FMO DATABASE

FMODB ID: 14Q9Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-734270.183169
FMO2-HF: Nuclear repulsion	693436.515706
FMO2-HF: Total energy	-40833.667463
FMO2-MP2: Total energy	-40951.553794

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.
-41.792	-55.809	53.594	-20.726	-18.855	-0.067

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 : -0.041 / q_NPA : -0.028

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	0	ALA	0	0.064	0.018	3.354	-0.434	2.667	0.027	-1.806	-1.323	0.004
4	A	1	MET	0	-0.073	-0.023	5.745	0.918	0.918	0.000	0.000	0.000	0.000
5	A	2	SER	0	-0.038	-0.014	2.444	-0.968	0.290	2.294	-1.555	-1.998	-0.012
6	A	3	GLN	0	-0.015	-0.002	4.275	-0.105	-0.084	-0.001	-0.044	0.024	0.000
7	A	4	GLN	0	-0.010	0.000	5.514	0.604	0.604	0.000	0.000	0.000	0.000
8	A	5	VAL	0	-0.025	-0.009	5.954	0.086	0.086	0.000	0.000	0.000	0.000
9	A	6	THR	0	0.000	-0.004	8.678	-0.291	-0.291	0.000	0.000	0.000	0.000
10	A	7	MET	0	-0.066	-0.028	8.508	0.061	0.061	0.000	0.000	0.000	0.000
11	A	8	SER	0	0.010	0.011	12.585	-0.097	-0.097	0.000	0.000	0.000	0.000
12	A	9	PHE	0	-0.003	-0.012	14.778	0.064	0.064	0.000	0.000	0.000	0.000
13	A	10	SER	0	0.045	0.029	16.854	-0.043	-0.043	0.000	0.000	0.000	0.000
14	A	11	VAL	0	0.001	-0.004	19.198	0.012	0.012	0.000	0.000	0.000	0.000
15	A	12	VAL	0	0.008	0.002	21.688	-0.012	-0.012	0.000	0.000	0.000	0.000
16	A	13	PRO	0	-0.009	-0.001	25.309	0.004	0.004	0.000	0.000	0.000	0.000
17	A	14	GLN	0	-0.021	0.002	26.778	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	15	ALA	0	0.057	0.015	29.846	-0.009	-0.009	0.000	0.000	0.000	0.000
19	A	16	LYS	1	0.898	0.955	31.783	0.018	0.018	0.000	0.000	0.000	0.000
20	A	17	THR	0	-0.054	-0.028	34.572	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	18	LYS	1	0.900	0.959	31.410	0.052	0.052	0.000	0.000	0.000	0.000
22	A	19	ASP	-1	-0.872	-0.919	33.742	-0.012	-0.012	0.000	0.000	0.000	0.000
23	A	20	VAL	0	0.040	0.003	28.684	-0.006	-0.006	0.000	0.000	0.000	0.000
24	A	21	TYR	0	0.010	-0.010	28.793	-0.004	-0.004	0.000	0.000	0.000	0.000
25	A	22	SER	0	0.016	0.011	28.679	-0.005	-0.005	0.000	0.000	0.000	0.000
26	A	23	VAL	0	-0.018	0.010	25.681	-0.012	-0.012	0.000	0.000	0.000	0.000
27	A	24	VAL	0	0.000	-0.018	23.633	-0.010	-0.010	0.000	0.000	0.000	0.000
28	A	25	ASP	-1	-0.933	-0.961	23.665	-0.082	-0.082	0.000	0.000	0.000	0.000
29	A	26	LYS	1	0.901	0.950	23.781	0.137	0.137	0.000	0.000	0.000	0.000
30	A	27	ALA	0	-0.003	0.004	20.031	-0.026	-0.026	0.000	0.000	0.000	0.000
31	A	28	ILE	0	-0.019	-0.020	19.109	-0.011	-0.011	0.000	0.000	0.000	0.000
32	A	29	GLU	-1	-0.842	-0.901	19.854	-0.199	-0.199	0.000	0.000	0.000	0.000
33	A	30	VAL	0	-0.028	-0.012	15.220	-0.046	-0.046	0.000	0.000	0.000	0.000
34	A	31	VAL	0	-0.036	-0.023	15.398	-0.045	-0.045	0.000	0.000	0.000	0.000
35	A	32	GLN	0	-0.044	-0.017	16.263	-0.050	-0.050	0.000	0.000	0.000	0.000
36	A	33	GLN	0	-0.038	-0.021	18.039	-0.039	-0.039	0.000	0.000	0.000	0.000
37	A	34	SER	0	-0.083	-0.040	12.350	-0.064	-0.064	0.000	0.000	0.000	0.000
38	A	35	GLY	0	0.004	0.008	12.973	-0.131	-0.131	0.000	0.000	0.000	0.000
39	A	36	VAL	0	-0.065	-0.014	9.693	0.003	0.003	0.000	0.000	0.000	0.000
40	A	37	ARG	1	0.924	0.954	12.792	-0.060	-0.060	0.000	0.000	0.000	0.000
41	A	38	TYR	0	-0.007	-0.019	14.307	0.080	0.080	0.000	0.000	0.000	0.000
42	A	39	GLU	-1	-0.821	-0.878	16.781	0.084	0.084	0.000	0.000	0.000	0.000
43	A	40	VAL	0	0.000	0.009	19.795	0.032	0.032	0.000	0.000	0.000	0.000
44	A	41	GLY	0	0.031	0.018	21.894	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	42	ALA	0	-0.043	-0.031	23.879	-0.007	-0.007	0.000	0.000	0.000	0.000
46	A	43	MET	0	-0.039	-0.013	24.759	-0.011	-0.011	0.000	0.000	0.000	0.000
47	A	44	GLU	-1	-0.871	-0.933	19.563	0.228	0.228	0.000	0.000	0.000	0.000
48	A	45	THR	0	-0.004	0.002	16.924	-0.031	-0.031	0.000	0.000	0.000	0.000
49	A	46	THR	0	-0.028	-0.023	15.805	0.066	0.066	0.000	0.000	0.000	0.000
50	A	47	LEU	0	-0.007	-0.010	11.759	-0.069	-0.069	0.000	0.000	0.000	0.000
51	A	48	GLU	-1	-0.817	-0.920	11.261	0.355	0.355	0.000	0.000	0.000	0.000
52	A	49	GLY	0	0.012	-0.003	8.477	-0.278	-0.278	0.000	0.000	0.000	0.000
53	A	50	GLU	-1	-0.787	-0.905	2.057	-21.805	-20.978	8.798	-5.023	-4.602	-0.041
54	A	51	LEU	0	-0.002	-0.006	2.867	-1.978	-0.351	0.357	-0.753	-1.232	0.005
55	A	52	ASP	-1	-0.826	-0.920	1.799	-14.487	-35.724	42.095	-11.478	-9.380	-0.024
56	A	53	VAL	0	-0.014	0.006	3.650	-1.279	-0.893	0.024	-0.067	-0.344	0.001
57	A	54	LEU	0	-0.003	-0.014	5.681	0.001	0.001	0.000	0.000	0.000	0.000
58	A	55	LEU	0	0.008	-0.003	6.166	-0.290	-0.290	0.000	0.000	0.000	0.000
59	A	56	ASP	-1	-0.901	-0.937	7.638	-1.126	-1.126	0.000	0.000	0.000	0.000
60	A	57	VAL	0	-0.005	0.000	9.472	0.036	0.036	0.000	0.000	0.000	0.000
61	A	58	VAL	0	0.010	0.007	11.406	0.017	0.017	0.000	0.000	0.000	0.000
62	A	59	LYS	1	0.900	0.949	10.275	0.485	0.485	0.000	0.000	0.000	0.000
63	A	60	ARG	1	0.919	0.946	11.477	0.711	0.711	0.000	0.000	0.000	0.000
64	A	61	ALA	0	0.028	0.036	15.395	0.015	0.015	0.000	0.000	0.000	0.000
65	A	62	GLN	0	0.042	0.014	16.919	0.048	0.048	0.000	0.000	0.000	0.000
66	A	63	GLN	0	-0.069	-0.033	18.113	0.014	0.014	0.000	0.000	0.000	0.000
67	A	64	ALA	0	0.040	0.019	19.464	0.006	0.006	0.000	0.000	0.000	0.000
68	A	65	CYS	0	-0.059	-0.022	21.411	0.020	0.020	0.000	0.000	0.000	0.000
69	A	66	VAL	0	0.018	0.007	23.121	0.007	0.007	0.000	0.000	0.000	0.000
70	A	67	ASP	-1	-0.890	-0.936	22.496	-0.194	-0.194	0.000	0.000	0.000	0.000
71	A	68	ALA	0	-0.077	-0.033	25.449	0.002	0.002	0.000	0.000	0.000	0.000
72	A	69	GLY	0	-0.080	-0.055	27.420	0.010	0.010	0.000	0.000	0.000	0.000
73	A	70	ALA	0	-0.043	-0.013	26.152	0.010	0.010	0.000	0.000	0.000	0.000
74	A	71	GLU	-1	-0.868	-0.952	27.726	-0.036	-0.036	0.000	0.000	0.000	0.000
75	A	72	GLU	-1	-0.957	-0.975	25.997	0.042	0.042	0.000	0.000	0.000	0.000
76	A	73	VAL	0	-0.003	-0.016	21.634	-0.005	-0.005	0.000	0.000	0.000	0.000
77	A	74	ILE	0	-0.025	0.007	23.097	0.013	0.013	0.000	0.000	0.000	0.000
78	A	75	THR	0	0.010	-0.026	16.928	-0.012	-0.012	0.000	0.000	0.000	0.000
79	A	76	SER	0	-0.023	0.004	19.049	0.033	0.033	0.000	0.000	0.000	0.000
80	A	77	ILE	0	0.033	0.008	12.351	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	78	LYS	1	0.906	0.959	15.239	-0.411	-0.411	0.000	0.000	0.000	0.000
82	A	79	ILE	0	0.035	0.016	8.987	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	80	HIS	0	0.007	0.015	12.086	-0.113	-0.113	0.000	0.000	0.000	0.000
84	A	81	TYR	0	0.045	0.009	5.183	0.154	0.154	0.000	0.000	0.000	0.000
85	A	82	ARG	1	0.822	0.885	9.480	-0.715	-0.715	0.000	0.000	0.000	0.000
86	A	83	PRO	0	0.032	0.020	6.822	-0.125	-0.125	0.000	0.000	0.000	0.000
87	A	84	SER	0	-0.017	0.003	8.303	-0.086	-0.086	0.000	0.000	0.000	0.000
88	A	85	THR	0	0.014	-0.016	11.429	-0.063	-0.063	0.000	0.000	0.000	0.000
89	A	86	GLY	0	0.033	0.044	9.699	-0.095	-0.095	0.000	0.000	0.000	0.000
90	A	87	VAL	0	-0.079	-0.044	10.543	-0.096	-0.096	0.000	0.000	0.000	0.000
91	A	88	THR	0	0.002	0.016	11.812	0.039	0.039	0.000	0.000	0.000	0.000
92	A	89	ILE	0	0.056	-0.001	14.362	0.007	0.007	0.000	0.000	0.000	0.000
93	A	90	ASP	-1	-0.792	-0.850	17.054	0.099	0.099	0.000	0.000	0.000	0.000
94	A	91	GLU	-1	-0.840	-0.912	15.881	0.413	0.413	0.000	0.000	0.000	0.000
95	A	92	LYS	1	0.815	0.897	16.494	-0.466	-0.466	0.000	0.000	0.000	0.000
96	A	93	VAL	0	-0.007	-0.008	20.420	-0.008	-0.008	0.000	0.000	0.000	0.000
97	A	94	TRP	0	0.032	0.026	22.486	-0.024	-0.024	0.000	0.000	0.000	0.000
98	A	95	LYS	1	0.858	0.937	24.496	-0.212	-0.212	0.000	0.000	0.000	0.000
99	A	96	TYR	0	-0.080	-0.046	25.122	0.002	0.002	0.000	0.000	0.000	0.000
100	A	97	ARG	1	0.771	0.875	23.414	-0.114	-0.114	0.000	0.000	0.000	0.000
101	A	98	ASP	-1	-0.857	-0.927	28.634	0.064	0.064	0.000	0.000	0.000	0.000
102	A	99	GLU	-1	-0.928	-0.966	26.588	0.061	0.061	0.000	0.000	0.000	0.000
103	A	100	TYR	0	-0.107	-0.089	21.503	-0.004	-0.004	0.000	0.000	0.000	0.000
104	A	101	ALA	0	-0.011	-0.004	28.117	0.005	0.005	0.000	0.000	0.000	0.000

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