FMO DATABASE

FMODB ID: YV4G2

Calculation Name: 1KNG-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1KNG

Chain ID: A

ChEMBL ID:

UniProt ID: P30960

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	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	143
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1303777.84625
FMO2-HF: Nuclear repulsion	1249572.956837
FMO2-HF: Total energy	-54204.889413
FMO2-MP2: Total energy	-54365.045465

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:50:ARG)

Summations of interaction energy for fragment #1(A:50: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.
-81.733	-71.131	15.295	-11.211	-14.686	-0.107

Interaction energy analysis for fragmet #1(A:50:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.935 / q_NPA : 0.971

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	52	ALA	0	0.027	0.019	2.795	-14.835	-11.216	0.505	-2.052	-2.071	-0.008
4	A	53	PRO	0	-0.016	-0.004	2.588	2.077	3.466	1.143	-0.544	-1.988	0.003
5	A	54	GLN	0	-0.032	-0.024	5.131	8.058	8.130	-0.001	-0.006	-0.066	0.000
6	A	55	THR	0	0.001	0.016	6.782	1.745	1.745	0.000	0.000	0.000	0.000
7	A	56	ALA	0	0.012	0.006	9.395	0.412	0.412	0.000	0.000	0.000	0.000
8	A	57	LEU	0	-0.058	-0.023	11.099	-0.105	-0.105	0.000	0.000	0.000	0.000
9	A	58	PRO	0	0.019	0.016	14.689	0.537	0.537	0.000	0.000	0.000	0.000
10	A	59	PRO	0	0.072	0.018	17.803	-0.759	-0.759	0.000	0.000	0.000	0.000
11	A	60	LEU	0	-0.018	0.006	20.188	0.158	0.158	0.000	0.000	0.000	0.000
12	A	61	GLU	-1	-0.928	-0.969	21.957	-11.407	-11.407	0.000	0.000	0.000	0.000
13	A	62	GLY	0	0.048	0.027	25.445	0.165	0.165	0.000	0.000	0.000	0.000
14	A	63	LEU	0	-0.058	-0.019	22.283	0.286	0.286	0.000	0.000	0.000	0.000
15	A	64	GLN	0	-0.008	-0.014	26.135	-0.018	-0.018	0.000	0.000	0.000	0.000
16	A	65	ALA	0	-0.013	-0.012	26.065	-0.064	-0.064	0.000	0.000	0.000	0.000
17	A	66	ASP	-1	-0.890	-0.936	28.112	-10.728	-10.728	0.000	0.000	0.000	0.000
18	A	67	ASN	0	-0.084	-0.048	31.255	0.237	0.237	0.000	0.000	0.000	0.000
19	A	68	VAL	0	0.027	0.024	28.351	0.163	0.163	0.000	0.000	0.000	0.000
20	A	69	GLN	0	-0.035	-0.027	23.736	0.181	0.181	0.000	0.000	0.000	0.000
21	A	70	VAL	0	0.005	0.013	21.179	-0.187	-0.187	0.000	0.000	0.000	0.000
22	A	71	PRO	0	-0.018	-0.008	20.540	-0.227	-0.227	0.000	0.000	0.000	0.000
23	A	72	GLY	0	0.078	0.036	18.059	-0.358	-0.358	0.000	0.000	0.000	0.000
24	A	73	LEU	0	-0.039	-0.003	10.324	0.121	0.121	0.000	0.000	0.000	0.000
25	A	74	ASP	-1	-0.849	-0.926	14.680	-19.654	-19.654	0.000	0.000	0.000	0.000
26	A	75	PRO	0	0.020	0.006	10.607	0.147	0.147	0.000	0.000	0.000	0.000
27	A	76	ALA	0	0.026	0.002	12.000	-0.772	-0.772	0.000	0.000	0.000	0.000
28	A	77	ALA	0	-0.064	-0.034	14.515	0.851	0.851	0.000	0.000	0.000	0.000
29	A	78	PHE	0	0.013	0.000	9.733	0.185	0.185	0.000	0.000	0.000	0.000
30	A	79	LYS	1	0.871	0.932	9.694	24.752	24.752	0.000	0.000	0.000	0.000
31	A	80	GLY	0	0.009	0.003	13.309	1.229	1.229	0.000	0.000	0.000	0.000
32	A	81	LYS	1	0.874	0.941	14.061	17.810	17.810	0.000	0.000	0.000	0.000
33	A	82	VAL	0	0.031	0.028	12.715	-1.186	-1.186	0.000	0.000	0.000	0.000
34	A	83	SER	0	-0.004	-0.007	11.907	1.534	1.534	0.000	0.000	0.000	0.000
35	A	84	LEU	0	0.013	0.021	12.042	-1.470	-1.470	0.000	0.000	0.000	0.000
36	A	85	VAL	0	0.003	0.000	8.978	0.923	0.923	0.000	0.000	0.000	0.000
37	A	86	ASN	0	-0.018	-0.032	10.624	-0.839	-0.839	0.000	0.000	0.000	0.000
38	A	87	VAL	0	-0.020	-0.005	8.693	0.515	0.515	0.000	0.000	0.000	0.000
39	A	88	TRP	0	0.062	0.020	12.085	1.088	1.088	0.000	0.000	0.000	0.000
40	A	89	ALA	0	0.004	-0.012	15.636	-0.199	-0.199	0.000	0.000	0.000	0.000
41	A	90	SER	0	-0.034	-0.047	18.528	0.507	0.507	0.000	0.000	0.000	0.000
42	A	91	TRP	0	-0.042	-0.031	17.038	0.463	0.463	0.000	0.000	0.000	0.000
43	A	92	CYS	0	-0.045	0.015	17.760	-0.297	-0.297	0.000	0.000	0.000	0.000
44	A	93	VAL	0	0.037	0.021	20.703	0.111	0.111	0.000	0.000	0.000	0.000
45	A	94	PRO	0	0.039	-0.004	18.911	0.193	0.193	0.000	0.000	0.000	0.000
46	A	96	HIS	0	-0.021	-0.001	19.815	0.396	0.396	0.000	0.000	0.000	0.000
47	A	97	ASP	-1	-0.886	-0.933	22.685	-12.242	-12.242	0.000	0.000	0.000	0.000
48	A	98	GLU	-1	-0.808	-0.902	16.777	-17.795	-17.795	0.000	0.000	0.000	0.000
49	A	99	ALA	0	-0.023	-0.001	21.437	-0.114	-0.114	0.000	0.000	0.000	0.000
50	A	100	PRO	0	-0.006	-0.013	22.403	0.042	0.042	0.000	0.000	0.000	0.000
51	A	101	LEU	0	-0.002	0.007	21.968	0.267	0.267	0.000	0.000	0.000	0.000
52	A	102	LEU	0	-0.003	0.003	16.976	-0.160	-0.160	0.000	0.000	0.000	0.000
53	A	103	THR	0	-0.017	-0.017	21.140	-0.223	-0.223	0.000	0.000	0.000	0.000
54	A	104	GLU	-1	-0.849	-0.910	24.323	-10.602	-10.602	0.000	0.000	0.000	0.000
55	A	105	LEU	0	0.002	0.015	18.563	0.036	0.036	0.000	0.000	0.000	0.000
56	A	106	GLY	0	0.049	0.024	22.160	-0.131	-0.131	0.000	0.000	0.000	0.000
57	A	107	LYS	1	0.750	0.863	23.004	11.013	11.013	0.000	0.000	0.000	0.000
58	A	108	ASP	-1	-0.813	-0.885	22.526	-12.755	-12.755	0.000	0.000	0.000	0.000
59	A	109	LYS	1	0.866	0.915	22.452	11.760	11.760	0.000	0.000	0.000	0.000
60	A	110	ARG	1	0.732	0.834	20.576	12.973	12.973	0.000	0.000	0.000	0.000
61	A	111	PHE	0	-0.050	-0.021	16.633	-0.713	-0.713	0.000	0.000	0.000	0.000
62	A	112	GLN	0	-0.070	-0.035	14.625	1.443	1.443	0.000	0.000	0.000	0.000
63	A	113	LEU	0	0.033	0.019	16.095	-1.227	-1.227	0.000	0.000	0.000	0.000
64	A	114	VAL	0	-0.024	-0.024	12.730	0.749	0.749	0.000	0.000	0.000	0.000
65	A	115	GLY	0	0.018	0.018	13.760	-0.908	-0.908	0.000	0.000	0.000	0.000
66	A	116	ILE	0	-0.003	-0.005	9.064	0.212	0.212	0.000	0.000	0.000	0.000
67	A	117	ASN	0	-0.046	-0.027	13.179	0.379	0.379	0.000	0.000	0.000	0.000
68	A	118	TYR	0	0.064	0.022	11.507	0.377	0.377	0.000	0.000	0.000	0.000
69	A	119	LYS	1	0.874	0.951	13.857	20.930	20.930	0.000	0.000	0.000	0.000
70	A	120	ASP	-1	-0.735	-0.834	17.315	-13.567	-13.567	0.000	0.000	0.000	0.000
71	A	121	ALA	0	0.007	0.019	20.258	-0.028	-0.028	0.000	0.000	0.000	0.000
72	A	122	ALA	0	0.074	0.014	23.415	-0.014	-0.014	0.000	0.000	0.000	0.000
73	A	123	ASP	-1	-0.823	-0.892	24.334	-10.698	-10.698	0.000	0.000	0.000	0.000
74	A	124	ASN	0	-0.037	-0.016	24.583	0.572	0.572	0.000	0.000	0.000	0.000
75	A	125	ALA	0	0.028	0.018	21.488	0.016	0.016	0.000	0.000	0.000	0.000
76	A	126	ARG	1	0.851	0.888	23.220	11.365	11.365	0.000	0.000	0.000	0.000
77	A	127	ARG	1	0.935	0.981	26.046	10.503	10.503	0.000	0.000	0.000	0.000
78	A	128	PHE	0	-0.015	-0.017	20.905	0.382	0.382	0.000	0.000	0.000	0.000
79	A	129	LEU	0	0.010	-0.002	20.912	0.077	0.077	0.000	0.000	0.000	0.000
80	A	130	GLY	0	-0.013	0.010	24.967	0.214	0.214	0.000	0.000	0.000	0.000
81	A	131	ARG	1	0.819	0.913	28.001	10.662	10.662	0.000	0.000	0.000	0.000
82	A	132	TYR	0	-0.014	-0.034	24.665	0.560	0.560	0.000	0.000	0.000	0.000
83	A	133	GLY	0	0.019	0.036	26.888	0.046	0.046	0.000	0.000	0.000	0.000
84	A	134	ASN	0	0.020	-0.017	22.077	-0.930	-0.930	0.000	0.000	0.000	0.000
85	A	135	PRO	0	-0.013	0.011	20.056	0.309	0.309	0.000	0.000	0.000	0.000
86	A	136	PHE	0	-0.013	-0.008	16.237	-0.473	-0.473	0.000	0.000	0.000	0.000
87	A	137	GLY	0	0.014	0.008	19.452	0.732	0.732	0.000	0.000	0.000	0.000
88	A	138	ARG	1	0.868	0.926	16.687	18.100	18.100	0.000	0.000	0.000	0.000
89	A	139	VAL	0	0.031	0.014	16.865	-0.708	-0.708	0.000	0.000	0.000	0.000
90	A	140	GLY	0	-0.028	-0.004	14.674	0.627	0.627	0.000	0.000	0.000	0.000
91	A	141	VAL	0	0.012	0.002	15.130	-0.588	-0.588	0.000	0.000	0.000	0.000
92	A	142	ASP	-1	-0.736	-0.862	10.877	-26.219	-26.219	0.000	0.000	0.000	0.000
93	A	143	ALA	0	0.017	-0.002	14.023	0.060	0.060	0.000	0.000	0.000	0.000
94	A	144	ASN	0	0.013	-0.006	14.117	-0.534	-0.534	0.000	0.000	0.000	0.000
95	A	145	GLY	0	0.003	-0.003	12.083	0.169	0.169	0.000	0.000	0.000	0.000
96	A	146	ARG	1	0.970	0.980	10.249	21.211	21.211	0.000	0.000	0.000	0.000
97	A	147	ALA	0	0.033	0.020	8.163	-2.851	-2.851	0.000	0.000	0.000	0.000
98	A	148	SER	0	0.012	-0.036	6.331	-5.600	-5.600	0.000	0.000	0.000	0.000
99	A	149	ILE	0	-0.031	-0.009	5.917	-4.161	-4.161	0.000	0.000	0.000	0.000
100	A	150	GLU	-1	-0.942	-0.953	4.092	-45.608	-44.643	-0.001	-0.565	-0.399	-0.002
101	A	151	TRP	0	-0.032	-0.030	1.846	-47.442	-47.394	11.729	-6.526	-5.250	-0.084
102	A	152	GLY	0	-0.053	-0.016	2.820	-4.884	-4.277	0.534	0.063	-1.203	-0.014
103	A	153	VAL	0	-0.059	-0.036	4.390	4.877	4.969	-0.001	-0.014	-0.077	0.000
104	A	154	TYR	0	-0.039	-0.024	7.447	1.385	1.385	0.000	0.000	0.000	0.000
105	A	155	GLY	0	-0.015	-0.007	10.585	1.932	1.932	0.000	0.000	0.000	0.000
106	A	156	VAL	0	-0.071	0.007	11.982	-1.340	-1.340	0.000	0.000	0.000	0.000
107	A	157	PRO	0	0.035	-0.006	13.756	1.102	1.102	0.000	0.000	0.000	0.000
108	A	158	GLU	-1	-0.764	-0.894	7.700	-34.008	-34.008	0.000	0.000	0.000	0.000
109	A	159	THR	0	0.008	0.004	10.724	0.530	0.530	0.000	0.000	0.000	0.000
110	A	160	PHE	0	-0.038	-0.018	3.999	-2.165	-2.007	-0.001	-0.015	-0.142	0.000
111	A	161	VAL	0	0.039	0.025	8.858	2.532	2.532	0.000	0.000	0.000	0.000
112	A	162	VAL	0	-0.035	-0.016	6.868	-3.424	-3.424	0.000	0.000	0.000	0.000
113	A	163	GLY	0	0.069	0.034	7.680	3.141	3.141	0.000	0.000	0.000	0.000
114	A	164	ARG	1	0.980	1.003	9.399	15.302	15.302	0.000	0.000	0.000	0.000
115	A	165	GLU	-1	-0.885	-0.947	7.548	-22.731	-22.731	0.000	0.000	0.000	0.000
116	A	166	GLY	0	-0.025	-0.003	8.400	-0.786	-0.786	0.000	0.000	0.000	0.000
117	A	167	THR	0	-0.011	-0.002	3.100	-4.613	-4.013	0.024	-0.213	-0.412	0.000
118	A	168	ILE	0	-0.026	-0.016	2.297	1.521	3.709	1.339	-0.926	-2.601	0.001
119	A	169	VAL	0	0.002	-0.001	3.373	-1.831	-0.967	0.025	-0.413	-0.477	-0.003
120	A	170	TYR	0	-0.014	-0.019	6.076	2.641	2.641	0.000	0.000	0.000	0.000
121	A	171	LYS	1	0.835	0.934	5.742	35.993	35.993	0.000	0.000	0.000	0.000
122	A	172	LEU	0	-0.039	-0.004	9.125	1.763	1.763	0.000	0.000	0.000	0.000
123	A	173	VAL	0	0.025	0.002	10.037	-1.161	-1.161	0.000	0.000	0.000	0.000
124	A	174	GLY	0	0.020	0.017	12.271	1.444	1.444	0.000	0.000	0.000	0.000
125	A	175	PRO	0	-0.004	0.001	15.034	-0.700	-0.700	0.000	0.000	0.000	0.000
126	A	176	ILE	0	0.002	-0.011	15.840	0.135	0.135	0.000	0.000	0.000	0.000
127	A	177	THR	0	0.002	-0.009	18.539	0.621	0.621	0.000	0.000	0.000	0.000
128	A	178	PRO	0	0.083	0.024	22.034	-0.254	-0.254	0.000	0.000	0.000	0.000
129	A	179	ASP	-1	-0.850	-0.910	24.329	-11.656	-11.656	0.000	0.000	0.000	0.000
130	A	180	ASN	0	-0.011	0.001	18.400	-0.109	-0.109	0.000	0.000	0.000	0.000
131	A	181	LEU	0	0.047	0.017	19.271	-0.658	-0.658	0.000	0.000	0.000	0.000
132	A	182	ARG	1	0.873	0.915	20.345	11.178	11.178	0.000	0.000	0.000	0.000
133	A	183	SER	0	0.013	0.008	21.640	0.156	0.156	0.000	0.000	0.000	0.000
134	A	184	VAL	0	-0.044	-0.010	15.526	-0.069	-0.069	0.000	0.000	0.000	0.000
135	A	185	LEU	0	-0.014	-0.021	13.845	-0.670	-0.670	0.000	0.000	0.000	0.000
136	A	186	LEU	0	0.041	0.022	15.811	-0.527	-0.527	0.000	0.000	0.000	0.000
137	A	187	PRO	0	0.022	0.010	17.817	-0.155	-0.155	0.000	0.000	0.000	0.000
138	A	188	GLN	0	-0.019	-0.006	12.108	0.629	0.629	0.000	0.000	0.000	0.000
139	A	189	MET	0	-0.042	-0.014	13.551	-0.729	-0.729	0.000	0.000	0.000	0.000
140	A	190	GLU	-1	-0.823	-0.908	14.845	-13.067	-13.067	0.000	0.000	0.000	0.000
141	A	191	LYS	1	0.912	0.966	14.333	15.193	15.193	0.000	0.000	0.000	0.000
142	A	192	ALA	0	-0.005	0.010	11.485	0.070	0.070	0.000	0.000	0.000	0.000
143	A	193	LEU	0	-0.103	-0.034	13.020	0.425	0.425	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:50:ARG)