FMO DATABASE

FMODB ID: YZQN2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1231136.60903
FMO2-HF: Nuclear repulsion	1176871.313283
FMO2-HF: Total energy	-54265.295747
FMO2-MP2: Total energy	-54422.554177

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.
1.149	2.298	0.001	-0.433	-0.717	0.001

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 : 0.028 / q_NPA : -0.003

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	1	MET	0	-0.014	-0.010	3.788	0.533	1.471	0.002	-0.405	-0.534	0.001
4	A	2	SER	0	0.016	0.023	4.229	0.136	0.347	-0.001	-0.028	-0.183	0.000
5	A	3	SER	0	-0.006	-0.009	5.681	0.464	0.464	0.000	0.000	0.000	0.000
6	A	4	VAL	0	0.019	0.010	9.370	-0.092	-0.092	0.000	0.000	0.000	0.000
7	A	5	GLN	0	-0.028	-0.021	10.303	0.147	0.147	0.000	0.000	0.000	0.000
8	A	6	LEU	0	0.005	0.013	13.078	0.061	0.061	0.000	0.000	0.000	0.000
9	A	7	SER	0	0.013	0.012	16.615	-0.009	-0.009	0.000	0.000	0.000	0.000
10	A	8	ARG	1	0.946	0.963	16.056	0.387	0.387	0.000	0.000	0.000	0.000
11	A	9	GLY	0	0.013	0.018	19.662	0.010	0.010	0.000	0.000	0.000	0.000
12	A	10	ASP	-1	-0.719	-0.817	22.713	-0.207	-0.207	0.000	0.000	0.000	0.000
13	A	11	PHE	0	-0.020	-0.014	24.417	0.018	0.018	0.000	0.000	0.000	0.000
14	A	12	HIS	0	-0.036	-0.033	26.810	0.004	0.004	0.000	0.000	0.000	0.000
15	A	13	SER	0	0.031	0.026	26.192	0.015	0.015	0.000	0.000	0.000	0.000
16	A	14	ILE	0	-0.016	-0.005	27.295	0.013	0.013	0.000	0.000	0.000	0.000
17	A	15	PHE	0	-0.024	-0.024	30.269	0.012	0.012	0.000	0.000	0.000	0.000
18	A	16	THR	0	-0.020	-0.030	30.855	0.009	0.009	0.000	0.000	0.000	0.000
19	A	17	ASN	0	-0.003	0.002	30.728	0.005	0.005	0.000	0.000	0.000	0.000
20	A	18	LYS	1	0.876	0.931	32.773	0.086	0.086	0.000	0.000	0.000	0.000
21	A	19	GLN	0	0.021	0.010	30.273	-0.007	-0.007	0.000	0.000	0.000	0.000
22	A	20	ARG	1	0.770	0.857	25.057	0.202	0.202	0.000	0.000	0.000	0.000
23	A	21	TYR	0	-0.043	-0.020	30.516	-0.005	-0.005	0.000	0.000	0.000	0.000
24	A	22	ASP	-1	-0.826	-0.928	33.396	-0.098	-0.098	0.000	0.000	0.000	0.000
25	A	23	ASN	0	-0.001	0.020	29.008	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	24	PRO	0	-0.016	0.011	28.989	-0.012	-0.012	0.000	0.000	0.000	0.000
27	A	25	THR	0	-0.047	-0.033	27.573	-0.013	-0.013	0.000	0.000	0.000	0.000
28	A	26	GLY	0	0.026	0.003	23.889	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	27	GLY	0	-0.024	0.001	21.825	-0.028	-0.028	0.000	0.000	0.000	0.000
30	A	28	VAL	0	-0.006	-0.010	16.842	0.003	0.003	0.000	0.000	0.000	0.000
31	A	29	TYR	0	-0.025	-0.041	19.799	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	30	GLN	0	-0.022	-0.023	17.369	-0.008	-0.008	0.000	0.000	0.000	0.000
33	A	31	VAL	0	0.003	0.004	21.337	0.033	0.033	0.000	0.000	0.000	0.000
34	A	32	TYR	0	0.038	0.009	23.693	-0.009	-0.009	0.000	0.000	0.000	0.000
35	A	33	ASN	0	-0.040	-0.044	25.775	0.013	0.013	0.000	0.000	0.000	0.000
36	A	34	THR	0	0.027	0.022	28.518	0.002	0.002	0.000	0.000	0.000	0.000
37	A	35	ARG	1	0.873	0.947	31.228	0.135	0.135	0.000	0.000	0.000	0.000
38	A	36	LYS	1	0.994	0.997	34.462	0.091	0.091	0.000	0.000	0.000	0.000
39	A	37	SER	0	0.002	0.032	37.710	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	38	ASP	-1	-0.790	-0.912	41.109	-0.076	-0.076	0.000	0.000	0.000	0.000
41	A	39	GLY	0	-0.108	-0.080	40.968	-0.004	-0.004	0.000	0.000	0.000	0.000
42	A	40	ALA	0	-0.013	0.020	41.880	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	41	ASN	0	-0.020	-0.005	44.557	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	42	SER	0	0.062	0.001	41.488	0.000	0.000	0.000	0.000	0.000	0.000
45	A	43	ASN	0	0.056	0.040	40.379	-0.004	-0.004	0.000	0.000	0.000	0.000
46	A	44	ARG	1	0.916	0.953	40.002	0.080	0.080	0.000	0.000	0.000	0.000
47	A	45	GLU	-1	-0.924	-0.967	38.370	-0.100	-0.100	0.000	0.000	0.000	0.000
48	A	46	ASN	0	-0.010	0.021	34.242	0.000	0.000	0.000	0.000	0.000	0.000
49	A	47	LEU	0	-0.018	0.006	34.766	-0.005	-0.005	0.000	0.000	0.000	0.000
50	A	48	ILE	0	-0.018	0.000	28.317	0.001	0.001	0.000	0.000	0.000	0.000
51	A	49	MET	0	-0.078	-0.025	29.132	0.007	0.007	0.000	0.000	0.000	0.000
52	A	50	ILE	0	0.025	0.019	25.375	-0.012	-0.012	0.000	0.000	0.000	0.000
53	A	51	SER	0	0.031	-0.002	22.250	0.015	0.015	0.000	0.000	0.000	0.000
54	A	52	ASP	-1	-0.727	-0.860	21.194	-0.274	-0.274	0.000	0.000	0.000	0.000
55	A	53	GLY	0	-0.007	-0.011	19.133	-0.034	-0.034	0.000	0.000	0.000	0.000
56	A	54	ILE	0	-0.086	-0.042	20.028	0.009	0.009	0.000	0.000	0.000	0.000
57	A	55	TYR	0	0.009	0.009	22.836	0.018	0.018	0.000	0.000	0.000	0.000
58	A	56	HIS	0	-0.036	-0.036	24.957	-0.007	-0.007	0.000	0.000	0.000	0.000
59	A	57	MET	0	-0.006	0.003	27.181	0.015	0.015	0.000	0.000	0.000	0.000
60	A	58	LYS	1	0.957	0.971	29.919	0.113	0.113	0.000	0.000	0.000	0.000
61	A	59	ALA	0	0.039	0.019	30.066	0.000	0.000	0.000	0.000	0.000	0.000
62	A	60	LEU	0	-0.030	-0.015	32.131	0.001	0.001	0.000	0.000	0.000	0.000
63	A	61	LEU	0	-0.006	0.002	29.918	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	62	ARG	1	0.943	0.966	34.200	0.120	0.120	0.000	0.000	0.000	0.000
65	A	63	ASN	0	-0.009	-0.016	35.993	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	64	GLN	0	0.041	0.014	33.828	0.006	0.006	0.000	0.000	0.000	0.000
67	A	65	ALA	0	0.004	0.019	31.865	-0.007	-0.007	0.000	0.000	0.000	0.000
68	A	66	ALA	0	0.008	0.004	32.573	-0.007	-0.007	0.000	0.000	0.000	0.000
69	A	67	SER	0	-0.014	-0.009	34.976	0.002	0.002	0.000	0.000	0.000	0.000
70	A	68	LYS	1	0.845	0.909	29.921	0.174	0.174	0.000	0.000	0.000	0.000
71	A	69	PHE	0	0.016	0.006	28.953	-0.005	-0.005	0.000	0.000	0.000	0.000
72	A	70	GLN	0	-0.087	-0.075	31.033	0.002	0.002	0.000	0.000	0.000	0.000
73	A	71	SER	0	-0.032	-0.003	32.655	0.001	0.001	0.000	0.000	0.000	0.000
74	A	72	MET	0	-0.040	-0.030	27.346	-0.006	-0.006	0.000	0.000	0.000	0.000
75	A	73	GLU	-1	-0.950	-0.953	28.038	-0.145	-0.145	0.000	0.000	0.000	0.000
76	A	74	LEU	0	-0.008	0.011	24.485	-0.009	-0.009	0.000	0.000	0.000	0.000
77	A	75	GLN	0	-0.100	-0.068	25.407	0.020	0.020	0.000	0.000	0.000	0.000
78	A	76	ARG	1	0.880	0.931	23.651	0.165	0.165	0.000	0.000	0.000	0.000
79	A	77	GLY	0	0.050	0.016	20.481	0.003	0.003	0.000	0.000	0.000	0.000
80	A	78	ASP	-1	-0.773	-0.859	19.296	-0.327	-0.327	0.000	0.000	0.000	0.000
81	A	79	ILE	0	-0.018	-0.013	15.643	0.013	0.013	0.000	0.000	0.000	0.000
82	A	80	ILE	0	0.008	0.004	19.835	0.002	0.002	0.000	0.000	0.000	0.000
83	A	81	ARG	1	0.940	0.974	17.986	0.375	0.375	0.000	0.000	0.000	0.000
84	A	82	VAL	0	0.006	0.004	22.628	0.020	0.020	0.000	0.000	0.000	0.000
85	A	83	ILE	0	-0.025	-0.013	24.809	-0.006	-0.006	0.000	0.000	0.000	0.000
86	A	84	ILE	0	0.017	0.013	28.070	0.009	0.009	0.000	0.000	0.000	0.000
87	A	85	ALA	0	-0.002	-0.021	30.558	-0.004	-0.004	0.000	0.000	0.000	0.000
88	A	86	GLU	-1	-0.928	-0.950	32.485	-0.102	-0.102	0.000	0.000	0.000	0.000
89	A	87	PRO	0	-0.007	0.002	33.115	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	88	ALA	0	0.019	0.019	35.000	0.007	0.007	0.000	0.000	0.000	0.000
91	A	89	ILE	0	-0.005	-0.011	37.269	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	90	VAL	0	-0.011	0.002	39.571	0.005	0.005	0.000	0.000	0.000	0.000
93	A	91	ARG	1	0.924	0.932	41.373	0.078	0.078	0.000	0.000	0.000	0.000
94	A	92	GLU	-1	-0.897	-0.948	44.118	-0.070	-0.070	0.000	0.000	0.000	0.000
95	A	93	ARG	1	0.878	0.927	43.791	0.074	0.074	0.000	0.000	0.000	0.000
96	A	94	LYS	1	0.955	0.990	40.930	0.069	0.069	0.000	0.000	0.000	0.000
97	A	95	LYS	1	0.944	0.988	38.620	0.087	0.087	0.000	0.000	0.000	0.000
98	A	96	TYR	0	0.023	0.025	34.609	0.004	0.004	0.000	0.000	0.000	0.000
99	A	97	VAL	0	-0.053	-0.031	34.454	-0.004	-0.004	0.000	0.000	0.000	0.000
100	A	98	LEU	0	0.043	0.022	28.701	0.003	0.003	0.000	0.000	0.000	0.000
101	A	99	LEU	0	-0.015	-0.009	32.848	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	100	VAL	0	0.004	-0.001	29.615	-0.004	-0.004	0.000	0.000	0.000	0.000
103	A	101	ASP	-1	-0.750	-0.880	32.670	-0.117	-0.117	0.000	0.000	0.000	0.000
104	A	102	ASP	-1	-0.837	-0.931	31.059	-0.169	-0.169	0.000	0.000	0.000	0.000
105	A	103	PHE	0	-0.056	-0.026	25.829	-0.004	-0.004	0.000	0.000	0.000	0.000
106	A	104	GLU	-1	-0.876	-0.930	23.651	-0.259	-0.259	0.000	0.000	0.000	0.000
107	A	105	LEU	0	-0.010	-0.016	21.218	-0.012	-0.012	0.000	0.000	0.000	0.000
108	A	106	VAL	0	-0.069	-0.028	16.370	-0.010	-0.010	0.000	0.000	0.000	0.000
109	A	107	GLN	0	0.027	-0.002	12.837	-0.094	-0.094	0.000	0.000	0.000	0.000
110	A	108	SER	0	-0.037	0.000	17.656	0.032	0.032	0.000	0.000	0.000	0.000
111	A	109	ARG	1	0.930	0.942	18.071	0.218	0.218	0.000	0.000	0.000	0.000
112	A	110	ALA	0	0.005	0.022	14.909	-0.018	-0.018	0.000	0.000	0.000	0.000
113	A	111	ASP	-1	-0.890	-0.943	13.023	-0.511	-0.511	0.000	0.000	0.000	0.000
114	A	112	MET	0	-0.071	-0.029	15.117	-0.007	-0.007	0.000	0.000	0.000	0.000
115	A	113	VAL	0	0.021	0.010	14.489	0.051	0.051	0.000	0.000	0.000	0.000
116	A	114	ASN	0	-0.033	-0.029	15.279	0.026	0.026	0.000	0.000	0.000	0.000
117	A	115	GLN	0	-0.020	-0.001	18.999	0.009	0.009	0.000	0.000	0.000	0.000
118	A	116	THR	0	0.027	0.003	21.324	0.016	0.016	0.000	0.000	0.000	0.000
119	A	117	SER	0	-0.014	0.037	23.138	0.013	0.013	0.000	0.000	0.000	0.000
120	A	118	THR	0	0.025	0.001	24.649	0.015	0.015	0.000	0.000	0.000	0.000
121	A	119	PHE	0	-0.024	-0.008	28.316	-0.008	-0.008	0.000	0.000	0.000	0.000
122	A	120	LEU	0	0.032	0.003	29.219	0.007	0.007	0.000	0.000	0.000	0.000
123	A	121	ASP	-1	-0.839	-0.943	31.278	-0.110	-0.110	0.000	0.000	0.000	0.000
124	A	122	ASN	0	-0.029	-0.020	33.704	0.010	0.010	0.000	0.000	0.000	0.000
125	A	123	TYR	0	-0.015	-0.016	31.163	0.004	0.004	0.000	0.000	0.000	0.000
126	A	124	PHE	0	0.020	-0.021	32.277	0.005	0.005	0.000	0.000	0.000	0.000
127	A	125	SER	0	-0.078	-0.022	35.890	0.007	0.007	0.000	0.000	0.000	0.000
128	A	126	GLU	-1	-0.934	-0.965	34.268	-0.088	-0.088	0.000	0.000	0.000	0.000
129	A	127	HIS	1	0.853	0.939	34.015	0.091	0.091	0.000	0.000	0.000	0.000
130	A	128	PRO	0	0.027	0.013	37.846	-0.003	-0.003	0.000	0.000	0.000	0.000
131	A	129	ASN	0	-0.079	-0.050	40.578	-0.001	-0.001	0.000	0.000	0.000	0.000
132	A	130	GLU	-1	-0.807	-0.850	32.824	-0.104	-0.104	0.000	0.000	0.000	0.000
133	A	131	THR	0	-0.031	-0.004	35.688	-0.001	-0.001	0.000	0.000	0.000	0.000
134	A	132	LEU	0	0.006	0.028	35.065	0.006	0.006	0.000	0.000	0.000	0.000

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