FMO DATABASE

FMODB ID: 22YMR

Calculation Name: 1AVG-I-Xray372

Preferred Name: Thrombin

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1AVG

Chain ID: I

ChEMBL ID: CHEMBL4471

UniProt ID: P00735

Base Structure: X-ray

Registration Date: 2023-06-20

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	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	139
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1349335.557495
FMO2-HF: Nuclear repulsion	1291965.923694
FMO2-HF: Total energy	-57369.633801
FMO2-MP2: Total energy	-57533.628781

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(I:1:ALA)

Summations of interaction energy for fragment #1(I:1:ALA)

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.
-25.079	-24.372	20.245	-10.249	-10.705	-0.078

Interaction energy analysis for fragmet #1(I:1:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.028 / q_NPA : -0.025

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	I	3	GLY	0	-0.037	-0.024	3.889	0.317	2.066	-0.008	-0.862	-0.880	0.003
4	I	4	ASP	-1	-0.813	-0.899	1.916	-14.730	-14.388	9.126	-4.975	-4.493	-0.060
5	I	5	ASP	-1	-0.809	-0.875	4.587	-1.344	-1.317	-0.001	-0.012	-0.014	0.000
6	I	6	CYS	0	-0.010	0.015	6.940	0.428	0.428	0.000	0.000	0.000	0.000
7	I	7	SER	0	-0.061	-0.059	9.129	0.332	0.332	0.000	0.000	0.000	0.000
8	I	8	ILE	0	-0.082	-0.037	11.032	0.195	0.195	0.000	0.000	0.000	0.000
9	I	9	GLU	-1	-0.819	-0.869	9.298	-0.904	-0.904	0.000	0.000	0.000	0.000
10	I	10	LYS	1	0.869	0.941	12.141	0.440	0.440	0.000	0.000	0.000	0.000
11	I	11	ALA	0	0.012	0.007	14.660	0.010	0.010	0.000	0.000	0.000	0.000
12	I	12	MET	0	-0.052	-0.026	16.510	0.016	0.016	0.000	0.000	0.000	0.000
13	I	13	GLY	0	-0.022	-0.002	18.861	0.020	0.020	0.000	0.000	0.000	0.000
14	I	14	ASP	-1	-0.924	-0.977	21.835	-0.069	-0.069	0.000	0.000	0.000	0.000
15	I	15	PHE	0	0.017	0.016	18.967	0.019	0.019	0.000	0.000	0.000	0.000
16	I	16	LYS	1	0.850	0.921	22.029	0.048	0.048	0.000	0.000	0.000	0.000
17	I	17	PRO	0	0.038	0.019	22.466	0.019	0.019	0.000	0.000	0.000	0.000
18	I	18	GLU	-1	-0.833	-0.910	23.485	0.027	0.027	0.000	0.000	0.000	0.000
19	I	19	GLU	-1	-0.940	-0.971	24.771	0.021	0.021	0.000	0.000	0.000	0.000
20	I	20	PHE	0	0.008	0.004	16.431	0.009	0.009	0.000	0.000	0.000	0.000
21	I	21	PHE	0	-0.033	-0.010	18.115	0.026	0.026	0.000	0.000	0.000	0.000
22	I	22	ASN	0	0.002	-0.004	22.763	-0.002	-0.002	0.000	0.000	0.000	0.000
23	I	23	GLY	0	0.045	0.047	24.706	0.013	0.013	0.000	0.000	0.000	0.000
24	I	24	THR	0	-0.089	-0.062	22.900	0.006	0.006	0.000	0.000	0.000	0.000
25	I	25	TRP	0	-0.013	0.007	18.206	-0.009	-0.009	0.000	0.000	0.000	0.000
26	I	26	TYR	0	0.051	0.029	18.328	-0.004	-0.004	0.000	0.000	0.000	0.000
27	I	27	LEU	0	0.025	0.016	10.639	-0.008	-0.008	0.000	0.000	0.000	0.000
28	I	28	ALA	0	0.053	0.031	13.873	0.060	0.060	0.000	0.000	0.000	0.000
29	I	29	HIS	0	-0.016	-0.024	8.304	0.620	0.620	0.000	0.000	0.000	0.000
30	I	30	GLY	0	0.007	-0.012	9.060	0.468	0.468	0.000	0.000	0.000	0.000
31	I	31	PRO	0	-0.009	-0.021	11.419	-0.126	-0.126	0.000	0.000	0.000	0.000
32	I	32	GLY	0	0.034	0.033	14.832	-0.090	-0.090	0.000	0.000	0.000	0.000
33	I	33	VAL	0	-0.076	-0.012	12.440	-0.069	-0.069	0.000	0.000	0.000	0.000
34	I	34	THR	0	0.034	0.008	15.799	0.023	0.023	0.000	0.000	0.000	0.000
35	I	35	SER	0	-0.051	-0.027	17.859	-0.081	-0.081	0.000	0.000	0.000	0.000
36	I	36	PRO	0	0.017	0.015	15.377	0.053	0.053	0.000	0.000	0.000	0.000
37	I	37	ALA	0	0.006	0.002	17.257	0.074	0.074	0.000	0.000	0.000	0.000
38	I	38	VAL	0	0.028	0.016	17.097	-0.046	-0.046	0.000	0.000	0.000	0.000
39	I	142	CYS	0	-0.101	-0.018	18.549	0.004	0.004	0.000	0.000	0.000	0.000
40	I	40	GLN	0	-0.006	-0.025	14.517	-0.067	-0.067	0.000	0.000	0.000	0.000
41	I	41	LYN	0	-0.011	0.011	19.665	-0.006	-0.006	0.000	0.000	0.000	0.000
42	I	42	PHE	0	0.031	0.001	15.677	-0.021	-0.021	0.000	0.000	0.000	0.000
43	I	43	THR	0	-0.049	-0.026	21.712	0.001	0.001	0.000	0.000	0.000	0.000
44	I	44	THR	0	0.004	-0.004	23.653	-0.013	-0.013	0.000	0.000	0.000	0.000
45	I	45	SER	0	-0.008	-0.021	24.784	0.011	0.011	0.000	0.000	0.000	0.000
46	I	46	GLY	0	0.016	-0.008	27.186	-0.012	-0.012	0.000	0.000	0.000	0.000
47	I	47	SER	0	-0.082	-0.052	28.609	0.002	0.002	0.000	0.000	0.000	0.000
48	I	48	LYS	1	0.904	0.965	28.927	-0.029	-0.029	0.000	0.000	0.000	0.000
49	I	49	GLY	0	0.106	0.052	25.893	0.004	0.004	0.000	0.000	0.000	0.000
50	I	50	PHE	0	-0.103	-0.041	24.762	0.009	0.009	0.000	0.000	0.000	0.000
51	I	51	THR	0	-0.015	-0.017	20.944	0.004	0.004	0.000	0.000	0.000	0.000
52	I	52	GLN	0	-0.055	-0.044	21.943	0.000	0.000	0.000	0.000	0.000	0.000
53	I	53	ILE	0	0.033	0.018	15.467	0.008	0.008	0.000	0.000	0.000	0.000
54	I	54	VAL	0	-0.002	-0.002	18.455	0.007	0.007	0.000	0.000	0.000	0.000
55	I	55	GLU	-1	-0.729	-0.806	11.152	0.962	0.962	0.000	0.000	0.000	0.000
56	I	56	ILE	0	-0.011	-0.014	14.521	-0.072	-0.072	0.000	0.000	0.000	0.000
57	I	57	GLY	0	0.046	0.015	13.650	0.160	0.160	0.000	0.000	0.000	0.000
58	I	58	TYR	0	-0.081	-0.067	7.971	0.090	0.090	0.000	0.000	0.000	0.000
59	I	59	ASN	0	-0.025	-0.034	10.116	-0.127	-0.127	0.000	0.000	0.000	0.000
60	I	60	LYS	1	0.856	0.948	9.692	-0.589	-0.589	0.000	0.000	0.000	0.000
61	I	61	PHE	0	-0.038	-0.014	13.104	-0.111	-0.111	0.000	0.000	0.000	0.000
62	I	62	GLU	-1	-0.825	-0.882	16.172	0.374	0.374	0.000	0.000	0.000	0.000
63	I	63	SER	0	-0.065	-0.074	19.762	-0.013	-0.013	0.000	0.000	0.000	0.000
64	I	64	ASN	0	-0.052	-0.029	21.333	-0.027	-0.027	0.000	0.000	0.000	0.000
65	I	65	VAL	0	-0.051	0.000	20.886	-0.035	-0.035	0.000	0.000	0.000	0.000
66	I	66	LYS	1	0.872	0.930	21.286	-0.149	-0.149	0.000	0.000	0.000	0.000
67	I	67	PHE	0	0.057	0.005	18.288	-0.021	-0.021	0.000	0.000	0.000	0.000
68	I	68	GLN	0	-0.041	-0.018	21.268	-0.009	-0.009	0.000	0.000	0.000	0.000
69	I	69	CYS	0	-0.076	0.003	17.401	0.013	0.013	0.000	0.000	0.000	0.000
70	I	70	ASN	0	0.029	0.012	21.164	0.010	0.010	0.000	0.000	0.000	0.000
71	I	71	GLN	0	0.043	0.043	20.752	0.008	0.008	0.000	0.000	0.000	0.000
72	I	72	VAL	0	-0.045	-0.032	20.470	0.008	0.008	0.000	0.000	0.000	0.000
73	I	73	ASP	-1	-0.913	-0.955	21.718	-0.125	-0.125	0.000	0.000	0.000	0.000
74	I	74	ASN	0	-0.085	-0.059	19.139	-0.006	-0.006	0.000	0.000	0.000	0.000
75	I	75	LYS	1	0.789	0.872	14.403	0.401	0.401	0.000	0.000	0.000	0.000
76	I	76	ASN	0	0.013	0.007	18.631	-0.037	-0.037	0.000	0.000	0.000	0.000
77	I	77	GLY	0	-0.026	0.002	20.042	0.023	0.023	0.000	0.000	0.000	0.000
78	I	78	GLU	-1	-0.913	-0.964	17.562	-0.420	-0.420	0.000	0.000	0.000	0.000
79	I	79	GLN	0	-0.005	0.005	12.186	0.027	0.027	0.000	0.000	0.000	0.000
80	I	80	TYR	0	-0.004	-0.006	16.100	0.059	0.059	0.000	0.000	0.000	0.000
81	I	81	SER	0	0.022	-0.018	15.877	-0.014	-0.014	0.000	0.000	0.000	0.000
82	I	82	PHE	0	-0.030	-0.027	16.793	0.033	0.033	0.000	0.000	0.000	0.000
83	I	83	LYS	1	0.871	0.924	17.329	0.036	0.036	0.000	0.000	0.000	0.000
84	I	85	LYS	1	0.908	0.944	19.408	-0.058	-0.058	0.000	0.000	0.000	0.000
85	I	86	SER	0	0.007	-0.036	21.027	0.008	0.008	0.000	0.000	0.000	0.000
86	I	87	SER	0	-0.033	-0.019	23.084	-0.010	-0.010	0.000	0.000	0.000	0.000
87	I	88	ASP	-1	-0.767	-0.835	21.389	0.186	0.186	0.000	0.000	0.000	0.000
88	I	89	ASN	0	-0.095	-0.053	24.463	-0.019	-0.019	0.000	0.000	0.000	0.000
89	I	90	THR	0	-0.033	-0.027	17.882	-0.021	-0.021	0.000	0.000	0.000	0.000
90	I	91	GLU	-1	-0.862	-0.928	19.777	-0.034	-0.034	0.000	0.000	0.000	0.000
91	I	92	PHE	0	-0.002	-0.003	14.362	0.012	0.012	0.000	0.000	0.000	0.000
92	I	93	GLU	-1	-0.859	-0.898	15.286	-0.257	-0.257	0.000	0.000	0.000	0.000
93	I	94	ALA	0	-0.012	-0.013	12.458	0.006	0.006	0.000	0.000	0.000	0.000
94	I	95	ASP	-1	-0.764	-0.839	11.653	-0.388	-0.388	0.000	0.000	0.000	0.000
95	I	96	PHE	0	-0.015	-0.018	11.254	0.005	0.005	0.000	0.000	0.000	0.000
96	I	97	THR	0	0.048	0.022	11.322	0.053	0.053	0.000	0.000	0.000	0.000
97	I	98	PHE	0	0.014	-0.004	12.044	-0.010	-0.010	0.000	0.000	0.000	0.000
98	I	99	ILE	0	0.028	0.031	10.535	0.022	0.022	0.000	0.000	0.000	0.000
99	I	100	SER	0	-0.027	-0.016	13.917	0.031	0.031	0.000	0.000	0.000	0.000
100	I	101	VAL	0	-0.025	-0.016	15.743	0.043	0.043	0.000	0.000	0.000	0.000
101	I	102	SER	0	-0.013	0.020	18.421	-0.015	-0.015	0.000	0.000	0.000	0.000
102	I	103	TYR	0	0.059	0.017	21.311	0.021	0.021	0.000	0.000	0.000	0.000
103	I	104	ASP	-1	-0.889	-0.947	22.899	0.102	0.102	0.000	0.000	0.000	0.000
104	I	105	ASN	0	-0.035	-0.021	21.849	0.037	0.037	0.000	0.000	0.000	0.000
105	I	106	PHE	0	0.006	0.007	15.419	0.033	0.033	0.000	0.000	0.000	0.000
106	I	107	ALA	0	0.020	0.013	15.503	-0.061	-0.061	0.000	0.000	0.000	0.000
107	I	108	LEU	0	-0.014	0.001	9.400	0.109	0.109	0.000	0.000	0.000	0.000
108	I	109	VAL	0	-0.015	-0.021	10.604	-0.128	-0.128	0.000	0.000	0.000	0.000
109	I	111	ARG	1	0.813	0.879	7.018	-0.513	-0.513	0.000	0.000	0.000	0.000
110	I	112	SER	0	0.032	-0.005	6.390	-0.219	-0.219	0.000	0.000	0.000	0.000
111	I	113	ILE	0	-0.063	-0.034	6.992	0.298	0.298	0.000	0.000	0.000	0.000
112	I	114	THR	0	-0.001	0.003	9.823	-0.166	-0.166	0.000	0.000	0.000	0.000
113	I	115	PHE	0	0.055	0.014	9.955	0.041	0.041	0.000	0.000	0.000	0.000
114	I	116	THR	0	-0.022	-0.014	14.544	-0.052	-0.052	0.000	0.000	0.000	0.000
115	I	117	SER	0	-0.036	-0.011	16.818	-0.011	-0.011	0.000	0.000	0.000	0.000
116	I	118	GLN	0	-0.041	-0.030	12.634	0.049	0.049	0.000	0.000	0.000	0.000
117	I	119	PRO	0	-0.010	-0.002	12.487	0.037	0.037	0.000	0.000	0.000	0.000
118	I	120	LYS	1	0.771	0.862	8.243	1.824	1.824	0.000	0.000	0.000	0.000
119	I	121	GLU	-1	-0.755	-0.825	5.126	0.887	0.887	0.000	0.000	0.000	0.000
120	I	122	ASP	-1	-0.743	-0.852	4.225	-1.736	-1.320	-0.001	-0.207	-0.208	0.000
121	I	123	ARG	1	0.873	0.929	1.958	-15.041	-16.059	11.020	-5.390	-4.613	-0.021
122	I	124	TYR	0	-0.077	-0.048	3.099	1.632	0.710	0.110	1.199	-0.387	0.000
123	I	125	LEU	0	-0.058	-0.032	5.353	1.327	1.440	-0.001	-0.002	-0.110	0.000
124	I	126	VAL	0	0.017	0.003	8.141	-0.368	-0.368	0.000	0.000	0.000	0.000
125	I	127	PHE	0	-0.026	-0.009	11.522	0.098	0.098	0.000	0.000	0.000	0.000
126	I	128	GLU	-1	-0.903	-0.960	14.923	0.467	0.467	0.000	0.000	0.000	0.000
127	I	129	ARG	1	0.780	0.875	18.179	-0.141	-0.141	0.000	0.000	0.000	0.000
128	I	130	THR	0	-0.039	-0.021	21.783	-0.026	-0.026	0.000	0.000	0.000	0.000
129	I	131	LYS	1	0.812	0.930	21.393	-0.243	-0.243	0.000	0.000	0.000	0.000
130	I	132	SER	0	0.035	0.016	19.424	-0.017	-0.017	0.000	0.000	0.000	0.000
131	I	133	ASP	-1	-0.963	-0.977	21.536	0.272	0.272	0.000	0.000	0.000	0.000
132	I	134	THR	0	-0.091	-0.063	21.229	-0.020	-0.020	0.000	0.000	0.000	0.000
133	I	135	ASP	-1	-0.823	-0.906	19.701	0.503	0.503	0.000	0.000	0.000	0.000
134	I	136	PRO	0	0.018	-0.006	21.406	-0.038	-0.038	0.000	0.000	0.000	0.000
135	I	137	ASP	-1	-0.829	-0.913	23.464	0.230	0.230	0.000	0.000	0.000	0.000
136	I	138	ALA	0	0.077	0.027	24.146	-0.001	-0.001	0.000	0.000	0.000	0.000
137	I	139	LYS	1	0.853	0.921	25.322	-0.150	-0.150	0.000	0.000	0.000	0.000
138	I	140	GLU	-1	-0.923	-0.955	27.310	0.225	0.225	0.000	0.000	0.000	0.000
139	I	141	ILE	0	0.005	0.013	21.595	-0.007	-0.007	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(I:1:ALA)