FMO DATABASE

FMODB ID: 76Z2K

Calculation Name: 1M8N-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1M8N

Chain ID: A

ChEMBL ID:

UniProt ID: Q9GSA6

Base Structure: X-ray

Registration Date: 2023-09-23

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	115
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-898215.854316
FMO2-HF: Nuclear repulsion	851834.994557
FMO2-HF: Total energy	-46380.859759
FMO2-MP2: Total energy	-46506.974021

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:GLY)

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

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.
-1.356	0.358	-0.004	-0.832	-0.877	0.001

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.069 / q_NPA : 0.021

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	4	CYS	0	0.000	-0.001	3.633	-0.015	1.630	-0.003	-0.828	-0.813	0.001
4	A	5	VAL	0	0.046	0.023	5.364	-0.454	-0.385	-0.001	-0.004	-0.064	0.000
5	A	6	ASN	0	0.007	-0.007	7.698	0.309	0.309	0.000	0.000	0.000	0.000
6	A	7	THR	0	-0.012	-0.005	9.424	-0.040	-0.040	0.000	0.000	0.000	0.000
7	A	8	ASN	0	-0.012	-0.021	13.048	0.052	0.052	0.000	0.000	0.000	0.000
8	A	9	SER	0	0.001	0.002	11.830	0.060	0.060	0.000	0.000	0.000	0.000
9	A	10	GLN	0	0.012	0.021	12.228	-0.031	-0.031	0.000	0.000	0.000	0.000
10	A	11	ILE	0	-0.022	-0.024	8.436	0.012	0.012	0.000	0.000	0.000	0.000
11	A	12	THR	0	0.017	0.008	11.249	0.006	0.006	0.000	0.000	0.000	0.000
12	A	13	ALA	0	0.021	-0.001	11.005	0.047	0.047	0.000	0.000	0.000	0.000
13	A	14	ASN	0	-0.068	-0.042	11.893	0.061	0.061	0.000	0.000	0.000	0.000
14	A	15	SER	0	0.001	0.010	11.706	-0.008	-0.008	0.000	0.000	0.000	0.000
15	A	16	GLN	0	-0.030	-0.021	8.048	0.107	0.107	0.000	0.000	0.000	0.000
16	A	18	VAL	0	-0.003	-0.004	5.405	0.442	0.442	0.000	0.000	0.000	0.000
17	A	19	LYS	1	0.920	0.956	6.614	-1.260	-1.260	0.000	0.000	0.000	0.000
18	A	20	SER	0	0.014	0.013	7.893	-0.119	-0.119	0.000	0.000	0.000	0.000
19	A	21	THR	0	0.008	0.007	8.643	-0.263	-0.263	0.000	0.000	0.000	0.000
20	A	22	ALA	0	0.014	0.006	10.761	0.106	0.106	0.000	0.000	0.000	0.000
21	A	23	THR	0	0.015	0.023	12.351	-0.076	-0.076	0.000	0.000	0.000	0.000
22	A	24	ASN	0	-0.019	-0.014	15.257	0.043	0.043	0.000	0.000	0.000	0.000
23	A	25	CYS	0	-0.034	0.027	14.128	0.042	0.042	0.000	0.000	0.000	0.000
24	A	26	TYR	0	0.031	0.015	15.730	-0.022	-0.022	0.000	0.000	0.000	0.000
25	A	27	ILE	0	-0.024	-0.016	11.651	0.014	0.014	0.000	0.000	0.000	0.000
26	A	28	ASP	-1	-0.770	-0.877	14.325	0.117	0.117	0.000	0.000	0.000	0.000
27	A	29	ASN	0	-0.012	0.016	16.253	0.007	0.007	0.000	0.000	0.000	0.000
28	A	30	SER	0	0.015	-0.002	14.757	-0.006	-0.006	0.000	0.000	0.000	0.000
29	A	31	GLN	0	-0.041	-0.025	12.249	0.045	0.045	0.000	0.000	0.000	0.000
30	A	32	LEU	0	-0.007	0.003	10.866	-0.070	-0.070	0.000	0.000	0.000	0.000
31	A	33	VAL	0	0.017	-0.003	9.969	0.094	0.094	0.000	0.000	0.000	0.000
32	A	34	ASP	-1	-0.828	-0.888	11.696	0.362	0.362	0.000	0.000	0.000	0.000
33	A	35	THR	0	0.022	-0.002	12.007	-0.044	-0.044	0.000	0.000	0.000	0.000
34	A	36	SER	0	0.006	0.006	12.812	-0.061	-0.061	0.000	0.000	0.000	0.000
35	A	37	ILE	0	-0.012	-0.017	13.028	-0.045	-0.045	0.000	0.000	0.000	0.000
36	A	39	THR	0	0.010	-0.006	15.661	-0.051	-0.051	0.000	0.000	0.000	0.000
37	A	40	ARG	1	0.809	0.872	18.343	0.081	0.081	0.000	0.000	0.000	0.000
38	A	41	SER	0	0.011	-0.012	18.641	0.014	0.014	0.000	0.000	0.000	0.000
39	A	42	GLN	0	-0.006	0.006	18.412	-0.010	-0.010	0.000	0.000	0.000	0.000
40	A	43	TYR	0	-0.037	-0.059	14.689	0.009	0.009	0.000	0.000	0.000	0.000
41	A	44	SER	0	0.009	-0.012	18.234	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	45	ASP	-1	-0.838	-0.914	19.285	0.147	0.147	0.000	0.000	0.000	0.000
43	A	46	ALA	0	-0.011	0.007	18.503	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	47	ASN	0	-0.034	-0.017	16.652	0.073	0.073	0.000	0.000	0.000	0.000
45	A	48	VAL	0	0.020	0.010	15.385	-0.027	-0.027	0.000	0.000	0.000	0.000
46	A	49	LYS	1	0.875	0.931	14.847	-0.412	-0.412	0.000	0.000	0.000	0.000
47	A	50	LYS	1	0.839	0.926	15.794	-0.317	-0.317	0.000	0.000	0.000	0.000
48	A	51	SER	0	-0.016	-0.014	16.927	-0.030	-0.030	0.000	0.000	0.000	0.000
49	A	52	VAL	0	0.023	0.012	17.213	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	53	THR	0	-0.018	-0.004	18.724	0.010	0.010	0.000	0.000	0.000	0.000
51	A	54	THR	0	-0.001	0.005	19.592	-0.022	-0.022	0.000	0.000	0.000	0.000
52	A	55	ASP	-1	-0.780	-0.852	22.248	-0.030	-0.030	0.000	0.000	0.000	0.000
53	A	56	CYS	0	-0.087	-0.013	22.211	0.005	0.005	0.000	0.000	0.000	0.000
54	A	57	ASN	0	-0.036	-0.019	22.355	0.004	0.004	0.000	0.000	0.000	0.000
55	A	58	ILE	0	-0.008	0.003	20.166	0.002	0.002	0.000	0.000	0.000	0.000
56	A	59	ASP	-1	-0.732	-0.845	21.556	0.091	0.091	0.000	0.000	0.000	0.000
57	A	60	LYS	1	0.896	0.950	23.017	-0.092	-0.092	0.000	0.000	0.000	0.000
58	A	61	SER	0	-0.027	-0.011	22.744	-0.006	-0.006	0.000	0.000	0.000	0.000
59	A	62	GLN	0	-0.065	-0.042	21.069	0.012	0.012	0.000	0.000	0.000	0.000
60	A	63	VAL	0	0.011	0.005	19.716	-0.016	-0.016	0.000	0.000	0.000	0.000
61	A	64	TYR	0	0.011	-0.003	19.220	0.035	0.035	0.000	0.000	0.000	0.000
62	A	65	LEU	0	-0.018	0.003	20.701	-0.018	-0.018	0.000	0.000	0.000	0.000
63	A	66	THR	0	0.003	-0.011	21.676	-0.017	-0.017	0.000	0.000	0.000	0.000
64	A	67	THR	0	0.016	0.014	21.807	0.003	0.003	0.000	0.000	0.000	0.000
65	A	69	THR	0	0.067	0.025	23.740	-0.011	-0.011	0.000	0.000	0.000	0.000
66	A	70	GLY	0	0.028	0.026	26.102	0.004	0.004	0.000	0.000	0.000	0.000
67	A	71	SER	0	-0.028	-0.060	26.576	0.002	0.002	0.000	0.000	0.000	0.000
68	A	72	GLN	0	0.006	-0.001	26.298	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	73	TYR	0	-0.003	-0.029	23.728	0.003	0.003	0.000	0.000	0.000	0.000
70	A	74	ASN	0	-0.017	-0.014	26.019	0.003	0.003	0.000	0.000	0.000	0.000
71	A	75	GLY	0	0.047	0.023	26.990	-0.005	-0.005	0.000	0.000	0.000	0.000
72	A	76	ILE	0	-0.020	-0.005	26.836	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	77	TYR	0	0.022	0.019	24.131	0.009	0.009	0.000	0.000	0.000	0.000
74	A	78	ILE	0	0.009	-0.001	24.776	-0.011	-0.011	0.000	0.000	0.000	0.000
75	A	79	ARG	1	0.917	0.955	24.744	-0.118	-0.118	0.000	0.000	0.000	0.000
76	A	80	SER	0	-0.014	0.003	25.334	-0.007	-0.007	0.000	0.000	0.000	0.000
77	A	81	SER	0	0.042	0.017	26.354	-0.011	-0.011	0.000	0.000	0.000	0.000
78	A	82	THR	0	-0.027	-0.020	26.520	-0.002	-0.002	0.000	0.000	0.000	0.000
79	A	83	THR	0	0.001	0.025	27.469	0.000	0.000	0.000	0.000	0.000	0.000
80	A	84	THR	0	0.001	-0.005	28.149	-0.005	-0.005	0.000	0.000	0.000	0.000
81	A	85	GLY	0	0.037	0.023	30.143	0.000	0.000	0.000	0.000	0.000	0.000
82	A	86	THR	0	-0.053	-0.027	30.219	0.000	0.000	0.000	0.000	0.000	0.000
83	A	87	SER	0	0.030	0.008	30.398	0.004	0.004	0.000	0.000	0.000	0.000
84	A	88	ILE	0	-0.028	-0.008	29.948	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	89	SER	0	0.011	0.005	30.272	0.003	0.003	0.000	0.000	0.000	0.000
86	A	90	GLY	0	0.066	0.026	31.994	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	91	PRO	0	0.009	-0.005	31.408	0.004	0.004	0.000	0.000	0.000	0.000
88	A	92	GLY	0	0.037	0.031	31.926	0.005	0.005	0.000	0.000	0.000	0.000
89	A	93	CYS	0	-0.163	-0.033	31.296	0.001	0.001	0.000	0.000	0.000	0.000
90	A	94	SER	0	0.019	0.000	30.364	0.008	0.008	0.000	0.000	0.000	0.000
91	A	95	ILE	0	0.031	-0.003	29.799	-0.008	-0.008	0.000	0.000	0.000	0.000
92	A	96	SER	0	-0.033	-0.029	29.425	0.012	0.012	0.000	0.000	0.000	0.000
93	A	97	THR	0	-0.035	-0.017	29.897	-0.005	-0.005	0.000	0.000	0.000	0.000
94	A	98	CYS	0	-0.060	0.014	31.067	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	99	THR	0	0.033	0.015	31.054	0.003	0.003	0.000	0.000	0.000	0.000
96	A	100	ILE	0	-0.023	-0.014	31.775	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	101	THR	0	0.029	0.005	32.447	0.000	0.000	0.000	0.000	0.000	0.000
98	A	102	ARG	1	0.878	0.931	34.343	-0.007	-0.007	0.000	0.000	0.000	0.000
99	A	103	GLY	0	0.027	0.019	35.421	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	104	VAL	0	-0.004	0.009	37.070	0.002	0.002	0.000	0.000	0.000	0.000
101	A	105	ALA	0	0.013	-0.001	36.152	0.000	0.000	0.000	0.000	0.000	0.000
102	A	106	THR	0	-0.002	-0.005	36.229	-0.003	-0.003	0.000	0.000	0.000	0.000
103	A	107	PRO	0	-0.003	-0.005	38.314	0.003	0.003	0.000	0.000	0.000	0.000
104	A	108	ALA	0	0.024	0.001	37.526	-0.002	-0.002	0.000	0.000	0.000	0.000
105	A	109	ALA	0	0.009	0.004	39.234	0.002	0.002	0.000	0.000	0.000	0.000
106	A	110	ALA	0	-0.011	-0.002	34.910	0.002	0.002	0.000	0.000	0.000	0.000
107	A	112	LYS	1	0.959	0.971	34.580	-0.067	-0.067	0.000	0.000	0.000	0.000
108	A	113	ILE	0	0.053	0.006	34.056	0.004	0.004	0.000	0.000	0.000	0.000
109	A	114	SER	0	-0.026	-0.005	35.014	-0.003	-0.003	0.000	0.000	0.000	0.000
110	A	115	GLY	0	0.059	0.022	34.988	0.004	0.004	0.000	0.000	0.000	0.000
111	A	117	SER	0	0.015	0.018	35.196	-0.004	-0.004	0.000	0.000	0.000	0.000
112	A	118	LEU	0	-0.016	-0.013	34.180	0.003	0.003	0.000	0.000	0.000	0.000
113	A	119	SER	0	0.001	-0.003	35.285	-0.003	-0.003	0.000	0.000	0.000	0.000
114	A	120	ALA	0	0.016	0.004	35.196	0.001	0.001	0.000	0.000	0.000	0.000
115	A	121	MET	0	-0.021	0.028	29.049	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:2:GLY)