FMO DATABASE

FMODB ID: N15KQ

Calculation Name: 4DFC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4DFC

Chain ID: A

ChEMBL ID:

UniProt ID: P30958

Base Structure: X-ray

Registration Date: 2023-06-20

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	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	85
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-608015.282159
FMO2-HF: Nuclear repulsion	573432.68269
FMO2-HF: Total energy	-34582.599469
FMO2-MP2: Total energy	-34682.997997

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:129:VAL)

Summations of interaction energy for fragment #1(A:129:VAL)

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.
-9.881	-4.311	10.774	-6.841	-9.501	-0.043

Interaction energy analysis for fragmet #1(A:129:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.025 / q_NPA : -0.020

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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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	131	LYS	1	0.905	0.950	2.413	-1.567	2.058	0.581	-1.569	-2.636	0.005
4	A	132	LYS	1	0.983	0.996	5.170	0.365	0.392	-0.001	-0.004	-0.022	0.000
5	A	133	GLY	0	-0.004	0.010	8.956	-0.019	-0.019	0.000	0.000	0.000	0.000
6	A	134	GLN	0	-0.016	0.013	4.809	-0.272	-0.272	0.000	0.000	0.000	0.000
7	A	135	ARG	1	0.905	0.946	9.089	0.120	0.120	0.000	0.000	0.000	0.000
8	A	136	LEU	0	-0.041	-0.034	7.630	-0.029	-0.029	0.000	0.000	0.000	0.000
9	A	137	SER	0	0.015	0.024	11.110	0.010	0.010	0.000	0.000	0.000	0.000
10	A	138	ARG	1	0.928	0.960	12.263	-0.119	-0.119	0.000	0.000	0.000	0.000
11	A	139	ASP	-1	-0.907	-0.965	14.048	0.306	0.306	0.000	0.000	0.000	0.000
12	A	140	ALA	0	-0.036	-0.010	11.835	0.019	0.019	0.000	0.000	0.000	0.000
13	A	141	LEU	0	0.043	0.019	7.925	0.080	0.080	0.000	0.000	0.000	0.000
14	A	142	ARG	1	0.954	0.981	10.968	-0.205	-0.205	0.000	0.000	0.000	0.000
15	A	143	THR	0	0.048	0.036	14.218	0.021	0.021	0.000	0.000	0.000	0.000
16	A	144	GLN	0	-0.006	0.001	7.078	0.009	0.009	0.000	0.000	0.000	0.000
17	A	145	LEU	0	-0.024	-0.026	9.280	0.052	0.052	0.000	0.000	0.000	0.000
18	A	146	ASP	-1	-0.819	-0.880	12.238	0.352	0.352	0.000	0.000	0.000	0.000
19	A	147	SER	0	-0.068	-0.036	14.478	-0.061	-0.061	0.000	0.000	0.000	0.000
20	A	148	ALA	0	-0.088	-0.035	11.164	-0.034	-0.034	0.000	0.000	0.000	0.000
21	A	149	GLY	0	-0.027	-0.009	13.153	-0.007	-0.007	0.000	0.000	0.000	0.000
22	A	150	TYR	0	-0.031	-0.014	9.644	0.012	0.012	0.000	0.000	0.000	0.000
23	A	151	ARG	1	0.963	0.976	15.309	-0.307	-0.307	0.000	0.000	0.000	0.000
24	A	152	HIS	0	-0.034	-0.005	17.544	0.013	0.013	0.000	0.000	0.000	0.000
25	A	153	VAL	0	0.001	-0.003	18.961	-0.028	-0.028	0.000	0.000	0.000	0.000
26	A	154	ASP	-1	-0.926	-0.966	20.728	0.139	0.139	0.000	0.000	0.000	0.000
27	A	155	GLN	0	-0.054	-0.039	21.462	-0.013	-0.013	0.000	0.000	0.000	0.000
28	A	156	VAL	0	-0.043	-0.014	15.531	0.007	0.007	0.000	0.000	0.000	0.000
29	A	157	MET	0	-0.001	0.006	18.780	-0.026	-0.026	0.000	0.000	0.000	0.000
30	A	158	GLU	-1	-0.939	-0.968	18.688	0.162	0.162	0.000	0.000	0.000	0.000
31	A	159	HIS	0	-0.082	-0.042	15.131	0.023	0.023	0.000	0.000	0.000	0.000
32	A	160	GLY	0	0.021	0.014	13.841	-0.013	-0.013	0.000	0.000	0.000	0.000
33	A	161	GLU	-1	-0.862	-0.930	14.838	0.216	0.216	0.000	0.000	0.000	0.000
34	A	162	TYR	0	-0.085	-0.080	13.378	0.046	0.046	0.000	0.000	0.000	0.000
35	A	163	ALA	0	0.047	0.033	15.164	-0.041	-0.041	0.000	0.000	0.000	0.000
36	A	164	THR	0	-0.064	-0.048	16.585	0.009	0.009	0.000	0.000	0.000	0.000
37	A	165	ARG	1	0.874	0.930	18.773	-0.147	-0.147	0.000	0.000	0.000	0.000
38	A	166	GLY	0	0.016	0.011	20.352	-0.011	-0.011	0.000	0.000	0.000	0.000
39	A	167	ALA	0	0.033	0.006	18.888	0.024	0.024	0.000	0.000	0.000	0.000
40	A	168	LEU	0	0.006	0.017	16.391	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	169	LEU	0	-0.038	-0.020	11.183	0.019	0.019	0.000	0.000	0.000	0.000
42	A	170	ASP	-1	-0.749	-0.841	12.995	0.141	0.141	0.000	0.000	0.000	0.000
43	A	171	LEU	0	0.033	-0.005	7.828	0.070	0.070	0.000	0.000	0.000	0.000
44	A	172	PHE	0	0.034	0.027	11.461	-0.049	-0.049	0.000	0.000	0.000	0.000
45	A	173	PRO	0	-0.031	-0.009	7.677	0.050	0.050	0.000	0.000	0.000	0.000
46	A	174	MET	0	0.028	0.001	9.775	-0.204	-0.204	0.000	0.000	0.000	0.000
47	A	175	GLY	0	-0.040	-0.016	10.857	0.062	0.062	0.000	0.000	0.000	0.000
48	A	176	SER	0	-0.066	-0.026	9.447	-0.105	-0.105	0.000	0.000	0.000	0.000
49	A	177	GLU	-1	-0.874	-0.950	11.491	-0.038	-0.038	0.000	0.000	0.000	0.000
50	A	178	LEU	0	-0.022	-0.009	11.961	0.015	0.015	0.000	0.000	0.000	0.000
51	A	179	PRO	0	-0.014	0.019	11.744	0.038	0.038	0.000	0.000	0.000	0.000
52	A	180	TYR	0	0.022	-0.022	9.026	-0.122	-0.122	0.000	0.000	0.000	0.000
53	A	181	ARG	1	0.809	0.897	11.488	0.008	0.008	0.000	0.000	0.000	0.000
54	A	182	LEU	0	-0.053	-0.023	7.981	-0.056	-0.056	0.000	0.000	0.000	0.000
55	A	183	ASP	-1	-0.934	-0.963	12.318	0.039	0.039	0.000	0.000	0.000	0.000
56	A	184	PHE	0	-0.029	-0.027	10.865	-0.017	-0.017	0.000	0.000	0.000	0.000
57	A	185	PHE	0	0.045	0.019	15.932	0.011	0.011	0.000	0.000	0.000	0.000
58	A	186	ASP	-1	-0.990	-0.988	17.480	0.011	0.011	0.000	0.000	0.000	0.000
59	A	187	ASP	-1	-0.868	-0.948	15.160	0.006	0.006	0.000	0.000	0.000	0.000
60	A	188	GLU	-1	-0.925	-0.967	12.698	-0.149	-0.149	0.000	0.000	0.000	0.000
61	A	189	ILE	0	-0.066	-0.017	8.069	0.034	0.034	0.000	0.000	0.000	0.000
62	A	190	ASP	-1	-0.895	-0.953	11.972	-0.159	-0.159	0.000	0.000	0.000	0.000
63	A	191	SER	0	-0.029	-0.035	12.762	-0.022	-0.022	0.000	0.000	0.000	0.000
64	A	192	LEU	0	-0.005	0.008	6.998	0.058	0.058	0.000	0.000	0.000	0.000
65	A	193	ARG	1	0.954	0.981	10.854	0.056	0.056	0.000	0.000	0.000	0.000
66	A	194	VAL	0	0.065	0.061	12.075	0.048	0.048	0.000	0.000	0.000	0.000
67	A	195	PHE	0	-0.063	-0.030	14.052	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	196	ASP	-1	-0.805	-0.890	17.005	0.047	0.047	0.000	0.000	0.000	0.000
69	A	197	VAL	0	0.010	-0.006	18.341	0.005	0.005	0.000	0.000	0.000	0.000
70	A	198	ASP	-1	-0.854	-0.913	20.483	0.066	0.066	0.000	0.000	0.000	0.000
71	A	199	SER	0	-0.138	-0.079	23.578	-0.004	-0.004	0.000	0.000	0.000	0.000
72	A	200	GLN	0	-0.008	-0.005	20.402	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	201	ARG	1	0.887	0.940	21.701	-0.012	-0.012	0.000	0.000	0.000	0.000
74	A	202	THR	0	-0.073	-0.066	18.284	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	203	LEU	0	-0.025	0.006	17.192	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	204	GLU	-1	-0.899	-0.952	14.743	-0.142	-0.142	0.000	0.000	0.000	0.000
77	A	205	GLU	-1	-0.944	-0.996	12.801	-0.211	-0.211	0.000	0.000	0.000	0.000
78	A	206	VAL	0	-0.020	-0.005	8.549	-0.016	-0.016	0.000	0.000	0.000	0.000
79	A	207	GLU	-1	-0.875	-0.953	8.498	-0.419	-0.419	0.000	0.000	0.000	0.000
80	A	208	ALA	0	-0.074	-0.048	3.384	-0.249	-0.050	0.018	-0.050	-0.167	0.000
81	A	209	ILE	0	0.053	0.049	3.540	-0.279	0.249	0.004	-0.168	-0.364	0.000
82	A	210	ASN	0	-0.017	-0.016	1.895	-7.800	-6.332	9.994	-6.364	-5.098	-0.049
83	A	211	LEU	0	0.045	0.003	2.893	1.396	0.943	0.179	1.339	-1.064	0.001
84	A	212	LEU	0	-0.006	0.012	4.358	-1.166	-0.990	-0.001	-0.025	-0.150	0.000
85	A	213	PRO	0	-0.010	0.007	6.545	0.084	0.084	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:129:VAL)