FMO DATABASE

FMODB ID: 39MNL

Calculation Name: 4DS1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4DS1

Chain ID: A

ChEMBL ID:

UniProt ID: Q02647

Base Structure: X-ray

Registration Date: 2023-06-22

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	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	86
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-605682.353023
FMO2-HF: Nuclear repulsion	572564.091433
FMO2-HF: Total energy	-33118.26159
FMO2-MP2: Total energy	-33218.312373

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:7:SER)

Summations of interaction energy for fragment #1(A:7:SER)

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.
-3.29	-0.68	0.304	-1.102	-1.813	0.001

Interaction energy analysis for fragmet #1(A:7:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.017 / q_NPA : -0.001

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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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	9	PRO	0	-0.002	-0.011	3.857	1.159	2.466	-0.009	-0.543	-0.754	0.002
4	A	10	ILE	0	-0.011	0.000	6.252	0.025	0.025	0.000	0.000	0.000	0.000
5	A	11	VAL	0	0.010	-0.013	8.772	-0.218	-0.218	0.000	0.000	0.000	0.000
6	A	12	LYS	1	0.861	0.952	10.650	-1.376	-1.376	0.000	0.000	0.000	0.000
7	A	13	ALA	0	0.028	0.015	14.822	-0.064	-0.064	0.000	0.000	0.000	0.000
8	A	14	SER	0	-0.002	-0.010	16.924	0.018	0.018	0.000	0.000	0.000	0.000
9	A	15	ASP	-1	-0.808	-0.886	19.147	0.160	0.160	0.000	0.000	0.000	0.000
10	A	16	ILE	0	-0.067	-0.015	17.637	-0.024	-0.024	0.000	0.000	0.000	0.000
11	A	17	THR	0	0.052	0.024	21.351	0.012	0.012	0.000	0.000	0.000	0.000
12	A	18	ASP	-1	-0.786	-0.897	18.160	0.281	0.281	0.000	0.000	0.000	0.000
13	A	19	LYS	1	0.970	0.983	17.637	-0.015	-0.015	0.000	0.000	0.000	0.000
14	A	20	LEU	0	-0.012	0.008	18.711	-0.030	-0.030	0.000	0.000	0.000	0.000
15	A	21	LYS	1	0.831	0.899	14.213	-0.407	-0.407	0.000	0.000	0.000	0.000
16	A	22	GLU	-1	-0.791	-0.902	12.573	0.319	0.319	0.000	0.000	0.000	0.000
17	A	23	ASP	-1	-0.797	-0.837	13.180	-0.201	-0.201	0.000	0.000	0.000	0.000
18	A	24	ILE	0	0.030	0.012	13.289	-0.064	-0.064	0.000	0.000	0.000	0.000
19	A	25	LEU	0	-0.034	-0.004	9.197	-0.039	-0.039	0.000	0.000	0.000	0.000
20	A	26	THR	0	-0.026	-0.025	9.410	-0.215	-0.215	0.000	0.000	0.000	0.000
21	A	27	ILE	0	-0.009	-0.008	10.675	-0.152	-0.152	0.000	0.000	0.000	0.000
22	A	28	SER	0	-0.019	-0.032	9.743	-0.019	-0.019	0.000	0.000	0.000	0.000
23	A	29	LYS	1	0.912	0.958	4.095	1.676	1.827	-0.001	-0.020	-0.130	0.000
24	A	30	ASP	-1	-0.801	-0.873	7.909	-0.708	-0.708	0.000	0.000	0.000	0.000
25	A	31	ALA	0	-0.010	-0.008	10.826	0.015	0.015	0.000	0.000	0.000	0.000
26	A	32	LEU	0	-0.010	-0.026	5.403	0.075	0.075	0.000	0.000	0.000	0.000
27	A	33	ASP	-1	-0.949	-0.954	7.539	-1.930	-1.930	0.000	0.000	0.000	0.000
28	A	34	LYS	1	0.760	0.865	9.877	0.709	0.709	0.000	0.000	0.000	0.000
29	A	35	TYR	0	-0.034	-0.014	12.946	0.110	0.110	0.000	0.000	0.000	0.000
30	A	36	GLN	0	0.026	0.009	13.117	-0.093	-0.093	0.000	0.000	0.000	0.000
31	A	37	LEU	0	-0.011	0.001	14.695	0.052	0.052	0.000	0.000	0.000	0.000
32	A	38	GLU	-1	-0.786	-0.892	12.718	-0.029	-0.029	0.000	0.000	0.000	0.000
33	A	39	ARG	1	0.857	0.892	14.725	0.168	0.168	0.000	0.000	0.000	0.000
34	A	40	ASP	-1	-0.808	-0.871	17.168	-0.184	-0.184	0.000	0.000	0.000	0.000
35	A	41	ILE	0	0.020	0.023	10.423	0.007	0.007	0.000	0.000	0.000	0.000
36	A	42	ALA	0	0.011	-0.005	14.196	0.014	0.014	0.000	0.000	0.000	0.000
37	A	43	GLY	0	-0.007	-0.010	16.179	0.013	0.013	0.000	0.000	0.000	0.000
38	A	44	THR	0	-0.032	-0.021	15.509	0.025	0.025	0.000	0.000	0.000	0.000
39	A	45	VAL	0	0.040	0.025	13.241	0.013	0.013	0.000	0.000	0.000	0.000
40	A	46	LYS	1	0.782	0.857	16.505	0.053	0.053	0.000	0.000	0.000	0.000
41	A	47	LYS	1	0.954	0.973	19.817	0.152	0.152	0.000	0.000	0.000	0.000
42	A	48	GLN	0	0.013	0.004	16.245	0.013	0.013	0.000	0.000	0.000	0.000
43	A	49	LEU	0	-0.002	-0.001	16.864	0.014	0.014	0.000	0.000	0.000	0.000
44	A	50	ASP	-1	-0.771	-0.876	20.921	-0.018	-0.018	0.000	0.000	0.000	0.000
45	A	51	VAL	0	-0.047	-0.020	24.056	0.008	0.008	0.000	0.000	0.000	0.000
46	A	52	LYS	1	0.814	0.915	18.575	0.133	0.133	0.000	0.000	0.000	0.000
47	A	53	TYR	0	-0.095	-0.087	19.719	0.016	0.016	0.000	0.000	0.000	0.000
48	A	54	GLY	0	0.040	0.039	25.113	0.014	0.014	0.000	0.000	0.000	0.000
49	A	55	ASN	0	-0.006	0.000	26.213	0.003	0.003	0.000	0.000	0.000	0.000
50	A	56	THR	0	-0.061	-0.057	26.533	0.001	0.001	0.000	0.000	0.000	0.000
51	A	57	TRP	0	0.026	0.002	19.577	0.025	0.025	0.000	0.000	0.000	0.000
52	A	58	HIS	0	-0.022	-0.010	21.749	-0.020	-0.020	0.000	0.000	0.000	0.000
53	A	59	VAL	0	-0.017	-0.008	15.734	0.020	0.020	0.000	0.000	0.000	0.000
54	A	60	ILE	0	-0.013	0.005	17.020	-0.022	-0.022	0.000	0.000	0.000	0.000
55	A	61	VAL	0	0.002	-0.002	11.399	0.041	0.041	0.000	0.000	0.000	0.000
56	A	62	GLY	0	0.047	0.029	12.828	-0.052	-0.052	0.000	0.000	0.000	0.000
57	A	63	LYS	1	0.887	0.914	11.172	0.120	0.120	0.000	0.000	0.000	0.000
58	A	64	ASN	0	-0.059	-0.028	13.543	0.043	0.043	0.000	0.000	0.000	0.000
59	A	65	PHE	0	0.014	0.016	14.495	-0.045	-0.045	0.000	0.000	0.000	0.000
60	A	66	GLY	0	0.040	0.027	18.953	0.045	0.045	0.000	0.000	0.000	0.000
61	A	67	SER	0	-0.035	-0.031	21.144	-0.032	-0.032	0.000	0.000	0.000	0.000
62	A	68	TYR	0	0.026	0.017	22.822	0.019	0.019	0.000	0.000	0.000	0.000
63	A	69	VAL	0	-0.017	0.004	22.347	-0.018	-0.018	0.000	0.000	0.000	0.000
64	A	70	THR	0	0.019	0.016	25.620	0.011	0.011	0.000	0.000	0.000	0.000
65	A	71	HIS	1	0.832	0.902	24.212	-0.169	-0.169	0.000	0.000	0.000	0.000
66	A	72	GLU	-1	-0.828	-0.914	26.236	0.055	0.055	0.000	0.000	0.000	0.000
67	A	73	LYS	1	0.919	0.959	25.727	-0.134	-0.134	0.000	0.000	0.000	0.000
68	A	74	GLY	0	-0.023	-0.012	24.260	-0.014	-0.014	0.000	0.000	0.000	0.000
69	A	75	HIS	1	0.861	0.924	21.935	-0.083	-0.083	0.000	0.000	0.000	0.000
70	A	76	PHE	0	0.025	0.003	19.162	-0.013	-0.013	0.000	0.000	0.000	0.000
71	A	77	VAL	0	0.018	0.008	14.099	0.025	0.025	0.000	0.000	0.000	0.000
72	A	78	TYR	0	0.029	0.018	14.722	-0.021	-0.021	0.000	0.000	0.000	0.000
73	A	79	PHE	0	0.002	-0.010	8.637	0.072	0.072	0.000	0.000	0.000	0.000
74	A	80	TYR	0	0.037	0.022	7.514	-0.208	-0.208	0.000	0.000	0.000	0.000
75	A	81	ILE	0	0.004	0.005	2.774	-0.218	0.177	0.269	-0.238	-0.426	-0.001
76	A	82	GLY	0	0.037	0.026	3.621	-1.266	-0.606	0.039	-0.237	-0.463	0.000
77	A	83	PRO	0	-0.015	-0.017	4.008	-0.698	-0.601	0.006	-0.064	-0.040	0.000
78	A	84	LEU	0	-0.046	0.000	6.853	-0.275	-0.275	0.000	0.000	0.000	0.000
79	A	85	ALA	0	0.023	0.016	8.085	0.243	0.243	0.000	0.000	0.000	0.000
80	A	86	PHE	0	0.053	-0.003	7.479	-0.209	-0.209	0.000	0.000	0.000	0.000
81	A	87	LEU	0	-0.016	0.001	12.230	0.089	0.089	0.000	0.000	0.000	0.000
82	A	88	VAL	0	0.006	0.006	14.454	-0.057	-0.057	0.000	0.000	0.000	0.000
83	A	89	PHE	0	0.001	-0.011	17.174	0.032	0.032	0.000	0.000	0.000	0.000
84	A	90	LYS	1	0.846	0.935	20.791	-0.054	-0.054	0.000	0.000	0.000	0.000
85	A	91	THR	0	0.030	0.024	24.086	0.015	0.015	0.000	0.000	0.000	0.000
86	A	92	ALA	0	0.072	0.065	27.826	-0.009	-0.009	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:SER)