FMO DATABASE

FMODB ID: R88N8

Calculation Name: 3N53-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3N53

Chain ID: B

ChEMBL ID:

UniProt ID: Q3A6W4

Base Structure: X-ray

Registration Date: 2023-09-21

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	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	93
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-743753.288119
FMO2-HF: Nuclear repulsion	705322.894267
FMO2-HF: Total energy	-38430.393853
FMO2-MP2: Total energy	-38543.928789

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(B:1:LEU)

Summations of interaction energy for fragment #1(B:1:LEU)

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.
-8.5	-2.482	1.772	-2.606	-5.184	-0.017

Interaction energy analysis for fragmet #1(B:1:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.024 / q_NPA : -0.021

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	B	3	LYS	1	0.849	0.932	3.859	-1.873	-0.475	-0.008	-0.612	-0.779	0.003
4	B	4	ILE	0	-0.008	-0.001	5.941	0.462	0.462	0.000	0.000	0.000	0.000
5	B	5	LEU	0	-0.020	0.004	8.615	-0.056	-0.056	0.000	0.000	0.000	0.000
6	B	6	ILE	0	0.013	0.009	11.765	0.085	0.085	0.000	0.000	0.000	0.000
7	B	7	ILE	0	-0.016	-0.001	14.117	0.014	0.014	0.000	0.000	0.000	0.000
8	B	8	ASP	-1	-0.768	-0.882	17.744	-0.243	-0.243	0.000	0.000	0.000	0.000
9	B	9	GLN	0	0.050	0.035	20.101	-0.010	-0.010	0.000	0.000	0.000	0.000
10	B	10	GLN	0	-0.030	-0.022	22.743	0.003	0.003	0.000	0.000	0.000	0.000
11	B	11	ASP	-1	-0.777	-0.876	20.582	-0.272	-0.272	0.000	0.000	0.000	0.000
12	B	12	PHE	0	-0.020	-0.007	19.794	-0.028	-0.028	0.000	0.000	0.000	0.000
13	B	13	SER	0	-0.032	-0.027	19.977	-0.016	-0.016	0.000	0.000	0.000	0.000
14	B	14	ARG	1	0.798	0.870	16.044	0.327	0.327	0.000	0.000	0.000	0.000
15	B	15	ILE	0	-0.005	0.000	15.566	-0.057	-0.057	0.000	0.000	0.000	0.000
16	B	16	GLU	-1	-0.832	-0.880	14.998	-0.403	-0.403	0.000	0.000	0.000	0.000
17	B	17	LEU	0	-0.031	-0.024	13.932	-0.033	-0.033	0.000	0.000	0.000	0.000
18	B	18	LYS	1	0.835	0.891	10.103	0.714	0.714	0.000	0.000	0.000	0.000
19	B	19	ASN	0	-0.009	-0.019	10.471	-0.181	-0.181	0.000	0.000	0.000	0.000
20	B	20	PHE	0	-0.062	-0.030	11.539	-0.025	-0.025	0.000	0.000	0.000	0.000
21	B	21	LEU	0	0.005	0.002	8.338	0.033	0.033	0.000	0.000	0.000	0.000
22	B	22	ASP	-1	-0.786	-0.889	6.221	-1.565	-1.565	0.000	0.000	0.000	0.000
23	B	23	SER	0	-0.112	-0.062	5.273	-0.450	-0.450	0.000	0.000	0.000	0.000
24	B	24	GLU	-1	-0.922	-0.944	3.404	-0.971	-0.614	0.024	-0.075	-0.307	0.000
25	B	25	TYR	0	-0.028	-0.017	2.682	-2.948	-0.618	1.093	-1.289	-2.133	-0.015
26	B	26	LEU	0	-0.026	-0.005	2.774	-1.858	-0.059	0.653	-0.611	-1.841	-0.005
27	B	27	VAL	0	-0.003	0.000	3.822	0.521	0.655	0.010	-0.019	-0.124	0.000
28	B	28	ILE	0	-0.016	-0.004	7.430	0.130	0.130	0.000	0.000	0.000	0.000
29	B	29	GLU	-1	-0.805	-0.885	10.455	-0.443	-0.443	0.000	0.000	0.000	0.000
30	B	30	SER	0	-0.010	-0.019	14.092	0.044	0.044	0.000	0.000	0.000	0.000
31	B	31	LYS	1	0.833	0.908	17.397	0.231	0.231	0.000	0.000	0.000	0.000
32	B	32	ASN	0	-0.060	-0.050	20.901	0.030	0.030	0.000	0.000	0.000	0.000
33	B	33	GLU	-1	-0.784	-0.883	21.489	-0.128	-0.128	0.000	0.000	0.000	0.000
34	B	34	LYS	1	0.805	0.889	22.343	0.164	0.164	0.000	0.000	0.000	0.000
35	B	35	GLU	-1	-0.780	-0.888	19.161	-0.261	-0.261	0.000	0.000	0.000	0.000
36	B	36	ALA	0	0.003	0.007	17.667	-0.024	-0.024	0.000	0.000	0.000	0.000
37	B	37	LEU	0	0.005	-0.005	17.711	-0.011	-0.011	0.000	0.000	0.000	0.000
38	B	38	GLU	-1	-0.805	-0.880	19.217	-0.175	-0.175	0.000	0.000	0.000	0.000
39	B	39	GLN	0	-0.012	-0.023	14.139	0.000	0.000	0.000	0.000	0.000	0.000
40	B	40	ILE	0	-0.039	-0.022	14.148	-0.043	-0.043	0.000	0.000	0.000	0.000
41	B	41	ASP	-1	-0.886	-0.940	15.292	-0.117	-0.117	0.000	0.000	0.000	0.000
42	B	42	HIS	0	-0.037	-0.012	15.823	0.028	0.028	0.000	0.000	0.000	0.000
43	B	43	HIS	0	-0.086	-0.051	10.493	-0.047	-0.047	0.000	0.000	0.000	0.000
44	B	44	HIS	0	-0.052	-0.008	10.452	-0.062	-0.062	0.000	0.000	0.000	0.000
45	B	45	PRO	0	-0.006	-0.007	9.571	-0.026	-0.026	0.000	0.000	0.000	0.000
46	B	46	ASP	-1	-0.796	-0.895	6.812	0.127	0.127	0.000	0.000	0.000	0.000
47	B	47	LEU	0	0.001	-0.002	9.754	0.139	0.139	0.000	0.000	0.000	0.000
48	B	48	VAL	0	-0.002	0.001	11.341	-0.134	-0.134	0.000	0.000	0.000	0.000
49	B	49	ILE	0	-0.004	0.003	12.297	0.046	0.046	0.000	0.000	0.000	0.000
50	B	50	LEU	0	-0.014	-0.005	15.557	-0.025	-0.025	0.000	0.000	0.000	0.000
51	B	51	ASP	-1	-0.791	-0.880	18.967	-0.179	-0.179	0.000	0.000	0.000	0.000
52	B	52	MET	0	-0.044	-0.025	21.533	0.011	0.011	0.000	0.000	0.000	0.000
53	B	53	ASP	-1	-0.869	-0.885	25.118	-0.127	-0.127	0.000	0.000	0.000	0.000
54	B	61	ASN	0	0.021	-0.010	28.648	0.002	0.002	0.000	0.000	0.000	0.000
55	B	62	LEU	0	0.031	0.019	23.191	0.005	0.005	0.000	0.000	0.000	0.000
56	B	63	CYS	0	0.009	-0.009	22.967	-0.009	-0.009	0.000	0.000	0.000	0.000
57	B	64	LEU	0	-0.005	0.003	23.460	0.005	0.005	0.000	0.000	0.000	0.000
58	B	65	LYS	1	0.799	0.902	25.248	0.098	0.098	0.000	0.000	0.000	0.000
59	B	66	LEU	0	0.016	0.022	19.025	0.004	0.004	0.000	0.000	0.000	0.000
60	B	75	VAL	0	-0.029	-0.004	13.310	0.025	0.025	0.000	0.000	0.000	0.000
61	B	76	PRO	0	-0.012	0.014	13.286	-0.017	-0.017	0.000	0.000	0.000	0.000
62	B	77	LEU	0	-0.022	-0.029	15.248	-0.058	-0.058	0.000	0.000	0.000	0.000
63	B	78	ILE	0	0.006	0.000	14.497	0.025	0.025	0.000	0.000	0.000	0.000
64	B	79	LEU	0	0.011	-0.004	18.082	-0.027	-0.027	0.000	0.000	0.000	0.000
65	B	80	LEU	0	-0.013	-0.002	18.326	0.009	0.009	0.000	0.000	0.000	0.000
66	B	81	PHE	0	0.002	-0.013	21.852	0.005	0.005	0.000	0.000	0.000	0.000
67	B	82	SER	0	-0.050	-0.047	25.544	0.005	0.005	0.000	0.000	0.000	0.000
68	B	97	ALA	0	0.012	0.002	21.806	-0.004	-0.004	0.000	0.000	0.000	0.000
69	B	98	ASP	-1	-0.873	-0.932	18.930	-0.013	-0.013	0.000	0.000	0.000	0.000
70	B	99	ASP	-1	-0.822	-0.890	19.106	-0.050	-0.050	0.000	0.000	0.000	0.000
71	B	100	TYR	0	-0.057	-0.032	21.141	-0.024	-0.024	0.000	0.000	0.000	0.000
72	B	101	LEU	0	-0.028	-0.011	19.130	0.007	0.007	0.000	0.000	0.000	0.000
73	B	102	THR	0	0.006	0.011	23.053	-0.006	-0.006	0.000	0.000	0.000	0.000
74	B	103	LYS	1	0.735	0.851	22.582	0.171	0.171	0.000	0.000	0.000	0.000
75	B	104	PRO	0	-0.025	-0.032	24.225	0.009	0.009	0.000	0.000	0.000	0.000
76	B	105	PHE	0	0.047	0.030	17.446	0.014	0.014	0.000	0.000	0.000	0.000
77	B	106	ASN	0	-0.002	-0.005	20.266	-0.030	-0.030	0.000	0.000	0.000	0.000
78	B	107	ARG	1	0.843	0.899	16.158	0.324	0.324	0.000	0.000	0.000	0.000
79	B	108	ASN	0	0.006	-0.006	15.641	-0.035	-0.035	0.000	0.000	0.000	0.000
80	B	109	ASP	-1	-0.855	-0.889	16.230	-0.085	-0.085	0.000	0.000	0.000	0.000
81	B	110	LEU	0	0.063	0.031	14.493	0.017	0.017	0.000	0.000	0.000	0.000
82	B	111	LEU	0	0.033	0.022	9.951	0.003	0.003	0.000	0.000	0.000	0.000
83	B	112	SER	0	-0.009	0.003	12.428	0.045	0.045	0.000	0.000	0.000	0.000
84	B	113	ARG	1	0.793	0.847	14.590	0.130	0.130	0.000	0.000	0.000	0.000
85	B	114	ILE	0	0.021	0.012	9.266	0.045	0.045	0.000	0.000	0.000	0.000
86	B	115	GLU	-1	-0.848	-0.899	9.748	0.326	0.326	0.000	0.000	0.000	0.000
87	B	116	ILE	0	-0.050	-0.026	11.124	0.126	0.126	0.000	0.000	0.000	0.000
88	B	117	HIS	0	-0.010	-0.013	13.595	0.078	0.078	0.000	0.000	0.000	0.000
89	B	118	LEU	0	-0.008	-0.009	6.845	0.059	0.059	0.000	0.000	0.000	0.000
90	B	119	ARG	1	0.798	0.875	10.742	-0.242	-0.242	0.000	0.000	0.000	0.000
91	B	120	THR	0	-0.026	-0.017	12.260	0.029	0.029	0.000	0.000	0.000	0.000
92	B	121	GLN	0	-0.019	-0.019	12.859	0.020	0.020	0.000	0.000	0.000	0.000
93	B	122	ASN	0	-0.147	-0.056	10.384	0.196	0.196	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:1:LEU)