FMO DATABASE

FMODB ID: 17J6Z

Calculation Name: 5M1X-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5M1X

Chain ID: A

ChEMBL ID:

UniProt ID: P22336

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	134
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1235249.656744
FMO2-HF: Nuclear repulsion	1180983.694484
FMO2-HF: Total energy	-54265.96226
FMO2-MP2: Total energy	-54423.28839

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:-1:GLY)

Summations of interaction energy for fragment #1(A:-1: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.
1.118	2.897	-0.002	-0.877	-0.898	0.003

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.058 / q_NPA : 0.026

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	1	MET	0	-0.026	-0.010	3.730	0.085	1.705	-0.001	-0.854	-0.764	0.003
4	A	2	SER	0	-0.019	0.005	4.453	0.459	0.618	-0.001	-0.023	-0.134	0.000
5	A	3	SER	0	0.015	0.001	5.671	0.523	0.523	0.000	0.000	0.000	0.000
6	A	4	VAL	0	0.005	-0.001	9.317	-0.089	-0.089	0.000	0.000	0.000	0.000
7	A	5	GLN	0	-0.018	-0.007	9.550	0.256	0.256	0.000	0.000	0.000	0.000
8	A	6	LEU	0	0.006	0.015	13.385	0.059	0.059	0.000	0.000	0.000	0.000
9	A	7	SER	0	0.009	0.006	17.018	-0.014	-0.014	0.000	0.000	0.000	0.000
10	A	8	ARG	1	0.877	0.936	15.946	0.394	0.394	0.000	0.000	0.000	0.000
11	A	9	GLY	0	0.047	0.034	19.965	0.005	0.005	0.000	0.000	0.000	0.000
12	A	10	ASP	-1	-0.749	-0.823	23.114	-0.259	-0.259	0.000	0.000	0.000	0.000
13	A	11	PHE	0	-0.017	-0.014	24.856	0.017	0.017	0.000	0.000	0.000	0.000
14	A	12	HIS	0	-0.031	-0.020	26.911	0.004	0.004	0.000	0.000	0.000	0.000
15	A	13	SER	0	0.021	0.008	26.304	0.013	0.013	0.000	0.000	0.000	0.000
16	A	14	ILE	0	-0.024	-0.011	27.591	0.013	0.013	0.000	0.000	0.000	0.000
17	A	15	PHE	0	-0.003	-0.011	30.686	0.012	0.012	0.000	0.000	0.000	0.000
18	A	16	THR	0	-0.022	-0.023	31.217	0.011	0.011	0.000	0.000	0.000	0.000
19	A	17	ASN	0	0.010	0.015	30.357	0.013	0.013	0.000	0.000	0.000	0.000
20	A	18	LYS	1	0.869	0.900	33.302	0.113	0.113	0.000	0.000	0.000	0.000
21	A	19	GLN	0	0.005	0.000	30.824	-0.008	-0.008	0.000	0.000	0.000	0.000
22	A	20	ARG	1	0.730	0.827	25.556	0.255	0.255	0.000	0.000	0.000	0.000
23	A	21	TYR	0	-0.051	-0.036	31.298	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	22	ASP	-1	-0.825	-0.901	34.126	-0.130	-0.130	0.000	0.000	0.000	0.000
25	A	23	ASN	0	0.020	0.027	30.453	-0.005	-0.005	0.000	0.000	0.000	0.000
26	A	24	PRO	0	0.031	0.033	29.415	-0.014	-0.014	0.000	0.000	0.000	0.000
27	A	25	THR	0	-0.063	-0.031	28.069	-0.020	-0.020	0.000	0.000	0.000	0.000
28	A	26	GLY	0	0.031	0.008	24.573	-0.005	-0.005	0.000	0.000	0.000	0.000
29	A	27	GLY	0	-0.005	0.012	22.491	-0.038	-0.038	0.000	0.000	0.000	0.000
30	A	28	VAL	0	-0.017	-0.018	17.394	0.008	0.008	0.000	0.000	0.000	0.000
31	A	29	TYR	0	-0.026	-0.045	20.120	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	30	GLN	0	-0.004	-0.016	17.309	0.000	0.000	0.000	0.000	0.000	0.000
33	A	31	VAL	0	0.001	0.001	21.044	0.037	0.037	0.000	0.000	0.000	0.000
34	A	32	TYR	0	0.046	0.012	23.614	0.004	0.004	0.000	0.000	0.000	0.000
35	A	33	ASN	0	-0.024	-0.034	25.676	0.019	0.019	0.000	0.000	0.000	0.000
36	A	34	THR	0	0.066	0.051	28.578	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	35	ARG	1	0.858	0.931	31.340	0.125	0.125	0.000	0.000	0.000	0.000
38	A	36	LYS	1	0.945	0.971	34.616	0.078	0.078	0.000	0.000	0.000	0.000
39	A	37	SER	0	-0.032	-0.019	37.985	0.002	0.002	0.000	0.000	0.000	0.000
40	A	38	ASP	-1	-0.799	-0.909	41.207	-0.073	-0.073	0.000	0.000	0.000	0.000
41	A	39	GLY	0	-0.046	-0.037	40.794	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	40	ALA	0	0.041	0.048	41.669	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	41	ASN	0	-0.010	0.002	44.420	-0.005	-0.005	0.000	0.000	0.000	0.000
44	A	42	SER	0	0.060	0.023	41.153	0.000	0.000	0.000	0.000	0.000	0.000
45	A	43	ASN	0	0.025	0.017	40.197	-0.005	-0.005	0.000	0.000	0.000	0.000
46	A	44	ARG	1	0.893	0.933	40.335	0.089	0.089	0.000	0.000	0.000	0.000
47	A	45	GLU	-1	-0.907	-0.948	38.351	-0.115	-0.115	0.000	0.000	0.000	0.000
48	A	46	ASN	0	-0.019	-0.014	34.547	0.000	0.000	0.000	0.000	0.000	0.000
49	A	47	LEU	0	-0.015	0.001	34.399	-0.008	-0.008	0.000	0.000	0.000	0.000
50	A	48	ILE	0	-0.018	0.001	28.610	0.003	0.003	0.000	0.000	0.000	0.000
51	A	49	MET	0	-0.088	-0.023	28.656	0.006	0.006	0.000	0.000	0.000	0.000
52	A	50	ILE	0	0.038	0.025	25.274	-0.009	-0.009	0.000	0.000	0.000	0.000
53	A	51	SER	0	0.039	0.000	21.709	0.026	0.026	0.000	0.000	0.000	0.000
54	A	52	ASP	-1	-0.710	-0.853	21.146	-0.293	-0.293	0.000	0.000	0.000	0.000
55	A	53	GLY	0	0.008	-0.004	19.030	-0.042	-0.042	0.000	0.000	0.000	0.000
56	A	54	ILE	0	-0.052	-0.026	20.058	0.012	0.012	0.000	0.000	0.000	0.000
57	A	55	TYR	0	-0.004	-0.012	22.648	0.022	0.022	0.000	0.000	0.000	0.000
58	A	56	HIS	0	-0.044	-0.031	24.504	-0.013	-0.013	0.000	0.000	0.000	0.000
59	A	57	MET	0	0.001	0.017	26.864	0.016	0.016	0.000	0.000	0.000	0.000
60	A	58	LYS	1	0.907	0.955	29.750	0.112	0.112	0.000	0.000	0.000	0.000
61	A	59	ALA	0	0.035	0.018	30.119	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	60	LEU	0	-0.002	-0.002	32.154	0.005	0.005	0.000	0.000	0.000	0.000
63	A	61	LEU	0	0.002	0.012	29.643	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	62	ARG	1	0.810	0.861	34.093	0.143	0.143	0.000	0.000	0.000	0.000
65	A	63	ASN	0	-0.024	-0.022	36.061	-0.003	-0.003	0.000	0.000	0.000	0.000
66	A	64	GLN	0	0.030	0.001	33.993	0.011	0.011	0.000	0.000	0.000	0.000
67	A	65	ALA	0	0.002	0.016	32.060	-0.007	-0.007	0.000	0.000	0.000	0.000
68	A	66	ALA	0	0.001	-0.001	32.796	-0.005	-0.005	0.000	0.000	0.000	0.000
69	A	67	SER	0	-0.037	-0.025	35.092	0.004	0.004	0.000	0.000	0.000	0.000
70	A	68	LYS	1	0.795	0.878	29.192	0.228	0.228	0.000	0.000	0.000	0.000
71	A	69	PHE	0	0.005	-0.012	29.408	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	70	GLN	0	-0.062	-0.050	31.383	0.006	0.006	0.000	0.000	0.000	0.000
73	A	71	SER	0	-0.041	-0.014	32.982	0.006	0.006	0.000	0.000	0.000	0.000
74	A	72	MET	0	-0.056	-0.026	27.786	-0.010	-0.010	0.000	0.000	0.000	0.000
75	A	73	GLU	-1	-0.950	-0.958	28.423	-0.139	-0.139	0.000	0.000	0.000	0.000
76	A	74	LEU	0	-0.005	0.019	25.098	-0.005	-0.005	0.000	0.000	0.000	0.000
77	A	75	GLN	0	-0.098	-0.071	25.832	0.027	0.027	0.000	0.000	0.000	0.000
78	A	76	ARG	1	0.846	0.912	23.448	0.132	0.132	0.000	0.000	0.000	0.000
79	A	77	GLY	0	0.063	0.029	20.324	0.010	0.010	0.000	0.000	0.000	0.000
80	A	78	ASP	-1	-0.769	-0.841	19.341	-0.328	-0.328	0.000	0.000	0.000	0.000
81	A	79	ILE	0	-0.019	-0.007	15.756	0.016	0.016	0.000	0.000	0.000	0.000
82	A	80	ILE	0	0.010	0.003	19.788	-0.011	-0.011	0.000	0.000	0.000	0.000
83	A	81	ARG	1	0.909	0.938	18.328	0.477	0.477	0.000	0.000	0.000	0.000
84	A	82	VAL	0	0.011	0.014	23.006	0.024	0.024	0.000	0.000	0.000	0.000
85	A	83	ILE	0	-0.030	-0.021	25.241	-0.008	-0.008	0.000	0.000	0.000	0.000
86	A	84	ILE	0	0.010	0.005	28.674	0.010	0.010	0.000	0.000	0.000	0.000
87	A	85	ALA	0	0.012	-0.006	31.079	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	86	GLU	-1	-0.800	-0.871	33.052	-0.128	-0.128	0.000	0.000	0.000	0.000
89	A	87	PRO	0	0.004	0.015	33.436	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	88	ALA	0	0.008	0.013	35.162	0.009	0.009	0.000	0.000	0.000	0.000
91	A	89	ILE	0	0.008	-0.008	37.274	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	90	VAL	0	-0.034	-0.007	39.644	0.005	0.005	0.000	0.000	0.000	0.000
93	A	91	ARG	1	0.950	0.948	41.463	0.096	0.096	0.000	0.000	0.000	0.000
94	A	92	GLU	-1	-0.884	-0.945	43.876	-0.077	-0.077	0.000	0.000	0.000	0.000
95	A	93	ARG	1	0.860	0.915	43.959	0.073	0.073	0.000	0.000	0.000	0.000
96	A	94	LYS	1	0.902	0.958	40.574	0.078	0.078	0.000	0.000	0.000	0.000
97	A	95	LYS	1	0.955	0.996	38.393	0.091	0.091	0.000	0.000	0.000	0.000
98	A	96	TYR	0	-0.017	-0.023	34.477	0.003	0.003	0.000	0.000	0.000	0.000
99	A	97	VAL	0	-0.047	-0.028	34.218	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	98	LEU	0	0.031	0.022	28.931	0.002	0.002	0.000	0.000	0.000	0.000
101	A	99	LEU	0	-0.005	0.001	32.886	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	100	VAL	0	0.000	-0.010	30.066	-0.008	-0.008	0.000	0.000	0.000	0.000
103	A	101	ASP	-1	-0.743	-0.832	33.189	-0.139	-0.139	0.000	0.000	0.000	0.000
104	A	102	ASP	-1	-0.774	-0.890	31.306	-0.203	-0.203	0.000	0.000	0.000	0.000
105	A	103	PHE	0	-0.044	-0.013	25.880	-0.006	-0.006	0.000	0.000	0.000	0.000
106	A	104	GLU	-1	-0.835	-0.893	23.675	-0.354	-0.354	0.000	0.000	0.000	0.000
107	A	105	LEU	0	-0.004	-0.008	21.379	-0.009	-0.009	0.000	0.000	0.000	0.000
108	A	106	VAL	0	-0.061	-0.025	16.373	-0.015	-0.015	0.000	0.000	0.000	0.000
109	A	107	GLN	0	0.036	0.006	13.219	-0.147	-0.147	0.000	0.000	0.000	0.000
110	A	108	SER	0	-0.047	-0.034	17.677	0.047	0.047	0.000	0.000	0.000	0.000
111	A	109	ARG	1	0.900	0.919	18.310	0.200	0.200	0.000	0.000	0.000	0.000
112	A	110	ALA	0	0.011	0.023	15.099	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	111	ASP	-1	-0.899	-0.946	12.752	-0.468	-0.468	0.000	0.000	0.000	0.000
114	A	112	MET	0	-0.054	-0.009	15.163	-0.017	-0.017	0.000	0.000	0.000	0.000
115	A	113	VAL	0	0.032	0.018	14.000	0.049	0.049	0.000	0.000	0.000	0.000
116	A	114	ASN	0	-0.014	-0.020	14.873	-0.008	-0.008	0.000	0.000	0.000	0.000
117	A	115	GLN	0	-0.033	-0.016	18.251	-0.004	-0.004	0.000	0.000	0.000	0.000
118	A	116	THR	0	0.024	0.005	20.146	0.017	0.017	0.000	0.000	0.000	0.000
119	A	117	SER	0	-0.054	0.004	22.458	0.013	0.013	0.000	0.000	0.000	0.000
120	A	118	THR	0	0.012	-0.003	23.971	0.016	0.016	0.000	0.000	0.000	0.000
121	A	119	PHE	0	0.019	-0.001	27.792	-0.010	-0.010	0.000	0.000	0.000	0.000
122	A	120	LEU	0	0.015	0.003	29.036	0.008	0.008	0.000	0.000	0.000	0.000
123	A	121	ASP	-1	-0.810	-0.915	31.133	-0.115	-0.115	0.000	0.000	0.000	0.000
124	A	122	ASN	0	-0.017	-0.010	33.578	0.007	0.007	0.000	0.000	0.000	0.000
125	A	123	TYR	0	0.021	0.000	31.011	0.005	0.005	0.000	0.000	0.000	0.000
126	A	124	PHE	0	0.009	-0.017	31.931	0.004	0.004	0.000	0.000	0.000	0.000
127	A	125	SER	0	-0.050	-0.023	35.778	0.006	0.006	0.000	0.000	0.000	0.000
128	A	126	GLU	-1	-0.925	-0.948	33.713	-0.081	-0.081	0.000	0.000	0.000	0.000
129	A	127	HIS	1	0.802	0.910	33.547	0.092	0.092	0.000	0.000	0.000	0.000
130	A	128	PRO	0	0.040	0.027	37.995	-0.004	-0.004	0.000	0.000	0.000	0.000
131	A	129	ASN	0	-0.035	-0.032	40.485	-0.001	-0.001	0.000	0.000	0.000	0.000
132	A	130	GLU	-1	-0.800	-0.866	32.861	-0.114	-0.114	0.000	0.000	0.000	0.000
133	A	131	THR	0	-0.015	0.028	35.162	-0.004	-0.004	0.000	0.000	0.000	0.000
134	A	132	LEU	0	-0.045	-0.010	35.405	0.010	0.010	0.000	0.000	0.000	0.000

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