FMO DATABASE

FMODB ID: VRN31

Calculation Name: 2GPR-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2GPR

Chain ID: A

ChEMBL ID:

UniProt ID: P45618

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	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	154
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1440522.838187
FMO2-HF: Nuclear repulsion	1382343.038644
FMO2-HF: Total energy	-58179.799543
FMO2-MP2: Total energy	-58351.161301

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:6:MET)

Summations of interaction energy for fragment #1(A:6:MET)

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.
0.418	-3.886	17.159	-4.472	-8.383	-0.004

Interaction energy analysis for fragmet #1(A:6:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.040 / q_NPA : 0.040

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	8	PHE	0	0.043	0.011	1.927	0.509	-3.934	17.147	-4.451	-8.253	-0.004
4	A	9	PHE	0	-0.002	-0.005	4.601	-0.995	-0.856	0.012	-0.021	-0.130	0.000
5	A	10	ASN	0	0.020	0.001	7.314	-0.316	-0.316	0.000	0.000	0.000	0.000
6	A	11	LYS	1	0.955	1.005	7.504	0.474	0.474	0.000	0.000	0.000	0.000
7	A	12	ASN	0	-0.021	-0.015	6.452	0.286	0.286	0.000	0.000	0.000	0.000
8	A	13	LEU	0	-0.039	-0.013	9.354	-0.104	-0.104	0.000	0.000	0.000	0.000
9	A	14	LYS	1	0.956	0.982	7.083	0.634	0.634	0.000	0.000	0.000	0.000
10	A	15	VAL	0	-0.003	-0.002	11.103	0.035	0.035	0.000	0.000	0.000	0.000
11	A	16	LEU	0	-0.019	-0.012	12.297	-0.005	-0.005	0.000	0.000	0.000	0.000
12	A	17	ALA	0	0.017	0.019	15.956	0.006	0.006	0.000	0.000	0.000	0.000
13	A	18	PRO	0	0.038	0.020	19.463	0.009	0.009	0.000	0.000	0.000	0.000
14	A	19	CYS	0	0.029	0.021	21.827	0.008	0.008	0.000	0.000	0.000	0.000
15	A	20	ASP	-1	-0.806	-0.896	23.316	-0.023	-0.023	0.000	0.000	0.000	0.000
16	A	21	GLY	0	0.001	-0.037	25.161	0.000	0.000	0.000	0.000	0.000	0.000
17	A	22	THR	0	-0.086	-0.066	25.133	0.000	0.000	0.000	0.000	0.000	0.000
18	A	23	ILE	0	-0.018	-0.003	21.067	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	24	ILE	0	-0.031	-0.014	24.463	0.006	0.006	0.000	0.000	0.000	0.000
20	A	25	THR	0	-0.009	-0.055	25.948	-0.008	-0.008	0.000	0.000	0.000	0.000
21	A	26	LEU	0	0.011	0.001	26.885	0.002	0.002	0.000	0.000	0.000	0.000
22	A	27	ASP	-1	-0.782	-0.906	29.320	-0.041	-0.041	0.000	0.000	0.000	0.000
23	A	28	GLU	-1	-0.941	-0.933	29.866	-0.032	-0.032	0.000	0.000	0.000	0.000
24	A	29	VAL	0	-0.041	-0.021	30.371	0.001	0.001	0.000	0.000	0.000	0.000
25	A	30	GLU	-1	-0.861	-0.945	33.434	-0.029	-0.029	0.000	0.000	0.000	0.000
26	A	31	ASP	-1	-0.854	-0.960	35.288	-0.037	-0.037	0.000	0.000	0.000	0.000
27	A	32	GLU	-1	-0.898	-0.963	35.436	-0.036	-0.036	0.000	0.000	0.000	0.000
28	A	33	VAL	0	0.037	0.021	33.336	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	34	PHE	0	-0.060	-0.041	30.515	-0.005	-0.005	0.000	0.000	0.000	0.000
30	A	35	LYS	1	0.907	0.965	31.163	0.028	0.028	0.000	0.000	0.000	0.000
31	A	36	GLU	-1	-0.951	-0.984	32.686	-0.032	-0.032	0.000	0.000	0.000	0.000
32	A	37	ARG	1	0.777	0.901	27.178	0.054	0.054	0.000	0.000	0.000	0.000
33	A	38	MET	0	-0.022	0.024	30.882	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	39	LEU	0	-0.010	-0.014	30.114	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	40	GLY	0	-0.028	-0.008	26.856	-0.006	-0.006	0.000	0.000	0.000	0.000
36	A	41	ASP	-1	-0.862	-0.906	23.778	-0.072	-0.072	0.000	0.000	0.000	0.000
37	A	42	GLY	0	-0.044	-0.041	22.194	-0.010	-0.010	0.000	0.000	0.000	0.000
38	A	43	PHE	0	-0.038	-0.015	19.333	0.003	0.003	0.000	0.000	0.000	0.000
39	A	44	ALA	0	0.041	0.023	24.468	0.000	0.000	0.000	0.000	0.000	0.000
40	A	45	ILE	0	0.015	0.000	23.105	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	46	ASN	0	0.029	0.028	26.634	0.004	0.004	0.000	0.000	0.000	0.000
42	A	47	PRO	0	-0.010	-0.002	28.204	0.001	0.001	0.000	0.000	0.000	0.000
43	A	48	LYS	1	0.832	0.925	28.067	0.020	0.020	0.000	0.000	0.000	0.000
44	A	49	SER	0	-0.033	-0.012	27.178	0.003	0.003	0.000	0.000	0.000	0.000
45	A	50	ASN	0	0.003	-0.013	29.485	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	51	ASP	-1	-0.878	-0.951	26.854	-0.024	-0.024	0.000	0.000	0.000	0.000
47	A	52	PHE	0	0.035	0.025	25.355	-0.003	-0.003	0.000	0.000	0.000	0.000
48	A	53	HIS	0	-0.057	-0.035	20.890	0.007	0.007	0.000	0.000	0.000	0.000
49	A	54	ALA	0	0.018	-0.005	19.558	-0.007	-0.007	0.000	0.000	0.000	0.000
50	A	55	PRO	0	0.027	0.023	17.878	-0.006	-0.006	0.000	0.000	0.000	0.000
51	A	56	VAL	0	0.011	-0.019	14.458	-0.039	-0.039	0.000	0.000	0.000	0.000
52	A	57	SER	0	0.028	0.025	14.630	0.023	0.023	0.000	0.000	0.000	0.000
53	A	58	GLY	0	-0.029	-0.032	16.334	-0.028	-0.028	0.000	0.000	0.000	0.000
54	A	59	LYS	1	0.963	0.993	19.013	0.108	0.108	0.000	0.000	0.000	0.000
55	A	60	LEU	0	0.019	0.018	22.765	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	61	VAL	0	-0.015	-0.014	24.639	0.007	0.007	0.000	0.000	0.000	0.000
57	A	62	THR	0	-0.008	0.054	27.068	0.007	0.007	0.000	0.000	0.000	0.000
58	A	63	ALA	0	0.052	0.023	28.645	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	64	PHE	0	0.023	0.000	30.866	0.002	0.002	0.000	0.000	0.000	0.000
60	A	65	PRO	0	0.028	0.024	34.419	0.000	0.000	0.000	0.000	0.000	0.000
61	A	66	THR	0	0.024	-0.018	36.215	0.002	0.002	0.000	0.000	0.000	0.000
62	A	67	LYS	1	0.796	0.908	33.055	0.032	0.032	0.000	0.000	0.000	0.000
63	A	68	HIS	0	0.093	0.070	32.564	0.000	0.000	0.000	0.000	0.000	0.000
64	A	69	ALA	0	-0.019	-0.008	29.760	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	70	PHE	0	-0.017	-0.013	25.965	0.001	0.001	0.000	0.000	0.000	0.000
66	A	71	GLY	0	0.015	-0.012	25.288	-0.005	-0.005	0.000	0.000	0.000	0.000
67	A	72	ILE	0	-0.001	-0.002	19.626	0.000	0.000	0.000	0.000	0.000	0.000
68	A	73	GLN	0	0.013	0.016	21.150	-0.010	-0.010	0.000	0.000	0.000	0.000
69	A	74	THR	0	0.014	0.040	15.736	-0.014	-0.014	0.000	0.000	0.000	0.000
70	A	75	LYS	1	0.998	0.973	13.176	0.304	0.304	0.000	0.000	0.000	0.000
71	A	76	SER	0	-0.078	-0.058	15.571	-0.008	-0.008	0.000	0.000	0.000	0.000
72	A	77	GLY	0	-0.023	0.001	17.420	0.011	0.011	0.000	0.000	0.000	0.000
73	A	78	VAL	0	-0.023	-0.013	17.137	0.008	0.008	0.000	0.000	0.000	0.000
74	A	79	GLU	-1	-0.901	-0.967	19.979	-0.112	-0.112	0.000	0.000	0.000	0.000
75	A	80	ILE	0	-0.045	-0.029	18.890	0.003	0.003	0.000	0.000	0.000	0.000
76	A	81	LEU	0	-0.002	-0.009	21.934	0.003	0.003	0.000	0.000	0.000	0.000
77	A	82	LEU	0	-0.005	0.022	23.877	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	83	HIS	0	-0.012	-0.018	25.519	0.005	0.005	0.000	0.000	0.000	0.000
79	A	84	ILE	0	0.020	-0.006	28.664	0.001	0.001	0.000	0.000	0.000	0.000
80	A	85	GLY	0	-0.029	-0.025	30.728	0.003	0.003	0.000	0.000	0.000	0.000
81	A	86	LEU	0	0.014	0.013	33.081	-0.003	-0.003	0.000	0.000	0.000	0.000
82	A	87	ASP	-1	-0.820	-0.935	35.813	-0.027	-0.027	0.000	0.000	0.000	0.000
83	A	88	THR	0	-0.038	-0.002	34.374	0.001	0.001	0.000	0.000	0.000	0.000
84	A	89	VAL	0	-0.013	0.004	37.526	0.001	0.001	0.000	0.000	0.000	0.000
85	A	90	SER	0	-0.022	-0.034	38.578	0.002	0.002	0.000	0.000	0.000	0.000
86	A	91	LEU	0	-0.078	-0.033	39.495	0.002	0.002	0.000	0.000	0.000	0.000
87	A	92	ASP	-1	-0.896	-0.955	41.327	-0.026	-0.026	0.000	0.000	0.000	0.000
88	A	93	GLY	0	0.015	0.011	37.993	0.000	0.000	0.000	0.000	0.000	0.000
89	A	94	ASN	0	-0.110	-0.064	38.969	0.001	0.001	0.000	0.000	0.000	0.000
90	A	95	GLY	0	0.028	0.013	38.676	0.000	0.000	0.000	0.000	0.000	0.000
91	A	96	PHE	0	-0.020	0.012	33.179	0.000	0.000	0.000	0.000	0.000	0.000
92	A	97	GLU	-1	-0.909	-0.952	34.110	-0.023	-0.023	0.000	0.000	0.000	0.000
93	A	98	SER	0	-0.030	-0.028	31.223	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	99	PHE	0	0.003	-0.011	28.476	0.004	0.004	0.000	0.000	0.000	0.000
95	A	100	VAL	0	-0.074	-0.017	25.759	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	101	THR	0	-0.002	-0.006	29.059	0.004	0.004	0.000	0.000	0.000	0.000
97	A	102	GLN	0	-0.015	-0.051	28.921	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	103	ASP	-1	-0.960	-0.971	27.951	-0.064	-0.064	0.000	0.000	0.000	0.000
99	A	104	GLN	0	0.022	0.025	25.051	0.000	0.000	0.000	0.000	0.000	0.000
100	A	105	GLU	-1	-0.963	-0.983	19.591	-0.137	-0.137	0.000	0.000	0.000	0.000
101	A	106	VAL	0	-0.073	-0.040	20.337	0.011	0.011	0.000	0.000	0.000	0.000
102	A	107	ASN	0	0.002	-0.022	16.621	-0.042	-0.042	0.000	0.000	0.000	0.000
103	A	108	ALA	0	-0.046	-0.013	14.393	0.010	0.010	0.000	0.000	0.000	0.000
104	A	109	GLY	0	0.031	0.008	16.294	0.011	0.011	0.000	0.000	0.000	0.000
105	A	110	ASP	-1	-0.837	-0.896	18.323	-0.047	-0.047	0.000	0.000	0.000	0.000
106	A	111	LYS	1	0.893	0.961	21.227	0.018	0.018	0.000	0.000	0.000	0.000
107	A	112	LEU	0	-0.029	-0.022	23.192	-0.002	-0.002	0.000	0.000	0.000	0.000
108	A	113	VAL	0	-0.009	-0.013	26.327	0.003	0.003	0.000	0.000	0.000	0.000
109	A	114	THR	0	-0.045	-0.002	28.991	0.000	0.000	0.000	0.000	0.000	0.000
110	A	115	VAL	0	0.032	0.016	31.389	0.001	0.001	0.000	0.000	0.000	0.000
111	A	116	ASP	-1	-0.853	-0.888	33.712	-0.014	-0.014	0.000	0.000	0.000	0.000
112	A	117	LEU	0	0.080	0.009	31.607	0.000	0.000	0.000	0.000	0.000	0.000
113	A	118	LYS	1	0.935	0.982	35.946	0.011	0.011	0.000	0.000	0.000	0.000
114	A	119	SER	0	-0.087	-0.082	39.314	0.001	0.001	0.000	0.000	0.000	0.000
115	A	120	VAL	0	0.002	-0.016	36.669	0.001	0.001	0.000	0.000	0.000	0.000
116	A	121	ALA	0	0.009	0.007	37.766	-0.001	-0.001	0.000	0.000	0.000	0.000
117	A	122	LYS	1	0.871	0.949	39.216	0.016	0.016	0.000	0.000	0.000	0.000
118	A	123	LYS	1	0.842	0.919	41.910	0.019	0.019	0.000	0.000	0.000	0.000
119	A	124	VAL	0	0.004	0.023	37.598	0.000	0.000	0.000	0.000	0.000	0.000
120	A	125	PRO	0	0.037	0.025	39.452	0.001	0.001	0.000	0.000	0.000	0.000
121	A	126	SER	0	0.017	0.008	35.179	0.001	0.001	0.000	0.000	0.000	0.000
122	A	127	ILE	0	0.028	0.016	32.932	-0.002	-0.002	0.000	0.000	0.000	0.000
123	A	128	LYS	1	0.860	0.939	31.112	0.027	0.027	0.000	0.000	0.000	0.000
124	A	129	SER	0	0.000	0.001	27.923	0.001	0.001	0.000	0.000	0.000	0.000
125	A	130	PRO	0	0.000	0.014	27.138	-0.005	-0.005	0.000	0.000	0.000	0.000
126	A	131	ILE	0	-0.049	-0.014	20.820	-0.004	-0.004	0.000	0.000	0.000	0.000
127	A	132	ILE	0	0.037	0.016	23.637	-0.004	-0.004	0.000	0.000	0.000	0.000
128	A	133	PHE	0	-0.020	-0.029	17.361	-0.012	-0.012	0.000	0.000	0.000	0.000
129	A	134	THR	0	0.014	0.014	22.789	0.008	0.008	0.000	0.000	0.000	0.000
130	A	135	ASN	0	-0.004	-0.013	23.448	0.005	0.005	0.000	0.000	0.000	0.000
131	A	136	ASN	0	0.123	0.123	19.762	-0.007	-0.007	0.000	0.000	0.000	0.000
132	A	137	GLY	0	0.027	-0.021	20.232	-0.007	-0.007	0.000	0.000	0.000	0.000
133	A	138	GLY	0	-0.011	-0.020	17.126	0.014	0.014	0.000	0.000	0.000	0.000
134	A	139	LYS	1	0.818	0.920	17.727	0.085	0.085	0.000	0.000	0.000	0.000
135	A	140	THR	0	-0.030	-0.010	16.758	0.013	0.013	0.000	0.000	0.000	0.000
136	A	141	LEU	0	0.081	0.022	16.841	-0.033	-0.033	0.000	0.000	0.000	0.000
137	A	142	GLU	-1	-0.976	-0.971	12.839	-0.105	-0.105	0.000	0.000	0.000	0.000
138	A	143	ILE	0	-0.023	-0.030	12.559	0.019	0.019	0.000	0.000	0.000	0.000
139	A	144	VAL	0	0.059	0.036	15.891	-0.033	-0.033	0.000	0.000	0.000	0.000
140	A	145	LYS	1	0.834	0.934	15.592	0.102	0.102	0.000	0.000	0.000	0.000
141	A	146	MET	0	0.013	0.006	18.407	0.000	0.000	0.000	0.000	0.000	0.000
142	A	147	GLY	0	0.006	0.011	22.063	0.005	0.005	0.000	0.000	0.000	0.000
143	A	148	GLU	-1	-0.810	-0.866	24.114	-0.023	-0.023	0.000	0.000	0.000	0.000
144	A	149	VAL	0	-0.081	-0.036	20.212	-0.001	-0.001	0.000	0.000	0.000	0.000
145	A	150	LYS	1	0.904	0.941	20.273	0.001	0.001	0.000	0.000	0.000	0.000
146	A	151	GLN	0	-0.018	0.002	19.598	-0.019	-0.019	0.000	0.000	0.000	0.000
147	A	152	GLY	0	0.001	-0.009	16.891	0.011	0.011	0.000	0.000	0.000	0.000
148	A	153	ASP	-1	-0.890	-0.921	15.215	-0.043	-0.043	0.000	0.000	0.000	0.000
149	A	154	VAL	0	-0.079	-0.065	10.480	-0.032	-0.032	0.000	0.000	0.000	0.000
150	A	155	VAL	0	0.049	0.010	13.882	0.027	0.027	0.000	0.000	0.000	0.000
151	A	156	ALA	0	0.040	0.015	14.738	0.021	0.021	0.000	0.000	0.000	0.000
152	A	157	ILE	0	-0.044	0.005	9.604	-0.068	-0.068	0.000	0.000	0.000	0.000
153	A	158	LEU	0	0.015	0.029	13.137	0.060	0.060	0.000	0.000	0.000	0.000
154	A	159	LYS	1	0.925	0.958	8.477	0.103	0.103	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:6:MET)