FMO DATABASE

FMODB ID: VQ511

Calculation Name: 3KTO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KTO

Chain ID: A

ChEMBL ID:

UniProt ID: Q15U25

Base Structure: X-ray

Registration Date: 2023-09-21

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	OptHSide
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	122
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1016273.508736
FMO2-HF: Nuclear repulsion	968870.80042
FMO2-HF: Total energy	-47402.708316
FMO2-MP2: Total energy	-47540.109446

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:12:PRO)

Summations of interaction energy for fragment #1(A:12: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.
-12.001	-3.177	4.508	-5.039	-8.291	-0.02

Interaction energy analysis for fragmet #1(A:12:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.003 / q_NPA : 0.009

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	14	ILE	0	0.015	0.015	3.789	-2.183	0.062	-0.033	-1.099	-1.112	0.004
4	A	15	TYR	0	-0.003	0.005	6.775	0.107	0.107	0.000	0.000	0.000	0.000
5	A	16	LEU	0	0.007	0.001	10.098	-0.061	-0.061	0.000	0.000	0.000	0.000
6	A	17	VAL	0	-0.011	-0.009	13.006	0.039	0.039	0.000	0.000	0.000	0.000
7	A	18	ASP	-1	-0.759	-0.911	16.560	0.001	0.001	0.000	0.000	0.000	0.000
8	A	19	HIS	0	0.089	0.075	19.231	0.021	0.021	0.000	0.000	0.000	0.000
9	A	20	GLN	0	-0.028	-0.015	21.876	0.006	0.006	0.000	0.000	0.000	0.000
10	A	21	LYS	1	0.875	0.911	21.021	-0.050	-0.050	0.000	0.000	0.000	0.000
11	A	22	ASP	-1	-0.838	-0.916	20.839	0.050	0.050	0.000	0.000	0.000	0.000
12	A	23	ALA	0	0.035	0.039	19.457	-0.004	-0.004	0.000	0.000	0.000	0.000
13	A	24	ARG	1	0.897	0.950	16.426	-0.108	-0.108	0.000	0.000	0.000	0.000
14	A	25	ALA	0	-0.009	0.012	16.033	0.008	0.008	0.000	0.000	0.000	0.000
15	A	26	ALA	0	-0.053	-0.052	17.116	-0.002	-0.002	0.000	0.000	0.000	0.000
16	A	27	LEU	0	0.042	0.012	13.952	-0.012	-0.012	0.000	0.000	0.000	0.000
17	A	28	SER	0	0.002	-0.009	12.352	-0.013	-0.013	0.000	0.000	0.000	0.000
18	A	29	LYS	1	0.872	0.938	12.691	-0.047	-0.047	0.000	0.000	0.000	0.000
19	A	30	LEU	0	0.008	0.008	14.506	-0.013	-0.013	0.000	0.000	0.000	0.000
20	A	31	LEU	0	0.021	0.006	9.363	-0.027	-0.027	0.000	0.000	0.000	0.000
21	A	32	SER	0	-0.028	-0.001	9.307	-0.062	-0.062	0.000	0.000	0.000	0.000
22	A	33	PRO	0	-0.078	-0.025	9.435	-0.019	-0.019	0.000	0.000	0.000	0.000
23	A	34	LEU	0	-0.017	-0.008	7.497	-0.034	-0.034	0.000	0.000	0.000	0.000
24	A	35	ASP	-1	-0.924	-0.958	4.006	-2.622	-2.192	0.003	-0.115	-0.319	-0.001
25	A	36	VAL	0	-0.006	-0.011	2.307	-3.565	-1.455	0.915	-0.972	-2.053	-0.003
26	A	37	THR	0	-0.005	0.010	3.714	-0.440	0.449	0.004	-0.274	-0.619	0.001
27	A	38	ILE	0	0.010	-0.005	5.636	-0.204	-0.204	0.000	0.000	0.000	0.000
28	A	39	GLN	0	0.016	0.021	8.528	0.189	0.189	0.000	0.000	0.000	0.000
29	A	40	CYS	0	-0.037	-0.016	10.311	-0.110	-0.110	0.000	0.000	0.000	0.000
30	A	41	PHE	0	0.004	-0.001	12.099	0.022	0.022	0.000	0.000	0.000	0.000
31	A	42	ALA	0	-0.041	-0.026	16.721	-0.024	-0.024	0.000	0.000	0.000	0.000
32	A	43	SER	0	0.078	0.036	19.800	-0.010	-0.010	0.000	0.000	0.000	0.000
33	A	44	ALA	0	0.091	0.039	19.607	0.012	0.012	0.000	0.000	0.000	0.000
34	A	45	GLU	-1	-0.862	-0.907	20.258	0.095	0.095	0.000	0.000	0.000	0.000
35	A	46	SER	0	-0.060	-0.037	19.544	0.015	0.015	0.000	0.000	0.000	0.000
36	A	47	PHE	0	0.079	0.025	12.105	0.013	0.013	0.000	0.000	0.000	0.000
37	A	48	MET	0	-0.019	-0.004	16.346	0.013	0.013	0.000	0.000	0.000	0.000
38	A	49	ARG	1	0.783	0.884	18.681	-0.121	-0.121	0.000	0.000	0.000	0.000
39	A	50	GLN	0	-0.064	-0.031	12.035	0.016	0.016	0.000	0.000	0.000	0.000
40	A	51	GLN	0	-0.019	-0.009	13.417	-0.055	-0.055	0.000	0.000	0.000	0.000
41	A	52	ILE	0	-0.018	-0.001	10.163	0.078	0.078	0.000	0.000	0.000	0.000
42	A	53	SER	0	-0.009	-0.025	6.768	-0.080	-0.080	0.000	0.000	0.000	0.000
43	A	54	ASP	-1	-0.925	-0.955	7.749	0.102	0.102	0.000	0.000	0.000	0.000
44	A	55	ASP	-1	-0.879	-0.926	3.038	0.434	1.029	0.056	-0.171	-0.480	0.000
45	A	56	ALA	0	-0.074	-0.026	2.388	-2.550	-1.307	2.441	-1.921	-1.763	-0.021
46	A	57	ILE	0	0.004	0.000	2.327	-1.218	-0.216	1.123	-0.453	-1.672	0.000
47	A	58	GLY	0	0.009	-0.007	5.379	-0.009	0.023	-0.001	0.000	-0.029	0.000
48	A	59	MET	0	-0.073	-0.028	8.071	0.059	0.059	0.000	0.000	0.000	0.000
49	A	60	ILE	0	0.016	0.012	10.470	-0.028	-0.028	0.000	0.000	0.000	0.000
50	A	61	ILE	0	-0.016	-0.009	13.333	0.034	0.034	0.000	0.000	0.000	0.000
51	A	62	GLU	-1	-0.801	-0.875	16.840	-0.014	-0.014	0.000	0.000	0.000	0.000
52	A	63	ALA	0	0.044	-0.005	20.093	0.006	0.006	0.000	0.000	0.000	0.000
53	A	64	HIS	0	-0.028	-0.001	22.758	0.006	0.006	0.000	0.000	0.000	0.000
54	A	65	LEU	0	0.008	0.010	20.155	0.005	0.005	0.000	0.000	0.000	0.000
55	A	66	GLU	-1	-0.917	-0.978	24.266	0.059	0.059	0.000	0.000	0.000	0.000
56	A	67	ASP	-1	-0.939	-0.963	27.097	0.015	0.015	0.000	0.000	0.000	0.000
57	A	68	LYS	1	0.806	0.918	27.957	-0.043	-0.043	0.000	0.000	0.000	0.000
58	A	69	LYS	1	0.858	0.908	27.836	0.007	0.007	0.000	0.000	0.000	0.000
59	A	70	ASP	-1	-0.769	-0.888	26.213	-0.007	-0.007	0.000	0.000	0.000	0.000
60	A	71	SER	0	0.004	-0.006	25.388	0.001	0.001	0.000	0.000	0.000	0.000
61	A	72	GLY	0	-0.017	-0.009	21.399	0.005	0.005	0.000	0.000	0.000	0.000
62	A	73	ILE	0	-0.023	-0.014	20.701	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	74	GLU	-1	-0.864	-0.907	22.374	0.012	0.012	0.000	0.000	0.000	0.000
64	A	75	LEU	0	-0.048	-0.013	17.465	0.003	0.003	0.000	0.000	0.000	0.000
65	A	76	LEU	0	0.017	0.006	16.491	0.005	0.005	0.000	0.000	0.000	0.000
66	A	77	GLU	-1	-0.762	-0.868	19.147	-0.011	-0.011	0.000	0.000	0.000	0.000
67	A	78	THR	0	-0.093	-0.056	21.304	0.001	0.001	0.000	0.000	0.000	0.000
68	A	79	LEU	0	-0.029	-0.023	15.065	0.005	0.005	0.000	0.000	0.000	0.000
69	A	80	VAL	0	0.054	0.042	17.937	0.000	0.000	0.000	0.000	0.000	0.000
70	A	81	LYS	1	0.904	0.960	19.261	-0.008	-0.008	0.000	0.000	0.000	0.000
71	A	82	ARG	1	0.821	0.903	19.313	-0.054	-0.054	0.000	0.000	0.000	0.000
72	A	83	GLY	0	0.033	0.023	18.737	0.007	0.007	0.000	0.000	0.000	0.000
73	A	84	PHE	0	-0.005	0.006	12.885	-0.007	-0.007	0.000	0.000	0.000	0.000
74	A	85	HIS	0	-0.038	-0.031	14.033	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	86	LEU	0	0.033	0.026	8.273	-0.022	-0.022	0.000	0.000	0.000	0.000
76	A	87	PRO	0	0.012	0.012	9.352	0.026	0.026	0.000	0.000	0.000	0.000
77	A	88	THR	0	0.013	0.001	11.007	0.001	0.001	0.000	0.000	0.000	0.000
78	A	89	ILE	0	-0.005	0.012	11.709	0.002	0.002	0.000	0.000	0.000	0.000
79	A	90	VAL	0	0.006	-0.001	14.975	0.017	0.017	0.000	0.000	0.000	0.000
80	A	91	MET	0	-0.019	-0.002	16.852	-0.007	-0.007	0.000	0.000	0.000	0.000
81	A	92	ALA	0	0.033	0.021	19.776	0.011	0.011	0.000	0.000	0.000	0.000
82	A	93	SER	0	-0.014	0.007	23.396	-0.004	-0.004	0.000	0.000	0.000	0.000
83	A	94	SER	0	-0.026	-0.011	25.839	0.000	0.000	0.000	0.000	0.000	0.000
84	A	95	SER	0	0.059	0.007	26.788	0.000	0.000	0.000	0.000	0.000	0.000
85	A	96	ASP	-1	-0.811	-0.869	28.922	-0.014	-0.014	0.000	0.000	0.000	0.000
86	A	97	ILE	0	0.045	-0.004	29.887	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	98	PRO	0	-0.016	-0.016	30.133	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	99	THR	0	0.007	-0.003	26.136	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	100	ALA	0	0.027	0.026	25.506	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	101	VAL	0	-0.022	-0.020	25.420	-0.004	-0.004	0.000	0.000	0.000	0.000
91	A	102	ARG	1	0.706	0.815	26.203	0.001	0.001	0.000	0.000	0.000	0.000
92	A	103	ALA	0	0.037	0.014	21.908	0.000	0.000	0.000	0.000	0.000	0.000
93	A	104	MET	0	-0.011	-0.004	20.566	-0.004	-0.004	0.000	0.000	0.000	0.000
94	A	105	ARG	1	0.891	0.942	22.891	0.027	0.027	0.000	0.000	0.000	0.000
95	A	106	ALA	0	-0.027	0.009	21.857	0.001	0.001	0.000	0.000	0.000	0.000
96	A	107	SER	0	-0.065	-0.043	18.593	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	108	ALA	0	-0.004	0.011	17.330	-0.011	-0.011	0.000	0.000	0.000	0.000
98	A	109	ALA	0	-0.033	-0.024	14.422	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	110	ASP	-1	-0.830	-0.891	16.400	-0.115	-0.115	0.000	0.000	0.000	0.000
100	A	111	PHE	0	-0.034	-0.024	18.312	0.009	0.009	0.000	0.000	0.000	0.000
101	A	112	ILE	0	-0.032	-0.016	16.283	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	113	GLU	-1	-0.933	-0.960	20.688	-0.032	-0.032	0.000	0.000	0.000	0.000
103	A	114	LYS	1	0.788	0.878	19.773	0.000	0.000	0.000	0.000	0.000	0.000
104	A	115	PRO	0	0.017	-0.013	23.630	0.005	0.005	0.000	0.000	0.000	0.000
105	A	116	PHE	0	0.017	0.019	17.267	0.000	0.000	0.000	0.000	0.000	0.000
106	A	117	ILE	0	0.011	0.010	21.583	0.003	0.003	0.000	0.000	0.000	0.000
107	A	118	GLU	-1	-0.905	-0.965	17.902	-0.094	-0.094	0.000	0.000	0.000	0.000
108	A	119	HIS	0	0.045	0.012	16.800	-0.014	-0.014	0.000	0.000	0.000	0.000
109	A	120	VAL	0	0.005	0.015	16.903	-0.020	-0.020	0.000	0.000	0.000	0.000
110	A	121	LEU	0	0.037	0.020	13.447	-0.015	-0.015	0.000	0.000	0.000	0.000
111	A	122	VAL	0	0.007	-0.009	12.411	-0.029	-0.029	0.000	0.000	0.000	0.000
112	A	123	HIS	0	-0.033	-0.010	11.951	-0.058	-0.058	0.000	0.000	0.000	0.000
113	A	124	ASH	0	-0.047	-0.074	12.801	-0.034	-0.034	0.000	0.000	0.000	0.000
114	A	125	VAL	0	0.004	0.000	7.488	-0.020	-0.020	0.000	0.000	0.000	0.000
115	A	126	GLN	0	0.024	0.011	8.046	-0.182	-0.182	0.000	0.000	0.000	0.000
116	A	127	GLN	0	-0.020	0.002	9.119	-0.052	-0.052	0.000	0.000	0.000	0.000
117	A	128	ILE	0	0.000	0.002	6.334	-0.009	-0.009	0.000	0.000	0.000	0.000
118	A	129	ILE	0	0.015	0.006	3.896	-0.242	-0.005	0.001	-0.030	-0.208	0.000
119	A	130	ASN	0	-0.035	-0.047	5.775	-0.160	-0.160	0.000	0.000	0.000	0.000
120	A	131	GLY	0	-0.042	-0.011	8.567	0.016	0.016	0.000	0.000	0.000	0.000
121	A	132	ALA	0	-0.021	0.010	4.709	0.005	0.046	-0.001	-0.004	-0.036	0.000
122	A	133	LYS	1	0.826	0.928	4.852	1.400	1.400	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:12:PRO)