FMO DATABASE

FMODB ID: QYKVY

Calculation Name: 5D90-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5D90

Chain ID: B

ChEMBL ID:

UniProt ID: P44558

Base Structure: X-ray

Registration Date: 2023-06-22

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	125
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-946050.513595
FMO2-HF: Nuclear repulsion	895460.9214
FMO2-HF: Total energy	-50589.592195
FMO2-MP2: Total energy	-50736.298661

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(B:0:GLY)

Summations of interaction energy for fragment #1(B:0: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.
-4.912	-0.646	0.869	-2.266	-2.867	-0.009

Interaction energy analysis for fragmet #1(B:0:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.015 / q_NPA : -0.001

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	B	2	THR	0	-0.057	-0.025	3.302	-2.417	-0.578	0.006	-1.027	-0.818	0.002
4	B	3	TYR	0	-0.039	-0.046	2.960	-1.107	1.208	0.866	-1.220	-1.961	-0.011
5	B	4	THR	0	0.067	0.033	5.362	-0.132	-0.131	-0.001	0.000	0.001	0.000
6	B	5	THR	0	0.021	-0.007	8.903	-0.111	-0.111	0.000	0.000	0.000	0.000
7	B	6	ALA	0	-0.009	0.004	11.424	-0.056	-0.056	0.000	0.000	0.000	0.000
8	B	7	LYS	1	0.872	0.907	6.390	-0.301	-0.301	0.000	0.000	0.000	0.000
9	B	8	ALA	0	0.006	0.001	7.657	-0.213	-0.213	0.000	0.000	0.000	0.000
10	B	9	ALA	0	-0.002	0.006	8.484	-0.057	-0.057	0.000	0.000	0.000	0.000
11	B	10	GLU	-1	-0.792	-0.876	8.143	-0.010	-0.010	0.000	0.000	0.000	0.000
12	B	11	LYS	1	0.825	0.923	4.563	1.607	1.659	-0.001	-0.004	-0.046	0.000
13	B	12	ILE	0	-0.027	-0.016	8.760	-0.049	-0.049	0.000	0.000	0.000	0.000
14	B	13	GLY	0	0.012	0.027	11.958	0.046	0.046	0.000	0.000	0.000	0.000
15	B	14	ILE	0	-0.060	-0.029	14.004	0.037	0.037	0.000	0.000	0.000	0.000
16	B	15	SER	0	0.025	0.009	14.969	0.018	0.018	0.000	0.000	0.000	0.000
17	B	16	ALA	0	0.073	0.002	14.964	-0.012	-0.012	0.000	0.000	0.000	0.000
18	B	17	TYR	0	-0.011	0.006	16.109	0.003	0.003	0.000	0.000	0.000	0.000
19	B	18	THR	0	0.027	0.016	18.383	0.002	0.002	0.000	0.000	0.000	0.000
20	B	19	LEU	0	0.007	0.020	12.148	0.000	0.000	0.000	0.000	0.000	0.000
21	B	20	ARG	1	0.978	0.976	16.249	-0.067	-0.067	0.000	0.000	0.000	0.000
22	B	21	PHE	0	-0.003	0.013	18.550	0.005	0.005	0.000	0.000	0.000	0.000
23	B	22	TYR	0	-0.004	-0.034	17.377	0.008	0.008	0.000	0.000	0.000	0.000
24	B	23	ASP	-1	-0.844	-0.909	17.603	-0.045	-0.045	0.000	0.000	0.000	0.000
25	B	24	LYS	1	0.887	0.939	19.414	0.034	0.034	0.000	0.000	0.000	0.000
26	B	25	GLU	-1	-0.860	-0.908	22.905	-0.045	-0.045	0.000	0.000	0.000	0.000
27	B	26	GLY	0	0.014	0.010	22.590	-0.001	-0.001	0.000	0.000	0.000	0.000
28	B	27	LEU	0	-0.015	-0.008	20.544	-0.007	-0.007	0.000	0.000	0.000	0.000
29	B	28	LEU	0	-0.041	-0.010	15.177	-0.028	-0.028	0.000	0.000	0.000	0.000
30	B	29	PRO	0	0.032	0.046	17.800	0.007	0.007	0.000	0.000	0.000	0.000
31	B	30	ASN	0	-0.004	-0.031	17.282	-0.011	-0.011	0.000	0.000	0.000	0.000
32	B	31	VAL	0	-0.049	-0.007	12.019	-0.007	-0.007	0.000	0.000	0.000	0.000
33	B	32	GLY	0	0.077	0.045	12.999	0.044	0.044	0.000	0.000	0.000	0.000
34	B	33	ARG	1	0.903	0.935	13.510	-0.023	-0.023	0.000	0.000	0.000	0.000
35	B	34	ASP	-1	-0.827	-0.908	12.881	0.317	0.317	0.000	0.000	0.000	0.000
36	B	35	GLU	-1	-0.907	-0.960	14.553	0.102	0.102	0.000	0.000	0.000	0.000
37	B	36	TYR	0	-0.033	-0.008	15.768	0.009	0.009	0.000	0.000	0.000	0.000
38	B	37	GLY	0	0.036	0.033	17.565	-0.015	-0.015	0.000	0.000	0.000	0.000
39	B	38	ASN	0	-0.108	-0.051	14.003	-0.062	-0.062	0.000	0.000	0.000	0.000
40	B	39	ARG	1	0.808	0.878	13.170	0.070	0.070	0.000	0.000	0.000	0.000
41	B	40	ARG	1	0.866	0.920	8.688	-0.308	-0.308	0.000	0.000	0.000	0.000
42	B	41	PHE	0	0.017	0.004	7.767	-0.038	-0.038	0.000	0.000	0.000	0.000
43	B	42	THR	0	0.044	-0.017	6.534	-0.034	-0.034	0.000	0.000	0.000	0.000
44	B	43	ASP	-1	-0.726	-0.866	4.445	-3.084	-3.025	-0.001	-0.015	-0.043	0.000
45	B	44	LYS	1	0.912	0.954	7.573	0.657	0.657	0.000	0.000	0.000	0.000
46	B	45	ASP	-1	-0.790	-0.859	10.153	-0.324	-0.324	0.000	0.000	0.000	0.000
47	B	46	LEU	0	-0.018	-0.009	6.062	0.095	0.095	0.000	0.000	0.000	0.000
48	B	47	GLN	0	0.017	0.021	10.431	0.127	0.127	0.000	0.000	0.000	0.000
49	B	48	TRP	0	0.024	0.016	13.092	0.050	0.050	0.000	0.000	0.000	0.000
50	B	49	LEU	0	-0.012	-0.011	11.357	0.049	0.049	0.000	0.000	0.000	0.000
51	B	50	SER	0	-0.011	-0.021	13.058	0.038	0.038	0.000	0.000	0.000	0.000
52	B	51	LEU	0	-0.019	0.008	15.560	0.037	0.037	0.000	0.000	0.000	0.000
53	B	52	LEU	0	0.014	0.004	17.415	0.030	0.030	0.000	0.000	0.000	0.000
54	B	53	GLN	0	0.014	0.006	16.948	0.039	0.039	0.000	0.000	0.000	0.000
55	B	54	CYS	0	-0.009	0.003	19.500	0.021	0.021	0.000	0.000	0.000	0.000
56	B	55	LEU	0	0.013	0.025	21.350	0.019	0.019	0.000	0.000	0.000	0.000
57	B	56	LYS	1	0.968	0.992	21.974	0.115	0.115	0.000	0.000	0.000	0.000
58	B	57	ASN	0	-0.075	-0.050	20.825	0.020	0.020	0.000	0.000	0.000	0.000
59	B	58	THR	0	0.018	0.008	24.322	0.007	0.007	0.000	0.000	0.000	0.000
60	B	59	GLY	0	0.011	0.012	27.077	0.007	0.007	0.000	0.000	0.000	0.000
61	B	60	MET	0	-0.017	0.018	26.679	0.007	0.007	0.000	0.000	0.000	0.000
62	B	61	SER	0	-0.025	-0.046	27.715	0.000	0.000	0.000	0.000	0.000	0.000
63	B	62	LEU	0	0.042	0.003	25.263	-0.004	-0.004	0.000	0.000	0.000	0.000
64	B	63	LYS	1	0.876	0.913	27.717	0.061	0.061	0.000	0.000	0.000	0.000
65	B	64	ASP	-1	-0.746	-0.816	29.625	-0.075	-0.075	0.000	0.000	0.000	0.000
66	B	65	ILE	0	-0.015	-0.002	23.144	-0.006	-0.006	0.000	0.000	0.000	0.000
67	B	66	LYS	1	0.835	0.898	25.262	0.057	0.057	0.000	0.000	0.000	0.000
68	B	67	ARG	1	0.808	0.869	26.753	0.072	0.072	0.000	0.000	0.000	0.000
69	B	68	PHE	0	0.025	0.005	22.308	-0.003	-0.003	0.000	0.000	0.000	0.000
70	B	69	ALA	0	0.005	-0.007	23.190	-0.005	-0.005	0.000	0.000	0.000	0.000
71	B	70	GLU	-1	-0.888	-0.927	24.511	-0.072	-0.072	0.000	0.000	0.000	0.000
72	B	71	CYS	0	-0.026	-0.012	27.627	0.003	0.003	0.000	0.000	0.000	0.000
73	B	72	THR	0	-0.054	-0.045	23.458	-0.006	-0.006	0.000	0.000	0.000	0.000
74	B	73	ILE	0	-0.083	-0.029	24.110	-0.005	-0.005	0.000	0.000	0.000	0.000
75	B	74	ILE	0	-0.043	-0.015	26.162	0.004	0.004	0.000	0.000	0.000	0.000
76	B	75	GLY	0	0.072	0.050	28.788	0.004	0.004	0.000	0.000	0.000	0.000
77	B	76	ASP	-1	-0.860	-0.939	28.764	-0.123	-0.123	0.000	0.000	0.000	0.000
78	B	77	ASP	-1	-0.892	-0.936	31.264	-0.073	-0.073	0.000	0.000	0.000	0.000
79	B	78	THR	0	-0.011	-0.013	30.507	0.000	0.000	0.000	0.000	0.000	0.000
80	B	79	ILE	0	-0.047	-0.019	29.110	-0.005	-0.005	0.000	0.000	0.000	0.000
81	B	80	GLU	-1	-0.896	-0.949	31.961	-0.075	-0.075	0.000	0.000	0.000	0.000
82	B	81	GLU	-1	-0.790	-0.849	32.741	-0.078	-0.078	0.000	0.000	0.000	0.000
83	B	82	ARG	1	0.818	0.884	26.612	0.121	0.121	0.000	0.000	0.000	0.000
84	B	83	LEU	0	-0.006	0.005	29.654	-0.007	-0.007	0.000	0.000	0.000	0.000
85	B	84	SER	0	0.017	0.004	31.437	0.000	0.000	0.000	0.000	0.000	0.000
86	B	85	LEU	0	-0.003	-0.003	28.355	0.002	0.002	0.000	0.000	0.000	0.000
87	B	86	PHE	0	0.007	-0.005	23.909	-0.003	-0.003	0.000	0.000	0.000	0.000
88	B	87	GLU	-1	-0.923	-0.934	29.412	-0.081	-0.081	0.000	0.000	0.000	0.000
89	B	88	ASN	0	-0.014	-0.014	32.778	0.006	0.006	0.000	0.000	0.000	0.000
90	B	89	GLN	0	0.030	0.011	27.926	0.010	0.010	0.000	0.000	0.000	0.000
91	B	90	THR	0	-0.045	-0.045	27.901	0.001	0.001	0.000	0.000	0.000	0.000
92	B	91	LYS	1	0.909	0.958	30.299	0.075	0.075	0.000	0.000	0.000	0.000
93	B	92	ASN	0	0.008	0.009	31.739	0.007	0.007	0.000	0.000	0.000	0.000
94	B	93	VAL	0	0.047	0.018	27.517	0.003	0.003	0.000	0.000	0.000	0.000
95	B	94	LYS	1	0.922	0.959	30.727	0.103	0.103	0.000	0.000	0.000	0.000
96	B	95	CYS	0	-0.024	-0.008	33.244	0.005	0.005	0.000	0.000	0.000	0.000
97	B	96	GLN	0	-0.053	-0.037	30.191	0.000	0.000	0.000	0.000	0.000	0.000
98	B	97	ILE	0	-0.013	-0.013	28.883	0.003	0.003	0.000	0.000	0.000	0.000
99	B	98	ALA	0	-0.027	-0.009	32.892	0.003	0.003	0.000	0.000	0.000	0.000
100	B	99	GLU	-1	-0.778	-0.856	36.479	-0.048	-0.048	0.000	0.000	0.000	0.000
101	B	100	LEU	0	-0.020	-0.017	31.006	0.003	0.003	0.000	0.000	0.000	0.000
102	B	101	LYS	1	0.944	0.974	33.316	0.080	0.080	0.000	0.000	0.000	0.000
103	B	102	ARG	1	0.870	0.919	36.731	0.050	0.050	0.000	0.000	0.000	0.000
104	B	103	TYR	0	-0.063	-0.047	37.498	0.005	0.005	0.000	0.000	0.000	0.000
105	B	104	LEU	0	-0.008	0.004	34.374	0.002	0.002	0.000	0.000	0.000	0.000
106	B	105	ASP	-1	-0.855	-0.918	37.919	-0.048	-0.048	0.000	0.000	0.000	0.000
107	B	106	LEU	0	-0.039	-0.021	41.147	0.003	0.003	0.000	0.000	0.000	0.000
108	B	107	LEU	0	-0.010	-0.010	37.357	0.003	0.003	0.000	0.000	0.000	0.000
109	B	108	GLU	-1	-0.890	-0.948	36.602	-0.049	-0.049	0.000	0.000	0.000	0.000
110	B	109	TYR	0	-0.007	0.002	40.749	0.003	0.003	0.000	0.000	0.000	0.000
111	B	110	LYS	1	0.869	0.929	43.818	0.028	0.028	0.000	0.000	0.000	0.000
112	B	111	LEU	0	-0.004	0.009	38.431	0.003	0.003	0.000	0.000	0.000	0.000
113	B	112	ALA	0	0.056	0.026	42.538	0.002	0.002	0.000	0.000	0.000	0.000
114	B	113	PHE	0	-0.049	-0.023	44.858	0.002	0.002	0.000	0.000	0.000	0.000
115	B	114	TYR	0	0.046	0.002	44.867	0.002	0.002	0.000	0.000	0.000	0.000
116	B	115	GLN	0	0.000	0.007	40.609	0.001	0.001	0.000	0.000	0.000	0.000
117	B	116	LYS	1	0.978	0.989	45.784	0.024	0.024	0.000	0.000	0.000	0.000
118	B	117	ALA	0	-0.015	-0.007	49.314	0.001	0.001	0.000	0.000	0.000	0.000
119	B	118	LYS	1	0.965	0.976	43.832	0.019	0.019	0.000	0.000	0.000	0.000
120	B	119	ALA	0	-0.030	-0.015	48.780	0.001	0.001	0.000	0.000	0.000	0.000
121	B	120	LEU	0	-0.024	-0.010	50.330	0.001	0.001	0.000	0.000	0.000	0.000
122	B	121	GLY	0	0.032	0.025	52.538	0.001	0.001	0.000	0.000	0.000	0.000
123	B	122	SER	0	0.007	0.007	53.541	0.001	0.001	0.000	0.000	0.000	0.000
124	B	123	VAL	0	-0.006	0.006	51.972	-0.001	-0.001	0.000	0.000	0.000	0.000
125	B	124	LYS	1	0.866	0.935	54.435	0.017	0.017	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(B:0:GLY)