FMO DATABASE

FMODB ID: V52K1

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	OptHSide
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	-1233314.514768
FMO2-HF: Nuclear repulsion	1179048.802201
FMO2-HF: Total energy	-54265.712567
FMO2-MP2: Total energy	-54423.038792

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.
1.15	2.94	-0.002	-0.855	-0.933	0.004

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 : 0.028

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	1	MET	0	-0.018	-0.011	3.793	-0.060	1.505	-0.001	-0.825	-0.739	0.004
4	A	2	SER	0	0.008	0.018	4.067	0.819	1.044	-0.001	-0.030	-0.194	0.000
5	A	3	SER	0	0.016	0.005	5.619	0.444	0.444	0.000	0.000	0.000	0.000
6	A	4	VAL	0	0.005	-0.003	9.287	-0.169	-0.169	0.000	0.000	0.000	0.000
7	A	5	GLN	0	-0.026	-0.017	9.577	0.178	0.178	0.000	0.000	0.000	0.000
8	A	6	LEU	0	-0.004	0.013	13.015	0.034	0.034	0.000	0.000	0.000	0.000
9	A	7	SER	0	0.022	0.011	16.547	-0.016	-0.016	0.000	0.000	0.000	0.000
10	A	8	ARG	1	0.908	0.952	15.921	0.250	0.250	0.000	0.000	0.000	0.000
11	A	9	GLY	0	0.023	0.022	19.550	-0.002	-0.002	0.000	0.000	0.000	0.000
12	A	10	ASP	-1	-0.733	-0.817	22.636	-0.224	-0.224	0.000	0.000	0.000	0.000
13	A	11	PHE	0	-0.018	-0.011	24.371	0.013	0.013	0.000	0.000	0.000	0.000
14	A	12	HIS	0	-0.027	-0.022	26.707	0.000	0.000	0.000	0.000	0.000	0.000
15	A	13	SER	0	0.017	0.018	25.827	0.009	0.009	0.000	0.000	0.000	0.000
16	A	14	ILE	0	-0.012	-0.007	27.289	0.009	0.009	0.000	0.000	0.000	0.000
17	A	15	PHE	0	-0.010	-0.017	30.252	0.009	0.009	0.000	0.000	0.000	0.000
18	A	16	THR	0	-0.022	-0.031	30.823	0.009	0.009	0.000	0.000	0.000	0.000
19	A	17	ASN	0	-0.004	0.004	30.719	0.004	0.004	0.000	0.000	0.000	0.000
20	A	18	LYS	1	0.859	0.895	32.797	0.099	0.099	0.000	0.000	0.000	0.000
21	A	19	GLN	0	0.018	0.008	30.233	-0.009	-0.009	0.000	0.000	0.000	0.000
22	A	20	ARG	1	0.747	0.839	24.993	0.225	0.225	0.000	0.000	0.000	0.000
23	A	21	TYR	0	-0.028	-0.016	30.588	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	22	ASP	-1	-0.823	-0.898	33.433	-0.113	-0.113	0.000	0.000	0.000	0.000
25	A	23	ASN	0	0.007	0.025	29.604	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	24	PRO	0	-0.008	0.018	29.059	-0.015	-0.015	0.000	0.000	0.000	0.000
27	A	25	THR	0	-0.041	-0.027	27.661	-0.011	-0.011	0.000	0.000	0.000	0.000
28	A	26	GLY	0	0.031	0.012	24.009	-0.006	-0.006	0.000	0.000	0.000	0.000
29	A	27	GLY	0	-0.020	0.005	21.920	-0.034	-0.034	0.000	0.000	0.000	0.000
30	A	28	VAL	0	-0.003	-0.006	16.914	0.004	0.004	0.000	0.000	0.000	0.000
31	A	29	TYR	0	-0.033	-0.051	19.731	0.008	0.008	0.000	0.000	0.000	0.000
32	A	30	GLN	0	-0.015	-0.019	17.420	-0.005	-0.005	0.000	0.000	0.000	0.000
33	A	31	VAL	0	0.000	0.005	21.150	0.031	0.031	0.000	0.000	0.000	0.000
34	A	32	TYR	0	0.052	0.013	23.698	0.005	0.005	0.000	0.000	0.000	0.000
35	A	33	ASN	0	-0.019	-0.028	25.720	0.019	0.019	0.000	0.000	0.000	0.000
36	A	34	THR	0	0.044	0.035	28.492	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	35	ARG	1	0.849	0.931	31.234	0.078	0.078	0.000	0.000	0.000	0.000
38	A	36	LYS	1	0.958	0.972	34.468	0.052	0.052	0.000	0.000	0.000	0.000
39	A	37	SER	0	0.004	0.025	37.715	0.001	0.001	0.000	0.000	0.000	0.000
40	A	38	ASP	-1	-0.796	-0.911	41.115	-0.050	-0.050	0.000	0.000	0.000	0.000
41	A	39	GLY	0	-0.084	-0.054	40.868	0.000	0.000	0.000	0.000	0.000	0.000
42	A	40	ALA	0	0.027	0.042	41.771	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	41	ASN	0	-0.012	-0.005	44.494	-0.006	-0.006	0.000	0.000	0.000	0.000
44	A	42	SER	0	0.055	-0.002	41.486	0.001	0.001	0.000	0.000	0.000	0.000
45	A	43	ASN	0	0.028	0.027	40.400	-0.005	-0.005	0.000	0.000	0.000	0.000
46	A	44	ARG	1	0.903	0.947	40.009	0.071	0.071	0.000	0.000	0.000	0.000
47	A	45	GLU	-1	-0.901	-0.956	38.300	-0.094	-0.094	0.000	0.000	0.000	0.000
48	A	46	ASN	0	-0.029	-0.007	34.246	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	47	LEU	0	-0.009	0.013	34.663	-0.006	-0.006	0.000	0.000	0.000	0.000
50	A	48	ILE	0	-0.015	0.001	28.433	0.005	0.005	0.000	0.000	0.000	0.000
51	A	49	MET	0	-0.087	-0.025	28.768	0.002	0.002	0.000	0.000	0.000	0.000
52	A	50	ILE	0	0.025	0.020	25.280	-0.007	-0.007	0.000	0.000	0.000	0.000
53	A	51	SER	0	0.035	-0.006	21.699	0.020	0.020	0.000	0.000	0.000	0.000
54	A	52	ASP	-1	-0.718	-0.854	21.057	-0.213	-0.213	0.000	0.000	0.000	0.000
55	A	53	GLY	0	-0.005	-0.011	18.907	-0.030	-0.030	0.000	0.000	0.000	0.000
56	A	54	ILE	0	-0.071	-0.039	19.788	0.026	0.026	0.000	0.000	0.000	0.000
57	A	55	TYR	0	0.020	0.008	22.596	0.022	0.022	0.000	0.000	0.000	0.000
58	A	56	HIS	0	-0.034	-0.023	24.743	-0.013	-0.013	0.000	0.000	0.000	0.000
59	A	57	MET	0	0.000	0.008	26.949	0.011	0.011	0.000	0.000	0.000	0.000
60	A	58	LYS	1	0.943	0.966	29.733	0.074	0.074	0.000	0.000	0.000	0.000
61	A	59	ALA	0	0.040	0.018	29.956	-0.004	-0.004	0.000	0.000	0.000	0.000
62	A	60	LEU	0	-0.020	-0.008	32.004	0.005	0.005	0.000	0.000	0.000	0.000
63	A	61	LEU	0	-0.016	0.000	29.852	-0.005	-0.005	0.000	0.000	0.000	0.000
64	A	62	ARG	1	0.837	0.871	34.126	0.124	0.124	0.000	0.000	0.000	0.000
65	A	63	ASN	0	-0.029	-0.031	35.981	-0.003	-0.003	0.000	0.000	0.000	0.000
66	A	64	GLN	0	0.018	-0.005	33.782	0.011	0.011	0.000	0.000	0.000	0.000
67	A	65	ALA	0	0.000	0.016	31.927	-0.006	-0.006	0.000	0.000	0.000	0.000
68	A	66	ALA	0	-0.001	0.001	32.580	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	67	SER	0	-0.015	-0.009	34.984	0.005	0.005	0.000	0.000	0.000	0.000
70	A	68	LYS	1	0.819	0.899	29.164	0.205	0.205	0.000	0.000	0.000	0.000
71	A	69	PHE	0	0.005	-0.003	29.072	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	70	GLN	0	-0.066	-0.052	31.040	0.007	0.007	0.000	0.000	0.000	0.000
73	A	71	SER	0	-0.022	0.002	32.614	0.004	0.004	0.000	0.000	0.000	0.000
74	A	72	MET	0	-0.066	-0.045	27.349	-0.005	-0.005	0.000	0.000	0.000	0.000
75	A	73	GLU	-1	-0.940	-0.947	28.030	-0.105	-0.105	0.000	0.000	0.000	0.000
76	A	74	LEU	0	-0.017	0.010	24.643	-0.003	-0.003	0.000	0.000	0.000	0.000
77	A	75	GLN	0	-0.102	-0.071	25.409	0.028	0.028	0.000	0.000	0.000	0.000
78	A	76	ARG	1	0.877	0.919	23.485	0.064	0.064	0.000	0.000	0.000	0.000
79	A	77	GLY	0	0.044	0.014	20.487	0.008	0.008	0.000	0.000	0.000	0.000
80	A	78	ASP	-1	-0.756	-0.838	19.302	-0.250	-0.250	0.000	0.000	0.000	0.000
81	A	79	ILE	0	-0.029	-0.018	15.820	0.012	0.012	0.000	0.000	0.000	0.000
82	A	80	ILE	0	0.016	0.007	19.842	-0.010	-0.010	0.000	0.000	0.000	0.000
83	A	81	ARG	1	0.917	0.947	18.146	0.446	0.446	0.000	0.000	0.000	0.000
84	A	82	VAL	0	0.009	0.005	22.660	0.020	0.020	0.000	0.000	0.000	0.000
85	A	83	ILE	0	-0.036	-0.021	24.927	-0.012	-0.012	0.000	0.000	0.000	0.000
86	A	84	ILE	0	0.007	0.010	28.167	0.005	0.005	0.000	0.000	0.000	0.000
87	A	85	ALA	0	0.013	-0.014	30.552	0.001	0.001	0.000	0.000	0.000	0.000
88	A	86	GLU	-1	-0.830	-0.890	32.521	-0.112	-0.112	0.000	0.000	0.000	0.000
89	A	87	PRO	0	-0.003	0.001	33.093	0.002	0.002	0.000	0.000	0.000	0.000
90	A	88	ALA	0	0.011	0.011	34.974	0.006	0.006	0.000	0.000	0.000	0.000
91	A	89	ILE	0	-0.012	-0.011	37.310	0.000	0.000	0.000	0.000	0.000	0.000
92	A	90	VAL	0	-0.024	-0.003	39.484	0.003	0.003	0.000	0.000	0.000	0.000
93	A	91	ARG	1	0.930	0.924	41.297	0.074	0.074	0.000	0.000	0.000	0.000
94	A	92	GLU	-1	-0.884	-0.941	43.998	-0.056	-0.056	0.000	0.000	0.000	0.000
95	A	93	ARG	1	0.878	0.925	43.723	0.051	0.051	0.000	0.000	0.000	0.000
96	A	94	LYS	1	0.950	0.990	40.664	0.054	0.054	0.000	0.000	0.000	0.000
97	A	95	LYS	1	0.942	0.984	38.438	0.065	0.065	0.000	0.000	0.000	0.000
98	A	96	TYR	0	-0.008	0.005	34.509	0.001	0.001	0.000	0.000	0.000	0.000
99	A	97	VAL	0	-0.052	-0.030	34.329	0.000	0.000	0.000	0.000	0.000	0.000
100	A	98	LEU	0	0.037	0.021	28.716	0.000	0.000	0.000	0.000	0.000	0.000
101	A	99	LEU	0	-0.012	-0.006	32.775	0.001	0.001	0.000	0.000	0.000	0.000
102	A	100	VAL	0	0.012	0.001	29.650	-0.008	-0.008	0.000	0.000	0.000	0.000
103	A	101	ASP	-1	-0.722	-0.829	32.650	-0.120	-0.120	0.000	0.000	0.000	0.000
104	A	102	ASP	-1	-0.789	-0.899	31.058	-0.187	-0.187	0.000	0.000	0.000	0.000
105	A	103	PHE	0	-0.029	-0.009	26.034	-0.004	-0.004	0.000	0.000	0.000	0.000
106	A	104	GLU	-1	-0.852	-0.908	23.539	-0.330	-0.330	0.000	0.000	0.000	0.000
107	A	105	LEU	0	-0.009	-0.013	21.308	-0.005	-0.005	0.000	0.000	0.000	0.000
108	A	106	VAL	0	-0.064	-0.024	16.363	-0.022	-0.022	0.000	0.000	0.000	0.000
109	A	107	GLN	0	0.026	-0.001	12.955	-0.118	-0.118	0.000	0.000	0.000	0.000
110	A	108	SER	0	-0.043	-0.021	17.663	0.042	0.042	0.000	0.000	0.000	0.000
111	A	109	ARG	1	0.909	0.930	18.077	0.148	0.148	0.000	0.000	0.000	0.000
112	A	110	ALA	0	0.003	0.020	14.944	0.000	0.000	0.000	0.000	0.000	0.000
113	A	111	ASP	-1	-0.891	-0.941	12.619	-0.155	-0.155	0.000	0.000	0.000	0.000
114	A	112	MET	0	-0.068	-0.025	15.121	-0.031	-0.031	0.000	0.000	0.000	0.000
115	A	113	VAL	0	0.028	0.015	14.336	0.032	0.032	0.000	0.000	0.000	0.000
116	A	114	ASN	0	-0.022	-0.018	15.312	-0.019	-0.019	0.000	0.000	0.000	0.000
117	A	115	GLN	0	-0.035	-0.016	18.603	-0.025	-0.025	0.000	0.000	0.000	0.000
118	A	116	THR	0	0.022	0.001	20.894	0.007	0.007	0.000	0.000	0.000	0.000
119	A	117	SER	0	-0.012	0.024	22.814	0.007	0.007	0.000	0.000	0.000	0.000
120	A	118	THR	0	0.015	0.005	24.335	0.011	0.011	0.000	0.000	0.000	0.000
121	A	119	PHE	0	-0.030	-0.015	28.050	-0.012	-0.012	0.000	0.000	0.000	0.000
122	A	120	LEU	0	0.027	0.000	28.992	0.005	0.005	0.000	0.000	0.000	0.000
123	A	121	ASP	-1	-0.829	-0.935	31.068	-0.078	-0.078	0.000	0.000	0.000	0.000
124	A	122	ASN	0	-0.008	-0.011	33.417	0.003	0.003	0.000	0.000	0.000	0.000
125	A	123	TYR	0	0.002	-0.006	30.863	0.005	0.005	0.000	0.000	0.000	0.000
126	A	124	PHE	0	0.018	-0.018	31.911	0.003	0.003	0.000	0.000	0.000	0.000
127	A	125	SER	0	-0.049	-0.014	35.701	0.004	0.004	0.000	0.000	0.000	0.000
128	A	126	GLU	-1	-0.923	-0.948	33.817	-0.034	-0.034	0.000	0.000	0.000	0.000
129	A	127	HIS	1	0.801	0.909	33.634	0.050	0.050	0.000	0.000	0.000	0.000
130	A	128	PRO	0	0.026	0.016	37.659	-0.005	-0.005	0.000	0.000	0.000	0.000
131	A	129	ASN	0	-0.074	-0.052	40.408	-0.003	-0.003	0.000	0.000	0.000	0.000
132	A	130	GLU	-1	-0.819	-0.873	32.677	-0.076	-0.076	0.000	0.000	0.000	0.000
133	A	131	THR	0	-0.036	-0.002	35.194	-0.003	-0.003	0.000	0.000	0.000	0.000
134	A	132	LEU	0	0.018	0.040	35.074	0.008	0.008	0.000	0.000	0.000	0.000

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