FMO DATABASE

FMODB ID: YY952

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1481576.002197
FMO2-HF: Nuclear repulsion	1422599.550743
FMO2-HF: Total energy	-58976.451454
FMO2-MP2: Total energy	-59150.247615

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.
74.05	68.251	32.375	-13.817	-12.758	0.121

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 : -0.860 / q_NPA : -0.919

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	0.027	0.022	3.930	-2.294	-1.351	-0.007	-0.369	-0.567	0.001
4	A	7	GLN	0	-0.076	-0.050	6.206	-0.218	-0.218	0.000	0.000	0.000	0.000
5	A	8	ASN	0	0.068	0.034	9.092	0.195	0.195	0.000	0.000	0.000	0.000
6	A	9	GLU	-1	-0.925	-0.968	12.512	16.308	16.308	0.000	0.000	0.000	0.000
7	A	10	ILE	0	-0.085	-0.040	14.901	-0.746	-0.746	0.000	0.000	0.000	0.000
8	A	11	GLY	0	-0.023	-0.003	11.933	-0.346	-0.346	0.000	0.000	0.000	0.000
9	A	12	GLU	-1	-0.826	-0.900	12.151	16.461	16.461	0.000	0.000	0.000	0.000
10	A	13	GLU	-1	-0.836	-0.901	7.387	30.038	30.038	0.000	0.000	0.000	0.000
11	A	14	VAL	0	-0.017	-0.015	9.825	-1.514	-1.514	0.000	0.000	0.000	0.000
12	A	15	PHE	0	0.012	-0.001	11.304	1.134	1.134	0.000	0.000	0.000	0.000
13	A	16	VAL	0	-0.036	-0.011	14.000	-1.131	-1.131	0.000	0.000	0.000	0.000
14	A	17	SER	0	0.000	-0.018	16.586	0.204	0.204	0.000	0.000	0.000	0.000
15	A	18	PRO	0	0.003	0.011	17.752	0.135	0.135	0.000	0.000	0.000	0.000
16	A	19	ILE	0	-0.006	-0.012	19.214	-0.227	-0.227	0.000	0.000	0.000	0.000
17	A	20	THR	0	0.003	-0.001	23.076	0.253	0.253	0.000	0.000	0.000	0.000
18	A	21	GLY	0	0.027	0.007	26.056	-0.234	-0.234	0.000	0.000	0.000	0.000
19	A	22	GLU	-1	-0.912	-0.919	28.435	9.301	9.301	0.000	0.000	0.000	0.000
20	A	23	ILE	0	-0.010	0.007	23.216	0.074	0.074	0.000	0.000	0.000	0.000
21	A	24	HIS	1	0.753	0.826	27.057	-10.195	-10.195	0.000	0.000	0.000	0.000
22	A	25	PRO	0	0.051	0.025	26.708	0.524	0.524	0.000	0.000	0.000	0.000
23	A	26	ILE	0	0.029	0.017	24.538	-0.223	-0.223	0.000	0.000	0.000	0.000
24	A	27	THR	0	-0.023	-0.027	27.448	-0.127	-0.127	0.000	0.000	0.000	0.000
25	A	28	ASP	-1	-0.846	-0.897	30.769	9.274	9.274	0.000	0.000	0.000	0.000
26	A	29	VAL	0	0.004	0.010	27.964	-0.126	-0.126	0.000	0.000	0.000	0.000
27	A	30	PRO	0	-0.049	-0.020	31.391	-0.131	-0.131	0.000	0.000	0.000	0.000
28	A	31	ASP	-1	-0.823	-0.929	31.284	9.583	9.583	0.000	0.000	0.000	0.000
29	A	32	GLN	0	0.005	0.005	31.775	0.304	0.304	0.000	0.000	0.000	0.000
30	A	33	VAL	0	0.004	-0.007	28.359	0.120	0.120	0.000	0.000	0.000	0.000
31	A	34	PHE	0	-0.004	-0.009	24.453	0.468	0.468	0.000	0.000	0.000	0.000
32	A	35	SER	0	-0.011	-0.004	28.087	0.142	0.142	0.000	0.000	0.000	0.000
33	A	36	GLY	0	-0.053	-0.025	30.559	-0.116	-0.116	0.000	0.000	0.000	0.000
34	A	37	LYS	1	0.833	0.888	25.809	-11.266	-11.266	0.000	0.000	0.000	0.000
35	A	38	MET	0	-0.059	-0.006	26.431	0.216	0.216	0.000	0.000	0.000	0.000
36	A	39	MET	0	-0.040	-0.013	23.459	0.066	0.066	0.000	0.000	0.000	0.000
37	A	40	GLY	0	0.043	0.026	21.637	0.714	0.714	0.000	0.000	0.000	0.000
38	A	41	ASP	-1	-0.775	-0.872	21.684	11.578	11.578	0.000	0.000	0.000	0.000
39	A	42	GLY	0	0.000	-0.018	20.926	0.788	0.788	0.000	0.000	0.000	0.000
40	A	43	PHE	0	-0.023	-0.008	18.901	-0.498	-0.498	0.000	0.000	0.000	0.000
41	A	44	ALA	0	0.030	0.010	23.897	0.149	0.149	0.000	0.000	0.000	0.000
42	A	45	ILE	0	0.016	0.016	22.446	-0.089	-0.089	0.000	0.000	0.000	0.000
43	A	46	LEU	0	0.026	0.011	26.574	-0.057	-0.057	0.000	0.000	0.000	0.000
44	A	47	PRO	0	-0.041	-0.012	27.283	-0.078	-0.078	0.000	0.000	0.000	0.000
45	A	48	SER	0	0.005	-0.011	29.130	-0.343	-0.343	0.000	0.000	0.000	0.000
46	A	49	GLU	-1	-0.846	-0.899	27.626	11.456	11.456	0.000	0.000	0.000	0.000
47	A	50	GLY	0	0.019	0.010	27.998	0.173	0.173	0.000	0.000	0.000	0.000
48	A	51	ILE	0	-0.045	-0.015	22.945	0.246	0.246	0.000	0.000	0.000	0.000
49	A	52	VAL	0	0.011	0.005	19.693	-0.048	-0.048	0.000	0.000	0.000	0.000
50	A	53	VAL	0	-0.003	-0.007	17.501	0.234	0.234	0.000	0.000	0.000	0.000
51	A	54	SER	0	0.001	-0.015	11.618	-0.695	-0.695	0.000	0.000	0.000	0.000
52	A	55	PRO	0	-0.001	0.012	13.766	-0.077	-0.077	0.000	0.000	0.000	0.000
53	A	56	VAL	0	0.021	0.011	9.301	-0.223	-0.223	0.000	0.000	0.000	0.000
54	A	57	ARG	1	0.773	0.877	1.773	-86.002	-89.790	12.584	-4.554	-4.242	0.054
55	A	58	GLY	0	0.082	0.030	6.429	-0.331	-0.331	0.000	0.000	0.000	0.000
56	A	59	LYS	1	0.809	0.924	7.034	-25.064	-25.064	0.000	0.000	0.000	0.000
57	A	60	ILE	0	0.029	0.022	8.730	-2.477	-2.477	0.000	0.000	0.000	0.000
58	A	61	LEU	0	-0.070	-0.039	11.205	0.776	0.776	0.000	0.000	0.000	0.000
59	A	62	ASN	0	-0.071	-0.049	14.191	-1.351	-1.351	0.000	0.000	0.000	0.000
60	A	63	VAL	0	0.022	0.009	17.591	0.175	0.175	0.000	0.000	0.000	0.000
61	A	64	PHE	0	0.052	0.035	20.098	-0.745	-0.745	0.000	0.000	0.000	0.000
62	A	65	PRO	0	-0.028	-0.020	23.692	-0.068	-0.068	0.000	0.000	0.000	0.000
63	A	66	THR	0	-0.014	-0.029	26.468	-0.016	-0.016	0.000	0.000	0.000	0.000
64	A	67	LYS	1	0.812	0.905	22.628	-13.836	-13.836	0.000	0.000	0.000	0.000
65	A	68	HIS	0	0.049	0.052	24.922	0.262	0.262	0.000	0.000	0.000	0.000
66	A	69	ALA	0	-0.001	-0.004	22.912	0.002	0.002	0.000	0.000	0.000	0.000
67	A	70	ILE	0	-0.013	-0.007	16.771	0.098	0.098	0.000	0.000	0.000	0.000
68	A	71	GLY	0	0.025	0.027	17.009	-0.363	-0.363	0.000	0.000	0.000	0.000
69	A	72	LEU	0	-0.025	-0.023	11.980	0.739	0.739	0.000	0.000	0.000	0.000
70	A	73	GLN	0	-0.016	-0.009	8.370	-0.473	-0.473	0.000	0.000	0.000	0.000
71	A	74	SER	0	-0.015	-0.023	7.801	2.918	2.918	0.000	0.000	0.000	0.000
72	A	75	ASP	-1	-0.732	-0.837	2.458	68.756	71.711	1.166	-1.596	-2.525	-0.016
73	A	76	GLY	0	-0.043	-0.015	4.050	1.707	1.926	0.001	-0.037	-0.182	0.000
74	A	77	GLY	0	-0.042	-0.014	6.560	-2.361	-2.361	0.000	0.000	0.000	0.000
75	A	78	ARG	1	0.838	0.891	8.294	-21.636	-21.636	0.000	0.000	0.000	0.000
76	A	79	GLU	-1	-0.904	-0.945	11.161	21.132	21.132	0.000	0.000	0.000	0.000
77	A	80	ILE	0	-0.019	-0.010	12.050	-1.193	-1.193	0.000	0.000	0.000	0.000
78	A	81	LEU	0	-0.026	-0.008	15.337	0.370	0.370	0.000	0.000	0.000	0.000
79	A	82	ILE	0	0.016	0.010	16.873	-0.486	-0.486	0.000	0.000	0.000	0.000
80	A	83	HIS	0	0.003	-0.007	20.421	-0.026	-0.026	0.000	0.000	0.000	0.000
81	A	84	PHE	0	0.055	0.015	24.125	-0.433	-0.433	0.000	0.000	0.000	0.000
82	A	85	GLY	0	0.013	0.015	26.239	-0.317	-0.317	0.000	0.000	0.000	0.000
83	A	86	ILE	0	-0.008	-0.003	29.040	0.243	0.243	0.000	0.000	0.000	0.000
84	A	87	ASP	-1	-0.846	-0.938	31.739	8.864	8.864	0.000	0.000	0.000	0.000
85	A	88	THR	0	0.007	-0.011	29.219	-0.234	-0.234	0.000	0.000	0.000	0.000
86	A	89	VAL	0	-0.001	0.014	30.351	-0.041	-0.041	0.000	0.000	0.000	0.000
87	A	90	SER	0	-0.037	-0.030	31.799	-0.196	-0.196	0.000	0.000	0.000	0.000
88	A	91	LEU	0	-0.004	0.006	33.564	-0.263	-0.263	0.000	0.000	0.000	0.000
89	A	92	LYS	1	0.817	0.895	32.734	-8.762	-8.762	0.000	0.000	0.000	0.000
90	A	93	GLY	0	0.052	0.025	30.179	0.200	0.200	0.000	0.000	0.000	0.000
91	A	94	GLU	-1	-0.974	-0.972	31.191	9.296	9.296	0.000	0.000	0.000	0.000
92	A	95	GLY	0	0.032	0.015	32.597	-0.026	-0.026	0.000	0.000	0.000	0.000
93	A	96	PHE	0	-0.038	-0.015	27.310	0.249	0.249	0.000	0.000	0.000	0.000
94	A	97	THR	0	-0.006	0.008	25.694	-0.170	-0.170	0.000	0.000	0.000	0.000
95	A	98	SER	0	-0.008	-0.019	20.810	0.380	0.380	0.000	0.000	0.000	0.000
96	A	99	PHE	0	-0.057	-0.041	19.986	-0.525	-0.525	0.000	0.000	0.000	0.000
97	A	100	VAL	0	-0.003	0.023	14.949	0.728	0.728	0.000	0.000	0.000	0.000
98	A	101	SER	0	-0.022	-0.019	15.732	-1.795	-1.795	0.000	0.000	0.000	0.000
99	A	102	GLU	-1	-0.832	-0.905	14.782	17.649	17.649	0.000	0.000	0.000	0.000
100	A	103	GLY	0	-0.073	-0.058	12.099	-0.256	-0.256	0.000	0.000	0.000	0.000
101	A	104	ASP	-1	-0.811	-0.901	10.186	25.283	25.283	0.000	0.000	0.000	0.000
102	A	105	ARG	1	0.699	0.803	1.695	-99.112	-105.240	18.631	-7.261	-5.242	0.082
103	A	106	VAL	0	-0.037	-0.024	8.112	-3.397	-3.397	0.000	0.000	0.000	0.000
104	A	107	GLU	-1	-0.778	-0.869	6.862	46.915	46.915	0.000	0.000	0.000	0.000
105	A	108	PRO	0	0.016	-0.007	9.014	-2.200	-2.200	0.000	0.000	0.000	0.000
106	A	109	GLY	0	0.049	0.019	12.244	-0.337	-0.337	0.000	0.000	0.000	0.000
107	A	110	GLN	0	-0.039	-0.004	12.141	0.187	0.187	0.000	0.000	0.000	0.000
108	A	111	LYS	1	0.779	0.882	15.481	-13.677	-13.677	0.000	0.000	0.000	0.000
109	A	112	LEU	0	-0.015	-0.003	14.785	0.688	0.688	0.000	0.000	0.000	0.000
110	A	113	LEU	0	-0.004	-0.009	18.652	-0.371	-0.371	0.000	0.000	0.000	0.000
111	A	114	GLU	-1	-0.843	-0.918	22.411	12.728	12.728	0.000	0.000	0.000	0.000
112	A	115	VAL	0	-0.017	0.002	25.826	-0.202	-0.202	0.000	0.000	0.000	0.000
113	A	116	ASP	-1	-0.861	-0.928	28.996	9.095	9.095	0.000	0.000	0.000	0.000
114	A	117	LEU	0	0.025	-0.002	30.141	-0.140	-0.140	0.000	0.000	0.000	0.000
115	A	118	ASP	-1	-0.854	-0.918	33.425	8.435	8.435	0.000	0.000	0.000	0.000
116	A	119	ALA	0	-0.007	0.012	35.430	-0.268	-0.268	0.000	0.000	0.000	0.000
117	A	120	VAL	0	0.008	-0.004	31.760	-0.159	-0.159	0.000	0.000	0.000	0.000
118	A	121	LYS	1	0.841	0.902	35.092	-8.647	-8.647	0.000	0.000	0.000	0.000
119	A	122	PRO	0	-0.071	-0.032	36.720	-0.133	-0.133	0.000	0.000	0.000	0.000
120	A	123	ASN	0	-0.093	-0.041	37.635	-0.378	-0.378	0.000	0.000	0.000	0.000
121	A	124	VAL	0	0.014	0.011	33.697	0.136	0.136	0.000	0.000	0.000	0.000
122	A	125	PRO	0	-0.019	0.009	35.686	-0.171	-0.171	0.000	0.000	0.000	0.000
123	A	126	SER	0	-0.001	-0.017	33.445	0.033	0.033	0.000	0.000	0.000	0.000
124	A	127	LEU	0	0.030	0.017	31.399	0.162	0.162	0.000	0.000	0.000	0.000
125	A	128	MET	0	-0.034	-0.011	29.367	0.493	0.493	0.000	0.000	0.000	0.000
126	A	129	THR	0	0.011	0.008	23.991	-0.003	-0.003	0.000	0.000	0.000	0.000
127	A	130	PRO	0	-0.027	-0.010	24.572	0.258	0.258	0.000	0.000	0.000	0.000
128	A	131	ILE	0	-0.029	-0.011	18.417	0.473	0.473	0.000	0.000	0.000	0.000
129	A	132	VAL	0	-0.015	-0.004	19.995	-0.335	-0.335	0.000	0.000	0.000	0.000
130	A	133	PHE	0	0.025	0.001	14.255	0.865	0.865	0.000	0.000	0.000	0.000
131	A	134	THR	0	-0.016	-0.018	16.883	-0.477	-0.477	0.000	0.000	0.000	0.000
132	A	135	ASN	0	-0.091	-0.053	12.347	-0.861	-0.861	0.000	0.000	0.000	0.000
133	A	136	LEU	0	-0.021	0.002	16.180	0.499	0.499	0.000	0.000	0.000	0.000
134	A	137	ALA	0	-0.011	-0.001	17.065	-0.456	-0.456	0.000	0.000	0.000	0.000
135	A	138	GLU	-1	-0.912	-0.978	18.855	10.978	10.978	0.000	0.000	0.000	0.000
136	A	139	GLY	0	-0.042	-0.013	21.999	0.175	0.175	0.000	0.000	0.000	0.000
137	A	140	GLU	-1	-0.829	-0.868	16.739	16.875	16.875	0.000	0.000	0.000	0.000
138	A	141	THR	0	-0.058	-0.034	21.298	-0.466	-0.466	0.000	0.000	0.000	0.000
139	A	142	VAL	0	-0.020	-0.009	19.584	0.515	0.515	0.000	0.000	0.000	0.000
140	A	143	SER	0	-0.041	-0.036	22.041	-0.706	-0.706	0.000	0.000	0.000	0.000
141	A	144	ILE	0	-0.038	-0.032	22.338	0.549	0.549	0.000	0.000	0.000	0.000
142	A	145	LYS	1	0.723	0.858	18.614	-15.279	-15.279	0.000	0.000	0.000	0.000
143	A	146	ALA	0	-0.019	0.000	24.371	-0.385	-0.385	0.000	0.000	0.000	0.000
144	A	147	SER	0	-0.022	-0.031	25.996	-0.252	-0.252	0.000	0.000	0.000	0.000
145	A	148	GLY	0	0.030	0.025	29.438	-0.038	-0.038	0.000	0.000	0.000	0.000
146	A	149	SER	0	-0.029	-0.026	29.477	0.170	0.170	0.000	0.000	0.000	0.000
147	A	150	VAL	0	-0.015	0.005	24.338	0.063	0.063	0.000	0.000	0.000	0.000
148	A	151	ASN	0	-0.021	-0.024	24.323	-0.466	-0.466	0.000	0.000	0.000	0.000
149	A	152	ARG	1	0.854	0.904	21.002	-12.652	-12.652	0.000	0.000	0.000	0.000
150	A	153	GLU	-1	-0.917	-0.968	16.963	16.011	16.011	0.000	0.000	0.000	0.000
151	A	154	GLN	0	-0.007	0.016	18.282	0.032	0.032	0.000	0.000	0.000	0.000
152	A	155	GLU	-1	-0.895	-0.961	15.422	17.564	17.564	0.000	0.000	0.000	0.000
153	A	156	ASP	-1	-0.836	-0.915	17.277	14.196	14.196	0.000	0.000	0.000	0.000
154	A	157	ILE	0	0.002	0.008	18.910	-0.790	-0.790	0.000	0.000	0.000	0.000
155	A	158	VAL	0	-0.042	-0.016	17.855	-0.715	-0.715	0.000	0.000	0.000	0.000
156	A	159	LYS	1	0.844	0.914	18.558	-12.618	-12.618	0.000	0.000	0.000	0.000
157	A	160	ILE	0	0.016	0.014	14.945	-0.260	-0.260	0.000	0.000	0.000	0.000
158	A	161	GLU	-1	-0.824	-0.851	18.760	12.389	12.389	0.000	0.000	0.000	0.000

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