FMO DATABASE

FMODB ID: 821QY

Calculation Name: 1YQH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YQH

Chain ID: A

ChEMBL ID:

UniProt ID: Q81IG4

Base Structure: X-ray

Registration Date: 2023-06-21

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	104
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-734904.268767
FMO2-HF: Nuclear repulsion	694070.124149
FMO2-HF: Total energy	-40834.144618
FMO2-MP2: Total energy	-40951.988343

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:-2:SER)

Summations of interaction energy for fragment #1(A:-2:SER)

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.
-48.684	-54.172	36.934	-18.434	-13.012	-0.084

Interaction energy analysis for fragmet #1(A:-2:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.068 / q_NPA : -0.063

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	0	ALA	0	0.061	0.033	3.764	-0.358	2.215	-0.007	-1.453	-1.113	0.004
4	A	1	MET	0	-0.071	-0.022	5.853	0.303	0.303	0.000	0.000	0.000	0.000
5	A	2	SER	0	-0.056	-0.024	2.656	-2.243	-0.283	0.928	-1.295	-1.594	-0.011
6	A	3	GLN	0	-0.026	-0.015	4.520	0.213	0.197	-0.001	-0.013	0.030	0.000
7	A	4	GLN	0	-0.013	-0.005	5.669	0.506	0.506	0.000	0.000	0.000	0.000
8	A	5	VAL	0	-0.037	-0.012	6.226	-0.162	-0.162	0.000	0.000	0.000	0.000
9	A	6	THR	0	0.007	-0.009	8.656	-0.139	-0.139	0.000	0.000	0.000	0.000
10	A	7	MET	0	-0.085	-0.039	8.085	-0.053	-0.053	0.000	0.000	0.000	0.000
11	A	8	SER	0	-0.059	-0.045	12.574	-0.045	-0.045	0.000	0.000	0.000	0.000
12	A	9	PHE	0	0.045	0.014	14.734	0.013	0.013	0.000	0.000	0.000	0.000
13	A	10	SER	0	0.017	0.000	16.771	-0.016	-0.016	0.000	0.000	0.000	0.000
14	A	11	VAL	0	0.007	-0.003	19.022	-0.012	-0.012	0.000	0.000	0.000	0.000
15	A	12	VAL	0	-0.010	-0.004	21.607	0.003	0.003	0.000	0.000	0.000	0.000
16	A	13	PRO	0	0.010	0.005	24.676	-0.009	-0.009	0.000	0.000	0.000	0.000
17	A	14	GLN	0	-0.013	0.005	26.258	0.007	0.007	0.000	0.000	0.000	0.000
18	A	15	ALA	0	0.063	0.012	29.402	-0.010	-0.010	0.000	0.000	0.000	0.000
19	A	16	LYS	1	0.783	0.878	31.512	0.047	0.047	0.000	0.000	0.000	0.000
20	A	17	THR	0	-0.046	-0.021	34.146	0.001	0.001	0.000	0.000	0.000	0.000
21	A	18	LYS	1	0.882	0.945	30.856	0.035	0.035	0.000	0.000	0.000	0.000
22	A	19	ASP	-1	-0.819	-0.878	33.219	0.004	0.004	0.000	0.000	0.000	0.000
23	A	20	VAL	0	0.031	0.005	28.473	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	21	TYR	0	0.009	-0.004	28.455	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	22	SER	0	-0.030	-0.034	28.588	0.003	0.003	0.000	0.000	0.000	0.000
26	A	23	VAL	0	-0.027	0.010	25.448	-0.006	-0.006	0.000	0.000	0.000	0.000
27	A	24	VAL	0	0.005	-0.009	23.576	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	25	ASP	-1	-0.863	-0.922	23.747	0.024	0.024	0.000	0.000	0.000	0.000
29	A	26	LYS	1	0.808	0.888	23.719	0.023	0.023	0.000	0.000	0.000	0.000
30	A	27	ALA	0	0.009	0.011	19.952	-0.009	-0.009	0.000	0.000	0.000	0.000
31	A	28	ILE	0	-0.030	-0.020	19.158	0.021	0.021	0.000	0.000	0.000	0.000
32	A	29	GLU	-1	-0.847	-0.908	20.329	-0.014	-0.014	0.000	0.000	0.000	0.000
33	A	30	VAL	0	-0.003	-0.006	15.666	-0.003	-0.003	0.000	0.000	0.000	0.000
34	A	31	VAL	0	-0.015	-0.011	15.704	0.021	0.021	0.000	0.000	0.000	0.000
35	A	32	GLN	0	-0.046	-0.006	16.837	0.018	0.018	0.000	0.000	0.000	0.000
36	A	33	GLN	0	-0.031	-0.022	18.627	-0.012	-0.012	0.000	0.000	0.000	0.000
37	A	34	SER	0	-0.067	-0.040	12.983	0.003	0.003	0.000	0.000	0.000	0.000
38	A	35	GLY	0	-0.014	0.000	13.522	0.005	0.005	0.000	0.000	0.000	0.000
39	A	36	VAL	0	-0.056	-0.018	9.980	0.056	0.056	0.000	0.000	0.000	0.000
40	A	37	ARG	1	0.825	0.883	13.079	-0.519	-0.519	0.000	0.000	0.000	0.000
41	A	38	TYR	0	0.002	-0.015	14.259	0.076	0.076	0.000	0.000	0.000	0.000
42	A	39	GLU	-1	-0.852	-0.900	16.821	0.229	0.229	0.000	0.000	0.000	0.000
43	A	40	VAL	0	-0.009	0.001	19.858	0.017	0.017	0.000	0.000	0.000	0.000
44	A	41	GLY	0	0.034	0.021	21.979	-0.010	-0.010	0.000	0.000	0.000	0.000
45	A	42	ALA	0	-0.042	-0.037	24.002	-0.010	-0.010	0.000	0.000	0.000	0.000
46	A	43	MET	0	-0.025	-0.010	24.894	-0.016	-0.016	0.000	0.000	0.000	0.000
47	A	44	GLU	-1	-0.822	-0.873	18.889	0.253	0.253	0.000	0.000	0.000	0.000
48	A	45	THR	0	-0.011	-0.004	17.216	-0.016	-0.016	0.000	0.000	0.000	0.000
49	A	46	THR	0	-0.008	-0.006	16.145	0.035	0.035	0.000	0.000	0.000	0.000
50	A	47	LEU	0	0.002	-0.005	11.878	-0.036	-0.036	0.000	0.000	0.000	0.000
51	A	48	GLU	-1	-0.795	-0.897	11.391	0.684	0.684	0.000	0.000	0.000	0.000
52	A	49	GLY	0	0.016	0.001	8.854	-0.229	-0.229	0.000	0.000	0.000	0.000
53	A	50	GLU	-1	-0.831	-0.922	3.018	-0.270	0.681	0.220	-0.433	-0.737	0.002
54	A	51	LEU	0	0.017	-0.003	2.712	-2.513	-0.546	0.718	-1.076	-1.609	0.011
55	A	52	ASP	-1	-0.777	-0.872	1.635	-41.305	-54.488	35.060	-14.113	-7.764	-0.090
56	A	53	VAL	0	0.002	0.013	3.573	-1.050	-0.790	0.016	-0.051	-0.225	0.000
57	A	54	LEU	0	0.000	-0.003	6.294	-0.572	-0.572	0.000	0.000	0.000	0.000
58	A	55	LEU	0	0.005	-0.004	5.495	-0.343	-0.343	0.000	0.000	0.000	0.000
59	A	56	ASP	-1	-0.818	-0.876	7.618	-0.900	-0.900	0.000	0.000	0.000	0.000
60	A	57	VAL	0	-0.001	0.005	9.462	-0.027	-0.027	0.000	0.000	0.000	0.000
61	A	58	VAL	0	0.011	0.010	11.374	-0.045	-0.045	0.000	0.000	0.000	0.000
62	A	59	LYS	1	0.815	0.891	9.271	1.001	1.001	0.000	0.000	0.000	0.000
63	A	60	ARG	1	0.880	0.916	11.115	0.279	0.279	0.000	0.000	0.000	0.000
64	A	61	ALA	0	0.025	0.031	15.360	0.010	0.010	0.000	0.000	0.000	0.000
65	A	62	GLN	0	0.042	0.018	15.890	0.044	0.044	0.000	0.000	0.000	0.000
66	A	63	GLN	0	-0.086	-0.049	17.816	-0.009	-0.009	0.000	0.000	0.000	0.000
67	A	64	ALA	0	0.064	0.027	19.428	0.009	0.009	0.000	0.000	0.000	0.000
68	A	65	CYS	0	-0.074	-0.031	21.360	0.021	0.021	0.000	0.000	0.000	0.000
69	A	66	VAL	0	0.007	0.001	22.784	0.006	0.006	0.000	0.000	0.000	0.000
70	A	67	ASP	-1	-0.876	-0.926	21.951	-0.154	-0.154	0.000	0.000	0.000	0.000
71	A	68	ALA	0	-0.034	-0.012	25.235	0.005	0.005	0.000	0.000	0.000	0.000
72	A	69	GLY	0	-0.056	-0.035	27.428	0.009	0.009	0.000	0.000	0.000	0.000
73	A	70	ALA	0	-0.046	-0.022	26.055	0.008	0.008	0.000	0.000	0.000	0.000
74	A	71	GLU	-1	-0.793	-0.887	27.174	-0.053	-0.053	0.000	0.000	0.000	0.000
75	A	72	GLU	-1	-0.964	-0.976	25.758	-0.031	-0.031	0.000	0.000	0.000	0.000
76	A	73	VAL	0	-0.002	-0.019	21.436	0.010	0.010	0.000	0.000	0.000	0.000
77	A	74	ILE	0	-0.013	0.025	22.638	-0.007	-0.007	0.000	0.000	0.000	0.000
78	A	75	THR	0	0.015	-0.024	16.591	0.013	0.013	0.000	0.000	0.000	0.000
79	A	76	SER	0	-0.042	-0.007	18.944	-0.007	-0.007	0.000	0.000	0.000	0.000
80	A	77	ILE	0	0.013	-0.001	12.241	0.015	0.015	0.000	0.000	0.000	0.000
81	A	78	LYS	1	0.898	0.949	14.839	-0.331	-0.331	0.000	0.000	0.000	0.000
82	A	79	ILE	0	0.037	0.020	8.873	0.050	0.050	0.000	0.000	0.000	0.000
83	A	80	HIS	0	0.014	0.030	12.222	-0.093	-0.093	0.000	0.000	0.000	0.000
84	A	81	TYR	0	0.046	0.009	5.333	-0.093	-0.093	0.000	0.000	0.000	0.000
85	A	82	ARG	1	0.811	0.865	9.447	-0.816	-0.816	0.000	0.000	0.000	0.000
86	A	83	PRO	0	0.028	0.016	6.680	-0.038	-0.038	0.000	0.000	0.000	0.000
87	A	84	SER	0	-0.005	0.009	8.232	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	85	THR	0	-0.022	-0.031	11.385	-0.060	-0.060	0.000	0.000	0.000	0.000
89	A	86	GLY	0	0.057	0.060	9.502	-0.049	-0.049	0.000	0.000	0.000	0.000
90	A	87	VAL	0	-0.085	-0.048	10.435	-0.157	-0.157	0.000	0.000	0.000	0.000
91	A	88	THR	0	-0.010	0.013	11.829	0.088	0.088	0.000	0.000	0.000	0.000
92	A	89	ILE	0	0.068	0.008	14.476	-0.033	-0.033	0.000	0.000	0.000	0.000
93	A	90	ASP	-1	-0.773	-0.833	17.264	0.326	0.326	0.000	0.000	0.000	0.000
94	A	91	GLU	-1	-0.786	-0.862	15.848	0.543	0.543	0.000	0.000	0.000	0.000
95	A	92	LYS	1	0.824	0.899	16.636	-0.555	-0.555	0.000	0.000	0.000	0.000
96	A	93	VAL	0	0.015	-0.010	20.715	-0.028	-0.028	0.000	0.000	0.000	0.000
97	A	94	TRP	0	0.025	0.018	22.665	-0.033	-0.033	0.000	0.000	0.000	0.000
98	A	95	LYS	1	0.813	0.922	23.369	-0.299	-0.299	0.000	0.000	0.000	0.000
99	A	96	TYR	0	-0.069	-0.035	24.786	-0.005	-0.005	0.000	0.000	0.000	0.000
100	A	97	ARG	1	0.788	0.868	23.337	-0.236	-0.236	0.000	0.000	0.000	0.000
101	A	98	ASP	-1	-0.871	-0.926	28.814	0.137	0.137	0.000	0.000	0.000	0.000
102	A	99	GLU	-1	-0.887	-0.941	26.118	0.189	0.189	0.000	0.000	0.000	0.000
103	A	100	TYR	0	-0.098	-0.069	21.553	0.004	0.004	0.000	0.000	0.000	0.000
104	A	101	ALA	0	-0.015	-0.002	28.184	-0.002	-0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-2:SER)