FMO DATABASE

FMODB ID: 4J86N

Calculation Name: 3C0D-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3C0D

Chain ID: A

ChEMBL ID:

UniProt ID: Q87HB1

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	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	109
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-842773.590502
FMO2-HF: Nuclear repulsion	798853.164739
FMO2-HF: Total energy	-43920.425764
FMO2-MP2: Total energy	-44044.081827

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:4:LEU)

Summations of interaction energy for fragment #1(A:4: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.
-11.043	-7.581	2.002	-2.548	-2.92	-0.019

Interaction energy analysis for fragmet #1(A:4:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.015 / 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

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	6	LYS	1	0.797	0.874	3.863	-0.521	1.022	-0.012	-0.842	-0.689	0.003
4	A	7	VAL	0	-0.004	0.005	6.705	0.296	0.296	0.000	0.000	0.000	0.000
5	A	8	LYS	1	0.957	0.967	9.704	0.783	0.783	0.000	0.000	0.000	0.000
6	A	9	LEU	0	-0.049	-0.013	13.182	0.013	0.013	0.000	0.000	0.000	0.000
7	A	10	CYS	0	-0.051	-0.022	15.025	0.062	0.062	0.000	0.000	0.000	0.000
8	A	11	GLN	0	-0.014	-0.010	17.619	-0.094	-0.094	0.000	0.000	0.000	0.000
9	A	12	LEU	0	-0.008	-0.010	18.871	0.007	0.007	0.000	0.000	0.000	0.000
10	A	13	ASP	-1	-0.858	-0.929	20.575	-0.242	-0.242	0.000	0.000	0.000	0.000
11	A	14	ASP	-1	-0.860	-0.914	21.874	-0.286	-0.286	0.000	0.000	0.000	0.000
12	A	15	LEU	0	-0.086	-0.050	18.931	0.013	0.013	0.000	0.000	0.000	0.000
13	A	16	MET	0	0.005	-0.004	23.572	0.011	0.011	0.000	0.000	0.000	0.000
14	A	17	PRO	0	-0.005	-0.010	25.219	0.000	0.000	0.000	0.000	0.000	0.000
15	A	18	PHE	0	-0.025	-0.016	25.200	0.007	0.007	0.000	0.000	0.000	0.000
16	A	19	ILE	0	-0.048	-0.015	26.271	0.011	0.011	0.000	0.000	0.000	0.000
17	A	20	GLY	0	0.010	0.014	24.052	-0.013	-0.013	0.000	0.000	0.000	0.000
18	A	21	ALA	0	-0.013	-0.012	22.430	0.006	0.006	0.000	0.000	0.000	0.000
19	A	22	THR	0	-0.038	-0.015	21.673	-0.009	-0.009	0.000	0.000	0.000	0.000
20	A	23	VAL	0	0.010	0.006	16.953	-0.012	-0.012	0.000	0.000	0.000	0.000
21	A	24	LEU	0	-0.028	-0.025	18.152	0.035	0.035	0.000	0.000	0.000	0.000
22	A	25	ILE	0	0.010	0.006	11.486	-0.056	-0.056	0.000	0.000	0.000	0.000
23	A	26	GLU	-1	-0.860	-0.908	11.596	-0.621	-0.621	0.000	0.000	0.000	0.000
24	A	27	GLY	0	0.016	0.022	14.665	0.056	0.056	0.000	0.000	0.000	0.000
25	A	28	GLU	-1	-0.826	-0.882	14.739	-0.131	-0.131	0.000	0.000	0.000	0.000
26	A	29	ARG	1	0.843	0.903	18.225	0.162	0.162	0.000	0.000	0.000	0.000
27	A	30	VAL	0	0.002	0.018	15.414	0.026	0.026	0.000	0.000	0.000	0.000
28	A	31	ALA	0	0.013	0.011	18.750	-0.011	-0.011	0.000	0.000	0.000	0.000
29	A	32	LEU	0	-0.001	-0.005	15.843	0.000	0.000	0.000	0.000	0.000	0.000
30	A	33	PHE	0	0.052	0.015	19.427	0.021	0.021	0.000	0.000	0.000	0.000
31	A	34	TYR	0	0.030	0.019	19.926	-0.008	-0.008	0.000	0.000	0.000	0.000
32	A	35	ILE	0	0.029	0.014	20.705	0.019	0.019	0.000	0.000	0.000	0.000
33	A	36	PRO	0	-0.003	-0.006	21.398	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	37	ASP	-1	-0.876	-0.931	22.593	-0.070	-0.070	0.000	0.000	0.000	0.000
35	A	38	SER	0	-0.078	-0.049	19.534	0.024	0.024	0.000	0.000	0.000	0.000
36	A	39	GLY	0	-0.004	0.028	16.752	0.002	0.002	0.000	0.000	0.000	0.000
37	A	40	VAL	0	0.000	-0.007	15.731	0.011	0.011	0.000	0.000	0.000	0.000
38	A	41	TYR	0	-0.070	-0.036	15.136	-0.009	-0.009	0.000	0.000	0.000	0.000
39	A	42	ALA	0	0.008	-0.001	14.223	-0.024	-0.024	0.000	0.000	0.000	0.000
40	A	43	VAL	0	0.049	0.026	15.927	0.029	0.029	0.000	0.000	0.000	0.000
41	A	44	GLN	0	-0.004	0.002	18.377	-0.022	-0.022	0.000	0.000	0.000	0.000
42	A	45	ASP	-1	-0.783	-0.908	19.794	-0.115	-0.115	0.000	0.000	0.000	0.000
43	A	46	TRP	0	-0.018	-0.005	22.727	0.008	0.008	0.000	0.000	0.000	0.000
44	A	47	ASP	-1	-0.721	-0.832	24.493	-0.021	-0.021	0.000	0.000	0.000	0.000
45	A	48	PRO	0	-0.020	0.003	25.089	0.000	0.000	0.000	0.000	0.000	0.000
46	A	49	ILE	0	0.011	0.011	27.200	0.006	0.006	0.000	0.000	0.000	0.000
47	A	50	GLY	0	-0.005	-0.026	30.616	0.001	0.001	0.000	0.000	0.000	0.000
48	A	51	LYS	1	0.774	0.894	29.735	0.005	0.005	0.000	0.000	0.000	0.000
49	A	52	ALA	0	0.060	0.021	29.399	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	53	TYR	0	-0.056	-0.027	23.779	-0.004	-0.004	0.000	0.000	0.000	0.000
51	A	54	VAL	0	0.017	0.006	26.794	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	55	MET	0	0.040	0.037	24.266	0.004	0.004	0.000	0.000	0.000	0.000
53	A	56	SER	0	-0.032	-0.033	24.245	0.004	0.004	0.000	0.000	0.000	0.000
54	A	57	ARG	1	0.838	0.910	25.628	0.100	0.100	0.000	0.000	0.000	0.000
55	A	58	GLY	0	0.023	0.019	28.134	0.008	0.008	0.000	0.000	0.000	0.000
56	A	59	ILE	0	-0.054	-0.024	29.037	-0.008	-0.008	0.000	0.000	0.000	0.000
57	A	60	VAL	0	-0.001	0.002	25.650	0.005	0.005	0.000	0.000	0.000	0.000
58	A	61	GLY	0	0.013	0.006	28.297	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	62	ASP	-1	-0.952	-0.970	28.282	-0.008	-0.008	0.000	0.000	0.000	0.000
60	A	63	ILE	0	0.012	-0.003	28.810	0.000	0.000	0.000	0.000	0.000	0.000
61	A	64	ASN	0	-0.072	-0.045	28.477	0.005	0.005	0.000	0.000	0.000	0.000
62	A	65	GLY	0	0.006	0.016	28.158	0.010	0.010	0.000	0.000	0.000	0.000
63	A	66	GLU	-1	-0.821	-0.871	22.954	0.031	0.031	0.000	0.000	0.000	0.000
64	A	67	MET	0	0.031	0.017	23.601	-0.012	-0.012	0.000	0.000	0.000	0.000
65	A	68	CYS	0	-0.023	0.022	23.820	0.003	0.003	0.000	0.000	0.000	0.000
66	A	69	VAL	0	-0.019	-0.010	24.202	-0.010	-0.010	0.000	0.000	0.000	0.000
67	A	70	ALA	0	0.047	0.025	26.890	0.008	0.008	0.000	0.000	0.000	0.000
68	A	71	SER	0	-0.029	-0.051	29.577	-0.010	-0.010	0.000	0.000	0.000	0.000
69	A	72	PRO	0	0.037	0.008	29.857	0.005	0.005	0.000	0.000	0.000	0.000
70	A	73	LEU	0	-0.061	-0.002	32.129	0.003	0.003	0.000	0.000	0.000	0.000
71	A	74	TYR	0	-0.014	-0.021	33.528	0.002	0.002	0.000	0.000	0.000	0.000
72	A	75	LYS	1	0.814	0.894	33.666	0.034	0.034	0.000	0.000	0.000	0.000
73	A	76	GLN	0	0.032	0.033	30.586	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	77	HIS	0	-0.018	-0.027	29.110	-0.014	-0.014	0.000	0.000	0.000	0.000
75	A	78	PHE	0	0.000	-0.013	24.002	0.008	0.008	0.000	0.000	0.000	0.000
76	A	79	SER	0	0.013	-0.025	21.877	-0.011	-0.011	0.000	0.000	0.000	0.000
77	A	80	LEU	0	0.002	-0.014	20.560	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	81	LYS	1	0.875	0.942	13.935	-0.118	-0.118	0.000	0.000	0.000	0.000
79	A	82	SER	0	-0.062	-0.051	16.932	0.026	0.026	0.000	0.000	0.000	0.000
80	A	83	GLY	0	0.041	0.022	18.886	0.014	0.014	0.000	0.000	0.000	0.000
81	A	84	GLN	0	0.006	-0.010	20.591	-0.012	-0.012	0.000	0.000	0.000	0.000
82	A	85	CYS	0	-0.076	-0.009	23.491	-0.012	-0.012	0.000	0.000	0.000	0.000
83	A	86	LEU	0	0.007	-0.002	27.002	0.011	0.011	0.000	0.000	0.000	0.000
84	A	87	GLU	-1	-0.818	-0.904	29.859	0.013	0.013	0.000	0.000	0.000	0.000
85	A	88	ASP	-1	-0.867	-0.961	30.930	0.036	0.036	0.000	0.000	0.000	0.000
86	A	89	GLU	-1	-0.943	-0.972	28.541	0.078	0.078	0.000	0.000	0.000	0.000
87	A	90	ALA	0	-0.033	0.003	27.507	0.011	0.011	0.000	0.000	0.000	0.000
88	A	91	HIS	0	-0.087	-0.038	26.004	-0.002	-0.002	0.000	0.000	0.000	0.000
89	A	92	CYS	0	-0.003	0.000	19.960	0.007	0.007	0.000	0.000	0.000	0.000
90	A	93	LEU	0	-0.087	-0.026	20.582	-0.008	-0.008	0.000	0.000	0.000	0.000
91	A	94	LYS	1	0.840	0.892	13.785	0.136	0.136	0.000	0.000	0.000	0.000
92	A	95	THR	0	0.009	0.000	14.850	-0.022	-0.022	0.000	0.000	0.000	0.000
93	A	96	TRP	0	-0.004	-0.008	10.760	0.047	0.047	0.000	0.000	0.000	0.000
94	A	97	ARG	1	0.934	0.964	4.249	-1.086	-0.986	-0.001	-0.007	-0.093	0.000
95	A	98	VAL	0	0.034	0.020	8.958	-0.291	-0.291	0.000	0.000	0.000	0.000
96	A	99	THR	0	-0.062	-0.025	8.250	0.033	0.033	0.000	0.000	0.000	0.000
97	A	100	VAL	0	0.025	-0.004	11.101	-0.043	-0.043	0.000	0.000	0.000	0.000
98	A	101	ASP	-1	-0.830	-0.883	11.532	-0.950	-0.950	0.000	0.000	0.000	0.000
99	A	102	ASP	-1	-0.939	-0.973	14.357	-0.353	-0.353	0.000	0.000	0.000	0.000
100	A	103	ASN	0	0.012	-0.008	18.141	0.055	0.055	0.000	0.000	0.000	0.000
101	A	104	GLN	0	-0.022	-0.005	14.636	-0.051	-0.051	0.000	0.000	0.000	0.000
102	A	105	VAL	0	0.034	0.023	14.360	-0.071	-0.071	0.000	0.000	0.000	0.000
103	A	106	CYS	0	-0.011	0.006	10.085	-0.034	-0.034	0.000	0.000	0.000	0.000
104	A	107	TYR	0	-0.004	-0.032	7.839	-0.034	-0.034	0.000	0.000	0.000	0.000
105	A	108	LEU	0	-0.053	-0.031	4.311	-0.384	-0.243	-0.001	-0.015	-0.125	0.000
106	A	109	ALA	0	0.017	0.008	3.737	0.996	1.214	-0.001	-0.063	-0.155	0.000
107	A	110	LYS	1	0.901	0.938	2.246	-6.142	-4.744	2.018	-1.607	-1.810	-0.022
108	A	111	GLU	-1	-0.797	-0.882	4.276	-2.747	-2.685	-0.001	-0.014	-0.048	0.000
109	A	112	LEU	0	-0.070	-0.022	6.028	0.367	0.367	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:LEU)