FMO DATABASE

FMODB ID: 8956Y

Calculation Name: 2YQY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YQY

Chain ID: A

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1082244.557272
FMO2-HF: Nuclear repulsion	1033421.044991
FMO2-HF: Total energy	-48823.512282
FMO2-MP2: Total energy	-48970.130602

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:9:THR)

Summations of interaction energy for fragment #1(A: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.
-41.147	-39.389	21.413	-11.795	-11.377	-0.054

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.021 / q_NPA : -0.047

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	A	11	ASP	-1	-0.839	-0.928	3.496	0.698	2.462	0.004	-0.673	-1.095	0.000
4	A	12	GLU	-1	-0.836	-0.882	1.717	-36.253	-38.470	21.072	-10.213	-8.643	-0.060
5	A	13	ALA	0	-0.027	-0.008	3.864	-0.976	-0.424	0.006	-0.195	-0.363	0.001
6	A	14	LEU	0	0.039	0.026	5.508	-0.110	-0.110	0.000	0.000	0.000	0.000
7	A	15	LYS	1	0.854	0.908	7.222	-0.631	-0.631	0.000	0.000	0.000	0.000
8	A	16	ARG	1	0.866	0.915	4.631	2.249	2.342	-0.001	-0.004	-0.088	0.000
9	A	17	LEU	0	0.073	0.044	9.038	-0.012	-0.012	0.000	0.000	0.000	0.000
10	A	18	GLU	-1	-0.839	-0.883	11.381	0.221	0.221	0.000	0.000	0.000	0.000
11	A	19	ALA	0	-0.035	-0.010	12.216	-0.023	-0.023	0.000	0.000	0.000	0.000
12	A	20	SER	0	-0.031	-0.045	13.099	-0.010	-0.010	0.000	0.000	0.000	0.000
13	A	21	ARG	1	0.776	0.864	14.918	-0.176	-0.176	0.000	0.000	0.000	0.000
14	A	22	LYS	1	0.864	0.918	14.805	-0.095	-0.095	0.000	0.000	0.000	0.000
15	A	23	ALA	0	0.022	0.011	17.834	-0.006	-0.006	0.000	0.000	0.000	0.000
16	A	24	LEU	0	-0.005	0.004	18.975	-0.003	-0.003	0.000	0.000	0.000	0.000
17	A	25	LEU	0	-0.037	-0.030	20.760	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	26	ALA	0	0.002	0.013	22.614	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	27	LEU	0	-0.001	-0.004	22.915	0.000	0.000	0.000	0.000	0.000	0.000
20	A	28	LEU	0	-0.020	-0.028	23.896	0.001	0.001	0.000	0.000	0.000	0.000
21	A	29	ARG	1	0.863	0.931	25.294	-0.064	-0.064	0.000	0.000	0.000	0.000
22	A	30	GLU	-1	-0.935	-0.959	27.110	-0.007	-0.007	0.000	0.000	0.000	0.000
23	A	31	ALA	0	-0.040	-0.001	29.168	-0.004	-0.004	0.000	0.000	0.000	0.000
24	A	32	ASP	-1	-0.801	-0.901	30.907	0.020	0.020	0.000	0.000	0.000	0.000
25	A	33	PRO	0	-0.001	-0.016	33.826	0.004	0.004	0.000	0.000	0.000	0.000
26	A	34	ALA	0	-0.031	-0.009	35.632	0.004	0.004	0.000	0.000	0.000	0.000
27	A	35	TRP	0	-0.003	-0.024	26.943	0.005	0.005	0.000	0.000	0.000	0.000
28	A	36	LEU	0	-0.009	-0.006	29.198	0.005	0.005	0.000	0.000	0.000	0.000
29	A	37	SER	0	-0.036	-0.023	31.855	0.006	0.006	0.000	0.000	0.000	0.000
30	A	38	ALA	0	0.007	0.013	34.131	0.001	0.001	0.000	0.000	0.000	0.000
31	A	39	PRO	0	-0.037	-0.032	32.876	0.003	0.003	0.000	0.000	0.000	0.000
32	A	40	LEU	0	-0.005	-0.001	26.788	-0.004	-0.004	0.000	0.000	0.000	0.000
33	A	41	ARG	1	0.834	0.892	31.206	-0.040	-0.040	0.000	0.000	0.000	0.000
34	A	42	DGL	-1	-0.827	-0.905	33.999	0.032	0.032	0.000	0.000	0.000	0.000
35	A	43	GLY	0	-0.002	0.013	35.702	0.002	0.002	0.000	0.000	0.000	0.000
36	A	44	ALA	0	-0.071	-0.019	30.699	0.005	0.005	0.000	0.000	0.000	0.000
37	A	45	TRP	0	0.024	0.004	23.944	0.000	0.000	0.000	0.000	0.000	0.000
38	A	46	THR	0	0.047	0.008	30.806	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	47	PRO	0	0.032	0.009	27.228	0.010	0.010	0.000	0.000	0.000	0.000
40	A	48	LEU	0	-0.008	0.012	26.642	0.009	0.009	0.000	0.000	0.000	0.000
41	A	49	MET	0	0.024	0.032	27.622	0.008	0.008	0.000	0.000	0.000	0.000
42	A	50	VAL	0	-0.021	0.004	22.767	0.014	0.014	0.000	0.000	0.000	0.000
43	A	51	ALA	0	0.003	-0.003	22.922	0.017	0.017	0.000	0.000	0.000	0.000
44	A	52	GLU	-1	-0.907	-0.964	23.317	0.114	0.114	0.000	0.000	0.000	0.000
45	A	53	HIS	0	0.026	0.002	21.978	0.026	0.026	0.000	0.000	0.000	0.000
46	A	54	VAL	0	-0.011	-0.012	17.904	0.023	0.023	0.000	0.000	0.000	0.000
47	A	55	ALA	0	0.021	0.022	19.638	0.028	0.028	0.000	0.000	0.000	0.000
48	A	56	LEU	0	0.002	-0.002	21.528	0.017	0.017	0.000	0.000	0.000	0.000
49	A	57	VAL	0	0.011	0.012	17.098	0.016	0.016	0.000	0.000	0.000	0.000
50	A	58	GLU	-1	-0.777	-0.844	16.136	0.300	0.300	0.000	0.000	0.000	0.000
51	A	59	ASP	-1	-0.750	-0.842	18.050	0.217	0.217	0.000	0.000	0.000	0.000
52	A	60	SER	0	-0.002	-0.006	20.358	0.000	0.000	0.000	0.000	0.000	0.000
53	A	61	THR	0	-0.030	-0.030	13.776	0.029	0.029	0.000	0.000	0.000	0.000
54	A	62	ALA	0	0.006	0.014	16.390	0.031	0.031	0.000	0.000	0.000	0.000
55	A	63	ARG	1	0.763	0.839	17.847	-0.194	-0.194	0.000	0.000	0.000	0.000
56	A	64	VAL	0	-0.011	0.007	15.875	-0.016	-0.016	0.000	0.000	0.000	0.000
57	A	65	LEU	0	0.002	0.006	11.857	0.004	0.004	0.000	0.000	0.000	0.000
58	A	66	ARG	1	0.942	0.991	15.825	-0.225	-0.225	0.000	0.000	0.000	0.000
59	A	67	ARG	1	0.905	0.957	19.242	-0.258	-0.258	0.000	0.000	0.000	0.000
60	A	68	LEU	0	0.007	-0.003	14.019	-0.017	-0.017	0.000	0.000	0.000	0.000
61	A	69	ARG	1	0.831	0.891	16.698	-0.272	-0.272	0.000	0.000	0.000	0.000
62	A	70	ARG	1	0.898	0.941	17.797	-0.197	-0.197	0.000	0.000	0.000	0.000
63	A	71	LEU	0	-0.044	-0.011	19.531	-0.019	-0.019	0.000	0.000	0.000	0.000
64	A	72	ALA	0	-0.053	-0.009	17.128	-0.031	-0.031	0.000	0.000	0.000	0.000
65	A	104	LEU	0	0.014	0.001	31.813	0.000	0.000	0.000	0.000	0.000	0.000
66	A	105	SER	0	0.028	0.017	33.844	-0.002	-0.002	0.000	0.000	0.000	0.000
67	A	106	LEU	0	0.060	0.016	28.922	0.006	0.006	0.000	0.000	0.000	0.000
68	A	107	DGL	-1	-0.920	-0.970	30.107	0.057	0.057	0.000	0.000	0.000	0.000
69	A	108	GLU	-1	-0.781	-0.866	30.700	0.095	0.095	0.000	0.000	0.000	0.000
70	A	109	VAL	0	0.024	0.005	26.642	0.010	0.010	0.000	0.000	0.000	0.000
71	A	110	LEU	0	-0.017	-0.004	25.812	0.011	0.011	0.000	0.000	0.000	0.000
72	A	111	ALA	0	0.061	0.036	25.743	0.009	0.009	0.000	0.000	0.000	0.000
73	A	112	LEU	0	-0.068	-0.004	25.460	0.010	0.010	0.000	0.000	0.000	0.000
74	A	113	LEU	0	0.024	0.005	20.770	0.017	0.017	0.000	0.000	0.000	0.000
75	A	114	ASP	-1	-0.856	-0.932	21.524	0.132	0.132	0.000	0.000	0.000	0.000
76	A	115	ARG	1	0.725	0.822	22.722	-0.097	-0.097	0.000	0.000	0.000	0.000
77	A	116	ALA	0	-0.007	0.009	20.940	0.012	0.012	0.000	0.000	0.000	0.000
78	A	117	ARG	1	0.761	0.838	14.523	-0.218	-0.218	0.000	0.000	0.000	0.000
79	A	118	ALA	0	-0.002	0.005	18.112	0.024	0.024	0.000	0.000	0.000	0.000
80	A	119	PHE	0	-0.033	-0.018	19.675	0.017	0.017	0.000	0.000	0.000	0.000
81	A	120	LEU	0	-0.012	-0.015	13.661	0.022	0.022	0.000	0.000	0.000	0.000
82	A	121	LEU	0	-0.006	-0.013	13.866	0.044	0.044	0.000	0.000	0.000	0.000
83	A	122	GLU	-1	-0.816	-0.880	15.747	0.231	0.231	0.000	0.000	0.000	0.000
84	A	123	GLU	-1	-0.765	-0.870	16.355	0.276	0.276	0.000	0.000	0.000	0.000
85	A	124	VAL	0	-0.035	-0.020	10.424	0.032	0.032	0.000	0.000	0.000	0.000
86	A	125	ALA	0	-0.040	-0.014	12.040	0.035	0.035	0.000	0.000	0.000	0.000
87	A	126	LYS	1	0.763	0.859	14.335	-0.248	-0.248	0.000	0.000	0.000	0.000
88	A	127	ALA	0	-0.051	-0.019	11.998	-0.021	-0.021	0.000	0.000	0.000	0.000
89	A	128	ASP	-1	-0.800	-0.896	11.229	0.424	0.424	0.000	0.000	0.000	0.000
90	A	129	PRO	0	-0.039	-0.030	6.245	0.041	0.041	0.000	0.000	0.000	0.000
91	A	130	GLN	0	-0.024	-0.033	6.955	0.209	0.209	0.000	0.000	0.000	0.000
92	A	131	ASN	0	0.013	0.023	9.597	-0.061	-0.061	0.000	0.000	0.000	0.000
93	A	132	PRO	0	0.014	0.007	12.179	0.079	0.079	0.000	0.000	0.000	0.000
94	A	133	ALA	0	-0.013	0.010	14.266	-0.010	-0.010	0.000	0.000	0.000	0.000
95	A	134	THR	0	-0.053	-0.066	14.219	0.061	0.061	0.000	0.000	0.000	0.000
96	A	135	PHE	0	-0.023	-0.021	16.154	-0.061	-0.061	0.000	0.000	0.000	0.000
97	A	136	PRO	0	0.035	0.032	16.905	0.055	0.055	0.000	0.000	0.000	0.000
98	A	137	HIS	0	0.034	0.017	15.524	-0.031	-0.031	0.000	0.000	0.000	0.000
99	A	138	PRO	0	-0.038	-0.029	17.948	-0.012	-0.012	0.000	0.000	0.000	0.000
100	A	139	PHE	0	-0.047	-0.017	16.711	-0.034	-0.034	0.000	0.000	0.000	0.000
101	A	140	PHE	0	-0.012	-0.017	13.797	0.015	0.015	0.000	0.000	0.000	0.000
102	A	141	GLY	0	0.049	0.040	16.240	0.017	0.017	0.000	0.000	0.000	0.000
103	A	142	GLU	-1	-0.850	-0.920	16.678	0.369	0.369	0.000	0.000	0.000	0.000
104	A	143	LEU	0	-0.029	0.002	11.155	0.100	0.100	0.000	0.000	0.000	0.000
105	A	144	ASN	0	0.053	0.018	8.738	0.119	0.119	0.000	0.000	0.000	0.000
106	A	145	PRO	0	0.014	0.003	9.983	0.099	0.099	0.000	0.000	0.000	0.000
107	A	146	LEU	0	0.025	0.021	2.788	-0.357	0.005	0.256	-0.105	-0.512	-0.001
108	A	147	GLY	0	-0.024	-0.003	6.591	0.676	0.676	0.000	0.000	0.000	0.000
109	A	148	TRP	0	0.020	-0.011	9.008	0.016	0.016	0.000	0.000	0.000	0.000
110	A	149	LEU	0	0.001	0.013	6.955	-0.068	-0.068	0.000	0.000	0.000	0.000
111	A	150	ARG	1	0.916	0.944	3.386	-6.945	-5.741	0.076	-0.605	-0.676	0.006
112	A	151	ALA	0	-0.007	0.009	7.699	-0.257	-0.257	0.000	0.000	0.000	0.000
113	A	152	ALA	0	0.021	0.009	11.389	-0.139	-0.139	0.000	0.000	0.000	0.000
114	A	153	ALA	0	-0.011	-0.017	8.234	-0.106	-0.106	0.000	0.000	0.000	0.000
115	A	154	TYR	0	-0.019	-0.012	10.255	-0.149	-0.149	0.000	0.000	0.000	0.000
116	A	155	HIS	0	-0.016	-0.006	11.698	-0.086	-0.086	0.000	0.000	0.000	0.000
117	A	156	GLU	-1	-0.678	-0.807	14.044	0.135	0.135	0.000	0.000	0.000	0.000
118	A	157	ALA	0	-0.004	-0.006	12.361	-0.054	-0.054	0.000	0.000	0.000	0.000
119	A	158	HIS	0	-0.061	-0.025	14.417	-0.052	-0.052	0.000	0.000	0.000	0.000
120	A	159	HIS	0	0.008	0.003	16.795	-0.046	-0.046	0.000	0.000	0.000	0.000
121	A	160	LEU	0	-0.013	0.010	16.314	-0.019	-0.019	0.000	0.000	0.000	0.000
122	A	161	LYS	1	0.934	0.969	16.522	0.039	0.039	0.000	0.000	0.000	0.000
123	A	162	ALA	0	0.008	0.005	19.715	-0.012	-0.012	0.000	0.000	0.000	0.000
124	A	163	LEU	0	0.011	0.016	22.453	-0.008	-0.008	0.000	0.000	0.000	0.000
125	A	164	GLN	0	-0.019	-0.023	19.326	-0.013	-0.013	0.000	0.000	0.000	0.000
126	A	165	ALA	0	-0.048	-0.019	23.650	-0.007	-0.007	0.000	0.000	0.000	0.000
127	A	166	SER	0	-0.055	-0.011	25.469	0.001	0.001	0.000	0.000	0.000	0.000

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