FMO DATABASE

FMODB ID: MNM5Z

Calculation Name: 4KIA-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4KIA

Chain ID: A

ChEMBL ID:

UniProt ID: Q8Y563

Base Structure: X-ray

Registration Date: 2023-09-20

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	159
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1681598.430227
FMO2-HF: Nuclear repulsion	1616856.495463
FMO2-HF: Total energy	-64741.934764
FMO2-MP2: Total energy	-64931.791044

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:2:LYS)

Summations of interaction energy for fragment #1(A:2:LYS)

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.
-120.007	-117.249	24.746	-14.197	-13.305	-0.128

Interaction energy analysis for fragmet #1(A:2:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.856 / q_NPA : 0.912

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	4	VAL	0	0.023	0.007	3.138	-19.363	-15.238	0.011	-2.299	-1.837	-0.009
4	A	5	PHE	0	-0.033	-0.026	5.164	4.996	5.060	-0.001	-0.004	-0.059	0.000
5	A	6	ILE	0	-0.003	-0.001	8.473	-0.690	-0.690	0.000	0.000	0.000	0.000
6	A	7	THR	0	0.037	0.016	11.268	0.973	0.973	0.000	0.000	0.000	0.000
7	A	8	THR	0	0.001	0.012	14.483	-0.081	-0.081	0.000	0.000	0.000	0.000
8	A	9	GLY	0	0.045	0.021	17.701	0.380	0.380	0.000	0.000	0.000	0.000
9	A	10	THR	0	0.031	0.011	20.806	-0.162	-0.162	0.000	0.000	0.000	0.000
10	A	11	GLU	-1	-0.742	-0.856	21.002	-14.403	-14.403	0.000	0.000	0.000	0.000
11	A	12	HIS	0	0.016	0.006	21.296	-0.637	-0.637	0.000	0.000	0.000	0.000
12	A	13	TYR	0	-0.021	-0.031	18.891	-0.111	-0.111	0.000	0.000	0.000	0.000
13	A	14	LEU	0	0.013	0.000	16.073	-0.496	-0.496	0.000	0.000	0.000	0.000
14	A	15	ARG	1	0.837	0.890	17.287	14.013	14.013	0.000	0.000	0.000	0.000
15	A	16	GLN	0	-0.062	-0.028	19.187	-0.084	-0.084	0.000	0.000	0.000	0.000
16	A	17	LEU	0	0.000	0.016	14.725	-0.286	-0.286	0.000	0.000	0.000	0.000
17	A	18	MET	0	0.001	-0.010	14.004	-0.528	-0.528	0.000	0.000	0.000	0.000
18	A	19	ALA	0	-0.010	0.007	14.673	-0.865	-0.865	0.000	0.000	0.000	0.000
19	A	20	ASN	0	-0.069	-0.028	15.424	1.387	1.387	0.000	0.000	0.000	0.000
20	A	21	TYR	0	-0.039	-0.025	10.810	-1.102	-1.102	0.000	0.000	0.000	0.000
21	A	22	THR	0	0.023	0.011	11.402	0.476	0.476	0.000	0.000	0.000	0.000
22	A	23	GLY	0	0.019	0.022	8.754	-0.806	-0.806	0.000	0.000	0.000	0.000
23	A	24	GLY	0	0.036	0.005	4.500	-0.089	-0.060	-0.001	-0.005	-0.023	0.000
24	A	25	ASN	0	-0.088	-0.059	4.088	3.630	3.734	-0.001	-0.016	-0.086	0.000
25	A	26	VAL	0	0.019	0.023	6.992	0.571	0.571	0.000	0.000	0.000	0.000
26	A	27	THR	0	-0.017	-0.015	9.328	2.698	2.698	0.000	0.000	0.000	0.000
27	A	28	LEU	0	-0.028	-0.009	11.579	-0.291	-0.291	0.000	0.000	0.000	0.000
28	A	29	LEU	0	-0.018	-0.009	12.864	0.409	0.409	0.000	0.000	0.000	0.000
29	A	30	GLN	0	-0.022	-0.022	16.582	0.682	0.682	0.000	0.000	0.000	0.000
30	A	31	ASN	0	0.075	0.045	19.975	0.334	0.334	0.000	0.000	0.000	0.000
31	A	32	PHE	0	0.018	0.000	22.549	0.156	0.156	0.000	0.000	0.000	0.000
32	A	33	SER	0	-0.033	-0.012	25.048	0.237	0.237	0.000	0.000	0.000	0.000
33	A	34	GLN	0	-0.010	0.017	20.181	-0.508	-0.508	0.000	0.000	0.000	0.000
34	A	35	SER	0	0.024	-0.003	18.987	-0.102	-0.102	0.000	0.000	0.000	0.000
35	A	36	LEU	0	-0.009	-0.010	12.776	0.075	0.075	0.000	0.000	0.000	0.000
36	A	37	LEU	0	-0.010	-0.007	11.704	-0.150	-0.150	0.000	0.000	0.000	0.000
37	A	38	TYR	0	-0.041	-0.047	4.727	0.190	0.231	-0.001	0.000	-0.040	0.000
38	A	39	GLN	0	0.035	0.014	7.366	1.432	1.432	0.000	0.000	0.000	0.000
39	A	40	GLU	-1	-0.814	-0.840	1.641	-119.691	-127.663	22.771	-9.049	-5.749	-0.097
40	A	41	SER	0	0.034	0.009	3.664	7.017	7.585	0.005	-0.126	-0.447	-0.001
41	A	42	THR	0	-0.043	-0.047	2.814	-12.805	-9.376	0.491	-1.758	-2.161	-0.018
42	A	43	GLY	0	0.042	0.038	4.461	1.899	1.965	-0.001	-0.016	-0.051	0.000
43	A	44	GLU	-1	-0.789	-0.918	7.379	-23.810	-23.810	0.000	0.000	0.000	0.000
44	A	45	LYS	1	0.799	0.897	9.800	17.510	17.510	0.000	0.000	0.000	0.000
45	A	46	LEU	0	0.031	0.028	8.586	1.060	1.060	0.000	0.000	0.000	0.000
46	A	47	PHE	0	-0.001	0.005	11.759	0.514	0.514	0.000	0.000	0.000	0.000
47	A	48	GLN	0	-0.006	0.009	12.894	0.494	0.494	0.000	0.000	0.000	0.000
48	A	49	GLU	-1	-0.841	-0.895	16.547	-16.031	-16.031	0.000	0.000	0.000	0.000
49	A	50	GLY	0	0.009	0.014	14.673	0.515	0.515	0.000	0.000	0.000	0.000
50	A	51	ALA	0	-0.048	-0.029	13.380	0.655	0.655	0.000	0.000	0.000	0.000
51	A	52	GLU	-1	-0.777	-0.887	8.373	-27.321	-27.321	0.000	0.000	0.000	0.000
52	A	53	TYR	0	-0.018	-0.020	8.147	3.587	3.587	0.000	0.000	0.000	0.000
53	A	54	ARG	1	0.970	0.989	4.039	20.824	20.972	-0.001	-0.033	-0.114	0.000
54	A	55	VAL	0	-0.021	-0.018	2.394	0.070	1.752	1.475	-0.788	-2.368	-0.003
55	A	56	LEU	0	-0.059	-0.032	3.987	0.584	0.904	0.001	-0.092	-0.229	0.000
56	A	57	GLN	0	0.026	-0.001	6.697	2.000	2.000	0.000	0.000	0.000	0.000
57	A	58	SER	0	0.008	0.011	4.560	-4.627	-4.577	-0.001	-0.003	-0.046	0.000
58	A	59	SER	0	-0.014	0.005	6.693	2.578	2.578	0.000	0.000	0.000	0.000
59	A	60	GLY	0	0.055	0.035	9.486	-1.140	-1.140	0.000	0.000	0.000	0.000
60	A	61	SER	0	-0.051	-0.039	8.834	-2.895	-2.895	0.000	0.000	0.000	0.000
61	A	62	ILE	0	-0.014	-0.002	7.423	1.601	1.601	0.000	0.000	0.000	0.000
62	A	63	LYS	1	0.897	0.932	10.821	18.132	18.132	0.000	0.000	0.000	0.000
63	A	64	GLY	0	-0.013	0.000	13.772	0.908	0.908	0.000	0.000	0.000	0.000
64	A	65	PHE	0	0.006	0.006	15.096	1.050	1.050	0.000	0.000	0.000	0.000
65	A	66	GLY	0	0.017	0.022	17.136	-0.724	-0.724	0.000	0.000	0.000	0.000
66	A	67	VAL	0	-0.036	-0.022	18.221	0.327	0.327	0.000	0.000	0.000	0.000
67	A	68	VAL	0	-0.024	-0.011	12.400	-0.950	-0.950	0.000	0.000	0.000	0.000
68	A	69	VAL	0	0.001	0.015	15.132	0.892	0.892	0.000	0.000	0.000	0.000
69	A	70	PHE	0	-0.023	-0.014	11.152	-2.071	-2.071	0.000	0.000	0.000	0.000
70	A	71	GLU	-1	-0.853	-0.941	15.031	-16.293	-16.293	0.000	0.000	0.000	0.000
71	A	72	TYR	0	-0.049	-0.030	14.641	-1.649	-1.649	0.000	0.000	0.000	0.000
72	A	73	ILE	0	0.029	-0.013	16.718	1.260	1.260	0.000	0.000	0.000	0.000
73	A	74	HIS	0	-0.037	-0.008	17.661	-1.105	-1.105	0.000	0.000	0.000	0.000
74	A	75	LEU	0	-0.032	-0.009	17.017	0.385	0.385	0.000	0.000	0.000	0.000
75	A	76	ARG	1	0.838	0.897	20.476	11.551	11.551	0.000	0.000	0.000	0.000
76	A	77	ASP	-1	-0.851	-0.933	20.161	-13.745	-13.745	0.000	0.000	0.000	0.000
77	A	78	GLU	-1	-0.896	-0.966	20.784	-12.110	-12.110	0.000	0.000	0.000	0.000
78	A	79	GLU	-1	-0.868	-0.934	21.928	-12.587	-12.587	0.000	0.000	0.000	0.000
79	A	80	ILE	0	-0.023	0.002	15.762	-0.616	-0.616	0.000	0.000	0.000	0.000
80	A	81	PRO	0	0.012	0.001	17.586	-0.715	-0.715	0.000	0.000	0.000	0.000
81	A	82	ILE	0	0.014	0.004	18.933	-0.366	-0.366	0.000	0.000	0.000	0.000
82	A	83	PHE	0	0.051	0.027	15.119	-0.253	-0.253	0.000	0.000	0.000	0.000
83	A	84	LEU	0	0.009	0.000	12.671	-0.812	-0.812	0.000	0.000	0.000	0.000
84	A	85	GLN	0	-0.019	-0.003	16.059	-0.204	-0.204	0.000	0.000	0.000	0.000
85	A	86	MET	0	-0.033	0.004	18.388	0.085	0.085	0.000	0.000	0.000	0.000
86	A	87	TYR	0	0.035	0.003	11.393	0.111	0.111	0.000	0.000	0.000	0.000
87	A	88	GLN	0	-0.029	-0.022	14.649	-0.913	-0.913	0.000	0.000	0.000	0.000
88	A	89	ARG	1	0.930	0.969	16.402	13.400	13.400	0.000	0.000	0.000	0.000
89	A	90	ALA	0	0.022	0.006	18.202	0.251	0.251	0.000	0.000	0.000	0.000
90	A	91	SER	0	-0.029	-0.028	13.772	-0.248	-0.248	0.000	0.000	0.000	0.000
91	A	92	LEU	0	-0.053	-0.023	15.726	-0.589	-0.589	0.000	0.000	0.000	0.000
92	A	93	HIS	0	0.006	0.004	17.979	0.523	0.523	0.000	0.000	0.000	0.000
93	A	94	PHE	0	-0.009	0.004	12.838	0.150	0.150	0.000	0.000	0.000	0.000
94	A	95	SER	0	-0.056	-0.055	16.940	-0.238	-0.238	0.000	0.000	0.000	0.000
95	A	96	GLU	-1	-0.863	-0.892	17.816	-14.258	-14.258	0.000	0.000	0.000	0.000
96	A	97	THR	0	-0.100	-0.039	18.768	0.796	0.796	0.000	0.000	0.000	0.000
97	A	98	PRO	0	0.025	-0.002	19.936	-0.560	-0.560	0.000	0.000	0.000	0.000
98	A	99	GLY	0	0.024	0.011	20.368	-0.062	-0.062	0.000	0.000	0.000	0.000
99	A	100	LEU	0	-0.040	-0.005	14.633	-0.620	-0.620	0.000	0.000	0.000	0.000
100	A	101	GLN	0	-0.085	-0.053	13.418	-1.513	-1.513	0.000	0.000	0.000	0.000
101	A	102	SER	0	-0.020	-0.027	8.740	-2.787	-2.787	0.000	0.000	0.000	0.000
102	A	103	THR	0	0.043	0.032	10.133	0.699	0.699	0.000	0.000	0.000	0.000
103	A	104	LYS	1	0.869	0.944	4.321	44.603	44.707	-0.001	-0.008	-0.095	0.000
104	A	105	LEU	0	0.008	0.033	7.851	3.399	3.399	0.000	0.000	0.000	0.000
105	A	106	THR	0	-0.028	-0.037	6.383	-3.858	-3.858	0.000	0.000	0.000	0.000
106	A	107	LYS	1	0.886	0.945	8.465	22.882	22.882	0.000	0.000	0.000	0.000
107	A	108	ALA	0	-0.006	0.004	9.517	-1.898	-1.898	0.000	0.000	0.000	0.000
108	A	109	MET	0	-0.031	-0.016	8.320	-0.199	-0.199	0.000	0.000	0.000	0.000
109	A	110	ASN	0	0.009	0.004	11.220	0.088	0.088	0.000	0.000	0.000	0.000
110	A	111	MET	0	0.062	0.050	14.635	0.898	0.898	0.000	0.000	0.000	0.000
111	A	112	ASN	0	0.007	0.018	14.855	-2.206	-2.206	0.000	0.000	0.000	0.000
112	A	113	LYS	1	0.916	0.960	15.661	18.842	18.842	0.000	0.000	0.000	0.000
113	A	114	PHE	0	0.017	-0.012	12.617	-1.547	-1.547	0.000	0.000	0.000	0.000
114	A	115	LEU	0	-0.014	0.002	10.786	1.426	1.426	0.000	0.000	0.000	0.000
115	A	116	ILE	0	0.013	0.017	11.011	-2.958	-2.958	0.000	0.000	0.000	0.000
116	A	117	ILE	0	-0.010	0.011	8.128	1.131	1.131	0.000	0.000	0.000	0.000
117	A	118	SER	0	0.023	0.012	10.989	-1.187	-1.187	0.000	0.000	0.000	0.000
118	A	119	PHE	0	0.007	0.003	8.744	0.653	0.653	0.000	0.000	0.000	0.000
119	A	120	TRP	0	0.054	0.008	13.536	0.424	0.424	0.000	0.000	0.000	0.000
120	A	121	ASP	-1	-0.797	-0.893	17.166	-16.625	-16.625	0.000	0.000	0.000	0.000
121	A	122	SER	0	-0.020	-0.020	19.628	0.636	0.636	0.000	0.000	0.000	0.000
122	A	123	GLU	-1	-0.807	-0.905	21.647	-13.380	-13.380	0.000	0.000	0.000	0.000
123	A	124	VAL	0	0.000	0.008	23.156	0.085	0.085	0.000	0.000	0.000	0.000
124	A	125	PHE	0	0.021	0.017	21.571	0.134	0.134	0.000	0.000	0.000	0.000
125	A	126	PHE	0	0.020	0.032	19.450	-0.090	-0.090	0.000	0.000	0.000	0.000
126	A	127	HIS	0	-0.001	-0.045	21.625	0.142	0.142	0.000	0.000	0.000	0.000
127	A	128	ASP	-1	-0.885	-0.929	25.170	-11.125	-11.125	0.000	0.000	0.000	0.000
128	A	129	TRP	0	0.035	0.016	18.607	0.334	0.334	0.000	0.000	0.000	0.000
129	A	130	LYS	1	0.871	0.937	22.407	13.779	13.779	0.000	0.000	0.000	0.000
130	A	131	LYS	1	0.781	0.887	24.699	11.384	11.384	0.000	0.000	0.000	0.000
131	A	132	SER	0	-0.034	-0.020	22.880	0.321	0.321	0.000	0.000	0.000	0.000
132	A	133	PRO	0	0.029	-0.010	25.161	-0.028	-0.028	0.000	0.000	0.000	0.000
133	A	134	LEU	0	0.041	0.031	17.265	0.055	0.055	0.000	0.000	0.000	0.000
134	A	135	SER	0	0.025	0.037	21.493	0.048	0.048	0.000	0.000	0.000	0.000
135	A	136	LYS	1	0.890	0.942	22.404	11.137	11.137	0.000	0.000	0.000	0.000
136	A	137	GLU	-1	-0.933	-0.965	23.020	-12.928	-12.928	0.000	0.000	0.000	0.000
137	A	138	ILE	0	0.047	0.017	17.761	0.216	0.216	0.000	0.000	0.000	0.000
138	A	139	THR	0	-0.005	-0.010	21.704	0.152	0.152	0.000	0.000	0.000	0.000
139	A	140	ASN	0	-0.012	-0.003	24.458	0.707	0.707	0.000	0.000	0.000	0.000
140	A	141	ILE	0	-0.005	-0.005	21.379	0.399	0.399	0.000	0.000	0.000	0.000
141	A	142	MET	0	-0.025	-0.001	19.540	0.320	0.320	0.000	0.000	0.000	0.000
142	A	143	ARG	1	0.851	0.923	24.147	10.616	10.616	0.000	0.000	0.000	0.000
143	A	144	LYS	1	0.922	0.959	27.402	11.145	11.145	0.000	0.000	0.000	0.000
144	A	145	ASN	0	0.019	0.015	24.540	0.054	0.054	0.000	0.000	0.000	0.000
145	A	146	ASN	0	0.030	0.012	26.359	0.530	0.530	0.000	0.000	0.000	0.000
146	A	147	THR	0	0.019	0.010	26.567	-0.342	-0.342	0.000	0.000	0.000	0.000
147	A	148	GLN	0	0.002	0.015	27.950	-0.206	-0.206	0.000	0.000	0.000	0.000
148	A	149	SER	0	-0.046	-0.018	22.645	-0.227	-0.227	0.000	0.000	0.000	0.000
149	A	150	GLY	0	0.020	0.021	22.969	-0.560	-0.560	0.000	0.000	0.000	0.000
150	A	151	PHE	0	0.002	-0.015	24.266	0.121	0.121	0.000	0.000	0.000	0.000
151	A	152	SER	0	0.004	0.006	21.356	-0.860	-0.860	0.000	0.000	0.000	0.000
152	A	153	HIS	1	0.768	0.866	19.241	16.420	16.420	0.000	0.000	0.000	0.000
153	A	154	GLU	-1	-0.797	-0.886	19.455	-15.334	-15.334	0.000	0.000	0.000	0.000
154	A	155	ASP	-1	-0.826	-0.885	18.029	-15.349	-15.349	0.000	0.000	0.000	0.000
155	A	156	ILE	0	0.027	0.005	18.196	-1.066	-1.066	0.000	0.000	0.000	0.000
156	A	157	TYR	0	-0.070	-0.047	16.660	0.463	0.463	0.000	0.000	0.000	0.000
157	A	158	HIS	0	0.025	0.012	18.458	-0.027	-0.027	0.000	0.000	0.000	0.000
158	A	159	TYR	0	0.037	0.009	14.124	-1.257	-1.257	0.000	0.000	0.000	0.000
159	A	160	PRO	0	-0.020	0.013	18.125	0.701	0.701	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:2:LYS)