FMO DATABASE

FMODB ID: VQ561

Calculation Name: 2YQY-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YQY

Chain ID: B

ChEMBL ID:

UniProt ID: Q5SLJ0

Base Structure: X-ray

Registration Date: 2023-09-21

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	127
LigandResidueName
LigandFragmentNumber	0
LigandCharge	DAS=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1075292.436886
FMO2-HF: Nuclear repulsion	1026619.296627
FMO2-HF: Total energy	-48673.140259
FMO2-MP2: Total energy	-48819.256798

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(B:9:THR)

Summations of interaction energy for fragment #1(B:9:THR)

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.
-19.538	-13.428	1.661	-2.766	-5.004	0.01

Interaction energy analysis for fragmet #1(B:9:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.012 / q_NPA : -0.011

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

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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	B	11	ASP	-1	-0.812	-0.916	3.393	-3.518	-1.665	0.008	-0.723	-1.138	0.000
4	B	12	GLU	-1	-0.809	-0.881	2.602	-1.325	0.693	1.341	-1.144	-2.216	0.007
5	B	13	ALA	0	-0.055	-0.007	4.229	-0.243	0.212	0.001	-0.136	-0.320	0.000
6	B	14	LEU	0	0.035	0.029	5.759	-0.167	-0.167	0.000	0.000	0.000	0.000
7	B	15	LYS	1	0.874	0.915	5.995	0.247	0.247	0.000	0.000	0.000	0.000
8	B	16	ARG	1	0.825	0.891	3.147	-6.082	-5.463	0.028	-0.271	-0.375	0.001
9	B	17	LEU	0	0.063	0.042	9.350	-0.134	-0.134	0.000	0.000	0.000	0.000
10	B	18	GLU	-1	-0.912	-0.939	11.711	-0.138	-0.138	0.000	0.000	0.000	0.000
11	B	19	ALA	0	-0.069	-0.034	12.480	-0.070	-0.070	0.000	0.000	0.000	0.000
12	B	20	SER	0	-0.040	-0.052	13.399	-0.016	-0.016	0.000	0.000	0.000	0.000
13	B	21	ARG	1	0.805	0.875	15.199	-0.376	-0.376	0.000	0.000	0.000	0.000
14	B	22	LYS	1	0.955	0.974	16.201	-0.141	-0.141	0.000	0.000	0.000	0.000
15	B	23	ALA	0	-0.002	-0.006	18.087	-0.029	-0.029	0.000	0.000	0.000	0.000
16	B	24	LEU	0	0.018	0.012	19.243	-0.020	-0.020	0.000	0.000	0.000	0.000
17	B	25	LEU	0	-0.014	-0.018	21.055	-0.025	-0.025	0.000	0.000	0.000	0.000
18	B	26	ALA	0	-0.061	-0.032	22.739	-0.021	-0.021	0.000	0.000	0.000	0.000
19	B	27	LEU	0	-0.021	0.003	23.402	-0.010	-0.010	0.000	0.000	0.000	0.000
20	B	28	LEU	0	0.005	-0.005	24.213	-0.010	-0.010	0.000	0.000	0.000	0.000
21	B	29	ARG	1	0.922	0.962	25.621	-0.126	-0.126	0.000	0.000	0.000	0.000
22	B	31	ALA	0	0.000	0.003	29.443	-0.003	-0.003	0.000	0.000	0.000	0.000
23	B	32	DAS	-1	-0.876	-0.939	31.204	0.106	0.106	0.000	0.000	0.000	0.000
24	B	33	PRO	0	0.016	0.007	34.198	0.008	0.008	0.000	0.000	0.000	0.000
25	B	34	DAL	0	-0.016	-0.011	35.760	0.004	0.004	0.000	0.000	0.000	0.000
26	B	35	TRP	0	0.012	-0.001	27.207	0.004	0.004	0.000	0.000	0.000	0.000
27	B	36	LEU	0	-0.003	-0.004	29.420	0.013	0.013	0.000	0.000	0.000	0.000
28	B	37	SER	0	0.003	-0.007	32.019	0.008	0.008	0.000	0.000	0.000	0.000
29	B	38	DAL	0	0.049	0.015	34.214	-0.003	-0.003	0.000	0.000	0.000	0.000
30	B	39	PRO	0	-0.048	-0.025	33.042	0.011	0.011	0.000	0.000	0.000	0.000
31	B	40	LEU	0	-0.027	0.004	31.247	0.008	0.008	0.000	0.000	0.000	0.000
32	B	41	ARG	1	0.841	0.885	33.727	-0.179	-0.179	0.000	0.000	0.000	0.000
33	B	42	GLU	-1	-0.824	-0.882	32.386	0.178	0.178	0.000	0.000	0.000	0.000
34	B	43	GLY	0	-0.028	-0.012	33.449	0.009	0.009	0.000	0.000	0.000	0.000
35	B	44	ALA	0	-0.022	-0.002	30.482	0.007	0.007	0.000	0.000	0.000	0.000
36	B	45	TRP	0	0.015	-0.002	24.421	-0.011	-0.011	0.000	0.000	0.000	0.000
37	B	46	THR	0	0.031	0.014	30.717	0.007	0.007	0.000	0.000	0.000	0.000
38	B	47	PRO	0	0.032	0.009	27.485	0.017	0.017	0.000	0.000	0.000	0.000
39	B	48	LEU	0	-0.014	0.008	26.946	0.017	0.017	0.000	0.000	0.000	0.000
40	B	49	MET	0	0.026	0.020	27.877	0.007	0.007	0.000	0.000	0.000	0.000
41	B	50	VAL	0	-0.041	-0.006	23.191	0.023	0.023	0.000	0.000	0.000	0.000
42	B	51	ALA	0	-0.003	-0.010	23.174	0.034	0.034	0.000	0.000	0.000	0.000
43	B	52	GLU	-1	-0.868	-0.946	23.403	0.215	0.215	0.000	0.000	0.000	0.000
44	B	53	HIS	0	0.008	0.004	22.099	0.045	0.045	0.000	0.000	0.000	0.000
45	B	54	VAL	0	-0.005	-0.009	17.936	0.033	0.033	0.000	0.000	0.000	0.000
46	B	55	ALA	0	0.019	0.020	19.703	0.024	0.024	0.000	0.000	0.000	0.000
47	B	56	LEU	0	0.005	-0.001	21.818	-0.006	-0.006	0.000	0.000	0.000	0.000
48	B	57	VAL	0	0.019	0.027	16.865	0.001	0.001	0.000	0.000	0.000	0.000
49	B	58	GLU	-1	-0.775	-0.847	16.186	0.435	0.435	0.000	0.000	0.000	0.000
50	B	59	ASP	-1	-0.744	-0.831	17.958	0.190	0.190	0.000	0.000	0.000	0.000
51	B	60	SER	0	-0.029	-0.035	19.966	-0.030	-0.030	0.000	0.000	0.000	0.000
52	B	61	THR	0	-0.021	-0.026	13.550	0.026	0.026	0.000	0.000	0.000	0.000
53	B	62	ALA	0	0.008	0.018	16.196	-0.010	-0.010	0.000	0.000	0.000	0.000
54	B	63	ARG	1	0.807	0.876	17.608	-0.237	-0.237	0.000	0.000	0.000	0.000
55	B	64	VAL	0	-0.010	0.007	15.696	-0.042	-0.042	0.000	0.000	0.000	0.000
56	B	65	LEU	0	0.004	0.011	11.679	-0.025	-0.025	0.000	0.000	0.000	0.000
57	B	66	ARG	1	0.946	0.986	15.530	-0.168	-0.168	0.000	0.000	0.000	0.000
58	B	67	ARG	1	0.896	0.955	18.977	-0.238	-0.238	0.000	0.000	0.000	0.000
59	B	68	LEU	0	0.009	-0.005	14.123	-0.029	-0.029	0.000	0.000	0.000	0.000
60	B	69	ARG	1	0.852	0.914	16.532	-0.030	-0.030	0.000	0.000	0.000	0.000
61	B	70	ARG	1	0.888	0.932	17.701	-0.073	-0.073	0.000	0.000	0.000	0.000
62	B	71	LEU	0	-0.037	-0.016	19.558	-0.009	-0.009	0.000	0.000	0.000	0.000
63	B	72	ALA	0	-0.004	0.017	17.085	-0.006	-0.006	0.000	0.000	0.000	0.000
64	B	73	DAL	0	-0.052	-0.011	19.179	-0.030	-0.030	0.000	0.000	0.000	0.000
65	B	104	LEU	0	-0.029	-0.019	31.038	-0.005	-0.005	0.000	0.000	0.000	0.000
66	B	105	SER	0	-0.006	-0.022	34.467	0.002	0.002	0.000	0.000	0.000	0.000
67	B	106	LEU	0	0.041	0.009	28.995	0.010	0.010	0.000	0.000	0.000	0.000
68	B	107	GLU	-1	-0.864	-0.923	30.215	0.109	0.109	0.000	0.000	0.000	0.000
69	B	108	GLU	-1	-0.882	-0.934	30.718	0.119	0.119	0.000	0.000	0.000	0.000
70	B	109	VAL	0	0.012	0.005	26.788	0.009	0.009	0.000	0.000	0.000	0.000
71	B	110	LEU	0	-0.031	-0.020	25.825	0.017	0.017	0.000	0.000	0.000	0.000
72	B	111	ALA	0	0.019	0.018	25.926	0.003	0.003	0.000	0.000	0.000	0.000
73	B	112	LEU	0	-0.027	-0.017	26.513	0.004	0.004	0.000	0.000	0.000	0.000
74	B	113	LEU	0	-0.002	-0.015	21.093	0.017	0.017	0.000	0.000	0.000	0.000
75	B	114	ASP	-1	-0.977	-0.967	21.710	0.118	0.118	0.000	0.000	0.000	0.000
76	B	115	ARG	1	0.903	0.936	22.265	-0.176	-0.176	0.000	0.000	0.000	0.000
77	B	116	ALA	0	-0.042	-0.009	20.901	-0.007	-0.007	0.000	0.000	0.000	0.000
78	B	117	ARG	1	0.770	0.844	14.798	-0.377	-0.377	0.000	0.000	0.000	0.000
79	B	118	ALA	0	0.011	0.008	17.885	-0.016	-0.016	0.000	0.000	0.000	0.000
80	B	119	PHE	0	-0.017	-0.008	19.460	-0.019	-0.019	0.000	0.000	0.000	0.000
81	B	120	LEU	0	-0.035	-0.027	13.462	-0.004	-0.004	0.000	0.000	0.000	0.000
82	B	121	LEU	0	0.010	-0.009	13.688	-0.014	-0.014	0.000	0.000	0.000	0.000
83	B	122	GLU	-1	-0.855	-0.896	15.701	-0.031	-0.031	0.000	0.000	0.000	0.000
84	B	123	GLU	-1	-0.768	-0.879	16.596	0.008	0.008	0.000	0.000	0.000	0.000
85	B	124	VAL	0	-0.023	-0.012	10.598	-0.022	-0.022	0.000	0.000	0.000	0.000
86	B	125	ALA	0	-0.021	-0.010	12.599	-0.101	-0.101	0.000	0.000	0.000	0.000
87	B	126	LYS	1	0.726	0.841	14.653	-0.031	-0.031	0.000	0.000	0.000	0.000
88	B	127	ALA	0	-0.051	-0.018	12.019	0.019	0.019	0.000	0.000	0.000	0.000
89	B	128	ASP	-1	-0.806	-0.899	11.329	-0.504	-0.504	0.000	0.000	0.000	0.000
90	B	129	PRO	0	-0.048	-0.035	6.341	0.155	0.155	0.000	0.000	0.000	0.000
91	B	130	GLN	0	-0.032	-0.034	6.639	0.007	0.007	0.000	0.000	0.000	0.000
92	B	131	ASN	0	0.013	0.021	9.410	0.117	0.117	0.000	0.000	0.000	0.000
93	B	132	PRO	0	0.015	0.005	11.773	0.123	0.123	0.000	0.000	0.000	0.000
94	B	133	ALA	0	-0.008	0.011	13.701	0.056	0.056	0.000	0.000	0.000	0.000
95	B	134	THR	0	-0.049	-0.062	13.848	0.044	0.044	0.000	0.000	0.000	0.000
96	B	135	PHE	0	-0.016	-0.017	15.877	-0.084	-0.084	0.000	0.000	0.000	0.000
97	B	136	PRO	0	0.034	0.029	16.720	0.087	0.087	0.000	0.000	0.000	0.000
98	B	137	HIS	0	0.041	0.017	15.274	-0.036	-0.036	0.000	0.000	0.000	0.000
99	B	138	PRO	0	-0.048	-0.032	17.759	-0.005	-0.005	0.000	0.000	0.000	0.000
100	B	139	PHE	0	-0.051	-0.020	16.637	-0.036	-0.036	0.000	0.000	0.000	0.000
101	B	140	PHE	0	-0.015	-0.019	13.778	0.051	0.051	0.000	0.000	0.000	0.000
102	B	141	GLY	0	0.047	0.042	15.735	0.028	0.028	0.000	0.000	0.000	0.000
103	B	142	GLU	-1	-0.842	-0.916	16.423	0.450	0.450	0.000	0.000	0.000	0.000
104	B	143	LEU	0	-0.035	-0.001	10.843	0.162	0.162	0.000	0.000	0.000	0.000
105	B	144	ASN	0	0.070	0.030	8.375	0.203	0.203	0.000	0.000	0.000	0.000
106	B	145	PRO	0	0.014	0.002	9.972	0.193	0.193	0.000	0.000	0.000	0.000
107	B	146	LEU	0	0.004	0.015	2.777	-0.223	0.192	0.275	-0.129	-0.560	-0.001
108	B	147	GLY	0	-0.009	-0.010	6.792	0.871	0.871	0.000	0.000	0.000	0.000
109	B	148	TRP	0	0.017	-0.011	8.806	0.185	0.185	0.000	0.000	0.000	0.000
110	B	149	LEU	0	0.018	0.020	6.910	0.028	0.028	0.000	0.000	0.000	0.000
111	B	150	ARG	1	0.922	0.951	3.742	-7.784	-7.034	0.008	-0.363	-0.395	0.003
112	B	151	ALA	0	-0.015	0.005	7.526	-0.158	-0.158	0.000	0.000	0.000	0.000
113	B	152	ALA	0	0.029	0.014	11.212	-0.149	-0.149	0.000	0.000	0.000	0.000
114	B	153	ALA	0	-0.012	-0.016	8.214	-0.103	-0.103	0.000	0.000	0.000	0.000
115	B	154	TYR	0	-0.042	-0.018	10.257	-0.104	-0.104	0.000	0.000	0.000	0.000
116	B	155	HIS	0	0.000	-0.001	11.703	-0.145	-0.145	0.000	0.000	0.000	0.000
117	B	156	GLU	-1	-0.671	-0.799	14.198	0.399	0.399	0.000	0.000	0.000	0.000
118	B	157	ALA	0	-0.003	-0.006	12.630	-0.097	-0.097	0.000	0.000	0.000	0.000
119	B	158	HIS	0	-0.065	-0.027	14.667	-0.096	-0.096	0.000	0.000	0.000	0.000
120	B	159	HIS	0	0.030	0.008	16.986	-0.049	-0.049	0.000	0.000	0.000	0.000
121	B	160	LEU	0	-0.020	0.008	16.521	-0.051	-0.051	0.000	0.000	0.000	0.000
122	B	161	LYS	1	0.961	0.975	15.415	-0.663	-0.663	0.000	0.000	0.000	0.000
123	B	162	ALA	0	0.005	0.014	20.044	-0.040	-0.040	0.000	0.000	0.000	0.000
124	B	163	LEU	0	0.009	0.014	22.678	-0.037	-0.037	0.000	0.000	0.000	0.000
125	B	164	GLN	0	-0.020	-0.031	19.744	0.004	0.004	0.000	0.000	0.000	0.000
126	B	165	ALA	0	-0.034	-0.008	24.001	-0.024	-0.024	0.000	0.000	0.000	0.000
127	B	166	SER	0	-0.065	-0.016	25.858	-0.042	-0.042	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:9:THR)