FMO DATABASE

FMODB ID: KGMV3

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

Total energy (hartree)

FMO2-HF: Electronic energy	-711423.253395
FMO2-HF: Nuclear repulsion	673144.612994
FMO2-HF: Total energy	-38278.640402
FMO2-MP2: Total energy	-38391.621224

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.
-87.805	-82.912	3.347	-2.439	-5.8	-0.011

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 : 0.976 / q_NPA : 0.965

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	0.007	0.011	3.881	2.230	3.502	-0.009	-0.484	-0.779	0.001
4	A	8	LYS	1	0.961	0.970	6.236	24.822	24.822	0.000	0.000	0.000	0.000
5	A	9	ASN	0	-0.044	-0.025	8.167	0.366	0.366	0.000	0.000	0.000	0.000
6	A	10	TRP	0	-0.038	-0.008	5.695	-1.146	-1.146	0.000	0.000	0.000	0.000
7	A	11	THR	0	-0.005	-0.008	10.877	1.156	1.156	0.000	0.000	0.000	0.000
8	A	12	ILE	0	-0.010	-0.008	13.003	-1.050	-1.050	0.000	0.000	0.000	0.000
9	A	13	GLN	0	-0.013	0.013	14.149	2.203	2.203	0.000	0.000	0.000	0.000
10	A	14	ARG	1	0.892	0.946	15.174	19.011	19.011	0.000	0.000	0.000	0.000
11	A	15	SER	0	0.010	-0.003	15.997	-1.148	-1.148	0.000	0.000	0.000	0.000
12	A	16	THR	0	-0.062	-0.013	18.198	0.774	0.774	0.000	0.000	0.000	0.000
13	A	17	PRO	0	0.004	-0.001	20.279	-0.166	-0.166	0.000	0.000	0.000	0.000
14	A	18	PHE	0	0.008	-0.008	20.591	-0.334	-0.334	0.000	0.000	0.000	0.000
15	A	19	PHE	0	-0.035	-0.024	21.092	0.305	0.305	0.000	0.000	0.000	0.000
16	A	20	THR	0	0.045	-0.006	23.697	-0.333	-0.333	0.000	0.000	0.000	0.000
17	A	21	LYS	1	0.818	0.877	26.123	10.557	10.557	0.000	0.000	0.000	0.000
18	A	22	ASP	-1	-0.876	-0.894	28.019	-9.589	-9.589	0.000	0.000	0.000	0.000
19	A	23	ASN	0	-0.028	-0.022	27.039	-0.005	-0.005	0.000	0.000	0.000	0.000
20	A	24	VAL	0	-0.008	0.013	22.621	-0.290	-0.290	0.000	0.000	0.000	0.000
21	A	25	PRO	0	-0.017	-0.007	22.461	0.176	0.176	0.000	0.000	0.000	0.000
22	A	26	GLU	-1	-0.884	-0.935	22.606	-11.864	-11.864	0.000	0.000	0.000	0.000
23	A	27	ALA	0	-0.013	-0.019	20.624	-0.404	-0.404	0.000	0.000	0.000	0.000
24	A	28	LEU	0	-0.066	-0.034	17.298	-0.930	-0.930	0.000	0.000	0.000	0.000
25	A	29	LEU	0	0.006	0.003	17.996	-0.833	-0.833	0.000	0.000	0.000	0.000
26	A	30	THR	0	0.026	0.018	19.694	-0.284	-0.284	0.000	0.000	0.000	0.000
27	A	31	HIS	0	-0.006	0.010	15.623	-1.133	-1.133	0.000	0.000	0.000	0.000
28	A	32	HIS	1	0.856	0.923	14.327	19.428	19.428	0.000	0.000	0.000	0.000
29	A	33	ASN	0	0.017	0.025	10.246	-1.653	-1.653	0.000	0.000	0.000	0.000
30	A	34	THR	0	-0.036	-0.028	7.869	1.842	1.842	0.000	0.000	0.000	0.000
31	A	35	ALA	0	0.048	0.006	9.617	-0.955	-0.955	0.000	0.000	0.000	0.000
32	A	36	VAL	0	0.002	-0.010	8.171	-2.351	-2.351	0.000	0.000	0.000	0.000
33	A	37	ASP	-1	-0.864	-0.928	6.385	-41.339	-41.339	0.000	0.000	0.000	0.000
34	A	38	VAL	0	-0.029	-0.029	7.519	2.644	2.644	0.000	0.000	0.000	0.000
35	A	39	PHE	0	0.006	0.017	2.210	-5.693	-4.103	2.856	-1.242	-3.204	-0.006
36	A	40	GLY	0	0.017	-0.002	7.362	3.826	3.826	0.000	0.000	0.000	0.000
37	A	41	GLN	0	-0.002	0.006	9.278	-0.283	-0.283	0.000	0.000	0.000	0.000
38	A	42	ILE	0	0.023	0.021	10.275	1.794	1.794	0.000	0.000	0.000	0.000
39	A	43	CYS	0	-0.037	-0.025	12.879	-0.570	-0.570	0.000	0.000	0.000	0.000
40	A	44	VAL	0	0.006	0.001	15.049	0.506	0.506	0.000	0.000	0.000	0.000
41	A	45	MET	0	-0.053	-0.024	18.229	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	46	GLU	-1	-0.932	-0.977	21.425	-9.909	-9.909	0.000	0.000	0.000	0.000
43	A	47	GLY	0	0.064	0.052	22.805	-0.357	-0.357	0.000	0.000	0.000	0.000
44	A	48	VAL	0	-0.056	-0.046	20.225	-0.418	-0.418	0.000	0.000	0.000	0.000
45	A	49	VAL	0	0.005	0.010	16.967	0.233	0.233	0.000	0.000	0.000	0.000
46	A	50	THR	0	-0.039	-0.028	17.710	-0.338	-0.338	0.000	0.000	0.000	0.000
47	A	51	TYR	0	-0.002	-0.024	10.247	-0.036	-0.036	0.000	0.000	0.000	0.000
48	A	52	TYR	0	-0.059	-0.072	15.361	0.676	0.676	0.000	0.000	0.000	0.000
49	A	53	GLY	0	0.034	0.012	11.871	-0.678	-0.678	0.000	0.000	0.000	0.000
50	A	54	PHE	0	-0.010	-0.020	12.356	1.438	1.438	0.000	0.000	0.000	0.000
51	A	55	ALA	0	0.046	0.029	11.722	-1.463	-1.463	0.000	0.000	0.000	0.000
52	A	56	ASN	0	-0.064	-0.040	11.540	-1.236	-1.236	0.000	0.000	0.000	0.000
53	A	57	SER	0	-0.017	-0.036	13.332	0.082	0.082	0.000	0.000	0.000	0.000
54	A	58	GLU	-1	-0.890	-0.923	15.667	-16.781	-16.781	0.000	0.000	0.000	0.000
55	A	59	ALA	0	-0.042	-0.004	16.106	0.842	0.842	0.000	0.000	0.000	0.000
56	A	60	THR	0	-0.023	-0.046	18.062	-0.435	-0.435	0.000	0.000	0.000	0.000
57	A	61	GLU	-1	-0.893	-0.917	20.495	-13.074	-13.074	0.000	0.000	0.000	0.000
58	A	62	PRO	0	-0.064	-0.029	16.613	-0.785	-0.785	0.000	0.000	0.000	0.000
59	A	63	GLU	-1	-0.850	-0.902	10.329	-25.798	-25.798	0.000	0.000	0.000	0.000
60	A	64	ILE	0	-0.054	-0.020	10.368	0.163	0.163	0.000	0.000	0.000	0.000
61	A	65	LYS	1	0.920	0.964	13.901	14.084	14.084	0.000	0.000	0.000	0.000
62	A	66	VAL	0	-0.030	-0.012	12.312	0.192	0.192	0.000	0.000	0.000	0.000
63	A	67	VAL	0	-0.015	0.000	15.768	0.258	0.258	0.000	0.000	0.000	0.000
64	A	68	ILE	0	-0.024	0.000	13.095	-0.501	-0.501	0.000	0.000	0.000	0.000
65	A	69	ASN	0	0.005	-0.018	16.369	0.934	0.934	0.000	0.000	0.000	0.000
66	A	70	ALA	0	0.053	0.027	18.334	-0.522	-0.522	0.000	0.000	0.000	0.000
67	A	71	GLY	0	-0.011	0.002	19.008	0.173	0.173	0.000	0.000	0.000	0.000
68	A	72	GLN	0	-0.022	0.008	14.635	-0.446	-0.446	0.000	0.000	0.000	0.000
69	A	73	PHE	0	0.000	-0.011	8.127	0.115	0.115	0.000	0.000	0.000	0.000
70	A	74	ALA	0	0.009	0.017	9.063	-0.378	-0.378	0.000	0.000	0.000	0.000
71	A	75	THR	0	-0.025	-0.032	5.203	1.645	1.645	0.000	0.000	0.000	0.000
72	A	76	SER	0	0.041	0.034	5.888	-3.384	-3.384	0.000	0.000	0.000	0.000
73	A	77	PRO	0	-0.015	-0.017	2.532	-3.776	-2.648	0.194	-0.383	-0.939	-0.003
74	A	78	PRO	0	-0.007	0.006	2.494	3.429	4.270	0.307	-0.330	-0.818	-0.003
75	A	79	GLN	0	-0.049	-0.014	4.997	-1.201	-1.139	-0.001	0.000	-0.060	0.000
76	A	80	TYR	0	-0.074	-0.053	5.968	1.687	1.687	0.000	0.000	0.000	0.000
77	A	81	TRP	0	0.040	0.024	7.757	2.625	2.625	0.000	0.000	0.000	0.000
78	A	82	HIS	0	-0.058	-0.031	10.651	0.377	0.377	0.000	0.000	0.000	0.000
79	A	83	ARG	1	0.846	0.920	13.398	15.227	15.227	0.000	0.000	0.000	0.000
80	A	84	ILE	0	-0.038	-0.019	15.712	-0.569	-0.569	0.000	0.000	0.000	0.000
81	A	85	GLU	-1	-0.767	-0.826	18.416	-12.555	-12.555	0.000	0.000	0.000	0.000
82	A	86	LEU	0	0.011	0.004	20.785	-0.400	-0.400	0.000	0.000	0.000	0.000
83	A	87	SER	0	-0.012	-0.034	23.228	0.240	0.240	0.000	0.000	0.000	0.000
84	A	88	ASP	-1	-0.855	-0.938	25.678	-10.025	-10.025	0.000	0.000	0.000	0.000
85	A	89	ASP	-1	-0.815	-0.872	27.017	-10.584	-10.584	0.000	0.000	0.000	0.000
86	A	90	ALA	0	-0.051	-0.012	22.468	-0.208	-0.208	0.000	0.000	0.000	0.000
87	A	91	GLN	0	0.009	0.018	23.528	0.375	0.375	0.000	0.000	0.000	0.000
88	A	92	PHE	0	-0.015	-0.020	17.618	-0.469	-0.469	0.000	0.000	0.000	0.000
89	A	93	ASN	0	-0.001	-0.027	17.013	0.086	0.086	0.000	0.000	0.000	0.000
90	A	94	ILE	0	0.004	0.006	13.503	-0.735	-0.735	0.000	0.000	0.000	0.000
91	A	95	ASN	0	0.024	0.042	13.012	1.612	1.612	0.000	0.000	0.000	0.000
92	A	96	PHE	0	0.018	-0.008	11.780	-1.672	-1.672	0.000	0.000	0.000	0.000
93	A	97	TRP	0	-0.032	-0.024	8.608	1.036	1.036	0.000	0.000	0.000	0.000
94	A	98	SER	0	0.020	-0.018	9.494	-2.563	-2.563	0.000	0.000	0.000	0.000
95	A	99	ASP	-1	-0.824	-0.902	9.736	-25.380	-25.380	0.000	0.000	0.000	0.000
96	A	100	GLN	0	-0.019	0.010	11.409	2.056	2.056	0.000	0.000	0.000	0.000

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