FMO DATABASE

FMODB ID: R8Q68

Calculation Name: 4D53-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4D53

Chain ID: A

ChEMBL ID:

UniProt ID: O51632

Base Structure: X-ray

Registration Date: 2023-09-22

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	133
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1255689.346667
FMO2-HF: Nuclear repulsion	1202327.881875
FMO2-HF: Total energy	-53361.464792
FMO2-MP2: Total energy	-53518.977194

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:4:MET)

Summations of interaction energy for fragment #1(A:4: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.
-27.293	-25.476	27.097	-7.929	-20.981	-0.057

Interaction energy analysis for fragmet #1(A:4:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.053 / 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	6	HIS	0	-0.010	-0.012	2.253	-3.638	-1.878	3.271	-2.430	-2.601	-0.017
4	A	7	LYS	1	0.958	0.975	2.799	-14.376	-16.083	5.555	-1.477	-2.370	0.014
5	A	8	ILE	0	-0.009	-0.014	6.140	-0.522	-0.522	0.000	0.000	0.000	0.000
6	A	9	ASP	-1	-0.911	-0.947	9.719	0.731	0.731	0.000	0.000	0.000	0.000
7	A	10	THR	0	0.004	-0.011	10.565	-0.103	-0.103	0.000	0.000	0.000	0.000
8	A	11	LYS	1	0.955	0.972	13.400	-0.341	-0.341	0.000	0.000	0.000	0.000
9	A	12	GLU	-1	-0.802	-0.895	16.200	0.130	0.130	0.000	0.000	0.000	0.000
10	A	13	ASP	-1	-0.807	-0.901	14.007	0.161	0.161	0.000	0.000	0.000	0.000
11	A	14	MET	0	-0.021	-0.003	14.367	-0.021	-0.021	0.000	0.000	0.000	0.000
12	A	15	LYS	1	0.810	0.901	17.083	-0.169	-0.169	0.000	0.000	0.000	0.000
13	A	16	ILE	0	0.011	0.005	19.868	-0.022	-0.022	0.000	0.000	0.000	0.000
14	A	17	LEU	0	0.011	0.005	16.379	-0.014	-0.014	0.000	0.000	0.000	0.000
15	A	18	TYR	0	-0.021	-0.061	17.914	-0.014	-0.014	0.000	0.000	0.000	0.000
16	A	19	SER	0	-0.004	-0.002	21.774	-0.018	-0.018	0.000	0.000	0.000	0.000
17	A	20	GLU	-1	-0.948	-0.970	22.084	0.079	0.079	0.000	0.000	0.000	0.000
18	A	21	ILE	0	-0.005	-0.010	19.959	-0.010	-0.010	0.000	0.000	0.000	0.000
19	A	22	ALA	0	-0.008	-0.003	24.433	-0.009	-0.009	0.000	0.000	0.000	0.000
20	A	23	GLU	-1	-0.787	-0.864	27.163	0.071	0.071	0.000	0.000	0.000	0.000
21	A	24	LEU	0	0.007	0.004	25.921	-0.009	-0.009	0.000	0.000	0.000	0.000
22	A	25	ARG	1	0.816	0.878	26.065	-0.155	-0.155	0.000	0.000	0.000	0.000
23	A	26	LYS	1	0.866	0.928	29.918	-0.089	-0.089	0.000	0.000	0.000	0.000
24	A	27	LYS	1	0.819	0.894	32.487	-0.071	-0.071	0.000	0.000	0.000	0.000
25	A	28	LEU	0	-0.034	-0.010	30.752	-0.006	-0.006	0.000	0.000	0.000	0.000
26	A	29	ASN	0	-0.058	-0.016	34.472	0.000	0.000	0.000	0.000	0.000	0.000
27	A	30	LEU	0	-0.008	0.010	30.360	0.002	0.002	0.000	0.000	0.000	0.000
28	A	31	ASN	0	-0.023	-0.023	29.752	-0.005	-0.005	0.000	0.000	0.000	0.000
29	A	32	HIS	0	0.024	0.004	28.586	0.000	0.000	0.000	0.000	0.000	0.000
30	A	33	LEU	0	-0.034	0.003	24.230	0.004	0.004	0.000	0.000	0.000	0.000
31	A	34	GLU	-1	-0.915	-0.941	26.426	0.177	0.177	0.000	0.000	0.000	0.000
32	A	35	ILE	0	0.021	-0.003	20.402	0.009	0.009	0.000	0.000	0.000	0.000
33	A	36	ASP	-1	-0.745	-0.862	21.315	0.304	0.304	0.000	0.000	0.000	0.000
34	A	37	ASP	-1	-0.865	-0.933	19.669	0.385	0.385	0.000	0.000	0.000	0.000
35	A	38	THR	0	-0.055	-0.036	18.360	0.069	0.069	0.000	0.000	0.000	0.000
36	A	39	LEU	0	-0.030	-0.003	17.441	0.057	0.057	0.000	0.000	0.000	0.000
37	A	40	GLU	-1	-0.806	-0.866	15.473	0.533	0.533	0.000	0.000	0.000	0.000
38	A	41	LYS	1	0.844	0.950	13.661	-0.416	-0.416	0.000	0.000	0.000	0.000
39	A	42	VAL	0	-0.013	-0.013	12.689	0.150	0.150	0.000	0.000	0.000	0.000
40	A	43	ALA	0	0.032	0.024	11.917	0.084	0.084	0.000	0.000	0.000	0.000
41	A	44	LYS	1	0.944	0.977	9.029	-1.357	-1.357	0.000	0.000	0.000	0.000
42	A	45	GLU	-1	-0.804	-0.875	7.681	1.329	1.329	0.000	0.000	0.000	0.000
43	A	46	TYR	0	-0.018	-0.043	7.584	0.218	0.218	0.000	0.000	0.000	0.000
44	A	47	ALA	0	0.065	0.031	6.598	-0.070	-0.070	0.000	0.000	0.000	0.000
45	A	48	ILE	0	-0.077	-0.037	3.061	-1.015	-0.110	0.114	-0.238	-0.781	0.000
46	A	49	LYS	1	0.934	0.976	2.797	-3.961	-2.407	0.368	-0.934	-0.987	-0.012
47	A	50	LEU	0	0.008	0.010	5.347	-0.203	-0.146	-0.001	-0.006	-0.050	0.000
48	A	51	GLY	0	0.012	-0.010	2.235	0.935	-0.610	3.463	-0.776	-1.142	0.000
49	A	52	GLU	-1	-0.987	-1.014	2.445	6.043	4.011	7.059	0.112	-5.139	-0.016
50	A	53	ASN	0	-0.056	-0.040	3.049	1.769	1.054	0.089	0.995	-0.369	0.000
51	A	54	ARG	1	0.895	0.968	5.240	-1.612	-1.612	0.000	0.000	0.000	0.000
52	A	55	THR	0	0.015	0.003	7.006	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	56	ILE	0	0.035	0.024	8.325	-0.022	-0.022	0.000	0.000	0.000	0.000
54	A	57	THR	0	0.038	0.013	10.904	-0.014	-0.014	0.000	0.000	0.000	0.000
55	A	58	HIS	0	0.002	0.003	12.495	0.023	0.023	0.000	0.000	0.000	0.000
56	A	59	THR	0	-0.015	-0.004	15.118	0.023	0.023	0.000	0.000	0.000	0.000
57	A	60	LEU	0	0.031	0.028	8.795	-0.019	-0.019	0.000	0.000	0.000	0.000
58	A	61	PHE	0	-0.036	-0.033	9.906	0.003	0.003	0.000	0.000	0.000	0.000
59	A	62	GLY	0	0.060	0.043	14.933	-0.009	-0.009	0.000	0.000	0.000	0.000
60	A	63	THR	0	-0.075	-0.012	14.608	-0.010	-0.010	0.000	0.000	0.000	0.000
61	A	64	THR	0	0.033	0.004	17.088	-0.012	-0.012	0.000	0.000	0.000	0.000
62	A	65	PRO	0	0.061	0.026	16.624	0.028	0.028	0.000	0.000	0.000	0.000
63	A	66	MET	0	0.025	0.010	17.652	0.024	0.024	0.000	0.000	0.000	0.000
64	A	67	GLN	0	0.034	0.021	19.273	-0.002	-0.002	0.000	0.000	0.000	0.000
65	A	68	ARG	1	0.762	0.849	12.981	-0.479	-0.479	0.000	0.000	0.000	0.000
66	A	69	ILE	0	0.019	0.013	16.865	0.034	0.034	0.000	0.000	0.000	0.000
67	A	70	HIS	0	-0.069	-0.054	18.902	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	71	LYS	1	0.803	0.922	14.216	-0.754	-0.754	0.000	0.000	0.000	0.000
69	A	72	TYR	0	-0.058	-0.068	14.556	-0.023	-0.023	0.000	0.000	0.000	0.000
70	A	73	ASP	-1	-0.731	-0.830	20.665	0.258	0.258	0.000	0.000	0.000	0.000
71	A	74	GLN	0	0.045	0.018	23.512	-0.016	-0.016	0.000	0.000	0.000	0.000
72	A	75	SER	0	-0.048	-0.043	25.776	-0.020	-0.020	0.000	0.000	0.000	0.000
73	A	76	PHE	0	0.009	0.024	22.573	-0.016	-0.016	0.000	0.000	0.000	0.000
74	A	77	ASN	0	0.000	-0.004	25.914	0.009	0.009	0.000	0.000	0.000	0.000
75	A	78	LEU	0	-0.002	0.006	26.102	-0.007	-0.007	0.000	0.000	0.000	0.000
76	A	79	THR	0	-0.033	-0.029	20.944	0.018	0.018	0.000	0.000	0.000	0.000
77	A	80	ARG	1	0.727	0.821	21.344	-0.182	-0.182	0.000	0.000	0.000	0.000
78	A	81	GLU	-1	-0.725	-0.850	14.473	0.459	0.459	0.000	0.000	0.000	0.000
79	A	82	ILE	0	-0.043	-0.008	16.754	-0.030	-0.030	0.000	0.000	0.000	0.000
80	A	83	LEU	0	0.004	0.007	11.230	0.048	0.048	0.000	0.000	0.000	0.000
81	A	84	ALA	0	-0.016	0.004	12.361	-0.046	-0.046	0.000	0.000	0.000	0.000
82	A	85	SER	0	-0.014	-0.021	8.786	0.007	0.007	0.000	0.000	0.000	0.000
83	A	86	GLY	0	0.032	0.029	10.371	-0.013	-0.013	0.000	0.000	0.000	0.000
84	A	87	ILE	0	-0.041	-0.015	12.015	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	88	GLU	-1	-0.765	-0.884	14.200	-0.081	-0.081	0.000	0.000	0.000	0.000
86	A	89	LEU	0	0.010	0.006	16.071	0.025	0.025	0.000	0.000	0.000	0.000
87	A	90	ASN	0	-0.003	0.004	17.104	0.008	0.008	0.000	0.000	0.000	0.000
88	A	91	ARG	1	0.915	0.946	19.032	0.031	0.031	0.000	0.000	0.000	0.000
89	A	92	VAL	0	0.026	0.029	15.538	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	93	VAL	0	0.036	0.027	18.504	0.008	0.008	0.000	0.000	0.000	0.000
91	A	94	ASN	0	0.007	-0.014	21.495	0.001	0.001	0.000	0.000	0.000	0.000
92	A	95	ALA	0	0.010	0.015	19.169	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	96	TRP	0	-0.021	-0.042	15.129	0.004	0.004	0.000	0.000	0.000	0.000
94	A	97	LEU	0	-0.021	-0.017	21.321	0.001	0.001	0.000	0.000	0.000	0.000
95	A	98	ASN	0	-0.051	-0.019	23.952	-0.004	-0.004	0.000	0.000	0.000	0.000
96	A	99	SER	0	0.001	0.013	21.800	-0.006	-0.006	0.000	0.000	0.000	0.000
97	A	100	PRO	0	0.030	0.001	24.400	0.010	0.010	0.000	0.000	0.000	0.000
98	A	101	SER	0	0.023	0.012	22.801	0.002	0.002	0.000	0.000	0.000	0.000
99	A	102	HIS	0	0.017	0.004	18.653	0.000	0.000	0.000	0.000	0.000	0.000
100	A	103	LYS	1	0.970	0.991	22.381	-0.064	-0.064	0.000	0.000	0.000	0.000
101	A	104	GLU	-1	-0.816	-0.863	25.463	0.145	0.145	0.000	0.000	0.000	0.000
102	A	105	ALA	0	0.009	0.009	22.104	0.004	0.004	0.000	0.000	0.000	0.000
103	A	106	LEU	0	-0.014	0.001	21.282	0.007	0.007	0.000	0.000	0.000	0.000
104	A	107	ILE	0	-0.036	-0.019	24.397	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	108	ASN	0	-0.018	0.026	25.132	-0.009	-0.009	0.000	0.000	0.000	0.000
106	A	109	THR	0	0.066	0.027	28.389	0.000	0.000	0.000	0.000	0.000	0.000
107	A	110	ASP	-1	-0.846	-0.900	28.329	0.146	0.146	0.000	0.000	0.000	0.000
108	A	111	THR	0	-0.105	-0.069	24.619	0.011	0.011	0.000	0.000	0.000	0.000
109	A	112	ASP	-1	-0.792	-0.910	27.460	0.177	0.177	0.000	0.000	0.000	0.000
110	A	113	LYS	1	0.832	0.927	23.668	-0.216	-0.216	0.000	0.000	0.000	0.000
111	A	114	ILE	0	0.014	-0.001	19.905	0.001	0.001	0.000	0.000	0.000	0.000
112	A	115	GLY	0	0.021	0.005	18.159	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	116	GLY	0	0.020	-0.001	14.494	-0.003	-0.003	0.000	0.000	0.000	0.000
114	A	117	TYR	0	-0.007	-0.015	7.142	0.281	0.281	0.000	0.000	0.000	0.000
115	A	118	ARG	1	0.802	0.857	9.941	-0.210	-0.210	0.000	0.000	0.000	0.000
116	A	119	LEU	0	-0.020	0.007	2.293	-0.269	-0.461	2.460	-0.351	-1.917	0.002
117	A	120	LYS	1	0.895	0.941	6.658	-0.361	-0.361	0.000	0.000	0.000	0.000
118	A	121	THR	0	-0.040	-0.059	2.406	0.521	1.318	1.174	-0.412	-1.558	-0.002
119	A	122	THR	0	0.015	0.006	5.430	-0.293	-0.293	0.000	0.000	0.000	0.000
120	A	123	ASP	-1	-0.857	-0.899	2.702	-11.209	-8.278	0.802	-1.891	-1.842	-0.018
121	A	124	ASN	0	-0.048	-0.021	6.273	0.298	0.298	0.000	0.000	0.000	0.000
122	A	125	ILE	0	0.046	0.039	2.304	-0.352	-0.348	2.743	-0.521	-2.225	-0.008
123	A	126	ASP	-1	-0.780	-0.874	5.635	0.370	0.370	0.000	0.000	0.000	0.000
124	A	127	ILE	0	0.003	0.012	4.917	-0.062	-0.062	0.000	0.000	0.000	0.000
125	A	128	PHE	0	0.005	-0.008	8.240	0.248	0.248	0.000	0.000	0.000	0.000
126	A	129	VAL	0	-0.013	0.003	9.179	-0.059	-0.059	0.000	0.000	0.000	0.000
127	A	130	VAL	0	0.007	-0.006	11.968	0.046	0.046	0.000	0.000	0.000	0.000
128	A	131	LEU	0	-0.031	-0.006	14.689	-0.028	-0.028	0.000	0.000	0.000	0.000
129	A	132	PHE	0	0.066	0.021	17.749	-0.007	-0.007	0.000	0.000	0.000	0.000
130	A	133	GLY	0	-0.009	-0.008	21.534	0.009	0.009	0.000	0.000	0.000	0.000
131	A	134	LYS	1	0.936	0.974	23.789	-0.176	-0.176	0.000	0.000	0.000	0.000
132	A	135	ARG	1	0.710	0.823	23.569	-0.273	-0.273	0.000	0.000	0.000	0.000
133	A	136	LYS	1	0.890	0.931	28.571	-0.223	-0.223	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:MET)