FMO DATABASE

FMODB ID: 6NG3Z

Calculation Name: 3C5R-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3C5R

Chain ID: A

ChEMBL ID:

UniProt ID: Q99728

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	125
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1042844.143032
FMO2-HF: Nuclear repulsion	995134.092478
FMO2-HF: Total energy	-47710.050554
FMO2-MP2: Total energy	-47851.588884

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:-2:PRO)

Summations of interaction energy for fragment #1(A:-2:PRO)

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.
0.461	2.402	-0.011	-0.839	-1.091	0.003

Interaction energy analysis for fragmet #1(A:-2:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.045 / q_NPA : 0.018

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	0	THR	0	0.008	0.000	3.866	-0.916	0.898	-0.010	-0.814	-0.990	0.003
4	A	425	ASN	0	-0.044	-0.025	6.292	0.101	0.101	0.000	0.000	0.000	0.000
5	A	426	HIS	0	0.030	-0.003	9.294	-0.097	-0.097	0.000	0.000	0.000	0.000
6	A	427	ARG	1	0.838	0.880	11.824	0.317	0.317	0.000	0.000	0.000	0.000
7	A	428	GLY	0	0.072	0.049	7.753	0.119	0.119	0.000	0.000	0.000	0.000
8	A	429	GLU	-1	-0.815	-0.859	7.676	-0.197	-0.197	0.000	0.000	0.000	0.000
9	A	430	THR	0	0.051	0.002	3.839	-0.409	-0.282	-0.001	-0.025	-0.101	0.000
10	A	431	LEU	0	0.014	-0.007	6.235	0.204	0.204	0.000	0.000	0.000	0.000
11	A	432	LEU	0	0.062	0.039	7.402	0.088	0.088	0.000	0.000	0.000	0.000
12	A	433	HIS	0	0.026	0.042	8.074	-0.045	-0.045	0.000	0.000	0.000	0.000
13	A	434	ILE	0	-0.005	-0.003	10.319	0.021	0.021	0.000	0.000	0.000	0.000
14	A	435	ALA	0	-0.015	-0.009	11.952	0.024	0.024	0.000	0.000	0.000	0.000
15	A	436	SER	0	0.008	-0.024	12.620	0.033	0.033	0.000	0.000	0.000	0.000
16	A	437	ILE	0	-0.030	-0.005	13.968	0.005	0.005	0.000	0.000	0.000	0.000
17	A	438	LYS	1	0.896	0.948	15.656	0.204	0.204	0.000	0.000	0.000	0.000
18	A	439	GLY	0	0.040	0.035	18.088	0.002	0.002	0.000	0.000	0.000	0.000
19	A	440	ASP	-1	-0.889	-0.922	16.291	-0.094	-0.094	0.000	0.000	0.000	0.000
20	A	441	ILE	0	0.033	0.002	16.819	0.007	0.007	0.000	0.000	0.000	0.000
21	A	442	PRO	0	-0.007	0.001	17.956	0.015	0.015	0.000	0.000	0.000	0.000
22	A	443	SER	0	-0.027	-0.031	13.649	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	444	VAL	0	-0.018	-0.014	13.225	0.012	0.012	0.000	0.000	0.000	0.000
24	A	445	GLU	-1	-0.876	-0.954	13.916	0.117	0.117	0.000	0.000	0.000	0.000
25	A	446	TYR	0	-0.024	-0.010	12.105	0.016	0.016	0.000	0.000	0.000	0.000
26	A	447	LEU	0	0.000	-0.010	8.327	0.008	0.008	0.000	0.000	0.000	0.000
27	A	448	LEU	0	-0.037	-0.007	10.569	0.095	0.095	0.000	0.000	0.000	0.000
28	A	449	GLN	0	-0.005	0.000	12.759	0.031	0.031	0.000	0.000	0.000	0.000
29	A	450	ASN	0	-0.103	-0.046	10.622	-0.036	-0.036	0.000	0.000	0.000	0.000
30	A	451	GLY	0	-0.002	0.008	9.826	0.003	0.003	0.000	0.000	0.000	0.000
31	A	452	SER	0	-0.075	-0.047	6.936	0.185	0.185	0.000	0.000	0.000	0.000
32	A	453	ASP	-1	-0.820	-0.907	7.091	1.094	1.094	0.000	0.000	0.000	0.000
33	A	454	PRO	0	0.006	0.000	7.822	0.142	0.142	0.000	0.000	0.000	0.000
34	A	455	ASN	0	-0.110	-0.050	10.394	-0.224	-0.224	0.000	0.000	0.000	0.000
35	A	456	VAL	0	-0.019	-0.006	4.856	0.141	0.141	0.000	0.000	0.000	0.000
36	A	457	LYS	1	0.859	0.902	8.021	-0.686	-0.686	0.000	0.000	0.000	0.000
37	A	458	ASP	-1	-0.806	-0.880	7.994	0.089	0.089	0.000	0.000	0.000	0.000
38	A	459	HIS	0	-0.030	-0.027	8.650	0.156	0.156	0.000	0.000	0.000	0.000
39	A	460	ALA	0	-0.060	-0.020	11.880	0.028	0.028	0.000	0.000	0.000	0.000
40	A	461	GLY	0	0.004	-0.014	13.488	0.016	0.016	0.000	0.000	0.000	0.000
41	A	462	TRP	0	-0.017	-0.013	13.882	0.065	0.065	0.000	0.000	0.000	0.000
42	A	463	THR	0	0.034	-0.007	11.669	0.030	0.030	0.000	0.000	0.000	0.000
43	A	464	PRO	0	0.004	-0.008	9.679	-0.084	-0.084	0.000	0.000	0.000	0.000
44	A	465	LEU	0	0.047	0.031	12.593	-0.053	-0.053	0.000	0.000	0.000	0.000
45	A	466	HIS	0	-0.012	0.025	15.672	-0.008	-0.008	0.000	0.000	0.000	0.000
46	A	467	GLU	-1	-0.856	-0.936	13.747	-0.016	-0.016	0.000	0.000	0.000	0.000
47	A	468	ALA	0	-0.003	0.002	16.569	-0.026	-0.026	0.000	0.000	0.000	0.000
48	A	469	CYS	0	-0.078	-0.035	18.333	-0.013	-0.013	0.000	0.000	0.000	0.000
49	A	470	ASN	0	-0.056	-0.021	20.249	-0.022	-0.022	0.000	0.000	0.000	0.000
50	A	471	HIS	0	-0.024	-0.021	18.629	-0.025	-0.025	0.000	0.000	0.000	0.000
51	A	472	GLY	0	0.032	0.033	22.120	-0.009	-0.009	0.000	0.000	0.000	0.000
52	A	473	HIS	0	-0.013	-0.003	19.296	0.005	0.005	0.000	0.000	0.000	0.000
53	A	474	LEU	0	0.014	0.009	21.162	0.016	0.016	0.000	0.000	0.000	0.000
54	A	475	LYS	1	0.888	0.946	21.304	-0.081	-0.081	0.000	0.000	0.000	0.000
55	A	476	VAL	0	0.022	0.014	16.113	0.011	0.011	0.000	0.000	0.000	0.000
56	A	477	VAL	0	0.009	-0.002	17.777	0.033	0.033	0.000	0.000	0.000	0.000
57	A	478	GLU	-1	-0.882	-0.929	19.394	0.132	0.132	0.000	0.000	0.000	0.000
58	A	479	LEU	0	-0.014	0.001	17.019	0.020	0.020	0.000	0.000	0.000	0.000
59	A	480	LEU	0	0.017	0.010	12.916	0.044	0.044	0.000	0.000	0.000	0.000
60	A	481	LEU	0	-0.025	-0.008	15.974	0.050	0.050	0.000	0.000	0.000	0.000
61	A	482	GLN	0	-0.050	-0.028	18.846	0.020	0.020	0.000	0.000	0.000	0.000
62	A	483	HIS	0	-0.102	-0.054	14.204	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	484	LYS	1	0.924	0.955	14.603	-0.257	-0.257	0.000	0.000	0.000	0.000
64	A	485	ALA	0	0.030	0.030	14.447	0.061	0.061	0.000	0.000	0.000	0.000
65	A	486	LEU	0	0.000	-0.011	15.364	-0.081	-0.081	0.000	0.000	0.000	0.000
66	A	487	VAL	0	0.025	0.018	17.497	-0.007	-0.007	0.000	0.000	0.000	0.000
67	A	488	ASN	0	-0.038	-0.010	20.213	-0.038	-0.038	0.000	0.000	0.000	0.000
68	A	489	THR	0	-0.047	-0.024	15.051	0.009	0.009	0.000	0.000	0.000	0.000
69	A	490	THR	0	0.018	0.016	18.472	-0.013	-0.013	0.000	0.000	0.000	0.000
70	A	491	GLY	0	0.036	0.012	16.624	0.048	0.048	0.000	0.000	0.000	0.000
71	A	492	TYR	0	0.003	0.013	17.517	-0.012	-0.012	0.000	0.000	0.000	0.000
72	A	493	GLN	0	-0.002	-0.007	18.578	-0.012	-0.012	0.000	0.000	0.000	0.000
73	A	494	ASN	0	-0.007	-0.010	20.408	0.010	0.010	0.000	0.000	0.000	0.000
74	A	495	ASP	-1	-0.758	-0.853	21.602	0.090	0.090	0.000	0.000	0.000	0.000
75	A	496	SER	0	0.002	-0.019	20.742	0.025	0.025	0.000	0.000	0.000	0.000
76	A	497	PRO	0	0.047	0.002	18.433	-0.022	-0.022	0.000	0.000	0.000	0.000
77	A	498	LEU	0	0.035	0.015	21.067	-0.018	-0.018	0.000	0.000	0.000	0.000
78	A	499	HIS	0	-0.025	0.004	24.220	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	500	ASP	-1	-0.792	-0.891	20.679	0.086	0.086	0.000	0.000	0.000	0.000
80	A	501	ALA	0	-0.002	0.005	23.901	-0.012	-0.012	0.000	0.000	0.000	0.000
81	A	502	ALA	0	-0.011	-0.027	25.624	-0.009	-0.009	0.000	0.000	0.000	0.000
82	A	503	LYS	1	0.764	0.867	23.516	-0.078	-0.078	0.000	0.000	0.000	0.000
83	A	504	ASN	0	-0.055	-0.032	24.657	-0.006	-0.006	0.000	0.000	0.000	0.000
84	A	505	GLY	0	0.008	0.015	28.229	-0.005	-0.005	0.000	0.000	0.000	0.000
85	A	506	HIS	0	0.013	0.014	25.287	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	507	VAL	0	0.024	-0.014	28.592	0.010	0.010	0.000	0.000	0.000	0.000
87	A	508	ASP	-1	-0.851	-0.932	28.089	0.063	0.063	0.000	0.000	0.000	0.000
88	A	509	ILE	0	0.014	0.008	23.156	0.010	0.010	0.000	0.000	0.000	0.000
89	A	510	VAL	0	-0.006	-0.002	26.079	0.013	0.013	0.000	0.000	0.000	0.000
90	A	511	LYS	1	0.909	0.960	28.199	-0.056	-0.056	0.000	0.000	0.000	0.000
91	A	512	LEU	0	0.008	0.018	23.177	0.005	0.005	0.000	0.000	0.000	0.000
92	A	513	LEU	0	0.046	0.022	21.475	0.013	0.013	0.000	0.000	0.000	0.000
93	A	514	LEU	0	-0.039	-0.022	25.137	0.010	0.010	0.000	0.000	0.000	0.000
94	A	515	SER	0	-0.100	-0.059	27.386	0.003	0.003	0.000	0.000	0.000	0.000
95	A	516	TYR	0	0.023	0.007	22.449	0.007	0.007	0.000	0.000	0.000	0.000
96	A	517	GLY	0	-0.014	0.004	24.845	0.016	0.016	0.000	0.000	0.000	0.000
97	A	518	ALA	0	-0.027	-0.003	24.801	0.009	0.009	0.000	0.000	0.000	0.000
98	A	519	SER	0	0.002	-0.028	25.802	-0.016	-0.016	0.000	0.000	0.000	0.000
99	A	520	ARG	1	0.862	0.922	27.800	-0.086	-0.086	0.000	0.000	0.000	0.000
100	A	521	ASN	0	-0.054	-0.021	30.528	-0.012	-0.012	0.000	0.000	0.000	0.000
101	A	522	ALA	0	0.030	0.026	26.466	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	523	VAL	0	-0.043	-0.028	27.772	-0.008	-0.008	0.000	0.000	0.000	0.000
103	A	524	ASN	0	0.014	0.004	25.147	0.010	0.010	0.000	0.000	0.000	0.000
104	A	525	ILE	0	-0.040	-0.039	23.749	-0.003	-0.003	0.000	0.000	0.000	0.000
105	A	526	PHE	0	-0.049	-0.019	26.550	-0.007	-0.007	0.000	0.000	0.000	0.000
106	A	527	GLY	0	-0.016	0.000	29.432	-0.005	-0.005	0.000	0.000	0.000	0.000
107	A	528	LEU	0	-0.030	0.004	30.180	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	529	ARG	1	0.941	0.958	29.323	-0.066	-0.066	0.000	0.000	0.000	0.000
109	A	530	PRO	0	-0.021	-0.019	27.382	-0.007	-0.007	0.000	0.000	0.000	0.000
110	A	531	VAL	0	0.011	-0.004	29.597	-0.005	-0.005	0.000	0.000	0.000	0.000
111	A	532	ASP	-1	-0.852	-0.911	32.809	0.059	0.059	0.000	0.000	0.000	0.000
112	A	533	TYR	0	-0.034	-0.009	29.285	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	534	THR	0	-0.010	-0.006	32.200	-0.004	-0.004	0.000	0.000	0.000	0.000
114	A	535	ASP	-1	-0.831	-0.925	34.328	0.030	0.030	0.000	0.000	0.000	0.000
115	A	536	ASP	-1	-0.776	-0.845	36.069	0.035	0.035	0.000	0.000	0.000	0.000
116	A	537	GLU	-1	-0.833	-0.927	37.737	0.040	0.040	0.000	0.000	0.000	0.000
117	A	538	SER	0	-0.073	-0.052	36.949	0.002	0.002	0.000	0.000	0.000	0.000
118	A	539	MET	0	-0.021	0.026	30.310	0.007	0.007	0.000	0.000	0.000	0.000
119	A	540	LYS	1	0.787	0.888	35.030	-0.030	-0.030	0.000	0.000	0.000	0.000
120	A	541	SER	0	-0.103	-0.061	37.329	0.004	0.004	0.000	0.000	0.000	0.000
121	A	542	LEU	0	-0.044	-0.021	32.380	0.003	0.003	0.000	0.000	0.000	0.000
122	A	543	LEU	0	-0.003	-0.011	30.666	0.008	0.008	0.000	0.000	0.000	0.000
123	A	544	LEU	0	0.008	0.027	34.568	0.003	0.003	0.000	0.000	0.000	0.000
124	A	545	LEU	0	-0.043	-0.038	37.947	0.005	0.005	0.000	0.000	0.000	0.000
125	A	546	PRO	0	0.012	0.023	40.750	-0.003	-0.003	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:-2:PRO)