FMO DATABASE

FMODB ID: G61V1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-830708.551813
FMO2-HF: Nuclear repulsion	788862.359992
FMO2-HF: Total energy	-41846.19182
FMO2-MP2: Total energy	-41968.437177

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.
-27.441	-10.481	15.247	-10.271	-21.935	-0.038

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 : 0.002 / q_NPA : 0.005

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	0.038	0.003	3.361	-3.406	0.761	0.635	-1.921	-2.881	0.006
4	A	1	MET	0	-0.076	-0.029	4.337	-0.545	-0.239	0.000	-0.010	-0.296	0.000
5	A	2	ASP	-1	-0.859	-0.921	2.352	-9.817	-6.115	4.099	-3.570	-4.231	-0.036
6	A	3	LEU	0	-0.078	-0.033	2.381	-1.433	-0.147	1.425	-0.465	-2.246	0.003
7	A	4	PRO	0	0.017	0.002	4.682	0.327	0.371	-0.001	-0.009	-0.034	0.000
8	A	5	ASP	-1	-0.861	-0.925	8.346	-0.589	-0.589	0.000	0.000	0.000	0.000
9	A	6	ILE	0	-0.034	-0.015	10.204	0.010	0.010	0.000	0.000	0.000	0.000
10	A	7	VAL	0	-0.015	-0.013	6.220	0.079	0.079	0.000	0.000	0.000	0.000
11	A	8	ASN	0	-0.022	-0.023	5.106	-0.215	-0.162	-0.001	-0.002	-0.049	0.000
12	A	9	MET	0	0.034	0.023	6.877	0.091	0.091	0.000	0.000	0.000	0.000
13	A	10	TYR	0	-0.027	-0.030	8.991	0.070	0.070	0.000	0.000	0.000	0.000
14	A	11	PHE	0	0.003	-0.013	5.729	0.132	0.132	0.000	0.000	0.000	0.000
15	A	12	ASP	-1	-0.841	-0.903	8.448	-0.570	-0.570	0.000	0.000	0.000	0.000
16	A	13	ALA	0	0.033	0.016	10.294	0.042	0.042	0.000	0.000	0.000	0.000
17	A	14	ASP	-1	-0.764	-0.847	11.297	-0.033	-0.033	0.000	0.000	0.000	0.000
18	A	15	SER	0	-0.035	-0.026	10.140	0.022	0.022	0.000	0.000	0.000	0.000
19	A	16	CYS	0	-0.081	-0.039	12.294	0.006	0.006	0.000	0.000	0.000	0.000
20	A	17	ASN	0	-0.084	-0.044	15.268	0.034	0.034	0.000	0.000	0.000	0.000
21	A	18	ASP	-1	-0.850	-0.915	16.372	-0.177	-0.177	0.000	0.000	0.000	0.000
22	A	19	THR	0	0.016	-0.025	17.770	0.001	0.001	0.000	0.000	0.000	0.000
23	A	20	ASP	-1	-0.926	-0.940	20.382	-0.112	-0.112	0.000	0.000	0.000	0.000
24	A	21	ALA	0	0.068	0.043	16.035	0.003	0.003	0.000	0.000	0.000	0.000
25	A	22	LEU	0	-0.015	0.008	14.328	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	23	SER	0	-0.100	-0.076	16.734	0.013	0.013	0.000	0.000	0.000	0.000
27	A	24	GLU	-1	-0.933	-0.958	18.403	-0.164	-0.164	0.000	0.000	0.000	0.000
28	A	25	THR	0	0.004	-0.015	12.905	-0.019	-0.019	0.000	0.000	0.000	0.000
29	A	26	PHE	0	-0.026	-0.017	15.343	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	27	ALA	0	0.036	0.024	18.370	-0.005	-0.005	0.000	0.000	0.000	0.000
31	A	28	PRO	0	-0.011	-0.028	21.501	0.009	0.009	0.000	0.000	0.000	0.000
32	A	29	ASP	-1	-0.915	-0.967	24.636	-0.040	-0.040	0.000	0.000	0.000	0.000
33	A	30	ALA	0	-0.002	0.022	19.777	0.011	0.011	0.000	0.000	0.000	0.000
34	A	31	VAL	0	-0.049	-0.039	20.689	0.007	0.007	0.000	0.000	0.000	0.000
35	A	32	VAL	0	0.034	0.019	17.186	-0.005	-0.005	0.000	0.000	0.000	0.000
36	A	33	GLU	-1	-0.996	-1.010	18.736	0.116	0.116	0.000	0.000	0.000	0.000
37	A	34	ASP	-1	-0.734	-0.880	17.945	0.137	0.137	0.000	0.000	0.000	0.000
38	A	35	GLU	-1	-0.988	-0.989	19.639	0.071	0.071	0.000	0.000	0.000	0.000
39	A	36	GLY	0	-0.016	0.015	21.948	-0.005	-0.005	0.000	0.000	0.000	0.000
40	A	37	ALA	0	-0.048	-0.021	23.394	-0.012	-0.012	0.000	0.000	0.000	0.000
41	A	38	ARG	1	0.886	0.932	23.053	-0.028	-0.028	0.000	0.000	0.000	0.000
42	A	39	HIS	0	-0.002	-0.001	21.416	-0.018	-0.018	0.000	0.000	0.000	0.000
43	A	40	GLN	0	-0.017	-0.012	23.107	0.009	0.009	0.000	0.000	0.000	0.000
44	A	41	GLY	0	0.031	0.031	24.246	0.000	0.000	0.000	0.000	0.000	0.000
45	A	42	VAL	0	0.051	0.021	21.570	0.006	0.006	0.000	0.000	0.000	0.000
46	A	43	VAL	0	0.014	0.006	23.396	0.000	0.000	0.000	0.000	0.000	0.000
47	A	44	ALA	0	-0.065	-0.034	24.957	0.003	0.003	0.000	0.000	0.000	0.000
48	A	45	ILE	0	0.026	0.030	18.786	0.006	0.006	0.000	0.000	0.000	0.000
49	A	46	LEU	0	0.036	0.015	20.806	0.002	0.002	0.000	0.000	0.000	0.000
50	A	47	ARG	1	0.882	0.940	22.251	0.013	0.013	0.000	0.000	0.000	0.000
51	A	48	TRP	0	-0.015	-0.013	15.139	-0.012	-0.012	0.000	0.000	0.000	0.000
52	A	49	TRP	0	-0.009	0.011	15.335	0.007	0.007	0.000	0.000	0.000	0.000
53	A	50	VAL	0	0.008	-0.007	19.528	0.000	0.000	0.000	0.000	0.000	0.000
54	A	51	ALA	0	-0.025	-0.016	22.297	0.001	0.001	0.000	0.000	0.000	0.000
55	A	52	ALA	0	0.090	0.047	19.075	0.002	0.002	0.000	0.000	0.000	0.000
56	A	53	LYS	1	0.811	0.923	14.724	0.099	0.099	0.000	0.000	0.000	0.000
57	A	54	LYS	1	0.873	0.930	20.529	0.042	0.042	0.000	0.000	0.000	0.000
58	A	55	ALA	0	0.008	0.007	23.055	0.001	0.001	0.000	0.000	0.000	0.000
59	A	56	ALA	0	0.024	0.000	19.804	0.001	0.001	0.000	0.000	0.000	0.000
60	A	57	SER	0	-0.095	-0.035	19.773	0.001	0.001	0.000	0.000	0.000	0.000
61	A	58	TYR	0	-0.060	-0.042	13.265	-0.005	-0.005	0.000	0.000	0.000	0.000
62	A	59	VAL	0	0.034	0.019	10.367	-0.027	-0.027	0.000	0.000	0.000	0.000
63	A	60	ALA	0	0.019	-0.004	9.870	0.056	0.056	0.000	0.000	0.000	0.000
64	A	61	GLU	-1	-0.797	-0.877	5.387	-0.345	-0.345	0.000	0.000	0.000	0.000
65	A	62	PRO	0	-0.024	-0.018	2.256	-0.689	-0.131	2.202	-0.731	-2.029	0.006
66	A	63	LEU	0	-0.038	-0.007	2.677	-3.963	-1.912	1.223	-1.142	-2.132	-0.008
67	A	64	GLU	-1	-0.824	-0.901	2.284	-0.995	2.168	4.588	-2.781	-4.970	-0.003
68	A	65	SER	0	-0.003	-0.007	2.683	-3.945	-2.819	1.077	0.431	-2.633	-0.006
69	A	66	THR	0	-0.022	0.001	4.531	-0.475	-0.269	-0.001	-0.018	-0.187	0.000
70	A	67	VAL	0	-0.011	-0.019	6.882	-0.067	-0.067	0.000	0.000	0.000	0.000
71	A	68	ASP	-1	-0.920	-0.957	9.456	0.173	0.173	0.000	0.000	0.000	0.000
72	A	69	GLY	0	0.024	0.015	13.287	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	70	ASP	-1	-0.845	-0.902	14.363	-0.096	-0.096	0.000	0.000	0.000	0.000
74	A	71	LYS	1	0.798	0.887	13.069	-0.105	-0.105	0.000	0.000	0.000	0.000
75	A	72	ALA	0	0.040	0.024	7.510	-0.050	-0.050	0.000	0.000	0.000	0.000
76	A	73	LEU	0	-0.043	-0.015	8.559	0.033	0.033	0.000	0.000	0.000	0.000
77	A	74	VAL	0	0.024	0.006	4.315	-0.228	0.070	0.001	-0.053	-0.247	0.000
78	A	75	ARG	1	0.840	0.922	6.740	-1.840	-1.840	0.000	0.000	0.000	0.000
79	A	76	ALA	0	0.050	0.015	6.249	0.719	0.719	0.000	0.000	0.000	0.000
80	A	77	LYS	1	0.814	0.893	7.478	-0.066	-0.066	0.000	0.000	0.000	0.000
81	A	78	VAL	0	0.031	0.022	9.565	-0.128	-0.128	0.000	0.000	0.000	0.000
82	A	79	SER	0	0.016	-0.012	12.228	0.021	0.021	0.000	0.000	0.000	0.000
83	A	80	GLY	0	0.006	-0.006	14.543	-0.033	-0.033	0.000	0.000	0.000	0.000
84	A	81	ARG	1	0.791	0.907	17.830	0.020	0.020	0.000	0.000	0.000	0.000
85	A	82	PHE	0	0.030	0.012	16.050	-0.006	-0.006	0.000	0.000	0.000	0.000
86	A	83	PRO	0	-0.009	-0.020	21.615	0.005	0.005	0.000	0.000	0.000	0.000
87	A	84	GLY	0	0.016	0.010	21.475	0.010	0.010	0.000	0.000	0.000	0.000
88	A	85	SER	0	0.012	0.050	17.538	0.026	0.026	0.000	0.000	0.000	0.000
89	A	86	PRO	0	-0.082	-0.044	13.869	-0.017	-0.017	0.000	0.000	0.000	0.000
90	A	87	VAL	0	0.036	0.003	14.518	0.023	0.023	0.000	0.000	0.000	0.000
91	A	88	THR	0	-0.036	-0.020	9.842	0.023	0.023	0.000	0.000	0.000	0.000
92	A	89	LEU	0	-0.021	-0.003	11.378	-0.018	-0.018	0.000	0.000	0.000	0.000
93	A	90	THR	0	0.009	-0.005	10.679	0.205	0.205	0.000	0.000	0.000	0.000
94	A	91	TYR	0	0.042	0.024	9.000	-0.134	-0.134	0.000	0.000	0.000	0.000
95	A	92	SER	0	0.021	-0.010	10.104	0.029	0.029	0.000	0.000	0.000	0.000
96	A	93	PHE	0	0.013	0.012	8.027	-0.063	-0.063	0.000	0.000	0.000	0.000
97	A	94	THR	0	-0.011	0.000	12.360	0.027	0.027	0.000	0.000	0.000	0.000
98	A	95	ILE	0	-0.012	0.003	12.057	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	96	LYS	1	0.810	0.887	15.499	0.077	0.077	0.000	0.000	0.000	0.000
100	A	97	ASP	-1	-0.903	-0.957	18.836	-0.112	-0.112	0.000	0.000	0.000	0.000
101	A	98	GLY	0	0.003	0.014	16.659	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	99	ARG	1	0.847	0.928	16.768	0.146	0.146	0.000	0.000	0.000	0.000
103	A	100	ILE	0	0.025	0.014	12.333	0.009	0.009	0.000	0.000	0.000	0.000
104	A	101	ALA	0	0.011	0.000	16.176	0.012	0.012	0.000	0.000	0.000	0.000
105	A	102	ARG	1	0.843	0.896	17.308	-0.062	-0.062	0.000	0.000	0.000	0.000
106	A	103	LEU	0	0.006	0.012	11.994	-0.009	-0.009	0.000	0.000	0.000	0.000
107	A	104	GLU	-1	-0.851	-0.920	14.728	0.162	0.162	0.000	0.000	0.000	0.000
108	A	105	ILE	0	-0.016	0.010	13.592	0.040	0.040	0.000	0.000	0.000	0.000
109	A	106	GLN	0	-0.024	-0.005	14.866	0.064	0.064	0.000	0.000	0.000	0.000

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