FMO DATABASE

FMODB ID: 94NK2

Calculation Name: 4EL6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4EL6

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-21

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	100
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-786707.109192
FMO2-HF: Nuclear repulsion	745086.007635
FMO2-HF: Total energy	-41621.101557
FMO2-MP2: Total energy	-41739.885252

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:23:CYS)

Summations of interaction energy for fragment #1(A:23:CYS)

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.
-21.819	-41.273	55.887	-14.655	-21.776	-0.065

Interaction energy analysis for fragmet #1(A:23:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.018 / q_NPA : 0.008

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

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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	25	TYR	0	0.019	-0.013	2.930	-4.354	-1.109	4.228	-2.116	-5.357	0.000
4	A	26	CYS	0	-0.046	-0.020	1.737	2.750	-15.084	32.791	-7.481	-7.476	0.000
5	A	27	LEU	0	0.015	0.035	3.775	1.202	-1.763	0.079	3.144	-0.257	0.002
6	A	28	GLN	0	0.039	-0.006	3.740	0.444	0.643	-0.001	-0.029	-0.169	0.000
7	A	29	LEU	0	-0.020	-0.004	7.106	0.594	0.594	0.000	0.000	0.000	0.000
8	A	30	TYR	0	0.014	0.004	7.989	-0.308	-0.308	0.000	0.000	0.000	0.000
9	A	31	ASP	-1	-0.811	-0.910	12.681	-0.755	-0.755	0.000	0.000	0.000	0.000
10	A	32	GLU	-1	-0.955	-0.973	15.994	-0.547	-0.547	0.000	0.000	0.000	0.000
11	A	33	THR	0	-0.029	-0.009	16.404	-0.086	-0.086	0.000	0.000	0.000	0.000
12	A	34	TYR	0	-0.062	-0.045	16.685	0.005	0.005	0.000	0.000	0.000	0.000
13	A	35	GLH	0	-0.061	-0.071	11.647	0.051	0.051	0.000	0.000	0.000	0.000
14	A	36	ARG	1	0.888	0.957	12.961	0.525	0.525	0.000	0.000	0.000	0.000
15	A	37	GLY	0	0.070	0.040	15.089	-0.016	-0.016	0.000	0.000	0.000	0.000
16	A	38	SER	0	-0.070	-0.038	12.866	-0.205	-0.205	0.000	0.000	0.000	0.000
17	A	39	TYR	0	0.020	-0.001	5.369	0.366	0.366	0.000	0.000	0.000	0.000
18	A	40	ILE	0	-0.002	0.016	8.872	-0.046	-0.046	0.000	0.000	0.000	0.000
19	A	41	GLU	-1	-0.853	-0.922	2.544	-22.782	-17.714	0.899	-3.115	-2.852	-0.036
20	A	42	VAL	0	0.009	0.009	5.660	0.750	0.750	0.000	0.000	0.000	0.000
21	A	43	TYR	0	0.006	-0.034	1.815	3.186	-4.212	17.893	-5.008	-5.486	-0.031
22	A	44	LYS	1	0.913	0.935	4.638	0.568	0.633	-0.001	-0.004	-0.060	0.000
23	A	45	SER	0	0.039	0.026	8.238	-0.184	-0.184	0.000	0.000	0.000	0.000
24	A	46	VAL	0	-0.011	0.000	11.656	0.012	0.012	0.000	0.000	0.000	0.000
25	A	47	GLY	0	0.060	0.022	13.582	-0.024	-0.024	0.000	0.000	0.000	0.000
26	A	48	SER	0	0.002	-0.003	16.936	0.005	0.005	0.000	0.000	0.000	0.000
27	A	49	LEU	0	-0.052	-0.004	13.572	-0.009	-0.009	0.000	0.000	0.000	0.000
28	A	50	SER	0	-0.021	0.014	17.729	0.012	0.012	0.000	0.000	0.000	0.000
29	A	51	PRO	0	0.065	0.005	20.650	0.001	0.001	0.000	0.000	0.000	0.000
30	A	52	PRO	0	-0.004	-0.007	19.636	-0.033	-0.033	0.000	0.000	0.000	0.000
31	A	53	TRP	0	0.004	0.006	10.950	-0.061	-0.061	0.000	0.000	0.000	0.000
32	A	54	THR	0	-0.002	-0.004	17.566	0.041	0.041	0.000	0.000	0.000	0.000
33	A	55	PRO	0	-0.016	0.018	14.295	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	56	GLY	0	0.056	0.023	16.292	0.098	0.098	0.000	0.000	0.000	0.000
35	A	57	SER	0	-0.049	-0.032	14.793	0.036	0.036	0.000	0.000	0.000	0.000
36	A	58	VAL	0	-0.005	0.008	11.016	-0.119	-0.119	0.000	0.000	0.000	0.000
37	A	59	CYS	0	0.007	0.019	8.943	0.018	0.018	0.000	0.000	0.000	0.000
38	A	60	VAL	0	-0.006	0.000	7.671	-0.208	-0.208	0.000	0.000	0.000	0.000
39	A	61	PRO	0	0.028	0.031	4.340	0.090	0.256	-0.001	-0.046	-0.119	0.000
40	A	62	PHE	0	0.038	0.029	7.148	0.590	0.590	0.000	0.000	0.000	0.000
41	A	63	VAL	0	-0.035	-0.002	8.523	0.012	0.012	0.000	0.000	0.000	0.000
42	A	64	ASN	0	-0.051	-0.037	10.716	-0.025	-0.025	0.000	0.000	0.000	0.000
43	A	65	ASP	-1	-0.728	-0.809	12.074	0.931	0.931	0.000	0.000	0.000	0.000
44	A	66	THR	0	-0.026	-0.045	14.193	-0.052	-0.052	0.000	0.000	0.000	0.000
45	A	67	LYS	1	0.948	0.971	15.930	-0.553	-0.553	0.000	0.000	0.000	0.000
46	A	68	ARG	1	0.847	0.898	12.026	-1.075	-1.075	0.000	0.000	0.000	0.000
47	A	69	GLU	-1	-0.812	-0.913	12.420	0.608	0.608	0.000	0.000	0.000	0.000
48	A	70	ARG	1	0.839	0.937	11.627	-0.118	-0.118	0.000	0.000	0.000	0.000
49	A	71	PRO	0	0.015	0.017	7.868	-0.020	-0.020	0.000	0.000	0.000	0.000
50	A	72	TYR	0	0.004	0.005	10.390	-0.205	-0.205	0.000	0.000	0.000	0.000
51	A	73	TRP	0	-0.001	-0.012	5.901	-0.033	-0.033	0.000	0.000	0.000	0.000
52	A	74	TYR	0	0.025	0.007	12.460	-0.080	-0.080	0.000	0.000	0.000	0.000
53	A	75	LEU	0	0.003	0.002	12.869	0.000	0.000	0.000	0.000	0.000	0.000
54	A	76	PHE	0	0.030	0.010	16.144	0.034	0.034	0.000	0.000	0.000	0.000
55	A	77	ASP	-1	-0.833	-0.914	19.237	-0.200	-0.200	0.000	0.000	0.000	0.000
56	A	78	ASN	0	0.012	0.022	21.899	-0.009	-0.009	0.000	0.000	0.000	0.000
57	A	79	VAL	0	0.045	-0.003	20.587	-0.006	-0.006	0.000	0.000	0.000	0.000
58	A	80	ASN	0	-0.072	-0.046	20.327	0.017	0.017	0.000	0.000	0.000	0.000
59	A	81	TYR	0	-0.051	-0.031	15.542	0.037	0.037	0.000	0.000	0.000	0.000
60	A	82	THR	0	0.012	0.012	20.269	0.013	0.013	0.000	0.000	0.000	0.000
61	A	83	GLY	0	0.038	0.016	22.732	-0.019	-0.019	0.000	0.000	0.000	0.000
62	A	84	ARG	1	0.892	0.950	23.805	0.174	0.174	0.000	0.000	0.000	0.000
63	A	85	ILE	0	0.010	0.001	19.631	-0.008	-0.008	0.000	0.000	0.000	0.000
64	A	86	THR	0	-0.005	0.002	17.347	0.014	0.014	0.000	0.000	0.000	0.000
65	A	87	GLY	0	-0.009	-0.007	16.582	-0.006	-0.006	0.000	0.000	0.000	0.000
66	A	88	LEU	0	-0.005	0.009	12.188	-0.039	-0.039	0.000	0.000	0.000	0.000
67	A	89	GLY	0	0.056	0.013	13.404	0.103	0.103	0.000	0.000	0.000	0.000
68	A	90	HIS	0	-0.001	-0.016	10.959	-0.118	-0.118	0.000	0.000	0.000	0.000
69	A	91	GLY	0	0.008	-0.018	10.560	0.062	0.062	0.000	0.000	0.000	0.000
70	A	92	THR	0	-0.049	0.000	11.862	0.006	0.006	0.000	0.000	0.000	0.000
71	A	94	ILE	0	-0.039	-0.033	13.839	0.136	0.136	0.000	0.000	0.000	0.000
72	A	95	ASP	-1	-0.794	-0.870	16.110	-0.696	-0.696	0.000	0.000	0.000	0.000
73	A	96	ASP	-1	-0.787	-0.898	17.566	-0.450	-0.450	0.000	0.000	0.000	0.000
74	A	97	PHE	0	-0.030	-0.027	16.895	0.047	0.047	0.000	0.000	0.000	0.000
75	A	98	THR	0	-0.073	-0.038	19.017	0.063	0.063	0.000	0.000	0.000	0.000
76	A	99	LYS	1	0.916	0.948	22.171	0.344	0.344	0.000	0.000	0.000	0.000
77	A	100	SER	0	-0.024	0.003	20.538	0.035	0.035	0.000	0.000	0.000	0.000
78	A	101	GLY	0	-0.003	-0.005	22.592	0.016	0.016	0.000	0.000	0.000	0.000
79	A	102	PHE	0	-0.046	-0.045	19.249	0.027	0.027	0.000	0.000	0.000	0.000
80	A	103	LYS	1	0.988	0.994	21.340	0.269	0.269	0.000	0.000	0.000	0.000
81	A	104	GLY	0	0.025	0.023	20.176	-0.048	-0.048	0.000	0.000	0.000	0.000
82	A	105	ILE	0	-0.043	-0.025	14.660	0.043	0.043	0.000	0.000	0.000	0.000
83	A	106	SER	0	0.023	0.014	18.006	-0.034	-0.034	0.000	0.000	0.000	0.000
84	A	107	SER	0	-0.038	-0.013	16.237	0.035	0.035	0.000	0.000	0.000	0.000
85	A	108	ILE	0	0.035	0.026	10.687	-0.009	-0.009	0.000	0.000	0.000	0.000
86	A	109	LYS	1	0.892	0.948	13.322	-0.087	-0.087	0.000	0.000	0.000	0.000
87	A	110	ARG	1	0.908	0.968	6.443	-2.255	-2.255	0.000	0.000	0.000	0.000
88	A	111	CYS	0	-0.165	-0.067	11.200	-0.042	-0.042	0.000	0.000	0.000	0.000
89	A	112	ILE	0	0.030	0.013	11.880	0.144	0.144	0.000	0.000	0.000	0.000
90	A	113	GLN	0	-0.008	0.001	14.112	-0.085	-0.085	0.000	0.000	0.000	0.000
91	A	114	THR	0	0.040	0.001	16.230	0.040	0.040	0.000	0.000	0.000	0.000
92	A	115	LYS	1	0.807	0.894	17.427	-0.441	-0.441	0.000	0.000	0.000	0.000
93	A	116	ASP	-1	-0.840	-0.912	20.438	0.164	0.164	0.000	0.000	0.000	0.000
94	A	117	GLY	0	-0.076	-0.036	20.389	-0.025	-0.025	0.000	0.000	0.000	0.000
95	A	118	LYS	1	0.927	0.985	21.070	-0.222	-0.222	0.000	0.000	0.000	0.000
96	A	119	VAL	0	0.009	-0.006	16.667	0.053	0.053	0.000	0.000	0.000	0.000
97	A	120	GLU	-1	-0.838	-0.929	19.127	0.150	0.150	0.000	0.000	0.000	0.000
98	A	122	ILE	0	0.007	-0.011	19.069	-0.008	-0.008	0.000	0.000	0.000	0.000
99	A	123	ASN	0	-0.041	-0.001	21.492	-0.037	-0.037	0.000	0.000	0.000	0.000
100	A	124	GLN	0	-0.002	0.004	24.420	0.007	0.007	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:23:CYS)