FMO DATABASE

FMODB ID: 52KGZ

Calculation Name: 3DO8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DO8

Chain ID: A

ChEMBL ID:

UniProt ID: O28077

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	135
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1266544.808282
FMO2-HF: Nuclear repulsion	1212008.968861
FMO2-HF: Total energy	-54535.839421
FMO2-MP2: Total energy	-54694.132398

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:MET)

Summations of interaction energy for fragment #1(A:1: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.
-27.015	-12.896	17.319	-9.945	-21.492	-0.098

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.017 / q_NPA : 0.017

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	3	VAL	0	-0.019	-0.017	3.818	-2.127	-0.078	0.045	-0.949	-1.146	0.005
4	A	4	ALA	0	0.015	0.018	4.132	1.804	2.732	0.071	-0.324	-0.674	-0.002
5	A	5	LEU	0	0.018	0.007	6.341	-0.678	-0.677	-0.001	-0.001	0.002	0.000
6	A	6	GLY	0	0.000	-0.007	9.018	0.168	0.168	0.000	0.000	0.000	0.000
7	A	7	GLY	0	0.012	0.013	11.763	-0.081	-0.081	0.000	0.000	0.000	0.000
8	A	8	THR	0	-0.021	-0.018	15.144	0.010	0.010	0.000	0.000	0.000	0.000
9	A	9	PHE	0	-0.016	-0.014	12.374	-0.028	-0.028	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.719	-0.814	17.543	0.049	0.049	0.000	0.000	0.000	0.000
11	A	11	PRO	0	0.023	0.006	21.282	0.003	0.003	0.000	0.000	0.000	0.000
12	A	12	LEU	0	0.007	-0.004	15.934	0.008	0.008	0.000	0.000	0.000	0.000
13	A	13	HIS	0	0.072	0.042	19.950	-0.019	-0.019	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.802	-0.911	19.901	-0.005	-0.005	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.058	0.024	20.210	-0.004	-0.004	0.000	0.000	0.000	0.000
16	A	16	HIS	0	0.030	0.003	16.141	0.001	0.001	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.859	0.932	15.341	0.014	0.014	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.839	0.923	16.202	-0.018	-0.018	0.000	0.000	0.000	0.000
19	A	19	LEU	0	0.004	0.013	13.723	-0.011	-0.011	0.000	0.000	0.000	0.000
20	A	20	ILE	0	0.002	-0.006	11.040	0.023	0.023	0.000	0.000	0.000	0.000
21	A	21	ASP	-1	-0.733	-0.821	11.550	-0.082	-0.082	0.000	0.000	0.000	0.000
22	A	22	VAL	0	-0.003	0.003	13.337	-0.028	-0.028	0.000	0.000	0.000	0.000
23	A	23	ALA	0	0.013	0.000	8.503	-0.034	-0.034	0.000	0.000	0.000	0.000
24	A	24	ILE	0	-0.005	0.002	8.864	-0.004	-0.004	0.000	0.000	0.000	0.000
25	A	25	LYS	1	0.811	0.888	9.883	0.025	0.025	0.000	0.000	0.000	0.000
26	A	26	LEU	0	-0.010	0.012	10.108	-0.028	-0.028	0.000	0.000	0.000	0.000
27	A	27	GLY	0	-0.011	-0.020	7.080	-0.157	-0.157	0.000	0.000	0.000	0.000
28	A	28	GLY	0	0.051	0.039	6.924	-0.177	-0.177	0.000	0.000	0.000	0.000
29	A	29	ARG	1	0.861	0.914	6.175	0.836	0.836	0.000	0.000	0.000	0.000
30	A	30	ASP	-1	-0.842	-0.907	2.517	-13.774	-7.958	3.588	-4.224	-5.180	-0.049
31	A	31	ILE	0	-0.005	-0.014	2.599	1.751	2.200	2.782	-0.337	-2.894	-0.005
32	A	32	THR	0	-0.034	-0.029	2.481	-0.331	-0.824	4.862	-0.423	-3.945	-0.021
33	A	33	ILE	0	-0.013	-0.008	3.958	-0.288	-0.173	0.010	0.043	-0.168	0.001
34	A	34	GLY	0	0.011	-0.008	7.542	-0.163	-0.163	0.000	0.000	0.000	0.000
35	A	35	VAL	0	0.006	-0.009	10.015	-0.087	-0.087	0.000	0.000	0.000	0.000
36	A	36	THR	0	0.002	0.009	13.328	-0.006	-0.006	0.000	0.000	0.000	0.000
37	A	37	SER	0	0.023	-0.009	16.468	-0.041	-0.041	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.778	-0.906	18.394	0.094	0.094	0.000	0.000	0.000	0.000
39	A	39	ARG	1	0.940	0.974	21.831	-0.102	-0.102	0.000	0.000	0.000	0.000
40	A	40	MET	0	0.030	0.019	18.424	0.002	0.002	0.000	0.000	0.000	0.000
41	A	41	ALA	0	-0.028	-0.007	20.594	0.000	0.000	0.000	0.000	0.000	0.000
42	A	42	ARG	1	0.992	0.982	21.974	-0.078	-0.078	0.000	0.000	0.000	0.000
43	A	43	ALA	0	-0.029	0.008	23.999	-0.006	-0.006	0.000	0.000	0.000	0.000
44	A	44	ARG	1	0.933	0.976	19.770	-0.134	-0.134	0.000	0.000	0.000	0.000
45	A	45	ILE	0	0.026	0.020	22.976	-0.007	-0.007	0.000	0.000	0.000	0.000
46	A	46	ARG	1	0.968	0.992	26.383	-0.035	-0.035	0.000	0.000	0.000	0.000
47	A	47	SER	0	-0.128	-0.091	23.438	-0.004	-0.004	0.000	0.000	0.000	0.000
48	A	48	VAL	0	-0.023	-0.034	25.691	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	49	LEU	0	-0.008	0.008	22.290	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	50	PRO	0	0.035	0.015	22.321	0.011	0.011	0.000	0.000	0.000	0.000
51	A	51	PHE	0	0.035	-0.007	13.249	-0.010	-0.010	0.000	0.000	0.000	0.000
52	A	52	ALA	0	0.008	0.011	17.147	0.000	0.000	0.000	0.000	0.000	0.000
53	A	53	ILE	0	0.035	0.017	17.889	-0.012	-0.012	0.000	0.000	0.000	0.000
54	A	54	ARG	1	0.758	0.880	17.469	-0.120	-0.120	0.000	0.000	0.000	0.000
55	A	55	ALA	0	0.046	0.017	13.485	0.002	0.002	0.000	0.000	0.000	0.000
56	A	56	GLU	-1	-0.790	-0.875	13.993	-0.090	-0.090	0.000	0.000	0.000	0.000
57	A	57	ASN	0	-0.043	-0.024	16.280	-0.026	-0.026	0.000	0.000	0.000	0.000
58	A	58	VAL	0	-0.009	0.003	11.207	-0.013	-0.013	0.000	0.000	0.000	0.000
59	A	59	LYS	1	0.862	0.922	10.826	0.106	0.106	0.000	0.000	0.000	0.000
60	A	60	ARG	1	0.884	0.923	12.906	0.017	0.017	0.000	0.000	0.000	0.000
61	A	61	TYR	0	-0.068	-0.037	14.330	-0.006	-0.006	0.000	0.000	0.000	0.000
62	A	62	VAL	0	0.018	0.008	9.785	0.003	0.003	0.000	0.000	0.000	0.000
63	A	63	MET	0	0.057	0.039	13.199	-0.015	-0.015	0.000	0.000	0.000	0.000
64	A	64	ARG	1	0.875	0.938	14.836	0.057	0.057	0.000	0.000	0.000	0.000
65	A	65	LYS	1	0.870	0.924	16.302	0.082	0.082	0.000	0.000	0.000	0.000
66	A	66	TYR	0	-0.049	-0.043	12.645	0.026	0.026	0.000	0.000	0.000	0.000
67	A	67	GLY	0	0.034	0.045	13.996	-0.028	-0.028	0.000	0.000	0.000	0.000
68	A	68	PHE	0	-0.007	-0.021	7.651	-0.053	-0.053	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.834	-0.913	10.090	-0.183	-0.183	0.000	0.000	0.000	0.000
70	A	70	PRO	0	-0.020	-0.007	6.366	-0.158	-0.158	0.000	0.000	0.000	0.000
71	A	71	GLU	-1	-0.706	-0.828	2.595	-0.956	0.003	0.924	-0.515	-1.368	-0.008
72	A	72	ILE	0	-0.044	-0.021	5.398	0.389	0.422	-0.001	0.000	-0.033	0.000
73	A	73	VAL	0	0.036	0.023	6.808	-0.038	-0.038	0.000	0.000	0.000	0.000
74	A	74	LYS	1	0.852	0.934	9.596	-0.111	-0.111	0.000	0.000	0.000	0.000
75	A	75	ILE	0	0.012	0.016	12.027	0.030	0.030	0.000	0.000	0.000	0.000
76	A	76	THR	0	0.020	-0.005	14.099	-0.048	-0.048	0.000	0.000	0.000	0.000
77	A	77	ASN	0	0.021	0.007	13.462	-0.049	-0.049	0.000	0.000	0.000	0.000
78	A	78	PRO	0	0.024	-0.007	15.344	0.042	0.042	0.000	0.000	0.000	0.000
79	A	79	TYR	0	0.082	0.055	12.877	-0.006	-0.006	0.000	0.000	0.000	0.000
80	A	80	GLY	0	-0.026	0.009	11.090	0.078	0.078	0.000	0.000	0.000	0.000
81	A	81	LYS	1	0.871	0.917	3.624	-3.173	-2.634	0.007	-0.199	-0.346	0.002
82	A	82	THR	0	-0.032	-0.025	7.426	-0.050	-0.050	0.000	0.000	0.000	0.000
83	A	83	LEU	0	-0.002	0.006	8.491	-0.153	-0.153	0.000	0.000	0.000	0.000
84	A	84	ASP	-1	-0.905	-0.940	8.738	0.595	0.595	0.000	0.000	0.000	0.000
85	A	85	VAL	0	0.029	0.021	3.056	-0.596	0.066	0.256	-0.167	-0.751	0.000
86	A	86	ASP	-1	-0.821	-0.871	4.097	-0.346	-0.050	-0.001	-0.079	-0.216	0.000
87	A	87	PHE	0	0.013	-0.007	2.153	-8.581	-6.103	4.778	-2.739	-4.517	-0.021
88	A	88	GLU	-1	-0.788	-0.846	3.968	-0.552	-0.265	-0.001	-0.031	-0.256	0.000
89	A	89	TYR	0	-0.036	-0.049	6.459	0.577	0.577	0.000	0.000	0.000	0.000
90	A	90	LEU	0	-0.005	-0.003	7.284	0.214	0.214	0.000	0.000	0.000	0.000
91	A	91	VAL	0	-0.008	0.007	9.719	-0.087	-0.087	0.000	0.000	0.000	0.000
92	A	92	VAL	0	-0.037	-0.017	12.050	0.079	0.079	0.000	0.000	0.000	0.000
93	A	93	SER	0	0.046	0.035	15.095	-0.033	-0.033	0.000	0.000	0.000	0.000
94	A	94	PRO	0	0.043	-0.001	18.650	0.004	0.004	0.000	0.000	0.000	0.000
95	A	95	GLU	-1	-0.874	-0.930	21.188	0.072	0.072	0.000	0.000	0.000	0.000
96	A	96	THR	0	-0.065	-0.044	16.280	0.020	0.020	0.000	0.000	0.000	0.000
97	A	97	TYR	0	0.039	0.024	17.074	0.016	0.016	0.000	0.000	0.000	0.000
98	A	98	GLU	-1	-0.882	-0.944	18.021	0.047	0.047	0.000	0.000	0.000	0.000
99	A	99	MET	0	-0.037	-0.008	15.661	-0.009	-0.009	0.000	0.000	0.000	0.000
100	A	100	ALA	0	0.020	0.008	13.952	0.010	0.010	0.000	0.000	0.000	0.000
101	A	101	LEU	0	0.030	0.016	14.841	-0.029	-0.029	0.000	0.000	0.000	0.000
102	A	102	LYS	1	0.851	0.929	17.609	-0.076	-0.076	0.000	0.000	0.000	0.000
103	A	103	ILE	0	-0.008	-0.012	11.051	0.002	0.002	0.000	0.000	0.000	0.000
104	A	104	ASN	0	0.035	0.003	12.549	-0.031	-0.031	0.000	0.000	0.000	0.000
105	A	105	GLN	0	0.001	0.025	14.673	-0.006	-0.006	0.000	0.000	0.000	0.000
106	A	106	LYS	1	0.843	0.898	16.159	-0.095	-0.095	0.000	0.000	0.000	0.000
107	A	107	ARG	1	0.754	0.836	7.463	0.153	0.153	0.000	0.000	0.000	0.000
108	A	108	GLU	-1	-0.811	-0.884	13.813	-0.017	-0.017	0.000	0.000	0.000	0.000
109	A	109	GLU	-1	-0.825	-0.913	16.405	0.081	0.081	0.000	0.000	0.000	0.000
110	A	110	LEU	0	-0.034	-0.009	15.147	0.009	0.009	0.000	0.000	0.000	0.000
111	A	111	GLY	0	0.015	0.023	15.940	0.018	0.018	0.000	0.000	0.000	0.000
112	A	112	LYS	1	0.778	0.881	8.163	-0.311	-0.311	0.000	0.000	0.000	0.000
113	A	113	ARG	1	0.928	0.950	5.781	0.263	0.263	0.000	0.000	0.000	0.000
114	A	114	LYS	1	0.827	0.898	10.128	0.001	0.001	0.000	0.000	0.000	0.000
115	A	115	ILE	0	-0.020	0.004	7.284	-0.062	-0.062	0.000	0.000	0.000	0.000
116	A	116	THR	0	0.015	0.010	9.738	0.187	0.187	0.000	0.000	0.000	0.000
117	A	117	ILE	0	-0.032	-0.016	11.659	0.031	0.031	0.000	0.000	0.000	0.000
118	A	118	VAL	0	-0.005	-0.001	12.619	-0.014	-0.014	0.000	0.000	0.000	0.000
119	A	119	LYS	1	0.882	0.917	14.698	0.041	0.041	0.000	0.000	0.000	0.000
120	A	120	VAL	0	0.009	0.005	16.085	-0.020	-0.020	0.000	0.000	0.000	0.000
121	A	121	ASP	-1	-0.777	-0.879	18.812	0.025	0.025	0.000	0.000	0.000	0.000
122	A	122	TRP	0	-0.070	-0.055	17.590	-0.001	-0.001	0.000	0.000	0.000	0.000
123	A	123	MET	0	-0.041	-0.013	22.082	-0.004	-0.004	0.000	0.000	0.000	0.000
124	A	124	MET	0	0.007	0.029	22.815	-0.004	-0.004	0.000	0.000	0.000	0.000
125	A	132	SER	0	0.032	0.025	30.218	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	133	SER	0	0.007	-0.029	25.907	0.004	0.004	0.000	0.000	0.000	0.000
127	A	134	THR	0	0.036	0.029	26.129	0.000	0.000	0.000	0.000	0.000	0.000
128	A	135	ARG	1	0.942	0.968	25.762	0.038	0.038	0.000	0.000	0.000	0.000
129	A	136	ILE	0	0.039	0.018	20.081	-0.003	-0.003	0.000	0.000	0.000	0.000
130	A	137	LYS	1	0.946	0.971	22.180	0.078	0.078	0.000	0.000	0.000	0.000
131	A	138	ARG	1	0.774	0.881	17.672	0.022	0.022	0.000	0.000	0.000	0.000
132	A	139	GLY	0	0.043	0.029	16.479	0.001	0.001	0.000	0.000	0.000	0.000
133	A	140	GLU	-1	-0.896	-0.965	11.794	-0.343	-0.343	0.000	0.000	0.000	0.000
134	A	141	ILE	0	-0.025	-0.025	15.584	0.022	0.022	0.000	0.000	0.000	0.000
135	A	142	ASP	-1	-0.957	-0.959	16.395	-0.193	-0.193	0.000	0.000	0.000	0.000

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