FMO DATABASE

FMODB ID: ZYL1N

Calculation Name: 2D4P-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2D4P

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SIW0

Base Structure: X-ray

Registration Date: 2023-03-13

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	130
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1070950.372422
FMO2-HF: Nuclear repulsion	1021447.856235
FMO2-HF: Total energy	-49502.516187
FMO2-MP2: Total energy	-49649.404508

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:MET)

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

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.
-52.121	-52.863	46.196	-20.334	-25.119	-0.113

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.010 / q_NPA : -0.005

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	PHE	0	0.028	0.009	3.178	-6.465	-1.198	1.504	-2.650	-4.121	0.004
4	A	4	ARG	1	0.730	0.842	5.412	-0.612	-0.612	0.000	0.000	0.000	0.000
5	A	5	PRO	0	0.051	0.026	8.860	0.098	0.098	0.000	0.000	0.000	0.000
6	A	6	PHE	0	-0.042	-0.011	11.536	-0.025	-0.025	0.000	0.000	0.000	0.000
7	A	7	THR	0	-0.008	-0.036	13.169	-0.021	-0.021	0.000	0.000	0.000	0.000
8	A	8	GLU	-1	-0.777	-0.894	16.516	0.223	0.223	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.857	-0.911	17.058	0.214	0.214	0.000	0.000	0.000	0.000
10	A	10	ASP	-1	-0.790	-0.875	12.803	0.385	0.385	0.000	0.000	0.000	0.000
11	A	11	LEU	0	0.000	-0.008	14.441	0.041	0.041	0.000	0.000	0.000	0.000
12	A	12	ASP	-1	-0.865	-0.936	16.414	0.128	0.128	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.892	0.947	10.114	-0.156	-0.156	0.000	0.000	0.000	0.000
14	A	14	LEU	0	0.001	0.000	11.717	0.066	0.066	0.000	0.000	0.000	0.000
15	A	15	ASN	0	-0.024	-0.027	13.394	0.025	0.025	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.923	0.970	11.300	0.225	0.225	0.000	0.000	0.000	0.000
17	A	17	LEU	0	-0.063	-0.004	8.332	-0.047	-0.047	0.000	0.000	0.000	0.000
18	A	18	ALA	0	-0.022	0.012	12.208	0.046	0.046	0.000	0.000	0.000	0.000
19	A	19	GLY	0	0.043	0.023	15.447	-0.026	-0.026	0.000	0.000	0.000	0.000
20	A	20	LYS	1	0.941	0.958	16.968	-0.056	-0.056	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.930	0.970	18.327	-0.318	-0.318	0.000	0.000	0.000	0.000
22	A	22	PRO	0	0.077	0.056	19.174	0.050	0.050	0.000	0.000	0.000	0.000
23	A	23	VAL	0	0.003	0.012	16.335	0.006	0.006	0.000	0.000	0.000	0.000
24	A	24	SER	0	0.022	0.007	19.708	-0.017	-0.017	0.000	0.000	0.000	0.000
25	A	25	LEU	0	0.099	0.035	21.230	0.028	0.028	0.000	0.000	0.000	0.000
26	A	26	GLY	0	-0.002	-0.002	22.435	0.013	0.013	0.000	0.000	0.000	0.000
27	A	27	ALA	0	0.003	-0.006	20.930	0.009	0.009	0.000	0.000	0.000	0.000
28	A	28	LEU	0	0.021	0.034	16.744	0.025	0.025	0.000	0.000	0.000	0.000
29	A	29	ARG	1	0.838	0.886	18.906	-0.172	-0.172	0.000	0.000	0.000	0.000
30	A	30	PHE	0	-0.067	-0.023	21.460	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	31	PHE	0	0.016	-0.013	17.071	0.003	0.003	0.000	0.000	0.000	0.000
32	A	32	ALA	0	0.026	0.027	16.836	0.038	0.038	0.000	0.000	0.000	0.000
33	A	33	ARG	1	0.930	0.967	17.887	-0.256	-0.256	0.000	0.000	0.000	0.000
34	A	34	THR	0	-0.070	-0.027	18.212	0.007	0.007	0.000	0.000	0.000	0.000
35	A	35	GLY	0	0.014	0.014	17.372	-0.019	-0.019	0.000	0.000	0.000	0.000
36	A	36	HIS	1	0.826	0.896	15.772	-0.462	-0.462	0.000	0.000	0.000	0.000
37	A	37	SER	0	0.028	0.029	13.704	0.058	0.058	0.000	0.000	0.000	0.000
38	A	38	PHE	0	-0.043	-0.015	8.648	-0.035	-0.035	0.000	0.000	0.000	0.000
39	A	39	LEU	0	0.001	-0.005	7.588	0.062	0.062	0.000	0.000	0.000	0.000
40	A	40	ALA	0	0.014	0.006	3.294	-0.971	-0.359	0.517	-0.315	-0.814	0.004
41	A	41	GLU	-1	-0.820	-0.895	3.277	-0.381	0.573	0.036	-0.297	-0.693	0.000
42	A	42	GLU	-1	-0.828	-0.902	1.606	-30.297	-41.737	38.232	-15.550	-11.243	-0.119
43	A	43	GLY	0	0.016	0.010	3.249	1.200	1.161	0.046	0.323	-0.330	-0.001
44	A	44	GLU	-1	-0.908	-0.967	5.765	0.254	0.254	0.000	0.000	0.000	0.000
45	A	45	GLU	-1	-0.869	-0.913	6.234	-0.490	-0.490	0.000	0.000	0.000	0.000
46	A	46	PRO	0	-0.033	-0.027	5.731	-0.146	-0.146	0.000	0.000	0.000	0.000
47	A	47	MET	0	0.011	-0.009	2.348	-1.393	-0.250	1.541	-0.472	-2.212	0.004
48	A	48	GLY	0	0.052	-0.002	5.398	0.241	0.337	-0.001	-0.009	-0.085	0.000
49	A	49	PHE	0	-0.050	-0.011	7.158	-0.143	-0.143	0.000	0.000	0.000	0.000
50	A	50	ALA	0	0.030	0.014	9.701	-0.059	-0.059	0.000	0.000	0.000	0.000
51	A	51	LEU	0	-0.058	-0.023	12.097	-0.071	-0.071	0.000	0.000	0.000	0.000
52	A	52	ALA	0	0.023	-0.006	15.682	-0.027	-0.027	0.000	0.000	0.000	0.000
53	A	53	GLN	0	-0.003	-0.014	17.424	-0.035	-0.035	0.000	0.000	0.000	0.000
54	A	54	ALA	0	-0.007	0.004	20.677	0.002	0.002	0.000	0.000	0.000	0.000
55	A	55	VAL	0	-0.019	-0.010	23.354	-0.013	-0.013	0.000	0.000	0.000	0.000
56	A	56	TRP	0	-0.001	0.010	26.487	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	57	GLN	0	-0.003	-0.022	28.392	0.007	0.007	0.000	0.000	0.000	0.000
58	A	58	GLY	0	-0.009	0.002	31.449	-0.011	-0.011	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.981	-0.988	32.906	0.135	0.135	0.000	0.000	0.000	0.000
60	A	60	ALA	0	0.034	0.033	29.137	0.008	0.008	0.000	0.000	0.000	0.000
61	A	61	THR	0	-0.004	-0.021	24.800	-0.008	-0.008	0.000	0.000	0.000	0.000
62	A	62	THR	0	0.048	0.040	23.600	0.001	0.001	0.000	0.000	0.000	0.000
63	A	63	VAL	0	-0.040	-0.020	18.011	0.002	0.002	0.000	0.000	0.000	0.000
64	A	64	LEU	0	0.009	0.011	20.638	0.011	0.011	0.000	0.000	0.000	0.000
65	A	65	VAL	0	0.008	-0.017	14.492	0.027	0.027	0.000	0.000	0.000	0.000
66	A	66	THR	0	-0.070	-0.026	17.696	-0.045	-0.045	0.000	0.000	0.000	0.000
67	A	67	ARG	1	0.748	0.831	15.168	-0.494	-0.494	0.000	0.000	0.000	0.000
68	A	68	ILE	0	0.024	0.028	9.843	0.051	0.051	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.837	-0.896	11.017	0.339	0.339	0.000	0.000	0.000	0.000
70	A	70	GLY	0	0.020	-0.018	7.237	0.556	0.556	0.000	0.000	0.000	0.000
71	A	71	ARG	1	0.809	0.909	5.246	0.015	0.015	0.000	0.000	0.000	0.000
72	A	72	SER	0	0.070	0.047	2.638	-0.335	0.301	0.129	-0.287	-0.478	-0.001
73	A	73	VAL	0	0.078	0.041	5.498	0.877	0.877	0.000	0.000	0.000	0.000
74	A	74	GLU	-1	-0.957	-0.970	2.992	-11.845	-8.782	0.717	-1.405	-2.375	-0.012
75	A	75	ALA	0	0.012	-0.005	2.650	0.943	2.226	3.460	-2.294	-2.449	0.008
76	A	76	LEU	0	-0.018	-0.008	3.672	1.111	-1.206	0.015	2.622	-0.319	0.000
77	A	77	ARG	1	0.869	0.914	7.197	-0.626	-0.626	0.000	0.000	0.000	0.000
78	A	78	GLY	0	-0.011	-0.004	5.536	-0.556	-0.556	0.000	0.000	0.000	0.000
79	A	79	LEU	0	-0.020	-0.007	6.087	-0.728	-0.728	0.000	0.000	0.000	0.000
80	A	80	LEU	0	-0.031	-0.004	8.025	-0.472	-0.472	0.000	0.000	0.000	0.000
81	A	81	ARG	1	0.928	0.976	5.889	-1.238	-1.238	0.000	0.000	0.000	0.000
82	A	82	ALA	0	-0.039	-0.003	8.545	-0.192	-0.192	0.000	0.000	0.000	0.000
83	A	83	VAL	0	0.005	-0.003	10.552	-0.171	-0.171	0.000	0.000	0.000	0.000
84	A	84	VAL	0	0.047	0.035	13.419	-0.115	-0.115	0.000	0.000	0.000	0.000
85	A	85	LYS	1	0.883	0.939	13.302	-0.625	-0.625	0.000	0.000	0.000	0.000
86	A	86	SER	0	-0.014	-0.010	14.700	-0.072	-0.072	0.000	0.000	0.000	0.000
87	A	87	ALA	0	-0.021	-0.018	16.445	-0.053	-0.053	0.000	0.000	0.000	0.000
88	A	88	TYR	0	0.037	0.009	17.830	-0.037	-0.037	0.000	0.000	0.000	0.000
89	A	89	ASP	-1	-0.885	-0.932	17.814	0.413	0.413	0.000	0.000	0.000	0.000
90	A	90	ALA	0	-0.089	-0.040	20.621	-0.026	-0.026	0.000	0.000	0.000	0.000
91	A	91	GLY	0	-0.013	0.003	22.661	-0.021	-0.021	0.000	0.000	0.000	0.000
92	A	92	VAL	0	-0.110	-0.057	21.691	-0.016	-0.016	0.000	0.000	0.000	0.000
93	A	93	TYR	0	-0.026	0.002	23.617	0.004	0.004	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.911	-0.955	22.922	0.249	0.249	0.000	0.000	0.000	0.000
95	A	95	VAL	0	0.017	0.001	17.019	0.019	0.019	0.000	0.000	0.000	0.000
96	A	96	ALA	0	0.028	0.022	20.465	-0.016	-0.016	0.000	0.000	0.000	0.000
97	A	97	LEU	0	0.016	-0.004	15.134	0.047	0.047	0.000	0.000	0.000	0.000
98	A	98	HIS	0	-0.018	-0.011	19.535	-0.035	-0.035	0.000	0.000	0.000	0.000
99	A	99	LEU	0	-0.007	-0.006	16.900	0.034	0.034	0.000	0.000	0.000	0.000
100	A	100	ASP	-1	-0.865	-0.929	18.947	0.142	0.142	0.000	0.000	0.000	0.000
101	A	101	PRO	0	0.057	0.012	18.831	0.018	0.018	0.000	0.000	0.000	0.000
102	A	102	GLU	-1	-0.945	-0.962	19.966	0.038	0.038	0.000	0.000	0.000	0.000
103	A	103	ARG	1	0.817	0.910	12.409	-0.540	-0.540	0.000	0.000	0.000	0.000
104	A	104	LYS	1	0.937	0.950	15.554	-0.022	-0.022	0.000	0.000	0.000	0.000
105	A	105	GLU	-1	-0.874	-0.931	8.740	-0.084	-0.084	0.000	0.000	0.000	0.000
106	A	106	LEU	0	-0.010	-0.012	11.526	0.096	0.096	0.000	0.000	0.000	0.000
107	A	107	GLU	-1	-0.927	-0.966	12.722	0.181	0.181	0.000	0.000	0.000	0.000
108	A	108	GLU	-1	-0.933	-0.965	12.228	-0.136	-0.136	0.000	0.000	0.000	0.000
109	A	109	ALA	0	-0.025	-0.033	9.989	0.008	0.008	0.000	0.000	0.000	0.000
110	A	110	LEU	0	-0.003	-0.012	11.851	0.033	0.033	0.000	0.000	0.000	0.000
111	A	111	LYS	1	0.980	1.001	14.981	-0.108	-0.108	0.000	0.000	0.000	0.000
112	A	112	ALA	0	-0.062	-0.031	12.798	-0.031	-0.031	0.000	0.000	0.000	0.000
113	A	113	GLU	-1	-0.818	-0.896	11.119	0.661	0.661	0.000	0.000	0.000	0.000
114	A	114	GLY	0	-0.017	0.000	14.570	0.016	0.016	0.000	0.000	0.000	0.000
115	A	115	PHE	0	-0.021	-0.004	15.128	-0.005	-0.005	0.000	0.000	0.000	0.000
116	A	116	ALA	0	-0.002	-0.001	19.142	-0.032	-0.032	0.000	0.000	0.000	0.000
117	A	117	LEU	0	-0.034	-0.027	19.741	0.016	0.016	0.000	0.000	0.000	0.000
118	A	118	GLY	0	0.018	0.032	23.571	-0.016	-0.016	0.000	0.000	0.000	0.000
119	A	119	PRO	0	-0.041	-0.030	26.816	0.009	0.009	0.000	0.000	0.000	0.000
120	A	120	LEU	0	0.014	-0.008	28.111	-0.009	-0.009	0.000	0.000	0.000	0.000
121	A	121	VAL	0	0.045	0.032	28.002	0.006	0.006	0.000	0.000	0.000	0.000
122	A	122	LEU	0	-0.021	-0.004	25.032	0.005	0.005	0.000	0.000	0.000	0.000
123	A	123	ALA	0	0.011	0.006	28.624	-0.012	-0.012	0.000	0.000	0.000	0.000
124	A	124	VAL	0	0.010	-0.007	27.912	0.008	0.008	0.000	0.000	0.000	0.000
125	A	125	ARG	1	0.979	0.990	31.337	-0.102	-0.102	0.000	0.000	0.000	0.000
126	A	126	VAL	0	-0.002	0.000	30.108	0.006	0.006	0.000	0.000	0.000	0.000
127	A	127	LEU	0	-0.028	-0.013	32.894	-0.010	-0.010	0.000	0.000	0.000	0.000
128	A	128	GLY	0	0.034	0.020	33.250	-0.008	-0.008	0.000	0.000	0.000	0.000
129	A	129	SER	0	-0.036	-0.015	32.139	0.008	0.008	0.000	0.000	0.000	0.000
130	A	130	ARG	1	1.009	1.006	34.376	-0.101	-0.101	0.000	0.000	0.000	0.000

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