FMO DATABASE

FMODB ID: 3QYLL

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:

Apendix: None

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	85
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-610921.682541
FMO2-HF: Nuclear repulsion	576338.13582
FMO2-HF: Total energy	-34583.546722
FMO2-MP2: Total energy	-34683.953581

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.
-13.653	-5.24	6.282	-6.037	-8.654	-0.034

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 : -0.028 / q_NPA : -0.014

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	131	LYS	1	0.907	0.944	2.195	-2.973	-0.204	1.456	-1.447	-2.779	0.009
4	A	132	LYS	1	0.852	0.902	5.293	0.231	0.264	-0.001	-0.003	-0.029	0.000
5	A	133	GLY	0	0.013	0.015	8.943	-0.004	-0.004	0.000	0.000	0.000	0.000
6	A	134	GLN	0	-0.018	0.000	5.021	-0.332	-0.332	0.000	0.000	0.000	0.000
7	A	135	ARG	1	0.779	0.855	9.177	-0.022	-0.022	0.000	0.000	0.000	0.000
8	A	136	LEU	0	-0.034	-0.028	7.658	0.020	0.020	0.000	0.000	0.000	0.000
9	A	137	SER	0	0.005	0.010	11.126	-0.014	-0.014	0.000	0.000	0.000	0.000
10	A	138	ARG	1	0.922	0.950	12.646	-0.161	-0.161	0.000	0.000	0.000	0.000
11	A	139	ASP	-1	-0.871	-0.943	14.066	0.330	0.330	0.000	0.000	0.000	0.000
12	A	140	ALA	0	-0.011	0.001	12.332	0.012	0.012	0.000	0.000	0.000	0.000
13	A	141	LEU	0	0.029	0.017	8.080	0.080	0.080	0.000	0.000	0.000	0.000
14	A	142	ARG	1	0.854	0.924	11.153	-0.237	-0.237	0.000	0.000	0.000	0.000
15	A	143	THR	0	0.046	0.022	14.506	0.028	0.028	0.000	0.000	0.000	0.000
16	A	144	GLN	0	-0.039	-0.001	6.892	0.058	0.058	0.000	0.000	0.000	0.000
17	A	145	LEU	0	-0.017	-0.011	9.425	0.036	0.036	0.000	0.000	0.000	0.000
18	A	146	ASP	-1	-0.811	-0.885	12.376	0.310	0.310	0.000	0.000	0.000	0.000
19	A	147	SER	0	-0.084	-0.057	14.300	-0.064	-0.064	0.000	0.000	0.000	0.000
20	A	148	ALA	0	-0.073	-0.027	11.420	-0.036	-0.036	0.000	0.000	0.000	0.000
21	A	149	GLY	0	-0.034	-0.011	13.397	-0.017	-0.017	0.000	0.000	0.000	0.000
22	A	150	TYR	0	-0.038	-0.013	9.380	-0.017	-0.017	0.000	0.000	0.000	0.000
23	A	151	ARG	1	0.786	0.854	15.452	-0.198	-0.198	0.000	0.000	0.000	0.000
24	A	152	HIS	0	0.036	0.029	17.928	0.021	0.021	0.000	0.000	0.000	0.000
25	A	153	VAL	0	-0.042	-0.017	19.196	-0.027	-0.027	0.000	0.000	0.000	0.000
26	A	154	ASP	-1	-0.876	-0.950	20.931	0.129	0.129	0.000	0.000	0.000	0.000
27	A	155	GLN	0	-0.052	-0.030	21.305	-0.009	-0.009	0.000	0.000	0.000	0.000
28	A	156	VAL	0	-0.013	0.013	15.511	0.001	0.001	0.000	0.000	0.000	0.000
29	A	157	MET	0	-0.004	0.002	18.864	-0.021	-0.021	0.000	0.000	0.000	0.000
30	A	158	GLU	-1	-0.849	-0.905	18.708	0.105	0.105	0.000	0.000	0.000	0.000
31	A	159	HIS	0	-0.047	-0.027	14.922	0.017	0.017	0.000	0.000	0.000	0.000
32	A	160	GLY	0	0.044	0.005	14.200	-0.011	-0.011	0.000	0.000	0.000	0.000
33	A	161	GLU	-1	-0.820	-0.886	15.104	0.170	0.170	0.000	0.000	0.000	0.000
34	A	162	TYR	0	-0.046	-0.079	13.736	0.056	0.056	0.000	0.000	0.000	0.000
35	A	163	ALA	0	0.028	0.032	15.378	-0.039	-0.039	0.000	0.000	0.000	0.000
36	A	164	THR	0	-0.028	-0.025	16.493	0.023	0.023	0.000	0.000	0.000	0.000
37	A	165	ARG	1	0.793	0.864	18.672	-0.161	-0.161	0.000	0.000	0.000	0.000
38	A	166	GLY	0	0.017	0.019	20.704	-0.011	-0.011	0.000	0.000	0.000	0.000
39	A	167	ALA	0	0.038	0.027	19.137	0.023	0.023	0.000	0.000	0.000	0.000
40	A	168	LEU	0	0.018	0.012	16.430	0.014	0.014	0.000	0.000	0.000	0.000
41	A	169	LEU	0	-0.052	-0.031	11.402	0.016	0.016	0.000	0.000	0.000	0.000
42	A	170	ASP	-1	-0.769	-0.811	13.451	0.139	0.139	0.000	0.000	0.000	0.000
43	A	171	LEU	0	0.022	-0.010	8.116	0.078	0.078	0.000	0.000	0.000	0.000
44	A	172	PHE	0	0.046	0.031	11.862	-0.060	-0.060	0.000	0.000	0.000	0.000
45	A	173	PRO	0	-0.017	-0.008	7.614	0.035	0.035	0.000	0.000	0.000	0.000
46	A	174	MET	0	0.016	0.015	9.897	-0.186	-0.186	0.000	0.000	0.000	0.000
47	A	175	GLY	0	-0.016	-0.008	11.180	-0.015	-0.015	0.000	0.000	0.000	0.000
48	A	176	SER	0	-0.052	-0.023	9.719	-0.107	-0.107	0.000	0.000	0.000	0.000
49	A	177	GLU	-1	-0.902	-0.967	11.652	-0.149	-0.149	0.000	0.000	0.000	0.000
50	A	178	LEU	0	-0.039	-0.011	11.887	0.019	0.019	0.000	0.000	0.000	0.000
51	A	179	PRO	0	-0.001	0.033	12.078	0.023	0.023	0.000	0.000	0.000	0.000
52	A	180	TYR	0	0.013	-0.022	8.458	-0.118	-0.118	0.000	0.000	0.000	0.000
53	A	181	ARG	1	0.759	0.839	11.603	-0.011	-0.011	0.000	0.000	0.000	0.000
54	A	182	LEU	0	-0.024	-0.011	7.636	-0.046	-0.046	0.000	0.000	0.000	0.000
55	A	183	ASP	-1	-0.880	-0.951	12.176	0.103	0.103	0.000	0.000	0.000	0.000
56	A	184	PHE	0	-0.040	-0.031	10.871	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	185	PHE	0	-0.004	0.004	15.870	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	186	ASP	-1	-0.919	-0.965	17.616	0.100	0.100	0.000	0.000	0.000	0.000
59	A	187	ASP	-1	-0.840	-0.903	15.791	0.126	0.126	0.000	0.000	0.000	0.000
60	A	188	GLU	-1	-0.884	-0.937	13.032	0.039	0.039	0.000	0.000	0.000	0.000
61	A	189	ILE	0	-0.026	-0.004	8.325	0.004	0.004	0.000	0.000	0.000	0.000
62	A	190	ASP	-1	-0.846	-0.890	11.744	-0.071	-0.071	0.000	0.000	0.000	0.000
63	A	191	SER	0	-0.046	-0.048	12.180	-0.035	-0.035	0.000	0.000	0.000	0.000
64	A	192	LEU	0	-0.012	0.014	6.540	0.048	0.048	0.000	0.000	0.000	0.000
65	A	193	ARG	1	0.833	0.900	11.021	0.009	0.009	0.000	0.000	0.000	0.000
66	A	194	VAL	0	0.079	0.056	12.627	0.042	0.042	0.000	0.000	0.000	0.000
67	A	195	PHE	0	-0.071	-0.046	14.269	0.011	0.011	0.000	0.000	0.000	0.000
68	A	196	ASP	-1	-0.760	-0.837	17.257	0.020	0.020	0.000	0.000	0.000	0.000
69	A	197	VAL	0	0.002	0.003	18.572	0.010	0.010	0.000	0.000	0.000	0.000
70	A	198	ASP	-1	-0.888	-0.938	20.833	0.043	0.043	0.000	0.000	0.000	0.000
71	A	199	SER	0	-0.152	-0.118	24.087	0.000	0.000	0.000	0.000	0.000	0.000
72	A	200	GLN	0	-0.010	-0.016	20.475	0.006	0.006	0.000	0.000	0.000	0.000
73	A	201	ARG	1	0.913	0.973	21.439	-0.004	-0.004	0.000	0.000	0.000	0.000
74	A	202	THR	0	-0.013	-0.010	17.669	0.003	0.003	0.000	0.000	0.000	0.000
75	A	203	LEU	0	-0.044	-0.023	17.550	0.000	0.000	0.000	0.000	0.000	0.000
76	A	204	GLU	-1	-0.899	-0.952	14.614	-0.119	-0.119	0.000	0.000	0.000	0.000
77	A	205	GLU	-1	-0.819	-0.898	12.925	-0.101	-0.101	0.000	0.000	0.000	0.000
78	A	206	VAL	0	0.000	-0.002	8.538	-0.017	-0.017	0.000	0.000	0.000	0.000
79	A	207	GLU	-1	-0.912	-0.957	8.393	-0.336	-0.336	0.000	0.000	0.000	0.000
80	A	208	ALA	0	-0.048	-0.038	3.335	-0.172	0.040	0.024	-0.057	-0.178	0.000
81	A	209	ILE	0	0.028	0.036	3.815	-0.130	0.214	0.000	-0.093	-0.250	0.000
82	A	210	ASN	0	-0.020	-0.026	2.232	-9.363	-5.225	4.692	-4.329	-4.500	-0.046
83	A	211	LEU	0	0.035	0.009	3.274	0.346	1.125	0.112	-0.099	-0.791	0.003
84	A	212	LEU	0	-0.013	0.006	4.603	-1.313	-1.175	-0.001	-0.009	-0.127	0.000
85	A	213	PRO	0	-0.003	0.006	7.009	0.176	0.176	0.000	0.000	0.000	0.000

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