FMO DATABASE

FMODB ID: 17R9Z

Calculation Name: 4U13-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4U13

Chain ID: A

ChEMBL ID:

UniProt ID: Q92YJ1

Base Structure: X-ray

Registration Date: 2023-09-20

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	109
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-826123.636065
FMO2-HF: Nuclear repulsion	784277.790089
FMO2-HF: Total energy	-41845.845976
FMO2-MP2: Total energy	-41967.97803

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:PHE)

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

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.
-26.73	-10.331	17.504	-9.77	-24.132	-0.034

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.004 / q_NPA : 0.002

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	0	SER	0	0.066	0.029	3.230	-3.548	0.768	1.208	-2.038	-3.486	0.006
4	A	1	MET	0	-0.057	-0.023	4.229	-0.790	-0.464	-0.001	0.000	-0.326	0.000
5	A	2	ASP	-1	-0.865	-0.926	2.490	-9.107	-4.695	2.702	-3.168	-3.946	-0.032
6	A	3	LEU	0	-0.096	-0.040	2.318	-1.372	-0.158	1.608	-0.494	-2.328	0.003
7	A	4	PRO	0	0.022	-0.003	4.659	0.352	0.403	-0.001	-0.009	-0.040	0.000
8	A	5	ASP	-1	-0.876	-0.941	8.242	-0.671	-0.671	0.000	0.000	0.000	0.000
9	A	6	ILE	0	-0.028	-0.013	10.128	0.011	0.011	0.000	0.000	0.000	0.000
10	A	7	VAL	0	-0.012	-0.006	6.083	0.068	0.068	0.000	0.000	0.000	0.000
11	A	8	ASN	0	-0.014	-0.025	5.379	-0.195	-0.195	0.000	0.000	0.000	0.000
12	A	9	MET	0	0.026	0.030	7.138	0.068	0.068	0.000	0.000	0.000	0.000
13	A	10	TYR	0	-0.030	-0.030	9.140	0.071	0.071	0.000	0.000	0.000	0.000
14	A	11	PHE	0	-0.002	-0.017	5.912	0.122	0.122	0.000	0.000	0.000	0.000
15	A	12	ASP	-1	-0.842	-0.909	8.662	-0.675	-0.675	0.000	0.000	0.000	0.000
16	A	13	ALA	0	0.027	0.014	10.444	0.051	0.051	0.000	0.000	0.000	0.000
17	A	14	ASP	-1	-0.779	-0.868	11.393	-0.069	-0.069	0.000	0.000	0.000	0.000
18	A	15	SER	0	-0.026	-0.019	10.270	0.026	0.026	0.000	0.000	0.000	0.000
19	A	16	CYS	0	-0.099	-0.039	12.423	0.013	0.013	0.000	0.000	0.000	0.000
20	A	17	ASN	0	-0.105	-0.059	15.430	0.033	0.033	0.000	0.000	0.000	0.000
21	A	18	ASP	-1	-0.840	-0.919	16.524	-0.212	-0.212	0.000	0.000	0.000	0.000
22	A	19	THR	0	0.013	-0.027	17.982	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	20	ASP	-1	-0.922	-0.942	20.425	-0.136	-0.136	0.000	0.000	0.000	0.000
24	A	21	ALA	0	0.082	0.055	16.029	0.002	0.002	0.000	0.000	0.000	0.000
25	A	22	LEU	0	-0.020	-0.012	14.483	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	23	SER	0	-0.081	-0.053	16.875	0.014	0.014	0.000	0.000	0.000	0.000
27	A	24	GLU	-1	-0.991	-0.980	18.287	-0.199	-0.199	0.000	0.000	0.000	0.000
28	A	25	THR	0	-0.012	-0.021	13.298	-0.024	-0.024	0.000	0.000	0.000	0.000
29	A	26	PHE	0	-0.043	-0.034	14.987	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	27	ALA	0	0.011	0.012	18.366	0.000	0.000	0.000	0.000	0.000	0.000
31	A	28	PRO	0	0.029	-0.013	21.277	0.008	0.008	0.000	0.000	0.000	0.000
32	A	29	ASP	-1	-0.962	-0.986	24.537	-0.053	-0.053	0.000	0.000	0.000	0.000
33	A	30	ALA	0	-0.009	0.021	19.638	0.011	0.011	0.000	0.000	0.000	0.000
34	A	31	VAL	0	-0.072	-0.057	20.648	0.009	0.009	0.000	0.000	0.000	0.000
35	A	32	VAL	0	0.058	0.034	17.203	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	33	GLU	-1	-1.053	-1.031	18.879	0.112	0.112	0.000	0.000	0.000	0.000
37	A	34	ASP	-1	-0.749	-0.890	18.092	0.117	0.117	0.000	0.000	0.000	0.000
38	A	35	GLU	-1	-0.971	-0.972	19.826	0.068	0.068	0.000	0.000	0.000	0.000
39	A	36	GLY	0	-0.026	-0.002	22.089	-0.010	-0.010	0.000	0.000	0.000	0.000
40	A	37	ALA	0	-0.050	-0.021	23.592	-0.012	-0.012	0.000	0.000	0.000	0.000
41	A	38	ARG	1	0.924	0.947	23.081	-0.018	-0.018	0.000	0.000	0.000	0.000
42	A	39	HIS	0	0.001	0.004	21.396	-0.016	-0.016	0.000	0.000	0.000	0.000
43	A	40	GLN	0	0.024	0.012	23.064	0.005	0.005	0.000	0.000	0.000	0.000
44	A	41	GLY	0	0.015	0.021	24.411	0.000	0.000	0.000	0.000	0.000	0.000
45	A	42	VAL	0	0.072	0.023	21.860	0.005	0.005	0.000	0.000	0.000	0.000
46	A	43	VAL	0	-0.002	0.000	23.655	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	44	ALA	0	-0.037	-0.031	25.310	0.001	0.001	0.000	0.000	0.000	0.000
48	A	45	ILE	0	0.062	0.052	18.957	0.005	0.005	0.000	0.000	0.000	0.000
49	A	46	LEU	0	0.035	0.018	20.750	0.001	0.001	0.000	0.000	0.000	0.000
50	A	47	ARG	1	0.864	0.930	22.405	0.022	0.022	0.000	0.000	0.000	0.000
51	A	48	TRP	0	-0.019	-0.008	15.387	-0.014	-0.014	0.000	0.000	0.000	0.000
52	A	49	TRP	0	-0.013	0.001	15.513	0.011	0.011	0.000	0.000	0.000	0.000
53	A	50	VAL	0	0.001	-0.011	19.804	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	51	ALA	0	-0.028	-0.026	22.582	0.001	0.001	0.000	0.000	0.000	0.000
55	A	52	ALA	0	0.094	0.058	19.245	0.004	0.004	0.000	0.000	0.000	0.000
56	A	53	LYS	1	0.831	0.939	14.774	0.143	0.143	0.000	0.000	0.000	0.000
57	A	54	LYS	1	0.870	0.933	20.331	0.059	0.059	0.000	0.000	0.000	0.000
58	A	55	ALA	0	-0.003	0.004	22.757	0.002	0.002	0.000	0.000	0.000	0.000
59	A	56	ALA	0	0.013	-0.004	19.519	0.004	0.004	0.000	0.000	0.000	0.000
60	A	57	SER	0	-0.085	-0.041	19.398	0.004	0.004	0.000	0.000	0.000	0.000
61	A	58	TYR	0	-0.063	-0.035	13.304	0.001	0.001	0.000	0.000	0.000	0.000
62	A	59	VAL	0	0.035	0.018	10.300	-0.030	-0.030	0.000	0.000	0.000	0.000
63	A	60	ALA	0	-0.003	-0.007	9.618	0.060	0.060	0.000	0.000	0.000	0.000
64	A	61	GLU	-1	-0.802	-0.886	5.329	-0.355	-0.355	0.000	0.000	0.000	0.000
65	A	62	PRO	0	-0.011	-0.013	2.318	-0.770	0.036	1.654	-0.646	-1.814	0.005
66	A	63	LEU	0	-0.038	-0.011	2.653	-4.217	-1.994	1.540	-1.264	-2.499	-0.008
67	A	64	GLU	-1	-0.832	-0.905	2.310	-0.479	1.867	7.679	-3.613	-6.412	-0.002
68	A	65	SER	0	0.010	-0.009	2.635	-3.623	-3.365	1.115	1.512	-2.885	-0.006
69	A	66	THR	0	-0.012	0.008	4.457	-0.303	-0.103	0.000	-0.020	-0.180	0.000
70	A	67	VAL	0	-0.020	-0.018	6.944	-0.048	-0.048	0.000	0.000	0.000	0.000
71	A	68	ASP	-1	-0.935	-0.964	9.294	0.202	0.202	0.000	0.000	0.000	0.000
72	A	69	GLY	0	0.008	0.007	13.072	0.008	0.008	0.000	0.000	0.000	0.000
73	A	70	ASP	-1	-0.857	-0.920	13.945	-0.118	-0.118	0.000	0.000	0.000	0.000
74	A	71	LYS	1	0.875	0.935	13.199	-0.107	-0.107	0.000	0.000	0.000	0.000
75	A	72	ALA	0	0.039	0.029	7.659	-0.033	-0.033	0.000	0.000	0.000	0.000
76	A	73	LEU	0	-0.017	0.002	8.484	0.023	0.023	0.000	0.000	0.000	0.000
77	A	74	VAL	0	0.024	0.010	4.466	-0.177	0.070	0.000	-0.030	-0.216	0.000
78	A	75	ARG	1	0.848	0.934	6.630	-2.023	-2.023	0.000	0.000	0.000	0.000
79	A	76	ALA	0	0.023	0.001	6.256	0.656	0.656	0.000	0.000	0.000	0.000
80	A	77	LYS	1	0.810	0.899	7.538	-0.049	-0.049	0.000	0.000	0.000	0.000
81	A	78	VAL	0	0.037	0.012	9.629	-0.131	-0.131	0.000	0.000	0.000	0.000
82	A	79	SER	0	0.018	0.003	12.321	0.025	0.025	0.000	0.000	0.000	0.000
83	A	80	GLY	0	0.009	-0.017	14.594	-0.034	-0.034	0.000	0.000	0.000	0.000
84	A	81	ARG	1	0.811	0.923	17.939	0.034	0.034	0.000	0.000	0.000	0.000
85	A	82	PHE	0	0.038	0.012	16.340	-0.007	-0.007	0.000	0.000	0.000	0.000
86	A	83	PRO	0	-0.015	-0.017	21.859	0.006	0.006	0.000	0.000	0.000	0.000
87	A	84	GLY	0	0.014	-0.001	21.814	0.010	0.010	0.000	0.000	0.000	0.000
88	A	85	SER	0	-0.010	0.057	17.785	0.025	0.025	0.000	0.000	0.000	0.000
89	A	86	PRO	0	-0.048	-0.029	14.033	-0.015	-0.015	0.000	0.000	0.000	0.000
90	A	87	VAL	0	0.035	-0.001	14.800	0.027	0.027	0.000	0.000	0.000	0.000
91	A	88	THR	0	-0.047	-0.021	10.162	0.027	0.027	0.000	0.000	0.000	0.000
92	A	89	LEU	0	-0.011	-0.001	11.400	-0.023	-0.023	0.000	0.000	0.000	0.000
93	A	90	THR	0	0.009	0.001	10.831	0.221	0.221	0.000	0.000	0.000	0.000
94	A	91	TYR	0	0.042	0.015	9.078	-0.125	-0.125	0.000	0.000	0.000	0.000
95	A	92	SER	0	-0.010	-0.008	10.086	0.027	0.027	0.000	0.000	0.000	0.000
96	A	93	PHE	0	0.024	0.007	8.082	-0.048	-0.048	0.000	0.000	0.000	0.000
97	A	94	THR	0	-0.072	-0.049	12.557	0.008	0.008	0.000	0.000	0.000	0.000
98	A	95	ILE	0	0.038	0.029	11.838	-0.004	-0.004	0.000	0.000	0.000	0.000
99	A	96	LYS	1	0.853	0.912	15.419	0.082	0.082	0.000	0.000	0.000	0.000
100	A	97	ASP	-1	-0.898	-0.959	19.005	-0.121	-0.121	0.000	0.000	0.000	0.000
101	A	98	GLY	0	-0.020	-0.005	16.162	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	99	ARG	1	0.924	0.983	16.693	0.165	0.165	0.000	0.000	0.000	0.000
103	A	100	ILE	0	0.028	0.017	12.354	0.007	0.007	0.000	0.000	0.000	0.000
104	A	101	ALA	0	-0.020	-0.017	16.187	0.016	0.016	0.000	0.000	0.000	0.000
105	A	102	ARG	1	0.887	0.919	17.149	-0.042	-0.042	0.000	0.000	0.000	0.000
106	A	103	LEU	0	-0.021	0.005	12.269	-0.018	-0.018	0.000	0.000	0.000	0.000
107	A	104	GLU	-1	-0.900	-0.937	15.288	0.151	0.151	0.000	0.000	0.000	0.000
108	A	105	ILE	0	0.007	0.007	13.549	0.040	0.040	0.000	0.000	0.000	0.000
109	A	106	GLN	0	-0.023	-0.004	15.162	0.065	0.065	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-2:PHE)