FMO DATABASE

FMODB ID: 6N7KZ

Calculation Name: 3F31-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3F31

Chain ID: A

ChEMBL ID:

UniProt ID: Q13813

Base Structure: X-ray

Registration Date: 2023-06-22

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	137
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1129783.58213
FMO2-HF: Nuclear repulsion	1072410.983199
FMO2-HF: Total energy	-57372.598931
FMO2-MP2: Total energy	-57541.409071

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:11:THR)

Summations of interaction energy for fragment #1(A:11:THR)

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.
-14.209	-11.968	9.318	-5.242	-6.316	-0.049

Interaction energy analysis for fragmet #1(A:11:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.027 / q_NPA : -0.004

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	13	GLU	-1	-0.876	-0.936	3.463	-3.026	-1.511	-0.007	-0.593	-0.914	0.001
4	A	14	ASP	-1	-0.816	-0.895	2.012	-17.143	-17.348	8.835	-4.297	-4.332	-0.049
5	A	15	ILE	0	-0.087	-0.058	2.435	1.841	2.717	0.491	-0.350	-1.017	-0.001
6	A	16	GLN	0	-0.028	0.007	5.319	1.040	1.095	-0.001	-0.002	-0.053	0.000
7	A	17	GLU	-1	-0.854	-0.932	7.896	-1.033	-1.033	0.000	0.000	0.000	0.000
8	A	18	ARG	1	0.927	0.962	5.445	1.691	1.691	0.000	0.000	0.000	0.000
9	A	19	ARG	1	0.868	0.916	7.718	1.276	1.276	0.000	0.000	0.000	0.000
10	A	20	GLN	0	0.053	0.038	11.854	0.176	0.176	0.000	0.000	0.000	0.000
11	A	21	GLN	0	0.005	-0.001	12.700	0.043	0.043	0.000	0.000	0.000	0.000
12	A	22	VAL	0	-0.029	-0.024	14.046	0.105	0.105	0.000	0.000	0.000	0.000
13	A	23	LEU	0	-0.014	-0.006	15.912	0.080	0.080	0.000	0.000	0.000	0.000
14	A	24	ASP	-1	-0.850	-0.911	17.717	-0.381	-0.381	0.000	0.000	0.000	0.000
15	A	25	ARG	1	0.823	0.891	19.223	0.443	0.443	0.000	0.000	0.000	0.000
16	A	26	TYR	0	-0.047	-0.012	19.991	0.043	0.043	0.000	0.000	0.000	0.000
17	A	27	HIS	0	0.004	-0.008	21.865	0.056	0.056	0.000	0.000	0.000	0.000
18	A	28	ARG	1	0.929	0.969	23.502	0.272	0.272	0.000	0.000	0.000	0.000
19	A	29	PHE	0	0.038	0.024	26.439	0.006	0.006	0.000	0.000	0.000	0.000
20	A	30	LYS	1	0.991	1.000	27.698	0.176	0.176	0.000	0.000	0.000	0.000
21	A	31	GLU	-1	-0.800	-0.895	30.101	-0.143	-0.143	0.000	0.000	0.000	0.000
22	A	32	LEU	0	0.019	0.005	30.087	0.005	0.005	0.000	0.000	0.000	0.000
23	A	33	SER	0	-0.032	-0.020	25.939	0.002	0.002	0.000	0.000	0.000	0.000
24	A	34	THR	0	-0.038	-0.013	28.756	0.007	0.007	0.000	0.000	0.000	0.000
25	A	35	LEU	0	0.039	0.015	31.801	0.007	0.007	0.000	0.000	0.000	0.000
26	A	36	ARG	1	0.873	0.930	26.964	0.186	0.186	0.000	0.000	0.000	0.000
27	A	37	ARG	1	0.866	0.921	28.742	0.105	0.105	0.000	0.000	0.000	0.000
28	A	38	GLN	0	0.039	0.023	30.365	0.003	0.003	0.000	0.000	0.000	0.000
29	A	39	LYS	1	0.984	0.997	32.857	0.088	0.088	0.000	0.000	0.000	0.000
30	A	40	LEU	0	-0.043	-0.005	27.876	0.006	0.006	0.000	0.000	0.000	0.000
31	A	41	GLU	-1	-0.809	-0.895	32.112	-0.078	-0.078	0.000	0.000	0.000	0.000
32	A	42	ASP	-1	-0.762	-0.883	34.437	-0.056	-0.056	0.000	0.000	0.000	0.000
33	A	43	SER	0	-0.066	-0.035	34.741	0.006	0.006	0.000	0.000	0.000	0.000
34	A	44	TYR	0	-0.052	-0.034	29.328	0.007	0.007	0.000	0.000	0.000	0.000
35	A	45	ARG	1	0.779	0.849	36.252	0.057	0.057	0.000	0.000	0.000	0.000
36	A	46	PHE	0	0.040	0.014	39.420	0.004	0.004	0.000	0.000	0.000	0.000
37	A	47	GLN	0	-0.001	0.003	34.896	0.006	0.006	0.000	0.000	0.000	0.000
38	A	48	PHE	0	-0.033	-0.026	35.749	0.004	0.004	0.000	0.000	0.000	0.000
39	A	49	PHE	0	0.042	0.027	41.096	0.003	0.003	0.000	0.000	0.000	0.000
40	A	50	GLN	0	0.031	0.016	43.468	0.004	0.004	0.000	0.000	0.000	0.000
41	A	51	ARG	1	0.894	0.949	37.385	0.017	0.017	0.000	0.000	0.000	0.000
42	A	52	ASP	-1	-0.806	-0.889	44.729	-0.012	-0.012	0.000	0.000	0.000	0.000
43	A	53	ALA	0	0.017	0.003	46.707	0.001	0.001	0.000	0.000	0.000	0.000
44	A	54	GLU	-1	-0.880	-0.930	47.524	-0.011	-0.011	0.000	0.000	0.000	0.000
45	A	55	GLU	-1	-0.976	-0.980	47.699	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	56	LEU	0	0.020	0.011	50.058	0.001	0.001	0.000	0.000	0.000	0.000
47	A	57	GLU	-1	-0.833	-0.893	52.573	-0.013	-0.013	0.000	0.000	0.000	0.000
48	A	58	LYS	1	0.805	0.884	51.866	0.000	0.000	0.000	0.000	0.000	0.000
49	A	59	TRP	0	0.013	0.005	54.282	0.000	0.000	0.000	0.000	0.000	0.000
50	A	60	ILE	0	0.013	-0.002	56.110	0.001	0.001	0.000	0.000	0.000	0.000
51	A	61	GLN	0	0.014	0.015	57.957	0.000	0.000	0.000	0.000	0.000	0.000
52	A	62	GLU	-1	-0.825	-0.894	55.990	0.002	0.002	0.000	0.000	0.000	0.000
53	A	63	LYS	1	0.806	0.899	58.989	0.001	0.001	0.000	0.000	0.000	0.000
54	A	64	LEU	0	0.001	-0.001	61.903	0.000	0.000	0.000	0.000	0.000	0.000
55	A	65	GLN	0	-0.035	-0.005	63.350	0.000	0.000	0.000	0.000	0.000	0.000
56	A	66	ILE	0	-0.005	-0.003	62.248	0.001	0.001	0.000	0.000	0.000	0.000
57	A	67	ALA	0	0.008	0.014	66.064	0.000	0.000	0.000	0.000	0.000	0.000
58	A	68	SER	0	-0.089	-0.063	68.457	0.000	0.000	0.000	0.000	0.000	0.000
59	A	69	ASP	-1	-0.803	-0.870	68.874	0.001	0.001	0.000	0.000	0.000	0.000
60	A	70	GLU	-1	-0.855	-0.937	70.375	0.003	0.003	0.000	0.000	0.000	0.000
61	A	71	ASN	0	0.012	-0.002	74.185	0.000	0.000	0.000	0.000	0.000	0.000
62	A	72	TYR	0	-0.004	-0.033	76.166	0.000	0.000	0.000	0.000	0.000	0.000
63	A	73	LYS	1	0.840	0.941	72.883	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	74	ASP	-1	-0.837	-0.918	79.507	0.003	0.003	0.000	0.000	0.000	0.000
65	A	75	PRO	0	0.025	0.014	76.970	0.000	0.000	0.000	0.000	0.000	0.000
66	A	76	THR	0	-0.096	-0.049	75.552	0.000	0.000	0.000	0.000	0.000	0.000
67	A	77	ASN	0	0.063	0.044	78.382	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	78	LEU	0	0.076	0.031	79.060	0.000	0.000	0.000	0.000	0.000	0.000
69	A	79	GLN	0	0.043	0.020	78.056	0.000	0.000	0.000	0.000	0.000	0.000
70	A	80	GLY	0	0.031	0.010	75.506	0.000	0.000	0.000	0.000	0.000	0.000
71	A	81	LYS	1	0.809	0.895	74.281	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	82	LEU	0	0.046	0.027	74.168	0.000	0.000	0.000	0.000	0.000	0.000
73	A	83	GLN	0	-0.006	0.006	70.717	0.000	0.000	0.000	0.000	0.000	0.000
74	A	84	LYS	1	0.908	0.938	70.004	-0.005	-0.005	0.000	0.000	0.000	0.000
75	A	85	HIS	0	-0.046	-0.015	69.191	0.000	0.000	0.000	0.000	0.000	0.000
76	A	86	GLN	0	0.028	0.003	69.455	0.000	0.000	0.000	0.000	0.000	0.000
77	A	87	ALA	0	-0.017	-0.003	66.262	0.000	0.000	0.000	0.000	0.000	0.000
78	A	88	PHE	0	-0.008	-0.001	64.536	0.000	0.000	0.000	0.000	0.000	0.000
79	A	89	GLU	-1	-0.836	-0.939	64.818	-0.003	-0.003	0.000	0.000	0.000	0.000
80	A	90	ALA	0	-0.031	-0.009	64.760	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	91	GLU	-1	-0.815	-0.893	58.748	0.000	0.000	0.000	0.000	0.000	0.000
82	A	92	VAL	0	0.009	-0.007	60.361	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	93	GLN	0	-0.002	-0.011	61.145	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	94	ALA	0	-0.036	0.002	59.023	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	95	ASN	0	-0.004	-0.006	55.080	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	96	SER	0	-0.012	-0.013	56.652	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	97	GLY	0	0.001	0.000	55.518	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	98	ALA	0	-0.014	-0.018	52.588	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	99	ILE	0	0.026	0.005	52.365	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	100	VAL	0	0.022	0.018	53.710	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	101	LYS	1	0.888	0.945	48.033	0.011	0.011	0.000	0.000	0.000	0.000
92	A	102	LEU	0	-0.009	0.022	48.184	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	103	ASP	-1	-0.802	-0.891	50.252	-0.022	-0.022	0.000	0.000	0.000	0.000
94	A	104	GLU	-1	-0.949	-0.966	48.566	-0.026	-0.026	0.000	0.000	0.000	0.000
95	A	105	THR	0	-0.032	-0.036	44.519	-0.003	-0.003	0.000	0.000	0.000	0.000
96	A	106	GLY	0	-0.001	-0.016	46.298	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	107	ASN	0	-0.042	-0.048	48.470	-0.003	-0.003	0.000	0.000	0.000	0.000
98	A	108	LEU	0	-0.002	0.033	44.170	-0.002	-0.002	0.000	0.000	0.000	0.000
99	A	109	MET	0	-0.002	0.007	43.141	-0.004	-0.004	0.000	0.000	0.000	0.000
100	A	110	ILE	0	-0.023	-0.013	45.619	-0.003	-0.003	0.000	0.000	0.000	0.000
101	A	111	SER	0	-0.098	-0.056	47.997	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	112	GLU	-1	-0.811	-0.873	42.190	-0.055	-0.055	0.000	0.000	0.000	0.000
103	A	113	GLY	0	-0.021	0.003	44.690	-0.003	-0.003	0.000	0.000	0.000	0.000
104	A	114	HIS	0	-0.018	-0.008	40.435	-0.002	-0.002	0.000	0.000	0.000	0.000
105	A	115	PHE	0	-0.005	-0.007	38.523	0.002	0.002	0.000	0.000	0.000	0.000
106	A	116	ALA	0	-0.013	-0.001	43.395	0.001	0.001	0.000	0.000	0.000	0.000
107	A	117	SER	0	0.016	-0.021	45.420	0.004	0.004	0.000	0.000	0.000	0.000
108	A	118	GLU	-1	-0.793	-0.855	48.269	-0.034	-0.034	0.000	0.000	0.000	0.000
109	A	119	THR	0	-0.010	0.004	47.457	0.002	0.002	0.000	0.000	0.000	0.000
110	A	120	ILE	0	-0.021	0.011	44.901	0.002	0.002	0.000	0.000	0.000	0.000
111	A	121	ARG	1	0.852	0.885	49.309	0.036	0.036	0.000	0.000	0.000	0.000
112	A	122	THR	0	-0.025	-0.031	52.834	0.002	0.002	0.000	0.000	0.000	0.000
113	A	123	ARG	1	0.730	0.816	48.059	0.018	0.018	0.000	0.000	0.000	0.000
114	A	124	LEU	0	0.002	0.012	51.337	0.002	0.002	0.000	0.000	0.000	0.000
115	A	125	MET	0	-0.043	-0.020	54.283	0.001	0.001	0.000	0.000	0.000	0.000
116	A	126	GLU	-1	-0.813	-0.887	56.493	-0.014	-0.014	0.000	0.000	0.000	0.000
117	A	127	LEU	0	0.012	0.008	52.287	0.001	0.001	0.000	0.000	0.000	0.000
118	A	128	HIS	1	0.801	0.867	56.898	0.018	0.018	0.000	0.000	0.000	0.000
119	A	129	ARG	1	0.808	0.900	59.643	0.014	0.014	0.000	0.000	0.000	0.000
120	A	130	GLN	0	0.013	-0.019	59.656	0.001	0.001	0.000	0.000	0.000	0.000
121	A	131	TRP	0	0.014	0.016	59.372	0.002	0.002	0.000	0.000	0.000	0.000
122	A	132	GLU	-1	-0.816	-0.920	61.415	-0.013	-0.013	0.000	0.000	0.000	0.000
123	A	133	LEU	0	-0.058	-0.019	64.664	0.001	0.001	0.000	0.000	0.000	0.000
124	A	134	LEU	0	-0.008	0.000	61.484	0.001	0.001	0.000	0.000	0.000	0.000
125	A	135	LEU	0	0.006	-0.001	63.925	0.001	0.001	0.000	0.000	0.000	0.000
126	A	136	GLU	-1	-0.867	-0.888	66.770	-0.008	-0.008	0.000	0.000	0.000	0.000
127	A	137	LYS	1	0.829	0.878	68.103	0.007	0.007	0.000	0.000	0.000	0.000
128	A	138	MET	0	-0.026	0.022	66.218	0.001	0.001	0.000	0.000	0.000	0.000
129	A	139	ARG	1	0.854	0.892	69.479	0.008	0.008	0.000	0.000	0.000	0.000
130	A	140	GLU	-1	-0.828	-0.895	72.426	-0.006	-0.006	0.000	0.000	0.000	0.000
131	A	141	LYS	1	0.791	0.895	69.954	0.001	0.001	0.000	0.000	0.000	0.000
132	A	142	GLY	0	0.048	0.019	73.355	0.001	0.001	0.000	0.000	0.000	0.000
133	A	143	ILE	0	-0.013	-0.019	74.721	0.000	0.000	0.000	0.000	0.000	0.000
134	A	144	LYS	1	0.819	0.929	77.318	0.002	0.002	0.000	0.000	0.000	0.000
135	A	145	LEU	0	-0.045	-0.023	74.633	0.000	0.000	0.000	0.000	0.000	0.000
136	A	146	LEU	0	-0.031	-0.013	78.782	0.000	0.000	0.000	0.000	0.000	0.000
137	A	147	GLN	0	-0.044	0.006	81.633	0.000	0.000	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:11:THR)