.000	0.000	0.000	0.000
75	A	80	SER	0	0.022	0.013	29.075	-0.112	-0.112	0.000	0.000	0.000	0.000
76	A	81	ASP	-1	-0.774	-0.891	30.611	-8.588	-8.588	0.000	0.000	0.000	0.000
77	A	82	ALA	0	-0.015	0.002	27.165	0.016	0.016	0.000	0.000	0.000	0.000
78	A	83	ASP	-1	-0.783	-0.880	24.948	-11.443	-11.443	0.000	0.000	0.000	0.000
79	A	84	LYS	1	0.827	0.908	27.800	8.687	8.687	0.000	0.000	0.000	0.000
80	A	85	VAL	0	0.039	0.026	30.702	0.115	0.115	0.000	0.000	0.000	0.000
81	A	86	ILE	0	0.028	0.001	24.317	-0.026	-0.026	0.000	0.000	0.000	0.000
82	A	87	SER	0	-0.057	-0.025	27.921	-0.150	-0.150	0.000	0.000	0.000	0.000
83	A	88	GLU	-1	-0.852	-0.897	29.123	-8.133	-8.133	0.000	0.000	0.000	0.000
84	A	89	ILE	0	0.000	-0.020	28.617	0.130	0.130	0.000	0.000	0.000	0.000
85	A	90	SER	0	-0.066	-0.047	25.989	-0.270	-0.270	0.000	0.000	0.000	0.000
86	A	91	ASP	-1	-0.941	-0.962	27.772	-10.226	-10.226	0.000	0.000	0.000	0.000
87	A	92	ILE	0	-0.061	-0.005	30.097	0.247	0.247	0.000	0.000	0.000	0.000
88	A	93	GLU	-1	-0.844	-0.938	30.968	-9.700	-9.700	0.000	0.000	0.000	0.000
89	A	94	TYR	0	0.045	0.032	30.853	-0.440	-0.440	0.000	0.000	0.000	0.000
90	A	95	VAL	0	0.000	-0.003	27.612	-0.120	-0.120	0.000	0.000	0.000	0.000
91	A	96	LYS	1	0.719	0.861	26.789	10.128	10.128	0.000	0.000	0.000	0.000
92	A	97	SER	0	-0.128	-0.093	22.674	-0.450	-0.450	0.000	0.000	0.000	0.000
93	A	98	VAL	0	0.071	0.038	23.099	0.537	0.537	0.000	0.000	0.000	0.000
94	A	99	GLU	-1	-0.883	-0.915	20.501	-14.157	-14.157	0.000	0.000	0.000	0.000
95	A	100	LYS	1	0.821	0.890	21.708	12.510	12.510	0.000	0.000	0.000	0.000
96	A	101	GLY	0	-0.014	-0.008	21.321	-0.690	-0.690	0.000	0.000	0.000	0.000
97	A	102	VAL	0	-0.023	-0.024	22.126	0.432	0.432	0.000	0.000	0.000	0.000
98	A	103	GLY	0	0.035	0.016	24.251	-0.320	-0.320	0.000	0.000	0.000	0.000
99	A	104	ARG	1	0.846	0.916	27.005	9.253	9.253	0.000	0.000	0.000	0.000
100	A	105	TYR	0	-0.073	-0.064	28.757	0.276	0.276	0.000	0.000	0.000	0.000
101	A	106	ASN	0	-0.022	-0.018	26.486	-0.069	-0.069	0.000	0.000	0.000	0.000
102	A	107	ILE	0	0.013	0.004	26.027	-0.333	-0.333	0.000	0.000	0.000	0.000
103	A	108	ILE	0	-0.011	0.016	24.532	0.376	0.376	0.000	0.000	0.000	0.000
104	A	109	VAL	0	0.019	0.015	25.848	-0.337	-0.337	0.000	0.000	0.000	0.000
105	A	110	ARG	1	0.922	0.978	23.906	12.594	12.594	0.000	0.000	0.000	0.000
106	A	111	LEU	0	0.036	0.025	28.628	-0.050	-0.050	0.000	0.000	0.000	0.000
107	A	112	LEU	0	-0.044	-0.028	31.104	-0.197	-0.197	0.000	0.000	0.000	0.000
108	A	113	LEU	0	0.018	0.016	32.882	0.163	0.163	0.000	0.000	0.000	0.000
109	A	114	PRO	0	0.055	0.022	36.626	-0.152	-0.152	0.000	0.000	0.000	0.000
110	A	115	LYS	1	0.816	0.873	37.704	8.291	8.291	0.000	0.000	0.000	0.000
111	A	116	ASP	-1	-0.816	-0.873	40.452	-6.843	-6.843	0.000	0.000	0.000	0.000
112	A	117	ILE	0	0.028	0.003	42.504	-0.103	-0.103	0.000	0.000	0.000	0.000
113	A	118	LYS	1	0.822	0.906	43.938	6.747	6.747	0.000	0.000	0.000	0.000
114	A	119	ASP	-1	-0.830	-0.931	43.177	-7.013	-7.013	0.000	0.000	0.000	0.000
115	A	120	ALA	0	-0.054	-0.023	39.821	-0.160	-0.160	0.000	0.000	0.000	0.000
116	A	121	GLU	-1	-0.887	-0.926	40.416	-7.131	-7.131	0.000	0.000	0.000	0.000
117	A	122	ASN	0	0.005	0.013	42.225	-0.134	-0.134	0.000	0.000	0.000	0.000
118	A	123	LEU	0	0.017	0.004	37.724	-0.049	-0.049	0.000	0.000	0.000	0.000
119	A	124	ILE	0	-0.020	-0.011	37.374	-0.210	-0.210	0.000	0.000	0.000	0.000
120	A	125	SER	0	-0.032	-0.047	38.937	-0.098	-0.098	0.000	0.000	0.000	0.000
121	A	126	GLU	-1	-0.859	-0.915	37.786	-8.144	-8.144	0.000	0.000	0.000	0.000
122	A	127	PHE	0	0.019	-0.006	31.536	-0.134	-0.134	0.000	0.000	0.000	0.000
123	A	128	LEU	0	-0.007	-0.023	36.505	-0.121	-0.121	0.000	0.000	0.000	0.000
124	A	129	GLN	0	-0.028	0.004	38.467	0.000	0.000	0.000	0.000	0.000	0.000
125	A	130	ARG	1	0.816	0.899	35.201	8.501	8.501	0.000	0.000	0.000	0.000
126	A	131	ILE	0	-0.069	-0.029	33.947	-0.122	-0.122	0.000	0.000	0.000	0.000
127	A	132	LYS	1	0.852	0.922	36.271	8.168	8.168	0.000	0.000	0.000	0.000
128	A	133	ASN	0	-0.023	-0.019	36.987	-0.046	-0.046	0.000	0.000	0.000	0.000
129	A	134	ALA	0	0.042	0.032	35.532	-0.087	-0.087	0.000	0.000	0.000	0.000
130	A	135	GLU	-1	-0.918	-0.943	36.199	-7.521	-7.521	0.000	0.000	0.000	0.000
131	A	136	ASN	0	-0.009	-0.010	35.705	-0.044	-0.044	0.000	0.000	0.000	0.000
132	A	137	VAL	0	0.048	0.014	35.092	-0.271	-0.271	0.000	0.000	0.000	0.000
133	A	138	GLU	-1	-0.797	-0.851	34.636	-8.345	-8.345	0.000	0.000	0.000	0.000
134	A	139	VAL	0	-0.006	-0.013	34.813	-0.276	-0.276	0.000	0.000	0.000	0.000
135	A	140	ILE	0	-0.015	-0.005	32.112	0.177	0.177	0.000	0.000	0.000	0.000
136	A	141	LEU	0	0.045	0.019	33.935	-0.270	-0.270	0.000	0.000	0.000	0.000
137	A	142	ILE	0	-0.058	-0.031	30.447	-0.052	-0.052	0.000	0.000	0.000	0.000
138	A	143	SER	0	0.023	0.012	33.686	0.008	0.008	0.000	0.000	0.000	0.000
139	A	144	GLU	-1	-0.841	-0.905	33.368	-9.231	-9.231	0.000	0.000	0.000	0.000
140	A	145	VAL	0	-0.029	-0.019	27.622	-0.261	-0.261	0.000	0.000	0.000	0.000
141	A	146	ARG	1	0.856	0.912	28.480	9.567	9.567	0.000	0.000	0.000	0.000
142	A	147	LYS	1	0.837	0.891	20.235	14.682	14.682	0.000	0.000	0.000	0.000
143	A	148	PHE	0	-0.006	-0.007	22.712	0.075	0.075	0.000	0.000	0.000	0.000
144	A	149	GLU	-1	-0.791	-0.862	18.130	-15.405	-15.405	0.000	0.000	0.000	0.000
145	A	150	ILE	0	-0.006	-0.002	15.681	0.031	0.031	0.000	0.000	0.000	0.000
146	A	151	ILE	0	0.015	0.012	10.473	-1.734	-1.734	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:6:LYS)