FMO DATABASE

FMODB ID: R82M8

Calculation Name: 3M8J-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3M8J

Chain ID: A

ChEMBL ID:

UniProt ID: Q93K76

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	90
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-601991.100439
FMO2-HF: Nuclear repulsion	566402.994851
FMO2-HF: Total energy	-35588.105588
FMO2-MP2: Total energy	-35690.74325

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:10:GLY)

Summations of interaction energy for fragment #1(A:10:GLY)

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.
1.282	3.116	0.005	-0.717	-1.121	0

Interaction energy analysis for fragmet #1(A:10:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.054 / q_NPA : 0.014

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].
3	A	12	ASP	-1	-0.881	-0.935	3.647	-1.657	-0.223	0.001	-0.607	-0.828
4	A	13	ALA	0	0.060	0.015	3.698	-0.109	0.132	0.005	-0.051	-0.195
5	A	14	PHE	0	-0.047	-0.017	4.424	0.741	0.900	-0.001	-0.059	-0.098
6	A	15	LEU	0	0.014	-0.005	6.069	0.532	0.532	0.000	0.000	0.000
7	A	16	LEU	0	0.031	0.024	8.175	0.168	0.168	0.000	0.000	0.000
8	A	17	LYS	1	0.961	0.991	8.759	0.670	0.670	0.000	0.000	0.000
9	A	18	LEU	0	-0.024	-0.032	10.294	0.142	0.142	0.000	0.000	0.000
10	A	19	ARG	1	0.930	0.968	12.304	0.283	0.283	0.000	0.000	0.000
11	A	20	GLU	-1	-0.988	-0.990	13.322	-0.361	-0.361	0.000	0.000	0.000
12	A	21	SER	0	-0.041	-0.027	14.295	0.024	0.024	0.000	0.000	0.000
13	A	22	ALA	0	-0.044	-0.002	16.101	0.013	0.013	0.000	0.000	0.000
14	A	23	LEU	0	0.004	0.005	17.928	0.018	0.018	0.000	0.000	0.000
15	A	24	SER	0	0.012	0.002	21.038	0.012	0.012	0.000	0.000	0.000
16	A	25	SER	0	-0.053	-0.016	24.376	0.000	0.000	0.000	0.000	0.000
17	A	26	GLY	0	0.009	0.004	27.518	0.000	0.000	0.000	0.000	0.000
18	A	27	SER	0	-0.077	-0.040	25.661	-0.002	-0.002	0.000	0.000	0.000
19	A	28	MET	0	-0.018	0.011	23.403	-0.005	-0.005	0.000	0.000	0.000
20	A	29	SER	0	0.077	0.037	28.650	0.006	0.006	0.000	0.000	0.000
21	A	30	GLU	-1	-0.867	-0.963	30.064	-0.072	-0.072	0.000	0.000	0.000
22	A	31	GLU	-1	-0.918	-0.953	31.025	-0.091	-0.091	0.000	0.000	0.000
23	A	32	GLN	0	0.034	0.012	24.319	0.004	0.004	0.000	0.000	0.000
24	A	33	PHE	0	0.009	-0.004	25.846	-0.011	-0.011	0.000	0.000	0.000
25	A	34	PHE	0	0.007	-0.022	26.519	-0.005	-0.005	0.000	0.000	0.000
26	A	35	LEU	0	0.031	0.034	26.789	-0.001	-0.001	0.000	0.000	0.000
27	A	36	LEU	0	-0.026	-0.017	20.855	-0.011	-0.011	0.000	0.000	0.000
28	A	37	ILE	0	-0.052	-0.030	22.757	-0.008	-0.008	0.000	0.000	0.000
29	A	38	GLY	0	0.010	0.019	24.331	0.002	0.002	0.000	0.000	0.000
30	A	39	ILE	0	0.001	0.011	19.877	-0.002	-0.002	0.000	0.000	0.000
31	A	40	SER	0	-0.105	-0.055	19.870	-0.006	-0.006	0.000	0.000	0.000
32	A	41	SER	0	-0.015	-0.017	19.140	0.009	0.009	0.000	0.000	0.000
33	A	42	ILE	0	-0.089	-0.056	20.467	0.014	0.014	0.000	0.000	0.000
34	A	43	HIS	0	0.083	0.038	22.763	0.001	0.001	0.000	0.000	0.000
35	A	44	SER	0	-0.031	-0.004	25.618	0.005	0.005	0.000	0.000	0.000
36	A	45	ASP	-1	-0.775	-0.891	27.649	-0.048	-0.048	0.000	0.000	0.000
37	A	46	ARG	1	0.830	0.878	28.190	0.019	0.019	0.000	0.000	0.000
38	A	47	VAL	0	-0.031	-0.021	23.957	-0.002	-0.002	0.000	0.000	0.000
39	A	48	ILE	0	0.033	0.021	26.654	-0.008	-0.008	0.000	0.000	0.000
40	A	49	LEU	0	0.002	-0.005	27.957	-0.005	-0.005	0.000	0.000	0.000
41	A	50	ALA	0	0.023	0.016	27.844	-0.002	-0.002	0.000	0.000	0.000
42	A	51	MET	0	-0.070	-0.043	23.614	-0.010	-0.010	0.000	0.000	0.000
43	A	52	LYS	1	0.951	1.007	26.848	0.058	0.058	0.000	0.000	0.000
44	A	53	ASP	-1	-0.798	-0.898	29.720	-0.055	-0.055	0.000	0.000	0.000
45	A	54	TYR	0	-0.060	-0.030	23.936	0.005	0.005	0.000	0.000	0.000
46	A	55	LEU	0	-0.013	-0.026	23.275	-0.003	-0.003	0.000	0.000	0.000
47	A	56	VAL	0	-0.042	-0.001	27.449	-0.003	-0.003	0.000	0.000	0.000
48	A	57	SER	0	-0.028	-0.017	30.828	0.001	0.001	0.000	0.000	0.000
49	A	58	GLY	0	0.043	0.032	31.124	0.004	0.004	0.000	0.000	0.000
50	A	59	HIS	0	-0.009	0.007	31.950	0.001	0.001	0.000	0.000	0.000
51	A	60	SER	0	0.019	0.010	30.197	-0.006	-0.006	0.000	0.000	0.000
52	A	61	ARG	1	0.975	0.967	24.292	0.059	0.059	0.000	0.000	0.000
53	A	62	LYS	1	0.927	0.952	28.006	0.040	0.040	0.000	0.000	0.000
54	A	63	ASP	-1	-0.785	-0.889	30.675	-0.037	-0.037	0.000	0.000	0.000
55	A	64	VAL	0	-0.030	-0.011	27.988	0.003	0.003	0.000	0.000	0.000
56	A	65	CYS	0	-0.103	-0.055	27.316	0.002	0.002	0.000	0.000	0.000
57	A	66	GLU	-1	-0.923	-0.952	29.764	-0.019	-0.019	0.000	0.000	0.000
58	A	67	LYS	1	0.935	0.988	33.435	0.040	0.040	0.000	0.000	0.000
59	A	68	TYR	0	-0.061	-0.053	30.627	0.004	0.004	0.000	0.000	0.000
60	A	69	GLN	0	0.023	0.030	31.062	0.000	0.000	0.000	0.000	0.000
61	A	70	MET	0	-0.057	0.008	24.853	0.002	0.002	0.000	0.000	0.000
62	A	71	ASN	0	0.075	0.034	24.362	-0.007	-0.007	0.000	0.000	0.000
63	A	72	ASN	0	0.083	0.016	23.100	-0.017	-0.017	0.000	0.000	0.000
64	A	73	GLY	0	0.031	0.027	20.227	-0.013	-0.013	0.000	0.000	0.000
65	A	74	TYR	0	0.013	0.005	19.972	-0.012	-0.012	0.000	0.000	0.000
66	A	75	PHE	0	0.079	0.043	21.610	-0.015	-0.015	0.000	0.000	0.000
67	A	76	SER	0	0.000	-0.009	18.294	-0.019	-0.019	0.000	0.000	0.000
68	A	77	THR	0	-0.014	-0.002	16.021	-0.032	-0.032	0.000	0.000	0.000
69	A	78	THR	0	-0.043	-0.041	17.211	-0.031	-0.031	0.000	0.000	0.000
70	A	79	LEU	0	0.054	0.028	19.371	-0.019	-0.019	0.000	0.000	0.000
71	A	80	GLY	0	0.015	0.015	15.291	-0.027	-0.027	0.000	0.000	0.000
72	A	81	ARG	1	0.890	0.940	14.957	0.073	0.073	0.000	0.000	0.000
73	A	82	LEU	0	0.066	0.029	16.245	-0.027	-0.027	0.000	0.000	0.000
74	A	83	THR	0	-0.007	0.006	14.694	-0.004	-0.004	0.000	0.000	0.000
75	A	84	ARG	1	0.945	0.970	10.668	0.471	0.471	0.000	0.000	0.000
76	A	85	LEU	0	-0.032	-0.015	13.877	-0.025	-0.025	0.000	0.000	0.000
77	A	86	ASN	0	0.060	0.038	16.828	0.025	0.025	0.000	0.000	0.000
78	A	87	VAL	0	-0.026	-0.012	12.495	0.000	0.000	0.000	0.000	0.000
79	A	88	LEU	0	-0.062	-0.048	11.697	-0.011	-0.011	0.000	0.000	0.000
80	A	89	VAL	0	0.052	0.027	15.547	0.017	0.017	0.000	0.000	0.000
81	A	90	ALA	0	0.001	0.008	18.093	0.019	0.019	0.000	0.000	0.000
82	A	91	ARG	1	0.895	0.930	10.240	0.604	0.604	0.000	0.000	0.000
83	A	92	LEU	0	0.013	0.015	17.747	0.010	0.010	0.000	0.000	0.000
84	A	93	ALA	0	0.018	0.014	20.186	0.019	0.019	0.000	0.000	0.000
85	A	94	PRO	0	0.034	0.012	21.266	0.015	0.015	0.000	0.000	0.000
86	A	95	TYR	0	-0.058	-0.001	19.292	0.014	0.014	0.000	0.000	0.000
87	A	96	TYR	0	-0.064	-0.030	23.330	0.004	0.004	0.000	0.000	0.000
88	A	97	THR	0	-0.067	-0.044	27.089	0.009	0.009	0.000	0.000	0.000
89	A	98	ASP	-1	-0.877	-0.943	29.441	-0.087	-0.087	0.000	0.000	0.000
90	A	99	SER	0	-0.095	-0.027	29.115	0.005	0.005	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:10:GLY)