FMO DATABASE

FMODB ID: 2J18R

Calculation Name: 3GPR-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GPR

Chain ID: C

ChEMBL ID:

UniProt ID: P81397

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	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	131
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1170704.178452
FMO2-HF: Nuclear repulsion	1114174.301266
FMO2-HF: Total energy	-56529.877186
FMO2-MP2: Total energy	-56688.768069

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(C:3002:PHE)

Summations of interaction energy for fragment #1(C:3002:PHE)

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.
-6.065	-2.993	0.043	-1.044	-2.072	0.004

Interaction energy analysis for fragmet #1(C:3002:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.008 / q_NPA : -0.015

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	C	3004	CYS	0	-0.046	0.002	3.810	-0.155	0.937	-0.002	-0.458	-0.632	0.001
4	C	3005	LEU	0	0.057	0.024	6.010	-0.383	-0.383	0.000	0.000	0.000	0.000
5	C	3006	PRO	0	0.017	0.002	9.420	-0.027	-0.027	0.000	0.000	0.000	0.000
6	C	3007	GLY	0	0.031	0.012	12.225	0.045	0.045	0.000	0.000	0.000	0.000
7	C	3008	TRP	0	-0.041	-0.009	9.655	0.110	0.110	0.000	0.000	0.000	0.000
8	C	3009	SER	0	0.005	0.010	9.651	-0.051	-0.051	0.000	0.000	0.000	0.000
9	C	3010	ALA	0	0.028	-0.010	7.120	0.140	0.140	0.000	0.000	0.000	0.000
10	C	3011	TYR	0	-0.038	-0.008	8.736	-0.161	-0.161	0.000	0.000	0.000	0.000
11	C	3012	ASP	-1	-0.901	-0.943	5.380	-0.307	-0.307	0.000	0.000	0.000	0.000
12	C	3013	GLN	0	0.011	-0.010	3.808	-1.062	-0.322	0.007	-0.180	-0.567	0.001
13	C	3014	HIS	0	-0.021	-0.003	5.702	0.576	0.576	0.000	0.000	0.000	0.000
14	C	3016	TYR	0	-0.006	-0.027	8.776	-0.062	-0.062	0.000	0.000	0.000	0.000
15	C	3017	GLN	0	0.002	-0.026	12.450	-0.020	-0.020	0.000	0.000	0.000	0.000
16	C	3018	ALA	0	-0.017	-0.005	15.093	0.014	0.014	0.000	0.000	0.000	0.000
17	C	3019	PHE	0	0.022	0.029	17.387	-0.023	-0.023	0.000	0.000	0.000	0.000
18	C	3020	ASN	0	-0.021	-0.027	21.134	-0.002	-0.002	0.000	0.000	0.000	0.000
19	C	3021	GLU	-1	-0.940	-0.969	24.480	0.116	0.116	0.000	0.000	0.000	0.000
20	C	3022	PRO	0	-0.052	-0.025	25.792	0.015	0.015	0.000	0.000	0.000	0.000
21	C	3023	LYS	1	0.917	0.976	24.715	-0.173	-0.173	0.000	0.000	0.000	0.000
22	C	3024	THR	0	0.058	0.035	28.872	-0.001	-0.001	0.000	0.000	0.000	0.000
23	C	3025	TRP	0	0.014	-0.003	25.911	0.014	0.014	0.000	0.000	0.000	0.000
24	C	3026	ASP	-1	-0.898	-0.968	26.501	0.169	0.169	0.000	0.000	0.000	0.000
25	C	3027	GLU	-1	-0.925	-0.981	26.146	0.147	0.147	0.000	0.000	0.000	0.000
26	C	3028	ALA	0	0.005	0.011	23.751	0.012	0.012	0.000	0.000	0.000	0.000
27	C	3029	GLU	-1	-0.761	-0.929	20.727	0.366	0.366	0.000	0.000	0.000	0.000
28	C	3030	ARG	1	0.855	0.926	21.277	-0.157	-0.157	0.000	0.000	0.000	0.000
29	C	3031	PHE	0	0.035	0.033	20.795	-0.001	-0.001	0.000	0.000	0.000	0.000
30	C	3032	CYS	0	-0.070	0.001	15.081	-0.003	-0.003	0.000	0.000	0.000	0.000
31	C	3033	THR	0	0.010	-0.009	16.849	0.043	0.043	0.000	0.000	0.000	0.000
32	C	3034	GLU	-1	-1.028	-0.990	18.019	0.242	0.242	0.000	0.000	0.000	0.000
33	C	3035	GLN	0	-0.043	-0.012	15.150	-0.036	-0.036	0.000	0.000	0.000	0.000
34	C	3036	ALA	0	-0.010	0.003	11.299	0.014	0.014	0.000	0.000	0.000	0.000
35	C	3037	LYS	1	0.924	0.984	8.524	-1.336	-1.336	0.000	0.000	0.000	0.000
36	C	3038	ARG	1	0.992	0.976	11.313	-0.582	-0.582	0.000	0.000	0.000	0.000
37	C	3039	GLY	0	-0.001	-0.005	13.606	0.084	0.084	0.000	0.000	0.000	0.000
38	C	3040	HIS	0	-0.042	-0.025	14.455	-0.098	-0.098	0.000	0.000	0.000	0.000
39	C	3041	LEU	0	0.004	0.019	16.183	0.044	0.044	0.000	0.000	0.000	0.000
40	C	3042	VAL	0	-0.040	-0.008	16.482	0.040	0.040	0.000	0.000	0.000	0.000
41	C	3043	SER	0	0.048	0.027	16.339	-0.031	-0.031	0.000	0.000	0.000	0.000
42	C	3044	ILE	0	-0.032	-0.013	17.196	0.027	0.027	0.000	0.000	0.000	0.000
43	C	3045	GLY	0	0.031	0.017	18.220	-0.025	-0.025	0.000	0.000	0.000	0.000
44	C	3046	SER	0	0.004	-0.010	16.492	-0.028	-0.028	0.000	0.000	0.000	0.000
45	C	3047	ASP	-1	-0.874	-0.932	19.074	0.096	0.096	0.000	0.000	0.000	0.000
46	C	3048	GLY	0	0.015	0.006	17.681	-0.004	-0.004	0.000	0.000	0.000	0.000
47	C	3049	GLU	-1	-0.902	-0.963	13.563	0.467	0.467	0.000	0.000	0.000	0.000
48	C	3050	ALA	0	-0.014	-0.008	17.251	0.022	0.022	0.000	0.000	0.000	0.000
49	C	3051	ASP	-1	-0.916	-0.975	20.197	0.096	0.096	0.000	0.000	0.000	0.000
50	C	3052	PHE	0	0.028	0.033	12.481	-0.009	-0.009	0.000	0.000	0.000	0.000
51	C	3053	VAL	0	0.055	0.026	16.210	-0.002	-0.002	0.000	0.000	0.000	0.000
52	C	3054	ALA	0	-0.062	-0.028	18.197	-0.012	-0.012	0.000	0.000	0.000	0.000
53	C	3055	GLN	0	0.041	0.012	19.663	-0.009	-0.009	0.000	0.000	0.000	0.000
54	C	3056	LEU	0	0.049	0.046	14.093	-0.013	-0.013	0.000	0.000	0.000	0.000
55	C	3057	VAL	0	0.000	-0.008	18.280	-0.013	-0.013	0.000	0.000	0.000	0.000
56	C	3058	THR	0	-0.044	-0.028	20.772	-0.017	-0.017	0.000	0.000	0.000	0.000
57	C	3059	ASN	0	-0.061	-0.034	19.889	-0.010	-0.010	0.000	0.000	0.000	0.000
58	C	3060	ASN	0	0.000	-0.006	18.485	-0.009	-0.009	0.000	0.000	0.000	0.000
59	C	3061	ILE	0	-0.119	-0.018	22.097	-0.006	-0.006	0.000	0.000	0.000	0.000
60	C	3062	LYS	1	0.964	0.956	25.070	-0.060	-0.060	0.000	0.000	0.000	0.000
61	C	3063	ARG	1	0.950	0.946	25.478	-0.044	-0.044	0.000	0.000	0.000	0.000
62	C	3064	PRO	0	-0.024	0.028	27.359	-0.002	-0.002	0.000	0.000	0.000	0.000
63	C	3065	GLU	-1	-0.918	-0.949	29.222	0.069	0.069	0.000	0.000	0.000	0.000
64	C	3066	LEU	0	-0.010	-0.034	25.355	0.002	0.002	0.000	0.000	0.000	0.000
65	C	3067	TYR	0	-0.024	-0.019	28.075	0.003	0.003	0.000	0.000	0.000	0.000
66	C	3068	VAL	0	0.003	0.019	21.866	0.002	0.002	0.000	0.000	0.000	0.000
67	C	3069	TRP	0	0.053	0.031	24.413	-0.002	-0.002	0.000	0.000	0.000	0.000
68	C	3070	ILE	0	-0.036	-0.015	21.945	0.021	0.021	0.000	0.000	0.000	0.000
69	C	3071	GLY	0	0.072	0.027	22.251	0.014	0.014	0.000	0.000	0.000	0.000
70	C	3072	LEU	0	-0.072	-0.023	23.320	0.005	0.005	0.000	0.000	0.000	0.000
71	C	3073	ARG	1	0.910	0.964	26.162	-0.195	-0.195	0.000	0.000	0.000	0.000
72	C	3074	ASP	-1	-0.878	-0.924	28.893	0.130	0.130	0.000	0.000	0.000	0.000
73	C	3075	ARG	1	0.873	0.954	31.747	-0.136	-0.136	0.000	0.000	0.000	0.000
74	C	3076	ARG	1	0.956	0.987	35.353	-0.086	-0.086	0.000	0.000	0.000	0.000
75	C	3077	LYS	1	0.863	0.909	37.236	-0.084	-0.084	0.000	0.000	0.000	0.000
76	C	3078	GLU	-1	-0.868	-0.932	34.863	0.116	0.116	0.000	0.000	0.000	0.000
77	C	3079	GLN	0	0.028	0.027	33.305	-0.001	-0.001	0.000	0.000	0.000	0.000
78	C	3080	GLN	0	-0.073	-0.047	29.185	0.015	0.015	0.000	0.000	0.000	0.000
79	C	3081	CYS	0	0.031	0.014	30.905	0.003	0.003	0.000	0.000	0.000	0.000
80	C	3082	SER	0	-0.044	-0.037	32.325	-0.010	-0.010	0.000	0.000	0.000	0.000
81	C	3083	SER	0	-0.048	-0.044	33.763	-0.008	-0.008	0.000	0.000	0.000	0.000
82	C	3084	GLU	-1	-0.935	-0.953	34.219	0.105	0.105	0.000	0.000	0.000	0.000
83	C	3085	TRP	0	-0.016	-0.006	37.917	-0.007	-0.007	0.000	0.000	0.000	0.000
84	C	3086	SER	0	-0.009	-0.010	39.668	0.003	0.003	0.000	0.000	0.000	0.000
85	C	3087	MET	0	0.004	-0.010	41.334	-0.002	-0.002	0.000	0.000	0.000	0.000
86	C	3088	SER	0	0.002	-0.005	37.051	0.001	0.001	0.000	0.000	0.000	0.000
87	C	3089	ALA	0	-0.026	0.006	38.657	0.003	0.003	0.000	0.000	0.000	0.000
88	C	3090	SER	0	0.019	0.013	37.951	0.002	0.002	0.000	0.000	0.000	0.000
89	C	3091	ILE	0	0.007	-0.002	38.052	-0.006	-0.006	0.000	0.000	0.000	0.000
90	C	3092	ILE	0	-0.006	-0.004	40.019	0.003	0.003	0.000	0.000	0.000	0.000
91	C	3093	TYR	0	-0.030	-0.022	42.787	-0.003	-0.003	0.000	0.000	0.000	0.000
92	C	3094	VAL	0	-0.007	0.005	42.316	0.000	0.000	0.000	0.000	0.000	0.000
93	C	3095	ASN	0	0.009	0.004	45.467	0.000	0.000	0.000	0.000	0.000	0.000
94	C	3096	TRP	0	0.015	0.006	39.659	-0.002	-0.002	0.000	0.000	0.000	0.000
95	C	3097	ASN	0	0.030	0.013	46.403	-0.003	-0.003	0.000	0.000	0.000	0.000
96	C	3098	THR	0	-0.015	-0.010	43.994	0.000	0.000	0.000	0.000	0.000	0.000
97	C	3099	GLY	0	0.041	0.023	44.985	0.000	0.000	0.000	0.000	0.000	0.000
98	C	3100	GLU	-1	-0.864	-0.913	42.372	0.073	0.073	0.000	0.000	0.000	0.000
99	C	3101	SER	0	-0.049	-0.030	39.581	0.001	0.001	0.000	0.000	0.000	0.000
100	C	3102	GLN	0	0.010	-0.021	34.116	0.006	0.006	0.000	0.000	0.000	0.000
101	C	3103	MET	0	0.011	0.005	34.861	0.001	0.001	0.000	0.000	0.000	0.000
102	C	3104	CYS	0	-0.018	-0.004	30.221	0.011	0.011	0.000	0.000	0.000	0.000
103	C	3105	GLN	0	0.031	0.011	28.236	-0.005	-0.005	0.000	0.000	0.000	0.000
104	C	3106	GLY	0	0.073	0.027	27.598	0.007	0.007	0.000	0.000	0.000	0.000
105	C	3107	LEU	0	-0.023	-0.001	22.931	-0.001	-0.001	0.000	0.000	0.000	0.000
106	C	3108	ALA	0	0.042	0.041	26.999	0.000	0.000	0.000	0.000	0.000	0.000
107	C	3109	ARG	1	0.854	0.930	23.237	-0.109	-0.109	0.000	0.000	0.000	0.000
108	C	3110	TRP	0	0.032	0.033	29.063	-0.006	-0.006	0.000	0.000	0.000	0.000
109	C	3111	THR	0	0.026	-0.005	32.162	-0.003	-0.003	0.000	0.000	0.000	0.000
110	C	3112	GLY	0	-0.014	0.010	29.118	-0.003	-0.003	0.000	0.000	0.000	0.000
111	C	3113	PHE	0	0.073	0.023	26.523	0.006	0.006	0.000	0.000	0.000	0.000
112	C	3114	ARG	1	0.803	0.899	22.805	-0.147	-0.147	0.000	0.000	0.000	0.000
113	C	3115	LYS	1	0.906	0.964	27.371	-0.072	-0.072	0.000	0.000	0.000	0.000
114	C	3116	TRP	0	0.029	-0.002	23.515	0.010	0.010	0.000	0.000	0.000	0.000
115	C	3117	ASP	-1	-0.950	-0.965	29.337	0.086	0.086	0.000	0.000	0.000	0.000
116	C	3118	TYR	0	-0.022	-0.010	31.283	0.008	0.008	0.000	0.000	0.000	0.000
117	C	3119	SER	0	0.057	0.032	32.888	-0.007	-0.007	0.000	0.000	0.000	0.000
118	C	3120	ASP	-1	-0.917	-0.977	34.246	0.096	0.096	0.000	0.000	0.000	0.000
119	C	3122	GLN	0	-0.030	0.001	32.358	0.012	0.012	0.000	0.000	0.000	0.000
120	C	3123	ALA	0	0.000	0.010	32.776	-0.006	-0.006	0.000	0.000	0.000	0.000
121	C	3124	LYS	1	0.943	0.963	31.290	-0.083	-0.083	0.000	0.000	0.000	0.000
122	C	3125	ASN	0	0.008	0.001	28.939	-0.009	-0.009	0.000	0.000	0.000	0.000
123	C	3126	PRO	0	-0.004	0.004	24.783	0.009	0.009	0.000	0.000	0.000	0.000
124	C	3127	PHE	0	0.014	-0.024	20.460	-0.004	-0.004	0.000	0.000	0.000	0.000
125	C	3128	VAL	0	0.002	-0.012	16.410	-0.013	-0.013	0.000	0.000	0.000	0.000
126	C	3130	LYS	1	0.895	0.944	12.708	-0.574	-0.574	0.000	0.000	0.000	0.000
127	C	3131	PHE	0	-0.052	-0.008	9.697	0.025	0.025	0.000	0.000	0.000	0.000
128	C	3132	SER	0	0.022	0.006	7.313	-0.051	-0.051	0.000	0.000	0.000	0.000
129	C	3133	SER	0	-0.010	-0.013	3.184	-2.981	-2.101	0.038	-0.370	-0.549	0.002
130	C	3134	GLU	-1	-0.951	-0.964	5.939	0.208	0.254	-0.001	-0.002	-0.043	0.000
131	C	3135	CYS	0	-0.006	0.002	4.611	-0.467	-0.153	0.001	-0.034	-0.281	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:3002:PHE)