FMO DATABASE

FMODB ID: 7613K

Calculation Name: 4KEE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4KEE

Chain ID: A

ChEMBL ID:

UniProt ID: Q03048

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	132
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1163305.140766
FMO2-HF: Nuclear repulsion	1111940.595292
FMO2-HF: Total energy	-51364.545474
FMO2-MP2: Total energy	-51516.121298

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:1:GLY)

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

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.
0.783	1.788	-0.002	-0.568	-0.436	0.003

Interaction energy analysis for fragmet #1(A:1:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.039 / q_NPA : 0.006

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	3	ARG	1	0.981	0.979	3.792	0.418	1.337	0.000	-0.544	-0.375	0.003
4	A	4	SER	0	-0.034	-0.032	6.595	0.152	0.152	0.000	0.000	0.000	0.000
5	A	5	GLY	0	0.011	0.028	4.139	0.185	0.265	-0.001	-0.019	-0.061	0.000
6	A	6	VAL	0	-0.052	-0.017	5.139	0.111	0.117	-0.001	-0.005	0.000	0.000
7	A	7	ALA	0	0.015	0.018	7.574	-0.114	-0.114	0.000	0.000	0.000	0.000
8	A	8	VAL	0	-0.020	-0.017	11.120	0.112	0.112	0.000	0.000	0.000	0.000
9	A	9	ALA	0	0.051	0.039	14.370	-0.042	-0.042	0.000	0.000	0.000	0.000
10	A	10	ASP	-1	-0.848	-0.939	16.804	-0.067	-0.067	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.875	-0.945	19.833	0.101	0.101	0.000	0.000	0.000	0.000
12	A	12	SER	0	-0.011	-0.018	17.381	0.011	0.011	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.007	0.003	19.952	0.003	0.003	0.000	0.000	0.000	0.000
14	A	14	THR	0	-0.050	-0.031	21.492	-0.005	-0.005	0.000	0.000	0.000	0.000
15	A	15	ALA	0	0.036	0.021	23.648	0.000	0.000	0.000	0.000	0.000	0.000
16	A	16	PHE	0	0.010	-0.003	22.724	0.000	0.000	0.000	0.000	0.000	0.000
17	A	17	ASN	0	-0.009	-0.018	24.758	0.000	0.000	0.000	0.000	0.000	0.000
18	A	18	ASP	-1	-0.884	-0.942	27.162	0.017	0.017	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.076	-0.025	27.273	0.000	0.000	0.000	0.000	0.000	0.000
20	A	20	LYS	1	0.856	0.928	26.287	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	21	LEU	0	-0.048	-0.036	29.797	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	22	GLY	0	-0.008	0.006	32.240	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.831	0.924	33.043	-0.036	-0.036	0.000	0.000	0.000	0.000
24	A	24	LYS	1	0.894	0.966	30.709	-0.031	-0.031	0.000	0.000	0.000	0.000
25	A	25	TYR	0	-0.042	-0.034	28.033	0.004	0.004	0.000	0.000	0.000	0.000
26	A	26	LYS	1	0.835	0.913	31.421	-0.066	-0.066	0.000	0.000	0.000	0.000
27	A	27	PHE	0	0.000	-0.019	26.718	0.002	0.002	0.000	0.000	0.000	0.000
28	A	28	ILE	0	-0.023	-0.005	22.574	-0.005	-0.005	0.000	0.000	0.000	0.000
29	A	29	LEU	0	0.008	0.012	22.192	0.010	0.010	0.000	0.000	0.000	0.000
30	A	30	PHE	0	0.025	-0.001	17.452	-0.010	-0.010	0.000	0.000	0.000	0.000
31	A	31	GLY	0	0.007	-0.016	15.737	0.025	0.025	0.000	0.000	0.000	0.000
32	A	32	LEU	0	-0.058	-0.013	9.084	-0.006	-0.006	0.000	0.000	0.000	0.000
33	A	33	ASN	0	0.086	0.046	11.307	0.082	0.082	0.000	0.000	0.000	0.000
34	A	34	ASP	-1	-0.872	-0.954	11.956	0.506	0.506	0.000	0.000	0.000	0.000
35	A	35	ALA	0	-0.083	-0.038	10.601	0.095	0.095	0.000	0.000	0.000	0.000
36	A	36	LYS	1	0.878	0.946	7.128	-0.775	-0.775	0.000	0.000	0.000	0.000
37	A	37	THR	0	-0.023	-0.014	6.546	0.241	0.241	0.000	0.000	0.000	0.000
38	A	38	GLU	-1	-0.920	-0.966	8.430	-0.156	-0.156	0.000	0.000	0.000	0.000
39	A	39	ILE	0	-0.042	-0.015	11.333	0.100	0.100	0.000	0.000	0.000	0.000
40	A	40	VAL	0	0.014	0.007	13.575	-0.064	-0.064	0.000	0.000	0.000	0.000
41	A	41	VAL	0	0.001	-0.006	16.937	0.027	0.027	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.862	0.941	18.379	-0.283	-0.283	0.000	0.000	0.000	0.000
43	A	43	GLU	-1	-0.879	-0.953	21.313	0.132	0.132	0.000	0.000	0.000	0.000
44	A	44	THR	0	-0.042	-0.008	24.801	0.002	0.002	0.000	0.000	0.000	0.000
45	A	45	SER	0	0.058	0.033	27.380	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	46	THR	0	0.011	-0.006	30.669	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	47	ASP	-1	-0.881	-0.938	33.610	0.074	0.074	0.000	0.000	0.000	0.000
48	A	48	PRO	0	0.003	-0.005	34.502	0.003	0.003	0.000	0.000	0.000	0.000
49	A	49	SER	0	-0.017	0.006	36.832	0.000	0.000	0.000	0.000	0.000	0.000
50	A	50	TYR	0	-0.007	-0.041	30.396	0.004	0.004	0.000	0.000	0.000	0.000
51	A	51	ASP	-1	-0.852	-0.926	33.124	0.099	0.099	0.000	0.000	0.000	0.000
52	A	52	ALA	0	0.002	0.008	33.630	0.007	0.007	0.000	0.000	0.000	0.000
53	A	53	PHE	0	-0.095	-0.048	26.083	0.009	0.009	0.000	0.000	0.000	0.000
54	A	54	LEU	0	0.006	-0.005	28.977	0.014	0.014	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.936	-0.967	29.440	0.118	0.118	0.000	0.000	0.000	0.000
56	A	56	LYS	1	0.862	0.938	27.170	-0.115	-0.115	0.000	0.000	0.000	0.000
57	A	57	LEU	0	-0.062	-0.012	24.115	0.017	0.017	0.000	0.000	0.000	0.000
58	A	58	PRO	0	-0.035	-0.002	21.423	-0.004	-0.004	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.856	-0.940	23.708	0.198	0.198	0.000	0.000	0.000	0.000
60	A	60	ASN	0	-0.040	0.001	22.958	0.004	0.004	0.000	0.000	0.000	0.000
61	A	61	ASP	-1	-0.877	-0.949	17.418	0.524	0.524	0.000	0.000	0.000	0.000
62	A	62	CYS	0	-0.066	-0.024	15.745	-0.024	-0.024	0.000	0.000	0.000	0.000
63	A	63	LEU	0	-0.058	-0.017	17.157	0.006	0.006	0.000	0.000	0.000	0.000
64	A	64	TYR	0	-0.031	-0.051	12.352	0.021	0.021	0.000	0.000	0.000	0.000
65	A	65	ALA	0	0.026	0.018	18.779	-0.009	-0.009	0.000	0.000	0.000	0.000
66	A	66	ILE	0	-0.033	0.001	22.071	-0.006	-0.006	0.000	0.000	0.000	0.000
67	A	67	TYR	0	0.037	0.011	24.399	-0.003	-0.003	0.000	0.000	0.000	0.000
68	A	68	ASP	-1	-0.792	-0.855	28.070	0.041	0.041	0.000	0.000	0.000	0.000
69	A	69	PHE	0	0.000	-0.004	31.063	0.001	0.001	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.833	-0.907	32.827	0.041	0.041	0.000	0.000	0.000	0.000
71	A	71	TYR	0	0.002	-0.001	35.523	0.004	0.004	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.941	-0.959	39.417	0.032	0.032	0.000	0.000	0.000	0.000
73	A	80	GLU	-1	-0.922	-0.967	37.613	0.024	0.024	0.000	0.000	0.000	0.000
74	A	81	SER	0	-0.112	-0.090	34.248	0.002	0.002	0.000	0.000	0.000	0.000
75	A	82	LYS	1	0.926	0.968	31.668	-0.033	-0.033	0.000	0.000	0.000	0.000
76	A	83	ILE	0	0.024	0.021	25.994	0.007	0.007	0.000	0.000	0.000	0.000
77	A	84	VAL	0	0.023	0.011	26.209	-0.004	-0.004	0.000	0.000	0.000	0.000
78	A	85	PHE	0	-0.011	-0.008	17.049	0.009	0.009	0.000	0.000	0.000	0.000
79	A	86	PHE	0	0.038	0.015	22.442	0.000	0.000	0.000	0.000	0.000	0.000
80	A	87	THR	0	-0.063	-0.052	17.405	0.017	0.017	0.000	0.000	0.000	0.000
81	A	88	TRP	0	-0.015	0.003	19.360	-0.016	-0.016	0.000	0.000	0.000	0.000
82	A	89	SER	0	-0.020	-0.042	17.755	0.073	0.073	0.000	0.000	0.000	0.000
83	A	90	PRO	0	0.052	0.051	19.406	-0.003	-0.003	0.000	0.000	0.000	0.000
84	A	91	ASP	-1	-0.850	-0.940	21.150	0.295	0.295	0.000	0.000	0.000	0.000
85	A	92	THR	0	-0.074	-0.070	22.316	0.027	0.027	0.000	0.000	0.000	0.000
86	A	93	ALA	0	0.001	0.023	18.355	0.011	0.011	0.000	0.000	0.000	0.000
87	A	94	PRO	0	-0.027	-0.023	16.404	0.027	0.027	0.000	0.000	0.000	0.000
88	A	95	VAL	0	0.059	0.019	14.157	0.051	0.051	0.000	0.000	0.000	0.000
89	A	96	ARG	1	0.962	0.966	11.656	-0.767	-0.767	0.000	0.000	0.000	0.000
90	A	97	SER	0	-0.027	-0.001	11.341	0.211	0.211	0.000	0.000	0.000	0.000
91	A	98	LYS	1	1.001	1.003	12.805	-0.357	-0.357	0.000	0.000	0.000	0.000
92	A	99	MET	0	-0.046	-0.014	9.308	-0.050	-0.050	0.000	0.000	0.000	0.000
93	A	100	VAL	0	0.004	0.012	6.627	0.085	0.085	0.000	0.000	0.000	0.000
94	A	101	TYR	0	0.084	0.058	8.911	-0.046	-0.046	0.000	0.000	0.000	0.000
95	A	102	ALA	0	0.010	0.023	11.735	-0.116	-0.116	0.000	0.000	0.000	0.000
96	A	103	SER	0	-0.079	-0.052	6.421	-0.081	-0.081	0.000	0.000	0.000	0.000
97	A	104	SER	0	-0.022	-0.021	7.835	-0.062	-0.062	0.000	0.000	0.000	0.000
98	A	105	LYS	1	0.959	1.004	8.956	-0.371	-0.371	0.000	0.000	0.000	0.000
99	A	106	ASP	-1	-0.912	-0.975	10.871	-0.118	-0.118	0.000	0.000	0.000	0.000
100	A	107	ALA	0	0.028	0.022	9.610	-0.068	-0.068	0.000	0.000	0.000	0.000
101	A	108	LEU	0	0.022	0.014	11.678	-0.041	-0.041	0.000	0.000	0.000	0.000
102	A	109	ARG	1	0.786	0.849	14.769	-0.099	-0.099	0.000	0.000	0.000	0.000
103	A	110	ARG	1	0.893	0.947	13.707	0.114	0.114	0.000	0.000	0.000	0.000
104	A	111	ALA	0	-0.022	0.007	16.073	-0.024	-0.024	0.000	0.000	0.000	0.000
105	A	112	LEU	0	-0.039	-0.002	17.848	-0.003	-0.003	0.000	0.000	0.000	0.000
106	A	113	ASN	0	-0.003	-0.005	20.860	0.000	0.000	0.000	0.000	0.000	0.000
107	A	114	GLY	0	0.015	-0.016	23.910	0.005	0.005	0.000	0.000	0.000	0.000
108	A	115	VAL	0	-0.018	0.004	22.428	0.004	0.004	0.000	0.000	0.000	0.000
109	A	116	SER	0	-0.053	-0.023	25.616	-0.008	-0.008	0.000	0.000	0.000	0.000
110	A	117	THR	0	0.003	-0.005	27.102	-0.003	-0.003	0.000	0.000	0.000	0.000
111	A	118	ASP	-1	-0.807	-0.859	21.259	0.096	0.096	0.000	0.000	0.000	0.000
112	A	119	VAL	0	0.002	-0.003	23.583	-0.006	-0.006	0.000	0.000	0.000	0.000
113	A	120	GLN	0	-0.052	-0.028	20.340	0.007	0.007	0.000	0.000	0.000	0.000
114	A	121	GLY	0	0.028	0.011	22.359	-0.009	-0.009	0.000	0.000	0.000	0.000
115	A	122	THR	0	-0.082	-0.066	21.694	0.031	0.031	0.000	0.000	0.000	0.000
116	A	123	ASP	-1	-0.718	-0.805	23.854	0.169	0.169	0.000	0.000	0.000	0.000
117	A	124	PHE	0	0.042	-0.015	27.215	-0.004	-0.004	0.000	0.000	0.000	0.000
118	A	125	SER	0	-0.123	-0.090	29.787	-0.012	-0.012	0.000	0.000	0.000	0.000
119	A	126	GLU	-1	-0.833	-0.907	26.102	0.168	0.168	0.000	0.000	0.000	0.000
120	A	127	VAL	0	-0.042	-0.015	25.932	-0.004	-0.004	0.000	0.000	0.000	0.000
121	A	128	SER	0	0.032	0.038	29.144	-0.008	-0.008	0.000	0.000	0.000	0.000
122	A	129	TYR	0	0.038	0.006	32.743	-0.002	-0.002	0.000	0.000	0.000	0.000
123	A	130	ASP	-1	-0.858	-0.941	34.639	0.067	0.067	0.000	0.000	0.000	0.000
124	A	131	SER	0	-0.020	-0.009	31.847	-0.007	-0.007	0.000	0.000	0.000	0.000
125	A	132	VAL	0	-0.038	-0.018	29.375	-0.002	-0.002	0.000	0.000	0.000	0.000
126	A	133	LEU	0	0.035	0.018	31.821	-0.006	-0.006	0.000	0.000	0.000	0.000
127	A	134	GLU	-1	-0.966	-0.949	34.644	0.064	0.064	0.000	0.000	0.000	0.000
128	A	135	ARG	1	0.911	0.947	28.084	-0.106	-0.106	0.000	0.000	0.000	0.000
129	A	136	VAL	0	-0.036	-0.022	30.852	-0.005	-0.005	0.000	0.000	0.000	0.000
130	A	137	SER	0	-0.080	-0.049	32.747	-0.007	-0.007	0.000	0.000	0.000	0.000
131	A	138	ARG	1	0.922	0.974	34.293	-0.046	-0.046	0.000	0.000	0.000	0.000
132	A	139	GLY	0	-0.037	-0.011	31.430	-0.007	-0.007	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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