FMO DATABASE

FMODB ID: Z6K3N

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1786147.901547
FMO2-HF: Nuclear repulsion	1718091.159914
FMO2-HF: Total energy	-68056.741633
FMO2-MP2: Total energy	-68256.1929

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.
-286.254	-287.528	33.021	-16.362	-15.384	-0.153

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 : 0.837 / q_NPA : 0.899

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	-0.023	-0.016	3.014	3.039	6.206	0.275	-1.527	-1.914	0.009
4	A	13	ALA	0	-0.010	-0.011	2.953	1.338	2.287	0.246	-0.326	-0.869	0.000
5	A	14	LEU	0	0.013	0.007	4.316	2.306	2.555	0.000	-0.046	-0.202	0.000
6	A	15	MET	0	0.032	0.019	6.300	4.198	4.198	0.000	0.000	0.000	0.000
7	A	16	GLN	0	0.004	-0.007	7.651	2.354	2.354	0.000	0.000	0.000	0.000
8	A	17	GLU	-1	-0.965	-0.988	8.563	-24.803	-24.803	0.000	0.000	0.000	0.000
9	A	18	GLN	0	0.024	0.019	10.286	0.557	0.557	0.000	0.000	0.000	0.000
10	A	19	ILE	0	-0.006	0.004	12.206	1.754	1.754	0.000	0.000	0.000	0.000
11	A	20	HIS	0	-0.042	-0.028	13.472	1.184	1.184	0.000	0.000	0.000	0.000
12	A	21	ASN	0	-0.024	-0.015	12.834	1.657	1.657	0.000	0.000	0.000	0.000
13	A	22	GLU	-1	-0.839	-0.927	16.282	-15.523	-15.523	0.000	0.000	0.000	0.000
14	A	23	PHE	0	-0.031	-0.022	17.610	1.074	1.074	0.000	0.000	0.000	0.000
15	A	24	THR	0	0.022	-0.003	19.033	1.039	1.039	0.000	0.000	0.000	0.000
16	A	25	ALA	0	0.003	0.003	20.342	0.664	0.664	0.000	0.000	0.000	0.000
17	A	26	ALA	0	-0.002	-0.014	22.144	0.645	0.645	0.000	0.000	0.000	0.000
18	A	27	GLN	0	0.017	0.008	23.820	0.531	0.531	0.000	0.000	0.000	0.000
19	A	28	GLN	0	-0.002	-0.014	25.001	0.405	0.405	0.000	0.000	0.000	0.000
20	A	29	TYR	0	-0.049	-0.087	25.124	0.663	0.663	0.000	0.000	0.000	0.000
21	A	30	VAL	0	0.013	0.016	28.167	0.450	0.450	0.000	0.000	0.000	0.000
22	A	31	ALA	0	-0.036	-0.003	29.723	0.382	0.382	0.000	0.000	0.000	0.000
23	A	32	ILE	0	-0.024	-0.013	29.281	0.311	0.311	0.000	0.000	0.000	0.000
24	A	33	ALA	0	-0.031	-0.017	32.496	0.280	0.280	0.000	0.000	0.000	0.000
25	A	34	VAL	0	0.000	-0.015	34.172	0.295	0.295	0.000	0.000	0.000	0.000
26	A	35	TYR	0	0.008	0.004	35.424	0.247	0.247	0.000	0.000	0.000	0.000
27	A	36	PHE	0	0.008	0.003	34.707	0.219	0.219	0.000	0.000	0.000	0.000
28	A	37	ASP	-1	-0.897	-0.932	38.539	-7.410	-7.410	0.000	0.000	0.000	0.000
29	A	38	SER	0	-0.081	-0.045	40.162	0.194	0.194	0.000	0.000	0.000	0.000
30	A	39	GLU	-1	-0.985	-0.991	40.883	-7.189	-7.189	0.000	0.000	0.000	0.000
31	A	40	ASP	-1	-0.941	-0.959	43.264	-6.586	-6.586	0.000	0.000	0.000	0.000
32	A	41	LEU	0	-0.092	-0.033	41.164	0.074	0.074	0.000	0.000	0.000	0.000
33	A	42	PRO	0	0.025	-0.003	41.107	-0.216	-0.216	0.000	0.000	0.000	0.000
34	A	43	GLN	0	-0.083	-0.037	40.926	-0.296	-0.296	0.000	0.000	0.000	0.000
35	A	44	LEU	0	0.006	-0.007	36.834	-0.246	-0.246	0.000	0.000	0.000	0.000
36	A	45	ALA	0	0.039	0.022	36.659	-0.288	-0.288	0.000	0.000	0.000	0.000
37	A	46	LYS	1	0.931	0.964	36.188	7.470	7.470	0.000	0.000	0.000	0.000
38	A	47	HIS	0	-0.008	0.000	31.860	0.043	0.043	0.000	0.000	0.000	0.000
39	A	48	PHE	0	0.038	0.002	30.268	-0.311	-0.311	0.000	0.000	0.000	0.000
40	A	49	TYR	0	-0.066	-0.049	31.351	-0.410	-0.410	0.000	0.000	0.000	0.000
41	A	50	SER	0	-0.062	-0.026	31.466	-0.334	-0.334	0.000	0.000	0.000	0.000
42	A	51	GLN	0	0.015	-0.007	26.854	0.116	0.116	0.000	0.000	0.000	0.000
43	A	52	ALA	0	0.036	0.011	27.155	-0.478	-0.478	0.000	0.000	0.000	0.000
44	A	53	VAL	0	-0.059	-0.018	26.379	-0.377	-0.377	0.000	0.000	0.000	0.000
45	A	54	GLU	-1	-0.752	-0.883	25.640	-12.196	-12.196	0.000	0.000	0.000	0.000
46	A	55	GLH	0	0.031	0.016	20.923	-0.371	-0.371	0.000	0.000	0.000	0.000
47	A	56	ARG	1	0.959	0.976	21.804	10.603	10.603	0.000	0.000	0.000	0.000
48	A	57	ASN	0	-0.069	-0.050	21.930	-0.333	-0.333	0.000	0.000	0.000	0.000
49	A	58	HIS	1	0.917	0.960	19.441	13.395	13.395	0.000	0.000	0.000	0.000
50	A	59	ALA	0	0.052	0.037	17.501	-0.833	-0.833	0.000	0.000	0.000	0.000
51	A	60	MET	0	-0.021	-0.016	17.376	-0.739	-0.739	0.000	0.000	0.000	0.000
52	A	61	MET	0	-0.046	-0.003	18.683	-0.139	-0.139	0.000	0.000	0.000	0.000
53	A	62	LEU	0	-0.008	0.011	13.337	-0.708	-0.708	0.000	0.000	0.000	0.000
54	A	63	VAL	0	-0.029	-0.027	13.942	-0.614	-0.614	0.000	0.000	0.000	0.000
55	A	64	GLN	0	-0.066	-0.044	15.346	0.366	0.366	0.000	0.000	0.000	0.000
56	A	65	HIS	0	0.060	0.047	10.771	-1.690	-1.690	0.000	0.000	0.000	0.000
57	A	66	LEU	0	-0.029	-0.022	8.720	-0.590	-0.590	0.000	0.000	0.000	0.000
58	A	67	LEU	0	-0.044	-0.020	12.164	0.270	0.270	0.000	0.000	0.000	0.000
59	A	68	ASP	-1	-0.877	-0.931	15.471	-14.554	-14.554	0.000	0.000	0.000	0.000
60	A	69	ARG	1	0.729	0.873	7.892	26.381	26.381	0.000	0.000	0.000	0.000
61	A	70	ASP	-1	-0.941	-0.960	11.968	-16.012	-16.012	0.000	0.000	0.000	0.000
62	A	71	LEU	0	-0.065	-0.028	7.060	-0.913	-0.913	0.000	0.000	0.000	0.000
63	A	72	ARG	1	0.916	0.947	9.835	17.337	17.337	0.000	0.000	0.000	0.000
64	A	73	VAL	0	0.040	0.029	10.252	-1.182	-1.182	0.000	0.000	0.000	0.000
65	A	74	GLU	-1	-0.977	-0.990	12.816	-16.037	-16.037	0.000	0.000	0.000	0.000
66	A	75	ILE	0	-0.039	-0.004	14.746	-0.449	-0.449	0.000	0.000	0.000	0.000
67	A	76	PRO	0	0.002	0.028	15.063	0.330	0.330	0.000	0.000	0.000	0.000
68	A	77	GLY	0	-0.020	-0.014	17.240	0.679	0.679	0.000	0.000	0.000	0.000
69	A	78	VAL	0	-0.021	-0.011	19.059	-0.494	-0.494	0.000	0.000	0.000	0.000
70	A	79	ASP	-1	-0.868	-0.914	19.320	-14.041	-14.041	0.000	0.000	0.000	0.000
71	A	80	THR	0	-0.069	-0.046	22.260	0.419	0.419	0.000	0.000	0.000	0.000
72	A	81	VAL	0	0.010	0.019	24.595	-0.293	-0.293	0.000	0.000	0.000	0.000
73	A	82	ARG	1	0.908	0.950	26.898	10.272	10.272	0.000	0.000	0.000	0.000
74	A	83	ASN	0	0.033	-0.008	29.675	0.137	0.137	0.000	0.000	0.000	0.000
75	A	84	GLN	0	-0.044	-0.008	33.136	0.208	0.208	0.000	0.000	0.000	0.000
76	A	85	PHE	0	-0.007	-0.016	31.210	-0.332	-0.332	0.000	0.000	0.000	0.000
77	A	86	ASP	-1	-0.908	-0.928	36.395	-7.964	-7.964	0.000	0.000	0.000	0.000
78	A	87	ARG	1	0.933	0.948	38.254	8.148	8.148	0.000	0.000	0.000	0.000
79	A	88	PRO	0	0.069	0.032	37.826	-0.261	-0.261	0.000	0.000	0.000	0.000
80	A	89	ARG	1	0.833	0.900	34.858	8.632	8.632	0.000	0.000	0.000	0.000
81	A	90	GLU	-1	-0.902	-0.964	33.716	-9.209	-9.209	0.000	0.000	0.000	0.000
82	A	91	ALA	0	0.036	0.029	32.781	-0.332	-0.332	0.000	0.000	0.000	0.000
83	A	92	LEU	0	0.018	-0.004	31.617	-0.342	-0.342	0.000	0.000	0.000	0.000
84	A	93	ALA	0	-0.058	-0.027	31.021	-0.314	-0.314	0.000	0.000	0.000	0.000
85	A	94	LEU	0	-0.004	0.018	26.507	-0.315	-0.315	0.000	0.000	0.000	0.000
86	A	95	ALA	0	0.025	0.021	26.776	-0.518	-0.518	0.000	0.000	0.000	0.000
87	A	96	LEU	0	-0.020	-0.011	26.304	-0.399	-0.399	0.000	0.000	0.000	0.000
88	A	97	ASP	-1	-0.994	-1.003	25.054	-13.166	-13.166	0.000	0.000	0.000	0.000
89	A	98	GLN	0	0.043	0.012	22.186	-0.760	-0.760	0.000	0.000	0.000	0.000
90	A	99	GLU	-1	-0.723	-0.798	21.352	-14.376	-14.376	0.000	0.000	0.000	0.000
91	A	100	ARG	1	0.909	0.953	21.220	11.517	11.517	0.000	0.000	0.000	0.000
92	A	101	THR	0	0.006	0.011	17.825	-0.852	-0.852	0.000	0.000	0.000	0.000
93	A	102	VAL	0	0.018	0.007	17.040	-1.397	-1.397	0.000	0.000	0.000	0.000
94	A	103	THR	0	-0.014	-0.014	16.369	-0.975	-0.975	0.000	0.000	0.000	0.000
95	A	104	ASP	-1	-0.924	-0.944	15.174	-19.027	-19.027	0.000	0.000	0.000	0.000
96	A	105	GLN	0	-0.055	-0.025	12.429	-1.904	-1.904	0.000	0.000	0.000	0.000
97	A	106	VAL	0	0.049	0.024	11.461	-2.793	-2.793	0.000	0.000	0.000	0.000
98	A	107	GLY	0	0.034	0.015	12.419	-1.391	-1.391	0.000	0.000	0.000	0.000
99	A	108	ARG	1	0.912	0.948	6.390	33.875	33.875	0.000	0.000	0.000	0.000
100	A	109	LEU	0	0.017	-0.006	7.090	-5.527	-5.527	0.000	0.000	0.000	0.000
101	A	110	THR	0	0.008	0.009	7.999	-3.215	-3.215	0.000	0.000	0.000	0.000
102	A	111	ALA	0	-0.052	-0.017	8.030	-1.090	-1.090	0.000	0.000	0.000	0.000
103	A	112	VAL	0	0.000	-0.007	2.561	-5.933	-5.145	0.716	-0.362	-1.142	-0.004
104	A	113	ALA	0	0.006	0.007	4.378	-9.359	-9.235	-0.001	-0.030	-0.094	0.000
105	A	114	ARG	1	0.924	0.980	6.571	31.636	31.636	0.000	0.000	0.000	0.000
106	A	115	ASP	-1	-0.959	-0.981	3.966	-44.209	-44.043	-0.001	-0.023	-0.142	0.000
107	A	116	GLU	-1	-0.917	-0.957	1.707	-132.080	-138.903	31.787	-14.025	-10.939	-0.158
108	A	117	GLY	0	0.008	0.010	4.511	5.274	5.380	-0.001	-0.023	-0.082	0.000
109	A	118	ASP	-1	-0.845	-0.909	6.698	-29.224	-29.224	0.000	0.000	0.000	0.000
110	A	119	PHE	0	0.033	-0.015	8.768	1.320	1.320	0.000	0.000	0.000	0.000
111	A	120	LEU	0	-0.046	-0.010	11.042	1.738	1.738	0.000	0.000	0.000	0.000
112	A	121	GLY	0	0.034	0.001	9.427	1.507	1.507	0.000	0.000	0.000	0.000
113	A	122	GLU	-1	-0.919	-0.970	10.472	-25.135	-25.135	0.000	0.000	0.000	0.000
114	A	123	GLN	0	-0.038	-0.032	11.772	1.493	1.493	0.000	0.000	0.000	0.000
115	A	124	PHE	0	-0.031	-0.007	13.010	1.395	1.395	0.000	0.000	0.000	0.000
116	A	125	MET	0	0.007	0.008	11.343	0.788	0.788	0.000	0.000	0.000	0.000
117	A	126	GLN	0	-0.023	-0.011	14.701	-0.141	-0.141	0.000	0.000	0.000	0.000
118	A	127	TRP	0	-0.029	0.074	17.491	0.739	0.739	0.000	0.000	0.000	0.000
119	A	128	PHE	0	0.044	0.007	16.489	0.676	0.676	0.000	0.000	0.000	0.000
120	A	129	LEU	0	0.000	0.014	15.357	0.517	0.517	0.000	0.000	0.000	0.000
121	A	130	GLN	0	-0.029	-0.017	18.872	0.909	0.909	0.000	0.000	0.000	0.000
122	A	131	GLU	-1	-0.765	-0.881	21.542	-11.926	-11.926	0.000	0.000	0.000	0.000
123	A	132	GLN	0	-0.007	-0.013	18.750	0.459	0.459	0.000	0.000	0.000	0.000
124	A	133	ILE	0	-0.088	-0.033	22.034	0.368	0.368	0.000	0.000	0.000	0.000
125	A	134	GLU	-1	-0.910	-0.959	24.432	-10.598	-10.598	0.000	0.000	0.000	0.000
126	A	135	GLU	-1	-0.808	-0.918	23.360	-12.467	-12.467	0.000	0.000	0.000	0.000
127	A	136	VAL	0	-0.028	-0.011	23.401	0.472	0.472	0.000	0.000	0.000	0.000
128	A	137	ALA	0	-0.032	-0.008	26.310	0.508	0.508	0.000	0.000	0.000	0.000
129	A	138	LEU	0	0.008	0.003	29.401	0.489	0.489	0.000	0.000	0.000	0.000
130	A	139	MET	0	0.033	0.024	27.481	0.490	0.490	0.000	0.000	0.000	0.000
131	A	140	ALA	0	-0.019	-0.016	29.824	0.330	0.330	0.000	0.000	0.000	0.000
132	A	141	THR	0	-0.088	-0.036	31.467	0.456	0.456	0.000	0.000	0.000	0.000
133	A	142	LEU	0	0.014	-0.002	33.241	0.368	0.368	0.000	0.000	0.000	0.000
134	A	143	VAL	0	0.014	0.015	31.965	0.271	0.271	0.000	0.000	0.000	0.000
135	A	144	ARG	1	0.954	0.971	33.168	9.543	9.543	0.000	0.000	0.000	0.000
136	A	145	VAL	0	-0.044	-0.014	37.483	0.281	0.281	0.000	0.000	0.000	0.000
137	A	146	ALA	0	0.006	-0.001	37.850	0.231	0.231	0.000	0.000	0.000	0.000
138	A	147	ASP	-1	-0.877	-0.905	37.903	-8.358	-8.358	0.000	0.000	0.000	0.000
139	A	148	ARG	1	0.873	0.924	40.688	7.730	7.730	0.000	0.000	0.000	0.000
140	A	149	ALA	0	-0.020	0.007	43.113	0.212	0.212	0.000	0.000	0.000	0.000
141	A	150	GLY	0	0.020	0.009	44.035	-0.063	-0.063	0.000	0.000	0.000	0.000
142	A	151	ALA	0	-0.025	-0.009	44.931	-0.118	-0.118	0.000	0.000	0.000	0.000
143	A	152	ASN	0	-0.018	-0.007	46.785	0.054	0.054	0.000	0.000	0.000	0.000
144	A	153	LEU	0	0.096	0.032	42.535	-0.093	-0.093	0.000	0.000	0.000	0.000
145	A	154	PHE	0	0.028	0.019	45.033	-0.090	-0.090	0.000	0.000	0.000	0.000
146	A	155	GLU	-1	-0.950	-0.971	46.478	-6.601	-6.601	0.000	0.000	0.000	0.000
147	A	156	LEU	0	-0.003	0.007	39.110	-0.078	-0.078	0.000	0.000	0.000	0.000
148	A	157	GLU	-1	-0.723	-0.881	41.953	-7.635	-7.635	0.000	0.000	0.000	0.000
149	A	158	ASN	0	-0.035	-0.030	43.663	-0.035	-0.035	0.000	0.000	0.000	0.000
150	A	159	PHE	0	-0.033	-0.015	38.367	-0.002	-0.002	0.000	0.000	0.000	0.000
151	A	160	VAL	0	0.022	-0.002	38.135	-0.097	-0.097	0.000	0.000	0.000	0.000
152	A	161	ALA	0	-0.019	0.000	40.437	-0.079	-0.079	0.000	0.000	0.000	0.000
153	A	162	ARG	1	0.749	0.858	43.037	7.063	7.063	0.000	0.000	0.000	0.000
154	A	163	GLU	-1	-0.839	-0.909	40.331	-7.393	-7.393	0.000	0.000	0.000	0.000
155	A	164	VAL	0	-0.063	-0.001	35.382	-0.222	-0.222	0.000	0.000	0.000	0.000
156	A	165	ASP	-1	-0.964	-0.982	37.610	-7.872	-7.872	0.000	0.000	0.000	0.000
157	A	166	VAL	0	-0.014	-0.021	34.093	0.114	0.114	0.000	0.000	0.000	0.000
158	A	167	ALA	0	-0.058	-0.019	31.812	-0.177	-0.177	0.000	0.000	0.000	0.000
159	A	168	PRO	0	-0.037	-0.010	28.547	0.082	0.082	0.000	0.000	0.000	0.000
160	A	169	ALA	0	0.001	0.006	27.050	-0.328	-0.328	0.000	0.000	0.000	0.000
161	A	170	ALA	0	0.006	0.001	25.926	0.357	0.357	0.000	0.000	0.000	0.000
162	A	171	SER	0	-0.072	-0.057	27.131	0.372	0.372	0.000	0.000	0.000	0.000
163	A	172	GLY	0	0.000	-0.064	24.548	-0.012	-0.012	0.000	0.000	0.000	0.000
164	A	173	ALA	0	-0.028	-0.028	23.327	0.348	0.348	0.000	0.000	0.000	0.000
165	A	174	PRO	0	-0.042	-0.008	19.197	0.378	0.378	0.000	0.000	0.000	0.000
166	A	175	HIS	0	0.042	0.012	21.142	0.311	0.311	0.000	0.000	0.000	0.000
167	A	176	ALA	0	0.043	0.014	20.408	-0.670	-0.670	0.000	0.000	0.000	0.000
168	A	177	ALA	0	0.004	0.021	20.071	0.580	0.580	0.000	0.000	0.000	0.000
169	A	178	GLY	0	-0.052	-0.033	21.937	0.059	0.059	0.000	0.000	0.000	0.000
170	A	179	GLY	0	-0.021	-0.019	25.177	0.479	0.479	0.000	0.000	0.000	0.000
171	A	180	ARG	1	0.857	0.943	25.314	11.059	11.059	0.000	0.000	0.000	0.000
172	A	181	LEU	0	-0.011	0.005	27.954	0.341	0.341	0.000	0.000	0.000	0.000

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