FMO DATABASE

FMODB ID: 2NV7R

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1163238.431523
FMO2-HF: Nuclear repulsion	1111873.399944
FMO2-HF: Total energy	-51365.031579
FMO2-MP2: Total energy	-51516.661876

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.
0.811	2.805	-0.006	-1.208	-0.78	0.007

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 : 0.060 / q_NPA : 0.033

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	0.970	0.976	3.792	-0.223	1.686	-0.004	-1.185	-0.720	0.007
4	A	4	SER	0	-0.031	-0.031	6.599	0.272	0.272	0.000	0.000	0.000	0.000
5	A	5	GLY	0	0.016	0.031	4.144	0.332	0.410	-0.001	-0.018	-0.059	0.000
6	A	6	VAL	0	-0.045	-0.014	5.144	-0.078	-0.071	-0.001	-0.005	-0.001	0.000
7	A	7	ALA	0	0.007	0.015	7.579	-0.035	-0.035	0.000	0.000	0.000	0.000
8	A	8	VAL	0	-0.011	-0.010	11.125	0.103	0.103	0.000	0.000	0.000	0.000
9	A	9	ALA	0	0.028	0.026	14.374	-0.056	-0.056	0.000	0.000	0.000	0.000
10	A	10	ASP	-1	-0.839	-0.934	16.800	-0.045	-0.045	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.874	-0.932	19.771	0.095	0.095	0.000	0.000	0.000	0.000
12	A	12	SER	0	0.003	-0.013	17.353	0.010	0.010	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.001	0.004	19.895	0.011	0.011	0.000	0.000	0.000	0.000
14	A	14	THR	0	-0.053	-0.041	21.496	-0.004	-0.004	0.000	0.000	0.000	0.000
15	A	15	ALA	0	0.037	0.022	23.633	0.000	0.000	0.000	0.000	0.000	0.000
16	A	16	PHE	0	0.027	0.003	22.713	0.002	0.002	0.000	0.000	0.000	0.000
17	A	17	ASN	0	-0.009	-0.023	24.483	0.004	0.004	0.000	0.000	0.000	0.000
18	A	18	ASP	-1	-0.772	-0.875	27.166	0.043	0.043	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.061	-0.016	27.298	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	20	LYS	1	0.830	0.924	26.013	-0.085	-0.085	0.000	0.000	0.000	0.000
21	A	21	LEU	0	-0.048	-0.033	29.800	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	22	GLY	0	-0.011	0.001	32.245	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.776	0.871	33.056	-0.083	-0.083	0.000	0.000	0.000	0.000
24	A	24	LYS	1	0.789	0.904	30.629	-0.045	-0.045	0.000	0.000	0.000	0.000
25	A	25	TYR	0	-0.061	-0.040	28.092	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	26	LYS	1	0.837	0.915	31.417	-0.104	-0.104	0.000	0.000	0.000	0.000
27	A	27	PHE	0	0.010	-0.012	26.988	0.008	0.008	0.000	0.000	0.000	0.000
28	A	28	ILE	0	-0.029	-0.009	22.592	-0.012	-0.012	0.000	0.000	0.000	0.000
29	A	29	LEU	0	0.007	0.016	22.233	0.023	0.023	0.000	0.000	0.000	0.000
30	A	30	PHE	0	0.027	-0.005	17.509	-0.019	-0.019	0.000	0.000	0.000	0.000
31	A	31	GLY	0	0.013	-0.010	15.733	0.038	0.038	0.000	0.000	0.000	0.000
32	A	32	LEU	0	-0.045	-0.006	9.088	-0.022	-0.022	0.000	0.000	0.000	0.000
33	A	33	ASN	0	0.079	0.046	11.324	0.045	0.045	0.000	0.000	0.000	0.000
34	A	34	ASP	-1	-0.855	-0.954	11.955	0.327	0.327	0.000	0.000	0.000	0.000
35	A	35	ALA	0	-0.052	-0.022	10.661	0.043	0.043	0.000	0.000	0.000	0.000
36	A	36	LYS	1	0.791	0.909	7.229	-0.573	-0.573	0.000	0.000	0.000	0.000
37	A	37	THR	0	-0.043	-0.040	6.544	0.166	0.166	0.000	0.000	0.000	0.000
38	A	38	GLU	-1	-0.854	-0.916	8.427	-0.192	-0.192	0.000	0.000	0.000	0.000
39	A	39	ILE	0	-0.057	-0.022	11.266	0.086	0.086	0.000	0.000	0.000	0.000
40	A	40	VAL	0	0.010	0.002	13.571	-0.063	-0.063	0.000	0.000	0.000	0.000
41	A	41	VAL	0	0.007	-0.009	16.934	0.046	0.046	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.870	0.946	18.487	-0.312	-0.312	0.000	0.000	0.000	0.000
43	A	43	GLU	-1	-0.871	-0.950	21.310	0.132	0.132	0.000	0.000	0.000	0.000
44	A	44	THR	0	-0.052	-0.016	24.797	0.008	0.008	0.000	0.000	0.000	0.000
45	A	45	SER	0	0.050	0.030	27.376	-0.008	-0.008	0.000	0.000	0.000	0.000
46	A	46	THR	0	0.018	-0.003	30.665	0.003	0.003	0.000	0.000	0.000	0.000
47	A	47	ASP	-1	-0.879	-0.935	33.595	0.095	0.095	0.000	0.000	0.000	0.000
48	A	48	PRO	0	0.001	-0.011	34.498	0.006	0.006	0.000	0.000	0.000	0.000
49	A	49	SER	0	-0.013	0.006	36.800	0.003	0.003	0.000	0.000	0.000	0.000
50	A	50	TYR	0	-0.004	-0.043	30.480	0.006	0.006	0.000	0.000	0.000	0.000
51	A	51	ASP	-1	-0.860	-0.932	33.120	0.132	0.132	0.000	0.000	0.000	0.000
52	A	52	ALA	0	0.021	0.020	33.627	0.006	0.006	0.000	0.000	0.000	0.000
53	A	53	PHE	0	-0.080	-0.042	25.975	0.008	0.008	0.000	0.000	0.000	0.000
54	A	54	LEU	0	0.009	-0.004	28.974	0.015	0.015	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.949	-0.972	29.438	0.137	0.137	0.000	0.000	0.000	0.000
56	A	56	LYS	1	0.840	0.930	27.185	-0.135	-0.135	0.000	0.000	0.000	0.000
57	A	57	LEU	0	-0.066	-0.011	24.239	0.017	0.017	0.000	0.000	0.000	0.000
58	A	58	PRO	0	-0.034	-0.007	21.504	-0.009	-0.009	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.864	-0.942	23.706	0.226	0.226	0.000	0.000	0.000	0.000
60	A	60	ASN	0	-0.044	-0.018	22.949	0.018	0.018	0.000	0.000	0.000	0.000
61	A	61	ASP	-1	-0.868	-0.944	17.318	0.519	0.519	0.000	0.000	0.000	0.000
62	A	62	CYS	0	-0.056	-0.009	15.760	0.003	0.003	0.000	0.000	0.000	0.000
63	A	63	LEU	0	-0.056	-0.016	17.150	-0.016	-0.016	0.000	0.000	0.000	0.000
64	A	64	TYR	0	-0.020	-0.041	12.292	0.036	0.036	0.000	0.000	0.000	0.000
65	A	65	ALA	0	0.025	0.018	18.776	-0.030	-0.030	0.000	0.000	0.000	0.000
66	A	66	ILE	0	-0.040	-0.002	22.104	0.009	0.009	0.000	0.000	0.000	0.000
67	A	67	TYR	0	0.034	0.011	24.401	-0.013	-0.013	0.000	0.000	0.000	0.000
68	A	68	ASP	-1	-0.788	-0.850	28.072	0.098	0.098	0.000	0.000	0.000	0.000
69	A	69	PHE	0	0.001	-0.003	31.065	-0.005	-0.005	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.807	-0.881	32.829	0.080	0.080	0.000	0.000	0.000	0.000
71	A	71	TYR	0	0.002	-0.001	35.425	0.005	0.005	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.944	-0.966	39.418	0.066	0.066	0.000	0.000	0.000	0.000
73	A	80	GLU	-1	-0.863	-0.924	37.606	0.083	0.083	0.000	0.000	0.000	0.000
74	A	81	SER	0	-0.036	-0.038	34.339	0.000	0.000	0.000	0.000	0.000	0.000
75	A	82	LYS	1	0.811	0.897	31.728	-0.095	-0.095	0.000	0.000	0.000	0.000
76	A	83	ILE	0	0.015	0.021	26.029	0.007	0.007	0.000	0.000	0.000	0.000
77	A	84	VAL	0	0.021	0.010	26.249	0.006	0.006	0.000	0.000	0.000	0.000
78	A	85	PHE	0	-0.005	-0.006	16.959	0.009	0.009	0.000	0.000	0.000	0.000
79	A	86	PHE	0	0.035	0.011	22.443	0.007	0.007	0.000	0.000	0.000	0.000
80	A	87	THR	0	-0.049	-0.040	17.405	0.035	0.035	0.000	0.000	0.000	0.000
81	A	88	TRP	0	-0.019	0.001	19.366	-0.012	-0.012	0.000	0.000	0.000	0.000
82	A	89	SER	0	-0.015	-0.045	17.588	0.081	0.081	0.000	0.000	0.000	0.000
83	A	90	PRO	0	0.043	0.046	19.403	0.008	0.008	0.000	0.000	0.000	0.000
84	A	91	ASP	-1	-0.780	-0.904	21.149	0.440	0.440	0.000	0.000	0.000	0.000
85	A	92	THR	0	-0.063	-0.033	22.316	0.028	0.028	0.000	0.000	0.000	0.000
86	A	93	ALA	0	-0.019	0.015	18.402	-0.006	-0.006	0.000	0.000	0.000	0.000
87	A	94	PRO	0	-0.023	-0.019	16.404	0.030	0.030	0.000	0.000	0.000	0.000
88	A	95	VAL	0	0.060	0.020	14.588	0.070	0.070	0.000	0.000	0.000	0.000
89	A	96	ARG	1	0.952	0.964	12.112	-0.507	-0.507	0.000	0.000	0.000	0.000
90	A	97	SER	0	-0.018	-0.009	11.341	0.263	0.263	0.000	0.000	0.000	0.000
91	A	98	LYS	1	0.915	0.946	12.804	-0.415	-0.415	0.000	0.000	0.000	0.000
92	A	99	MET	0	-0.046	-0.014	9.799	-0.023	-0.023	0.000	0.000	0.000	0.000
93	A	100	VAL	0	0.009	0.019	6.504	0.301	0.301	0.000	0.000	0.000	0.000
94	A	101	TYR	0	0.074	0.050	8.910	0.037	0.037	0.000	0.000	0.000	0.000
95	A	102	ALA	0	0.010	0.019	11.732	-0.098	-0.098	0.000	0.000	0.000	0.000
96	A	103	SER	0	-0.078	-0.057	6.432	0.082	0.082	0.000	0.000	0.000	0.000
97	A	104	SER	0	-0.026	-0.021	7.834	0.054	0.054	0.000	0.000	0.000	0.000
98	A	105	LYS	1	0.962	1.007	8.957	-0.812	-0.812	0.000	0.000	0.000	0.000
99	A	106	ASP	-1	-0.868	-0.948	10.982	0.298	0.298	0.000	0.000	0.000	0.000
100	A	107	ALA	0	0.017	0.018	9.580	-0.126	-0.126	0.000	0.000	0.000	0.000
101	A	108	LEU	0	0.022	0.012	11.681	-0.096	-0.096	0.000	0.000	0.000	0.000
102	A	109	ARG	1	0.809	0.868	14.771	-0.309	-0.309	0.000	0.000	0.000	0.000
103	A	110	ARG	1	0.844	0.913	13.683	-0.283	-0.283	0.000	0.000	0.000	0.000
104	A	111	ALA	0	-0.023	0.007	16.046	-0.044	-0.044	0.000	0.000	0.000	0.000
105	A	112	LEU	0	-0.047	-0.008	17.851	-0.028	-0.028	0.000	0.000	0.000	0.000
106	A	113	ASN	0	-0.018	-0.013	20.863	0.009	0.009	0.000	0.000	0.000	0.000
107	A	114	GLY	0	0.041	-0.004	23.913	-0.005	-0.005	0.000	0.000	0.000	0.000
108	A	115	VAL	0	-0.028	-0.003	22.374	-0.003	-0.003	0.000	0.000	0.000	0.000
109	A	116	SER	0	-0.029	-0.012	25.618	-0.005	-0.005	0.000	0.000	0.000	0.000
110	A	117	THR	0	0.003	-0.003	27.115	-0.003	-0.003	0.000	0.000	0.000	0.000
111	A	118	ASP	-1	-0.815	-0.871	21.009	0.287	0.287	0.000	0.000	0.000	0.000
112	A	119	VAL	0	-0.006	-0.007	23.576	-0.009	-0.009	0.000	0.000	0.000	0.000
113	A	120	GLN	0	-0.049	-0.026	20.240	0.040	0.040	0.000	0.000	0.000	0.000
114	A	121	GLY	0	0.034	0.014	22.353	-0.017	-0.017	0.000	0.000	0.000	0.000
115	A	122	THR	0	-0.078	-0.064	21.671	0.037	0.037	0.000	0.000	0.000	0.000
116	A	123	ASP	-1	-0.771	-0.865	23.852	0.233	0.233	0.000	0.000	0.000	0.000
117	A	124	PHE	0	0.056	-0.004	27.213	0.002	0.002	0.000	0.000	0.000	0.000
118	A	125	SER	0	-0.084	-0.049	29.785	-0.015	-0.015	0.000	0.000	0.000	0.000
119	A	126	GLU	-1	-0.839	-0.896	25.981	0.290	0.290	0.000	0.000	0.000	0.000
120	A	127	VAL	0	-0.044	-0.017	25.865	0.002	0.002	0.000	0.000	0.000	0.000
121	A	128	SER	0	0.022	0.030	29.144	-0.014	-0.014	0.000	0.000	0.000	0.000
122	A	129	TYR	0	0.038	0.007	32.743	0.003	0.003	0.000	0.000	0.000	0.000
123	A	130	ASP	-1	-0.852	-0.937	34.640	0.119	0.119	0.000	0.000	0.000	0.000
124	A	131	SER	0	-0.030	-0.015	31.935	-0.006	-0.006	0.000	0.000	0.000	0.000
125	A	132	VAL	0	-0.037	-0.018	29.337	0.006	0.006	0.000	0.000	0.000	0.000
126	A	133	LEU	0	0.034	0.021	31.821	-0.003	-0.003	0.000	0.000	0.000	0.000
127	A	134	GLU	-1	-0.967	-0.952	34.653	0.141	0.141	0.000	0.000	0.000	0.000
128	A	135	ARG	1	0.924	0.952	27.607	-0.223	-0.223	0.000	0.000	0.000	0.000
129	A	136	VAL	0	-0.002	-0.007	30.814	-0.003	-0.003	0.000	0.000	0.000	0.000
130	A	137	SER	0	-0.062	-0.026	32.747	-0.008	-0.008	0.000	0.000	0.000	0.000
131	A	138	ARG	1	0.911	0.971	34.278	-0.129	-0.129	0.000	0.000	0.000	0.000
132	A	139	GLY	0	-0.080	-0.045	31.430	-0.003	-0.003	0.000	0.000	0.000	0.000

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