FMO DATABASE

FMODB ID: J3JN9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-608860.551019
FMO2-HF: Nuclear repulsion	574277.243328
FMO2-HF: Total energy	-34583.307691
FMO2-MP2: Total energy	-34683.698827

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.
-10.692	-5.094	10.734	-6.744	-9.588	-0.044

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 : -0.038 / q_NPA : -0.025

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	0.912	0.962	2.267	-2.812	0.268	1.573	-1.706	-2.947	0.005
4	A	132	LYS	1	0.868	0.908	5.272	0.208	0.237	-0.001	-0.003	-0.024	0.000
5	A	133	GLY	0	0.010	0.011	9.055	-0.002	-0.002	0.000	0.000	0.000	0.000
6	A	134	GLN	0	-0.022	0.002	5.175	-0.346	-0.358	-0.001	-0.016	0.029	0.000
7	A	135	ARG	1	0.807	0.878	9.178	-0.003	-0.003	0.000	0.000	0.000	0.000
8	A	136	LEU	0	-0.030	-0.031	7.698	0.007	0.007	0.000	0.000	0.000	0.000
9	A	137	SER	0	0.009	0.014	11.210	-0.016	-0.016	0.000	0.000	0.000	0.000
10	A	138	ARG	1	0.915	0.950	12.378	-0.157	-0.157	0.000	0.000	0.000	0.000
11	A	139	ASP	-1	-0.891	-0.958	14.168	0.319	0.319	0.000	0.000	0.000	0.000
12	A	140	ALA	0	-0.029	-0.011	12.007	0.012	0.012	0.000	0.000	0.000	0.000
13	A	141	LEU	0	0.040	0.018	8.012	0.069	0.069	0.000	0.000	0.000	0.000
14	A	142	ARG	1	0.878	0.937	11.079	-0.237	-0.237	0.000	0.000	0.000	0.000
15	A	143	THR	0	0.046	0.028	14.285	0.014	0.014	0.000	0.000	0.000	0.000
16	A	144	GLN	0	-0.027	-0.006	7.013	0.052	0.052	0.000	0.000	0.000	0.000
17	A	145	LEU	0	-0.014	-0.018	9.097	0.030	0.030	0.000	0.000	0.000	0.000
18	A	146	ASP	-1	-0.805	-0.876	12.238	0.314	0.314	0.000	0.000	0.000	0.000
19	A	147	SER	0	-0.075	-0.037	14.350	-0.063	-0.063	0.000	0.000	0.000	0.000
20	A	148	ALA	0	-0.092	-0.041	11.105	-0.038	-0.038	0.000	0.000	0.000	0.000
21	A	149	GLY	0	-0.025	-0.005	13.060	-0.020	-0.020	0.000	0.000	0.000	0.000
22	A	150	TYR	0	-0.036	-0.014	9.389	-0.017	-0.017	0.000	0.000	0.000	0.000
23	A	151	ARG	1	0.805	0.878	15.309	-0.221	-0.221	0.000	0.000	0.000	0.000
24	A	152	HIS	0	0.012	0.015	17.537	0.017	0.017	0.000	0.000	0.000	0.000
25	A	153	VAL	0	-0.018	-0.009	18.887	-0.026	-0.026	0.000	0.000	0.000	0.000
26	A	154	ASP	-1	-0.912	-0.962	20.727	0.130	0.130	0.000	0.000	0.000	0.000
27	A	155	GLN	0	-0.036	-0.031	21.452	-0.009	-0.009	0.000	0.000	0.000	0.000
28	A	156	VAL	0	-0.026	-0.004	15.453	0.004	0.004	0.000	0.000	0.000	0.000
29	A	157	MET	0	0.007	0.017	18.779	-0.022	-0.022	0.000	0.000	0.000	0.000
30	A	158	GLU	-1	-0.851	-0.911	18.740	0.125	0.125	0.000	0.000	0.000	0.000
31	A	159	HIS	0	-0.057	-0.038	15.087	0.013	0.013	0.000	0.000	0.000	0.000
32	A	160	GLY	0	0.053	0.019	13.832	-0.008	-0.008	0.000	0.000	0.000	0.000
33	A	161	GLU	-1	-0.835	-0.905	14.826	0.182	0.182	0.000	0.000	0.000	0.000
34	A	162	TYR	0	-0.069	-0.085	13.412	0.045	0.045	0.000	0.000	0.000	0.000
35	A	163	ALA	0	0.027	0.029	15.161	-0.037	-0.037	0.000	0.000	0.000	0.000
36	A	164	THR	0	-0.040	-0.027	16.588	0.018	0.018	0.000	0.000	0.000	0.000
37	A	165	ARG	1	0.852	0.917	18.777	-0.155	-0.155	0.000	0.000	0.000	0.000
38	A	166	GLY	0	0.025	0.021	20.362	-0.008	-0.008	0.000	0.000	0.000	0.000
39	A	167	ALA	0	0.027	0.012	19.000	0.025	0.025	0.000	0.000	0.000	0.000
40	A	168	LEU	0	0.013	0.024	16.389	0.006	0.006	0.000	0.000	0.000	0.000
41	A	169	LEU	0	-0.048	-0.028	11.406	0.015	0.015	0.000	0.000	0.000	0.000
42	A	170	ASP	-1	-0.765	-0.819	13.003	0.148	0.148	0.000	0.000	0.000	0.000
43	A	171	LEU	0	0.044	-0.003	7.892	0.067	0.067	0.000	0.000	0.000	0.000
44	A	172	PHE	0	0.027	0.026	11.463	-0.053	-0.053	0.000	0.000	0.000	0.000
45	A	173	PRO	0	-0.018	-0.007	7.571	0.033	0.033	0.000	0.000	0.000	0.000
46	A	174	MET	0	0.033	0.019	9.765	-0.173	-0.173	0.000	0.000	0.000	0.000
47	A	175	GLY	0	-0.026	-0.017	10.842	0.019	0.019	0.000	0.000	0.000	0.000
48	A	176	SER	0	-0.065	-0.027	9.510	-0.104	-0.104	0.000	0.000	0.000	0.000
49	A	177	GLU	-1	-0.894	-0.961	11.484	-0.122	-0.122	0.000	0.000	0.000	0.000
50	A	178	LEU	0	-0.025	-0.009	11.748	0.027	0.027	0.000	0.000	0.000	0.000
51	A	179	PRO	0	-0.014	0.022	11.746	0.017	0.017	0.000	0.000	0.000	0.000
52	A	180	TYR	0	0.028	-0.017	8.429	-0.109	-0.109	0.000	0.000	0.000	0.000
53	A	181	ARG	1	0.780	0.848	11.497	-0.011	-0.011	0.000	0.000	0.000	0.000
54	A	182	LEU	0	-0.047	-0.014	7.791	-0.044	-0.044	0.000	0.000	0.000	0.000
55	A	183	ASP	-1	-0.910	-0.957	12.332	0.084	0.084	0.000	0.000	0.000	0.000
56	A	184	PHE	0	-0.038	-0.031	10.745	-0.006	-0.006	0.000	0.000	0.000	0.000
57	A	185	PHE	0	0.021	0.015	15.948	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	186	ASP	-1	-0.963	-0.988	17.599	0.081	0.081	0.000	0.000	0.000	0.000
59	A	187	ASP	-1	-0.843	-0.916	15.374	0.104	0.104	0.000	0.000	0.000	0.000
60	A	188	GLU	-1	-0.877	-0.932	13.076	0.008	0.008	0.000	0.000	0.000	0.000
61	A	189	ILE	0	-0.058	-0.013	8.348	0.014	0.014	0.000	0.000	0.000	0.000
62	A	190	ASP	-1	-0.905	-0.945	12.097	-0.070	-0.070	0.000	0.000	0.000	0.000
63	A	191	SER	0	0.016	-0.008	12.815	-0.029	-0.029	0.000	0.000	0.000	0.000
64	A	192	LEU	0	-0.002	0.014	6.556	0.048	0.048	0.000	0.000	0.000	0.000
65	A	193	ARG	1	0.881	0.934	10.977	0.012	0.012	0.000	0.000	0.000	0.000
66	A	194	VAL	0	0.078	0.059	12.321	0.040	0.040	0.000	0.000	0.000	0.000
67	A	195	PHE	0	-0.045	-0.023	14.157	0.003	0.003	0.000	0.000	0.000	0.000
68	A	196	ASP	-1	-0.764	-0.840	17.012	0.026	0.026	0.000	0.000	0.000	0.000
69	A	197	VAL	0	0.010	0.003	18.204	0.008	0.008	0.000	0.000	0.000	0.000
70	A	198	ASP	-1	-0.884	-0.924	20.486	0.047	0.047	0.000	0.000	0.000	0.000
71	A	199	SER	0	-0.156	-0.120	23.631	0.001	0.001	0.000	0.000	0.000	0.000
72	A	200	GLN	0	-0.028	-0.028	20.443	0.007	0.007	0.000	0.000	0.000	0.000
73	A	201	ARG	1	0.906	0.964	21.710	-0.010	-0.010	0.000	0.000	0.000	0.000
74	A	202	THR	0	-0.048	-0.031	18.103	0.002	0.002	0.000	0.000	0.000	0.000
75	A	203	LEU	0	-0.031	-0.021	17.329	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	204	GLU	-1	-0.919	-0.962	14.954	-0.117	-0.117	0.000	0.000	0.000	0.000
77	A	205	GLU	-1	-0.830	-0.912	12.838	-0.113	-0.113	0.000	0.000	0.000	0.000
78	A	206	VAL	0	0.003	0.002	8.541	-0.022	-0.022	0.000	0.000	0.000	0.000
79	A	207	GLU	-1	-0.902	-0.956	8.546	-0.303	-0.303	0.000	0.000	0.000	0.000
80	A	208	ALA	0	-0.056	-0.048	3.455	-0.151	0.031	0.013	-0.048	-0.147	0.000
81	A	209	ILE	0	0.042	0.046	3.665	-0.277	0.143	0.002	-0.119	-0.303	0.000
82	A	210	ASN	0	-0.014	-0.014	1.917	-7.661	-5.525	8.978	-6.130	-4.985	-0.048
83	A	211	LEU	0	0.034	0.002	2.889	1.597	1.165	0.171	1.311	-1.050	-0.001
84	A	212	LEU	0	-0.016	0.008	4.259	-1.284	-1.089	-0.001	-0.033	-0.161	0.000
85	A	213	PRO	0	0.000	0.008	6.356	0.171	0.171	0.000	0.000	0.000	0.000

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