FMO DATABASE

FMODB ID: 229YR

Calculation Name: 3KIO-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KIO

Chain ID: C

ChEMBL ID:

UniProt ID: Q9CWY8

Base Structure: X-ray

Registration Date: 2023-06-19

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	OptH
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	113
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-734294.725627
FMO2-HF: Nuclear repulsion	692102.765472
FMO2-HF: Total energy	-42191.960155
FMO2-MP2: Total energy	-42316.410692

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(C:13:ARG)

Summations of interaction energy for fragment #1(C:13:ARG)

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.
-24.812	-23.397	-0.027	-0.625	-0.762	0.001

Interaction energy analysis for fragmet #1(C:13:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.964 / q_NPA : 0.974

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	C	15	HIS	0	0.002	0.000	3.817	1.761	3.176	-0.027	-0.625	-0.762	0.001
4	C	16	LEU	0	0.053	0.025	6.574	0.509	0.509	0.000	0.000	0.000	0.000
5	C	17	ARG	1	0.816	0.920	10.164	18.973	18.973	0.000	0.000	0.000	0.000
6	C	18	PRO	0	0.088	-0.001	12.943	0.376	0.376	0.000	0.000	0.000	0.000
7	C	19	GLY	0	-0.049	-0.038	15.888	0.748	0.748	0.000	0.000	0.000	0.000
8	C	20	SER	0	0.010	0.014	15.099	0.537	0.537	0.000	0.000	0.000	0.000
9	C	21	LEU	0	0.004	0.040	14.384	0.564	0.564	0.000	0.000	0.000	0.000
10	C	22	ARG	1	0.917	0.937	17.857	12.860	12.860	0.000	0.000	0.000	0.000
11	C	23	GLY	0	-0.026	0.000	21.016	-0.054	-0.054	0.000	0.000	0.000	0.000
12	C	24	ALA	0	0.008	0.012	20.314	0.310	0.310	0.000	0.000	0.000	0.000
13	C	25	ALA	0	0.015	0.012	22.445	0.323	0.323	0.000	0.000	0.000	0.000
14	C	26	PRO	0	0.019	0.010	24.652	-0.312	-0.312	0.000	0.000	0.000	0.000
15	C	27	ALA	0	0.013	0.014	24.331	0.017	0.017	0.000	0.000	0.000	0.000
16	C	28	LYS	1	0.938	0.976	26.346	8.673	8.673	0.000	0.000	0.000	0.000
17	C	29	LEU	0	-0.034	-0.034	22.700	-0.313	-0.313	0.000	0.000	0.000	0.000
18	C	30	HIS	0	0.045	0.024	26.917	0.181	0.181	0.000	0.000	0.000	0.000
19	C	31	LEU	0	-0.007	0.008	25.213	-0.359	-0.359	0.000	0.000	0.000	0.000
20	C	32	LEU	0	0.023	0.008	28.058	0.256	0.256	0.000	0.000	0.000	0.000
21	C	33	PRO	0	0.025	0.042	29.202	-0.264	-0.264	0.000	0.000	0.000	0.000
22	C	34	CYS	0	-0.079	-0.068	30.377	0.229	0.229	0.000	0.000	0.000	0.000
23	C	35	ASP	-1	-0.868	-0.914	25.526	-10.944	-10.944	0.000	0.000	0.000	0.000
24	C	36	VAL	0	-0.060	-0.039	27.441	0.246	0.246	0.000	0.000	0.000	0.000
25	C	37	LEU	0	0.014	0.005	25.745	-0.276	-0.276	0.000	0.000	0.000	0.000
26	C	38	VAL	0	-0.037	-0.014	23.944	-0.331	-0.331	0.000	0.000	0.000	0.000
27	C	39	SER	0	0.025	0.016	20.081	0.450	0.450	0.000	0.000	0.000	0.000
28	C	40	ARG	1	0.937	0.964	22.914	9.702	9.702	0.000	0.000	0.000	0.000
29	C	41	PRO	0	0.020	0.025	25.075	0.164	0.164	0.000	0.000	0.000	0.000
30	C	42	ALA	0	0.042	-0.002	27.057	0.213	0.213	0.000	0.000	0.000	0.000
31	C	43	PRO	0	-0.010	0.005	30.140	-0.036	-0.036	0.000	0.000	0.000	0.000
32	C	44	VAL	0	0.083	0.035	29.801	0.311	0.311	0.000	0.000	0.000	0.000
33	C	45	ASP	-1	-0.809	-0.908	33.030	-8.327	-8.327	0.000	0.000	0.000	0.000
34	C	46	ARG	1	0.825	0.916	35.599	7.859	7.859	0.000	0.000	0.000	0.000
35	C	47	PHE	0	-0.047	-0.050	36.226	0.188	0.188	0.000	0.000	0.000	0.000
36	C	48	PHE	0	0.007	0.033	33.453	0.130	0.130	0.000	0.000	0.000	0.000
37	C	49	THR	0	0.046	0.018	35.213	0.137	0.137	0.000	0.000	0.000	0.000
38	C	50	PRO	0	-0.050	-0.020	37.304	0.128	0.128	0.000	0.000	0.000	0.000
39	C	51	ALA	0	-0.037	-0.033	39.798	0.208	0.208	0.000	0.000	0.000	0.000
40	C	52	VAL	0	-0.011	0.007	36.886	0.113	0.113	0.000	0.000	0.000	0.000
41	C	53	ARG	1	0.803	0.921	40.282	6.662	6.662	0.000	0.000	0.000	0.000
42	C	54	HIS	0	0.067	0.026	39.908	-0.015	-0.015	0.000	0.000	0.000	0.000
43	C	55	ASP	-1	-0.875	-0.919	43.787	-6.326	-6.326	0.000	0.000	0.000	0.000
44	C	56	ALA	0	-0.011	-0.005	44.824	-0.063	-0.063	0.000	0.000	0.000	0.000
45	C	57	ASP	-1	-0.927	-0.942	43.396	-6.377	-6.377	0.000	0.000	0.000	0.000
46	C	58	GLY	0	0.044	0.009	39.695	0.002	0.002	0.000	0.000	0.000	0.000
47	C	59	LEU	0	0.024	0.003	37.076	0.011	0.011	0.000	0.000	0.000	0.000
48	C	60	GLN	0	-0.043	0.010	40.311	-0.046	-0.046	0.000	0.000	0.000	0.000
49	C	61	ALA	0	0.028	-0.001	38.046	-0.068	-0.068	0.000	0.000	0.000	0.000
50	C	62	SER	0	0.011	0.019	39.957	0.011	0.011	0.000	0.000	0.000	0.000
51	C	63	PHE	0	0.027	-0.006	32.518	-0.178	-0.178	0.000	0.000	0.000	0.000
52	C	64	ARG	1	0.892	0.944	33.831	8.286	8.286	0.000	0.000	0.000	0.000
53	C	65	GLY	0	-0.003	0.002	38.616	0.084	0.084	0.000	0.000	0.000	0.000
54	C	66	ARG	1	0.872	0.936	38.227	7.490	7.490	0.000	0.000	0.000	0.000
55	C	67	GLY	0	0.018	0.004	39.969	-0.093	-0.093	0.000	0.000	0.000	0.000
56	C	68	LEU	0	-0.031	-0.012	35.303	-0.073	-0.073	0.000	0.000	0.000	0.000
57	C	69	ARG	1	0.787	0.852	38.309	6.917	6.917	0.000	0.000	0.000	0.000
58	C	70	GLY	0	0.056	0.031	36.150	-0.145	-0.145	0.000	0.000	0.000	0.000
59	C	71	GLU	-1	-0.916	-0.931	34.953	-7.179	-7.179	0.000	0.000	0.000	0.000
60	C	72	GLU	-1	-0.925	-0.947	33.063	-8.565	-8.565	0.000	0.000	0.000	0.000
61	C	73	VAL	0	0.078	0.046	28.779	0.062	0.062	0.000	0.000	0.000	0.000
62	C	74	ALA	0	-0.074	-0.039	30.009	-0.198	-0.198	0.000	0.000	0.000	0.000
63	C	75	VAL	0	-0.036	-0.022	23.979	-0.189	-0.189	0.000	0.000	0.000	0.000
64	C	76	PRO	0	0.014	0.010	24.168	0.237	0.237	0.000	0.000	0.000	0.000
65	C	77	PRO	0	0.053	0.019	26.544	-0.138	-0.138	0.000	0.000	0.000	0.000
66	C	78	GLY	0	-0.013	-0.014	26.080	-0.146	-0.146	0.000	0.000	0.000	0.000
67	C	79	PHE	0	-0.061	-0.021	19.798	-0.524	-0.524	0.000	0.000	0.000	0.000
68	C	80	ALA	0	0.013	-0.005	21.402	0.330	0.330	0.000	0.000	0.000	0.000
69	C	81	GLY	0	0.030	0.001	20.722	-0.455	-0.455	0.000	0.000	0.000	0.000
70	C	82	PHE	0	-0.048	-0.034	17.389	0.099	0.099	0.000	0.000	0.000	0.000
71	C	83	VAL	0	0.016	0.027	18.256	-0.142	-0.142	0.000	0.000	0.000	0.000
72	C	84	MET	0	-0.019	0.006	12.968	-0.044	-0.044	0.000	0.000	0.000	0.000
73	C	85	VAL	0	0.015	0.014	14.577	0.353	0.353	0.000	0.000	0.000	0.000
74	C	86	THR	0	-0.051	-0.030	9.861	-1.355	-1.355	0.000	0.000	0.000	0.000
75	C	87	GLU	-1	-0.991	-0.985	9.515	-21.377	-21.377	0.000	0.000	0.000	0.000
76	C	88	GLU	-1	-0.790	-0.885	9.727	-21.484	-21.484	0.000	0.000	0.000	0.000
77	C	89	LYS	1	0.752	0.851	5.579	29.733	29.733	0.000	0.000	0.000	0.000
78	C	90	GLY	0	0.069	0.035	9.059	1.351	1.351	0.000	0.000	0.000	0.000
79	C	91	GLU	-1	-0.787	-0.873	10.305	-17.048	-17.048	0.000	0.000	0.000	0.000
80	C	92	GLY	0	0.004	-0.010	13.677	0.400	0.400	0.000	0.000	0.000	0.000
81	C	93	LEU	0	-0.048	-0.032	16.708	0.259	0.259	0.000	0.000	0.000	0.000
82	C	94	ILE	0	-0.008	-0.034	19.249	0.618	0.618	0.000	0.000	0.000	0.000
83	C	95	GLY	0	-0.007	0.001	20.864	-0.520	-0.520	0.000	0.000	0.000	0.000
84	C	96	LYS	1	0.861	0.961	21.081	12.117	12.117	0.000	0.000	0.000	0.000
85	C	97	LEU	0	0.047	0.017	24.678	-0.282	-0.282	0.000	0.000	0.000	0.000
86	C	98	ASN	0	-0.007	-0.013	27.309	0.009	0.009	0.000	0.000	0.000	0.000
87	C	99	PHE	0	-0.036	-0.017	25.638	-0.322	-0.322	0.000	0.000	0.000	0.000
88	C	100	SER	0	0.010	-0.001	28.958	0.175	0.175	0.000	0.000	0.000	0.000
89	C	101	GLY	0	-0.017	-0.013	30.324	-0.322	-0.322	0.000	0.000	0.000	0.000
90	C	102	ASP	-1	-0.906	-0.963	31.654	-7.975	-7.975	0.000	0.000	0.000	0.000
91	C	103	ALA	0	0.043	0.039	32.924	-0.196	-0.196	0.000	0.000	0.000	0.000
92	C	104	GLU	-1	-0.865	-0.950	35.410	-7.290	-7.290	0.000	0.000	0.000	0.000
93	C	105	ASP	-1	-0.936	-0.948	38.073	-6.562	-6.562	0.000	0.000	0.000	0.000
94	C	106	LYS	1	0.756	0.844	40.055	6.855	6.855	0.000	0.000	0.000	0.000
95	C	107	ALA	0	-0.005	-0.003	38.901	-0.113	-0.113	0.000	0.000	0.000	0.000
96	C	108	ASP	-1	-0.908	-0.973	34.227	-8.327	-8.327	0.000	0.000	0.000	0.000
97	C	109	GLU	-1	-0.824	-0.910	36.126	-7.087	-7.087	0.000	0.000	0.000	0.000
98	C	110	ALA	0	-0.061	-0.028	36.706	-0.101	-0.101	0.000	0.000	0.000	0.000
99	C	111	GLN	0	-0.060	-0.041	33.722	-0.039	-0.039	0.000	0.000	0.000	0.000
100	C	112	GLU	-1	-0.798	-0.879	31.997	-8.003	-8.003	0.000	0.000	0.000	0.000
101	C	113	PRO	0	-0.113	-0.080	27.640	-0.146	-0.146	0.000	0.000	0.000	0.000
102	C	114	LEU	0	0.001	0.017	26.189	-0.312	-0.312	0.000	0.000	0.000	0.000
103	C	115	GLU	-1	-0.916	-0.946	27.763	-8.629	-8.629	0.000	0.000	0.000	0.000
104	C	116	ARG	1	0.878	0.945	27.259	8.510	8.510	0.000	0.000	0.000	0.000
105	C	136	LEU	0	0.003	-0.020	25.201	0.049	0.049	0.000	0.000	0.000	0.000
106	C	137	TRP	0	-0.042	-0.022	25.735	0.291	0.291	0.000	0.000	0.000	0.000
107	C	138	GLY	0	0.053	0.044	25.442	0.067	0.067	0.000	0.000	0.000	0.000
108	C	139	LEU	0	-0.046	-0.027	19.878	-0.189	-0.189	0.000	0.000	0.000	0.000
109	C	140	GLU	-1	-0.912	-0.967	18.669	-12.328	-12.328	0.000	0.000	0.000	0.000
110	C	141	THR	0	-0.061	-0.022	13.174	-0.371	-0.371	0.000	0.000	0.000	0.000
111	C	142	VAL	0	0.028	0.000	10.410	0.108	0.108	0.000	0.000	0.000	0.000
112	C	143	PRO	0	-0.057	-0.036	9.513	-0.374	-0.374	0.000	0.000	0.000	0.000
113	C	144	GLY	0	0.032	0.044	8.168	0.868	0.868	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:13:ARG)