FMO DATABASE

FMODB ID: R96R8

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	OptHSide
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	-1787343.144403
FMO2-HF: Nuclear repulsion	1719285.359821
FMO2-HF: Total energy	-68057.784582
FMO2-MP2: Total energy	-68257.168807

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.
-289.966	-285.857	25.164	-15.486	-13.785	-0.143

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 : 0.822 / q_NPA : 0.880

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	-0.019	-0.018	3.010	3.041	6.146	0.282	-1.473	-1.913	0.009
4	A	13	ALA	0	-0.014	-0.013	2.882	1.422	2.402	0.303	-0.378	-0.905	0.000
5	A	14	LEU	0	0.005	0.006	4.299	2.281	2.516	0.000	-0.045	-0.190	0.000
6	A	15	MET	0	0.038	0.024	6.289	3.993	3.993	0.000	0.000	0.000	0.000
7	A	16	GLN	0	0.005	-0.005	7.604	2.625	2.625	0.000	0.000	0.000	0.000
8	A	17	GLU	-1	-0.961	-0.981	8.537	-26.457	-26.457	0.000	0.000	0.000	0.000
9	A	18	GLN	0	0.017	-0.005	10.266	0.456	0.456	0.000	0.000	0.000	0.000
10	A	19	ILE	0	-0.017	0.000	12.103	1.759	1.759	0.000	0.000	0.000	0.000
11	A	20	HIS	0	-0.053	-0.048	13.441	1.024	1.024	0.000	0.000	0.000	0.000
12	A	21	ASN	0	-0.018	-0.018	13.019	1.794	1.794	0.000	0.000	0.000	0.000
13	A	22	GLU	-1	-0.795	-0.861	16.112	-15.998	-15.998	0.000	0.000	0.000	0.000
14	A	23	PHE	0	-0.026	-0.027	17.556	1.067	1.067	0.000	0.000	0.000	0.000
15	A	24	THR	0	-0.017	-0.034	19.206	0.923	0.923	0.000	0.000	0.000	0.000
16	A	25	ALA	0	0.017	0.015	20.320	0.687	0.687	0.000	0.000	0.000	0.000
17	A	26	ALA	0	-0.002	-0.015	22.119	0.653	0.653	0.000	0.000	0.000	0.000
18	A	27	GLN	0	0.008	0.003	23.793	0.599	0.599	0.000	0.000	0.000	0.000
19	A	28	GLN	0	0.004	-0.011	24.983	0.422	0.422	0.000	0.000	0.000	0.000
20	A	29	TYR	0	-0.018	-0.031	25.370	0.690	0.690	0.000	0.000	0.000	0.000
21	A	30	VAL	0	0.016	0.018	28.301	0.455	0.455	0.000	0.000	0.000	0.000
22	A	31	ALA	0	-0.033	-0.001	29.701	0.386	0.386	0.000	0.000	0.000	0.000
23	A	32	ILE	0	-0.008	-0.010	29.302	0.333	0.333	0.000	0.000	0.000	0.000
24	A	33	ALA	0	-0.033	-0.018	32.475	0.285	0.285	0.000	0.000	0.000	0.000
25	A	34	VAL	0	-0.001	-0.016	34.151	0.304	0.304	0.000	0.000	0.000	0.000
26	A	35	TYR	0	-0.068	-0.055	35.408	0.165	0.165	0.000	0.000	0.000	0.000
27	A	36	PHE	0	0.020	-0.002	34.453	0.227	0.227	0.000	0.000	0.000	0.000
28	A	37	ASP	-1	-0.887	-0.915	38.521	-7.439	-7.439	0.000	0.000	0.000	0.000
29	A	38	SER	0	-0.072	-0.041	40.143	0.202	0.202	0.000	0.000	0.000	0.000
30	A	39	GLU	-1	-0.910	-0.929	40.807	-7.284	-7.284	0.000	0.000	0.000	0.000
31	A	40	ASP	-1	-0.949	-0.966	43.330	-6.573	-6.573	0.000	0.000	0.000	0.000
32	A	41	LEU	0	-0.087	-0.032	41.062	0.074	0.074	0.000	0.000	0.000	0.000
33	A	42	PRO	0	0.037	0.001	41.121	-0.223	-0.223	0.000	0.000	0.000	0.000
34	A	43	GLN	0	-0.034	-0.009	40.902	-0.315	-0.315	0.000	0.000	0.000	0.000
35	A	44	LEU	0	-0.002	-0.011	37.078	-0.244	-0.244	0.000	0.000	0.000	0.000
36	A	45	ALA	0	0.033	0.020	36.726	-0.288	-0.288	0.000	0.000	0.000	0.000
37	A	46	LYS	1	0.885	0.939	36.163	7.579	7.579	0.000	0.000	0.000	0.000
38	A	47	HIS	0	-0.028	-0.011	31.962	0.066	0.066	0.000	0.000	0.000	0.000
39	A	48	PHE	0	0.034	0.002	30.346	-0.309	-0.309	0.000	0.000	0.000	0.000
40	A	49	TYR	0	-0.077	-0.062	31.326	-0.425	-0.425	0.000	0.000	0.000	0.000
41	A	50	SER	0	-0.050	-0.022	31.434	-0.329	-0.329	0.000	0.000	0.000	0.000
42	A	51	GLN	0	-0.006	-0.023	27.106	0.151	0.151	0.000	0.000	0.000	0.000
43	A	52	ALA	0	0.032	0.013	27.134	-0.483	-0.483	0.000	0.000	0.000	0.000
44	A	53	VAL	0	-0.074	-0.029	26.346	-0.389	-0.389	0.000	0.000	0.000	0.000
45	A	54	GLU	-1	-0.720	-0.836	25.540	-12.160	-12.160	0.000	0.000	0.000	0.000
46	A	55	GLH	0	0.032	-0.006	20.413	-0.499	-0.499	0.000	0.000	0.000	0.000
47	A	56	ARG	1	0.960	0.978	21.769	10.665	10.665	0.000	0.000	0.000	0.000
48	A	57	ASN	0	-0.091	-0.069	21.888	-0.325	-0.325	0.000	0.000	0.000	0.000
49	A	58	HIS	1	0.902	0.932	19.458	13.335	13.335	0.000	0.000	0.000	0.000
50	A	59	ALA	0	0.053	0.039	17.461	-0.830	-0.830	0.000	0.000	0.000	0.000
51	A	60	MET	0	-0.038	-0.024	17.329	-0.660	-0.660	0.000	0.000	0.000	0.000
52	A	61	MET	0	-0.047	-0.002	18.722	-0.097	-0.097	0.000	0.000	0.000	0.000
53	A	62	LEU	0	-0.014	0.011	13.222	-0.710	-0.710	0.000	0.000	0.000	0.000
54	A	63	VAL	0	-0.022	-0.025	13.942	-0.577	-0.577	0.000	0.000	0.000	0.000
55	A	64	GLN	0	-0.074	-0.059	15.346	0.322	0.322	0.000	0.000	0.000	0.000
56	A	65	HIS	0	0.057	0.048	10.768	-1.806	-1.806	0.000	0.000	0.000	0.000
57	A	66	LEU	0	-0.024	-0.023	8.642	-0.565	-0.565	0.000	0.000	0.000	0.000
58	A	67	LEU	0	-0.034	-0.015	12.164	0.273	0.273	0.000	0.000	0.000	0.000
59	A	68	ASP	-1	-0.863	-0.911	15.471	-14.483	-14.483	0.000	0.000	0.000	0.000
60	A	69	ARG	1	0.693	0.833	8.183	26.108	26.108	0.000	0.000	0.000	0.000
61	A	70	ASP	-1	-0.948	-0.961	11.949	-15.675	-15.675	0.000	0.000	0.000	0.000
62	A	71	LEU	0	-0.071	-0.029	7.129	-0.897	-0.897	0.000	0.000	0.000	0.000
63	A	72	ARG	1	0.890	0.945	9.772	17.171	17.171	0.000	0.000	0.000	0.000
64	A	73	VAL	0	0.035	0.018	10.252	-1.150	-1.150	0.000	0.000	0.000	0.000
65	A	74	GLU	-1	-0.959	-0.988	12.816	-16.444	-16.444	0.000	0.000	0.000	0.000
66	A	75	ILE	0	-0.027	-0.004	14.689	-0.446	-0.446	0.000	0.000	0.000	0.000
67	A	76	PRO	0	-0.026	0.020	15.201	0.397	0.397	0.000	0.000	0.000	0.000
68	A	77	GLY	0	-0.012	-0.012	17.199	0.679	0.679	0.000	0.000	0.000	0.000
69	A	78	VAL	0	0.004	0.000	19.029	-0.462	-0.462	0.000	0.000	0.000	0.000
70	A	79	ASP	-1	-0.857	-0.892	19.361	-14.339	-14.339	0.000	0.000	0.000	0.000
71	A	80	THR	0	-0.045	-0.027	22.245	0.382	0.382	0.000	0.000	0.000	0.000
72	A	81	VAL	0	0.007	0.015	24.560	-0.290	-0.290	0.000	0.000	0.000	0.000
73	A	82	ARG	1	0.788	0.866	26.890	10.007	10.007	0.000	0.000	0.000	0.000
74	A	83	ASN	0	-0.002	-0.020	29.854	0.170	0.170	0.000	0.000	0.000	0.000
75	A	84	GLN	0	-0.024	0.005	33.217	0.184	0.184	0.000	0.000	0.000	0.000
76	A	85	PHE	0	0.012	-0.008	31.175	-0.313	-0.313	0.000	0.000	0.000	0.000
77	A	86	ASP	-1	-0.911	-0.934	36.630	-7.997	-7.997	0.000	0.000	0.000	0.000
78	A	87	ARG	1	0.937	0.957	38.414	8.151	8.151	0.000	0.000	0.000	0.000
79	A	88	PRO	0	0.089	0.043	37.920	-0.264	-0.264	0.000	0.000	0.000	0.000
80	A	89	ARG	1	0.808	0.876	34.567	8.653	8.653	0.000	0.000	0.000	0.000
81	A	90	GLU	-1	-0.823	-0.901	34.011	-9.422	-9.422	0.000	0.000	0.000	0.000
82	A	91	ALA	0	0.048	0.034	32.877	-0.328	-0.328	0.000	0.000	0.000	0.000
83	A	92	LEU	0	0.008	-0.003	31.637	-0.332	-0.332	0.000	0.000	0.000	0.000
84	A	93	ALA	0	-0.063	-0.030	31.063	-0.308	-0.308	0.000	0.000	0.000	0.000
85	A	94	LEU	0	0.016	0.025	26.406	-0.336	-0.336	0.000	0.000	0.000	0.000
86	A	95	ALA	0	0.032	0.022	26.782	-0.518	-0.518	0.000	0.000	0.000	0.000
87	A	96	LEU	0	-0.025	-0.017	26.361	-0.410	-0.410	0.000	0.000	0.000	0.000
88	A	97	ASP	-1	-0.984	-0.999	25.133	-13.110	-13.110	0.000	0.000	0.000	0.000
89	A	98	GLN	0	0.016	-0.001	22.205	-0.623	-0.623	0.000	0.000	0.000	0.000
90	A	99	GLU	-1	-0.761	-0.858	21.397	-14.330	-14.330	0.000	0.000	0.000	0.000
91	A	100	ARG	1	0.911	0.960	21.343	11.485	11.485	0.000	0.000	0.000	0.000
92	A	101	THR	0	0.001	0.006	17.651	-0.837	-0.837	0.000	0.000	0.000	0.000
93	A	102	VAL	0	0.013	0.009	17.104	-1.387	-1.387	0.000	0.000	0.000	0.000
94	A	103	THR	0	-0.017	-0.026	16.511	-0.914	-0.914	0.000	0.000	0.000	0.000
95	A	104	ASP	-1	-0.920	-0.945	15.308	-19.067	-19.067	0.000	0.000	0.000	0.000
96	A	105	GLN	0	-0.057	-0.017	12.506	-1.709	-1.709	0.000	0.000	0.000	0.000
97	A	106	VAL	0	0.048	0.024	11.624	-2.764	-2.764	0.000	0.000	0.000	0.000
98	A	107	GLY	0	0.040	0.021	12.572	-1.363	-1.363	0.000	0.000	0.000	0.000
99	A	108	ARG	1	0.894	0.942	7.074	32.474	32.474	0.000	0.000	0.000	0.000
100	A	109	LEU	0	0.007	-0.007	7.452	-5.423	-5.423	0.000	0.000	0.000	0.000
101	A	110	THR	0	0.002	-0.004	7.986	-3.001	-3.001	0.000	0.000	0.000	0.000
102	A	111	ALA	0	-0.053	-0.013	8.528	-0.944	-0.944	0.000	0.000	0.000	0.000
103	A	112	VAL	0	0.004	-0.008	2.481	-5.422	-4.617	0.522	-0.362	-0.965	-0.004
104	A	113	ALA	0	0.000	0.012	4.543	-8.187	-8.095	-0.001	-0.016	-0.074	0.000
105	A	114	ARG	1	0.875	0.925	6.718	32.838	32.838	0.000	0.000	0.000	0.000
106	A	115	ASP	-1	-0.917	-0.936	4.207	-41.271	-41.161	-0.001	-0.010	-0.099	0.000
107	A	116	GLU	-1	-0.894	-0.941	1.656	-139.335	-140.628	24.060	-13.196	-9.571	-0.148
108	A	117	GLY	0	0.009	0.009	4.854	4.822	4.897	-0.001	-0.006	-0.068	0.000
109	A	118	ASP	-1	-0.817	-0.889	6.687	-27.776	-27.776	0.000	0.000	0.000	0.000
110	A	119	PHE	0	0.018	-0.015	8.824	1.152	1.152	0.000	0.000	0.000	0.000
111	A	120	LEU	0	-0.046	-0.010	11.002	1.621	1.621	0.000	0.000	0.000	0.000
112	A	121	GLY	0	0.044	0.009	9.410	1.403	1.403	0.000	0.000	0.000	0.000
113	A	122	GLU	-1	-0.918	-0.968	10.454	-24.526	-24.526	0.000	0.000	0.000	0.000
114	A	123	GLN	0	-0.037	-0.033	11.936	1.340	1.340	0.000	0.000	0.000	0.000
115	A	124	PHE	0	-0.017	-0.001	12.791	1.393	1.393	0.000	0.000	0.000	0.000
116	A	125	MET	0	0.020	0.014	11.523	0.764	0.764	0.000	0.000	0.000	0.000
117	A	126	GLN	0	-0.026	-0.013	14.795	0.248	0.248	0.000	0.000	0.000	0.000
118	A	127	TRP	0	-0.040	-0.019	17.563	0.597	0.597	0.000	0.000	0.000	0.000
119	A	128	PHE	0	0.058	0.013	16.781	0.627	0.627	0.000	0.000	0.000	0.000
120	A	129	LEU	0	0.013	0.014	15.325	0.499	0.499	0.000	0.000	0.000	0.000
121	A	130	GLN	0	-0.019	-0.011	18.917	0.669	0.669	0.000	0.000	0.000	0.000
122	A	131	GLU	-1	-0.746	-0.866	21.730	-12.003	-12.003	0.000	0.000	0.000	0.000
123	A	132	GLN	0	0.010	-0.001	19.062	0.389	0.389	0.000	0.000	0.000	0.000
124	A	133	ILE	0	-0.073	-0.024	22.273	0.408	0.408	0.000	0.000	0.000	0.000
125	A	134	GLU	-1	-0.916	-0.961	24.562	-10.464	-10.464	0.000	0.000	0.000	0.000
126	A	135	GLU	-1	-0.814	-0.912	23.693	-12.378	-12.378	0.000	0.000	0.000	0.000
127	A	136	VAL	0	-0.027	-0.010	23.447	0.478	0.478	0.000	0.000	0.000	0.000
128	A	137	ALA	0	-0.021	-0.001	26.489	0.506	0.506	0.000	0.000	0.000	0.000
129	A	138	LEU	0	0.012	0.008	29.614	0.493	0.493	0.000	0.000	0.000	0.000
130	A	139	MET	0	0.040	0.035	27.718	0.530	0.530	0.000	0.000	0.000	0.000
131	A	140	ALA	0	-0.017	-0.013	29.983	0.326	0.326	0.000	0.000	0.000	0.000
132	A	141	THR	0	-0.092	-0.051	31.608	0.456	0.456	0.000	0.000	0.000	0.000
133	A	142	LEU	0	0.016	0.006	32.914	0.369	0.369	0.000	0.000	0.000	0.000
134	A	143	VAL	0	0.020	0.017	32.115	0.275	0.275	0.000	0.000	0.000	0.000
135	A	144	ARG	1	0.929	0.964	33.116	9.664	9.664	0.000	0.000	0.000	0.000
136	A	145	VAL	0	-0.057	-0.022	37.601	0.291	0.291	0.000	0.000	0.000	0.000
137	A	146	ALA	0	0.013	0.002	37.898	0.233	0.233	0.000	0.000	0.000	0.000
138	A	147	ASP	-1	-0.875	-0.901	37.910	-8.363	-8.363	0.000	0.000	0.000	0.000
139	A	148	ARG	1	0.866	0.928	40.758	7.720	7.720	0.000	0.000	0.000	0.000
140	A	149	ALA	0	-0.023	0.006	43.212	0.211	0.211	0.000	0.000	0.000	0.000
141	A	150	GLY	0	0.031	0.011	44.092	-0.067	-0.067	0.000	0.000	0.000	0.000
142	A	151	ALA	0	-0.030	-0.011	44.967	-0.118	-0.118	0.000	0.000	0.000	0.000
143	A	152	ASN	0	-0.022	-0.013	46.801	0.069	0.069	0.000	0.000	0.000	0.000
144	A	153	LEU	0	0.092	0.032	42.504	-0.091	-0.091	0.000	0.000	0.000	0.000
145	A	154	PHE	0	0.032	0.021	45.101	-0.092	-0.092	0.000	0.000	0.000	0.000
146	A	155	GLU	-1	-0.941	-0.965	46.617	-6.636	-6.636	0.000	0.000	0.000	0.000
147	A	156	LEU	0	0.000	0.002	39.047	-0.077	-0.077	0.000	0.000	0.000	0.000
148	A	157	GLU	-1	-0.730	-0.875	42.046	-7.646	-7.646	0.000	0.000	0.000	0.000
149	A	158	ASN	0	-0.044	-0.036	43.782	-0.015	-0.015	0.000	0.000	0.000	0.000
150	A	159	PHE	0	-0.019	-0.008	38.284	-0.015	-0.015	0.000	0.000	0.000	0.000
151	A	160	VAL	0	0.031	0.002	38.263	-0.094	-0.094	0.000	0.000	0.000	0.000
152	A	161	ALA	0	-0.049	-0.017	40.596	-0.081	-0.081	0.000	0.000	0.000	0.000
153	A	162	ARG	1	0.766	0.869	43.189	7.045	7.045	0.000	0.000	0.000	0.000
154	A	163	GLU	-1	-0.836	-0.907	40.433	-7.337	-7.337	0.000	0.000	0.000	0.000
155	A	164	VAL	0	-0.055	-0.004	35.460	-0.216	-0.216	0.000	0.000	0.000	0.000
156	A	165	ASP	-1	-0.975	-0.988	37.806	-7.885	-7.885	0.000	0.000	0.000	0.000
157	A	166	VAL	0	-0.003	-0.011	34.215	0.124	0.124	0.000	0.000	0.000	0.000
158	A	167	ALA	0	-0.039	-0.008	32.051	-0.177	-0.177	0.000	0.000	0.000	0.000
159	A	168	PRO	0	-0.024	-0.010	28.777	0.056	0.056	0.000	0.000	0.000	0.000
160	A	169	ALA	0	-0.015	0.002	27.272	-0.359	-0.359	0.000	0.000	0.000	0.000
161	A	170	ALA	0	0.011	0.001	26.241	0.345	0.345	0.000	0.000	0.000	0.000
162	A	171	SER	0	-0.082	-0.058	27.386	0.356	0.356	0.000	0.000	0.000	0.000
163	A	172	GLY	0	-0.043	0.004	24.519	0.047	0.047	0.000	0.000	0.000	0.000
164	A	173	ALA	0	0.033	0.000	23.346	0.326	0.326	0.000	0.000	0.000	0.000
165	A	174	PRO	0	-0.066	-0.010	19.106	0.374	0.374	0.000	0.000	0.000	0.000
166	A	175	HIS	0	0.046	0.012	21.120	0.312	0.312	0.000	0.000	0.000	0.000
167	A	176	ALA	0	0.035	0.013	20.385	-0.665	-0.665	0.000	0.000	0.000	0.000
168	A	177	ALA	0	0.003	0.022	20.003	0.589	0.589	0.000	0.000	0.000	0.000
169	A	178	GLY	0	-0.050	-0.036	21.937	0.057	0.057	0.000	0.000	0.000	0.000
170	A	179	GLY	0	-0.020	-0.019	25.180	0.477	0.477	0.000	0.000	0.000	0.000
171	A	180	ARG	1	0.822	0.906	24.739	11.236	11.236	0.000	0.000	0.000	0.000
172	A	181	LEU	0	0.006	0.011	27.954	0.347	0.347	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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