FMO DATABASE

FMODB ID: JLVM9

Calculation Name: 4DS1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4DS1

Chain ID: A

ChEMBL ID:

UniProt ID: Q02647

Base Structure: X-ray

Registration Date: 2023-06-22

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	86
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-604653.991736
FMO2-HF: Nuclear repulsion	571535.814767
FMO2-HF: Total energy	-33118.17697
FMO2-MP2: Total energy	-33218.227425

3D Structure Molmil

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:7:SER)

Summations of interaction energy for fragment #1(A:7:SER)

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.
-1.842	0.858	0.146	-1.148	-1.7	0

Interaction energy analysis for fragmet #1(A:7:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.007 / q_NPA : -0.009

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	9	PRO	0	0.006	0.002	3.800	-2.557	-1.111	-0.008	-0.617	-0.821	0.002
4	A	10	ILE	0	-0.018	0.001	5.258	0.656	0.656	0.000	0.000	0.000	0.000
5	A	11	VAL	0	0.009	-0.007	7.745	-0.050	-0.050	0.000	0.000	0.000	0.000
6	A	12	LYS	1	0.888	0.958	9.558	0.822	0.822	0.000	0.000	0.000	0.000
7	A	13	ALA	0	0.024	0.009	13.402	0.066	0.066	0.000	0.000	0.000	0.000
8	A	14	SER	0	-0.023	-0.020	16.289	-0.034	-0.034	0.000	0.000	0.000	0.000
9	A	15	ASP	-1	-0.845	-0.913	18.435	-0.100	-0.100	0.000	0.000	0.000	0.000
10	A	16	ILE	0	-0.049	-0.013	17.640	-0.002	-0.002	0.000	0.000	0.000	0.000
11	A	17	THR	0	0.035	0.016	21.113	0.009	0.009	0.000	0.000	0.000	0.000
12	A	18	ASP	-1	-0.761	-0.895	18.060	-0.033	-0.033	0.000	0.000	0.000	0.000
13	A	19	LYS	1	0.961	0.982	17.706	-0.030	-0.030	0.000	0.000	0.000	0.000
14	A	20	LEU	0	-0.008	0.005	18.465	0.002	0.002	0.000	0.000	0.000	0.000
15	A	21	LYS	1	0.851	0.919	14.157	0.047	0.047	0.000	0.000	0.000	0.000
16	A	22	GLU	-1	-0.831	-0.915	12.924	-0.039	-0.039	0.000	0.000	0.000	0.000
17	A	23	ASP	-1	-0.790	-0.836	13.503	-0.035	-0.035	0.000	0.000	0.000	0.000
18	A	24	ILE	0	0.020	0.008	13.496	-0.021	-0.021	0.000	0.000	0.000	0.000
19	A	25	LEU	0	-0.022	0.006	9.140	-0.108	-0.108	0.000	0.000	0.000	0.000
20	A	26	THR	0	-0.033	-0.028	9.848	-0.059	-0.059	0.000	0.000	0.000	0.000
21	A	27	ILE	0	-0.016	-0.013	11.169	-0.005	-0.005	0.000	0.000	0.000	0.000
22	A	28	SER	0	-0.019	-0.031	10.139	-0.011	-0.011	0.000	0.000	0.000	0.000
23	A	29	LYS	1	0.927	0.956	4.410	-1.338	-1.253	-0.001	-0.008	-0.076	0.000
24	A	30	ASP	-1	-0.794	-0.863	7.928	-0.013	-0.013	0.000	0.000	0.000	0.000
25	A	31	ALA	0	-0.008	-0.007	10.723	0.006	0.006	0.000	0.000	0.000	0.000
26	A	32	LEU	0	-0.039	-0.036	6.020	-0.034	-0.034	0.000	0.000	0.000	0.000
27	A	33	ASP	-1	-0.926	-0.939	8.325	0.046	0.046	0.000	0.000	0.000	0.000
28	A	34	LYS	1	0.750	0.856	10.500	0.081	0.081	0.000	0.000	0.000	0.000
29	A	35	TYR	0	-0.045	-0.022	13.277	0.037	0.037	0.000	0.000	0.000	0.000
30	A	36	GLN	0	0.048	0.021	13.261	-0.066	-0.066	0.000	0.000	0.000	0.000
31	A	37	LEU	0	-0.036	-0.009	14.836	-0.040	-0.040	0.000	0.000	0.000	0.000
32	A	38	GLU	-1	-0.807	-0.910	13.152	-0.596	-0.596	0.000	0.000	0.000	0.000
33	A	39	ARG	1	0.873	0.909	15.203	0.218	0.218	0.000	0.000	0.000	0.000
34	A	40	ASP	-1	-0.818	-0.886	17.733	-0.209	-0.209	0.000	0.000	0.000	0.000
35	A	41	ILE	0	0.029	0.026	11.085	0.023	0.023	0.000	0.000	0.000	0.000
36	A	42	ALA	0	0.008	-0.004	14.867	0.014	0.014	0.000	0.000	0.000	0.000
37	A	43	GLY	0	-0.016	-0.013	16.641	0.032	0.032	0.000	0.000	0.000	0.000
38	A	44	THR	0	-0.008	-0.005	15.791	0.034	0.034	0.000	0.000	0.000	0.000
39	A	45	VAL	0	0.045	0.028	13.732	0.030	0.030	0.000	0.000	0.000	0.000
40	A	46	LYS	1	0.784	0.860	17.045	0.185	0.185	0.000	0.000	0.000	0.000
41	A	47	LYS	1	0.943	0.963	20.240	0.163	0.163	0.000	0.000	0.000	0.000
42	A	48	GLN	0	0.013	0.007	16.461	0.039	0.039	0.000	0.000	0.000	0.000
43	A	49	LEU	0	-0.012	-0.004	17.433	0.020	0.020	0.000	0.000	0.000	0.000
44	A	50	ASP	-1	-0.754	-0.868	21.449	-0.118	-0.118	0.000	0.000	0.000	0.000
45	A	51	VAL	0	-0.049	-0.014	24.329	0.012	0.012	0.000	0.000	0.000	0.000
46	A	52	LYS	1	0.815	0.909	19.022	0.032	0.032	0.000	0.000	0.000	0.000
47	A	53	TYR	0	-0.105	-0.100	19.957	0.017	0.017	0.000	0.000	0.000	0.000
48	A	54	GLY	0	0.032	0.039	25.457	0.003	0.003	0.000	0.000	0.000	0.000
49	A	55	ASN	0	-0.027	-0.007	26.384	-0.007	-0.007	0.000	0.000	0.000	0.000
50	A	56	THR	0	-0.034	-0.048	26.888	0.010	0.010	0.000	0.000	0.000	0.000
51	A	57	TRP	0	0.009	-0.001	19.928	-0.015	-0.015	0.000	0.000	0.000	0.000
52	A	58	HIS	0	-0.017	-0.008	21.875	0.001	0.001	0.000	0.000	0.000	0.000
53	A	59	VAL	0	-0.013	-0.010	15.820	-0.013	-0.013	0.000	0.000	0.000	0.000
54	A	60	ILE	0	-0.017	0.003	17.117	0.021	0.021	0.000	0.000	0.000	0.000
55	A	61	VAL	0	0.010	0.005	11.561	-0.041	-0.041	0.000	0.000	0.000	0.000
56	A	62	GLY	0	0.048	0.028	13.079	0.060	0.060	0.000	0.000	0.000	0.000
57	A	63	LYS	1	0.900	0.927	11.106	0.627	0.627	0.000	0.000	0.000	0.000
58	A	64	ASN	0	-0.064	-0.033	13.629	0.036	0.036	0.000	0.000	0.000	0.000
59	A	65	PHE	0	0.028	0.023	14.756	0.038	0.038	0.000	0.000	0.000	0.000
60	A	66	GLY	0	0.038	0.036	18.570	-0.023	-0.023	0.000	0.000	0.000	0.000
61	A	67	SER	0	-0.035	-0.037	20.878	0.018	0.018	0.000	0.000	0.000	0.000
62	A	68	TYR	0	0.028	0.021	22.539	0.000	0.000	0.000	0.000	0.000	0.000
63	A	69	VAL	0	-0.012	0.006	22.314	0.008	0.008	0.000	0.000	0.000	0.000
64	A	70	THR	0	0.013	0.006	25.461	0.009	0.009	0.000	0.000	0.000	0.000
65	A	71	HIS	1	0.834	0.916	23.872	0.158	0.158	0.000	0.000	0.000	0.000
66	A	72	GLU	-1	-0.825	-0.906	26.029	-0.086	-0.086	0.000	0.000	0.000	0.000
67	A	73	LYS	1	1.004	1.001	25.789	0.058	0.058	0.000	0.000	0.000	0.000
68	A	74	GLY	0	-0.027	-0.011	24.258	0.009	0.009	0.000	0.000	0.000	0.000
69	A	75	HIS	1	0.839	0.914	22.133	0.105	0.105	0.000	0.000	0.000	0.000
70	A	76	PHE	0	0.035	0.003	19.094	-0.010	-0.010	0.000	0.000	0.000	0.000
71	A	77	VAL	0	0.012	0.008	14.101	0.015	0.015	0.000	0.000	0.000	0.000
72	A	78	TYR	0	0.029	0.017	14.518	-0.019	-0.019	0.000	0.000	0.000	0.000
73	A	79	PHE	0	0.012	0.002	8.493	0.057	0.057	0.000	0.000	0.000	0.000
74	A	80	TYR	0	0.015	0.011	6.712	0.138	0.138	0.000	0.000	0.000	0.000
75	A	81	ILE	0	0.016	0.017	3.170	-0.632	-0.298	0.077	-0.148	-0.264	-0.001
76	A	82	GLY	0	0.023	0.014	3.192	-0.249	0.530	0.074	-0.329	-0.524	-0.001
77	A	83	PRO	0	-0.011	-0.017	4.015	0.380	0.436	0.004	-0.046	-0.015	0.000
78	A	84	LEU	0	-0.038	-0.004	6.780	0.336	0.336	0.000	0.000	0.000	0.000
79	A	85	ALA	0	0.012	0.014	8.180	-0.206	-0.206	0.000	0.000	0.000	0.000
80	A	86	PHE	0	0.053	0.004	7.784	0.110	0.110	0.000	0.000	0.000	0.000
81	A	87	LEU	0	-0.020	-0.005	12.315	0.024	0.024	0.000	0.000	0.000	0.000
82	A	88	VAL	0	0.008	0.006	14.648	0.027	0.027	0.000	0.000	0.000	0.000
83	A	89	PHE	0	0.009	-0.013	17.351	0.017	0.017	0.000	0.000	0.000	0.000
84	A	90	LYS	1	0.849	0.933	20.942	0.101	0.101	0.000	0.000	0.000	0.000
85	A	91	THR	0	0.030	0.027	24.229	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	92	ALA	0	0.050	0.046	27.818	0.001	0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:SER)