FMO DATABASE

FMODB ID: 164YZ

Calculation Name: 3DA7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DA7

Chain ID: A

ChEMBL ID:

UniProt ID: P11540

Base Structure: X-ray

Registration Date: 2023-09-26

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	109
LigandResidueName
LigandFragmentNumber	0
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-864912.322669
FMO2-HF: Nuclear repulsion	822227.374154
FMO2-HF: Total energy	-42684.948515
FMO2-MP2: Total energy	-42812.150211

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:ARG)

Summations of interaction energy for fragment #1(A:4:ARG)

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.
-69.571	-75.855	59.873	-23.668	-29.924	-0.19

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.833 / q_NPA : 0.927

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	TRP	0	0.033	0.010	3.594	-6.336	-3.127	0.003	-1.384	-1.828	0.005
4	A	7	ARG	1	0.891	0.947	5.809	24.982	24.982	0.000	0.000	0.000	0.000
5	A	8	GLU	-1	-0.851	-0.881	9.433	-20.772	-20.772	0.000	0.000	0.000	0.000
6	A	9	ALA	0	0.011	0.003	12.399	1.033	1.033	0.000	0.000	0.000	0.000
7	A	10	ASP	-1	-0.754	-0.832	15.777	-15.196	-15.196	0.000	0.000	0.000	0.000
8	A	11	ILE	0	0.016	0.010	16.896	-0.033	-0.033	0.000	0.000	0.000	0.000
9	A	12	ASN	0	0.004	0.018	20.000	0.521	0.521	0.000	0.000	0.000	0.000
10	A	13	TYR	0	-0.033	-0.007	23.456	0.392	0.392	0.000	0.000	0.000	0.000
11	A	14	THR	0	-0.012	0.000	25.101	0.075	0.075	0.000	0.000	0.000	0.000
12	A	15	SER	0	-0.006	-0.018	28.612	0.121	0.121	0.000	0.000	0.000	0.000
13	A	16	GLY	0	0.056	0.052	30.433	-0.087	-0.087	0.000	0.000	0.000	0.000
14	A	17	PHE	0	-0.018	-0.023	29.137	-0.255	-0.255	0.000	0.000	0.000	0.000
15	A	18	ARG	1	0.784	0.858	19.080	13.810	13.810	0.000	0.000	0.000	0.000
16	A	19	ASN	0	0.039	0.015	22.507	-0.178	-0.178	0.000	0.000	0.000	0.000
17	A	20	SER	0	0.005	-0.011	21.953	-0.162	-0.162	0.000	0.000	0.000	0.000
18	A	21	ASP	-1	-0.861	-0.919	19.534	-14.616	-14.616	0.000	0.000	0.000	0.000
19	A	22	ARG	1	0.780	0.885	15.243	15.615	15.615	0.000	0.000	0.000	0.000
20	A	23	ILE	0	0.009	0.013	12.256	-0.584	-0.584	0.000	0.000	0.000	0.000
21	A	24	LEU	0	-0.036	-0.026	9.070	0.019	0.019	0.000	0.000	0.000	0.000
22	A	25	TYR	0	0.043	0.016	7.312	-1.110	-1.110	0.000	0.000	0.000	0.000
23	A	26	SER	0	-0.015	-0.038	2.262	2.453	4.514	1.132	-1.452	-1.741	0.010
24	A	27	SER	0	0.015	0.005	2.267	1.361	3.043	2.519	-1.876	-2.326	-0.014
25	A	28	ASP	-1	-0.808	-0.871	2.001	-97.142	-117.501	41.270	-10.411	-10.501	-0.121
26	A	29	TRP	0	-0.022	0.006	4.280	1.679	1.821	-0.001	-0.032	-0.109	0.000
27	A	30	LEU	0	0.029	0.023	2.692	3.240	4.512	0.875	-0.437	-1.710	-0.001
28	A	31	ILE	0	0.014	-0.006	5.617	1.230	1.230	0.000	0.000	0.000	0.000
29	A	32	TYR	0	-0.025	-0.015	6.754	1.856	1.856	0.000	0.000	0.000	0.000
30	A	33	LYS	1	0.969	1.004	10.570	17.470	17.470	0.000	0.000	0.000	0.000
31	A	34	THR	0	-0.023	-0.012	13.993	-0.211	-0.211	0.000	0.000	0.000	0.000
32	A	35	THR	0	0.066	0.017	16.346	0.086	0.086	0.000	0.000	0.000	0.000
33	A	36	ASP	-1	-0.783	-0.824	18.777	-15.586	-15.586	0.000	0.000	0.000	0.000
34	A	37	HIS	0	0.013	-0.001	19.351	-0.278	-0.278	0.000	0.000	0.000	0.000
35	A	38	TYR	0	-0.097	-0.101	14.139	0.418	0.418	0.000	0.000	0.000	0.000
36	A	39	GLN	0	-0.033	0.005	15.837	-0.956	-0.956	0.000	0.000	0.000	0.000
37	A	40	THR	0	-0.044	-0.075	15.631	-0.856	-0.856	0.000	0.000	0.000	0.000
38	A	41	PHE	0	0.034	0.013	11.742	-0.382	-0.382	0.000	0.000	0.000	0.000
39	A	42	THR	0	-0.068	-0.037	13.706	0.064	0.064	0.000	0.000	0.000	0.000
40	A	43	LYS	1	0.917	0.959	10.279	22.591	22.591	0.000	0.000	0.000	0.000
41	A	44	ILE	0	0.004	-0.008	11.536	1.931	1.931	0.000	0.000	0.000	0.000
42	A	45	ARG	1	0.860	0.908	12.572	20.664	20.664	0.000	0.000	0.000	0.000
43	A	46	CYM	-1	-0.724	-0.817	14.962	-15.990	-15.990	0.000	0.000	0.000	0.000
44	A	47	ALA	0	-0.115	-0.079	17.342	0.043	0.043	0.000	0.000	0.000	0.000
45	A	48	GLN	0	0.015	0.003	20.821	0.327	0.327	0.000	0.000	0.000	0.000
46	A	49	VAL	0	0.041	0.026	20.202	-0.174	-0.174	0.000	0.000	0.000	0.000
47	A	50	ILE	0	-0.028	0.003	22.485	0.576	0.576	0.000	0.000	0.000	0.000
48	A	51	ASN	0	-0.018	-0.039	19.841	0.438	0.438	0.000	0.000	0.000	0.000
49	A	52	THR	0	0.029	-0.004	21.474	-0.694	-0.694	0.000	0.000	0.000	0.000
50	A	53	PHE	0	-0.027	-0.019	16.215	-0.631	-0.631	0.000	0.000	0.000	0.000
51	A	54	ASP	-1	-0.808	-0.900	16.603	-16.726	-16.726	0.000	0.000	0.000	0.000
52	A	55	GLY	0	0.005	0.000	17.879	-0.374	-0.374	0.000	0.000	0.000	0.000
53	A	56	VAL	0	-0.007	-0.009	15.259	-0.193	-0.193	0.000	0.000	0.000	0.000
54	A	57	ALA	0	-0.007	-0.014	13.187	-0.874	-0.874	0.000	0.000	0.000	0.000
55	A	58	ASP	-1	-0.848	-0.918	13.766	-17.675	-17.675	0.000	0.000	0.000	0.000
56	A	59	TYR	0	-0.010	0.021	16.394	0.168	0.168	0.000	0.000	0.000	0.000
57	A	60	LEU	0	-0.046	-0.034	11.499	-0.328	-0.328	0.000	0.000	0.000	0.000
58	A	61	GLN	0	-0.025	-0.025	9.021	-0.201	-0.201	0.000	0.000	0.000	0.000
59	A	62	THR	0	-0.043	-0.013	13.133	0.000	0.000	0.000	0.000	0.000	0.000
60	A	63	TYR	0	-0.032	-0.028	16.244	0.550	0.550	0.000	0.000	0.000	0.000
61	A	64	HIS	1	0.802	0.909	11.278	22.964	22.964	0.000	0.000	0.000	0.000
62	A	65	LYS	1	0.968	0.982	13.201	14.118	14.118	0.000	0.000	0.000	0.000
63	A	66	LEU	0	-0.033	-0.006	14.333	-0.230	-0.230	0.000	0.000	0.000	0.000
64	A	67	PRO	0	0.027	0.018	16.444	0.453	0.453	0.000	0.000	0.000	0.000
65	A	68	ASP	-1	-0.839	-0.922	19.945	-12.848	-12.848	0.000	0.000	0.000	0.000
66	A	69	ASN	0	-0.058	-0.026	21.874	0.190	0.190	0.000	0.000	0.000	0.000
67	A	70	TYR	0	-0.018	-0.035	18.849	-0.074	-0.074	0.000	0.000	0.000	0.000
68	A	71	ILE	0	0.004	0.016	21.273	0.204	0.204	0.000	0.000	0.000	0.000
69	A	72	THR	0	0.008	0.010	17.252	-0.162	-0.162	0.000	0.000	0.000	0.000
70	A	73	LYS	1	0.949	0.958	17.817	15.728	15.728	0.000	0.000	0.000	0.000
71	A	74	SER	0	-0.016	-0.003	20.749	0.596	0.596	0.000	0.000	0.000	0.000
72	A	75	GLU	-1	-0.809	-0.910	20.835	-12.760	-12.760	0.000	0.000	0.000	0.000
73	A	76	ALA	0	0.031	0.014	23.838	0.491	0.491	0.000	0.000	0.000	0.000
74	A	77	GLN	0	-0.055	-0.045	24.064	-0.045	-0.045	0.000	0.000	0.000	0.000
75	A	78	ALA	0	-0.013	0.016	26.782	0.419	0.419	0.000	0.000	0.000	0.000
76	A	79	LEU	0	-0.019	0.001	28.065	0.330	0.330	0.000	0.000	0.000	0.000
77	A	80	GLY	0	0.019	0.006	30.605	0.247	0.247	0.000	0.000	0.000	0.000
78	A	81	TRP	0	-0.028	-0.018	23.403	-0.100	-0.100	0.000	0.000	0.000	0.000
79	A	82	VAL	0	-0.032	-0.032	29.499	-0.027	-0.027	0.000	0.000	0.000	0.000
80	A	83	ALA	0	0.022	0.000	26.543	0.112	0.112	0.000	0.000	0.000	0.000
81	A	84	SER	0	0.005	-0.013	28.525	-0.046	-0.046	0.000	0.000	0.000	0.000
82	A	85	LYS	1	0.940	0.979	31.393	8.661	8.661	0.000	0.000	0.000	0.000
83	A	86	GLY	0	0.002	0.020	30.263	0.112	0.112	0.000	0.000	0.000	0.000
84	A	87	ASN	0	0.018	0.009	31.350	-0.176	-0.176	0.000	0.000	0.000	0.000
85	A	88	LEU	0	0.021	0.015	25.217	0.062	0.062	0.000	0.000	0.000	0.000
86	A	89	ALA	0	-0.028	-0.017	29.497	-0.014	-0.014	0.000	0.000	0.000	0.000
87	A	90	ASP	-1	-0.919	-0.955	31.441	-8.426	-8.426	0.000	0.000	0.000	0.000
88	A	91	VAL	0	-0.046	-0.024	29.962	0.145	0.145	0.000	0.000	0.000	0.000
89	A	92	ALA	0	-0.023	-0.013	28.126	-0.050	-0.050	0.000	0.000	0.000	0.000
90	A	93	PRO	0	0.051	0.024	29.210	-0.324	-0.324	0.000	0.000	0.000	0.000
91	A	94	GLY	0	-0.007	0.001	29.142	-0.084	-0.084	0.000	0.000	0.000	0.000
92	A	95	LYS	1	0.861	0.944	25.243	11.054	11.054	0.000	0.000	0.000	0.000
93	A	96	SER	0	-0.018	-0.010	21.873	0.113	0.113	0.000	0.000	0.000	0.000
94	A	97	ILE	0	0.017	0.010	18.906	-0.114	-0.114	0.000	0.000	0.000	0.000
95	A	98	GLY	0	-0.025	-0.031	16.766	-0.460	-0.460	0.000	0.000	0.000	0.000
96	A	99	GLY	0	0.022	0.011	14.011	0.489	0.489	0.000	0.000	0.000	0.000
97	A	100	ASP	-1	-0.857	-0.918	13.756	-16.279	-16.279	0.000	0.000	0.000	0.000
98	A	101	ILE	0	-0.015	-0.015	9.436	-1.582	-1.582	0.000	0.000	0.000	0.000
99	A	102	PHE	0	0.038	0.020	8.332	0.916	0.916	0.000	0.000	0.000	0.000
100	A	103	SER	0	-0.072	-0.059	8.152	-1.891	-1.891	0.000	0.000	0.000	0.000
101	A	104	ASN	0	-0.028	-0.007	6.272	2.705	2.705	0.000	0.000	0.000	0.000
102	A	105	ARG	1	0.987	0.976	9.481	17.918	17.918	0.000	0.000	0.000	0.000
103	A	106	GLU	-1	-0.902	-0.948	12.665	-17.509	-17.509	0.000	0.000	0.000	0.000
104	A	107	GLY	0	-0.034	-0.005	8.903	0.365	0.365	0.000	0.000	0.000	0.000
105	A	108	LYS	1	0.864	0.943	8.854	18.149	18.149	0.000	0.000	0.000	0.000
106	A	109	LEU	0	-0.040	0.000	5.978	-0.618	-0.618	0.000	0.000	0.000	0.000
107	A	110	PRO	0	0.022	0.008	2.463	0.629	-2.203	6.719	-1.149	-2.738	0.002
108	A	111	GLY	0	0.025	0.015	2.756	-10.757	-8.655	0.646	-1.114	-1.635	-0.014
109	A	112	LYS	1	0.982	1.001	2.219	-7.278	-0.839	6.710	-5.813	-7.336	-0.057

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