FMO DATABASE

FMODB ID: 1N73Z

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	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	127
LigandCharge	DGL=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1076602.491546
FMO2-HF: Nuclear repulsion	1027779.598658
FMO2-HF: Total energy	-48822.892888
FMO2-MP2: Total energy	-48969.536709

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.
-36.589	-26.391	9.416	-8.42	-11.192	-0.023

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 : 0.018 / q_NPA : -0.008

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	-0.833	-0.920	3.187	-0.748	1.897	0.159	-1.156	-1.647	0.004
4	A	12	GLU	-1	-0.960	-0.977	2.096	-32.759	-26.801	9.128	-6.740	-8.346	-0.028
5	A	13	ALA	0	-0.032	-0.016	3.233	-0.053	0.627	0.012	-0.254	-0.438	0.000
6	A	14	LEU	0	0.066	0.034	4.927	0.167	0.276	-0.001	-0.009	-0.099	0.000
7	A	15	LYS	1	0.851	0.928	7.124	0.144	0.144	0.000	0.000	0.000	0.000
8	A	16	ARG	1	0.944	0.952	6.009	1.575	1.575	0.000	0.000	0.000	0.000
9	A	17	LEU	0	0.046	0.040	8.990	0.097	0.097	0.000	0.000	0.000	0.000
10	A	18	GLU	-1	-0.889	-0.934	11.057	0.039	0.039	0.000	0.000	0.000	0.000
11	A	19	ALA	0	-0.059	-0.024	12.254	0.031	0.031	0.000	0.000	0.000	0.000
12	A	20	SER	0	-0.031	-0.053	13.100	0.015	0.015	0.000	0.000	0.000	0.000
13	A	21	ARG	1	0.864	0.942	14.859	0.013	0.013	0.000	0.000	0.000	0.000
14	A	22	LYS	1	0.932	0.957	15.716	0.197	0.197	0.000	0.000	0.000	0.000
15	A	23	ALA	0	0.005	0.011	17.828	0.011	0.011	0.000	0.000	0.000	0.000
16	A	24	LEU	0	0.012	0.006	18.874	0.013	0.013	0.000	0.000	0.000	0.000
17	A	25	LEU	0	-0.016	-0.023	20.703	0.011	0.011	0.000	0.000	0.000	0.000
18	A	26	ALA	0	-0.025	-0.006	22.586	0.008	0.008	0.000	0.000	0.000	0.000
19	A	27	LEU	0	0.041	0.024	23.271	0.005	0.005	0.000	0.000	0.000	0.000
20	A	28	LEU	0	-0.028	-0.033	24.187	0.008	0.008	0.000	0.000	0.000	0.000
21	A	29	ARG	1	0.908	0.948	24.698	0.039	0.039	0.000	0.000	0.000	0.000
22	A	30	GLU	-1	-0.956	-0.965	27.601	-0.083	-0.083	0.000	0.000	0.000	0.000
23	A	31	ALA	0	-0.051	-0.004	29.307	0.000	0.000	0.000	0.000	0.000	0.000
24	A	32	ASP	-1	-0.839	-0.935	31.026	-0.019	-0.019	0.000	0.000	0.000	0.000
25	A	33	PRO	0	0.004	-0.016	34.005	0.003	0.003	0.000	0.000	0.000	0.000
26	A	34	ALA	0	-0.038	-0.012	35.655	0.004	0.004	0.000	0.000	0.000	0.000
27	A	35	TRP	0	0.023	0.005	27.094	0.003	0.003	0.000	0.000	0.000	0.000
28	A	36	LEU	0	-0.005	-0.004	29.418	0.004	0.004	0.000	0.000	0.000	0.000
29	A	37	SER	0	-0.025	-0.017	31.803	0.006	0.006	0.000	0.000	0.000	0.000
30	A	38	ALA	0	0.009	0.016	34.145	0.003	0.003	0.000	0.000	0.000	0.000
31	A	39	PRO	0	-0.039	-0.029	33.069	0.000	0.000	0.000	0.000	0.000	0.000
32	A	40	LEU	0	0.005	0.002	27.096	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	41	ARG	1	0.855	0.911	31.465	-0.021	-0.021	0.000	0.000	0.000	0.000
34	A	42	DGL	-1	-0.804	-0.901	33.932	0.013	0.013	0.000	0.000	0.000	0.000
35	A	43	GLY	0	-0.037	-0.007	35.417	0.003	0.003	0.000	0.000	0.000	0.000
36	A	44	ALA	0	-0.086	-0.024	30.761	0.005	0.005	0.000	0.000	0.000	0.000
37	A	45	TRP	0	0.035	0.012	23.815	0.000	0.000	0.000	0.000	0.000	0.000
38	A	46	THR	0	0.043	0.002	30.787	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	47	PRO	0	0.048	0.016	27.277	0.006	0.006	0.000	0.000	0.000	0.000
40	A	48	LEU	0	-0.015	-0.002	26.694	0.002	0.002	0.000	0.000	0.000	0.000
41	A	49	MET	0	-0.007	0.023	27.797	0.007	0.007	0.000	0.000	0.000	0.000
42	A	50	VAL	0	-0.013	0.016	22.800	0.009	0.009	0.000	0.000	0.000	0.000
43	A	51	ALA	0	-0.001	-0.012	22.926	0.009	0.009	0.000	0.000	0.000	0.000
44	A	52	GLU	-1	-0.876	-0.944	23.137	0.066	0.066	0.000	0.000	0.000	0.000
45	A	53	HIS	0	0.015	0.002	21.375	0.022	0.022	0.000	0.000	0.000	0.000
46	A	54	VAL	0	0.001	-0.006	17.873	0.019	0.019	0.000	0.000	0.000	0.000
47	A	55	ALA	0	0.016	0.015	19.267	0.017	0.017	0.000	0.000	0.000	0.000
48	A	56	LEU	0	-0.008	-0.005	21.168	0.018	0.018	0.000	0.000	0.000	0.000
49	A	57	VAL	0	-0.003	0.002	16.860	0.022	0.022	0.000	0.000	0.000	0.000
50	A	58	GLU	-1	-0.795	-0.861	15.443	0.121	0.121	0.000	0.000	0.000	0.000
51	A	59	ASP	-1	-0.776	-0.867	17.693	0.163	0.163	0.000	0.000	0.000	0.000
52	A	60	SER	0	-0.025	-0.009	20.058	0.021	0.021	0.000	0.000	0.000	0.000
53	A	61	THR	0	-0.012	-0.033	13.516	0.033	0.033	0.000	0.000	0.000	0.000
54	A	62	ALA	0	0.025	0.023	16.506	0.040	0.040	0.000	0.000	0.000	0.000
55	A	63	ARG	1	0.785	0.869	17.816	-0.143	-0.143	0.000	0.000	0.000	0.000
56	A	64	VAL	0	-0.020	0.009	15.788	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	65	LEU	0	0.007	0.005	12.066	0.021	0.021	0.000	0.000	0.000	0.000
58	A	66	ARG	1	0.955	0.993	15.917	-0.186	-0.186	0.000	0.000	0.000	0.000
59	A	67	ARG	1	0.888	0.938	19.185	-0.252	-0.252	0.000	0.000	0.000	0.000
60	A	68	LEU	0	0.005	-0.008	14.280	-0.011	-0.011	0.000	0.000	0.000	0.000
61	A	69	ARG	1	0.825	0.920	16.968	-0.256	-0.256	0.000	0.000	0.000	0.000
62	A	70	ARG	1	0.880	0.929	17.921	-0.199	-0.199	0.000	0.000	0.000	0.000
63	A	71	LEU	0	-0.037	-0.018	19.685	-0.018	-0.018	0.000	0.000	0.000	0.000
64	A	72	ALA	0	-0.015	0.027	17.240	-0.015	-0.015	0.000	0.000	0.000	0.000
65	A	104	LEU	0	0.012	-0.002	31.816	0.000	0.000	0.000	0.000	0.000	0.000
66	A	105	SER	0	0.041	0.018	33.572	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	106	LEU	0	0.047	0.021	28.555	0.003	0.003	0.000	0.000	0.000	0.000
68	A	107	DGL	-1	-0.912	-0.972	29.982	0.005	0.005	0.000	0.000	0.000	0.000
69	A	108	GLU	-1	-0.843	-0.892	30.773	0.044	0.044	0.000	0.000	0.000	0.000
70	A	109	VAL	0	0.019	-0.002	26.161	0.006	0.006	0.000	0.000	0.000	0.000
71	A	110	LEU	0	-0.019	-0.024	25.868	0.003	0.003	0.000	0.000	0.000	0.000
72	A	111	ALA	0	0.085	0.059	25.682	0.003	0.003	0.000	0.000	0.000	0.000
73	A	112	LEU	0	-0.057	-0.006	25.186	0.009	0.009	0.000	0.000	0.000	0.000
74	A	113	LEU	0	-0.025	-0.022	20.858	0.011	0.011	0.000	0.000	0.000	0.000
75	A	114	ASP	-1	-0.917	-0.950	21.358	0.023	0.023	0.000	0.000	0.000	0.000
76	A	115	ARG	1	0.776	0.847	22.212	-0.042	-0.042	0.000	0.000	0.000	0.000
77	A	116	ALA	0	0.025	0.022	20.606	0.012	0.012	0.000	0.000	0.000	0.000
78	A	117	ARG	1	0.764	0.860	14.364	-0.002	-0.002	0.000	0.000	0.000	0.000
79	A	118	ALA	0	0.000	-0.006	17.772	0.016	0.016	0.000	0.000	0.000	0.000
80	A	119	PHE	0	-0.057	-0.024	19.525	0.021	0.021	0.000	0.000	0.000	0.000
81	A	120	LEU	0	0.015	-0.011	13.242	0.029	0.029	0.000	0.000	0.000	0.000
82	A	121	LEU	0	0.002	-0.008	13.555	0.041	0.041	0.000	0.000	0.000	0.000
83	A	122	GLU	-1	-0.821	-0.880	15.489	0.211	0.211	0.000	0.000	0.000	0.000
84	A	123	GLU	-1	-0.805	-0.921	16.157	0.277	0.277	0.000	0.000	0.000	0.000
85	A	124	VAL	0	-0.063	-0.033	10.211	0.050	0.050	0.000	0.000	0.000	0.000
86	A	125	ALA	0	-0.029	-0.013	12.003	0.064	0.064	0.000	0.000	0.000	0.000
87	A	126	LYS	1	0.782	0.872	14.048	-0.194	-0.194	0.000	0.000	0.000	0.000
88	A	127	ALA	0	-0.047	-0.003	11.564	-0.007	-0.007	0.000	0.000	0.000	0.000
89	A	128	ASP	-1	-0.811	-0.902	11.097	0.588	0.588	0.000	0.000	0.000	0.000
90	A	129	PRO	0	-0.046	-0.033	6.043	0.034	0.034	0.000	0.000	0.000	0.000
91	A	130	GLN	0	-0.035	-0.031	6.550	0.215	0.215	0.000	0.000	0.000	0.000
92	A	131	ASN	0	0.007	0.008	9.436	-0.097	-0.097	0.000	0.000	0.000	0.000
93	A	132	PRO	0	0.003	-0.009	11.781	0.088	0.088	0.000	0.000	0.000	0.000
94	A	133	ALA	0	-0.030	0.002	13.764	-0.011	-0.011	0.000	0.000	0.000	0.000
95	A	134	THR	0	-0.037	-0.057	14.193	0.066	0.066	0.000	0.000	0.000	0.000
96	A	135	PHE	0	-0.034	-0.022	16.080	-0.068	-0.068	0.000	0.000	0.000	0.000
97	A	136	PRO	0	0.037	0.027	16.961	0.048	0.048	0.000	0.000	0.000	0.000
98	A	137	HIS	0	0.003	0.006	15.398	-0.027	-0.027	0.000	0.000	0.000	0.000
99	A	138	PRO	0	-0.011	-0.023	18.224	-0.003	-0.003	0.000	0.000	0.000	0.000
100	A	139	PHE	0	-0.041	-0.007	16.775	-0.024	-0.024	0.000	0.000	0.000	0.000
101	A	140	PHE	0	-0.019	-0.037	14.385	0.012	0.012	0.000	0.000	0.000	0.000
102	A	141	GLY	0	0.050	0.047	16.132	0.044	0.044	0.000	0.000	0.000	0.000
103	A	142	GLU	-1	-0.857	-0.911	16.904	0.382	0.382	0.000	0.000	0.000	0.000
104	A	143	LEU	0	-0.023	-0.001	11.539	0.108	0.108	0.000	0.000	0.000	0.000
105	A	144	ASN	0	0.067	0.039	9.227	0.055	0.055	0.000	0.000	0.000	0.000
106	A	145	PRO	0	0.051	0.009	10.168	0.045	0.045	0.000	0.000	0.000	0.000
107	A	146	LEU	0	0.022	0.023	3.051	-0.396	-0.012	0.115	-0.099	-0.399	0.000
108	A	147	GLY	0	-0.050	-0.025	7.079	0.150	0.150	0.000	0.000	0.000	0.000
109	A	148	TRP	0	0.017	-0.011	9.112	-0.124	-0.124	0.000	0.000	0.000	0.000
110	A	149	LEU	0	0.004	0.022	6.637	-0.103	-0.103	0.000	0.000	0.000	0.000
111	A	150	ARG	1	0.951	0.955	4.061	-5.838	-5.416	0.003	-0.162	-0.263	0.001
112	A	151	ALA	0	-0.021	0.005	7.411	-0.207	-0.207	0.000	0.000	0.000	0.000
113	A	152	ALA	0	0.037	0.020	11.071	-0.101	-0.101	0.000	0.000	0.000	0.000
114	A	153	ALA	0	0.009	-0.006	8.007	-0.086	-0.086	0.000	0.000	0.000	0.000
115	A	154	TYR	0	-0.060	-0.028	9.970	-0.098	-0.098	0.000	0.000	0.000	0.000
116	A	155	HIS	0	-0.028	-0.007	11.447	-0.053	-0.053	0.000	0.000	0.000	0.000
117	A	156	GLU	-1	-0.661	-0.802	13.878	-0.068	-0.068	0.000	0.000	0.000	0.000
118	A	157	ALA	0	-0.038	-0.021	12.399	-0.031	-0.031	0.000	0.000	0.000	0.000
119	A	158	HIS	0	-0.045	-0.020	14.441	-0.016	-0.016	0.000	0.000	0.000	0.000
120	A	159	HIS	0	0.001	-0.011	16.845	-0.024	-0.024	0.000	0.000	0.000	0.000
121	A	160	LEU	0	0.001	0.015	16.579	-0.009	-0.009	0.000	0.000	0.000	0.000
122	A	161	LYS	1	0.954	0.975	15.714	0.140	0.140	0.000	0.000	0.000	0.000
123	A	162	ALA	0	-0.018	-0.006	19.897	-0.002	-0.002	0.000	0.000	0.000	0.000
124	A	163	LEU	0	0.003	0.007	22.599	-0.001	-0.001	0.000	0.000	0.000	0.000
125	A	164	GLN	0	-0.005	-0.020	19.777	-0.005	-0.005	0.000	0.000	0.000	0.000
126	A	165	ALA	0	-0.068	-0.020	24.022	-0.002	-0.002	0.000	0.000	0.000	0.000
127	A	166	SER	0	-0.021	0.013	25.788	0.008	0.008	0.000	0.000	0.000	0.000

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