FMO DATABASE

FMODB ID: 1N7GZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1019456.362571
FMO2-HF: Nuclear repulsion	972053.509586
FMO2-HF: Total energy	-47402.852985
FMO2-MP2: Total energy	-47540.230616

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.
-12.437	-2.44	3.847	-5.205	-8.64	-0.029

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 : 0.012 / q_NPA : 0.017

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	0.002	0.012	3.880	-1.404	0.304	-0.016	-0.840	-0.852	0.003
4	A	15	TYR	0	-0.001	0.005	6.545	0.109	0.109	0.000	0.000	0.000	0.000
5	A	16	LEU	0	0.003	0.004	10.173	-0.047	-0.047	0.000	0.000	0.000	0.000
6	A	17	VAL	0	-0.006	-0.003	12.682	0.045	0.045	0.000	0.000	0.000	0.000
7	A	18	ASP	-1	-0.756	-0.893	16.172	-0.052	-0.052	0.000	0.000	0.000	0.000
8	A	19	HIS	0	0.091	0.069	18.807	0.016	0.016	0.000	0.000	0.000	0.000
9	A	20	GLN	0	-0.013	-0.006	21.902	0.013	0.013	0.000	0.000	0.000	0.000
10	A	21	LYS	1	0.852	0.900	20.905	-0.024	-0.024	0.000	0.000	0.000	0.000
11	A	22	ASP	-1	-0.814	-0.893	20.704	0.010	0.010	0.000	0.000	0.000	0.000
12	A	23	ALA	0	0.030	0.026	19.663	-0.008	-0.008	0.000	0.000	0.000	0.000
13	A	24	ARG	1	0.886	0.935	16.425	-0.064	-0.064	0.000	0.000	0.000	0.000
14	A	25	ALA	0	0.012	0.017	16.001	-0.006	-0.006	0.000	0.000	0.000	0.000
15	A	26	ALA	0	-0.064	-0.039	17.443	-0.008	-0.008	0.000	0.000	0.000	0.000
16	A	27	LEU	0	0.048	0.014	13.685	-0.015	-0.015	0.000	0.000	0.000	0.000
17	A	28	SER	0	0.008	-0.012	12.428	-0.030	-0.030	0.000	0.000	0.000	0.000
18	A	29	LYS	1	0.883	0.946	12.758	0.012	0.012	0.000	0.000	0.000	0.000
19	A	30	LEU	0	0.003	0.010	14.430	-0.018	-0.018	0.000	0.000	0.000	0.000
20	A	31	LEU	0	0.005	-0.005	9.447	-0.029	-0.029	0.000	0.000	0.000	0.000
21	A	32	SER	0	-0.035	-0.007	9.451	-0.089	-0.089	0.000	0.000	0.000	0.000
22	A	33	PRO	0	-0.071	-0.021	9.775	-0.018	-0.018	0.000	0.000	0.000	0.000
23	A	34	LEU	0	-0.011	-0.021	7.863	-0.013	-0.013	0.000	0.000	0.000	0.000
24	A	35	ASP	-1	-0.875	-0.916	3.779	-3.034	-2.483	0.009	-0.179	-0.381	-0.001
25	A	36	VAL	0	-0.011	-0.019	2.556	-4.736	-1.997	0.904	-1.285	-2.359	-0.011
26	A	37	THR	0	-0.015	0.008	3.350	-0.388	0.764	0.011	-0.391	-0.772	0.001
27	A	38	ILE	0	0.016	-0.002	5.294	-0.187	-0.159	-0.001	-0.009	-0.018	0.000
28	A	39	GLN	0	0.009	0.008	8.417	0.234	0.234	0.000	0.000	0.000	0.000
29	A	40	CYS	0	-0.037	-0.013	10.095	-0.085	-0.085	0.000	0.000	0.000	0.000
30	A	41	PHE	0	-0.009	-0.008	12.009	0.039	0.039	0.000	0.000	0.000	0.000
31	A	42	ALA	0	-0.032	-0.023	16.438	-0.027	-0.027	0.000	0.000	0.000	0.000
32	A	43	SER	0	0.060	0.028	19.788	-0.009	-0.009	0.000	0.000	0.000	0.000
33	A	44	ALA	0	0.089	0.038	19.604	0.011	0.011	0.000	0.000	0.000	0.000
34	A	45	GLU	-1	-0.849	-0.896	20.317	0.086	0.086	0.000	0.000	0.000	0.000
35	A	46	SER	0	-0.077	-0.038	19.434	0.015	0.015	0.000	0.000	0.000	0.000
36	A	47	PHE	0	0.064	0.016	12.089	0.014	0.014	0.000	0.000	0.000	0.000
37	A	48	MET	0	-0.030	-0.006	16.525	0.020	0.020	0.000	0.000	0.000	0.000
38	A	49	ARG	1	0.806	0.886	18.524	-0.114	-0.114	0.000	0.000	0.000	0.000
39	A	50	GLN	0	-0.047	-0.017	11.913	0.025	0.025	0.000	0.000	0.000	0.000
40	A	51	GLN	0	-0.013	-0.015	12.722	-0.070	-0.070	0.000	0.000	0.000	0.000
41	A	52	ILE	0	-0.016	0.009	9.979	0.072	0.072	0.000	0.000	0.000	0.000
42	A	53	SER	0	-0.014	-0.028	6.921	-0.119	-0.119	0.000	0.000	0.000	0.000
43	A	54	ASP	-1	-0.908	-0.954	7.459	0.273	0.273	0.000	0.000	0.000	0.000
44	A	55	ASP	-1	-0.882	-0.919	2.935	1.213	1.816	0.125	-0.210	-0.519	0.000
45	A	56	ALA	0	-0.067	-0.031	2.562	-3.272	-1.257	1.289	-1.749	-1.555	-0.020
46	A	57	ILE	0	0.024	0.012	2.546	-1.262	-0.303	1.527	-0.518	-1.968	-0.001
47	A	58	GLY	0	0.006	-0.010	5.183	-0.055	-0.016	-0.001	-0.001	-0.036	0.000
48	A	59	MET	0	-0.087	-0.040	8.227	0.043	0.043	0.000	0.000	0.000	0.000
49	A	60	ILE	0	0.014	0.009	10.269	-0.030	-0.030	0.000	0.000	0.000	0.000
50	A	61	ILE	0	-0.019	-0.009	12.949	0.035	0.035	0.000	0.000	0.000	0.000
51	A	62	GLU	-1	-0.805	-0.885	16.542	-0.051	-0.051	0.000	0.000	0.000	0.000
52	A	63	ALA	0	0.041	0.001	19.924	0.010	0.010	0.000	0.000	0.000	0.000
53	A	64	HIS	0	-0.036	-0.005	22.566	0.010	0.010	0.000	0.000	0.000	0.000
54	A	65	LEU	0	0.009	0.003	19.937	0.006	0.006	0.000	0.000	0.000	0.000
55	A	66	GLU	-1	-0.910	-0.968	24.040	0.043	0.043	0.000	0.000	0.000	0.000
56	A	67	ASP	-1	-0.927	-0.957	26.891	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	68	LYS	1	0.821	0.914	27.756	-0.025	-0.025	0.000	0.000	0.000	0.000
58	A	69	LYS	1	0.833	0.909	27.497	0.024	0.024	0.000	0.000	0.000	0.000
59	A	70	ASP	-1	-0.746	-0.864	26.035	-0.026	-0.026	0.000	0.000	0.000	0.000
60	A	71	SER	0	-0.001	-0.015	25.307	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	72	GLY	0	-0.016	-0.012	21.306	0.006	0.006	0.000	0.000	0.000	0.000
62	A	73	ILE	0	-0.037	-0.016	20.404	-0.006	-0.006	0.000	0.000	0.000	0.000
63	A	74	GLU	-1	-0.844	-0.893	22.373	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	75	LEU	0	-0.044	-0.005	17.812	0.007	0.007	0.000	0.000	0.000	0.000
65	A	76	LEU	0	0.036	0.019	16.380	0.008	0.008	0.000	0.000	0.000	0.000
66	A	77	GLU	-1	-0.771	-0.866	19.179	-0.021	-0.021	0.000	0.000	0.000	0.000
67	A	78	THR	0	-0.082	-0.054	21.484	0.005	0.005	0.000	0.000	0.000	0.000
68	A	79	LEU	0	-0.041	-0.024	15.164	0.011	0.011	0.000	0.000	0.000	0.000
69	A	80	VAL	0	0.062	0.036	17.872	0.006	0.006	0.000	0.000	0.000	0.000
70	A	81	LYS	1	0.911	0.959	19.159	-0.005	-0.005	0.000	0.000	0.000	0.000
71	A	82	ARG	1	0.856	0.916	19.170	-0.054	-0.054	0.000	0.000	0.000	0.000
72	A	83	GLY	0	0.031	0.024	18.573	0.010	0.010	0.000	0.000	0.000	0.000
73	A	84	PHE	0	0.001	0.001	12.787	-0.009	-0.009	0.000	0.000	0.000	0.000
74	A	85	HIS	0	-0.048	-0.028	15.009	-0.011	-0.011	0.000	0.000	0.000	0.000
75	A	86	LEU	0	0.017	0.015	8.773	-0.020	-0.020	0.000	0.000	0.000	0.000
76	A	87	PRO	0	0.010	0.011	9.471	0.015	0.015	0.000	0.000	0.000	0.000
77	A	88	THR	0	0.014	0.004	10.836	-0.022	-0.022	0.000	0.000	0.000	0.000
78	A	89	ILE	0	-0.015	0.000	11.502	0.013	0.013	0.000	0.000	0.000	0.000
79	A	90	VAL	0	0.021	0.011	14.567	0.015	0.015	0.000	0.000	0.000	0.000
80	A	91	MET	0	-0.023	-0.007	16.655	-0.014	-0.014	0.000	0.000	0.000	0.000
81	A	92	ALA	0	0.034	0.011	19.470	0.013	0.013	0.000	0.000	0.000	0.000
82	A	93	SER	0	-0.043	-0.003	23.051	-0.004	-0.004	0.000	0.000	0.000	0.000
83	A	94	SER	0	-0.007	0.001	25.622	0.003	0.003	0.000	0.000	0.000	0.000
84	A	95	SER	0	0.055	0.012	26.849	-0.003	-0.003	0.000	0.000	0.000	0.000
85	A	96	ASP	-1	-0.815	-0.879	28.768	-0.029	-0.029	0.000	0.000	0.000	0.000
86	A	97	ILE	0	0.043	0.001	29.683	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	98	PRO	0	-0.022	-0.019	29.966	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	99	THR	0	-0.021	-0.023	25.626	0.000	0.000	0.000	0.000	0.000	0.000
89	A	100	ALA	0	0.032	0.030	25.245	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	101	VAL	0	-0.029	-0.024	25.421	-0.005	-0.005	0.000	0.000	0.000	0.000
91	A	102	ARG	1	0.703	0.806	26.042	0.016	0.016	0.000	0.000	0.000	0.000
92	A	103	ALA	0	0.042	0.012	21.603	0.000	0.000	0.000	0.000	0.000	0.000
93	A	104	MET	0	-0.009	-0.004	20.779	-0.005	-0.005	0.000	0.000	0.000	0.000
94	A	105	ARG	1	0.894	0.943	23.222	0.040	0.040	0.000	0.000	0.000	0.000
95	A	106	ALA	0	-0.014	0.008	21.657	0.002	0.002	0.000	0.000	0.000	0.000
96	A	107	SER	0	-0.076	-0.039	18.999	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	108	ALA	0	-0.001	0.002	17.427	-0.012	-0.012	0.000	0.000	0.000	0.000
98	A	109	ALA	0	-0.036	-0.019	14.316	0.000	0.000	0.000	0.000	0.000	0.000
99	A	110	ASP	-1	-0.828	-0.881	16.324	-0.169	-0.169	0.000	0.000	0.000	0.000
100	A	111	PHE	0	-0.049	-0.041	18.028	0.009	0.009	0.000	0.000	0.000	0.000
101	A	112	ILE	0	-0.021	-0.003	16.307	0.003	0.003	0.000	0.000	0.000	0.000
102	A	113	GLU	-1	-0.921	-0.957	20.611	-0.061	-0.061	0.000	0.000	0.000	0.000
103	A	114	LYS	1	0.770	0.872	19.576	0.047	0.047	0.000	0.000	0.000	0.000
104	A	115	PRO	0	-0.005	-0.020	23.539	0.008	0.008	0.000	0.000	0.000	0.000
105	A	116	PHE	0	0.036	0.021	17.201	0.002	0.002	0.000	0.000	0.000	0.000
106	A	117	ILE	0	0.001	-0.001	22.114	0.002	0.002	0.000	0.000	0.000	0.000
107	A	118	GLU	-1	-0.917	-0.966	18.236	-0.160	-0.160	0.000	0.000	0.000	0.000
108	A	119	HIS	0	0.050	0.008	16.945	-0.022	-0.022	0.000	0.000	0.000	0.000
109	A	120	VAL	0	0.012	0.018	16.865	-0.026	-0.026	0.000	0.000	0.000	0.000
110	A	121	LEU	0	0.038	0.024	13.227	-0.020	-0.020	0.000	0.000	0.000	0.000
111	A	122	VAL	0	0.010	0.000	12.416	-0.046	-0.046	0.000	0.000	0.000	0.000
112	A	123	HIS	0	-0.034	-0.011	11.995	-0.078	-0.078	0.000	0.000	0.000	0.000
113	A	124	ASH	0	-0.031	-0.067	12.670	-0.041	-0.041	0.000	0.000	0.000	0.000
114	A	125	VAL	0	0.006	-0.001	7.430	-0.022	-0.022	0.000	0.000	0.000	0.000
115	A	126	GLN	0	0.035	0.019	7.900	-0.227	-0.227	0.000	0.000	0.000	0.000
116	A	127	GLN	0	-0.010	0.002	9.475	-0.035	-0.035	0.000	0.000	0.000	0.000
117	A	128	ILE	0	-0.010	-0.003	6.498	0.012	0.012	0.000	0.000	0.000	0.000
118	A	129	ILE	0	-0.003	-0.002	4.041	-0.144	0.059	0.000	-0.023	-0.180	0.000
119	A	130	ASN	0	-0.097	-0.076	6.033	-0.078	-0.078	0.000	0.000	0.000	0.000
120	A	131	GLY	0	-0.020	0.009	8.816	0.056	0.056	0.000	0.000	0.000	0.000
121	A	132	ALA	0	-0.018	0.013	4.978	0.066	0.066	0.000	0.000	0.000	0.000
122	A	133	LYS	1	0.799	0.896	5.006	1.492	1.492	0.000	0.000	0.000	0.000

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