FMO DATABASE

FMODB ID: ZYKMN

Calculation Name: 3LYS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LYS

Chain ID: A

ChEMBL ID:

UniProt ID: Q9CGT4

Base Structure: X-ray

Registration Date: 2023-06-19

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	105
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-874974.416697
FMO2-HF: Nuclear repulsion	831801.34611
FMO2-HF: Total energy	-43173.070586
FMO2-MP2: Total energy	-43298.900659

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:55:PRO)

Summations of interaction energy for fragment #1(A:55:PRO)

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.
0.0030000000000003	3.861	0.304	-1.864	-2.299	-0.004

Interaction energy analysis for fragmet #1(A:55:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.027 / q_NPA : 0.000

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	57	LYS	1	0.837	0.910	3.866	0.299	2.059	-0.017	-0.895	-0.849	0.000
4	A	58	GLN	0	0.026	0.006	5.975	-0.165	-0.165	0.000	0.000	0.000	0.000
5	A	59	GLU	-1	-0.768	-0.853	9.502	-0.106	-0.106	0.000	0.000	0.000	0.000
6	A	60	ILE	0	-0.011	-0.012	12.910	-0.031	-0.031	0.000	0.000	0.000	0.000
7	A	61	SER	0	-0.016	-0.026	14.075	0.010	0.010	0.000	0.000	0.000	0.000
8	A	62	GLU	-1	-0.912	-0.948	13.448	-0.479	-0.479	0.000	0.000	0.000	0.000
9	A	63	TYR	0	0.029	-0.007	10.722	0.008	0.008	0.000	0.000	0.000	0.000
10	A	64	PHE	0	-0.026	-0.016	13.190	0.042	0.042	0.000	0.000	0.000	0.000
11	A	65	LYS	1	0.851	0.890	16.271	0.242	0.242	0.000	0.000	0.000	0.000
12	A	66	ASP	-1	-0.901	-0.943	12.449	-0.470	-0.470	0.000	0.000	0.000	0.000
13	A	67	TRP	0	0.070	0.028	13.575	0.047	0.047	0.000	0.000	0.000	0.000
14	A	68	MET	0	-0.052	-0.022	15.381	0.036	0.036	0.000	0.000	0.000	0.000
15	A	69	GLU	-1	-0.867	-0.920	18.785	-0.173	-0.173	0.000	0.000	0.000	0.000
16	A	70	LEU	0	-0.005	0.014	14.029	0.021	0.021	0.000	0.000	0.000	0.000
17	A	71	TYR	0	-0.058	-0.041	12.128	0.025	0.025	0.000	0.000	0.000	0.000
18	A	72	LYS	1	0.849	0.925	18.826	0.023	0.023	0.000	0.000	0.000	0.000
19	A	73	LYS	1	0.845	0.929	22.150	0.084	0.084	0.000	0.000	0.000	0.000
20	A	74	ASN	0	-0.010	-0.020	24.358	0.000	0.000	0.000	0.000	0.000	0.000
21	A	75	ALA	0	0.009	0.013	23.955	0.005	0.005	0.000	0.000	0.000	0.000
22	A	76	ILE	0	-0.073	-0.028	25.624	0.012	0.012	0.000	0.000	0.000	0.000
23	A	77	ASP	-1	-0.742	-0.852	27.692	-0.022	-0.022	0.000	0.000	0.000	0.000
24	A	78	GLU	-1	-0.750	-0.858	29.750	-0.058	-0.058	0.000	0.000	0.000	0.000
25	A	79	MET	0	-0.028	-0.021	30.984	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	80	THR	0	-0.041	-0.051	27.672	0.003	0.003	0.000	0.000	0.000	0.000
27	A	81	TYR	0	-0.014	0.004	22.990	0.000	0.000	0.000	0.000	0.000	0.000
28	A	82	LYS	1	0.891	0.947	26.875	0.045	0.045	0.000	0.000	0.000	0.000
29	A	83	GLY	0	-0.017	0.001	28.192	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	84	TYR	0	-0.006	-0.023	21.395	0.007	0.007	0.000	0.000	0.000	0.000
31	A	85	GLU	-1	-0.810	-0.918	23.755	-0.079	-0.079	0.000	0.000	0.000	0.000
32	A	86	GLN	0	0.014	0.007	25.695	-0.008	-0.008	0.000	0.000	0.000	0.000
33	A	87	THR	0	-0.005	0.006	21.194	0.003	0.003	0.000	0.000	0.000	0.000
34	A	88	LEU	0	0.055	0.028	19.620	0.001	0.001	0.000	0.000	0.000	0.000
35	A	89	LYS	1	0.920	0.964	22.163	0.041	0.041	0.000	0.000	0.000	0.000
36	A	90	TYR	0	-0.020	-0.018	24.482	0.002	0.002	0.000	0.000	0.000	0.000
37	A	91	LEU	0	-0.001	0.003	17.015	0.007	0.007	0.000	0.000	0.000	0.000
38	A	92	LYS	1	0.895	0.937	19.190	0.183	0.183	0.000	0.000	0.000	0.000
39	A	93	THR	0	-0.062	-0.016	21.844	0.000	0.000	0.000	0.000	0.000	0.000
40	A	94	TYR	0	-0.042	-0.036	23.393	0.002	0.002	0.000	0.000	0.000	0.000
41	A	95	MET	0	-0.097	-0.051	16.848	0.019	0.019	0.000	0.000	0.000	0.000
42	A	96	PRO	0	0.071	0.047	18.579	-0.017	-0.017	0.000	0.000	0.000	0.000
43	A	97	ASN	0	-0.030	-0.017	16.958	0.002	0.002	0.000	0.000	0.000	0.000
44	A	98	VAL	0	-0.038	-0.016	14.704	0.004	0.004	0.000	0.000	0.000	0.000
45	A	99	LEU	0	0.044	0.017	9.203	-0.038	-0.038	0.000	0.000	0.000	0.000
46	A	100	ILE	0	-0.023	-0.019	7.537	0.108	0.108	0.000	0.000	0.000	0.000
47	A	101	SER	0	-0.014	-0.029	6.408	0.060	0.060	0.000	0.000	0.000	0.000
48	A	102	GLU	-1	-0.818	-0.886	8.431	0.056	0.056	0.000	0.000	0.000	0.000
49	A	103	ILE	0	-0.056	-0.007	11.783	0.012	0.012	0.000	0.000	0.000	0.000
50	A	104	THR	0	0.030	0.024	12.767	0.055	0.055	0.000	0.000	0.000	0.000
51	A	105	ALA	0	0.050	0.008	15.095	-0.029	-0.029	0.000	0.000	0.000	0.000
52	A	106	SER	0	-0.026	-0.007	17.322	-0.028	-0.028	0.000	0.000	0.000	0.000
53	A	107	SER	0	-0.008	-0.019	17.087	-0.023	-0.023	0.000	0.000	0.000	0.000
54	A	108	TYR	0	0.063	0.012	16.756	-0.019	-0.019	0.000	0.000	0.000	0.000
55	A	109	GLN	0	-0.018	-0.022	18.778	-0.005	-0.005	0.000	0.000	0.000	0.000
56	A	110	ARG	1	0.959	0.984	21.593	-0.083	-0.083	0.000	0.000	0.000	0.000
57	A	111	ALA	0	0.022	0.020	20.980	-0.010	-0.010	0.000	0.000	0.000	0.000
58	A	112	LEU	0	0.006	-0.007	21.151	-0.009	-0.009	0.000	0.000	0.000	0.000
59	A	113	ASN	0	-0.064	-0.036	24.402	0.000	0.000	0.000	0.000	0.000	0.000
60	A	114	LYS	1	0.853	0.909	26.244	-0.017	-0.017	0.000	0.000	0.000	0.000
61	A	115	PHE	0	-0.020	-0.008	25.801	-0.005	-0.005	0.000	0.000	0.000	0.000
62	A	116	ALA	0	-0.023	-0.022	27.970	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	117	GLU	-1	-0.793	-0.866	30.379	0.014	0.014	0.000	0.000	0.000	0.000
64	A	118	THR	0	0.017	0.017	31.151	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	119	HIS	1	0.816	0.908	30.024	0.001	0.001	0.000	0.000	0.000	0.000
66	A	120	ALA	0	0.087	0.055	32.919	0.004	0.004	0.000	0.000	0.000	0.000
67	A	121	LYS	1	0.906	0.951	31.272	-0.050	-0.050	0.000	0.000	0.000	0.000
68	A	122	ALA	0	0.012	-0.001	30.763	0.003	0.003	0.000	0.000	0.000	0.000
69	A	123	SER	0	-0.002	0.008	29.733	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	124	THR	0	0.013	0.016	27.073	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	125	LYS	1	0.952	0.973	25.929	-0.058	-0.058	0.000	0.000	0.000	0.000
72	A	126	GLY	0	-0.007	-0.007	25.766	0.006	0.006	0.000	0.000	0.000	0.000
73	A	127	PHE	0	-0.014	-0.002	21.566	-0.002	-0.002	0.000	0.000	0.000	0.000
74	A	128	HIS	0	0.018	0.011	20.237	-0.009	-0.009	0.000	0.000	0.000	0.000
75	A	129	THR	0	-0.017	-0.013	20.757	0.008	0.008	0.000	0.000	0.000	0.000
76	A	130	ARG	1	0.884	0.952	21.229	0.014	0.014	0.000	0.000	0.000	0.000
77	A	131	VAL	0	0.033	0.026	16.635	-0.005	-0.005	0.000	0.000	0.000	0.000
78	A	132	ARG	1	0.853	0.915	16.407	-0.206	-0.206	0.000	0.000	0.000	0.000
79	A	133	ALA	0	-0.021	-0.012	16.321	0.025	0.025	0.000	0.000	0.000	0.000
80	A	134	SER	0	-0.016	-0.016	15.071	0.001	0.001	0.000	0.000	0.000	0.000
81	A	135	ILE	0	-0.003	0.001	11.687	-0.011	-0.011	0.000	0.000	0.000	0.000
82	A	136	GLN	0	-0.012	-0.028	11.634	0.068	0.068	0.000	0.000	0.000	0.000
83	A	137	CYS	0	-0.002	0.005	12.037	0.079	0.079	0.000	0.000	0.000	0.000
84	A	138	LEU	0	0.003	0.017	6.970	0.040	0.040	0.000	0.000	0.000	0.000
85	A	139	ILE	0	-0.073	-0.042	7.565	0.347	0.347	0.000	0.000	0.000	0.000
86	A	140	GLU	-1	-0.920	-0.960	9.538	0.636	0.636	0.000	0.000	0.000	0.000
87	A	141	GLU	-1	-0.802	-0.871	7.480	-0.135	-0.135	0.000	0.000	0.000	0.000
88	A	142	GLY	0	-0.004	0.004	6.596	0.134	0.134	0.000	0.000	0.000	0.000
89	A	143	ARG	1	0.849	0.920	3.446	2.148	3.157	0.060	-0.300	-0.769	0.002
90	A	144	LEU	0	-0.043	-0.024	3.021	-1.993	-0.904	0.261	-0.669	-0.681	-0.006
91	A	145	GLN	0	0.032	0.010	5.206	0.250	0.250	0.000	0.000	0.000	0.000
92	A	146	LYS	1	0.939	0.963	7.212	-0.758	-0.758	0.000	0.000	0.000	0.000
93	A	147	ASP	-1	-0.665	-0.796	10.536	0.225	0.225	0.000	0.000	0.000	0.000
94	A	148	PHE	0	-0.002	-0.009	10.665	-0.046	-0.046	0.000	0.000	0.000	0.000
95	A	149	THR	0	-0.020	-0.022	14.417	-0.051	-0.051	0.000	0.000	0.000	0.000
96	A	150	THR	0	-0.039	-0.013	16.490	-0.041	-0.041	0.000	0.000	0.000	0.000
97	A	151	ARG	1	0.984	0.985	18.273	-0.171	-0.171	0.000	0.000	0.000	0.000
98	A	152	ALA	0	-0.001	0.019	20.022	-0.015	-0.015	0.000	0.000	0.000	0.000
99	A	153	VAL	0	0.000	-0.002	21.707	-0.014	-0.014	0.000	0.000	0.000	0.000
100	A	154	VAL	0	0.004	0.015	24.435	-0.011	-0.011	0.000	0.000	0.000	0.000
101	A	155	LYN	0	0.044	0.030	26.326	-0.009	-0.009	0.000	0.000	0.000	0.000
102	A	156	GLY	0	0.003	-0.004	27.357	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	157	LEU	0	-0.049	-0.052	30.141	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	158	GLU	-1	-0.800	-0.885	33.553	0.016	0.016	0.000	0.000	0.000	0.000
105	A	159	HIS	0	-0.048	-0.027	36.338	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:55:PRO)