FMO DATABASE

FMODB ID: VQY11

Calculation Name: 3KXY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KXY

Chain ID: A

ChEMBL ID:

UniProt ID: P26995

Base Structure: X-ray

Registration Date: 2023-09-23

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	133
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1130836.71989
FMO2-HF: Nuclear repulsion	1078666.005078
FMO2-HF: Total energy	-52170.714812
FMO2-MP2: Total energy	-52323.606327

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:1:MET)

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

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.
-3.454	2.891	7.016	-4.334	-9.027	-0.02

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / 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	3	LEU	0	0.015	0.023	3.355	-3.490	-1.068	0.028	-1.384	-1.066	0.002
4	A	4	THR	0	0.064	0.006	5.682	0.014	0.014	0.000	0.000	0.000	0.000
5	A	5	SER	0	-0.039	-0.055	2.837	-2.137	-0.690	3.954	-2.138	-3.262	-0.012
6	A	6	LYS	1	0.820	0.902	2.445	1.833	4.826	2.927	-1.841	-4.079	-0.009
7	A	7	VAL	0	0.056	0.029	2.976	1.781	0.901	0.092	1.088	-0.301	-0.001
8	A	8	ASN	0	0.090	0.043	5.782	0.220	0.220	0.000	0.000	0.000	0.000
9	A	9	ARG	1	0.797	0.889	3.395	0.631	0.964	0.016	-0.058	-0.291	0.000
10	A	10	LEU	0	-0.016	-0.014	5.278	0.376	0.406	-0.001	-0.001	-0.028	0.000
11	A	11	LEU	0	0.044	0.016	8.257	0.217	0.217	0.000	0.000	0.000	0.000
12	A	12	ALA	0	0.010	0.011	8.256	0.145	0.145	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.884	-0.928	9.200	-0.497	-0.497	0.000	0.000	0.000	0.000
14	A	14	PHE	0	0.004	-0.008	11.024	0.078	0.078	0.000	0.000	0.000	0.000
15	A	15	ALA	0	0.005	0.008	13.171	0.055	0.055	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.014	0.007	13.923	0.043	0.043	0.000	0.000	0.000	0.000
17	A	17	ARG	1	0.723	0.819	14.438	0.351	0.351	0.000	0.000	0.000	0.000
18	A	18	ILE	0	-0.023	0.003	17.316	0.016	0.016	0.000	0.000	0.000	0.000
19	A	19	GLY	0	-0.026	-0.001	18.947	0.016	0.016	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.005	0.003	17.320	0.024	0.024	0.000	0.000	0.000	0.000
21	A	21	PRO	0	-0.048	-0.037	16.869	-0.004	-0.004	0.000	0.000	0.000	0.000
22	A	22	SER	0	-0.042	-0.022	12.959	0.018	0.018	0.000	0.000	0.000	0.000
23	A	23	LEU	0	0.048	0.024	12.441	-0.004	-0.004	0.000	0.000	0.000	0.000
24	A	24	SER	0	-0.115	-0.066	10.124	-0.006	-0.006	0.000	0.000	0.000	0.000
25	A	25	LEU	0	-0.038	-0.019	9.916	-0.013	-0.013	0.000	0.000	0.000	0.000
26	A	26	ASP	-1	-0.862	-0.928	12.701	-0.110	-0.110	0.000	0.000	0.000	0.000
27	A	27	GLU	-1	-0.969	-0.994	14.157	-0.105	-0.105	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.952	-0.973	15.216	-0.240	-0.240	0.000	0.000	0.000	0.000
29	A	29	GLY	0	-0.053	-0.021	13.174	-0.057	-0.057	0.000	0.000	0.000	0.000
30	A	30	MET	0	-0.054	-0.023	14.172	-0.064	-0.064	0.000	0.000	0.000	0.000
31	A	31	ALA	0	0.067	0.036	15.048	0.012	0.012	0.000	0.000	0.000	0.000
32	A	32	SER	0	-0.015	-0.018	16.968	-0.021	-0.021	0.000	0.000	0.000	0.000
33	A	33	LEU	0	-0.054	-0.028	17.548	0.011	0.011	0.000	0.000	0.000	0.000
34	A	34	LEU	0	-0.017	-0.008	21.480	0.003	0.003	0.000	0.000	0.000	0.000
35	A	35	PHE	0	0.020	0.009	20.812	0.001	0.001	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.865	-0.944	26.553	-0.117	-0.117	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.990	-0.990	29.215	-0.064	-0.064	0.000	0.000	0.000	0.000
38	A	38	GLN	0	-0.084	-0.039	30.399	0.007	0.007	0.000	0.000	0.000	0.000
39	A	39	VAL	0	-0.026	-0.005	26.723	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	40	GLY	0	0.041	0.023	26.005	-0.005	-0.005	0.000	0.000	0.000	0.000
41	A	41	VAL	0	-0.023	-0.020	20.476	-0.009	-0.009	0.000	0.000	0.000	0.000
42	A	42	THR	0	0.021	0.016	20.111	0.015	0.015	0.000	0.000	0.000	0.000
43	A	43	LEU	0	-0.030	-0.001	14.736	-0.033	-0.033	0.000	0.000	0.000	0.000
44	A	44	LEU	0	0.048	0.022	16.451	0.009	0.009	0.000	0.000	0.000	0.000
45	A	45	LEU	0	-0.013	-0.005	9.103	-0.081	-0.081	0.000	0.000	0.000	0.000
46	A	46	LEU	0	0.039	0.022	13.539	0.024	0.024	0.000	0.000	0.000	0.000
47	A	47	ALA	0	0.018	-0.003	10.783	-0.052	-0.052	0.000	0.000	0.000	0.000
48	A	48	GLU	-1	-0.848	-0.892	12.429	-0.610	-0.610	0.000	0.000	0.000	0.000
49	A	49	ARG	1	0.739	0.830	14.704	0.556	0.556	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.922	-0.963	10.668	-1.438	-1.438	0.000	0.000	0.000	0.000
51	A	51	ARG	1	0.859	0.937	13.324	0.585	0.585	0.000	0.000	0.000	0.000
52	A	52	LEU	0	0.011	0.019	11.860	-0.029	-0.029	0.000	0.000	0.000	0.000
53	A	53	LEU	0	-0.026	-0.020	14.455	0.041	0.041	0.000	0.000	0.000	0.000
54	A	54	LEU	0	-0.006	-0.004	16.189	-0.018	-0.018	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.870	-0.951	19.629	-0.267	-0.267	0.000	0.000	0.000	0.000
56	A	56	ALA	0	0.015	0.006	22.911	0.001	0.001	0.000	0.000	0.000	0.000
57	A	57	ASP	-1	-0.796	-0.877	25.543	-0.156	-0.156	0.000	0.000	0.000	0.000
58	A	58	VAL	0	-0.064	-0.025	29.017	0.000	0.000	0.000	0.000	0.000	0.000
59	A	59	VAL	0	0.000	-0.015	31.899	0.008	0.008	0.000	0.000	0.000	0.000
60	A	60	GLY	0	0.047	0.044	35.089	-0.005	-0.005	0.000	0.000	0.000	0.000
61	A	61	ILE	0	0.009	-0.025	37.155	0.002	0.002	0.000	0.000	0.000	0.000
62	A	62	ASP	-1	-0.935	-0.965	39.588	-0.087	-0.087	0.000	0.000	0.000	0.000
63	A	63	VAL	0	-0.006	0.003	40.284	0.005	0.005	0.000	0.000	0.000	0.000
64	A	64	LEU	0	-0.023	0.008	38.528	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	65	GLY	0	0.027	0.004	42.739	0.005	0.005	0.000	0.000	0.000	0.000
66	A	66	GLU	-1	-0.883	-0.941	44.749	-0.088	-0.088	0.000	0.000	0.000	0.000
67	A	67	GLY	0	-0.042	-0.037	45.342	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	68	ILE	0	0.013	0.013	39.622	-0.005	-0.005	0.000	0.000	0.000	0.000
69	A	69	PHE	0	0.092	0.039	36.689	-0.006	-0.006	0.000	0.000	0.000	0.000
70	A	70	ARG	1	0.934	0.971	39.442	0.095	0.095	0.000	0.000	0.000	0.000
71	A	71	GLN	0	-0.030	-0.003	41.137	-0.004	-0.004	0.000	0.000	0.000	0.000
72	A	72	LEU	0	0.077	0.042	35.540	-0.004	-0.004	0.000	0.000	0.000	0.000
73	A	73	ALA	0	0.004	0.009	36.119	-0.010	-0.010	0.000	0.000	0.000	0.000
74	A	74	SER	0	-0.085	-0.059	37.429	-0.004	-0.004	0.000	0.000	0.000	0.000
75	A	75	PHE	0	-0.019	0.000	31.690	0.002	0.002	0.000	0.000	0.000	0.000
76	A	76	ASN	0	0.075	0.034	32.176	-0.009	-0.009	0.000	0.000	0.000	0.000
77	A	77	ARG	1	0.852	0.935	33.477	0.136	0.136	0.000	0.000	0.000	0.000
78	A	78	HIS	0	-0.122	-0.083	35.097	0.004	0.004	0.000	0.000	0.000	0.000
79	A	79	TRP	0	0.058	0.032	27.147	0.014	0.014	0.000	0.000	0.000	0.000
80	A	80	HIS	0	-0.002	0.009	29.377	-0.004	-0.004	0.000	0.000	0.000	0.000
81	A	81	ARG	1	0.874	0.939	30.322	0.159	0.159	0.000	0.000	0.000	0.000
82	A	82	PHE	0	-0.026	-0.020	29.528	0.011	0.011	0.000	0.000	0.000	0.000
83	A	83	ASP	-1	-0.899	-0.944	24.566	-0.332	-0.332	0.000	0.000	0.000	0.000
84	A	84	LEU	0	-0.005	0.018	24.923	-0.019	-0.019	0.000	0.000	0.000	0.000
85	A	85	HIS	0	-0.069	-0.033	25.349	0.015	0.015	0.000	0.000	0.000	0.000
86	A	86	PHE	0	0.023	-0.003	28.531	-0.006	-0.006	0.000	0.000	0.000	0.000
87	A	87	GLY	0	-0.004	-0.008	30.381	-0.006	-0.006	0.000	0.000	0.000	0.000
88	A	88	PHE	0	-0.053	-0.032	31.293	0.007	0.007	0.000	0.000	0.000	0.000
89	A	89	ASP	-1	-0.750	-0.841	30.399	-0.147	-0.147	0.000	0.000	0.000	0.000
90	A	90	GLU	-1	-0.913	-0.975	32.529	-0.107	-0.107	0.000	0.000	0.000	0.000
91	A	91	LEU	0	-0.107	-0.047	30.877	0.010	0.010	0.000	0.000	0.000	0.000
92	A	92	THR	0	-0.065	-0.055	30.647	0.007	0.007	0.000	0.000	0.000	0.000
93	A	93	GLY	0	0.015	0.015	33.873	0.004	0.004	0.000	0.000	0.000	0.000
94	A	94	LYS	1	0.882	0.941	31.112	0.134	0.134	0.000	0.000	0.000	0.000
95	A	95	VAL	0	-0.008	-0.007	32.920	-0.007	-0.007	0.000	0.000	0.000	0.000
96	A	96	GLN	0	-0.005	-0.006	27.039	-0.008	-0.008	0.000	0.000	0.000	0.000
97	A	97	LEU	0	-0.024	-0.018	27.440	0.005	0.005	0.000	0.000	0.000	0.000
98	A	98	TYR	0	-0.012	-0.007	24.040	-0.007	-0.007	0.000	0.000	0.000	0.000
99	A	99	ALA	0	0.051	0.016	21.336	0.012	0.012	0.000	0.000	0.000	0.000
100	A	100	GLN	0	-0.017	-0.007	18.736	-0.041	-0.041	0.000	0.000	0.000	0.000
101	A	101	ILE	0	0.017	0.023	14.691	0.018	0.018	0.000	0.000	0.000	0.000
102	A	102	LEU	0	0.019	0.007	15.071	-0.058	-0.058	0.000	0.000	0.000	0.000
103	A	103	ALA	0	0.035	0.008	9.984	-0.018	-0.018	0.000	0.000	0.000	0.000
104	A	104	ALA	0	-0.045	-0.022	11.275	-0.088	-0.088	0.000	0.000	0.000	0.000
105	A	105	GLN	0	0.004	-0.014	13.403	0.059	0.059	0.000	0.000	0.000	0.000
106	A	106	LEU	0	0.002	0.028	10.002	0.077	0.077	0.000	0.000	0.000	0.000
107	A	107	THR	0	0.015	0.003	10.257	-0.160	-0.160	0.000	0.000	0.000	0.000
108	A	108	LEU	0	0.021	0.006	11.318	0.024	0.024	0.000	0.000	0.000	0.000
109	A	109	GLU	-1	-0.921	-0.960	12.774	-0.372	-0.372	0.000	0.000	0.000	0.000
110	A	110	CYS	0	-0.041	-0.014	14.903	0.060	0.060	0.000	0.000	0.000	0.000
111	A	111	PHE	0	0.021	0.010	13.351	0.022	0.022	0.000	0.000	0.000	0.000
112	A	112	GLU	-1	-0.763	-0.851	15.455	-0.314	-0.314	0.000	0.000	0.000	0.000
113	A	113	ALA	0	-0.003	0.005	18.003	0.039	0.039	0.000	0.000	0.000	0.000
114	A	114	THR	0	-0.034	-0.036	18.512	0.034	0.034	0.000	0.000	0.000	0.000
115	A	115	LEU	0	-0.021	-0.004	18.222	0.025	0.025	0.000	0.000	0.000	0.000
116	A	116	ALA	0	0.010	0.007	20.602	0.027	0.027	0.000	0.000	0.000	0.000
117	A	117	ASN	0	0.057	0.026	23.552	0.036	0.036	0.000	0.000	0.000	0.000
118	A	118	LEU	0	-0.021	-0.007	22.147	0.017	0.017	0.000	0.000	0.000	0.000
119	A	119	LEU	0	0.006	0.005	23.342	0.019	0.019	0.000	0.000	0.000	0.000
120	A	120	ASP	-1	-0.892	-0.939	26.482	-0.180	-0.180	0.000	0.000	0.000	0.000
121	A	121	HIS	0	-0.088	-0.059	28.282	0.025	0.025	0.000	0.000	0.000	0.000
122	A	122	ALA	0	-0.016	-0.001	28.265	0.012	0.012	0.000	0.000	0.000	0.000
123	A	123	GLU	-1	-0.775	-0.878	30.211	-0.124	-0.124	0.000	0.000	0.000	0.000
124	A	124	PHE	0	-0.062	-0.030	32.478	0.013	0.013	0.000	0.000	0.000	0.000
125	A	125	TRP	0	-0.009	-0.019	32.263	0.015	0.015	0.000	0.000	0.000	0.000
126	A	126	GLN	0	-0.016	-0.003	32.631	0.012	0.012	0.000	0.000	0.000	0.000
127	A	127	ARG	1	0.764	0.862	34.148	0.129	0.129	0.000	0.000	0.000	0.000
128	A	128	LEU	0	-0.080	-0.027	38.314	0.006	0.006	0.000	0.000	0.000	0.000
129	A	129	LEU	0	-0.025	-0.019	36.119	0.002	0.002	0.000	0.000	0.000	0.000
130	A	130	PRO	0	-0.023	0.000	39.299	0.003	0.003	0.000	0.000	0.000	0.000
131	A	131	CYS	0	-0.079	-0.021	42.288	0.003	0.003	0.000	0.000	0.000	0.000
132	A	132	ALA	0	-0.020	-0.011	45.767	0.004	0.004	0.000	0.000	0.000	0.000
133	A	133	SER	0	-0.003	0.002	45.773	-0.001	-0.001	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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