FMO DATABASE

FMODB ID: 6YGKZ

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	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	97
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-742572.61303
FMO2-HF: Nuclear repulsion	701760.553287
FMO2-HF: Total energy	-40812.059744
FMO2-MP2: Total energy	-40930.64263

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.
-4.501	-1.532	0.189	-1.327	-1.831	0.008

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 : 0.008

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	0.012	0.013	3.224	-2.610	-0.082	0.191	-1.260	-1.459	0.008
4	A	13	ASP	-1	-0.752	-0.864	4.269	-0.186	0.157	-0.001	-0.049	-0.293	0.000
5	A	14	ILE	0	0.018	0.000	6.161	0.081	0.081	0.000	0.000	0.000	0.000
6	A	15	LEU	0	-0.019	-0.004	7.244	0.153	0.153	0.000	0.000	0.000	0.000
7	A	16	ILE	0	0.020	0.005	8.344	-0.009	-0.009	0.000	0.000	0.000	0.000
8	A	17	VAL	0	0.018	0.010	10.564	-0.035	-0.035	0.000	0.000	0.000	0.000
9	A	18	SER	0	-0.045	-0.028	12.093	-0.012	-0.012	0.000	0.000	0.000	0.000
10	A	19	ILE	0	-0.059	-0.010	12.693	0.006	0.006	0.000	0.000	0.000	0.000
11	A	20	LEU	0	-0.007	-0.014	14.484	-0.011	-0.011	0.000	0.000	0.000	0.000
12	A	21	GLU	-1	-0.840	-0.889	16.881	-0.071	-0.071	0.000	0.000	0.000	0.000
13	A	22	LYS	1	0.810	0.882	18.747	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	23	LYS	1	0.861	0.904	20.490	-0.130	-0.130	0.000	0.000	0.000	0.000
15	A	24	ASP	-1	-0.685	-0.778	19.965	0.099	0.099	0.000	0.000	0.000	0.000
16	A	25	CYS	0	-0.072	-0.029	17.826	-0.004	-0.004	0.000	0.000	0.000	0.000
17	A	26	TYR	0	0.039	0.024	18.826	0.017	0.017	0.000	0.000	0.000	0.000
18	A	27	GLY	0	0.024	-0.003	15.995	0.010	0.010	0.000	0.000	0.000	0.000
19	A	28	TYR	0	0.027	0.014	16.216	0.041	0.041	0.000	0.000	0.000	0.000
20	A	29	GLU	-1	-0.770	-0.881	18.185	0.167	0.167	0.000	0.000	0.000	0.000
21	A	30	ILE	0	-0.008	0.002	12.412	-0.004	-0.004	0.000	0.000	0.000	0.000
22	A	31	ALA	0	0.025	-0.003	13.508	0.037	0.037	0.000	0.000	0.000	0.000
23	A	32	LYS	1	0.791	0.893	14.569	-0.159	-0.159	0.000	0.000	0.000	0.000
24	A	33	GLN	0	0.067	0.027	15.878	-0.030	-0.030	0.000	0.000	0.000	0.000
25	A	34	VAL	0	-0.032	-0.021	9.588	-0.011	-0.011	0.000	0.000	0.000	0.000
26	A	35	ARG	1	0.826	0.909	12.778	-0.500	-0.500	0.000	0.000	0.000	0.000
27	A	36	GLU	-1	-0.803	-0.878	14.851	0.122	0.122	0.000	0.000	0.000	0.000
28	A	37	ARG	1	0.856	0.930	14.813	-0.123	-0.123	0.000	0.000	0.000	0.000
29	A	38	SER	0	-0.073	-0.047	11.368	-0.010	-0.010	0.000	0.000	0.000	0.000
30	A	39	GLU	-1	-0.838	-0.913	12.374	0.109	0.109	0.000	0.000	0.000	0.000
31	A	40	PHE	0	-0.069	-0.036	5.415	0.128	0.128	0.000	0.000	0.000	0.000
32	A	41	GLU	-1	-0.811	-0.882	10.083	0.415	0.415	0.000	0.000	0.000	0.000
33	A	42	LEU	0	-0.047	-0.034	7.885	0.147	0.147	0.000	0.000	0.000	0.000
34	A	43	LYS	1	0.896	0.935	10.360	-0.531	-0.531	0.000	0.000	0.000	0.000
35	A	44	GLU	-1	-0.757	-0.868	10.767	0.632	0.632	0.000	0.000	0.000	0.000
36	A	45	GLY	0	0.021	0.000	12.283	0.060	0.060	0.000	0.000	0.000	0.000
37	A	46	THR	0	0.013	0.000	5.935	-0.086	-0.086	0.000	0.000	0.000	0.000
38	A	47	MET	0	-0.006	0.020	7.718	0.406	0.406	0.000	0.000	0.000	0.000
39	A	48	TYR	0	0.004	-0.006	9.772	-0.083	-0.083	0.000	0.000	0.000	0.000
40	A	49	LEU	0	0.019	0.013	8.722	-0.093	-0.093	0.000	0.000	0.000	0.000
41	A	50	ALA	0	-0.023	-0.008	6.531	-0.071	-0.071	0.000	0.000	0.000	0.000
42	A	51	LEU	0	0.004	-0.001	7.779	-0.291	-0.291	0.000	0.000	0.000	0.000
43	A	52	LYS	1	0.888	0.942	11.277	-0.369	-0.369	0.000	0.000	0.000	0.000
44	A	53	ARG	1	0.878	0.916	4.105	-1.820	-1.722	-0.001	-0.018	-0.079	0.000
45	A	54	MET	0	-0.023	-0.002	8.361	-0.066	-0.066	0.000	0.000	0.000	0.000
46	A	55	GLU	-1	-0.751	-0.834	10.770	0.182	0.182	0.000	0.000	0.000	0.000
47	A	56	SER	0	-0.039	-0.015	12.644	-0.039	-0.039	0.000	0.000	0.000	0.000
48	A	57	LYS	1	0.854	0.927	6.411	0.273	0.273	0.000	0.000	0.000	0.000
49	A	58	ASN	0	0.003	0.010	13.049	-0.040	-0.040	0.000	0.000	0.000	0.000
50	A	59	LEU	0	0.038	0.046	9.967	-0.012	-0.012	0.000	0.000	0.000	0.000
51	A	60	ILE	0	-0.051	-0.026	12.431	0.005	0.005	0.000	0.000	0.000	0.000
52	A	61	LYS	1	0.940	0.965	15.577	-0.086	-0.086	0.000	0.000	0.000	0.000
53	A	62	SER	0	-0.037	-0.036	18.269	-0.009	-0.009	0.000	0.000	0.000	0.000
54	A	63	TYR	0	-0.107	-0.083	19.823	-0.018	-0.018	0.000	0.000	0.000	0.000
55	A	64	TYR	0	0.023	-0.003	22.393	0.024	0.024	0.000	0.000	0.000	0.000
56	A	65	SER	0	0.005	0.008	25.613	-0.007	-0.007	0.000	0.000	0.000	0.000
57	A	66	ASN	0	0.046	0.007	28.245	0.005	0.005	0.000	0.000	0.000	0.000
58	A	67	GLU	-1	-0.802	-0.877	31.542	0.096	0.096	0.000	0.000	0.000	0.000
59	A	68	GLN	0	0.031	0.015	32.801	0.001	0.001	0.000	0.000	0.000	0.000
60	A	69	SER	0	-0.040	-0.014	30.943	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	70	SER	0	0.046	0.001	31.970	0.001	0.001	0.000	0.000	0.000	0.000
62	A	71	GLY	0	-0.005	0.011	28.585	0.002	0.002	0.000	0.000	0.000	0.000
63	A	72	GLY	0	0.011	0.018	28.482	0.011	0.011	0.000	0.000	0.000	0.000
64	A	73	ARG	1	0.823	0.906	26.322	-0.104	-0.104	0.000	0.000	0.000	0.000
65	A	74	ARG	1	0.873	0.935	23.500	-0.140	-0.140	0.000	0.000	0.000	0.000
66	A	75	LYS	1	0.843	0.903	16.877	-0.272	-0.272	0.000	0.000	0.000	0.000
67	A	76	TYR	0	-0.003	0.000	19.871	0.031	0.031	0.000	0.000	0.000	0.000
68	A	77	TYR	0	0.020	-0.008	15.637	0.007	0.007	0.000	0.000	0.000	0.000
69	A	78	ASN	0	-0.013	-0.011	18.577	-0.010	-0.010	0.000	0.000	0.000	0.000
70	A	79	LEU	0	-0.013	0.011	14.910	0.013	0.013	0.000	0.000	0.000	0.000
71	A	80	THR	0	0.037	-0.002	17.138	-0.018	-0.018	0.000	0.000	0.000	0.000
72	A	81	ASN	0	0.032	0.010	18.590	-0.005	-0.005	0.000	0.000	0.000	0.000
73	A	82	GLU	-1	-0.816	-0.896	16.597	-0.058	-0.058	0.000	0.000	0.000	0.000
74	A	83	GLY	0	0.000	-0.008	14.224	-0.035	-0.035	0.000	0.000	0.000	0.000
75	A	84	LYS	1	0.810	0.885	14.820	-0.020	-0.020	0.000	0.000	0.000	0.000
76	A	85	ASP	-1	-0.868	-0.926	17.357	-0.111	-0.111	0.000	0.000	0.000	0.000
77	A	86	PHE	0	-0.018	-0.019	7.954	-0.052	-0.052	0.000	0.000	0.000	0.000
78	A	87	LEU	0	-0.012	-0.003	13.224	-0.069	-0.069	0.000	0.000	0.000	0.000
79	A	88	GLU	-1	-0.769	-0.871	14.221	-0.172	-0.172	0.000	0.000	0.000	0.000
80	A	89	ILE	0	0.036	0.017	14.266	-0.014	-0.014	0.000	0.000	0.000	0.000
81	A	90	LYS	1	0.767	0.867	9.411	0.569	0.569	0.000	0.000	0.000	0.000
82	A	91	LYS	1	0.854	0.912	12.935	0.104	0.104	0.000	0.000	0.000	0.000
83	A	92	GLN	0	-0.060	-0.013	15.836	0.013	0.013	0.000	0.000	0.000	0.000
84	A	93	GLU	-1	-0.772	-0.864	11.654	-0.561	-0.561	0.000	0.000	0.000	0.000
85	A	94	TRP	0	0.010	-0.001	13.197	0.003	0.003	0.000	0.000	0.000	0.000
86	A	95	ARG	1	0.790	0.852	14.735	0.206	0.206	0.000	0.000	0.000	0.000
87	A	96	PHE	0	0.012	0.015	17.238	0.019	0.019	0.000	0.000	0.000	0.000
88	A	97	ILE	0	0.039	0.007	12.545	0.017	0.017	0.000	0.000	0.000	0.000
89	A	98	LYS	1	0.927	0.979	16.347	0.235	0.235	0.000	0.000	0.000	0.000
90	A	99	LYS	1	0.971	0.998	17.388	0.152	0.152	0.000	0.000	0.000	0.000
91	A	100	VAL	0	0.007	0.007	18.626	0.017	0.017	0.000	0.000	0.000	0.000
92	A	101	MET	0	0.009	-0.009	14.850	0.001	0.001	0.000	0.000	0.000	0.000
93	A	102	ASN	0	0.001	-0.010	18.310	0.005	0.005	0.000	0.000	0.000	0.000
94	A	103	GLN	0	-0.060	-0.023	21.080	0.017	0.017	0.000	0.000	0.000	0.000
95	A	104	PHE	0	-0.014	-0.010	21.173	0.013	0.013	0.000	0.000	0.000	0.000
96	A	105	LEU	0	-0.001	0.010	16.769	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	106	GLY	0	-0.073	-0.017	20.843	0.022	0.022	0.000	0.000	0.000	0.000

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