FMO DATABASE

FMODB ID: 72MJK

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	OptH
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	-1039434.195072
FMO2-HF: Nuclear repulsion	991724.706763
FMO2-HF: Total energy	-47709.48831
FMO2-MP2: Total energy	-47851.010189

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.
0.759	2.803	-0.011	-0.797	-1.236	0.002

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 : 0.057 / 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

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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	0.031	0.029	3.682	-0.772	1.114	-0.011	-0.764	-1.111	0.002
4	A	425	ASN	0	-0.047	-0.012	6.014	0.064	0.064	0.000	0.000	0.000	0.000
5	A	426	HIS	0	0.037	-0.002	9.251	-0.055	-0.055	0.000	0.000	0.000	0.000
6	A	427	ARG	1	0.841	0.912	11.531	0.218	0.218	0.000	0.000	0.000	0.000
7	A	428	GLY	0	0.050	0.034	7.409	0.115	0.115	0.000	0.000	0.000	0.000
8	A	429	GLU	-1	-0.816	-0.896	7.459	0.101	0.101	0.000	0.000	0.000	0.000
9	A	430	THR	0	0.029	-0.016	3.718	-0.476	-0.318	0.000	-0.033	-0.125	0.000
10	A	431	LEU	0	0.021	-0.010	6.171	0.096	0.096	0.000	0.000	0.000	0.000
11	A	432	LEU	0	0.054	0.039	7.451	0.026	0.026	0.000	0.000	0.000	0.000
12	A	433	HIS	0	0.064	0.047	7.855	-0.078	-0.078	0.000	0.000	0.000	0.000
13	A	434	ILE	0	-0.004	-0.001	10.354	-0.031	-0.031	0.000	0.000	0.000	0.000
14	A	435	ALA	0	-0.011	-0.009	11.923	-0.003	-0.003	0.000	0.000	0.000	0.000
15	A	436	SER	0	-0.016	-0.014	12.840	0.014	0.014	0.000	0.000	0.000	0.000
16	A	437	ILE	0	-0.012	0.004	13.974	-0.013	-0.013	0.000	0.000	0.000	0.000
17	A	438	LYS	1	0.885	0.938	16.130	0.091	0.091	0.000	0.000	0.000	0.000
18	A	439	GLY	0	0.052	0.038	17.699	-0.005	-0.005	0.000	0.000	0.000	0.000
19	A	440	ASP	-1	-0.904	-0.932	16.510	-0.022	-0.022	0.000	0.000	0.000	0.000
20	A	441	ILE	0	0.040	-0.005	16.947	0.015	0.015	0.000	0.000	0.000	0.000
21	A	442	PRO	0	0.018	0.014	17.932	0.017	0.017	0.000	0.000	0.000	0.000
22	A	443	SER	0	-0.032	-0.035	13.779	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	444	VAL	0	-0.027	-0.012	13.356	0.023	0.023	0.000	0.000	0.000	0.000
24	A	445	GLU	-1	-0.946	-0.978	13.896	0.140	0.140	0.000	0.000	0.000	0.000
25	A	446	TYR	0	0.023	0.020	12.181	0.016	0.016	0.000	0.000	0.000	0.000
26	A	447	LEU	0	-0.005	-0.005	8.234	-0.003	-0.003	0.000	0.000	0.000	0.000
27	A	448	LEU	0	-0.039	-0.021	10.527	0.082	0.082	0.000	0.000	0.000	0.000
28	A	449	GLN	0	-0.017	-0.009	12.645	0.013	0.013	0.000	0.000	0.000	0.000
29	A	450	ASN	0	-0.121	-0.068	10.975	-0.031	-0.031	0.000	0.000	0.000	0.000
30	A	451	GLY	0	-0.022	0.002	9.958	-0.029	-0.029	0.000	0.000	0.000	0.000
31	A	452	SER	0	-0.078	-0.037	6.900	0.162	0.162	0.000	0.000	0.000	0.000
32	A	453	ASP	-1	-0.860	-0.944	6.742	1.191	1.191	0.000	0.000	0.000	0.000
33	A	454	PRO	0	-0.004	0.001	8.072	0.249	0.249	0.000	0.000	0.000	0.000
34	A	455	ASN	0	-0.072	-0.025	10.499	-0.212	-0.212	0.000	0.000	0.000	0.000
35	A	456	VAL	0	0.001	0.004	5.296	0.182	0.182	0.000	0.000	0.000	0.000
36	A	457	LYS	1	0.866	0.931	8.293	-0.745	-0.745	0.000	0.000	0.000	0.000
37	A	458	ASP	-1	-0.829	-0.894	8.018	0.320	0.320	0.000	0.000	0.000	0.000
38	A	459	HIS	0	-0.027	-0.048	8.188	0.117	0.117	0.000	0.000	0.000	0.000
39	A	460	ALA	0	-0.037	-0.002	11.517	0.008	0.008	0.000	0.000	0.000	0.000
40	A	461	GLY	0	-0.016	-0.011	13.034	-0.004	-0.004	0.000	0.000	0.000	0.000
41	A	462	TRP	0	-0.012	-0.012	13.805	0.058	0.058	0.000	0.000	0.000	0.000
42	A	463	THR	0	-0.003	-0.019	11.805	0.078	0.078	0.000	0.000	0.000	0.000
43	A	464	PRO	0	0.032	-0.001	9.940	-0.107	-0.107	0.000	0.000	0.000	0.000
44	A	465	LEU	0	0.025	0.016	12.778	-0.074	-0.074	0.000	0.000	0.000	0.000
45	A	466	HIS	0	-0.034	0.009	15.842	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	467	GLU	-1	-0.842	-0.934	14.098	0.087	0.087	0.000	0.000	0.000	0.000
47	A	468	ALA	0	-0.011	0.003	16.862	-0.033	-0.033	0.000	0.000	0.000	0.000
48	A	469	CYS	0	-0.081	-0.034	18.618	-0.024	-0.024	0.000	0.000	0.000	0.000
49	A	470	ASN	0	-0.073	-0.038	20.456	-0.029	-0.029	0.000	0.000	0.000	0.000
50	A	471	HIS	0	-0.049	-0.037	19.031	-0.032	-0.032	0.000	0.000	0.000	0.000
51	A	472	GLY	0	0.009	0.018	22.341	-0.011	-0.011	0.000	0.000	0.000	0.000
52	A	473	HIS	0	-0.001	0.002	19.365	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	474	LEU	0	0.033	0.010	21.468	0.020	0.020	0.000	0.000	0.000	0.000
54	A	475	LYS	1	0.976	0.986	21.635	-0.100	-0.100	0.000	0.000	0.000	0.000
55	A	476	VAL	0	0.022	0.018	16.464	0.012	0.012	0.000	0.000	0.000	0.000
56	A	477	VAL	0	0.021	0.002	18.094	0.036	0.036	0.000	0.000	0.000	0.000
57	A	478	GLU	-1	-0.965	-0.984	19.559	0.155	0.155	0.000	0.000	0.000	0.000
58	A	479	LEU	0	-0.009	-0.002	17.459	0.012	0.012	0.000	0.000	0.000	0.000
59	A	480	LEU	0	0.012	0.012	13.292	0.039	0.039	0.000	0.000	0.000	0.000
60	A	481	LEU	0	-0.029	-0.016	16.460	0.040	0.040	0.000	0.000	0.000	0.000
61	A	482	GLN	0	-0.026	-0.014	19.327	0.011	0.011	0.000	0.000	0.000	0.000
62	A	483	HIS	0	-0.079	-0.030	14.484	-0.015	-0.015	0.000	0.000	0.000	0.000
63	A	484	LYS	1	0.921	0.958	14.732	-0.257	-0.257	0.000	0.000	0.000	0.000
64	A	485	ALA	0	0.035	0.034	14.928	0.058	0.058	0.000	0.000	0.000	0.000
65	A	486	LEU	0	-0.041	-0.031	15.711	-0.078	-0.078	0.000	0.000	0.000	0.000
66	A	487	VAL	0	0.027	0.009	17.984	0.002	0.002	0.000	0.000	0.000	0.000
67	A	488	ASN	0	-0.025	-0.015	20.787	-0.026	-0.026	0.000	0.000	0.000	0.000
68	A	489	THR	0	-0.036	0.003	15.114	-0.006	-0.006	0.000	0.000	0.000	0.000
69	A	490	THR	0	0.007	0.012	18.532	-0.009	-0.009	0.000	0.000	0.000	0.000
70	A	491	GLY	0	0.053	0.012	16.398	0.053	0.053	0.000	0.000	0.000	0.000
71	A	492	TYR	0	0.030	0.019	17.362	-0.022	-0.022	0.000	0.000	0.000	0.000
72	A	493	GLN	0	-0.015	-0.017	18.698	-0.016	-0.016	0.000	0.000	0.000	0.000
73	A	494	ASN	0	0.016	-0.004	20.571	0.002	0.002	0.000	0.000	0.000	0.000
74	A	495	ASP	-1	-0.817	-0.887	21.567	0.121	0.121	0.000	0.000	0.000	0.000
75	A	496	SER	0	-0.011	-0.032	20.566	0.030	0.030	0.000	0.000	0.000	0.000
76	A	497	PRO	0	0.051	0.007	18.947	-0.021	-0.021	0.000	0.000	0.000	0.000
77	A	498	LEU	0	0.026	0.009	21.432	-0.018	-0.018	0.000	0.000	0.000	0.000
78	A	499	HIS	0	-0.033	-0.002	24.369	-0.004	-0.004	0.000	0.000	0.000	0.000
79	A	500	ASP	-1	-0.822	-0.898	20.955	0.140	0.140	0.000	0.000	0.000	0.000
80	A	501	ALA	0	0.016	0.019	23.913	-0.012	-0.012	0.000	0.000	0.000	0.000
81	A	502	ALA	0	-0.038	-0.035	25.670	-0.012	-0.012	0.000	0.000	0.000	0.000
82	A	503	LYS	1	0.900	0.954	24.878	-0.104	-0.104	0.000	0.000	0.000	0.000
83	A	504	ASN	0	-0.063	-0.025	25.170	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	505	GLY	0	0.012	0.022	28.232	-0.005	-0.005	0.000	0.000	0.000	0.000
85	A	506	HIS	0	0.034	0.027	25.650	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	507	VAL	0	0.030	-0.011	28.778	0.009	0.009	0.000	0.000	0.000	0.000
87	A	508	ASP	-1	-0.883	-0.940	28.666	0.088	0.088	0.000	0.000	0.000	0.000
88	A	509	ILE	0	0.021	0.003	23.461	0.009	0.009	0.000	0.000	0.000	0.000
89	A	510	VAL	0	0.000	0.007	26.422	0.012	0.012	0.000	0.000	0.000	0.000
90	A	511	LYS	1	0.908	0.953	28.542	-0.069	-0.069	0.000	0.000	0.000	0.000
91	A	512	LEU	0	0.020	0.024	23.856	0.003	0.003	0.000	0.000	0.000	0.000
92	A	513	LEU	0	0.043	0.024	21.898	0.011	0.011	0.000	0.000	0.000	0.000
93	A	514	LEU	0	-0.012	-0.015	25.578	0.009	0.009	0.000	0.000	0.000	0.000
94	A	515	SER	0	-0.106	-0.045	27.766	0.001	0.001	0.000	0.000	0.000	0.000
95	A	516	TYR	0	0.022	0.006	23.247	0.006	0.006	0.000	0.000	0.000	0.000
96	A	517	GLY	0	-0.027	-0.013	25.481	0.015	0.015	0.000	0.000	0.000	0.000
97	A	518	ALA	0	-0.018	-0.008	25.227	0.006	0.006	0.000	0.000	0.000	0.000
98	A	519	SER	0	-0.038	-0.035	26.225	-0.018	-0.018	0.000	0.000	0.000	0.000
99	A	520	ARG	1	0.921	0.959	28.288	-0.093	-0.093	0.000	0.000	0.000	0.000
100	A	521	ASN	0	-0.064	-0.037	31.010	-0.006	-0.006	0.000	0.000	0.000	0.000
101	A	522	ALA	0	0.031	0.022	26.229	-0.003	-0.003	0.000	0.000	0.000	0.000
102	A	523	VAL	0	-0.033	-0.017	27.836	-0.007	-0.007	0.000	0.000	0.000	0.000
103	A	524	ASN	0	0.020	0.002	25.006	0.006	0.006	0.000	0.000	0.000	0.000
104	A	525	ILE	0	-0.049	-0.047	23.632	-0.005	-0.005	0.000	0.000	0.000	0.000
105	A	526	PHE	0	-0.066	-0.025	26.547	-0.008	-0.008	0.000	0.000	0.000	0.000
106	A	527	GLY	0	-0.020	0.000	29.299	-0.006	-0.006	0.000	0.000	0.000	0.000
107	A	528	LEU	0	-0.027	0.003	30.092	-0.003	-0.003	0.000	0.000	0.000	0.000
108	A	529	ARG	1	0.961	0.970	29.421	-0.072	-0.072	0.000	0.000	0.000	0.000
109	A	530	PRO	0	0.013	0.005	27.871	-0.007	-0.007	0.000	0.000	0.000	0.000
110	A	531	VAL	0	0.015	-0.005	30.075	-0.005	-0.005	0.000	0.000	0.000	0.000
111	A	532	ASP	-1	-0.874	-0.917	32.742	0.069	0.069	0.000	0.000	0.000	0.000
112	A	533	TYR	0	-0.054	-0.025	29.281	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	534	THR	0	-0.003	0.004	32.589	-0.004	-0.004	0.000	0.000	0.000	0.000
114	A	535	ASP	-1	-0.894	-0.960	34.834	0.041	0.041	0.000	0.000	0.000	0.000
115	A	536	ASP	-1	-0.860	-0.935	35.986	0.051	0.051	0.000	0.000	0.000	0.000
116	A	537	GLU	-1	-0.869	-0.951	37.923	0.051	0.051	0.000	0.000	0.000	0.000
117	A	538	SER	0	-0.040	-0.015	37.436	0.002	0.002	0.000	0.000	0.000	0.000
118	A	539	MET	0	-0.040	0.008	30.687	0.007	0.007	0.000	0.000	0.000	0.000
119	A	540	LYS	1	0.917	0.956	35.194	-0.044	-0.044	0.000	0.000	0.000	0.000
120	A	541	SER	0	-0.080	-0.031	37.466	0.002	0.002	0.000	0.000	0.000	0.000
121	A	542	LEU	0	-0.017	-0.011	32.991	0.002	0.002	0.000	0.000	0.000	0.000
122	A	543	LEU	0	-0.001	-0.005	30.795	0.006	0.006	0.000	0.000	0.000	0.000
123	A	544	LEU	0	-0.030	0.001	34.894	0.003	0.003	0.000	0.000	0.000	0.000
124	A	545	LEU	0	-0.047	-0.027	38.417	0.002	0.002	0.000	0.000	0.000	0.000
125	A	546	PRO	0	0.028	0.025	41.009	-0.003	-0.003	0.000	0.000	0.000	0.000

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