FMO DATABASE

FMODB ID: 6Y1LZ

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	OptAll
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	-1166879.729679
FMO2-HF: Nuclear repulsion	1115514.501785
FMO2-HF: Total energy	-51365.227894
FMO2-MP2: Total energy	-51516.920435

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.
1.565	3.175	-0.003	-0.914	-0.693	0.004

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 : 0.031

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	0.947	0.962	3.853	0.540	2.030	-0.002	-0.886	-0.603	0.004
4	A	4	SER	0	-0.023	-0.022	6.369	0.479	0.479	0.000	0.000	0.000	0.000
5	A	5	GLY	0	-0.007	0.023	3.839	0.448	0.556	0.000	-0.022	-0.086	0.000
6	A	6	VAL	0	0.007	0.017	4.894	-0.374	-0.362	-0.001	-0.006	-0.004	0.000
7	A	7	ALA	0	0.010	0.012	7.354	0.050	0.050	0.000	0.000	0.000	0.000
8	A	8	VAL	0	-0.004	-0.003	11.043	0.116	0.116	0.000	0.000	0.000	0.000
9	A	9	ALA	0	0.032	0.023	14.269	-0.055	-0.055	0.000	0.000	0.000	0.000
10	A	10	ASP	-1	-0.856	-0.944	16.689	-0.048	-0.048	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.862	-0.909	19.309	0.076	0.076	0.000	0.000	0.000	0.000
12	A	12	SER	0	0.006	-0.016	17.101	0.010	0.010	0.000	0.000	0.000	0.000
13	A	13	LEU	0	0.006	0.004	19.441	0.014	0.014	0.000	0.000	0.000	0.000
14	A	14	THR	0	-0.040	-0.032	21.072	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	15	ALA	0	0.036	0.014	23.417	0.002	0.002	0.000	0.000	0.000	0.000
16	A	16	PHE	0	0.025	0.003	22.421	0.004	0.004	0.000	0.000	0.000	0.000
17	A	17	ASN	0	-0.028	-0.032	24.023	0.002	0.002	0.000	0.000	0.000	0.000
18	A	18	ASP	-1	-0.740	-0.853	26.932	0.041	0.041	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.056	-0.007	27.297	-0.003	-0.003	0.000	0.000	0.000	0.000
20	A	20	LYS	1	0.829	0.914	25.758	-0.087	-0.087	0.000	0.000	0.000	0.000
21	A	21	LEU	0	-0.050	-0.030	29.488	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	22	GLY	0	-0.012	0.002	32.152	-0.006	-0.006	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.749	0.850	32.912	-0.085	-0.085	0.000	0.000	0.000	0.000
24	A	24	LYS	1	0.782	0.900	30.388	-0.040	-0.040	0.000	0.000	0.000	0.000
25	A	25	TYR	0	-0.074	-0.060	27.811	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	26	LYS	1	0.852	0.924	31.318	-0.103	-0.103	0.000	0.000	0.000	0.000
27	A	27	PHE	0	0.007	-0.012	27.026	0.009	0.009	0.000	0.000	0.000	0.000
28	A	28	ILE	0	-0.027	-0.011	22.581	-0.014	-0.014	0.000	0.000	0.000	0.000
29	A	29	LEU	0	0.000	0.016	21.963	0.024	0.024	0.000	0.000	0.000	0.000
30	A	30	PHE	0	-0.001	-0.015	17.425	-0.022	-0.022	0.000	0.000	0.000	0.000
31	A	31	GLY	0	0.007	-0.009	15.115	0.045	0.045	0.000	0.000	0.000	0.000
32	A	32	LEU	0	-0.054	-0.007	8.653	-0.039	-0.039	0.000	0.000	0.000	0.000
33	A	33	ASN	0	0.053	0.035	11.123	0.041	0.041	0.000	0.000	0.000	0.000
34	A	34	ASP	-1	-0.864	-0.946	11.795	0.228	0.228	0.000	0.000	0.000	0.000
35	A	35	ALA	0	-0.038	-0.017	10.438	0.057	0.057	0.000	0.000	0.000	0.000
36	A	36	LYS	1	0.773	0.888	6.891	-0.493	-0.493	0.000	0.000	0.000	0.000
37	A	37	THR	0	-0.039	-0.043	6.504	0.120	0.120	0.000	0.000	0.000	0.000
38	A	38	GLU	-1	-0.823	-0.894	8.400	-0.245	-0.245	0.000	0.000	0.000	0.000
39	A	39	ILE	0	-0.049	-0.019	10.879	0.084	0.084	0.000	0.000	0.000	0.000
40	A	40	VAL	0	0.014	0.010	13.277	-0.060	-0.060	0.000	0.000	0.000	0.000
41	A	41	VAL	0	0.007	-0.009	16.656	0.051	0.051	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.812	0.918	17.379	-0.359	-0.359	0.000	0.000	0.000	0.000
43	A	43	GLU	-1	-0.867	-0.944	20.915	0.122	0.122	0.000	0.000	0.000	0.000
44	A	44	THR	0	-0.040	-0.016	24.456	0.010	0.010	0.000	0.000	0.000	0.000
45	A	45	SER	0	0.044	0.031	27.074	-0.011	-0.011	0.000	0.000	0.000	0.000
46	A	46	THR	0	0.006	-0.011	30.387	0.004	0.004	0.000	0.000	0.000	0.000
47	A	47	ASP	-1	-0.882	-0.932	33.349	0.093	0.093	0.000	0.000	0.000	0.000
48	A	48	PRO	0	0.003	-0.011	34.147	0.006	0.006	0.000	0.000	0.000	0.000
49	A	49	SER	0	-0.005	0.006	36.238	0.004	0.004	0.000	0.000	0.000	0.000
50	A	50	TYR	0	0.004	-0.029	30.190	0.005	0.005	0.000	0.000	0.000	0.000
51	A	51	ASP	-1	-0.874	-0.937	32.633	0.130	0.130	0.000	0.000	0.000	0.000
52	A	52	ALA	0	0.027	0.022	33.018	0.008	0.008	0.000	0.000	0.000	0.000
53	A	53	PHE	0	-0.041	-0.017	25.556	0.004	0.004	0.000	0.000	0.000	0.000
54	A	54	LEU	0	0.007	-0.005	28.511	0.015	0.015	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.946	-0.980	29.011	0.130	0.130	0.000	0.000	0.000	0.000
56	A	56	LYS	1	0.798	0.908	26.866	-0.129	-0.129	0.000	0.000	0.000	0.000
57	A	57	LEU	0	-0.037	-0.001	23.948	0.018	0.018	0.000	0.000	0.000	0.000
58	A	58	PRO	0	-0.038	-0.006	21.350	-0.008	-0.008	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.871	-0.952	23.107	0.224	0.224	0.000	0.000	0.000	0.000
60	A	60	ASN	0	-0.038	-0.014	22.491	0.024	0.024	0.000	0.000	0.000	0.000
61	A	61	ASP	-1	-0.835	-0.928	16.875	0.480	0.480	0.000	0.000	0.000	0.000
62	A	62	CYS	0	-0.054	0.006	15.373	0.009	0.009	0.000	0.000	0.000	0.000
63	A	63	LEU	0	-0.047	-0.027	17.030	-0.021	-0.021	0.000	0.000	0.000	0.000
64	A	64	TYR	0	-0.025	-0.035	11.896	0.029	0.029	0.000	0.000	0.000	0.000
65	A	65	ALA	0	0.018	0.010	18.390	-0.032	-0.032	0.000	0.000	0.000	0.000
66	A	66	ILE	0	-0.047	-0.019	21.924	0.012	0.012	0.000	0.000	0.000	0.000
67	A	67	TYR	0	0.043	0.018	24.389	-0.013	-0.013	0.000	0.000	0.000	0.000
68	A	68	ASP	-1	-0.782	-0.850	28.081	0.101	0.101	0.000	0.000	0.000	0.000
69	A	69	PHE	0	0.000	0.002	30.799	-0.005	-0.005	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.809	-0.884	32.569	0.081	0.081	0.000	0.000	0.000	0.000
71	A	71	TYR	0	-0.033	-0.036	35.095	0.006	0.006	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.960	-0.972	39.258	0.066	0.066	0.000	0.000	0.000	0.000
73	A	80	GLU	-1	-0.818	-0.880	37.523	0.091	0.091	0.000	0.000	0.000	0.000
74	A	81	SER	0	-0.049	-0.034	34.302	0.001	0.001	0.000	0.000	0.000	0.000
75	A	82	LYS	1	0.835	0.906	31.459	-0.102	-0.102	0.000	0.000	0.000	0.000
76	A	83	ILE	0	0.009	0.020	25.934	0.006	0.006	0.000	0.000	0.000	0.000
77	A	84	VAL	0	0.036	0.019	26.270	0.009	0.009	0.000	0.000	0.000	0.000
78	A	85	PHE	0	-0.007	-0.008	16.911	0.008	0.008	0.000	0.000	0.000	0.000
79	A	86	PHE	0	0.030	0.009	21.893	0.005	0.005	0.000	0.000	0.000	0.000
80	A	87	THR	0	-0.055	-0.044	17.238	0.032	0.032	0.000	0.000	0.000	0.000
81	A	88	TRP	0	-0.009	0.008	19.252	0.008	0.008	0.000	0.000	0.000	0.000
82	A	89	SER	0	0.000	-0.039	17.492	0.087	0.087	0.000	0.000	0.000	0.000
83	A	90	PRO	0	0.027	0.049	19.247	0.011	0.011	0.000	0.000	0.000	0.000
84	A	91	ASP	-1	-0.826	-0.925	21.219	0.445	0.445	0.000	0.000	0.000	0.000
85	A	92	THR	0	-0.009	0.000	22.468	0.019	0.019	0.000	0.000	0.000	0.000
86	A	93	ALA	0	-0.018	0.011	18.508	-0.005	-0.005	0.000	0.000	0.000	0.000
87	A	94	PRO	0	-0.013	-0.015	16.538	0.040	0.040	0.000	0.000	0.000	0.000
88	A	95	VAL	0	0.053	0.021	14.574	0.075	0.075	0.000	0.000	0.000	0.000
89	A	96	ARG	1	0.956	0.965	11.930	-0.453	-0.453	0.000	0.000	0.000	0.000
90	A	97	SER	0	-0.020	-0.005	11.187	0.236	0.236	0.000	0.000	0.000	0.000
91	A	98	LYS	1	0.896	0.923	12.499	-0.382	-0.382	0.000	0.000	0.000	0.000
92	A	99	MET	0	-0.042	-0.017	9.634	-0.014	-0.014	0.000	0.000	0.000	0.000
93	A	100	VAL	0	0.010	0.023	6.266	0.355	0.355	0.000	0.000	0.000	0.000
94	A	101	TYR	0	0.076	0.043	8.675	0.065	0.065	0.000	0.000	0.000	0.000
95	A	102	ALA	0	0.014	0.016	11.506	-0.066	-0.066	0.000	0.000	0.000	0.000
96	A	103	SER	0	-0.073	-0.055	6.527	0.076	0.076	0.000	0.000	0.000	0.000
97	A	104	SER	0	-0.024	-0.017	7.543	0.061	0.061	0.000	0.000	0.000	0.000
98	A	105	LYS	1	0.898	0.956	8.763	-0.916	-0.916	0.000	0.000	0.000	0.000
99	A	106	ASP	-1	-0.839	-0.915	11.066	0.379	0.379	0.000	0.000	0.000	0.000
100	A	107	ALA	0	0.015	0.016	9.634	-0.124	-0.124	0.000	0.000	0.000	0.000
101	A	108	LEU	0	0.034	0.018	11.729	-0.097	-0.097	0.000	0.000	0.000	0.000
102	A	109	ARG	1	0.806	0.861	14.745	-0.324	-0.324	0.000	0.000	0.000	0.000
103	A	110	ARG	1	0.861	0.921	13.469	-0.349	-0.349	0.000	0.000	0.000	0.000
104	A	111	ALA	0	0.021	0.028	16.288	-0.043	-0.043	0.000	0.000	0.000	0.000
105	A	112	LEU	0	-0.033	-0.004	17.952	-0.030	-0.030	0.000	0.000	0.000	0.000
106	A	113	ASN	0	-0.045	-0.035	20.614	0.007	0.007	0.000	0.000	0.000	0.000
107	A	114	GLY	0	0.027	-0.007	23.371	-0.014	-0.014	0.000	0.000	0.000	0.000
108	A	115	VAL	0	-0.044	-0.009	22.068	-0.005	-0.005	0.000	0.000	0.000	0.000
109	A	116	SER	0	-0.029	-0.010	25.265	-0.003	-0.003	0.000	0.000	0.000	0.000
110	A	117	THR	0	0.012	0.006	26.805	-0.005	-0.005	0.000	0.000	0.000	0.000
111	A	118	ASP	-1	-0.801	-0.865	21.135	0.298	0.298	0.000	0.000	0.000	0.000
112	A	119	VAL	0	-0.007	-0.005	23.346	-0.007	-0.007	0.000	0.000	0.000	0.000
113	A	120	GLN	0	-0.031	-0.011	20.385	0.050	0.050	0.000	0.000	0.000	0.000
114	A	121	GLY	0	0.059	0.019	21.768	-0.033	-0.033	0.000	0.000	0.000	0.000
115	A	122	THR	0	-0.080	-0.057	21.459	0.019	0.019	0.000	0.000	0.000	0.000
116	A	123	ASP	-1	-0.776	-0.871	23.449	0.230	0.230	0.000	0.000	0.000	0.000
117	A	124	PHE	0	0.046	0.008	26.751	0.004	0.004	0.000	0.000	0.000	0.000
118	A	125	SER	0	-0.078	-0.054	29.296	-0.014	-0.014	0.000	0.000	0.000	0.000
119	A	126	GLU	-1	-0.813	-0.879	25.219	0.305	0.305	0.000	0.000	0.000	0.000
120	A	127	VAL	0	-0.019	-0.002	25.489	-0.002	-0.002	0.000	0.000	0.000	0.000
121	A	128	SER	0	0.017	0.016	28.708	-0.015	-0.015	0.000	0.000	0.000	0.000
122	A	129	TYR	0	0.024	-0.004	32.453	0.003	0.003	0.000	0.000	0.000	0.000
123	A	130	ASP	-1	-0.849	-0.935	34.413	0.122	0.122	0.000	0.000	0.000	0.000
124	A	131	SER	0	-0.036	-0.018	31.569	-0.006	-0.006	0.000	0.000	0.000	0.000
125	A	132	VAL	0	-0.024	-0.006	29.059	0.009	0.009	0.000	0.000	0.000	0.000
126	A	133	LEU	0	0.022	0.013	31.495	-0.002	-0.002	0.000	0.000	0.000	0.000
127	A	134	GLU	-1	-0.974	-0.955	34.103	0.151	0.151	0.000	0.000	0.000	0.000
128	A	135	ARG	1	0.871	0.921	25.968	-0.247	-0.247	0.000	0.000	0.000	0.000
129	A	136	VAL	0	0.002	0.005	30.654	-0.002	-0.002	0.000	0.000	0.000	0.000
130	A	137	SER	0	-0.069	-0.033	32.521	-0.007	-0.007	0.000	0.000	0.000	0.000
131	A	138	ARG	1	0.908	0.962	33.836	-0.140	-0.140	0.000	0.000	0.000	0.000
132	A	139	GLY	0	-0.085	-0.054	30.650	0.004	0.004	0.000	0.000	0.000	0.000

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