FMO DATABASE

FMODB ID: 53R7Z

Calculation Name: 1GPR-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1GPR

Chain ID: A

ChEMBL ID:

UniProt ID: P20166

Base Structure: X-ray

Registration Date: 2023-03-13

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	OptHSide
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	158
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1480753.167759
FMO2-HF: Nuclear repulsion	1421777.430597
FMO2-HF: Total energy	-58975.737162
FMO2-MP2: Total energy	-59149.421869

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:4:GLU)

Summations of interaction energy for fragment #1(A:4:GLU)

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.
96.715	102.34	13.563	-9.233	-9.955	0.087

Interaction energy analysis for fragmet #1(A:4:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.899 / q_NPA : -0.967

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	6	LEU	0	0.018	0.021	3.842	-1.908	-0.936	-0.011	-0.420	-0.542	0.003
4	A	7	GLN	0	-0.060	-0.046	6.286	-0.208	-0.208	0.000	0.000	0.000	0.000
5	A	8	ASN	0	0.071	0.041	9.014	0.096	0.096	0.000	0.000	0.000	0.000
6	A	9	GLU	-1	-0.912	-0.952	12.363	16.363	16.363	0.000	0.000	0.000	0.000
7	A	10	ILE	0	-0.080	-0.035	14.842	-0.786	-0.786	0.000	0.000	0.000	0.000
8	A	11	GLY	0	-0.056	-0.038	11.433	-0.180	-0.180	0.000	0.000	0.000	0.000
9	A	12	GLU	-1	-0.887	-0.938	12.102	16.726	16.726	0.000	0.000	0.000	0.000
10	A	13	GLU	-1	-0.813	-0.885	6.878	32.355	32.355	0.000	0.000	0.000	0.000
11	A	14	VAL	0	-0.030	-0.024	9.552	-1.613	-1.613	0.000	0.000	0.000	0.000
12	A	15	PHE	0	0.005	-0.017	11.136	1.008	1.008	0.000	0.000	0.000	0.000
13	A	16	VAL	0	-0.025	0.003	13.854	-1.202	-1.202	0.000	0.000	0.000	0.000
14	A	17	SER	0	-0.007	-0.006	16.489	0.215	0.215	0.000	0.000	0.000	0.000
15	A	18	PRO	0	0.034	0.040	17.888	0.111	0.111	0.000	0.000	0.000	0.000
16	A	19	ILE	0	-0.005	-0.015	19.395	-0.276	-0.276	0.000	0.000	0.000	0.000
17	A	20	THR	0	-0.006	0.002	23.269	0.192	0.192	0.000	0.000	0.000	0.000
18	A	21	GLY	0	0.044	0.024	26.266	-0.247	-0.247	0.000	0.000	0.000	0.000
19	A	22	GLU	-1	-0.928	-0.926	28.422	9.375	9.375	0.000	0.000	0.000	0.000
20	A	23	ILE	0	-0.020	0.007	23.219	0.087	0.087	0.000	0.000	0.000	0.000
21	A	24	HIS	1	0.772	0.835	27.146	-10.212	-10.212	0.000	0.000	0.000	0.000
22	A	25	PRO	0	0.056	0.025	26.866	0.526	0.526	0.000	0.000	0.000	0.000
23	A	26	ILE	0	0.009	0.005	24.714	-0.222	-0.222	0.000	0.000	0.000	0.000
24	A	27	THR	0	-0.015	-0.023	27.487	-0.107	-0.107	0.000	0.000	0.000	0.000
25	A	28	ASP	-1	-0.845	-0.902	30.932	9.215	9.215	0.000	0.000	0.000	0.000
26	A	29	VAL	0	-0.006	0.006	27.977	-0.119	-0.119	0.000	0.000	0.000	0.000
27	A	30	PRO	0	-0.054	-0.014	31.389	-0.130	-0.130	0.000	0.000	0.000	0.000
28	A	31	ASP	-1	-0.780	-0.914	31.576	9.659	9.659	0.000	0.000	0.000	0.000
29	A	32	GLN	0	-0.026	-0.015	31.925	0.352	0.352	0.000	0.000	0.000	0.000
30	A	33	VAL	0	0.001	-0.005	28.572	0.104	0.104	0.000	0.000	0.000	0.000
31	A	34	PHE	0	-0.001	-0.011	24.676	0.446	0.446	0.000	0.000	0.000	0.000
32	A	35	SER	0	-0.013	-0.005	28.143	0.151	0.151	0.000	0.000	0.000	0.000
33	A	36	GLY	0	-0.048	-0.011	30.504	-0.073	-0.073	0.000	0.000	0.000	0.000
34	A	37	LYS	1	0.825	0.888	25.864	-11.318	-11.318	0.000	0.000	0.000	0.000
35	A	38	MET	0	-0.065	-0.016	26.634	0.149	0.149	0.000	0.000	0.000	0.000
36	A	39	MET	0	-0.043	-0.011	23.148	0.178	0.178	0.000	0.000	0.000	0.000
37	A	40	GLY	0	0.059	0.028	21.722	0.654	0.654	0.000	0.000	0.000	0.000
38	A	41	ASP	-1	-0.804	-0.885	21.714	11.775	11.775	0.000	0.000	0.000	0.000
39	A	42	GLY	0	0.020	-0.012	20.999	0.715	0.715	0.000	0.000	0.000	0.000
40	A	43	PHE	0	-0.029	-0.003	18.876	-0.485	-0.485	0.000	0.000	0.000	0.000
41	A	44	ALA	0	0.029	0.001	23.785	0.215	0.215	0.000	0.000	0.000	0.000
42	A	45	ILE	0	0.008	0.015	22.380	-0.154	-0.154	0.000	0.000	0.000	0.000
43	A	46	LEU	0	0.014	0.009	26.465	-0.052	-0.052	0.000	0.000	0.000	0.000
44	A	47	PRO	0	-0.037	-0.022	27.252	-0.063	-0.063	0.000	0.000	0.000	0.000
45	A	48	SER	0	0.005	-0.008	29.192	-0.321	-0.321	0.000	0.000	0.000	0.000
46	A	49	GLU	-1	-0.852	-0.904	28.059	11.201	11.201	0.000	0.000	0.000	0.000
47	A	50	GLY	0	0.021	0.018	28.216	0.211	0.211	0.000	0.000	0.000	0.000
48	A	51	ILE	0	-0.011	0.000	23.116	0.236	0.236	0.000	0.000	0.000	0.000
49	A	52	VAL	0	0.004	0.001	19.948	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	53	VAL	0	-0.008	-0.006	18.035	0.208	0.208	0.000	0.000	0.000	0.000
51	A	54	SER	0	-0.015	-0.024	12.025	-0.540	-0.540	0.000	0.000	0.000	0.000
52	A	55	PRO	0	0.019	0.020	13.749	-0.117	-0.117	0.000	0.000	0.000	0.000
53	A	56	VAL	0	0.011	0.002	9.189	0.129	0.129	0.000	0.000	0.000	0.000
54	A	57	ARG	1	0.818	0.907	2.693	-69.882	-67.276	0.423	-1.444	-1.584	0.016
55	A	58	GLY	0	0.040	0.011	6.306	1.465	1.465	0.000	0.000	0.000	0.000
56	A	59	LYS	1	0.833	0.928	7.028	-27.321	-27.321	0.000	0.000	0.000	0.000
57	A	60	ILE	0	0.010	0.017	8.764	-2.298	-2.298	0.000	0.000	0.000	0.000
58	A	61	LEU	0	-0.042	-0.041	11.011	0.352	0.352	0.000	0.000	0.000	0.000
59	A	62	ASN	0	-0.046	-0.036	13.978	-1.261	-1.261	0.000	0.000	0.000	0.000
60	A	63	VAL	0	0.019	0.023	17.594	0.052	0.052	0.000	0.000	0.000	0.000
61	A	64	PHE	0	0.037	0.027	19.976	-0.731	-0.731	0.000	0.000	0.000	0.000
62	A	65	PRO	0	-0.019	-0.032	23.513	-0.033	-0.033	0.000	0.000	0.000	0.000
63	A	66	THR	0	-0.025	-0.045	26.251	-0.099	-0.099	0.000	0.000	0.000	0.000
64	A	67	LYS	1	0.852	0.929	22.994	-13.575	-13.575	0.000	0.000	0.000	0.000
65	A	68	HIS	0	0.063	0.070	24.894	0.157	0.157	0.000	0.000	0.000	0.000
66	A	69	ALA	0	0.013	0.005	22.914	-0.040	-0.040	0.000	0.000	0.000	0.000
67	A	70	ILE	0	-0.019	-0.009	16.681	0.060	0.060	0.000	0.000	0.000	0.000
68	A	71	GLY	0	0.025	0.026	16.832	-0.304	-0.304	0.000	0.000	0.000	0.000
69	A	72	LEU	0	-0.038	-0.024	12.099	0.906	0.906	0.000	0.000	0.000	0.000
70	A	73	GLN	0	-0.032	-0.015	8.473	0.435	0.435	0.000	0.000	0.000	0.000
71	A	74	SER	0	-0.009	-0.010	7.626	2.951	2.951	0.000	0.000	0.000	0.000
72	A	75	ASP	-1	-0.730	-0.845	2.094	74.791	77.360	2.138	-1.783	-2.925	-0.009
73	A	76	GLY	0	-0.049	-0.030	3.858	1.136	1.382	0.000	-0.023	-0.223	0.000
74	A	77	GLY	0	-0.048	-0.010	5.936	-2.674	-2.674	0.000	0.000	0.000	0.000
75	A	78	ARG	1	0.838	0.896	8.303	-22.662	-22.662	0.000	0.000	0.000	0.000
76	A	79	GLU	-1	-0.918	-0.964	10.912	22.780	22.780	0.000	0.000	0.000	0.000
77	A	80	ILE	0	-0.023	-0.010	12.244	-1.323	-1.323	0.000	0.000	0.000	0.000
78	A	81	LEU	0	-0.014	0.002	15.502	0.392	0.392	0.000	0.000	0.000	0.000
79	A	82	ILE	0	0.005	0.000	17.050	-0.484	-0.484	0.000	0.000	0.000	0.000
80	A	83	HIS	0	0.008	-0.002	20.473	-0.062	-0.062	0.000	0.000	0.000	0.000
81	A	84	PHE	0	0.029	-0.008	24.079	-0.424	-0.424	0.000	0.000	0.000	0.000
82	A	85	GLY	0	0.017	0.018	26.272	-0.318	-0.318	0.000	0.000	0.000	0.000
83	A	86	ILE	0	-0.011	-0.006	29.196	0.210	0.210	0.000	0.000	0.000	0.000
84	A	87	ASP	-1	-0.870	-0.953	31.851	8.915	8.915	0.000	0.000	0.000	0.000
85	A	88	THR	0	0.011	-0.012	29.376	-0.252	-0.252	0.000	0.000	0.000	0.000
86	A	89	VAL	0	-0.007	0.013	30.315	-0.007	-0.007	0.000	0.000	0.000	0.000
87	A	90	SER	0	-0.029	-0.034	31.804	-0.095	-0.095	0.000	0.000	0.000	0.000
88	A	91	LEU	0	0.002	0.008	33.293	-0.243	-0.243	0.000	0.000	0.000	0.000
89	A	92	LYS	1	0.854	0.924	32.836	-8.765	-8.765	0.000	0.000	0.000	0.000
90	A	93	GLY	0	0.054	0.019	30.085	0.009	0.009	0.000	0.000	0.000	0.000
91	A	94	GLU	-1	-0.999	-0.978	31.020	9.315	9.315	0.000	0.000	0.000	0.000
92	A	95	GLY	0	0.060	0.032	32.533	-0.074	-0.074	0.000	0.000	0.000	0.000
93	A	96	PHE	0	-0.061	-0.029	27.018	0.227	0.227	0.000	0.000	0.000	0.000
94	A	97	THR	0	-0.014	0.004	25.685	-0.197	-0.197	0.000	0.000	0.000	0.000
95	A	98	SER	0	0.007	-0.009	20.893	0.353	0.353	0.000	0.000	0.000	0.000
96	A	99	PHE	0	-0.059	-0.041	20.362	-0.507	-0.507	0.000	0.000	0.000	0.000
97	A	100	VAL	0	-0.001	0.015	15.452	0.729	0.729	0.000	0.000	0.000	0.000
98	A	101	SER	0	-0.045	-0.027	16.266	-1.743	-1.743	0.000	0.000	0.000	0.000
99	A	102	GLU	-1	-0.828	-0.908	15.045	18.000	18.000	0.000	0.000	0.000	0.000
100	A	103	GLY	0	-0.073	-0.047	11.490	-0.245	-0.245	0.000	0.000	0.000	0.000
101	A	104	ASP	-1	-0.827	-0.900	10.648	23.875	23.875	0.000	0.000	0.000	0.000
102	A	105	ARG	1	0.698	0.815	1.853	-97.787	-98.555	11.013	-5.563	-4.681	0.077
103	A	106	VAL	0	-0.040	-0.021	8.833	-2.814	-2.814	0.000	0.000	0.000	0.000
104	A	107	GLU	-1	-0.767	-0.862	7.898	42.680	42.680	0.000	0.000	0.000	0.000
105	A	108	PRO	0	0.007	-0.015	9.511	-1.953	-1.953	0.000	0.000	0.000	0.000
106	A	109	GLY	0	0.060	0.031	12.717	-0.444	-0.444	0.000	0.000	0.000	0.000
107	A	110	GLN	0	-0.028	0.008	12.844	0.227	0.227	0.000	0.000	0.000	0.000
108	A	111	LYS	1	0.797	0.889	16.001	-13.423	-13.423	0.000	0.000	0.000	0.000
109	A	112	LEU	0	-0.015	-0.013	15.033	0.599	0.599	0.000	0.000	0.000	0.000
110	A	113	LEU	0	-0.014	-0.013	18.948	-0.329	-0.329	0.000	0.000	0.000	0.000
111	A	114	GLU	-1	-0.860	-0.918	22.618	12.264	12.264	0.000	0.000	0.000	0.000
112	A	115	VAL	0	-0.019	-0.007	26.062	-0.150	-0.150	0.000	0.000	0.000	0.000
113	A	116	ASP	-1	-0.885	-0.942	29.034	9.134	9.134	0.000	0.000	0.000	0.000
114	A	117	LEU	0	0.021	-0.019	30.326	-0.176	-0.176	0.000	0.000	0.000	0.000
115	A	118	ASP	-1	-0.930	-0.961	33.902	8.397	8.397	0.000	0.000	0.000	0.000
116	A	119	ALA	0	-0.032	0.000	35.428	-0.251	-0.251	0.000	0.000	0.000	0.000
117	A	120	VAL	0	-0.006	-0.015	31.961	-0.104	-0.104	0.000	0.000	0.000	0.000
118	A	121	LYS	1	0.942	0.973	35.310	-8.620	-8.620	0.000	0.000	0.000	0.000
119	A	122	PRO	0	-0.056	-0.032	36.895	-0.120	-0.120	0.000	0.000	0.000	0.000
120	A	123	ASN	0	-0.083	-0.038	37.630	-0.355	-0.355	0.000	0.000	0.000	0.000
121	A	124	VAL	0	0.015	0.031	33.801	0.066	0.066	0.000	0.000	0.000	0.000
122	A	125	PRO	0	-0.017	0.004	35.812	-0.159	-0.159	0.000	0.000	0.000	0.000
123	A	126	SER	0	0.004	-0.020	34.028	-0.004	-0.004	0.000	0.000	0.000	0.000
124	A	127	LEU	0	0.024	0.017	31.569	0.146	0.146	0.000	0.000	0.000	0.000
125	A	128	MET	0	-0.057	-0.026	29.058	0.476	0.476	0.000	0.000	0.000	0.000
126	A	129	THR	0	0.040	0.020	23.965	0.057	0.057	0.000	0.000	0.000	0.000
127	A	130	PRO	0	-0.022	0.002	24.580	0.240	0.240	0.000	0.000	0.000	0.000
128	A	131	ILE	0	-0.024	-0.008	18.463	0.446	0.446	0.000	0.000	0.000	0.000
129	A	132	VAL	0	-0.021	-0.001	20.138	-0.330	-0.330	0.000	0.000	0.000	0.000
130	A	133	PHE	0	0.032	0.001	14.287	0.864	0.864	0.000	0.000	0.000	0.000
131	A	134	THR	0	0.003	-0.014	17.013	-0.551	-0.551	0.000	0.000	0.000	0.000
132	A	135	ASN	0	-0.083	-0.030	12.396	-0.883	-0.883	0.000	0.000	0.000	0.000
133	A	136	LEU	0	-0.007	0.006	15.971	0.644	0.644	0.000	0.000	0.000	0.000
134	A	137	ALA	0	-0.028	-0.011	16.946	-0.492	-0.492	0.000	0.000	0.000	0.000
135	A	138	GLU	-1	-0.918	-0.980	18.751	11.226	11.226	0.000	0.000	0.000	0.000
136	A	139	GLY	0	-0.017	-0.006	21.869	0.112	0.112	0.000	0.000	0.000	0.000
137	A	140	GLU	-1	-0.849	-0.874	16.144	17.416	17.416	0.000	0.000	0.000	0.000
138	A	141	THR	0	-0.046	-0.028	20.783	-0.444	-0.444	0.000	0.000	0.000	0.000
139	A	142	VAL	0	-0.012	-0.002	19.334	0.583	0.583	0.000	0.000	0.000	0.000
140	A	143	SER	0	-0.028	-0.039	21.548	-0.714	-0.714	0.000	0.000	0.000	0.000
141	A	144	ILE	0	-0.053	-0.027	22.448	0.477	0.477	0.000	0.000	0.000	0.000
142	A	145	LYS	1	0.749	0.868	18.909	-15.064	-15.064	0.000	0.000	0.000	0.000
143	A	146	ALA	0	-0.024	0.000	24.215	-0.409	-0.409	0.000	0.000	0.000	0.000
144	A	147	SER	0	-0.004	-0.015	25.821	-0.222	-0.222	0.000	0.000	0.000	0.000
145	A	148	GLY	0	0.011	0.013	29.342	-0.022	-0.022	0.000	0.000	0.000	0.000
146	A	149	SER	0	-0.008	-0.025	29.534	0.131	0.131	0.000	0.000	0.000	0.000
147	A	150	VAL	0	-0.040	-0.004	24.243	0.086	0.086	0.000	0.000	0.000	0.000
148	A	151	ASN	0	-0.002	-0.018	24.691	-0.462	-0.462	0.000	0.000	0.000	0.000
149	A	152	ARG	1	0.812	0.890	21.437	-12.411	-12.411	0.000	0.000	0.000	0.000
150	A	153	GLU	-1	-0.928	-1.000	17.827	16.097	16.097	0.000	0.000	0.000	0.000
151	A	154	GLN	0	0.001	0.019	18.898	-0.046	-0.046	0.000	0.000	0.000	0.000
152	A	155	GLU	-1	-0.917	-0.976	15.774	17.176	17.176	0.000	0.000	0.000	0.000
153	A	156	ASP	-1	-0.836	-0.911	17.396	13.945	13.945	0.000	0.000	0.000	0.000
154	A	157	ILE	0	0.019	0.015	19.081	-0.832	-0.832	0.000	0.000	0.000	0.000
155	A	158	VAL	0	-0.020	-0.002	18.004	-0.674	-0.674	0.000	0.000	0.000	0.000
156	A	159	LYS	1	0.865	0.920	18.524	-12.418	-12.418	0.000	0.000	0.000	0.000
157	A	160	ILE	0	0.016	0.018	14.767	-0.435	-0.435	0.000	0.000	0.000	0.000
158	A	161	GLU	-1	-0.820	-0.861	18.159	12.516	12.516	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:GLU)