FMO DATABASE

FMODB ID: 7G9KK

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1346688.617175
FMO2-HF: Nuclear repulsion	1289319.589204
FMO2-HF: Total energy	-57369.027971
FMO2-MP2: Total energy	-57533.032653

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.
-26.184	-29.463	25.217	-11.954	-9.983	-0.075

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 : -0.041 / q_NPA : -0.031

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	-0.018	-0.011	3.808	-0.456	1.495	-0.013	-0.959	-0.979	0.006
4	I	4	ASP	-1	-0.866	-0.921	1.826	-14.038	-16.559	13.066	-6.031	-4.513	-0.061
5	I	5	ASP	-1	-0.818	-0.895	4.407	-1.295	-1.242	-0.001	-0.016	-0.036	0.000
6	I	6	CYS	0	-0.010	0.022	7.058	0.544	0.544	0.000	0.000	0.000	0.000
7	I	7	SER	0	-0.036	-0.048	8.818	0.323	0.323	0.000	0.000	0.000	0.000
8	I	8	ILE	0	-0.106	-0.040	10.912	0.214	0.214	0.000	0.000	0.000	0.000
9	I	9	GLU	-1	-0.829	-0.879	9.381	-0.993	-0.993	0.000	0.000	0.000	0.000
10	I	10	LYS	1	0.886	0.944	12.286	0.454	0.454	0.000	0.000	0.000	0.000
11	I	11	ALA	0	-0.005	0.000	15.031	0.023	0.023	0.000	0.000	0.000	0.000
12	I	12	MET	0	-0.041	-0.016	16.585	0.014	0.014	0.000	0.000	0.000	0.000
13	I	13	GLY	0	-0.019	0.005	18.864	0.019	0.019	0.000	0.000	0.000	0.000
14	I	14	ASP	-1	-0.938	-0.983	22.062	-0.053	-0.053	0.000	0.000	0.000	0.000
15	I	15	PHE	0	0.030	0.020	19.537	0.018	0.018	0.000	0.000	0.000	0.000
16	I	16	LYS	1	0.838	0.909	22.369	0.033	0.033	0.000	0.000	0.000	0.000
17	I	17	PRO	0	0.048	0.017	22.424	0.020	0.020	0.000	0.000	0.000	0.000
18	I	18	GLU	-1	-0.861	-0.910	23.444	0.049	0.049	0.000	0.000	0.000	0.000
19	I	19	GLU	-1	-0.945	-0.973	25.186	0.032	0.032	0.000	0.000	0.000	0.000
20	I	20	PHE	0	-0.013	-0.009	16.949	0.010	0.010	0.000	0.000	0.000	0.000
21	I	21	PHE	0	-0.020	-0.009	18.396	0.025	0.025	0.000	0.000	0.000	0.000
22	I	22	ASN	0	0.025	0.000	23.139	-0.003	-0.003	0.000	0.000	0.000	0.000
23	I	23	GLY	0	0.014	0.030	24.905	0.010	0.010	0.000	0.000	0.000	0.000
24	I	24	THR	0	-0.042	-0.035	22.956	0.002	0.002	0.000	0.000	0.000	0.000
25	I	25	TRP	0	-0.020	0.004	18.435	-0.004	-0.004	0.000	0.000	0.000	0.000
26	I	26	TYR	0	0.038	0.008	18.775	-0.001	-0.001	0.000	0.000	0.000	0.000
27	I	27	LEU	0	0.031	0.017	11.045	0.008	0.008	0.000	0.000	0.000	0.000
28	I	28	ALA	0	0.070	0.049	13.787	0.037	0.037	0.000	0.000	0.000	0.000
29	I	29	HIS	0	-0.037	-0.036	8.870	0.602	0.602	0.000	0.000	0.000	0.000
30	I	30	GLY	0	-0.017	-0.027	9.251	0.324	0.324	0.000	0.000	0.000	0.000
31	I	31	PRO	0	-0.023	-0.016	11.648	-0.101	-0.101	0.000	0.000	0.000	0.000
32	I	32	GLY	0	-0.006	0.008	15.076	-0.053	-0.053	0.000	0.000	0.000	0.000
33	I	33	VAL	0	-0.032	-0.008	12.535	-0.059	-0.059	0.000	0.000	0.000	0.000
34	I	34	THR	0	0.100	0.041	15.786	-0.012	-0.012	0.000	0.000	0.000	0.000
35	I	35	SER	0	-0.074	-0.019	17.628	-0.074	-0.074	0.000	0.000	0.000	0.000
36	I	36	PRO	0	-0.006	0.004	15.507	0.050	0.050	0.000	0.000	0.000	0.000
37	I	37	ALA	0	0.041	0.007	17.354	0.070	0.070	0.000	0.000	0.000	0.000
38	I	38	VAL	0	0.027	0.021	17.741	-0.039	-0.039	0.000	0.000	0.000	0.000
39	I	142	CYS	0	-0.123	-0.035	19.125	0.011	0.011	0.000	0.000	0.000	0.000
40	I	40	GLN	0	-0.039	-0.033	15.001	-0.065	-0.065	0.000	0.000	0.000	0.000
41	I	41	LYN	0	0.011	0.034	20.347	-0.005	-0.005	0.000	0.000	0.000	0.000
42	I	42	PHE	0	0.028	-0.008	16.272	-0.013	-0.013	0.000	0.000	0.000	0.000
43	I	43	THR	0	-0.045	-0.014	22.244	-0.005	-0.005	0.000	0.000	0.000	0.000
44	I	44	THR	0	-0.014	-0.008	23.795	-0.010	-0.010	0.000	0.000	0.000	0.000
45	I	45	SER	0	0.001	-0.013	24.831	0.007	0.007	0.000	0.000	0.000	0.000
46	I	46	GLY	0	0.023	0.000	27.055	-0.013	-0.013	0.000	0.000	0.000	0.000
47	I	47	SER	0	-0.100	-0.060	29.181	0.001	0.001	0.000	0.000	0.000	0.000
48	I	48	LYS	1	0.918	0.955	29.359	-0.048	-0.048	0.000	0.000	0.000	0.000
49	I	49	GLY	0	0.134	0.070	26.461	0.003	0.003	0.000	0.000	0.000	0.000
50	I	50	PHE	0	-0.094	-0.051	25.181	0.010	0.010	0.000	0.000	0.000	0.000
51	I	51	THR	0	-0.019	0.011	21.300	0.003	0.003	0.000	0.000	0.000	0.000
52	I	52	GLN	0	-0.054	-0.037	22.611	-0.002	-0.002	0.000	0.000	0.000	0.000
53	I	53	ILE	0	0.034	0.021	15.829	0.003	0.003	0.000	0.000	0.000	0.000
54	I	54	VAL	0	-0.002	-0.004	19.159	-0.001	-0.001	0.000	0.000	0.000	0.000
55	I	55	GLU	-1	-0.738	-0.812	11.621	1.060	1.060	0.000	0.000	0.000	0.000
56	I	56	ILE	0	-0.006	-0.016	15.108	-0.053	-0.053	0.000	0.000	0.000	0.000
57	I	57	GLY	0	0.020	-0.002	13.311	0.152	0.152	0.000	0.000	0.000	0.000
58	I	58	TYR	0	-0.061	-0.048	8.136	0.090	0.090	0.000	0.000	0.000	0.000
59	I	59	ASN	0	-0.026	-0.041	9.680	-0.179	-0.179	0.000	0.000	0.000	0.000
60	I	60	LYS	1	0.871	0.956	9.510	-0.801	-0.801	0.000	0.000	0.000	0.000
61	I	61	PHE	0	-0.051	-0.019	13.321	-0.099	-0.099	0.000	0.000	0.000	0.000
62	I	62	GLU	-1	-0.818	-0.888	16.311	0.383	0.383	0.000	0.000	0.000	0.000
63	I	63	SER	0	-0.047	-0.061	19.820	-0.010	-0.010	0.000	0.000	0.000	0.000
64	I	64	ASN	0	-0.079	-0.032	21.503	-0.022	-0.022	0.000	0.000	0.000	0.000
65	I	65	VAL	0	-0.013	0.004	21.376	-0.035	-0.035	0.000	0.000	0.000	0.000
66	I	66	LYS	1	0.876	0.931	22.151	-0.173	-0.173	0.000	0.000	0.000	0.000
67	I	67	PHE	0	0.047	0.004	18.662	-0.019	-0.019	0.000	0.000	0.000	0.000
68	I	68	GLN	0	-0.037	-0.023	21.797	-0.007	-0.007	0.000	0.000	0.000	0.000
69	I	69	CYS	0	-0.064	-0.011	17.789	0.010	0.010	0.000	0.000	0.000	0.000
70	I	70	ASN	0	0.026	-0.003	21.514	-0.001	-0.001	0.000	0.000	0.000	0.000
71	I	71	GLN	0	0.060	0.048	21.004	0.010	0.010	0.000	0.000	0.000	0.000
72	I	72	VAL	0	-0.071	-0.029	20.245	0.001	0.001	0.000	0.000	0.000	0.000
73	I	73	ASP	-1	-0.891	-0.956	22.308	-0.093	-0.093	0.000	0.000	0.000	0.000
74	I	74	ASN	0	-0.132	-0.071	19.432	-0.010	-0.010	0.000	0.000	0.000	0.000
75	I	75	LYS	1	0.798	0.882	14.418	0.326	0.326	0.000	0.000	0.000	0.000
76	I	76	ASN	0	0.040	0.012	18.807	-0.026	-0.026	0.000	0.000	0.000	0.000
77	I	77	GLY	0	-0.028	-0.006	19.781	0.017	0.017	0.000	0.000	0.000	0.000
78	I	78	GLU	-1	-0.903	-0.948	17.265	-0.415	-0.415	0.000	0.000	0.000	0.000
79	I	79	GLN	0	-0.004	-0.002	12.202	-0.005	-0.005	0.000	0.000	0.000	0.000
80	I	80	TYR	0	0.016	0.014	16.323	0.044	0.044	0.000	0.000	0.000	0.000
81	I	81	SER	0	0.023	-0.015	16.078	0.001	0.001	0.000	0.000	0.000	0.000
82	I	82	PHE	0	-0.033	-0.027	16.685	0.026	0.026	0.000	0.000	0.000	0.000
83	I	83	LYS	1	0.901	0.953	17.287	-0.001	-0.001	0.000	0.000	0.000	0.000
84	I	85	LYS	1	0.929	0.959	19.751	-0.094	-0.094	0.000	0.000	0.000	0.000
85	I	86	SER	0	0.024	-0.019	21.465	0.006	0.006	0.000	0.000	0.000	0.000
86	I	87	SER	0	-0.016	0.001	23.348	-0.012	-0.012	0.000	0.000	0.000	0.000
87	I	88	ASP	-1	-0.799	-0.856	22.202	0.227	0.227	0.000	0.000	0.000	0.000
88	I	89	ASN	0	-0.126	-0.072	24.809	-0.017	-0.017	0.000	0.000	0.000	0.000
89	I	90	THR	0	-0.013	-0.012	18.301	-0.009	-0.009	0.000	0.000	0.000	0.000
90	I	91	GLU	-1	-0.880	-0.958	19.956	0.019	0.019	0.000	0.000	0.000	0.000
91	I	92	PHE	0	-0.027	-0.005	14.589	0.013	0.013	0.000	0.000	0.000	0.000
92	I	93	GLU	-1	-0.902	-0.925	15.201	-0.176	-0.176	0.000	0.000	0.000	0.000
93	I	94	ALA	0	0.011	-0.001	12.502	0.022	0.022	0.000	0.000	0.000	0.000
94	I	95	ASP	-1	-0.760	-0.834	11.856	-0.308	-0.308	0.000	0.000	0.000	0.000
95	I	96	PHE	0	-0.022	-0.022	11.317	0.024	0.024	0.000	0.000	0.000	0.000
96	I	97	THR	0	0.071	0.038	11.379	0.011	0.011	0.000	0.000	0.000	0.000
97	I	98	PHE	0	-0.012	-0.012	12.293	0.004	0.004	0.000	0.000	0.000	0.000
98	I	99	ILE	0	0.036	0.028	10.635	-0.018	-0.018	0.000	0.000	0.000	0.000
99	I	100	SER	0	-0.019	-0.014	14.059	0.013	0.013	0.000	0.000	0.000	0.000
100	I	101	VAL	0	0.004	-0.003	15.958	0.052	0.052	0.000	0.000	0.000	0.000
101	I	102	SER	0	0.010	0.042	18.585	-0.018	-0.018	0.000	0.000	0.000	0.000
102	I	103	TYR	0	0.025	-0.003	21.632	0.025	0.025	0.000	0.000	0.000	0.000
103	I	104	ASP	-1	-0.893	-0.948	23.067	0.108	0.108	0.000	0.000	0.000	0.000
104	I	105	ASN	0	-0.031	-0.023	22.065	0.031	0.031	0.000	0.000	0.000	0.000
105	I	106	PHE	0	0.011	0.010	15.796	0.034	0.034	0.000	0.000	0.000	0.000
106	I	107	ALA	0	0.004	-0.001	16.104	-0.062	-0.062	0.000	0.000	0.000	0.000
107	I	108	LEU	0	-0.011	0.011	9.374	0.102	0.102	0.000	0.000	0.000	0.000
108	I	109	VAL	0	-0.032	-0.035	10.746	-0.122	-0.122	0.000	0.000	0.000	0.000
109	I	111	ARG	1	0.826	0.879	7.040	-0.852	-0.852	0.000	0.000	0.000	0.000
110	I	112	SER	0	0.043	-0.002	6.507	-0.052	-0.052	0.000	0.000	0.000	0.000
111	I	113	ILE	0	-0.064	-0.021	7.351	0.155	0.155	0.000	0.000	0.000	0.000
112	I	114	THR	0	-0.028	-0.014	9.804	-0.155	-0.155	0.000	0.000	0.000	0.000
113	I	115	PHE	0	0.034	-0.005	10.711	0.004	0.004	0.000	0.000	0.000	0.000
114	I	116	THR	0	-0.015	-0.010	14.831	-0.050	-0.050	0.000	0.000	0.000	0.000
115	I	117	SER	0	-0.047	-0.015	16.364	-0.015	-0.015	0.000	0.000	0.000	0.000
116	I	118	GLN	0	-0.021	-0.008	12.620	0.025	0.025	0.000	0.000	0.000	0.000
117	I	119	PRO	0	-0.008	-0.011	12.659	0.049	0.049	0.000	0.000	0.000	0.000
118	I	120	LYS	1	0.808	0.885	7.632	1.853	1.853	0.000	0.000	0.000	0.000
119	I	121	GLU	-1	-0.760	-0.851	5.410	1.344	1.344	0.000	0.000	0.000	0.000
120	I	122	ASP	-1	-0.782	-0.859	4.032	-1.736	-1.231	-0.001	-0.277	-0.227	-0.001
121	I	123	ARG	1	0.925	0.960	1.855	-13.109	-16.290	12.114	-5.011	-3.922	-0.020
122	I	124	TYR	0	-0.068	-0.047	3.357	-0.854	-0.940	0.052	0.340	-0.306	0.001
123	I	125	LEU	0	-0.065	-0.039	5.864	0.907	0.907	0.000	0.000	0.000	0.000
124	I	126	VAL	0	0.035	0.003	8.806	-0.353	-0.353	0.000	0.000	0.000	0.000
125	I	127	PHE	0	-0.047	-0.015	11.894	0.069	0.069	0.000	0.000	0.000	0.000
126	I	128	GLU	-1	-0.887	-0.953	15.377	0.440	0.440	0.000	0.000	0.000	0.000
127	I	129	ARG	1	0.792	0.895	18.443	-0.166	-0.166	0.000	0.000	0.000	0.000
128	I	130	THR	0	-0.037	-0.027	21.892	-0.025	-0.025	0.000	0.000	0.000	0.000
129	I	131	LYS	1	0.803	0.919	21.501	-0.239	-0.239	0.000	0.000	0.000	0.000
130	I	132	SER	0	0.042	0.021	19.818	-0.030	-0.030	0.000	0.000	0.000	0.000
131	I	133	ASP	-1	-0.977	-0.996	21.781	0.275	0.275	0.000	0.000	0.000	0.000
132	I	134	THR	0	-0.071	-0.043	21.249	-0.024	-0.024	0.000	0.000	0.000	0.000
133	I	135	ASP	-1	-0.867	-0.924	19.558	0.495	0.495	0.000	0.000	0.000	0.000
134	I	136	PRO	0	0.028	0.005	21.577	-0.034	-0.034	0.000	0.000	0.000	0.000
135	I	137	ASP	-1	-0.820	-0.912	24.099	0.228	0.228	0.000	0.000	0.000	0.000
136	I	138	ALA	0	0.061	0.022	24.505	0.000	0.000	0.000	0.000	0.000	0.000
137	I	139	LYS	1	0.868	0.940	25.769	-0.156	-0.156	0.000	0.000	0.000	0.000
138	I	140	GLU	-1	-0.958	-0.974	28.008	0.227	0.227	0.000	0.000	0.000	0.000
139	I	141	ILE	0	0.006	0.001	21.989	-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)