FMO DATABASE

FMODB ID: 2J38R

Calculation Name: 3B83-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3B83

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-09-19

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	OptHSide
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	95
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-638699.69573
FMO2-HF: Nuclear repulsion	602548.683137
FMO2-HF: Total energy	-36151.012593
FMO2-MP2: Total energy	-36258.210012

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:0:MET)

Summations of interaction energy for fragment #1(A:0:MET)

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.
-1.472	0.747	-0.02	-0.822	-1.377	0.001

Interaction energy analysis for fragmet #1(A:0:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.021 / q_NPA : -0.025

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	2	GLN	0	-0.030	-0.016	3.813	1.409	2.927	-0.023	-0.675	-0.820	0.001
4	A	3	PRO	0	0.046	0.012	6.490	-0.110	-0.110	0.000	0.000	0.000	0.000
5	A	4	PRO	0	0.011	0.023	8.602	-0.170	-0.170	0.000	0.000	0.000	0.000
6	A	5	PHE	0	0.012	-0.019	12.055	0.095	0.095	0.000	0.000	0.000	0.000
7	A	6	ASN	0	-0.027	-0.031	14.735	-0.047	-0.047	0.000	0.000	0.000	0.000
8	A	7	ILE	0	0.043	0.029	15.485	-0.023	-0.023	0.000	0.000	0.000	0.000
9	A	8	LYS	1	0.900	0.957	19.381	-0.044	-0.044	0.000	0.000	0.000	0.000
10	A	9	VAL	0	0.029	0.009	23.163	-0.007	-0.007	0.000	0.000	0.000	0.000
11	A	10	THR	0	-0.006	-0.011	25.717	0.002	0.002	0.000	0.000	0.000	0.000
12	A	11	ASN	0	-0.037	-0.030	29.229	-0.002	-0.002	0.000	0.000	0.000	0.000
13	A	12	ILE	0	-0.001	0.024	28.603	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	13	THR	0	0.006	-0.007	32.355	0.000	0.000	0.000	0.000	0.000	0.000
15	A	14	LEU	0	0.019	0.010	34.655	0.001	0.001	0.000	0.000	0.000	0.000
16	A	15	THR	0	0.015	0.011	34.246	0.000	0.000	0.000	0.000	0.000	0.000
17	A	16	THR	0	-0.018	-0.010	32.271	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	17	ALA	0	0.029	0.019	28.214	0.004	0.004	0.000	0.000	0.000	0.000
19	A	18	VAL	0	-0.012	0.018	27.382	-0.005	-0.005	0.000	0.000	0.000	0.000
20	A	19	VAL	0	0.033	0.022	21.530	0.008	0.008	0.000	0.000	0.000	0.000
21	A	20	THR	0	-0.012	0.005	22.681	-0.009	-0.009	0.000	0.000	0.000	0.000
22	A	21	TRP	0	0.011	0.012	16.709	0.025	0.025	0.000	0.000	0.000	0.000
23	A	22	GLN	0	-0.057	-0.027	17.109	-0.026	-0.026	0.000	0.000	0.000	0.000
24	A	23	PRO	0	0.014	0.005	15.322	0.029	0.029	0.000	0.000	0.000	0.000
25	A	24	PRO	0	0.007	0.002	10.325	0.024	0.024	0.000	0.000	0.000	0.000
26	A	25	ILE	0	-0.005	0.005	11.186	-0.042	-0.042	0.000	0.000	0.000	0.000
27	A	26	LEU	0	-0.018	0.001	7.027	-0.027	-0.027	0.000	0.000	0.000	0.000
28	A	27	PRO	0	0.032	0.001	10.893	0.032	0.032	0.000	0.000	0.000	0.000
29	A	28	ILE	0	-0.035	-0.008	9.814	-0.140	-0.140	0.000	0.000	0.000	0.000
30	A	29	GLU	-1	-0.879	-0.933	12.432	-0.401	-0.401	0.000	0.000	0.000	0.000
31	A	30	GLY	0	-0.015	-0.006	13.301	0.056	0.056	0.000	0.000	0.000	0.000
32	A	31	ILE	0	-0.051	-0.024	12.935	-0.029	-0.029	0.000	0.000	0.000	0.000
33	A	32	LEU	0	0.018	0.014	12.349	0.011	0.011	0.000	0.000	0.000	0.000
34	A	33	VAL	0	-0.010	0.000	14.854	0.040	0.040	0.000	0.000	0.000	0.000
35	A	34	THR	0	0.002	-0.002	16.597	-0.020	-0.020	0.000	0.000	0.000	0.000
36	A	35	PHE	0	-0.007	-0.013	18.841	0.019	0.019	0.000	0.000	0.000	0.000
37	A	36	GLY	0	0.114	0.066	21.950	-0.010	-0.010	0.000	0.000	0.000	0.000
38	A	37	ARG	1	0.764	0.846	24.587	0.024	0.024	0.000	0.000	0.000	0.000
39	A	38	LYS	1	0.875	0.932	21.601	-0.058	-0.058	0.000	0.000	0.000	0.000
40	A	39	ASN	0	-0.065	-0.041	24.593	0.003	0.003	0.000	0.000	0.000	0.000
41	A	40	ASP	-1	-0.799	-0.876	26.835	-0.021	-0.021	0.000	0.000	0.000	0.000
42	A	41	PRO	0	0.014	0.012	22.451	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	42	SER	0	-0.093	-0.061	22.805	-0.008	-0.008	0.000	0.000	0.000	0.000
44	A	43	ASP	-1	-0.830	-0.887	25.223	-0.023	-0.023	0.000	0.000	0.000	0.000
45	A	44	GLU	-1	-0.864	-0.927	19.742	-0.024	-0.024	0.000	0.000	0.000	0.000
46	A	45	THR	0	-0.009	0.023	22.565	-0.007	-0.007	0.000	0.000	0.000	0.000
47	A	46	THR	0	-0.029	-0.036	17.182	0.005	0.005	0.000	0.000	0.000	0.000
48	A	47	VAL	0	-0.024	0.001	19.850	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	48	ASP	-1	-0.800	-0.874	16.340	-0.222	-0.222	0.000	0.000	0.000	0.000
50	A	49	LEU	0	-0.022	-0.008	17.787	0.009	0.009	0.000	0.000	0.000	0.000
51	A	50	THR	0	0.079	0.024	17.525	-0.022	-0.022	0.000	0.000	0.000	0.000
52	A	51	SER	0	0.041	0.002	16.161	0.022	0.022	0.000	0.000	0.000	0.000
53	A	52	SER	0	-0.056	-0.023	18.045	0.013	0.013	0.000	0.000	0.000	0.000
54	A	53	ILE	0	-0.014	0.007	20.823	0.013	0.013	0.000	0.000	0.000	0.000
55	A	54	THR	0	-0.007	-0.007	20.081	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	55	SER	0	-0.030	-0.049	21.733	0.015	0.015	0.000	0.000	0.000	0.000
57	A	56	LEU	0	0.023	0.022	21.823	-0.008	-0.008	0.000	0.000	0.000	0.000
58	A	57	THR	0	-0.001	-0.001	25.555	0.006	0.006	0.000	0.000	0.000	0.000
59	A	58	LEU	0	-0.009	0.008	24.482	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	59	THR	0	0.005	-0.020	28.746	0.003	0.003	0.000	0.000	0.000	0.000
61	A	60	ASN	0	-0.029	-0.018	31.563	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	61	LEU	0	-0.019	0.018	28.610	0.000	0.000	0.000	0.000	0.000	0.000
63	A	62	GLU	-1	-0.877	-0.947	32.517	-0.011	-0.011	0.000	0.000	0.000	0.000
64	A	63	PRO	0	0.037	0.012	33.864	0.003	0.003	0.000	0.000	0.000	0.000
65	A	64	ASN	0	-0.064	-0.029	35.181	0.001	0.001	0.000	0.000	0.000	0.000
66	A	65	THR	0	-0.052	-0.017	30.270	0.000	0.000	0.000	0.000	0.000	0.000
67	A	66	THR	0	-0.035	-0.021	26.632	0.001	0.001	0.000	0.000	0.000	0.000
68	A	67	TYR	0	0.028	0.017	25.495	-0.004	-0.004	0.000	0.000	0.000	0.000
69	A	68	GLU	-1	-0.841	-0.927	18.342	0.081	0.081	0.000	0.000	0.000	0.000
70	A	69	ILE	0	-0.031	-0.011	18.566	-0.012	-0.012	0.000	0.000	0.000	0.000
71	A	70	ARG	1	0.825	0.892	14.765	0.026	0.026	0.000	0.000	0.000	0.000
72	A	71	ILE	0	0.000	-0.002	13.587	-0.033	-0.033	0.000	0.000	0.000	0.000
73	A	72	VAL	0	-0.016	-0.006	8.694	0.083	0.083	0.000	0.000	0.000	0.000
74	A	73	ALA	0	0.008	0.025	8.830	-0.086	-0.086	0.000	0.000	0.000	0.000
75	A	74	ARG	1	0.859	0.890	8.366	0.241	0.241	0.000	0.000	0.000	0.000
76	A	75	ASN	0	0.036	-0.006	8.274	0.168	0.168	0.000	0.000	0.000	0.000
77	A	76	GLY	0	0.004	0.011	8.584	-0.230	-0.230	0.000	0.000	0.000	0.000
78	A	77	GLN	0	-0.063	-0.043	9.555	0.058	0.058	0.000	0.000	0.000	0.000
79	A	78	GLN	0	-0.026	-0.004	3.988	-1.191	-0.875	0.001	-0.054	-0.263	0.000
80	A	79	TYR	0	0.036	0.000	5.574	0.325	0.325	0.000	0.000	0.000	0.000
81	A	80	SER	0	-0.013	0.020	4.350	-0.480	-0.366	-0.001	-0.019	-0.094	0.000
82	A	81	PRO	0	-0.005	-0.001	3.942	-0.736	-0.465	0.003	-0.074	-0.200	0.000
83	A	82	PRO	0	-0.002	-0.011	6.653	-0.028	-0.028	0.000	0.000	0.000	0.000
84	A	83	VAL	0	-0.025	0.005	10.370	0.062	0.062	0.000	0.000	0.000	0.000
85	A	84	SER	0	0.017	-0.013	12.835	-0.058	-0.058	0.000	0.000	0.000	0.000
86	A	85	THR	0	-0.039	-0.014	16.405	0.010	0.010	0.000	0.000	0.000	0.000
87	A	86	THR	0	0.018	0.009	20.049	-0.009	-0.009	0.000	0.000	0.000	0.000
88	A	87	PHE	0	-0.028	-0.010	23.302	0.003	0.003	0.000	0.000	0.000	0.000
89	A	88	THR	0	0.029	0.005	26.755	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	89	THR	0	-0.011	-0.009	30.223	0.001	0.001	0.000	0.000	0.000	0.000
91	A	90	GLY	0	0.029	0.019	32.696	0.001	0.001	0.000	0.000	0.000	0.000
92	A	91	SER	0	0.036	0.015	36.197	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	92	LEU	0	-0.047	-0.032	39.030	0.000	0.000	0.000	0.000	0.000	0.000
94	A	93	GLU	-1	-0.941	-0.962	42.310	0.002	0.002	0.000	0.000	0.000	0.000
95	A	94	HIS	0	-0.027	-0.004	45.321	0.000	0.000	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:0:MET)