FMO DATABASE

FMODB ID: R5J78

Calculation Name: 5DTC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5DTC

Chain ID: A

ChEMBL ID:

UniProt ID: Q12024

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	87
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-615924.549464
FMO2-HF: Nuclear repulsion	581437.933079
FMO2-HF: Total energy	-34486.616385
FMO2-MP2: Total energy	-34589.302554

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:5:LYS)

Summations of interaction energy for fragment #1(A:5:LYS)

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.
-22.716	-18.559	0.911	-2.181	-2.884	-0.012

Interaction energy analysis for fragmet #1(A:5:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.002 / q_NPA : 0.981

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	7	GLN	0	-0.009	-0.005	3.103	3.132	5.405	-0.024	-0.976	-1.273	0.000
4	A	8	VAL	0	0.040	0.025	4.554	-4.466	-4.345	-0.001	-0.015	-0.104	0.000
5	A	9	LYS	1	0.940	0.987	7.288	21.139	21.139	0.000	0.000	0.000	0.000
6	A	10	ILE	0	-0.005	0.001	10.269	-0.220	-0.220	0.000	0.000	0.000	0.000
7	A	11	ARG	1	0.980	0.989	13.535	15.222	15.222	0.000	0.000	0.000	0.000
8	A	12	PHE	0	0.025	0.013	17.130	-0.234	-0.234	0.000	0.000	0.000	0.000
9	A	13	PHE	0	0.024	0.022	20.031	0.420	0.420	0.000	0.000	0.000	0.000
10	A	14	THR	0	0.038	0.010	23.458	-0.010	-0.010	0.000	0.000	0.000	0.000
11	A	15	ARG	1	0.942	0.972	26.377	9.819	9.819	0.000	0.000	0.000	0.000
12	A	16	GLU	-1	-0.823	-0.908	29.386	-8.820	-8.820	0.000	0.000	0.000	0.000
13	A	17	LYS	1	0.941	0.961	31.408	7.716	7.716	0.000	0.000	0.000	0.000
14	A	18	ASP	-1	-0.908	-0.946	33.608	-8.135	-8.135	0.000	0.000	0.000	0.000
15	A	19	GLU	-1	-0.864	-0.928	32.648	-8.289	-8.289	0.000	0.000	0.000	0.000
16	A	20	LEU	0	-0.017	-0.009	32.103	-0.187	-0.187	0.000	0.000	0.000	0.000
17	A	21	LEU	0	-0.049	-0.024	29.481	-0.221	-0.221	0.000	0.000	0.000	0.000
18	A	22	HIS	0	-0.037	0.001	27.946	-0.434	-0.434	0.000	0.000	0.000	0.000
19	A	23	VAL	0	0.009	0.016	22.539	0.077	0.077	0.000	0.000	0.000	0.000
20	A	24	GLN	0	-0.014	-0.025	23.508	-0.050	-0.050	0.000	0.000	0.000	0.000
21	A	25	ASP	-1	-0.901	-0.956	22.223	-12.398	-12.398	0.000	0.000	0.000	0.000
22	A	26	THR	0	-0.054	-0.012	18.411	-0.510	-0.510	0.000	0.000	0.000	0.000
23	A	27	PRO	0	-0.054	-0.024	14.651	-0.388	-0.388	0.000	0.000	0.000	0.000
24	A	28	MET	0	0.015	0.012	13.862	0.462	0.462	0.000	0.000	0.000	0.000
25	A	29	TYR	0	-0.017	-0.017	7.302	-0.303	-0.303	0.000	0.000	0.000	0.000
26	A	30	ALA	0	0.032	0.024	9.596	1.202	1.202	0.000	0.000	0.000	0.000
27	A	31	PRO	0	0.040	0.012	8.005	-2.217	-2.217	0.000	0.000	0.000	0.000
28	A	32	ILE	0	0.028	0.007	4.282	1.732	1.922	-0.001	-0.040	-0.148	0.000
29	A	33	SER	0	-0.016	-0.008	8.238	0.955	0.955	0.000	0.000	0.000	0.000
30	A	34	LEU	0	-0.020	0.007	10.546	1.529	1.529	0.000	0.000	0.000	0.000
31	A	35	LYS	1	1.007	0.984	13.590	15.370	15.370	0.000	0.000	0.000	0.000
32	A	36	ARG	1	0.948	0.988	16.504	11.828	11.828	0.000	0.000	0.000	0.000
33	A	37	TYR	0	-0.014	-0.011	19.872	0.282	0.282	0.000	0.000	0.000	0.000
34	A	38	GLY	0	0.075	0.042	17.287	0.253	0.253	0.000	0.000	0.000	0.000
35	A	39	LEU	0	0.000	-0.001	14.693	0.041	0.041	0.000	0.000	0.000	0.000
36	A	40	SER	0	0.029	0.008	18.303	0.397	0.397	0.000	0.000	0.000	0.000
37	A	41	GLU	-1	-0.954	-0.965	20.117	-12.288	-12.288	0.000	0.000	0.000	0.000
38	A	42	ILE	0	-0.016	-0.012	15.174	0.164	0.164	0.000	0.000	0.000	0.000
39	A	43	VAL	0	0.010	0.005	19.654	0.274	0.274	0.000	0.000	0.000	0.000
40	A	44	ASN	0	-0.005	-0.014	22.210	0.748	0.748	0.000	0.000	0.000	0.000
41	A	45	HIS	0	-0.008	0.015	21.777	0.439	0.439	0.000	0.000	0.000	0.000
42	A	46	LEU	0	-0.063	-0.040	19.634	0.220	0.220	0.000	0.000	0.000	0.000
43	A	47	LEU	0	-0.046	-0.011	23.823	0.207	0.207	0.000	0.000	0.000	0.000
44	A	48	GLY	0	-0.026	0.011	26.805	0.327	0.327	0.000	0.000	0.000	0.000
45	A	49	SER	0	-0.059	-0.048	28.334	0.316	0.316	0.000	0.000	0.000	0.000
46	A	50	GLU	-1	-0.928	-0.949	30.242	-7.936	-7.936	0.000	0.000	0.000	0.000
47	A	51	LYS	1	0.908	0.944	32.621	7.798	7.798	0.000	0.000	0.000	0.000
48	A	52	PRO	0	-0.004	0.005	27.922	-0.049	-0.049	0.000	0.000	0.000	0.000
49	A	53	VAL	0	0.016	0.001	28.745	0.246	0.246	0.000	0.000	0.000	0.000
50	A	54	PRO	0	-0.038	-0.007	27.298	-0.395	-0.395	0.000	0.000	0.000	0.000
51	A	55	PHE	0	0.057	0.023	24.003	0.191	0.191	0.000	0.000	0.000	0.000
52	A	56	ASP	-1	-0.852	-0.938	23.614	-11.579	-11.579	0.000	0.000	0.000	0.000
53	A	57	PHE	0	0.008	-0.011	19.344	-0.043	-0.043	0.000	0.000	0.000	0.000
54	A	58	LEU	0	-0.026	-0.007	20.926	-0.082	-0.082	0.000	0.000	0.000	0.000
55	A	59	ILE	0	-0.016	-0.006	14.706	-0.310	-0.310	0.000	0.000	0.000	0.000
56	A	60	GLU	-1	-0.907	-0.957	18.620	-14.364	-14.364	0.000	0.000	0.000	0.000
57	A	61	GLY	0	0.016	0.016	21.237	0.288	0.288	0.000	0.000	0.000	0.000
58	A	62	GLU	-1	-0.906	-0.941	20.158	-14.058	-14.058	0.000	0.000	0.000	0.000
59	A	63	LEU	0	-0.023	-0.014	20.828	-0.393	-0.393	0.000	0.000	0.000	0.000
60	A	64	LEU	0	-0.008	-0.009	15.220	-0.363	-0.363	0.000	0.000	0.000	0.000
61	A	65	ARG	1	0.930	0.962	19.295	12.372	12.372	0.000	0.000	0.000	0.000
62	A	66	THR	0	-0.052	-0.034	15.762	0.373	0.373	0.000	0.000	0.000	0.000
63	A	67	SER	0	-0.013	0.004	11.905	-0.203	-0.203	0.000	0.000	0.000	0.000
64	A	68	LEU	0	0.049	0.022	10.396	-0.004	-0.004	0.000	0.000	0.000	0.000
65	A	69	HIS	0	0.035	0.005	6.769	-2.065	-2.065	0.000	0.000	0.000	0.000
66	A	70	ASP	-1	-0.860	-0.932	9.115	-21.390	-21.390	0.000	0.000	0.000	0.000
67	A	71	TYR	0	-0.016	-0.004	12.201	0.571	0.571	0.000	0.000	0.000	0.000
68	A	72	LEU	0	-0.006	-0.019	6.836	0.397	0.397	0.000	0.000	0.000	0.000
69	A	73	THR	0	-0.001	0.003	9.407	-1.195	-1.195	0.000	0.000	0.000	0.000
70	A	74	LYS	1	0.884	0.951	10.987	16.768	16.768	0.000	0.000	0.000	0.000
71	A	75	LYS	1	0.826	0.905	13.722	17.067	17.067	0.000	0.000	0.000	0.000
72	A	76	GLY	0	0.005	0.024	11.367	0.563	0.563	0.000	0.000	0.000	0.000
73	A	77	LEU	0	-0.036	-0.012	10.357	-0.351	-0.351	0.000	0.000	0.000	0.000
74	A	78	SER	0	0.050	0.022	5.244	-1.174	-1.174	0.000	0.000	0.000	0.000
75	A	79	SER	0	-0.003	-0.018	2.628	-1.841	-0.329	0.938	-1.148	-1.302	-0.012
76	A	80	GLU	-1	-0.966	-0.987	5.036	-39.084	-39.023	-0.001	-0.002	-0.057	0.000
77	A	81	ALA	0	-0.041	-0.003	6.942	3.340	3.340	0.000	0.000	0.000	0.000
78	A	82	SER	0	-0.039	-0.031	9.409	0.035	0.035	0.000	0.000	0.000	0.000
79	A	83	LEU	0	-0.037	-0.021	10.694	0.801	0.801	0.000	0.000	0.000	0.000
80	A	84	ASN	0	0.021	-0.001	13.803	0.375	0.375	0.000	0.000	0.000	0.000
81	A	85	VAL	0	-0.041	-0.021	15.292	0.006	0.006	0.000	0.000	0.000	0.000
82	A	86	GLU	-1	-0.879	-0.936	18.256	-10.966	-10.966	0.000	0.000	0.000	0.000
83	A	87	TYR	0	-0.067	-0.074	21.567	-0.479	-0.479	0.000	0.000	0.000	0.000
84	A	88	THR	0	0.006	0.009	23.577	0.450	0.450	0.000	0.000	0.000	0.000
85	A	89	ARG	1	0.890	0.947	26.751	8.428	8.428	0.000	0.000	0.000	0.000
86	A	90	ALA	0	-0.038	-0.027	27.773	-0.034	-0.034	0.000	0.000	0.000	0.000
87	A	91	ILE	0	-0.066	-0.028	27.584	0.472	0.472	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:LYS)