FMO DATABASE

FMODB ID: 17ZVZ

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-713064.306141
FMO2-HF: Nuclear repulsion	671979.652584
FMO2-HF: Total energy	-41084.653558
FMO2-MP2: Total energy	-41200.844038

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.
-0.661	1.014	-0.009	-0.708	-0.957	0.003

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 : 0.007 / q_NPA : -0.011

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	0.003	3.737	-0.013	1.662	-0.009	-0.708	-0.957	0.003
4	M	153	SER	0	0.003	0.002	5.898	0.237	0.237	0.000	0.000	0.000	0.000
5	M	154	VAL	0	0.001	-0.009	8.538	0.017	0.017	0.000	0.000	0.000	0.000
6	M	155	LEU	0	0.020	0.018	9.840	-0.152	-0.152	0.000	0.000	0.000	0.000
7	M	156	GLN	0	-0.005	0.000	7.807	-0.050	-0.050	0.000	0.000	0.000	0.000
8	M	157	VAL	0	-0.021	-0.023	11.237	0.069	0.069	0.000	0.000	0.000	0.000
9	M	158	VAL	0	0.033	0.013	12.824	-0.023	-0.023	0.000	0.000	0.000	0.000
10	M	159	ASN	0	-0.038	-0.001	14.926	0.021	0.021	0.000	0.000	0.000	0.000
11	M	160	LEU	0	0.012	0.008	14.976	-0.001	-0.001	0.000	0.000	0.000	0.000
12	M	161	PRO	0	0.024	0.018	19.158	0.018	0.018	0.000	0.000	0.000	0.000
13	M	162	LEU	0	-0.011	-0.010	21.944	-0.009	-0.009	0.000	0.000	0.000	0.000
14	M	163	VAL	0	-0.024	0.005	22.126	0.009	0.009	0.000	0.000	0.000	0.000
15	M	164	GLU	-1	-0.811	-0.898	25.155	-0.121	-0.121	0.000	0.000	0.000	0.000
16	M	165	ARG	1	0.938	0.919	27.788	0.102	0.102	0.000	0.000	0.000	0.000
17	M	166	PRO	0	-0.035	-0.012	28.525	-0.001	-0.001	0.000	0.000	0.000	0.000
18	M	167	VAL	0	0.060	0.038	24.591	0.002	0.002	0.000	0.000	0.000	0.000
19	M	168	CYS	0	-0.016	0.017	20.864	-0.011	-0.011	0.000	0.000	0.000	0.000
20	M	169	LYS	1	0.916	0.938	24.677	0.087	0.087	0.000	0.000	0.000	0.000
21	M	170	ALA	0	0.041	0.027	26.457	0.000	0.000	0.000	0.000	0.000	0.000
22	M	171	SER	0	-0.067	-0.021	21.270	-0.003	-0.003	0.000	0.000	0.000	0.000
23	M	172	THR	0	-0.034	-0.036	21.136	-0.004	-0.004	0.000	0.000	0.000	0.000
24	M	173	ARG	1	0.929	0.966	20.541	0.130	0.130	0.000	0.000	0.000	0.000
25	M	174	ILE	0	-0.009	0.014	20.752	0.010	0.010	0.000	0.000	0.000	0.000
26	M	175	ARG	1	0.976	0.979	24.857	0.078	0.078	0.000	0.000	0.000	0.000
27	M	176	ILE	0	0.012	0.018	23.642	0.002	0.002	0.000	0.000	0.000	0.000
28	M	177	THR	0	0.041	0.010	27.239	0.009	0.009	0.000	0.000	0.000	0.000
29	M	178	ASP	-1	-0.829	-0.906	28.673	-0.094	-0.094	0.000	0.000	0.000	0.000
30	M	179	ASN	0	-0.033	-0.009	28.501	0.002	0.002	0.000	0.000	0.000	0.000
31	M	180	MET	0	-0.008	0.035	23.400	-0.007	-0.007	0.000	0.000	0.000	0.000
32	M	181	PHE	0	-0.034	-0.011	22.745	0.013	0.013	0.000	0.000	0.000	0.000
33	M	183	ALA	0	0.024	0.013	19.409	0.015	0.015	0.000	0.000	0.000	0.000
34	M	184	GLY	0	0.049	0.027	18.005	-0.022	-0.022	0.000	0.000	0.000	0.000
35	M	184	TYR	0	-0.027	-0.018	16.999	0.037	0.037	0.000	0.000	0.000	0.000
36	M	185	LYS	1	0.863	0.927	19.491	0.134	0.134	0.000	0.000	0.000	0.000
37	M	186	PRO	0	0.012	-0.018	20.334	-0.001	-0.001	0.000	0.000	0.000	0.000
38	M	186	GLY	0	-0.002	0.000	21.395	-0.003	-0.003	0.000	0.000	0.000	0.000
39	M	186	GLU	-1	-0.904	-0.947	22.110	-0.163	-0.163	0.000	0.000	0.000	0.000
40	M	186	GLY	0	-0.003	0.016	20.342	0.000	0.000	0.000	0.000	0.000	0.000
41	M	186	LYS	1	0.922	0.954	17.934	0.209	0.209	0.000	0.000	0.000	0.000
42	M	187	ARG	1	0.779	0.879	12.663	0.348	0.348	0.000	0.000	0.000	0.000
43	M	188	GLY	0	-0.023	-0.024	11.959	0.007	0.007	0.000	0.000	0.000	0.000
44	M	189	ASP	-1	-0.883	-0.939	10.933	-0.349	-0.349	0.000	0.000	0.000	0.000
45	M	190	ALA	0	-0.034	0.005	10.818	-0.072	-0.072	0.000	0.000	0.000	0.000
46	M	191	CYS	0	0.069	0.021	6.508	-0.036	-0.036	0.000	0.000	0.000	0.000
47	M	192	GLU	-1	-0.886	-0.972	6.099	-0.482	-0.482	0.000	0.000	0.000	0.000
48	M	193	GLY	0	-0.035	-0.011	6.942	-0.154	-0.154	0.000	0.000	0.000	0.000
49	M	194	ASP	-1	-0.893	-0.930	9.434	-0.773	-0.773	0.000	0.000	0.000	0.000
50	M	195	SER	0	-0.107	-0.060	11.364	0.089	0.089	0.000	0.000	0.000	0.000
51	M	196	GLY	0	0.001	-0.002	13.757	0.018	0.018	0.000	0.000	0.000	0.000
52	M	197	GLY	0	0.021	0.014	15.631	0.028	0.028	0.000	0.000	0.000	0.000
53	M	198	PRO	0	-0.031	-0.024	16.985	0.011	0.011	0.000	0.000	0.000	0.000
54	M	199	PHE	0	0.068	0.053	18.362	-0.019	-0.019	0.000	0.000	0.000	0.000
55	M	200	VAL	0	-0.026	-0.040	20.607	0.024	0.024	0.000	0.000	0.000	0.000
56	M	201	MET	0	0.007	0.009	23.055	-0.007	-0.007	0.000	0.000	0.000	0.000
57	M	202	LYS	1	0.908	0.969	25.813	0.110	0.110	0.000	0.000	0.000	0.000
58	M	203	SER	0	-0.007	-0.003	28.254	0.002	0.002	0.000	0.000	0.000	0.000
59	M	204	PRO	0	0.026	0.002	31.849	0.003	0.003	0.000	0.000	0.000	0.000
60	M	204	TYR	0	0.024	0.016	33.726	0.005	0.005	0.000	0.000	0.000	0.000
61	M	204	ASN	0	-0.001	-0.013	34.977	0.003	0.003	0.000	0.000	0.000	0.000
62	M	205	ASN	0	0.052	0.015	32.058	-0.009	-0.009	0.000	0.000	0.000	0.000
63	M	206	ARG	1	0.963	1.003	30.780	0.067	0.067	0.000	0.000	0.000	0.000
64	M	207	TRP	0	0.037	0.011	23.497	-0.002	-0.002	0.000	0.000	0.000	0.000
65	M	208	TYR	0	-0.028	-0.012	27.682	0.007	0.007	0.000	0.000	0.000	0.000
66	M	209	GLN	0	0.029	0.013	23.133	-0.015	-0.015	0.000	0.000	0.000	0.000
67	M	210	MET	0	-0.032	-0.029	24.829	0.013	0.013	0.000	0.000	0.000	0.000
68	M	211	GLY	0	0.003	-0.024	23.286	0.010	0.010	0.000	0.000	0.000	0.000
69	M	212	ILE	0	-0.039	0.000	19.192	-0.001	-0.001	0.000	0.000	0.000	0.000
70	M	213	VAL	0	0.027	0.021	13.869	0.015	0.015	0.000	0.000	0.000	0.000
71	M	214	SER	0	-0.042	-0.005	17.133	0.010	0.010	0.000	0.000	0.000	0.000
72	M	215	TRP	0	0.024	-0.034	15.953	-0.006	-0.006	0.000	0.000	0.000	0.000
73	M	216	GLY	0	0.090	0.038	15.154	-0.011	-0.011	0.000	0.000	0.000	0.000
74	M	217	GLU	-1	-0.814	-0.878	15.180	-0.153	-0.153	0.000	0.000	0.000	0.000
75	M	219	GLY	0	-0.023	-0.009	10.915	0.009	0.009	0.000	0.000	0.000	0.000
76	M	221	ASP	-1	-0.820	-0.902	9.791	-0.459	-0.459	0.000	0.000	0.000	0.000
77	M	221	ARG	1	0.916	0.963	11.765	0.284	0.284	0.000	0.000	0.000	0.000
78	M	222	ASP	-1	-0.807	-0.912	13.843	-0.224	-0.224	0.000	0.000	0.000	0.000
79	M	223	GLY	0	-0.019	-0.010	17.366	0.013	0.013	0.000	0.000	0.000	0.000
80	M	224	LYS	1	0.735	0.872	16.120	0.187	0.187	0.000	0.000	0.000	0.000
81	M	225	TYR	0	0.024	0.002	17.515	-0.005	-0.005	0.000	0.000	0.000	0.000
82	M	226	GLY	0	0.074	0.051	16.380	-0.001	-0.001	0.000	0.000	0.000	0.000
83	M	227	PHE	0	-0.027	-0.045	16.951	0.034	0.034	0.000	0.000	0.000	0.000
84	M	228	TYR	0	0.025	-0.004	16.231	-0.014	-0.014	0.000	0.000	0.000	0.000
85	M	229	THR	0	-0.020	-0.003	21.123	0.014	0.014	0.000	0.000	0.000	0.000
86	M	230	HIS	0	0.034	0.014	23.713	-0.002	-0.002	0.000	0.000	0.000	0.000
87	M	231	VAL	0	0.035	0.016	24.953	0.011	0.011	0.000	0.000	0.000	0.000
88	M	232	PHE	0	0.017	0.013	27.540	0.009	0.009	0.000	0.000	0.000	0.000
89	M	233	ARG	1	0.833	0.904	30.553	0.097	0.097	0.000	0.000	0.000	0.000
90	M	234	LEU	0	0.036	0.019	27.644	0.008	0.008	0.000	0.000	0.000	0.000
91	M	235	LYS	1	0.980	0.996	31.427	0.076	0.076	0.000	0.000	0.000	0.000
92	M	236	LYS	1	0.861	0.921	32.772	0.075	0.075	0.000	0.000	0.000	0.000
93	M	237	TRP	0	-0.019	-0.004	28.599	0.003	0.003	0.000	0.000	0.000	0.000
94	M	238	ILE	0	0.070	0.017	28.605	0.003	0.003	0.000	0.000	0.000	0.000
95	M	239	GLN	0	-0.004	0.005	32.539	0.000	0.000	0.000	0.000	0.000	0.000
96	M	240	LYS	1	0.942	0.974	36.126	0.053	0.053	0.000	0.000	0.000	0.000
97	M	241	VAL	0	-0.044	-0.022	31.558	0.003	0.003	0.000	0.000	0.000	0.000
98	M	242	ILE	0	-0.049	-0.011	31.394	-0.002	-0.002	0.000	0.000	0.000	0.000
99	M	243	ASP	-1	-0.955	-0.954	34.507	-0.037	-0.037	0.000	0.000	0.000	0.000

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