FMO DATABASE

FMODB ID: G6971

Calculation Name: 1YCP-M-Xray372

Preferred Name: Fibrinogen

Target Type: PROTEIN FAMILY

Ligand Name:

ligand 3-letter code:

PDB ID: 1YCP

Chain ID: M

ChEMBL ID: CHEMBL2364709

UniProt ID: P02671

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	99
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-712493.772937
FMO2-HF: Nuclear repulsion	671408.62891
FMO2-HF: Total energy	-41085.144027
FMO2-MP2: Total energy	-41201.235725

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(M:150:VAL)

Summations of interaction energy for fragment #1(M:150:VAL)

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.
-0.503	1.007	-0.007	-0.653	-0.851	0.002

Interaction energy analysis for fragmet #1(M:150:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / q_NPA : -0.009

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	M	152	PRO	0	-0.010	0.008	3.869	-0.128	1.382	-0.007	-0.653	-0.851	0.002
4	M	153	SER	0	0.012	-0.008	5.901	0.244	0.244	0.000	0.000	0.000	0.000
5	M	154	VAL	0	-0.011	0.000	8.563	0.038	0.038	0.000	0.000	0.000	0.000
6	M	155	LEU	0	0.019	0.014	10.269	-0.129	-0.129	0.000	0.000	0.000	0.000
7	M	156	GLN	0	-0.012	-0.005	8.437	-0.061	-0.061	0.000	0.000	0.000	0.000
8	M	157	VAL	0	-0.003	-0.015	11.931	0.059	0.059	0.000	0.000	0.000	0.000
9	M	158	VAL	0	0.019	0.014	13.298	-0.021	-0.021	0.000	0.000	0.000	0.000
10	M	159	ASN	0	-0.029	-0.006	15.362	0.032	0.032	0.000	0.000	0.000	0.000
11	M	160	LEU	0	0.019	0.018	15.339	-0.005	-0.005	0.000	0.000	0.000	0.000
12	M	161	PRO	0	0.011	0.015	19.544	0.017	0.017	0.000	0.000	0.000	0.000
13	M	162	LEU	0	-0.006	-0.005	21.941	-0.009	-0.009	0.000	0.000	0.000	0.000
14	M	163	VAL	0	-0.032	-0.003	21.878	0.006	0.006	0.000	0.000	0.000	0.000
15	M	164	GLU	-1	-0.785	-0.887	24.910	-0.118	-0.118	0.000	0.000	0.000	0.000
16	M	165	ARG	1	0.851	0.897	27.815	0.094	0.094	0.000	0.000	0.000	0.000
17	M	166	PRO	0	-0.020	-0.020	28.849	0.000	0.000	0.000	0.000	0.000	0.000
18	M	167	VAL	0	0.050	0.035	24.770	0.002	0.002	0.000	0.000	0.000	0.000
19	M	168	CYS	0	-0.011	0.011	20.912	-0.011	-0.011	0.000	0.000	0.000	0.000
20	M	169	LYS	1	0.903	0.942	24.658	0.080	0.080	0.000	0.000	0.000	0.000
21	M	170	ALA	0	0.017	0.005	26.708	0.000	0.000	0.000	0.000	0.000	0.000
22	M	171	SER	0	-0.044	-0.005	21.166	-0.002	-0.002	0.000	0.000	0.000	0.000
23	M	172	THR	0	-0.026	-0.033	21.349	-0.005	-0.005	0.000	0.000	0.000	0.000
24	M	173	ARG	1	0.897	0.932	20.314	0.126	0.126	0.000	0.000	0.000	0.000
25	M	174	ILE	0	0.004	0.025	20.789	0.010	0.010	0.000	0.000	0.000	0.000
26	M	175	ARG	1	0.969	0.982	24.963	0.068	0.068	0.000	0.000	0.000	0.000
27	M	176	ILE	0	0.018	0.009	23.900	0.003	0.003	0.000	0.000	0.000	0.000
28	M	177	THR	0	-0.010	-0.005	27.450	0.009	0.009	0.000	0.000	0.000	0.000
29	M	178	ASP	-1	-0.747	-0.868	28.921	-0.085	-0.085	0.000	0.000	0.000	0.000
30	M	179	ASN	0	-0.044	-0.019	28.776	0.000	0.000	0.000	0.000	0.000	0.000
31	M	180	MET	0	0.001	0.028	23.677	-0.005	-0.005	0.000	0.000	0.000	0.000
32	M	181	PHE	0	-0.046	-0.016	22.705	0.012	0.012	0.000	0.000	0.000	0.000
33	M	183	ALA	0	0.010	-0.002	19.603	0.015	0.015	0.000	0.000	0.000	0.000
34	M	184	GLY	0	0.040	0.019	18.025	-0.025	-0.025	0.000	0.000	0.000	0.000
35	M	184	TYR	0	-0.022	-0.021	17.275	0.034	0.034	0.000	0.000	0.000	0.000
36	M	185	LYS	1	0.853	0.916	19.514	0.132	0.132	0.000	0.000	0.000	0.000
37	M	186	PRO	0	0.027	-0.003	20.077	-0.001	-0.001	0.000	0.000	0.000	0.000
38	M	186	GLY	0	-0.007	0.009	21.245	0.000	0.000	0.000	0.000	0.000	0.000
39	M	186	GLU	-1	-0.896	-0.952	22.374	-0.156	-0.156	0.000	0.000	0.000	0.000
40	M	186	GLY	0	-0.010	0.003	21.213	-0.002	-0.002	0.000	0.000	0.000	0.000
41	M	186	LYS	1	0.886	0.947	18.315	0.194	0.194	0.000	0.000	0.000	0.000
42	M	187	ARG	1	0.809	0.890	12.357	0.360	0.360	0.000	0.000	0.000	0.000
43	M	188	GLY	0	-0.021	-0.015	12.352	0.002	0.002	0.000	0.000	0.000	0.000
44	M	189	ASP	-1	-0.874	-0.942	11.246	-0.321	-0.321	0.000	0.000	0.000	0.000
45	M	190	ALA	0	-0.044	-0.007	11.347	-0.059	-0.059	0.000	0.000	0.000	0.000
46	M	191	CYS	0	-0.004	-0.008	6.808	-0.003	-0.003	0.000	0.000	0.000	0.000
47	M	192	GLU	-1	-0.893	-0.978	6.180	-0.404	-0.404	0.000	0.000	0.000	0.000
48	M	193	GLY	0	-0.025	-0.005	6.698	-0.133	-0.133	0.000	0.000	0.000	0.000
49	M	194	ASP	-1	-0.852	-0.912	9.337	-0.600	-0.600	0.000	0.000	0.000	0.000
50	M	195	SER	0	-0.084	-0.045	11.840	0.071	0.071	0.000	0.000	0.000	0.000
51	M	196	GLY	0	0.011	0.005	14.213	0.018	0.018	0.000	0.000	0.000	0.000
52	M	197	GLY	0	0.021	0.017	15.918	0.023	0.023	0.000	0.000	0.000	0.000
53	M	198	PRO	0	-0.051	-0.029	17.092	0.007	0.007	0.000	0.000	0.000	0.000
54	M	199	PHE	0	0.037	0.013	18.788	-0.017	-0.017	0.000	0.000	0.000	0.000
55	M	200	VAL	0	-0.033	-0.035	20.862	0.023	0.023	0.000	0.000	0.000	0.000
56	M	201	MET	0	0.020	0.011	23.501	-0.007	-0.007	0.000	0.000	0.000	0.000
57	M	202	LYS	1	0.927	0.973	26.247	0.100	0.100	0.000	0.000	0.000	0.000
58	M	203	SER	0	-0.006	-0.004	28.580	0.000	0.000	0.000	0.000	0.000	0.000
59	M	204	PRO	0	0.018	-0.002	32.222	0.002	0.002	0.000	0.000	0.000	0.000
60	M	204	TYR	0	0.024	0.017	34.267	0.004	0.004	0.000	0.000	0.000	0.000
61	M	204	ASN	0	0.027	0.012	35.502	0.002	0.002	0.000	0.000	0.000	0.000
62	M	205	ASN	0	0.040	0.033	32.799	-0.009	-0.009	0.000	0.000	0.000	0.000
63	M	206	ARG	1	0.952	0.982	31.155	0.059	0.059	0.000	0.000	0.000	0.000
64	M	207	TRP	0	0.045	0.018	23.803	-0.003	-0.003	0.000	0.000	0.000	0.000
65	M	208	TYR	0	-0.049	-0.036	28.056	0.008	0.008	0.000	0.000	0.000	0.000
66	M	209	GLN	0	0.029	0.006	23.549	-0.010	-0.010	0.000	0.000	0.000	0.000
67	M	210	MET	0	-0.011	-0.010	25.699	0.010	0.010	0.000	0.000	0.000	0.000
68	M	211	GLY	0	-0.014	-0.022	23.620	0.007	0.007	0.000	0.000	0.000	0.000
69	M	212	ILE	0	-0.015	0.014	19.584	0.000	0.000	0.000	0.000	0.000	0.000
70	M	213	VAL	0	0.029	0.020	14.007	0.012	0.012	0.000	0.000	0.000	0.000
71	M	214	SER	0	-0.046	-0.009	17.375	0.013	0.013	0.000	0.000	0.000	0.000
72	M	215	TRP	0	0.036	-0.009	15.606	-0.003	-0.003	0.000	0.000	0.000	0.000
73	M	216	GLY	0	0.134	0.056	14.924	-0.008	-0.008	0.000	0.000	0.000	0.000
74	M	217	GLU	-1	-0.790	-0.843	15.173	-0.142	-0.142	0.000	0.000	0.000	0.000
75	M	219	GLY	0	-0.022	0.000	11.437	0.013	0.013	0.000	0.000	0.000	0.000
76	M	221	ASP	-1	-0.825	-0.904	9.886	-0.464	-0.464	0.000	0.000	0.000	0.000
77	M	221	ARG	1	0.877	0.919	11.654	0.276	0.276	0.000	0.000	0.000	0.000
78	M	222	ASP	-1	-0.802	-0.906	13.845	-0.231	-0.231	0.000	0.000	0.000	0.000
79	M	223	GLY	0	-0.006	-0.001	17.443	0.016	0.016	0.000	0.000	0.000	0.000
80	M	224	LYS	1	0.734	0.875	16.079	0.179	0.179	0.000	0.000	0.000	0.000
81	M	225	TYR	0	0.027	0.000	17.253	-0.003	-0.003	0.000	0.000	0.000	0.000
82	M	226	GLY	0	0.106	0.077	16.054	0.001	0.001	0.000	0.000	0.000	0.000
83	M	227	PHE	0	-0.028	-0.046	16.652	0.034	0.034	0.000	0.000	0.000	0.000
84	M	228	TYR	0	0.022	0.016	16.558	-0.012	-0.012	0.000	0.000	0.000	0.000
85	M	229	THR	0	0.000	0.003	21.104	0.013	0.013	0.000	0.000	0.000	0.000
86	M	230	HIS	0	0.036	-0.001	23.796	-0.001	-0.001	0.000	0.000	0.000	0.000
87	M	231	VAL	0	0.057	0.034	25.291	0.010	0.010	0.000	0.000	0.000	0.000
88	M	232	PHE	0	0.007	0.007	27.895	0.008	0.008	0.000	0.000	0.000	0.000
89	M	233	ARG	1	0.797	0.883	30.671	0.085	0.085	0.000	0.000	0.000	0.000
90	M	234	LEU	0	0.095	0.036	27.609	0.006	0.006	0.000	0.000	0.000	0.000
91	M	235	LYS	1	0.943	0.988	31.502	0.067	0.067	0.000	0.000	0.000	0.000
92	M	236	LYS	1	0.848	0.919	32.856	0.066	0.066	0.000	0.000	0.000	0.000
93	M	237	TRP	0	-0.006	-0.002	28.765	0.002	0.002	0.000	0.000	0.000	0.000
94	M	238	ILE	0	0.056	0.017	28.946	0.002	0.002	0.000	0.000	0.000	0.000
95	M	239	GLN	0	0.028	0.003	32.598	0.000	0.000	0.000	0.000	0.000	0.000
96	M	240	LYS	1	0.920	0.969	36.063	0.042	0.042	0.000	0.000	0.000	0.000
97	M	241	VAL	0	-0.039	-0.014	31.744	0.002	0.002	0.000	0.000	0.000	0.000
98	M	242	ILE	0	-0.058	-0.018	31.199	-0.001	-0.001	0.000	0.000	0.000	0.000
99	M	243	ASP	-1	-0.952	-0.955	34.419	-0.027	-0.027	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(M:150:VAL)