FMO DATABASE

FMODB ID: R8VL8

Calculation Name: 3DL3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DL3

Chain ID: A

ChEMBL ID:

UniProt ID: Q5E3X2

Base Structure: X-ray

Registration Date: 2023-09-23

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	96
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-709916.230804
FMO2-HF: Nuclear repulsion	671638.295697
FMO2-HF: Total energy	-38277.935107
FMO2-MP2: Total energy	-38390.955764

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:5:ARG)

Summations of interaction energy for fragment #1(A:5: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.
-80.854	-77.716	5.425	-3.005	-5.558	-0.017

Interaction energy analysis for fragmet #1(A:5:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.950 / q_NPA : 0.958

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	7	PRO	0	-0.014	0.003	3.798	2.731	4.224	-0.016	-0.578	-0.900	0.001
4	A	8	LYS	1	0.988	0.980	5.807	23.541	23.541	0.000	0.000	0.000	0.000
5	A	9	ASN	0	-0.024	-0.011	7.874	0.273	0.273	0.000	0.000	0.000	0.000
6	A	10	TRP	0	0.003	0.022	7.495	-0.651	-0.651	0.000	0.000	0.000	0.000
7	A	11	THR	0	-0.010	-0.012	10.722	0.962	0.962	0.000	0.000	0.000	0.000
8	A	12	ILE	0	-0.014	-0.012	12.658	-1.102	-1.102	0.000	0.000	0.000	0.000
9	A	13	GLN	0	-0.024	0.003	14.158	2.242	2.242	0.000	0.000	0.000	0.000
10	A	14	ARG	1	0.920	0.953	15.534	18.465	18.465	0.000	0.000	0.000	0.000
11	A	15	SER	0	0.027	0.000	15.847	-1.167	-1.167	0.000	0.000	0.000	0.000
12	A	16	THR	0	-0.060	0.001	17.792	0.781	0.781	0.000	0.000	0.000	0.000
13	A	17	PRO	0	0.022	0.004	19.865	-0.118	-0.118	0.000	0.000	0.000	0.000
14	A	18	PHE	0	0.028	-0.006	20.509	-0.396	-0.396	0.000	0.000	0.000	0.000
15	A	19	PHE	0	-0.034	-0.021	20.688	0.278	0.278	0.000	0.000	0.000	0.000
16	A	20	THR	0	0.068	0.030	23.492	-0.080	-0.080	0.000	0.000	0.000	0.000
17	A	21	LYS	1	0.944	0.957	25.798	10.819	10.819	0.000	0.000	0.000	0.000
18	A	22	ASP	-1	-0.899	-0.934	27.734	-9.389	-9.389	0.000	0.000	0.000	0.000
19	A	23	ASN	0	-0.038	-0.028	27.014	0.063	0.063	0.000	0.000	0.000	0.000
20	A	24	VAL	0	-0.043	-0.003	22.578	-0.324	-0.324	0.000	0.000	0.000	0.000
21	A	25	PRO	0	-0.023	-0.009	22.787	0.151	0.151	0.000	0.000	0.000	0.000
22	A	26	GLU	-1	-0.857	-0.934	23.072	-11.501	-11.501	0.000	0.000	0.000	0.000
23	A	27	ALA	0	-0.022	-0.021	20.823	-0.410	-0.410	0.000	0.000	0.000	0.000
24	A	28	LEU	0	-0.078	-0.040	17.737	-0.875	-0.875	0.000	0.000	0.000	0.000
25	A	29	LEU	0	0.004	0.000	18.236	-0.870	-0.870	0.000	0.000	0.000	0.000
26	A	30	THR	0	0.006	0.031	19.341	0.010	0.010	0.000	0.000	0.000	0.000
27	A	31	HIS	0	0.002	0.024	16.364	-0.838	-0.838	0.000	0.000	0.000	0.000
28	A	32	HIS	1	0.838	0.895	14.645	19.276	19.276	0.000	0.000	0.000	0.000
29	A	33	ASN	0	0.026	0.032	10.290	-2.436	-2.436	0.000	0.000	0.000	0.000
30	A	34	THR	0	-0.045	-0.025	8.165	1.734	1.734	0.000	0.000	0.000	0.000
31	A	35	ALA	0	0.022	-0.002	10.351	-0.286	-0.286	0.000	0.000	0.000	0.000
32	A	36	VAL	0	0.052	0.013	8.915	-2.115	-2.115	0.000	0.000	0.000	0.000
33	A	37	ASP	-1	-0.863	-0.927	7.370	-38.520	-38.520	0.000	0.000	0.000	0.000
34	A	38	VAL	0	-0.044	-0.042	7.868	2.524	2.524	0.000	0.000	0.000	0.000
35	A	39	PHE	0	-0.021	0.003	1.902	-5.574	-6.504	4.893	-1.381	-2.581	-0.006
36	A	40	GLY	0	0.017	0.001	7.325	3.471	3.471	0.000	0.000	0.000	0.000
37	A	41	GLN	0	0.041	0.037	8.913	-1.132	-1.132	0.000	0.000	0.000	0.000
38	A	42	ILE	0	0.033	0.004	9.852	1.818	1.818	0.000	0.000	0.000	0.000
39	A	43	CYS	0	-0.027	-0.017	12.794	-0.718	-0.718	0.000	0.000	0.000	0.000
40	A	44	VAL	0	0.032	0.026	14.887	0.528	0.528	0.000	0.000	0.000	0.000
41	A	45	MET	0	-0.062	-0.048	17.928	-0.046	-0.046	0.000	0.000	0.000	0.000
42	A	46	GLU	-1	-0.930	-0.973	20.960	-10.047	-10.047	0.000	0.000	0.000	0.000
43	A	47	GLY	0	0.075	0.069	22.672	-0.355	-0.355	0.000	0.000	0.000	0.000
44	A	48	VAL	0	-0.055	-0.042	20.439	-0.412	-0.412	0.000	0.000	0.000	0.000
45	A	49	VAL	0	0.000	0.007	16.813	0.195	0.195	0.000	0.000	0.000	0.000
46	A	50	THR	0	-0.037	-0.019	17.722	-0.404	-0.404	0.000	0.000	0.000	0.000
47	A	51	TYR	0	-0.014	-0.032	9.836	-0.189	-0.189	0.000	0.000	0.000	0.000
48	A	52	TYR	0	-0.050	-0.040	15.174	0.256	0.256	0.000	0.000	0.000	0.000
49	A	53	GLY	0	0.030	0.005	11.784	-0.638	-0.638	0.000	0.000	0.000	0.000
50	A	54	PHE	0	-0.028	-0.022	12.227	1.705	1.705	0.000	0.000	0.000	0.000
51	A	55	ALA	0	0.047	0.039	11.412	-1.573	-1.573	0.000	0.000	0.000	0.000
52	A	56	ASN	0	-0.031	-0.031	11.185	-0.914	-0.914	0.000	0.000	0.000	0.000
53	A	57	SER	0	-0.046	-0.030	13.046	0.798	0.798	0.000	0.000	0.000	0.000
54	A	58	GLU	-1	-0.854	-0.921	15.290	-16.546	-16.546	0.000	0.000	0.000	0.000
55	A	59	ALA	0	-0.077	-0.015	15.849	0.809	0.809	0.000	0.000	0.000	0.000
56	A	60	THR	0	0.031	-0.003	17.890	-0.190	-0.190	0.000	0.000	0.000	0.000
57	A	61	GLU	-1	-0.974	-0.979	19.950	-13.041	-13.041	0.000	0.000	0.000	0.000
58	A	62	PRO	0	-0.073	-0.043	16.378	-0.769	-0.769	0.000	0.000	0.000	0.000
59	A	63	GLU	-1	-0.848	-0.901	10.790	-26.311	-26.311	0.000	0.000	0.000	0.000
60	A	64	ILE	0	-0.035	-0.011	10.320	-0.020	-0.020	0.000	0.000	0.000	0.000
61	A	65	LYS	1	0.945	0.984	13.772	14.125	14.125	0.000	0.000	0.000	0.000
62	A	66	VAL	0	-0.028	-0.018	12.346	0.408	0.408	0.000	0.000	0.000	0.000
63	A	67	VAL	0	-0.020	0.005	15.364	-0.080	-0.080	0.000	0.000	0.000	0.000
64	A	68	ILE	0	-0.022	-0.011	13.217	-0.592	-0.592	0.000	0.000	0.000	0.000
65	A	69	ASN	0	0.027	0.003	16.654	1.164	1.164	0.000	0.000	0.000	0.000
66	A	70	ALA	0	0.084	0.040	17.904	-0.582	-0.582	0.000	0.000	0.000	0.000
67	A	71	GLY	0	-0.037	-0.009	18.458	0.121	0.121	0.000	0.000	0.000	0.000
68	A	72	GLN	0	-0.028	-0.012	14.260	-0.548	-0.548	0.000	0.000	0.000	0.000
69	A	73	PHE	0	0.000	-0.018	7.790	0.210	0.210	0.000	0.000	0.000	0.000
70	A	74	ALA	0	0.019	0.024	9.162	-0.767	-0.767	0.000	0.000	0.000	0.000
71	A	75	THR	0	-0.027	-0.019	4.636	1.040	1.117	-0.001	-0.002	-0.074	0.000
72	A	76	SER	0	0.003	0.023	6.300	-2.589	-2.589	0.000	0.000	0.000	0.000
73	A	77	PRO	0	-0.032	-0.018	2.447	-3.319	-1.734	0.358	-0.699	-1.245	-0.008
74	A	78	PRO	0	0.005	-0.013	2.577	2.861	3.774	0.191	-0.345	-0.758	-0.004
75	A	79	GLN	0	-0.029	0.004	5.247	0.063	0.063	0.000	0.000	0.000	0.000
76	A	80	TYR	0	-0.074	-0.051	5.994	1.333	1.333	0.000	0.000	0.000	0.000
77	A	81	TRP	0	0.044	0.013	7.834	2.464	2.464	0.000	0.000	0.000	0.000
78	A	82	HIS	0	-0.056	-0.029	10.692	0.582	0.582	0.000	0.000	0.000	0.000
79	A	83	ARG	1	0.963	0.987	13.417	15.810	15.810	0.000	0.000	0.000	0.000
80	A	84	ILE	0	-0.002	-0.005	15.466	-0.501	-0.501	0.000	0.000	0.000	0.000
81	A	85	GLU	-1	-0.890	-0.931	17.965	-12.573	-12.573	0.000	0.000	0.000	0.000
82	A	86	LEU	0	-0.006	-0.010	20.539	-0.318	-0.318	0.000	0.000	0.000	0.000
83	A	87	SER	0	0.002	0.016	23.059	0.215	0.215	0.000	0.000	0.000	0.000
84	A	88	ASP	-1	-0.912	-0.990	25.566	-9.829	-9.829	0.000	0.000	0.000	0.000
85	A	89	ASP	-1	-0.893	-0.945	27.216	-10.568	-10.568	0.000	0.000	0.000	0.000
86	A	90	ALA	0	-0.037	-0.002	22.461	-0.229	-0.229	0.000	0.000	0.000	0.000
87	A	91	GLN	0	0.009	0.003	22.926	0.493	0.493	0.000	0.000	0.000	0.000
88	A	92	PHE	0	-0.025	-0.019	17.196	-0.520	-0.520	0.000	0.000	0.000	0.000
89	A	93	ASN	0	-0.013	-0.011	16.913	0.304	0.304	0.000	0.000	0.000	0.000
90	A	94	ILE	0	-0.031	-0.010	12.901	-0.738	-0.738	0.000	0.000	0.000	0.000
91	A	95	ASN	0	0.001	0.019	12.222	1.807	1.807	0.000	0.000	0.000	0.000
92	A	96	PHE	0	-0.038	-0.033	11.572	-1.718	-1.718	0.000	0.000	0.000	0.000
93	A	97	TRP	0	-0.003	0.004	8.489	1.112	1.112	0.000	0.000	0.000	0.000
94	A	98	SER	0	0.033	0.000	9.756	-1.894	-1.894	0.000	0.000	0.000	0.000
95	A	99	ASP	-1	-0.899	-0.950	11.244	-22.863	-22.863	0.000	0.000	0.000	0.000
96	A	100	GLN	0	-0.010	0.005	12.637	1.789	1.789	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:ARG)