FMO DATABASE

FMODB ID: QYZQY

Calculation Name: 3QD8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3QD8

Chain ID: A

ChEMBL ID:

UniProt ID: P9WNE5

Base Structure: X-ray

Registration Date: 2023-09-19

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	172
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1791592.723093
FMO2-HF: Nuclear repulsion	1723534.179104
FMO2-HF: Total energy	-68058.543989
FMO2-MP2: Total energy	-68257.805136

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:10:LYS)

Summations of interaction energy for fragment #1(A:10: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.
-300.812	-299.142	30.848	-16.709	-15.812	-0.169

Interaction energy analysis for fragmet #1(A:10:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.804 / q_NPA : 0.878

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	12	HIS	0	-0.018	-0.012	2.950	2.755	5.667	0.327	-1.405	-1.835	0.008
4	A	13	ALA	0	-0.005	-0.006	2.932	1.106	2.020	0.192	-0.351	-0.756	0.000
5	A	14	LEU	0	-0.006	-0.001	4.131	2.549	2.896	-0.001	-0.110	-0.237	0.000
6	A	15	MET	0	0.035	0.025	6.197	3.968	3.968	0.000	0.000	0.000	0.000
7	A	16	GLN	0	0.014	0.001	7.658	2.677	2.677	0.000	0.000	0.000	0.000
8	A	17	GLU	-1	-0.841	-0.889	8.315	-28.006	-28.006	0.000	0.000	0.000	0.000
9	A	18	GLN	0	-0.005	-0.017	10.085	0.573	0.573	0.000	0.000	0.000	0.000
10	A	19	ILE	0	-0.018	-0.006	11.845	1.776	1.776	0.000	0.000	0.000	0.000
11	A	20	HIS	0	-0.045	-0.034	13.431	1.019	1.019	0.000	0.000	0.000	0.000
12	A	21	ASN	0	-0.034	-0.027	12.643	1.958	1.958	0.000	0.000	0.000	0.000
13	A	22	GLU	-1	-0.770	-0.852	15.921	-16.755	-16.755	0.000	0.000	0.000	0.000
14	A	23	PHE	0	-0.027	-0.018	17.614	1.095	1.095	0.000	0.000	0.000	0.000
15	A	24	THR	0	-0.018	-0.047	19.293	0.953	0.953	0.000	0.000	0.000	0.000
16	A	25	ALA	0	0.016	0.020	20.423	0.682	0.682	0.000	0.000	0.000	0.000
17	A	26	ALA	0	0.002	-0.004	22.134	0.651	0.651	0.000	0.000	0.000	0.000
18	A	27	GLN	0	0.019	0.002	23.856	0.659	0.659	0.000	0.000	0.000	0.000
19	A	28	GLN	0	-0.012	-0.017	24.962	0.417	0.417	0.000	0.000	0.000	0.000
20	A	29	TYR	0	-0.013	-0.039	25.075	0.685	0.685	0.000	0.000	0.000	0.000
21	A	30	VAL	0	-0.011	0.002	28.164	0.444	0.444	0.000	0.000	0.000	0.000
22	A	31	ALA	0	-0.030	-0.007	29.681	0.380	0.380	0.000	0.000	0.000	0.000
23	A	32	ILE	0	-0.025	-0.014	28.722	0.332	0.332	0.000	0.000	0.000	0.000
24	A	33	ALA	0	-0.012	0.000	32.373	0.287	0.287	0.000	0.000	0.000	0.000
25	A	34	VAL	0	0.012	0.000	34.216	0.300	0.300	0.000	0.000	0.000	0.000
26	A	35	TYR	0	-0.067	-0.054	35.225	0.151	0.151	0.000	0.000	0.000	0.000
27	A	36	PHE	0	0.014	-0.005	33.850	0.220	0.220	0.000	0.000	0.000	0.000
28	A	37	ASP	-1	-0.881	-0.923	38.396	-7.511	-7.511	0.000	0.000	0.000	0.000
29	A	38	SER	0	-0.089	-0.056	40.070	0.203	0.203	0.000	0.000	0.000	0.000
30	A	39	GLU	-1	-0.880	-0.911	40.221	-7.425	-7.425	0.000	0.000	0.000	0.000
31	A	40	ASP	-1	-0.953	-0.966	42.976	-6.609	-6.609	0.000	0.000	0.000	0.000
32	A	41	LEU	0	-0.095	-0.038	40.434	0.065	0.065	0.000	0.000	0.000	0.000
33	A	42	PRO	0	0.046	0.009	40.808	-0.221	-0.221	0.000	0.000	0.000	0.000
34	A	43	GLN	0	-0.029	-0.015	40.786	-0.288	-0.288	0.000	0.000	0.000	0.000
35	A	44	LEU	0	0.013	-0.007	36.452	-0.260	-0.260	0.000	0.000	0.000	0.000
36	A	45	ALA	0	0.026	0.024	36.199	-0.296	-0.296	0.000	0.000	0.000	0.000
37	A	46	LYS	1	0.847	0.928	36.123	7.763	7.763	0.000	0.000	0.000	0.000
38	A	47	HIS	0	-0.033	-0.015	31.506	0.076	0.076	0.000	0.000	0.000	0.000
39	A	48	PHE	0	0.013	-0.012	29.871	-0.315	-0.315	0.000	0.000	0.000	0.000
40	A	49	TYR	0	-0.054	-0.050	31.246	-0.427	-0.427	0.000	0.000	0.000	0.000
41	A	50	SER	0	-0.034	-0.009	31.279	-0.321	-0.321	0.000	0.000	0.000	0.000
42	A	51	GLN	0	0.003	-0.021	26.705	0.140	0.140	0.000	0.000	0.000	0.000
43	A	52	ALA	0	0.026	0.012	27.068	-0.503	-0.503	0.000	0.000	0.000	0.000
44	A	53	VAL	0	-0.062	-0.029	26.208	-0.426	-0.426	0.000	0.000	0.000	0.000
45	A	54	GLU	-1	-0.737	-0.831	25.292	-12.297	-12.297	0.000	0.000	0.000	0.000
46	A	55	GLH	0	0.039	-0.003	19.716	-0.515	-0.515	0.000	0.000	0.000	0.000
47	A	56	ARG	1	0.959	0.977	21.566	10.847	10.847	0.000	0.000	0.000	0.000
48	A	57	ASN	0	-0.085	-0.072	21.948	-0.259	-0.259	0.000	0.000	0.000	0.000
49	A	58	HIS	1	0.860	0.909	19.476	13.528	13.528	0.000	0.000	0.000	0.000
50	A	59	ALA	0	0.060	0.036	17.475	-0.809	-0.809	0.000	0.000	0.000	0.000
51	A	60	MET	0	-0.047	-0.025	17.378	-0.571	-0.571	0.000	0.000	0.000	0.000
52	A	61	MET	0	-0.043	0.004	18.542	0.015	0.015	0.000	0.000	0.000	0.000
53	A	62	LEU	0	-0.011	0.008	13.179	-0.697	-0.697	0.000	0.000	0.000	0.000
54	A	63	VAL	0	-0.013	-0.015	13.650	-0.657	-0.657	0.000	0.000	0.000	0.000
55	A	64	GLN	0	-0.073	-0.058	15.190	0.284	0.284	0.000	0.000	0.000	0.000
56	A	65	HIS	0	0.049	0.039	10.508	-1.807	-1.807	0.000	0.000	0.000	0.000
57	A	66	LEU	0	-0.021	-0.015	8.650	-0.851	-0.851	0.000	0.000	0.000	0.000
58	A	67	LEU	0	-0.018	-0.005	12.147	0.286	0.286	0.000	0.000	0.000	0.000
59	A	68	ASP	-1	-0.887	-0.929	15.265	-14.599	-14.599	0.000	0.000	0.000	0.000
60	A	69	ARG	1	0.707	0.817	8.197	25.465	25.465	0.000	0.000	0.000	0.000
61	A	70	ASP	-1	-0.936	-0.954	12.049	-15.643	-15.643	0.000	0.000	0.000	0.000
62	A	71	LEU	0	-0.061	-0.017	7.320	-0.573	-0.573	0.000	0.000	0.000	0.000
63	A	72	ARG	1	0.871	0.940	9.933	17.114	17.114	0.000	0.000	0.000	0.000
64	A	73	VAL	0	0.050	0.029	10.390	-1.240	-1.240	0.000	0.000	0.000	0.000
65	A	74	GLU	-1	-0.966	-0.987	12.896	-16.384	-16.384	0.000	0.000	0.000	0.000
66	A	75	ILE	0	-0.009	-0.004	14.909	-0.472	-0.472	0.000	0.000	0.000	0.000
67	A	76	PRO	0	-0.025	0.013	15.327	0.412	0.412	0.000	0.000	0.000	0.000
68	A	77	GLY	0	-0.012	-0.013	17.292	0.682	0.682	0.000	0.000	0.000	0.000
69	A	78	VAL	0	-0.002	-0.008	19.245	-0.435	-0.435	0.000	0.000	0.000	0.000
70	A	79	ASP	-1	-0.833	-0.867	19.461	-14.416	-14.416	0.000	0.000	0.000	0.000
71	A	80	THR	0	-0.059	-0.034	22.487	0.430	0.430	0.000	0.000	0.000	0.000
72	A	81	VAL	0	0.000	0.010	24.676	-0.254	-0.254	0.000	0.000	0.000	0.000
73	A	82	ARG	1	0.798	0.873	27.000	10.055	10.055	0.000	0.000	0.000	0.000
74	A	83	ASN	0	0.010	-0.014	29.835	0.128	0.128	0.000	0.000	0.000	0.000
75	A	84	GLN	0	-0.021	-0.001	33.151	0.226	0.226	0.000	0.000	0.000	0.000
76	A	85	PHE	0	-0.013	-0.011	30.830	-0.345	-0.345	0.000	0.000	0.000	0.000
77	A	86	ASP	-1	-0.888	-0.928	36.212	-8.090	-8.090	0.000	0.000	0.000	0.000
78	A	87	ARG	1	0.866	0.927	38.150	8.322	8.322	0.000	0.000	0.000	0.000
79	A	88	PRO	0	0.073	0.043	37.532	-0.282	-0.282	0.000	0.000	0.000	0.000
80	A	89	ARG	1	0.817	0.886	34.005	8.771	8.771	0.000	0.000	0.000	0.000
81	A	90	GLU	-1	-0.834	-0.893	33.332	-9.478	-9.478	0.000	0.000	0.000	0.000
82	A	91	ALA	0	0.044	0.028	32.209	-0.353	-0.353	0.000	0.000	0.000	0.000
83	A	92	LEU	0	-0.001	-0.005	31.016	-0.339	-0.339	0.000	0.000	0.000	0.000
84	A	93	ALA	0	-0.039	-0.018	30.642	-0.271	-0.271	0.000	0.000	0.000	0.000
85	A	94	LEU	0	-0.002	0.007	25.880	-0.351	-0.351	0.000	0.000	0.000	0.000
86	A	95	ALA	0	0.036	0.019	26.279	-0.500	-0.500	0.000	0.000	0.000	0.000
87	A	96	LEU	0	-0.036	-0.023	25.894	-0.419	-0.419	0.000	0.000	0.000	0.000
88	A	97	ASP	-1	-0.852	-0.936	24.450	-12.756	-12.756	0.000	0.000	0.000	0.000
89	A	98	GLN	0	-0.045	-0.009	21.935	-0.631	-0.631	0.000	0.000	0.000	0.000
90	A	99	GLU	-1	-0.721	-0.844	20.839	-14.704	-14.704	0.000	0.000	0.000	0.000
91	A	100	ARG	1	0.837	0.930	20.807	11.723	11.723	0.000	0.000	0.000	0.000
92	A	101	THR	0	0.010	0.002	17.164	-0.899	-0.899	0.000	0.000	0.000	0.000
93	A	102	VAL	0	0.008	0.010	16.497	-1.433	-1.433	0.000	0.000	0.000	0.000
94	A	103	THR	0	-0.017	-0.027	16.032	-1.073	-1.073	0.000	0.000	0.000	0.000
95	A	104	ASP	-1	-0.931	-0.960	14.978	-19.414	-19.414	0.000	0.000	0.000	0.000
96	A	105	GLN	0	-0.047	-0.015	12.145	-1.788	-1.788	0.000	0.000	0.000	0.000
97	A	106	VAL	0	0.047	0.023	11.271	-2.856	-2.856	0.000	0.000	0.000	0.000
98	A	107	GLY	0	0.015	0.022	12.207	-1.448	-1.448	0.000	0.000	0.000	0.000
99	A	108	ARG	1	0.748	0.834	7.003	30.902	30.902	0.000	0.000	0.000	0.000
100	A	109	LEU	0	0.022	-0.006	7.480	-5.918	-5.918	0.000	0.000	0.000	0.000
101	A	110	THR	0	-0.003	-0.015	7.690	-3.431	-3.431	0.000	0.000	0.000	0.000
102	A	111	ALA	0	-0.043	-0.020	8.191	-1.031	-1.031	0.000	0.000	0.000	0.000
103	A	112	VAL	0	-0.009	-0.007	2.231	-7.046	-6.323	1.275	-0.602	-1.396	-0.007
104	A	113	ALA	0	-0.009	0.006	3.997	-10.162	-9.917	-0.001	-0.103	-0.142	-0.001
105	A	114	ARG	1	0.849	0.902	6.452	33.569	33.569	0.000	0.000	0.000	0.000
106	A	115	ASP	-1	-0.896	-0.919	3.987	-40.916	-40.771	-0.001	-0.018	-0.125	0.000
107	A	116	GLU	-1	-0.822	-0.893	1.649	-143.593	-147.301	29.058	-14.111	-11.239	-0.169
108	A	117	GLY	0	-0.002	0.011	4.757	5.700	5.792	-0.001	-0.009	-0.082	0.000
109	A	118	ASP	-1	-0.796	-0.873	6.216	-26.555	-26.555	0.000	0.000	0.000	0.000
110	A	119	PHE	0	0.015	-0.013	8.310	0.856	0.856	0.000	0.000	0.000	0.000
111	A	120	LEU	0	-0.041	-0.015	10.759	1.855	1.855	0.000	0.000	0.000	0.000
112	A	121	GLY	0	0.049	0.011	8.824	1.419	1.419	0.000	0.000	0.000	0.000
113	A	122	GLU	-1	-0.921	-0.978	9.878	-25.140	-25.140	0.000	0.000	0.000	0.000
114	A	123	GLN	0	-0.059	-0.040	11.572	1.431	1.431	0.000	0.000	0.000	0.000
115	A	124	PHE	0	0.000	0.008	12.485	1.510	1.510	0.000	0.000	0.000	0.000
116	A	125	MET	0	0.007	0.007	11.247	0.822	0.822	0.000	0.000	0.000	0.000
117	A	126	GLN	0	-0.011	-0.006	14.470	0.333	0.333	0.000	0.000	0.000	0.000
118	A	127	TRP	0	-0.030	-0.015	17.260	0.705	0.705	0.000	0.000	0.000	0.000
119	A	128	PHE	0	0.061	0.014	16.380	0.622	0.622	0.000	0.000	0.000	0.000
120	A	129	LEU	0	0.002	0.013	15.170	0.412	0.412	0.000	0.000	0.000	0.000
121	A	130	GLN	0	-0.014	-0.009	18.668	0.512	0.512	0.000	0.000	0.000	0.000
122	A	131	GLU	-1	-0.798	-0.895	21.272	-12.095	-12.095	0.000	0.000	0.000	0.000
123	A	132	GLN	0	-0.002	-0.023	18.794	0.377	0.377	0.000	0.000	0.000	0.000
124	A	133	ILE	0	-0.044	-0.008	21.879	0.429	0.429	0.000	0.000	0.000	0.000
125	A	134	GLU	-1	-0.901	-0.951	24.017	-10.583	-10.583	0.000	0.000	0.000	0.000
126	A	135	GLU	-1	-0.810	-0.885	23.293	-12.633	-12.633	0.000	0.000	0.000	0.000
127	A	136	VAL	0	-0.011	-0.005	23.008	0.520	0.520	0.000	0.000	0.000	0.000
128	A	137	ALA	0	-0.016	-0.001	26.074	0.500	0.500	0.000	0.000	0.000	0.000
129	A	138	LEU	0	0.006	0.017	29.195	0.549	0.549	0.000	0.000	0.000	0.000
130	A	139	MET	0	0.020	0.024	27.459	0.596	0.596	0.000	0.000	0.000	0.000
131	A	140	ALA	0	0.019	0.006	29.489	0.345	0.345	0.000	0.000	0.000	0.000
132	A	141	THR	0	-0.114	-0.052	31.256	0.472	0.472	0.000	0.000	0.000	0.000
133	A	142	LEU	0	0.029	0.012	32.429	0.373	0.373	0.000	0.000	0.000	0.000
134	A	143	VAL	0	0.007	0.002	31.571	0.314	0.314	0.000	0.000	0.000	0.000
135	A	144	ARG	1	0.879	0.916	32.898	9.845	9.845	0.000	0.000	0.000	0.000
136	A	145	VAL	0	-0.058	-0.026	37.082	0.320	0.320	0.000	0.000	0.000	0.000
137	A	146	ALA	0	0.018	0.011	37.342	0.245	0.245	0.000	0.000	0.000	0.000
138	A	147	ASP	-1	-0.814	-0.885	37.836	-8.477	-8.477	0.000	0.000	0.000	0.000
139	A	148	ARG	1	0.877	0.942	40.695	7.837	7.837	0.000	0.000	0.000	0.000
140	A	149	ALA	0	0.006	0.019	42.823	0.207	0.207	0.000	0.000	0.000	0.000
141	A	150	GLY	0	0.004	0.001	43.268	-0.122	-0.122	0.000	0.000	0.000	0.000
142	A	151	ALA	0	0.000	-0.017	44.764	-0.085	-0.085	0.000	0.000	0.000	0.000
143	A	152	ASN	0	-0.049	-0.024	46.863	0.057	0.057	0.000	0.000	0.000	0.000
144	A	153	LEU	0	0.074	0.027	42.043	-0.069	-0.069	0.000	0.000	0.000	0.000
145	A	154	PHE	0	0.050	0.025	44.482	-0.105	-0.105	0.000	0.000	0.000	0.000
146	A	155	GLU	-1	-0.902	-0.935	45.959	-6.722	-6.722	0.000	0.000	0.000	0.000
147	A	156	LEU	0	-0.001	0.001	38.367	-0.076	-0.076	0.000	0.000	0.000	0.000
148	A	157	GLU	-1	-0.738	-0.867	41.578	-7.718	-7.718	0.000	0.000	0.000	0.000
149	A	158	ASN	0	-0.065	-0.057	43.333	0.023	0.023	0.000	0.000	0.000	0.000
150	A	159	PHE	0	-0.023	-0.005	37.541	0.001	0.001	0.000	0.000	0.000	0.000
151	A	160	VAL	0	0.028	0.004	37.709	-0.086	-0.086	0.000	0.000	0.000	0.000
152	A	161	ALA	0	-0.049	-0.017	40.115	-0.069	-0.069	0.000	0.000	0.000	0.000
153	A	162	ARG	1	0.725	0.837	42.689	7.152	7.152	0.000	0.000	0.000	0.000
154	A	163	GLU	-1	-0.805	-0.874	40.020	-7.398	-7.398	0.000	0.000	0.000	0.000
155	A	164	VAL	0	-0.085	-0.039	35.128	-0.234	-0.234	0.000	0.000	0.000	0.000
156	A	165	ASP	-1	-0.931	-0.959	37.536	-8.000	-8.000	0.000	0.000	0.000	0.000
157	A	166	VAL	0	-0.014	-0.011	33.754	0.082	0.082	0.000	0.000	0.000	0.000
158	A	167	ALA	0	-0.020	-0.005	31.258	-0.024	-0.024	0.000	0.000	0.000	0.000
159	A	168	PRO	0	-0.045	-0.012	28.535	0.040	0.040	0.000	0.000	0.000	0.000
160	A	169	ALA	0	0.007	0.012	27.072	-0.396	-0.396	0.000	0.000	0.000	0.000
161	A	170	ALA	0	0.017	0.013	26.230	0.422	0.422	0.000	0.000	0.000	0.000
162	A	171	SER	0	-0.046	-0.045	28.038	0.046	0.046	0.000	0.000	0.000	0.000
163	A	172	GLY	0	-0.054	-0.014	24.306	0.098	0.098	0.000	0.000	0.000	0.000
164	A	173	ALA	0	0.005	0.000	23.040	0.230	0.230	0.000	0.000	0.000	0.000
165	A	174	PRO	0	-0.023	0.011	18.693	0.312	0.312	0.000	0.000	0.000	0.000
166	A	175	HIS	0	0.042	0.019	20.846	0.454	0.454	0.000	0.000	0.000	0.000
167	A	176	ALA	0	0.010	-0.009	20.168	-0.694	-0.694	0.000	0.000	0.000	0.000
168	A	177	ALA	0	0.020	0.014	19.645	0.612	0.612	0.000	0.000	0.000	0.000
169	A	178	GLY	0	-0.045	-0.023	21.679	0.140	0.140	0.000	0.000	0.000	0.000
170	A	179	GLY	0	-0.039	-0.018	24.925	0.517	0.517	0.000	0.000	0.000	0.000
171	A	180	ARG	1	0.829	0.886	24.115	11.477	11.477	0.000	0.000	0.000	0.000
172	A	181	LEU	0	0.003	0.020	27.872	0.426	0.426	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:10:LYS)