FMO DATABASE

FMODB ID: LNJK9

Calculation Name: 1Z9M-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1Z9M

Chain ID: A

ChEMBL ID:

UniProt ID: Q8N126

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	103
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-758405.90631
FMO2-HF: Nuclear repulsion	718045.276822
FMO2-HF: Total energy	-40360.629488
FMO2-MP2: Total energy	-40478.131921

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:38:GLN)

Summations of interaction energy for fragment #1(A:38:GLN)

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.
0.288	2.66	-0.035	-1.146	-1.191	-0.004

Interaction energy analysis for fragmet #1(A:38:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.059 / q_NPA : -0.058

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	40	ASP	-1	-0.872	-0.926	3.801	1.429	3.801	-0.035	-1.146	-1.191	-0.004
4	A	41	SER	0	0.042	-0.011	6.793	0.452	0.452	0.000	0.000	0.000	0.000
5	A	42	GLN	0	-0.125	-0.062	4.874	0.112	0.112	0.000	0.000	0.000	0.000
6	A	43	PRO	0	-0.025	-0.022	7.001	0.228	0.228	0.000	0.000	0.000	0.000
7	A	44	TRP	0	-0.037	-0.010	8.202	0.223	0.223	0.000	0.000	0.000	0.000
8	A	45	THR	0	0.034	-0.001	10.147	-0.049	-0.049	0.000	0.000	0.000	0.000
9	A	46	SER	0	-0.040	-0.006	13.000	0.052	0.052	0.000	0.000	0.000	0.000
10	A	47	ASP	-1	-0.849	-0.915	15.466	0.224	0.224	0.000	0.000	0.000	0.000
11	A	48	GLU	-1	-0.944	-0.970	18.486	0.371	0.371	0.000	0.000	0.000	0.000
12	A	49	THR	0	-0.024	-0.011	21.916	-0.036	-0.036	0.000	0.000	0.000	0.000
13	A	50	VAL	0	-0.018	-0.009	25.016	0.012	0.012	0.000	0.000	0.000	0.000
14	A	51	VAL	0	-0.007	0.014	28.215	-0.014	-0.014	0.000	0.000	0.000	0.000
15	A	52	ALA	0	0.037	0.008	31.954	0.005	0.005	0.000	0.000	0.000	0.000
16	A	53	GLY	0	-0.032	-0.014	33.783	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	54	GLY	0	-0.034	-0.016	32.149	0.003	0.003	0.000	0.000	0.000	0.000
18	A	55	THR	0	-0.044	-0.039	28.443	-0.011	-0.011	0.000	0.000	0.000	0.000
19	A	56	VAL	0	0.023	0.036	23.883	0.010	0.010	0.000	0.000	0.000	0.000
20	A	57	VAL	0	-0.010	-0.028	22.406	-0.011	-0.011	0.000	0.000	0.000	0.000
21	A	58	LEU	0	0.034	0.035	19.832	0.015	0.015	0.000	0.000	0.000	0.000
22	A	59	LYS	1	0.958	0.977	17.084	-0.630	-0.630	0.000	0.000	0.000	0.000
23	A	60	CYS	0	-0.072	-0.017	14.158	0.018	0.018	0.000	0.000	0.000	0.000
24	A	61	GLN	0	0.008	-0.006	12.407	-0.004	-0.004	0.000	0.000	0.000	0.000
25	A	62	VAL	0	0.047	0.020	9.792	0.036	0.036	0.000	0.000	0.000	0.000
26	A	63	LYS	1	0.883	0.960	7.479	-3.054	-3.054	0.000	0.000	0.000	0.000
27	A	64	ASP	-1	-0.878	-0.944	10.152	0.171	0.171	0.000	0.000	0.000	0.000
28	A	65	HIS	0	0.007	0.017	11.638	-0.162	-0.162	0.000	0.000	0.000	0.000
29	A	66	GLU	-1	-0.909	-0.958	12.882	-0.375	-0.375	0.000	0.000	0.000	0.000
30	A	67	ASP	-1	-0.955	-0.982	15.673	0.129	0.129	0.000	0.000	0.000	0.000
31	A	68	SER	0	-0.092	-0.040	16.044	-0.045	-0.045	0.000	0.000	0.000	0.000
32	A	69	SER	0	-0.020	-0.022	17.565	0.038	0.038	0.000	0.000	0.000	0.000
33	A	70	LEU	0	0.051	0.033	14.401	-0.017	-0.017	0.000	0.000	0.000	0.000
34	A	71	GLN	0	-0.004	-0.032	17.850	-0.028	-0.028	0.000	0.000	0.000	0.000
35	A	72	TRP	0	0.003	0.018	17.074	-0.009	-0.009	0.000	0.000	0.000	0.000
36	A	73	SER	0	-0.041	-0.027	20.348	-0.029	-0.029	0.000	0.000	0.000	0.000
37	A	74	ASN	0	0.042	0.012	21.904	0.009	0.009	0.000	0.000	0.000	0.000
38	A	75	PRO	0	0.058	0.036	23.522	-0.007	-0.007	0.000	0.000	0.000	0.000
39	A	76	ALA	0	-0.049	-0.006	24.690	-0.015	-0.015	0.000	0.000	0.000	0.000
40	A	77	GLN	0	-0.012	-0.020	20.759	0.000	0.000	0.000	0.000	0.000	0.000
41	A	78	GLN	0	-0.033	-0.003	24.529	0.001	0.001	0.000	0.000	0.000	0.000
42	A	79	THR	0	0.021	0.002	24.290	0.012	0.012	0.000	0.000	0.000	0.000
43	A	80	LEU	0	-0.010	-0.009	23.842	-0.007	-0.007	0.000	0.000	0.000	0.000
44	A	81	TYR	0	-0.020	-0.021	23.929	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	82	PHE	0	0.000	0.024	22.412	0.010	0.010	0.000	0.000	0.000	0.000
46	A	83	GLY	0	0.056	0.027	22.078	-0.010	-0.010	0.000	0.000	0.000	0.000
47	A	84	GLU	-1	-0.918	-0.976	23.190	0.177	0.177	0.000	0.000	0.000	0.000
48	A	85	LYS	1	0.902	0.952	26.092	-0.096	-0.096	0.000	0.000	0.000	0.000
49	A	86	ARG	1	0.886	0.939	27.322	-0.126	-0.126	0.000	0.000	0.000	0.000
50	A	87	ALA	0	-0.021	-0.001	27.824	-0.011	-0.011	0.000	0.000	0.000	0.000
51	A	88	LEU	0	-0.025	-0.007	29.127	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	89	ARG	1	0.892	0.937	30.987	-0.076	-0.076	0.000	0.000	0.000	0.000
53	A	90	ASP	-1	-0.765	-0.882	31.826	0.092	0.092	0.000	0.000	0.000	0.000
54	A	91	ASN	0	-0.056	-0.043	33.108	0.012	0.012	0.000	0.000	0.000	0.000
55	A	92	ARG	1	0.730	0.860	31.736	-0.098	-0.098	0.000	0.000	0.000	0.000
56	A	93	ILE	0	0.021	0.017	27.565	0.011	0.011	0.000	0.000	0.000	0.000
57	A	94	GLN	0	-0.028	-0.008	29.232	-0.009	-0.009	0.000	0.000	0.000	0.000
58	A	95	LEU	0	0.012	0.014	24.480	0.008	0.008	0.000	0.000	0.000	0.000
59	A	96	VAL	0	-0.057	-0.035	24.364	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	97	THR	0	-0.010	-0.029	22.147	-0.007	-0.007	0.000	0.000	0.000	0.000
61	A	98	SER	0	0.015	0.007	22.071	0.008	0.008	0.000	0.000	0.000	0.000
62	A	99	THR	0	-0.040	-0.015	19.987	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	100	PRO	0	0.023	-0.004	19.064	0.001	0.001	0.000	0.000	0.000	0.000
64	A	101	HIS	0	0.004	0.017	14.272	-0.037	-0.037	0.000	0.000	0.000	0.000
65	A	102	GLU	-1	-0.894	-0.952	15.186	0.595	0.595	0.000	0.000	0.000	0.000
66	A	103	LEU	0	-0.002	0.024	17.584	-0.055	-0.055	0.000	0.000	0.000	0.000
67	A	104	SER	0	0.006	0.003	18.943	0.028	0.028	0.000	0.000	0.000	0.000
68	A	105	ILE	0	-0.016	0.003	21.345	-0.028	-0.028	0.000	0.000	0.000	0.000
69	A	106	SER	0	-0.006	0.004	24.058	0.011	0.011	0.000	0.000	0.000	0.000
70	A	107	ILE	0	0.037	0.021	25.725	-0.015	-0.015	0.000	0.000	0.000	0.000
71	A	108	SER	0	-0.034	-0.020	28.890	0.000	0.000	0.000	0.000	0.000	0.000
72	A	109	ASN	0	-0.028	-0.026	32.103	-0.013	-0.013	0.000	0.000	0.000	0.000
73	A	110	VAL	0	0.006	0.017	28.889	-0.009	-0.009	0.000	0.000	0.000	0.000
74	A	111	ALA	0	0.027	0.000	31.956	-0.006	-0.006	0.000	0.000	0.000	0.000
75	A	112	LEU	0	0.076	0.021	31.440	0.004	0.004	0.000	0.000	0.000	0.000
76	A	113	ALA	0	-0.053	-0.014	31.176	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	114	ASP	-1	-0.747	-0.838	28.527	0.101	0.101	0.000	0.000	0.000	0.000
78	A	115	GLU	-1	-0.836	-0.875	26.874	0.089	0.089	0.000	0.000	0.000	0.000
79	A	116	GLY	0	-0.002	-0.006	24.476	-0.014	-0.014	0.000	0.000	0.000	0.000
80	A	117	GLU	-1	-0.920	-0.959	18.178	0.105	0.105	0.000	0.000	0.000	0.000
81	A	118	TYR	0	-0.065	-0.058	20.200	-0.016	-0.016	0.000	0.000	0.000	0.000
82	A	119	THR	0	0.003	-0.013	15.849	0.025	0.025	0.000	0.000	0.000	0.000
83	A	121	SER	0	-0.030	-0.034	14.226	0.008	0.008	0.000	0.000	0.000	0.000
84	A	122	ILE	0	0.056	0.042	11.391	0.027	0.027	0.000	0.000	0.000	0.000
85	A	123	PHE	0	-0.082	-0.053	14.516	-0.046	-0.046	0.000	0.000	0.000	0.000
86	A	124	THR	0	0.057	0.051	12.883	0.009	0.009	0.000	0.000	0.000	0.000
87	A	125	MET	0	-0.064	-0.008	14.928	-0.004	-0.004	0.000	0.000	0.000	0.000
88	A	126	PRO	0	-0.023	-0.030	11.392	-0.056	-0.056	0.000	0.000	0.000	0.000
89	A	127	VAL	0	0.037	0.011	12.979	0.004	0.004	0.000	0.000	0.000	0.000
90	A	128	ARG	1	0.931	0.976	7.282	0.694	0.694	0.000	0.000	0.000	0.000
91	A	129	THR	0	-0.023	-0.022	11.124	0.014	0.014	0.000	0.000	0.000	0.000
92	A	130	ALA	0	0.017	0.024	10.490	0.112	0.112	0.000	0.000	0.000	0.000
93	A	131	LYS	1	0.900	0.956	12.174	-0.141	-0.141	0.000	0.000	0.000	0.000
94	A	132	SER	0	0.001	0.006	14.798	0.029	0.029	0.000	0.000	0.000	0.000
95	A	133	LEU	0	0.002	-0.005	17.336	-0.036	-0.036	0.000	0.000	0.000	0.000
96	A	134	VAL	0	-0.019	-0.012	20.080	0.019	0.019	0.000	0.000	0.000	0.000
97	A	135	THR	0	-0.016	-0.007	23.201	-0.027	-0.027	0.000	0.000	0.000	0.000
98	A	136	VAL	0	-0.058	-0.053	25.857	0.014	0.014	0.000	0.000	0.000	0.000
99	A	137	LEU	0	0.006	-0.004	28.800	-0.012	-0.012	0.000	0.000	0.000	0.000
100	A	138	GLY	0	-0.005	-0.001	31.712	0.002	0.002	0.000	0.000	0.000	0.000
101	A	139	ILE	0	-0.018	-0.023	35.394	0.004	0.004	0.000	0.000	0.000	0.000
102	A	140	PRO	0	-0.029	-0.007	36.743	-0.006	-0.006	0.000	0.000	0.000	0.000
103	A	141	GLN	0	0.017	0.014	39.645	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:38:GLN)