FMO DATABASE

FMODB ID: MN3QZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-757904.946067
FMO2-HF: Nuclear repulsion	717543.353737
FMO2-HF: Total energy	-40361.592331
FMO2-MP2: Total energy	-40479.000371

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.
1.012	3.033	-0.017	-0.988	-1.015	0.003

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 : -0.020 / q_NPA : -0.019

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	-0.799	-0.874	3.877	1.535	3.556	-0.017	-0.988	-1.015	0.003
4	A	41	SER	0	0.015	-0.020	6.560	0.493	0.493	0.000	0.000	0.000	0.000
5	A	42	GLN	0	-0.078	-0.047	4.842	-0.241	-0.241	0.000	0.000	0.000	0.000
6	A	43	PRO	0	-0.033	-0.021	6.990	0.446	0.446	0.000	0.000	0.000	0.000
7	A	44	TRP	0	-0.040	-0.008	8.133	0.083	0.083	0.000	0.000	0.000	0.000
8	A	45	THR	0	0.015	-0.012	10.356	-0.043	-0.043	0.000	0.000	0.000	0.000
9	A	46	SER	0	-0.053	-0.024	13.276	0.071	0.071	0.000	0.000	0.000	0.000
10	A	47	ASP	-1	-0.826	-0.891	15.858	0.145	0.145	0.000	0.000	0.000	0.000
11	A	48	GLU	-1	-0.907	-0.931	18.351	0.328	0.328	0.000	0.000	0.000	0.000
12	A	49	THR	0	-0.019	-0.016	21.836	-0.033	-0.033	0.000	0.000	0.000	0.000
13	A	50	VAL	0	-0.040	-0.010	25.103	0.014	0.014	0.000	0.000	0.000	0.000
14	A	51	VAL	0	-0.019	-0.001	28.570	-0.009	-0.009	0.000	0.000	0.000	0.000
15	A	52	ALA	0	0.031	0.004	32.315	0.000	0.000	0.000	0.000	0.000	0.000
16	A	53	GLY	0	-0.028	-0.009	34.371	0.001	0.001	0.000	0.000	0.000	0.000
17	A	54	GLY	0	-0.034	-0.011	32.579	0.002	0.002	0.000	0.000	0.000	0.000
18	A	55	THR	0	-0.032	-0.042	29.276	-0.014	-0.014	0.000	0.000	0.000	0.000
19	A	56	VAL	0	0.011	0.024	24.200	0.013	0.013	0.000	0.000	0.000	0.000
20	A	57	VAL	0	-0.008	-0.028	22.219	-0.016	-0.016	0.000	0.000	0.000	0.000
21	A	58	LEU	0	0.020	0.029	20.255	0.018	0.018	0.000	0.000	0.000	0.000
22	A	59	LYS	1	0.861	0.909	17.172	-0.460	-0.460	0.000	0.000	0.000	0.000
23	A	60	CYS	0	-0.051	0.009	14.400	0.016	0.016	0.000	0.000	0.000	0.000
24	A	61	GLN	0	-0.020	-0.035	13.068	0.077	0.077	0.000	0.000	0.000	0.000
25	A	62	VAL	0	0.033	0.012	9.807	-0.041	-0.041	0.000	0.000	0.000	0.000
26	A	63	LYS	1	0.798	0.895	7.056	-2.181	-2.181	0.000	0.000	0.000	0.000
27	A	64	ASP	-1	-0.871	-0.945	10.298	-0.029	-0.029	0.000	0.000	0.000	0.000
28	A	65	HIS	0	0.002	0.012	11.382	-0.210	-0.210	0.000	0.000	0.000	0.000
29	A	66	GLU	-1	-0.852	-0.921	12.723	-0.889	-0.889	0.000	0.000	0.000	0.000
30	A	67	ASP	-1	-0.921	-0.957	15.788	-0.072	-0.072	0.000	0.000	0.000	0.000
31	A	68	SER	0	-0.065	-0.023	16.306	-0.017	-0.017	0.000	0.000	0.000	0.000
32	A	69	SER	0	-0.054	-0.039	17.859	0.030	0.030	0.000	0.000	0.000	0.000
33	A	70	LEU	0	0.067	0.035	14.550	-0.048	-0.048	0.000	0.000	0.000	0.000
34	A	71	GLN	0	-0.013	-0.007	17.959	0.023	0.023	0.000	0.000	0.000	0.000
35	A	72	TRP	0	0.021	0.019	17.422	-0.036	-0.036	0.000	0.000	0.000	0.000
36	A	73	SER	0	-0.034	-0.032	20.255	-0.014	-0.014	0.000	0.000	0.000	0.000
37	A	74	ASN	0	0.051	0.013	21.742	0.002	0.002	0.000	0.000	0.000	0.000
38	A	75	PRO	0	0.058	0.038	23.525	-0.022	-0.022	0.000	0.000	0.000	0.000
39	A	76	ALA	0	-0.050	-0.011	24.657	-0.010	-0.010	0.000	0.000	0.000	0.000
40	A	77	GLN	0	-0.017	-0.017	19.665	0.002	0.002	0.000	0.000	0.000	0.000
41	A	78	GLN	0	0.002	0.019	24.039	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	79	THR	0	-0.006	-0.018	24.238	0.009	0.009	0.000	0.000	0.000	0.000
43	A	80	LEU	0	-0.040	-0.021	24.019	0.010	0.010	0.000	0.000	0.000	0.000
44	A	81	TYR	0	-0.006	-0.012	24.242	0.011	0.011	0.000	0.000	0.000	0.000
45	A	82	PHE	0	0.003	0.005	22.827	-0.011	-0.011	0.000	0.000	0.000	0.000
46	A	83	GLY	0	0.048	0.027	22.069	0.003	0.003	0.000	0.000	0.000	0.000
47	A	84	GLU	-1	-0.926	-0.977	23.283	0.050	0.050	0.000	0.000	0.000	0.000
48	A	85	LYS	1	0.912	0.954	26.463	0.040	0.040	0.000	0.000	0.000	0.000
49	A	86	ARG	1	0.848	0.922	27.340	-0.041	-0.041	0.000	0.000	0.000	0.000
50	A	87	ALA	0	-0.027	-0.006	28.090	-0.008	-0.008	0.000	0.000	0.000	0.000
51	A	88	LEU	0	0.020	0.012	29.168	0.003	0.003	0.000	0.000	0.000	0.000
52	A	89	ARG	1	0.882	0.925	31.014	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	90	ASP	-1	-0.755	-0.864	32.185	0.030	0.030	0.000	0.000	0.000	0.000
54	A	91	ASN	0	-0.026	-0.025	33.172	0.002	0.002	0.000	0.000	0.000	0.000
55	A	92	ARG	1	0.734	0.837	31.959	-0.036	-0.036	0.000	0.000	0.000	0.000
56	A	93	ILE	0	0.002	0.024	27.731	0.010	0.010	0.000	0.000	0.000	0.000
57	A	94	GLN	0	-0.043	-0.016	28.994	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	95	LEU	0	-0.004	0.005	24.695	0.001	0.001	0.000	0.000	0.000	0.000
59	A	96	VAL	0	-0.030	-0.012	24.395	0.002	0.002	0.000	0.000	0.000	0.000
60	A	97	THR	0	-0.001	-0.017	21.931	0.001	0.001	0.000	0.000	0.000	0.000
61	A	98	SER	0	0.024	0.008	22.273	-0.015	-0.015	0.000	0.000	0.000	0.000
62	A	99	THR	0	-0.045	-0.012	19.965	0.016	0.016	0.000	0.000	0.000	0.000
63	A	100	PRO	0	0.035	0.003	18.793	-0.008	-0.008	0.000	0.000	0.000	0.000
64	A	101	HIS	0	0.006	0.016	14.080	-0.075	-0.075	0.000	0.000	0.000	0.000
65	A	102	GLU	-1	-0.786	-0.841	15.209	0.455	0.455	0.000	0.000	0.000	0.000
66	A	103	LEU	0	-0.044	-0.003	17.572	-0.037	-0.037	0.000	0.000	0.000	0.000
67	A	104	SER	0	-0.004	-0.026	18.972	0.007	0.007	0.000	0.000	0.000	0.000
68	A	105	ILE	0	0.002	0.012	21.352	-0.014	-0.014	0.000	0.000	0.000	0.000
69	A	106	SER	0	0.010	0.004	23.912	0.017	0.017	0.000	0.000	0.000	0.000
70	A	107	ILE	0	0.027	0.016	26.121	-0.018	-0.018	0.000	0.000	0.000	0.000
71	A	108	SER	0	-0.017	-0.017	29.014	0.011	0.011	0.000	0.000	0.000	0.000
72	A	109	ASN	0	-0.035	-0.023	32.292	-0.010	-0.010	0.000	0.000	0.000	0.000
73	A	110	VAL	0	0.022	0.025	29.130	-0.010	-0.010	0.000	0.000	0.000	0.000
74	A	111	ALA	0	0.018	-0.006	32.271	0.002	0.002	0.000	0.000	0.000	0.000
75	A	112	LEU	0	0.049	0.008	31.754	0.000	0.000	0.000	0.000	0.000	0.000
76	A	113	ALA	0	-0.044	-0.018	31.647	-0.005	-0.005	0.000	0.000	0.000	0.000
77	A	114	ASP	-1	-0.767	-0.828	28.648	0.035	0.035	0.000	0.000	0.000	0.000
78	A	115	GLU	-1	-0.827	-0.901	27.013	0.060	0.060	0.000	0.000	0.000	0.000
79	A	116	GLY	0	0.008	-0.003	24.587	-0.017	-0.017	0.000	0.000	0.000	0.000
80	A	117	GLU	-1	-0.871	-0.932	18.104	-0.076	-0.076	0.000	0.000	0.000	0.000
81	A	118	TYR	0	-0.049	-0.037	20.519	-0.025	-0.025	0.000	0.000	0.000	0.000
82	A	119	THR	0	-0.004	-0.018	16.241	0.007	0.007	0.000	0.000	0.000	0.000
83	A	121	SER	0	-0.034	-0.033	14.889	-0.072	-0.072	0.000	0.000	0.000	0.000
84	A	122	ILE	0	0.050	0.025	11.612	0.085	0.085	0.000	0.000	0.000	0.000
85	A	123	PHE	0	-0.067	-0.032	14.608	-0.102	-0.102	0.000	0.000	0.000	0.000
86	A	124	THR	0	0.021	0.011	12.831	0.025	0.025	0.000	0.000	0.000	0.000
87	A	125	MET	0	-0.058	-0.019	15.026	0.029	0.029	0.000	0.000	0.000	0.000
88	A	126	PRO	0	0.009	-0.001	11.093	-0.019	-0.019	0.000	0.000	0.000	0.000
89	A	127	VAL	0	0.030	0.027	12.787	-0.045	-0.045	0.000	0.000	0.000	0.000
90	A	128	ARG	1	0.793	0.880	8.107	1.532	1.532	0.000	0.000	0.000	0.000
91	A	129	THR	0	-0.029	-0.031	10.772	0.194	0.194	0.000	0.000	0.000	0.000
92	A	130	ALA	0	-0.001	0.018	10.761	-0.071	-0.071	0.000	0.000	0.000	0.000
93	A	131	LYS	1	0.813	0.898	12.342	0.148	0.148	0.000	0.000	0.000	0.000
94	A	132	SER	0	-0.007	-0.019	14.816	0.053	0.053	0.000	0.000	0.000	0.000
95	A	133	LEU	0	-0.020	-0.013	17.634	-0.037	-0.037	0.000	0.000	0.000	0.000
96	A	134	VAL	0	-0.009	0.004	20.472	0.029	0.029	0.000	0.000	0.000	0.000
97	A	135	THR	0	-0.017	-0.004	23.442	-0.023	-0.023	0.000	0.000	0.000	0.000
98	A	136	VAL	0	-0.048	-0.043	26.036	0.016	0.016	0.000	0.000	0.000	0.000
99	A	137	LEU	0	0.020	0.014	28.487	-0.010	-0.010	0.000	0.000	0.000	0.000
100	A	138	GLY	0	0.019	0.006	31.954	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	139	ILE	0	-0.006	-0.010	35.612	0.007	0.007	0.000	0.000	0.000	0.000
102	A	140	PRO	0	-0.030	-0.004	36.913	-0.006	-0.006	0.000	0.000	0.000	0.000
103	A	141	GLN	0	0.008	0.002	39.666	-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:38:GLN)