FMO DATABASE

FMODB ID: 76MQK

Calculation Name: 5DYM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5DYM

Chain ID: A

ChEMBL ID:

UniProt ID: C9YK90

Base Structure: X-ray

Registration Date: 2023-09-22

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

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	97
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-739684.4544
FMO2-HF: Nuclear repulsion	698873.292531
FMO2-HF: Total energy	-40811.161869
FMO2-MP2: Total energy	-40929.714156

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:10:GLY)

Summations of interaction energy for fragment #1(A:10:GLY)

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.
-1.344	1.233	0.367	-0.908	-2.036	0.003

Interaction energy analysis for fragmet #1(A:10:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.032 / q_NPA : 0.007

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

Sort

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	12	ILE	0	-0.009	-0.008	2.637	-2.507	-0.376	0.370	-0.851	-1.650	0.003
4	A	13	ASP	-1	-0.768	-0.898	4.267	-1.619	-1.302	-0.001	-0.034	-0.282	0.000
5	A	14	ILE	0	0.024	0.009	6.290	0.300	0.300	0.000	0.000	0.000	0.000
6	A	15	LEU	0	-0.021	-0.006	7.157	0.094	0.094	0.000	0.000	0.000	0.000
7	A	16	ILE	0	0.007	-0.002	8.213	0.008	0.008	0.000	0.000	0.000	0.000
8	A	17	VAL	0	0.005	-0.005	10.422	0.035	0.035	0.000	0.000	0.000	0.000
9	A	18	SER	0	-0.040	-0.014	12.113	0.033	0.033	0.000	0.000	0.000	0.000
10	A	19	ILE	0	-0.056	-0.024	11.798	0.014	0.014	0.000	0.000	0.000	0.000
11	A	20	LEU	0	-0.038	-0.025	14.170	0.002	0.002	0.000	0.000	0.000	0.000
12	A	21	GLU	-1	-0.904	-0.942	16.683	-0.040	-0.040	0.000	0.000	0.000	0.000
13	A	22	LYS	1	0.898	0.944	18.693	0.009	0.009	0.000	0.000	0.000	0.000
14	A	23	LYS	1	0.844	0.900	20.297	0.004	0.004	0.000	0.000	0.000	0.000
15	A	24	ASP	-1	-0.730	-0.817	19.601	-0.064	-0.064	0.000	0.000	0.000	0.000
16	A	25	CYS	0	-0.053	-0.015	16.944	0.021	0.021	0.000	0.000	0.000	0.000
17	A	26	TYR	0	0.046	0.022	18.073	-0.017	-0.017	0.000	0.000	0.000	0.000
18	A	27	GLY	0	0.037	0.000	14.933	0.011	0.011	0.000	0.000	0.000	0.000
19	A	28	TYR	0	0.012	0.006	15.142	0.019	0.019	0.000	0.000	0.000	0.000
20	A	29	GLU	-1	-0.797	-0.896	17.095	0.032	0.032	0.000	0.000	0.000	0.000
21	A	30	ILE	0	0.005	0.002	11.545	0.019	0.019	0.000	0.000	0.000	0.000
22	A	31	ALA	0	0.030	-0.006	12.271	0.045	0.045	0.000	0.000	0.000	0.000
23	A	32	LYS	1	0.903	0.964	13.336	-0.046	-0.046	0.000	0.000	0.000	0.000
24	A	33	GLN	0	0.034	0.013	14.816	0.024	0.024	0.000	0.000	0.000	0.000
25	A	34	VAL	0	-0.024	-0.015	8.836	0.031	0.031	0.000	0.000	0.000	0.000
26	A	35	ARG	1	0.936	0.971	12.104	-0.150	-0.150	0.000	0.000	0.000	0.000
27	A	36	GLU	-1	-0.908	-0.951	14.193	0.146	0.146	0.000	0.000	0.000	0.000
28	A	37	ARG	1	0.884	0.950	14.992	-0.172	-0.172	0.000	0.000	0.000	0.000
29	A	38	SER	0	-0.079	-0.032	11.191	0.095	0.095	0.000	0.000	0.000	0.000
30	A	39	GLU	-1	-0.825	-0.910	12.229	0.332	0.332	0.000	0.000	0.000	0.000
31	A	40	PHE	0	-0.102	-0.044	5.042	0.223	0.271	-0.001	-0.004	-0.043	0.000
32	A	41	GLU	-1	-0.898	-0.951	9.903	0.198	0.198	0.000	0.000	0.000	0.000
33	A	42	LEU	0	-0.053	-0.038	6.952	-0.088	-0.088	0.000	0.000	0.000	0.000
34	A	43	LYS	1	0.986	1.020	8.803	-0.143	-0.143	0.000	0.000	0.000	0.000
35	A	44	GLU	-1	-0.859	-0.955	9.623	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	45	GLY	0	-0.049	-0.041	11.402	-0.039	-0.039	0.000	0.000	0.000	0.000
37	A	46	THR	0	0.039	0.016	5.013	-0.051	-0.051	0.000	0.000	0.000	0.000
38	A	47	MET	0	0.003	0.019	7.086	-0.144	-0.144	0.000	0.000	0.000	0.000
39	A	48	TYR	0	0.007	-0.003	8.832	-0.076	-0.076	0.000	0.000	0.000	0.000
40	A	49	LEU	0	-0.002	-0.001	8.317	-0.029	-0.029	0.000	0.000	0.000	0.000
41	A	50	ALA	0	-0.026	-0.013	5.776	-0.060	-0.060	0.000	0.000	0.000	0.000
42	A	51	LEU	0	0.018	0.009	7.566	-0.013	-0.013	0.000	0.000	0.000	0.000
43	A	52	LYS	1	0.935	0.980	11.020	0.175	0.175	0.000	0.000	0.000	0.000
44	A	53	ARG	1	0.862	0.933	4.322	1.055	1.136	-0.001	-0.019	-0.061	0.000
45	A	54	MET	0	-0.010	-0.006	8.419	0.001	0.001	0.000	0.000	0.000	0.000
46	A	55	GLU	-1	-0.803	-0.895	10.812	-0.122	-0.122	0.000	0.000	0.000	0.000
47	A	56	SER	0	-0.064	-0.026	12.873	0.029	0.029	0.000	0.000	0.000	0.000
48	A	57	LYS	1	0.929	0.971	7.745	0.695	0.695	0.000	0.000	0.000	0.000
49	A	58	ASN	0	0.040	0.035	13.823	0.000	0.000	0.000	0.000	0.000	0.000
50	A	59	LEU	0	0.043	0.046	10.296	0.008	0.008	0.000	0.000	0.000	0.000
51	A	60	ILE	0	-0.050	-0.027	12.375	0.031	0.031	0.000	0.000	0.000	0.000
52	A	61	LYS	1	0.982	0.988	15.646	0.097	0.097	0.000	0.000	0.000	0.000
53	A	62	SER	0	-0.060	-0.045	18.179	0.019	0.019	0.000	0.000	0.000	0.000
54	A	63	TYR	0	-0.099	-0.079	19.858	0.005	0.005	0.000	0.000	0.000	0.000
55	A	64	TYR	0	0.024	-0.001	22.372	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	65	SER	0	0.029	0.033	25.324	0.000	0.000	0.000	0.000	0.000	0.000
57	A	66	ASN	0	0.050	0.012	27.470	0.001	0.001	0.000	0.000	0.000	0.000
58	A	67	GLU	-1	-0.915	-0.950	30.657	-0.017	-0.017	0.000	0.000	0.000	0.000
59	A	68	GLN	0	0.007	0.002	31.830	0.001	0.001	0.000	0.000	0.000	0.000
60	A	69	SER	0	-0.076	-0.045	30.020	0.002	0.002	0.000	0.000	0.000	0.000
61	A	70	SER	0	0.044	0.010	30.677	0.001	0.001	0.000	0.000	0.000	0.000
62	A	71	GLY	0	-0.029	-0.011	27.547	0.003	0.003	0.000	0.000	0.000	0.000
63	A	72	GLY	0	0.053	0.040	27.687	0.000	0.000	0.000	0.000	0.000	0.000
64	A	73	ARG	1	0.934	0.968	26.054	0.029	0.029	0.000	0.000	0.000	0.000
65	A	74	ARG	1	0.907	0.961	22.431	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	75	LYS	1	0.881	0.945	17.419	0.112	0.112	0.000	0.000	0.000	0.000
67	A	76	TYR	0	-0.016	-0.011	19.415	0.005	0.005	0.000	0.000	0.000	0.000
68	A	77	TYR	0	-0.016	-0.025	15.645	-0.020	-0.020	0.000	0.000	0.000	0.000
69	A	78	ASN	0	0.010	0.012	18.339	0.000	0.000	0.000	0.000	0.000	0.000
70	A	79	LEU	0	0.007	0.018	14.746	-0.022	-0.022	0.000	0.000	0.000	0.000
71	A	80	THR	0	0.019	-0.006	17.301	0.017	0.017	0.000	0.000	0.000	0.000
72	A	81	ASN	0	0.018	-0.010	18.837	0.000	0.000	0.000	0.000	0.000	0.000
73	A	82	GLU	-1	-0.831	-0.909	16.918	-0.203	-0.203	0.000	0.000	0.000	0.000
74	A	83	GLY	0	0.001	-0.009	14.652	-0.028	-0.028	0.000	0.000	0.000	0.000
75	A	84	LYS	1	0.844	0.918	15.318	0.088	0.088	0.000	0.000	0.000	0.000
76	A	85	ASP	-1	-0.860	-0.916	17.903	-0.132	-0.132	0.000	0.000	0.000	0.000
77	A	86	PHE	0	-0.029	-0.024	8.397	-0.025	-0.025	0.000	0.000	0.000	0.000
78	A	87	LEU	0	-0.030	-0.018	13.717	-0.015	-0.015	0.000	0.000	0.000	0.000
79	A	88	GLU	-1	-0.868	-0.940	14.699	-0.049	-0.049	0.000	0.000	0.000	0.000
80	A	89	ILE	0	0.053	0.023	14.590	0.014	0.014	0.000	0.000	0.000	0.000
81	A	90	LYS	1	0.879	0.949	9.587	0.519	0.519	0.000	0.000	0.000	0.000
82	A	91	LYS	1	0.871	0.942	13.473	0.089	0.089	0.000	0.000	0.000	0.000
83	A	92	GLN	0	-0.054	-0.030	16.145	0.025	0.025	0.000	0.000	0.000	0.000
84	A	93	GLU	-1	-0.872	-0.943	12.852	-0.262	-0.262	0.000	0.000	0.000	0.000
85	A	94	TRP	0	0.011	0.007	12.833	0.024	0.024	0.000	0.000	0.000	0.000
86	A	95	ARG	1	0.876	0.935	15.194	0.059	0.059	0.000	0.000	0.000	0.000
87	A	96	PHE	0	0.010	0.011	17.521	0.016	0.016	0.000	0.000	0.000	0.000
88	A	97	ILE	0	0.050	0.016	12.646	0.014	0.014	0.000	0.000	0.000	0.000
89	A	98	LYS	1	0.909	0.962	16.739	-0.059	-0.059	0.000	0.000	0.000	0.000
90	A	99	LYS	1	0.949	0.981	17.866	0.000	0.000	0.000	0.000	0.000	0.000
91	A	100	VAL	0	0.013	0.007	19.149	0.005	0.005	0.000	0.000	0.000	0.000
92	A	101	MET	0	0.041	0.004	15.426	0.006	0.006	0.000	0.000	0.000	0.000
93	A	102	ASN	0	0.002	0.007	18.860	0.024	0.024	0.000	0.000	0.000	0.000
94	A	103	GLN	0	-0.039	-0.005	21.333	0.000	0.000	0.000	0.000	0.000	0.000
95	A	104	PHE	0	-0.050	-0.034	21.368	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	105	LEU	0	-0.039	-0.018	17.096	0.002	0.002	0.000	0.000	0.000	0.000
97	A	106	GLY	0	-0.035	0.010	21.096	0.010	0.010	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:10:GLY)