FMO DATABASE

FMODB ID: R81L8

Calculation Name: 3M8F-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3M8F

Chain ID: A

ChEMBL ID:

UniProt ID: Q8KNP2

Base Structure: X-ray

Registration Date: 2023-09-20

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	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. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-687720.294397
FMO2-HF: Nuclear repulsion	648395.021646
FMO2-HF: Total energy	-39325.272751
FMO2-MP2: Total energy	-39435.887269

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:HIS)

Summations of interaction energy for fragment #1(A:5:HIS)

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.
-2.655	0.567	0.072	-1.543	-1.75	0.004

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.007 / q_NPA : 0.005

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	TYR	0	-0.009	-0.007	3.692	-0.633	2.589	0.072	-1.543	-1.750	0.004
4	A	8	THR	0	-0.013	-0.005	5.511	-0.119	-0.119	0.000	0.000	0.000	0.000
5	A	9	LEU	0	0.032	0.012	9.214	-0.114	-0.114	0.000	0.000	0.000	0.000
6	A	10	ASN	0	0.040	0.018	11.613	0.122	0.122	0.000	0.000	0.000	0.000
7	A	11	ILE	0	0.038	0.015	15.072	-0.046	-0.046	0.000	0.000	0.000	0.000
8	A	12	ALA	0	0.076	0.037	16.481	-0.005	-0.005	0.000	0.000	0.000	0.000
9	A	13	GLU	-1	-0.857	-0.910	17.432	-0.676	-0.676	0.000	0.000	0.000	0.000
10	A	14	ILE	0	-0.024	-0.013	13.319	-0.015	-0.015	0.000	0.000	0.000	0.000
11	A	15	ALA	0	0.043	0.022	17.918	0.020	0.020	0.000	0.000	0.000	0.000
12	A	16	GLU	-1	-0.826	-0.893	21.262	-0.324	-0.324	0.000	0.000	0.000	0.000
13	A	17	ARG	1	0.760	0.866	17.646	0.755	0.755	0.000	0.000	0.000	0.000
14	A	18	ILE	0	0.012	0.001	18.857	0.020	0.020	0.000	0.000	0.000	0.000
15	A	19	GLY	0	0.013	0.006	22.588	0.028	0.028	0.000	0.000	0.000	0.000
16	A	20	ASN	0	-0.120	-0.060	24.979	0.047	0.047	0.000	0.000	0.000	0.000
17	A	21	ASP	-1	-0.881	-0.932	24.535	-0.423	-0.423	0.000	0.000	0.000	0.000
18	A	22	ASP	-1	-0.872	-0.945	26.480	-0.270	-0.270	0.000	0.000	0.000	0.000
19	A	23	CYS	0	-0.021	0.003	26.854	0.019	0.019	0.000	0.000	0.000	0.000
20	A	24	ALA	0	-0.026	-0.028	22.879	0.000	0.000	0.000	0.000	0.000	0.000
21	A	25	TYR	0	0.016	0.013	24.935	0.003	0.003	0.000	0.000	0.000	0.000
22	A	26	GLN	0	-0.026	-0.025	26.734	0.025	0.025	0.000	0.000	0.000	0.000
23	A	27	VAL	0	-0.030	-0.033	24.425	0.013	0.013	0.000	0.000	0.000	0.000
24	A	28	LEU	0	-0.033	-0.007	21.957	-0.006	-0.006	0.000	0.000	0.000	0.000
25	A	29	MET	0	0.001	-0.001	25.188	0.007	0.007	0.000	0.000	0.000	0.000
26	A	30	ALA	0	0.024	0.022	28.598	0.019	0.019	0.000	0.000	0.000	0.000
27	A	31	PHE	0	-0.071	-0.033	24.818	0.014	0.014	0.000	0.000	0.000	0.000
28	A	32	ILE	0	-0.008	0.002	26.426	0.000	0.000	0.000	0.000	0.000	0.000
29	A	33	ASN	0	-0.026	-0.017	29.799	0.003	0.003	0.000	0.000	0.000	0.000
30	A	34	GLU	-1	-0.918	-0.976	33.198	-0.141	-0.141	0.000	0.000	0.000	0.000
31	A	35	ASN	0	-0.118	-0.058	34.501	0.009	0.009	0.000	0.000	0.000	0.000
32	A	36	GLY	0	-0.019	-0.005	32.126	0.005	0.005	0.000	0.000	0.000	0.000
33	A	37	GLU	-1	-0.884	-0.914	29.622	-0.142	-0.142	0.000	0.000	0.000	0.000
34	A	38	ALA	0	0.013	0.004	25.244	-0.009	-0.009	0.000	0.000	0.000	0.000
35	A	39	GLN	0	-0.055	-0.032	27.297	0.031	0.031	0.000	0.000	0.000	0.000
36	A	40	MET	0	-0.038	-0.017	26.702	-0.017	-0.017	0.000	0.000	0.000	0.000
37	A	41	LEU	0	0.016	0.014	27.199	0.016	0.016	0.000	0.000	0.000	0.000
38	A	42	ASN	0	-0.006	-0.017	27.375	-0.011	-0.011	0.000	0.000	0.000	0.000
39	A	43	LYS	1	0.852	0.910	23.089	0.365	0.365	0.000	0.000	0.000	0.000
40	A	44	THR	0	-0.048	-0.028	28.591	-0.006	-0.006	0.000	0.000	0.000	0.000
41	A	45	ALA	0	0.107	0.057	31.920	0.000	0.000	0.000	0.000	0.000	0.000
42	A	46	VAL	0	0.053	0.026	27.326	0.004	0.004	0.000	0.000	0.000	0.000
43	A	47	ALA	0	-0.043	-0.030	30.654	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	48	GLU	-1	-0.858	-0.917	32.558	-0.176	-0.176	0.000	0.000	0.000	0.000
45	A	49	MET	0	-0.040	-0.018	32.838	0.007	0.007	0.000	0.000	0.000	0.000
46	A	50	ILE	0	0.008	0.028	29.814	0.000	0.000	0.000	0.000	0.000	0.000
47	A	51	GLN	0	-0.016	0.007	34.127	0.006	0.006	0.000	0.000	0.000	0.000
48	A	52	LEU	0	0.032	0.011	31.008	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	53	SER	0	-0.053	-0.037	32.415	0.008	0.008	0.000	0.000	0.000	0.000
50	A	54	LYS	1	0.900	0.932	32.049	0.188	0.188	0.000	0.000	0.000	0.000
51	A	55	PRO	0	-0.010	-0.012	30.517	-0.014	-0.014	0.000	0.000	0.000	0.000
52	A	56	THR	0	0.037	0.034	28.348	-0.016	-0.016	0.000	0.000	0.000	0.000
53	A	57	VAL	0	0.059	0.055	27.207	-0.031	-0.031	0.000	0.000	0.000	0.000
54	A	58	PHE	0	-0.029	-0.026	26.529	-0.019	-0.019	0.000	0.000	0.000	0.000
55	A	59	ALA	0	-0.035	-0.016	24.253	-0.024	-0.024	0.000	0.000	0.000	0.000
56	A	60	THR	0	0.027	0.004	22.627	-0.047	-0.047	0.000	0.000	0.000	0.000
57	A	61	VAL	0	0.009	0.011	21.880	-0.040	-0.040	0.000	0.000	0.000	0.000
58	A	62	ASN	0	-0.006	-0.012	20.814	-0.017	-0.017	0.000	0.000	0.000	0.000
59	A	63	TRP	0	0.044	0.023	17.560	-0.035	-0.035	0.000	0.000	0.000	0.000
60	A	64	PHE	0	0.029	0.007	17.010	-0.097	-0.097	0.000	0.000	0.000	0.000
61	A	65	TYR	0	-0.033	-0.008	17.061	-0.051	-0.051	0.000	0.000	0.000	0.000
62	A	66	CYS	0	-0.091	-0.050	14.284	-0.043	-0.043	0.000	0.000	0.000	0.000
63	A	67	ALA	0	-0.044	-0.017	12.559	-0.168	-0.168	0.000	0.000	0.000	0.000
64	A	68	GLY	0	0.029	0.024	13.169	-0.073	-0.073	0.000	0.000	0.000	0.000
65	A	69	TYR	0	-0.014	-0.006	14.107	0.076	0.076	0.000	0.000	0.000	0.000
66	A	70	ILE	0	-0.031	-0.012	17.405	0.078	0.078	0.000	0.000	0.000	0.000
67	A	71	ASP	-1	-0.831	-0.907	15.713	-0.573	-0.573	0.000	0.000	0.000	0.000
68	A	72	GLU	-1	-0.817	-0.891	18.234	-0.292	-0.292	0.000	0.000	0.000	0.000
69	A	73	THR	0	-0.031	-0.015	19.789	0.021	0.021	0.000	0.000	0.000	0.000
70	A	74	ARG	1	0.866	0.905	22.162	0.265	0.265	0.000	0.000	0.000	0.000
71	A	75	VAL	0	0.044	0.024	24.973	0.018	0.018	0.000	0.000	0.000	0.000
72	A	76	GLY	0	0.030	0.019	28.389	0.000	0.000	0.000	0.000	0.000	0.000
73	A	77	ARG	1	0.866	0.919	31.165	0.108	0.108	0.000	0.000	0.000	0.000
74	A	78	SER	0	-0.035	-0.003	29.681	-0.008	-0.008	0.000	0.000	0.000	0.000
75	A	79	LYN	0	0.018	0.032	24.158	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	80	ILE	0	-0.030	-0.011	25.349	-0.003	-0.003	0.000	0.000	0.000	0.000
77	A	81	TYR	0	0.019	-0.035	20.685	-0.006	-0.006	0.000	0.000	0.000	0.000
78	A	82	THR	0	0.045	0.019	21.012	0.040	0.040	0.000	0.000	0.000	0.000
79	A	83	LEU	0	-0.024	0.000	20.901	-0.039	-0.039	0.000	0.000	0.000	0.000
80	A	84	SER	0	0.039	0.029	15.775	0.046	0.046	0.000	0.000	0.000	0.000
81	A	85	ASP	-1	-0.893	-0.960	15.373	-0.358	-0.358	0.000	0.000	0.000	0.000
82	A	86	LEU	0	-0.029	-0.007	13.038	0.009	0.009	0.000	0.000	0.000	0.000
83	A	87	GLY	0	0.039	0.008	16.577	0.004	0.004	0.000	0.000	0.000	0.000
84	A	88	VAL	0	-0.020	-0.017	19.740	0.029	0.029	0.000	0.000	0.000	0.000
85	A	89	GLU	-1	-0.894	-0.947	17.657	-0.325	-0.325	0.000	0.000	0.000	0.000
86	A	90	ILE	0	-0.040	-0.016	17.435	0.017	0.017	0.000	0.000	0.000	0.000
87	A	91	VAL	0	0.028	0.005	21.231	0.025	0.025	0.000	0.000	0.000	0.000
88	A	92	GLU	-1	-0.790	-0.871	23.458	-0.181	-0.181	0.000	0.000	0.000	0.000
89	A	93	CYS	0	-0.044	-0.016	21.636	0.014	0.014	0.000	0.000	0.000	0.000
90	A	94	PHE	0	-0.010	-0.015	23.706	0.017	0.017	0.000	0.000	0.000	0.000
91	A	95	LYS	1	0.821	0.894	27.192	0.208	0.208	0.000	0.000	0.000	0.000
92	A	96	GLN	0	-0.057	-0.036	25.279	0.018	0.018	0.000	0.000	0.000	0.000
93	A	97	LYS	1	0.859	0.903	24.165	0.354	0.354	0.000	0.000	0.000	0.000
94	A	98	ALA	0	-0.046	-0.004	29.749	0.007	0.007	0.000	0.000	0.000	0.000
95	A	99	MET	0	-0.086	-0.034	32.394	0.015	0.015	0.000	0.000	0.000	0.000
96	A	100	GLU	-1	-1.027	-1.002	30.039	-0.161	-0.161	0.000	0.000	0.000	0.000

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