FMO DATABASE

FMODB ID: 85LKY

Calculation Name: 5A15-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5A15

Chain ID: A

ChEMBL ID:

UniProt ID: Q68DU8

Base Structure: X-ray

Registration Date: 2023-09-20

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

DOI:

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	95
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-749526.341513
FMO2-HF: Nuclear repulsion	710998.890396
FMO2-HF: Total energy	-38527.451117
FMO2-MP2: Total energy	-38643.110282

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:23:PHE)

Summations of interaction energy for fragment #1(A:23:PHE)

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.
-22.284	-8.835	10.126	-6.01	-17.564	-0.006

Interaction energy analysis for fragmet #1(A:23:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.026 / q_NPA : -0.024

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	25	GLU	-1	-0.873	-0.940	3.344	-3.359	-1.164	0.031	-1.076	-1.150	0.001
4	A	26	VAL	0	-0.045	-0.031	6.099	0.263	0.263	0.000	0.000	0.000	0.000
5	A	27	VAL	0	-0.025	-0.013	3.467	-0.181	0.190	0.010	-0.062	-0.319	0.000
6	A	28	GLU	-1	-0.857	-0.939	6.193	0.426	0.426	0.000	0.000	0.000	0.000
7	A	29	LEU	0	-0.040	-0.024	6.647	0.181	0.181	0.000	0.000	0.000	0.000
8	A	30	ASN	0	-0.038	-0.036	9.531	-0.134	-0.134	0.000	0.000	0.000	0.000
9	A	31	VAL	0	0.031	0.001	12.027	0.005	0.005	0.000	0.000	0.000	0.000
10	A	32	GLY	0	0.045	0.040	14.045	-0.028	-0.028	0.000	0.000	0.000	0.000
11	A	33	GLY	0	-0.019	-0.007	15.921	-0.018	-0.018	0.000	0.000	0.000	0.000
12	A	34	GLN	0	-0.058	-0.021	16.903	-0.001	-0.001	0.000	0.000	0.000	0.000
13	A	35	VAL	0	-0.029	-0.011	13.220	0.025	0.025	0.000	0.000	0.000	0.000
14	A	36	TYR	0	-0.051	-0.041	12.636	-0.063	-0.063	0.000	0.000	0.000	0.000
15	A	37	PHE	0	0.025	0.021	10.907	0.077	0.077	0.000	0.000	0.000	0.000
16	A	38	THR	0	-0.016	-0.020	8.632	-0.101	-0.101	0.000	0.000	0.000	0.000
17	A	39	ARG	1	0.996	1.014	7.992	0.292	0.292	0.000	0.000	0.000	0.000
18	A	40	HIS	0	0.038	0.001	2.875	-3.191	-0.882	0.933	-0.909	-2.334	0.002
19	A	41	SER	0	0.011	-0.007	5.670	0.125	0.125	0.000	0.000	0.000	0.000
20	A	42	THR	0	-0.036	-0.021	8.880	0.038	0.038	0.000	0.000	0.000	0.000
21	A	43	LEU	0	-0.008	0.002	5.460	0.015	0.015	0.000	0.000	0.000	0.000
22	A	44	ILE	0	-0.012	0.000	5.903	0.021	0.021	0.000	0.000	0.000	0.000
23	A	45	SER	0	-0.018	0.005	9.162	-0.096	-0.096	0.000	0.000	0.000	0.000
24	A	46	ILE	0	-0.010	-0.007	12.748	0.003	0.003	0.000	0.000	0.000	0.000
25	A	47	PRO	0	0.045	0.021	11.960	0.000	0.000	0.000	0.000	0.000	0.000
26	A	48	HIS	0	0.021	0.009	12.081	0.058	0.058	0.000	0.000	0.000	0.000
27	A	49	SER	0	0.025	0.022	12.475	0.076	0.076	0.000	0.000	0.000	0.000
28	A	50	LEU	0	-0.023	-0.007	10.856	-0.096	-0.096	0.000	0.000	0.000	0.000
29	A	51	LEU	0	0.047	0.005	8.706	-0.065	-0.065	0.000	0.000	0.000	0.000
30	A	52	TRP	0	0.031	0.035	7.491	0.108	0.108	0.000	0.000	0.000	0.000
31	A	53	LYS	1	0.804	0.892	6.737	0.129	0.129	0.000	0.000	0.000	0.000
32	A	54	MET	0	-0.068	-0.011	5.299	-0.341	-0.341	0.000	0.000	0.000	0.000
33	A	55	PHE	0	0.014	0.002	2.733	-6.642	-3.167	4.364	-2.287	-5.551	0.014
34	A	56	SER	0	-0.004	0.004	2.967	-1.679	-1.163	1.929	0.089	-2.534	-0.008
35	A	57	PRO	0	-0.024	-0.005	2.870	-3.648	-1.376	0.408	-0.700	-1.979	-0.007
36	A	65	LEU	0	-0.015	-0.016	2.322	-0.581	-0.210	1.541	-0.402	-1.510	0.000
37	A	66	ALA	0	0.029	0.028	6.615	0.196	0.196	0.000	0.000	0.000	0.000
38	A	67	LYS	1	0.949	0.972	6.074	-1.534	-1.534	0.000	0.000	0.000	0.000
39	A	68	ASP	-1	-0.735	-0.843	9.407	0.456	0.456	0.000	0.000	0.000	0.000
40	A	69	SER	0	0.007	-0.002	12.739	0.069	0.069	0.000	0.000	0.000	0.000
41	A	70	LYS	1	0.916	0.959	14.198	-0.364	-0.364	0.000	0.000	0.000	0.000
42	A	71	GLY	0	-0.005	0.006	10.753	0.059	0.059	0.000	0.000	0.000	0.000
43	A	72	ARG	1	0.812	0.909	8.570	-0.244	-0.244	0.000	0.000	0.000	0.000
44	A	73	PHE	0	0.027	0.003	3.036	-2.452	-0.512	0.910	-0.663	-2.187	-0.008
45	A	74	PHE	0	-0.014	-0.017	6.861	-0.049	-0.049	0.000	0.000	0.000	0.000
46	A	75	ILE	0	-0.056	-0.030	8.059	-0.057	-0.057	0.000	0.000	0.000	0.000
47	A	76	ASP	-1	-0.901	-0.949	11.327	0.112	0.112	0.000	0.000	0.000	0.000
48	A	77	ARG	1	0.786	0.852	14.764	-0.056	-0.056	0.000	0.000	0.000	0.000
49	A	78	ASP	-1	-0.770	-0.882	16.822	0.080	0.080	0.000	0.000	0.000	0.000
50	A	79	GLY	0	0.070	0.028	17.192	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	80	PHE	0	0.017	0.016	18.237	0.000	0.000	0.000	0.000	0.000	0.000
52	A	81	LEU	0	-0.002	-0.012	20.536	-0.011	-0.011	0.000	0.000	0.000	0.000
53	A	82	PHE	0	0.015	0.008	11.429	-0.017	-0.017	0.000	0.000	0.000	0.000
54	A	83	ARG	1	0.904	0.962	17.090	-0.008	-0.008	0.000	0.000	0.000	0.000
55	A	84	TYR	0	0.021	0.001	18.703	-0.018	-0.018	0.000	0.000	0.000	0.000
56	A	85	ILE	0	-0.025	-0.001	15.701	-0.024	-0.024	0.000	0.000	0.000	0.000
57	A	86	LEU	0	-0.044	-0.020	11.984	-0.026	-0.026	0.000	0.000	0.000	0.000
58	A	87	ASP	-1	-0.782	-0.889	15.627	-0.061	-0.061	0.000	0.000	0.000	0.000
59	A	88	TYR	0	0.002	0.016	18.328	-0.030	-0.030	0.000	0.000	0.000	0.000
60	A	89	LEU	0	-0.029	-0.004	12.650	-0.027	-0.027	0.000	0.000	0.000	0.000
61	A	90	ARG	1	0.746	0.864	14.792	0.027	0.027	0.000	0.000	0.000	0.000
62	A	91	ASP	-1	-0.815	-0.903	15.880	-0.157	-0.157	0.000	0.000	0.000	0.000
63	A	92	ARG	1	0.848	0.922	16.392	0.308	0.308	0.000	0.000	0.000	0.000
64	A	93	GLN	0	-0.048	-0.027	20.566	0.016	0.016	0.000	0.000	0.000	0.000
65	A	94	VAL	0	-0.009	-0.016	21.857	0.004	0.004	0.000	0.000	0.000	0.000
66	A	95	VAL	0	0.018	0.019	24.281	0.001	0.001	0.000	0.000	0.000	0.000
67	A	96	LEU	0	-0.052	-0.027	25.795	0.006	0.006	0.000	0.000	0.000	0.000
68	A	97	PRO	0	0.018	0.003	27.712	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	98	ASP	-1	-0.886	-0.939	30.880	-0.026	-0.026	0.000	0.000	0.000	0.000
70	A	99	HIS	0	-0.034	-0.021	34.588	0.004	0.004	0.000	0.000	0.000	0.000
71	A	100	PHE	0	0.001	0.001	26.041	0.003	0.003	0.000	0.000	0.000	0.000
72	A	101	PRO	0	0.028	0.016	30.882	-0.004	-0.004	0.000	0.000	0.000	0.000
73	A	102	GLU	-1	-0.819	-0.892	26.840	0.020	0.020	0.000	0.000	0.000	0.000
74	A	103	LYS	1	1.007	0.996	27.357	0.043	0.043	0.000	0.000	0.000	0.000
75	A	104	GLY	0	-0.016	-0.003	27.634	-0.005	-0.005	0.000	0.000	0.000	0.000
76	A	105	ARG	1	0.805	0.865	24.315	-0.030	-0.030	0.000	0.000	0.000	0.000
77	A	106	LEU	0	0.034	0.026	21.775	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	107	LYS	1	0.886	0.934	22.828	0.057	0.057	0.000	0.000	0.000	0.000
79	A	108	ARG	1	0.927	0.954	21.718	0.051	0.051	0.000	0.000	0.000	0.000
80	A	109	GLU	-1	-0.789	-0.872	18.933	0.003	0.003	0.000	0.000	0.000	0.000
81	A	110	ALA	0	-0.001	-0.003	18.671	-0.009	-0.009	0.000	0.000	0.000	0.000
82	A	111	GLU	-1	-0.880	-0.930	19.191	-0.095	-0.095	0.000	0.000	0.000	0.000
83	A	112	TYR	0	-0.050	-0.009	13.127	-0.029	-0.029	0.000	0.000	0.000	0.000
84	A	113	PHE	0	0.032	-0.012	12.348	-0.019	-0.019	0.000	0.000	0.000	0.000
85	A	114	GLN	0	0.000	0.010	14.795	-0.089	-0.089	0.000	0.000	0.000	0.000
86	A	115	LEU	0	0.007	0.004	15.455	-0.033	-0.033	0.000	0.000	0.000	0.000
87	A	116	PRO	0	0.063	0.017	19.000	0.021	0.021	0.000	0.000	0.000	0.000
88	A	117	ASP	-1	-0.834	-0.914	21.902	-0.174	-0.174	0.000	0.000	0.000	0.000
89	A	118	LEU	0	-0.008	0.008	20.337	0.013	0.013	0.000	0.000	0.000	0.000
90	A	119	VAL	0	0.027	-0.001	22.497	0.016	0.016	0.000	0.000	0.000	0.000
91	A	120	LYS	1	0.870	0.933	24.993	0.159	0.159	0.000	0.000	0.000	0.000
92	A	121	LEU	0	-0.009	0.001	24.848	0.008	0.008	0.000	0.000	0.000	0.000
93	A	122	LEU	0	-0.012	0.004	24.784	0.010	0.010	0.000	0.000	0.000	0.000
94	A	123	THR	0	-0.085	-0.036	28.690	0.009	0.009	0.000	0.000	0.000	0.000
95	A	124	PRO	0	0.004	0.017	31.177	-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:23:PHE)