FMO DATABASE

FMODB ID: M3Q8Z

Calculation Name: 3S63-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3S63

Chain ID: A

ChEMBL ID:

UniProt ID: H2L2M0

Base Structure: X-ray

Registration Date: 2023-06-20

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	85
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-675823.501332
FMO2-HF: Nuclear repulsion	637675.29394
FMO2-HF: Total energy	-38148.207392
FMO2-MP2: Total energy	-38252.864744

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:1:LEU)

Summations of interaction energy for fragment #1(A: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.
-21.398	-9.55	10.118	-7.578	-14.39	-0.044

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.020 / q_NPA : -0.007

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	A	3	PRO	0	0.064	0.010	3.014	-2.968	0.012	0.180	-1.595	-1.566	0.002
4	A	4	LYS	1	0.985	0.995	5.603	1.446	1.446	0.000	0.000	0.000	0.000
5	A	5	GLU	-1	-0.840	-0.930	2.304	-9.368	-6.012	5.010	-3.491	-4.876	-0.040
6	A	6	THR	0	-0.035	-0.023	2.388	-0.621	1.536	1.785	-1.404	-2.538	-0.011
7	A	7	CYS	0	-0.025	0.040	3.588	0.637	0.826	0.019	0.030	-0.238	0.000
8	A	8	ASP	-1	-0.840	-0.942	6.499	-0.443	-0.443	0.000	0.000	0.000	0.000
9	A	9	LEU	0	-0.028	-0.040	2.619	-0.206	0.436	0.828	-0.203	-1.267	0.001
10	A	10	CYS	0	-0.076	-0.031	6.145	0.274	0.274	0.000	0.000	0.000	0.000
11	A	11	GLN	0	0.026	-0.003	7.964	0.105	0.105	0.000	0.000	0.000	0.000
12	A	12	ILE	0	-0.019	-0.017	8.069	0.037	0.037	0.000	0.000	0.000	0.000
13	A	13	ALA	0	-0.009	0.004	9.099	0.005	0.005	0.000	0.000	0.000	0.000
14	A	14	LEU	0	0.020	-0.005	10.992	-0.033	-0.033	0.000	0.000	0.000	0.000
15	A	15	ARG	1	0.980	1.000	13.577	-0.142	-0.142	0.000	0.000	0.000	0.000
16	A	16	THR	0	-0.036	-0.014	13.703	-0.047	-0.047	0.000	0.000	0.000	0.000
17	A	17	VAL	0	-0.009	-0.009	14.630	-0.016	-0.016	0.000	0.000	0.000	0.000
18	A	18	PHE	0	0.003	-0.005	17.051	-0.021	-0.021	0.000	0.000	0.000	0.000
19	A	19	GLY	0	0.025	0.006	18.893	-0.023	-0.023	0.000	0.000	0.000	0.000
20	A	20	HIS	0	-0.054	-0.016	19.421	-0.010	-0.010	0.000	0.000	0.000	0.000
21	A	21	PHE	0	-0.080	-0.045	19.909	0.000	0.000	0.000	0.000	0.000	0.000
22	A	22	GLY	0	0.037	0.023	23.486	-0.016	-0.016	0.000	0.000	0.000	0.000
23	A	23	GLY	0	-0.009	0.002	23.648	-0.016	-0.016	0.000	0.000	0.000	0.000
24	A	24	ASN	0	-0.036	-0.002	24.861	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	25	ILE	0	0.007	-0.008	22.030	0.019	0.019	0.000	0.000	0.000	0.000
26	A	26	PRO	0	-0.003	0.013	24.633	-0.007	-0.007	0.000	0.000	0.000	0.000
27	A	27	SER	0	0.080	0.013	25.476	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	28	ARG	1	1.003	1.016	21.150	-0.200	-0.200	0.000	0.000	0.000	0.000
29	A	29	ARG	1	0.919	0.965	20.917	-0.256	-0.256	0.000	0.000	0.000	0.000
30	A	30	LYS	1	1.010	1.010	22.197	-0.223	-0.223	0.000	0.000	0.000	0.000
31	A	31	LEU	0	0.041	0.019	18.231	0.029	0.029	0.000	0.000	0.000	0.000
32	A	32	VAL	0	-0.002	-0.007	17.392	0.047	0.047	0.000	0.000	0.000	0.000
33	A	33	HIS	0	-0.052	-0.032	17.236	0.059	0.059	0.000	0.000	0.000	0.000
34	A	34	GLN	0	0.016	0.012	17.786	0.057	0.057	0.000	0.000	0.000	0.000
35	A	35	LEU	0	0.050	0.033	13.854	0.061	0.061	0.000	0.000	0.000	0.000
36	A	36	LYS	1	0.930	0.951	12.855	-0.405	-0.405	0.000	0.000	0.000	0.000
37	A	37	HIS	0	-0.023	-0.010	13.088	0.102	0.102	0.000	0.000	0.000	0.000
38	A	38	GLU	-1	-0.763	-0.866	11.239	0.763	0.763	0.000	0.000	0.000	0.000
39	A	39	CYS	0	-0.002	0.013	5.813	-0.575	-0.575	0.000	0.000	0.000	0.000
40	A	40	LYS	1	0.841	0.911	8.548	-0.450	-0.450	0.000	0.000	0.000	0.000
41	A	41	ARG	1	0.909	0.965	10.888	-0.667	-0.667	0.000	0.000	0.000	0.000
42	A	42	HIS	0	-0.025	-0.007	5.548	0.058	0.058	0.000	0.000	0.000	0.000
43	A	43	PHE	0	0.019	0.009	6.523	0.467	0.467	0.000	0.000	0.000	0.000
44	A	44	ASN	0	0.039	0.004	2.773	-1.167	-0.465	0.289	-0.192	-0.799	0.001
45	A	45	TYR	0	0.068	0.040	2.276	-0.675	0.863	1.963	-0.987	-2.514	0.003
46	A	46	ARG	1	0.976	1.003	3.330	-1.870	-2.054	0.017	0.347	-0.180	0.000
47	A	47	ARG	1	0.963	0.956	6.717	-1.698	-1.698	0.000	0.000	0.000	0.000
48	A	48	ARG	1	0.843	0.876	3.249	-1.622	-1.154	0.027	-0.083	-0.412	0.000
49	A	50	LEU	0	-0.047	-0.035	7.347	-0.415	-0.415	0.000	0.000	0.000	0.000
50	A	51	LEU	0	-0.045	-0.025	9.506	-0.215	-0.215	0.000	0.000	0.000	0.000
51	A	52	LEU	0	0.061	0.041	7.861	-0.157	-0.157	0.000	0.000	0.000	0.000
52	A	53	MET	0	0.028	0.013	9.693	-0.187	-0.187	0.000	0.000	0.000	0.000
53	A	54	LYS	1	0.859	0.935	13.325	-0.523	-0.523	0.000	0.000	0.000	0.000
54	A	55	VAL	0	-0.047	-0.030	13.991	-0.052	-0.052	0.000	0.000	0.000	0.000
55	A	56	ASN	0	0.051	0.038	13.155	-0.095	-0.095	0.000	0.000	0.000	0.000
56	A	57	SER	0	-0.017	-0.005	16.335	-0.037	-0.037	0.000	0.000	0.000	0.000
57	A	58	ASP	-1	-0.913	-0.952	17.983	0.171	0.171	0.000	0.000	0.000	0.000
58	A	59	LEU	0	0.059	0.026	16.430	-0.015	-0.015	0.000	0.000	0.000	0.000
59	A	60	ILE	0	-0.005	-0.018	13.787	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	61	PHE	0	-0.029	-0.033	17.930	-0.006	-0.006	0.000	0.000	0.000	0.000
61	A	62	ARG	1	0.898	0.954	21.205	-0.072	-0.072	0.000	0.000	0.000	0.000
62	A	63	GLU	-1	-0.810	-0.908	19.389	0.038	0.038	0.000	0.000	0.000	0.000
63	A	64	MET	0	-0.105	-0.042	16.643	0.000	0.000	0.000	0.000	0.000	0.000
64	A	65	THR	0	-0.080	-0.054	21.469	-0.010	-0.010	0.000	0.000	0.000	0.000
65	A	66	ASP	-1	-0.849	-0.904	24.746	0.055	0.055	0.000	0.000	0.000	0.000
66	A	67	GLY	0	-0.049	-0.014	25.203	-0.010	-0.010	0.000	0.000	0.000	0.000
67	A	68	SER	0	-0.054	-0.034	23.268	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	69	PHE	0	-0.007	-0.016	16.044	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	70	LYS	1	1.006	1.015	19.198	0.016	0.016	0.000	0.000	0.000	0.000
70	A	71	PRO	0	-0.001	0.000	14.083	-0.008	-0.008	0.000	0.000	0.000	0.000
71	A	72	MET	0	0.046	-0.011	12.776	0.008	0.008	0.000	0.000	0.000	0.000
72	A	73	GLU	-1	-0.897	-0.938	14.659	-0.133	-0.133	0.000	0.000	0.000	0.000
73	A	74	VAL	0	0.024	0.009	14.420	-0.002	-0.002	0.000	0.000	0.000	0.000
74	A	76	LEU	0	0.008	0.018	12.046	-0.053	-0.053	0.000	0.000	0.000	0.000
75	A	77	ILE	0	-0.023	-0.001	14.534	-0.016	-0.016	0.000	0.000	0.000	0.000
76	A	78	MET	0	-0.081	-0.036	11.212	0.043	0.043	0.000	0.000	0.000	0.000
77	A	79	ARG	1	0.875	0.939	12.411	0.400	0.400	0.000	0.000	0.000	0.000
78	A	80	GLU	-1	-0.797	-0.855	6.406	0.322	0.322	0.000	0.000	0.000	0.000
79	A	82	ASN	0	0.003	0.001	10.927	0.179	0.179	0.000	0.000	0.000	0.000
80	A	83	PRO	0	0.038	-0.007	13.458	-0.024	-0.024	0.000	0.000	0.000	0.000
81	A	84	HIS	0	-0.060	-0.020	12.030	0.065	0.065	0.000	0.000	0.000	0.000
82	A	85	ASP	-1	-0.873	-0.922	10.472	-1.131	-1.131	0.000	0.000	0.000	0.000
83	A	86	SER	0	0.027	-0.001	12.710	0.085	0.085	0.000	0.000	0.000	0.000
84	A	87	PRO	0	0.005	-0.003	13.057	-0.030	-0.030	0.000	0.000	0.000	0.000
85	A	88	LEU	0	-0.033	0.004	10.981	0.007	0.007	0.000	0.000	0.000	0.000

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