FMO DATABASE

FMODB ID: 5J46Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1303193.054942
FMO2-HF: Nuclear repulsion	1248988.603785
FMO2-HF: Total energy	-54204.451157
FMO2-MP2: Total energy	-54364.583811

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.
-84.924	-74.258	15.079	-11.107	-14.637	-0.114

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 : 0.899 / q_NPA : 0.938

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	0.034	0.022	2.809	-15.501	-12.415	0.496	-1.646	-1.936	-0.012
4	A	53	PRO	0	-0.018	-0.002	2.583	1.847	3.256	1.232	-0.560	-2.081	0.003
5	A	54	GLN	0	-0.030	-0.023	4.979	9.038	9.130	-0.001	-0.009	-0.081	0.000
6	A	55	THR	0	-0.001	0.011	6.555	1.819	1.819	0.000	0.000	0.000	0.000
7	A	56	ALA	0	0.025	0.013	9.249	0.434	0.434	0.000	0.000	0.000	0.000
8	A	57	LEU	0	-0.068	-0.026	11.039	-0.080	-0.080	0.000	0.000	0.000	0.000
9	A	58	PRO	0	0.017	0.016	14.666	0.570	0.570	0.000	0.000	0.000	0.000
10	A	59	PRO	0	0.077	0.020	17.785	-0.767	-0.767	0.000	0.000	0.000	0.000
11	A	60	LEU	0	-0.014	0.006	20.169	0.163	0.163	0.000	0.000	0.000	0.000
12	A	61	GLU	-1	-0.934	-0.969	21.945	-11.332	-11.332	0.000	0.000	0.000	0.000
13	A	62	GLY	0	0.041	0.016	25.431	0.162	0.162	0.000	0.000	0.000	0.000
14	A	63	LEU	0	-0.056	-0.021	22.287	0.291	0.291	0.000	0.000	0.000	0.000
15	A	64	GLN	0	-0.009	-0.009	26.119	-0.024	-0.024	0.000	0.000	0.000	0.000
16	A	65	ALA	0	-0.012	-0.016	26.125	-0.065	-0.065	0.000	0.000	0.000	0.000
17	A	66	ASP	-1	-0.901	-0.938	28.126	-10.619	-10.619	0.000	0.000	0.000	0.000
18	A	67	ASN	0	-0.071	-0.039	31.266	0.150	0.150	0.000	0.000	0.000	0.000
19	A	68	VAL	0	0.025	0.021	28.118	0.156	0.156	0.000	0.000	0.000	0.000
20	A	69	GLN	0	-0.036	-0.026	23.807	0.186	0.186	0.000	0.000	0.000	0.000
21	A	70	VAL	0	-0.002	0.008	21.201	-0.179	-0.179	0.000	0.000	0.000	0.000
22	A	71	PRO	0	-0.014	-0.004	20.498	-0.213	-0.213	0.000	0.000	0.000	0.000
23	A	72	GLY	0	0.078	0.036	18.038	-0.357	-0.357	0.000	0.000	0.000	0.000
24	A	73	LEU	0	-0.036	-0.002	10.290	0.133	0.133	0.000	0.000	0.000	0.000
25	A	74	ASP	-1	-0.845	-0.930	14.650	-19.831	-19.831	0.000	0.000	0.000	0.000
26	A	75	PRO	0	0.013	0.007	10.415	0.207	0.207	0.000	0.000	0.000	0.000
27	A	76	ALA	0	0.022	0.003	12.174	-0.661	-0.661	0.000	0.000	0.000	0.000
28	A	77	ALA	0	-0.057	-0.029	14.696	0.889	0.889	0.000	0.000	0.000	0.000
29	A	78	PHE	0	0.010	-0.003	9.838	0.262	0.262	0.000	0.000	0.000	0.000
30	A	79	LYS	1	0.888	0.953	10.043	23.213	23.213	0.000	0.000	0.000	0.000
31	A	80	GLY	0	0.006	0.003	13.445	1.169	1.169	0.000	0.000	0.000	0.000
32	A	81	LYS	1	0.872	0.929	13.981	17.528	17.528	0.000	0.000	0.000	0.000
33	A	82	VAL	0	0.039	0.028	12.343	-1.081	-1.081	0.000	0.000	0.000	0.000
34	A	83	SER	0	-0.001	-0.001	11.825	1.479	1.479	0.000	0.000	0.000	0.000
35	A	84	LEU	0	0.021	0.023	11.842	-1.437	-1.437	0.000	0.000	0.000	0.000
36	A	85	VAL	0	0.000	0.000	8.846	0.906	0.906	0.000	0.000	0.000	0.000
37	A	86	ASN	0	-0.008	-0.019	10.656	-0.805	-0.805	0.000	0.000	0.000	0.000
38	A	87	VAL	0	-0.028	-0.008	8.774	0.522	0.522	0.000	0.000	0.000	0.000
39	A	88	TRP	0	0.061	0.019	12.130	1.073	1.073	0.000	0.000	0.000	0.000
40	A	89	ALA	0	0.016	-0.006	15.684	-0.213	-0.213	0.000	0.000	0.000	0.000
41	A	90	SER	0	-0.044	-0.048	18.564	0.540	0.540	0.000	0.000	0.000	0.000
42	A	91	TRP	0	-0.043	-0.026	17.233	0.471	0.471	0.000	0.000	0.000	0.000
43	A	92	CYS	0	-0.027	0.025	17.839	-0.295	-0.295	0.000	0.000	0.000	0.000
44	A	93	VAL	0	0.054	0.028	20.758	0.094	0.094	0.000	0.000	0.000	0.000
45	A	94	PRO	0	0.038	-0.008	18.986	0.205	0.205	0.000	0.000	0.000	0.000
46	A	96	HIS	0	-0.041	-0.003	19.867	0.475	0.475	0.000	0.000	0.000	0.000
47	A	97	ASP	-1	-0.895	-0.934	22.754	-12.137	-12.137	0.000	0.000	0.000	0.000
48	A	98	GLU	-1	-0.828	-0.926	17.045	-17.666	-17.666	0.000	0.000	0.000	0.000
49	A	99	ALA	0	-0.023	0.000	21.485	-0.103	-0.103	0.000	0.000	0.000	0.000
50	A	100	PRO	0	-0.015	-0.019	22.447	0.039	0.039	0.000	0.000	0.000	0.000
51	A	101	LEU	0	0.005	0.010	22.043	0.277	0.277	0.000	0.000	0.000	0.000
52	A	102	LEU	0	0.002	0.004	17.010	-0.149	-0.149	0.000	0.000	0.000	0.000
53	A	103	THR	0	-0.027	-0.019	21.174	-0.210	-0.210	0.000	0.000	0.000	0.000
54	A	104	GLU	-1	-0.871	-0.923	24.355	-10.532	-10.532	0.000	0.000	0.000	0.000
55	A	105	LEU	0	0.001	0.011	18.498	0.052	0.052	0.000	0.000	0.000	0.000
56	A	106	GLY	0	0.041	0.023	22.178	-0.116	-0.116	0.000	0.000	0.000	0.000
57	A	107	LYS	1	0.790	0.881	23.024	10.923	10.923	0.000	0.000	0.000	0.000
58	A	108	ASP	-1	-0.812	-0.888	22.354	-12.631	-12.631	0.000	0.000	0.000	0.000
59	A	109	LYS	1	0.882	0.931	22.204	11.602	11.602	0.000	0.000	0.000	0.000
60	A	110	ARG	1	0.747	0.861	20.295	12.850	12.850	0.000	0.000	0.000	0.000
61	A	111	PHE	0	-0.054	-0.022	16.429	-0.663	-0.663	0.000	0.000	0.000	0.000
62	A	112	GLN	0	-0.073	-0.035	14.773	1.421	1.421	0.000	0.000	0.000	0.000
63	A	113	LEU	0	0.031	0.019	16.085	-1.203	-1.203	0.000	0.000	0.000	0.000
64	A	114	VAL	0	-0.025	-0.024	12.729	0.733	0.733	0.000	0.000	0.000	0.000
65	A	115	GLY	0	0.027	0.022	13.783	-0.916	-0.916	0.000	0.000	0.000	0.000
66	A	116	ILE	0	-0.006	-0.008	9.100	0.217	0.217	0.000	0.000	0.000	0.000
67	A	117	ASN	0	-0.052	-0.026	13.174	0.387	0.387	0.000	0.000	0.000	0.000
68	A	118	TYR	0	0.051	0.004	11.604	0.350	0.350	0.000	0.000	0.000	0.000
69	A	119	LYS	1	0.896	0.963	14.031	20.379	20.379	0.000	0.000	0.000	0.000
70	A	120	ASP	-1	-0.723	-0.824	17.325	-13.710	-13.710	0.000	0.000	0.000	0.000
71	A	121	ALA	0	-0.002	0.013	20.265	-0.014	-0.014	0.000	0.000	0.000	0.000
72	A	122	ALA	0	0.061	0.006	23.411	0.007	0.007	0.000	0.000	0.000	0.000
73	A	123	ASP	-1	-0.835	-0.911	24.333	-10.513	-10.513	0.000	0.000	0.000	0.000
74	A	124	ASN	0	-0.041	-0.018	24.688	0.540	0.540	0.000	0.000	0.000	0.000
75	A	125	ALA	0	0.032	0.020	21.512	0.021	0.021	0.000	0.000	0.000	0.000
76	A	126	ARG	1	0.875	0.916	23.222	11.458	11.458	0.000	0.000	0.000	0.000
77	A	127	ARG	1	0.946	0.990	26.044	10.505	10.505	0.000	0.000	0.000	0.000
78	A	128	PHE	0	-0.024	-0.024	21.206	0.369	0.369	0.000	0.000	0.000	0.000
79	A	129	LEU	0	0.016	-0.004	20.979	0.090	0.090	0.000	0.000	0.000	0.000
80	A	130	GLY	0	-0.011	0.014	25.003	0.215	0.215	0.000	0.000	0.000	0.000
81	A	131	ARG	1	0.818	0.919	27.995	10.658	10.658	0.000	0.000	0.000	0.000
82	A	132	TYR	0	-0.013	-0.050	25.043	0.506	0.506	0.000	0.000	0.000	0.000
83	A	133	GLY	0	0.012	0.028	26.921	0.053	0.053	0.000	0.000	0.000	0.000
84	A	134	ASN	0	0.029	-0.008	22.078	-0.938	-0.938	0.000	0.000	0.000	0.000
85	A	135	PRO	0	-0.020	0.011	20.107	0.324	0.324	0.000	0.000	0.000	0.000
86	A	136	PHE	0	-0.013	-0.013	16.275	-0.455	-0.455	0.000	0.000	0.000	0.000
87	A	137	GLY	0	0.007	0.005	19.451	0.720	0.720	0.000	0.000	0.000	0.000
88	A	138	ARG	1	0.873	0.924	16.715	17.903	17.903	0.000	0.000	0.000	0.000
89	A	139	VAL	0	0.031	0.013	16.859	-0.688	-0.688	0.000	0.000	0.000	0.000
90	A	140	GLY	0	-0.032	-0.005	14.657	0.632	0.632	0.000	0.000	0.000	0.000
91	A	141	VAL	0	0.014	0.002	15.120	-0.588	-0.588	0.000	0.000	0.000	0.000
92	A	142	ASP	-1	-0.739	-0.872	10.890	-26.415	-26.415	0.000	0.000	0.000	0.000
93	A	143	ALA	0	0.014	-0.003	14.019	0.066	0.066	0.000	0.000	0.000	0.000
94	A	144	ASN	0	0.015	-0.005	14.177	-0.442	-0.442	0.000	0.000	0.000	0.000
95	A	145	GLY	0	-0.001	0.006	12.086	0.157	0.157	0.000	0.000	0.000	0.000
96	A	146	ARG	1	0.952	0.967	10.258	20.835	20.835	0.000	0.000	0.000	0.000
97	A	147	ALA	0	0.033	0.023	8.162	-2.799	-2.799	0.000	0.000	0.000	0.000
98	A	148	SER	0	0.004	-0.029	6.326	-5.766	-5.766	0.000	0.000	0.000	0.000
99	A	149	ILE	0	-0.002	0.018	5.935	-4.449	-4.449	0.000	0.000	0.000	0.000
100	A	150	GLU	-1	-0.921	-0.954	3.863	-47.820	-46.787	0.000	-0.598	-0.435	-0.003
101	A	151	TRP	0	-0.042	-0.040	1.840	-48.330	-48.275	11.914	-6.655	-5.314	-0.085
102	A	152	GLY	0	-0.065	-0.023	2.878	-4.397	-3.865	0.427	0.149	-1.109	-0.013
103	A	153	VAL	0	-0.071	-0.039	4.429	4.771	4.859	-0.001	-0.013	-0.074	0.000
104	A	154	TYR	0	-0.039	-0.020	7.505	1.201	1.201	0.000	0.000	0.000	0.000
105	A	155	GLY	0	-0.021	-0.008	10.642	1.929	1.929	0.000	0.000	0.000	0.000
106	A	156	VAL	0	-0.056	0.010	12.041	-1.315	-1.315	0.000	0.000	0.000	0.000
107	A	157	PRO	0	0.026	-0.010	13.828	1.075	1.075	0.000	0.000	0.000	0.000
108	A	158	GLU	-1	-0.771	-0.907	8.070	-32.492	-32.492	0.000	0.000	0.000	0.000
109	A	159	THR	0	0.024	0.017	10.771	0.502	0.502	0.000	0.000	0.000	0.000
110	A	160	PHE	0	-0.037	-0.016	4.072	-2.331	-2.181	-0.001	-0.013	-0.135	0.000
111	A	161	VAL	0	0.036	0.021	8.884	2.523	2.523	0.000	0.000	0.000	0.000
112	A	162	VAL	0	-0.034	-0.014	6.959	-3.229	-3.229	0.000	0.000	0.000	0.000
113	A	163	GLY	0	0.075	0.038	7.393	3.043	3.043	0.000	0.000	0.000	0.000
114	A	164	ARG	1	1.000	1.008	9.291	15.074	15.074	0.000	0.000	0.000	0.000
115	A	165	GLU	-1	-0.928	-0.962	8.241	-20.624	-20.624	0.000	0.000	0.000	0.000
116	A	166	GLY	0	-0.024	-0.013	8.347	-0.689	-0.689	0.000	0.000	0.000	0.000
117	A	167	THR	0	-0.007	0.000	3.201	-5.329	-4.653	0.027	-0.240	-0.463	0.001
118	A	168	ILE	0	-0.036	-0.020	2.372	1.242	3.573	0.946	-0.906	-2.371	0.000
119	A	169	VAL	0	-0.001	-0.002	3.196	-1.751	-0.537	0.040	-0.616	-0.638	-0.005
120	A	170	TYR	0	-0.006	-0.010	5.880	2.209	2.209	0.000	0.000	0.000	0.000
121	A	171	LYS	1	0.854	0.942	5.592	37.034	37.034	0.000	0.000	0.000	0.000
122	A	172	LEU	0	-0.038	-0.012	9.175	1.810	1.810	0.000	0.000	0.000	0.000
123	A	173	VAL	0	0.031	0.012	10.130	-1.163	-1.163	0.000	0.000	0.000	0.000
124	A	174	GLY	0	0.020	0.014	12.324	1.450	1.450	0.000	0.000	0.000	0.000
125	A	175	PRO	0	-0.012	0.004	15.086	-0.712	-0.712	0.000	0.000	0.000	0.000
126	A	176	ILE	0	-0.007	-0.019	15.821	0.130	0.130	0.000	0.000	0.000	0.000
127	A	177	THR	0	0.005	-0.002	18.583	0.635	0.635	0.000	0.000	0.000	0.000
128	A	178	PRO	0	0.076	0.019	22.078	-0.232	-0.232	0.000	0.000	0.000	0.000
129	A	179	ASP	-1	-0.846	-0.907	24.368	-11.655	-11.655	0.000	0.000	0.000	0.000
130	A	180	ASN	0	-0.016	0.000	18.491	-0.100	-0.100	0.000	0.000	0.000	0.000
131	A	181	LEU	0	0.044	0.017	19.268	-0.641	-0.641	0.000	0.000	0.000	0.000
132	A	182	ARG	1	0.879	0.916	20.271	11.200	11.200	0.000	0.000	0.000	0.000
133	A	183	SER	0	0.024	0.017	21.593	0.155	0.155	0.000	0.000	0.000	0.000
134	A	184	VAL	0	-0.054	-0.016	15.550	-0.114	-0.114	0.000	0.000	0.000	0.000
135	A	185	LEU	0	-0.008	-0.024	13.838	-0.614	-0.614	0.000	0.000	0.000	0.000
136	A	186	LEU	0	0.031	0.019	15.681	-0.496	-0.496	0.000	0.000	0.000	0.000
137	A	187	PRO	0	0.023	0.011	17.647	-0.144	-0.144	0.000	0.000	0.000	0.000
138	A	188	GLN	0	0.001	0.000	12.205	0.131	0.131	0.000	0.000	0.000	0.000
139	A	189	MET	0	-0.054	-0.017	13.317	-0.642	-0.642	0.000	0.000	0.000	0.000
140	A	190	GLU	-1	-0.869	-0.952	14.611	-12.935	-12.935	0.000	0.000	0.000	0.000
141	A	191	LYS	1	0.908	0.962	14.344	14.874	14.874	0.000	0.000	0.000	0.000
142	A	192	ALA	0	-0.006	0.015	11.497	0.034	0.034	0.000	0.000	0.000	0.000
143	A	193	LEU	0	-0.097	-0.031	13.076	0.101	0.101	0.000	0.000	0.000	0.000

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