FMO DATABASE

FMODB ID: V57Z1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-713314.447907
FMO2-HF: Nuclear repulsion	672230.629768
FMO2-HF: Total energy	-41083.81814
FMO2-MP2: Total energy	-41200.083548

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.
-0.542	0.921	0.012	-0.483	-0.992	0.004

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 : 0.018 / q_NPA : -0.006

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	-0.029	0.001	3.517	0.357	1.820	0.012	-0.483	-0.992	0.004
4	M	153	SER	0	0.016	0.005	5.916	0.152	0.152	0.000	0.000	0.000	0.000
5	M	154	VAL	0	-0.002	-0.008	8.559	-0.003	-0.003	0.000	0.000	0.000	0.000
6	M	155	LEU	0	0.003	0.009	9.853	-0.141	-0.141	0.000	0.000	0.000	0.000
7	M	156	GLN	0	0.016	0.012	7.879	-0.019	-0.019	0.000	0.000	0.000	0.000
8	M	157	VAL	0	-0.010	-0.017	11.241	0.055	0.055	0.000	0.000	0.000	0.000
9	M	158	VAL	0	0.015	0.004	12.872	-0.015	-0.015	0.000	0.000	0.000	0.000
10	M	159	ASN	0	-0.036	-0.002	14.935	0.013	0.013	0.000	0.000	0.000	0.000
11	M	160	LEU	0	0.004	-0.004	15.107	0.001	0.001	0.000	0.000	0.000	0.000
12	M	161	PRO	0	0.021	0.016	19.160	0.014	0.014	0.000	0.000	0.000	0.000
13	M	162	LEU	0	-0.002	-0.003	22.162	-0.011	-0.011	0.000	0.000	0.000	0.000
14	M	163	VAL	0	-0.013	0.013	22.187	0.009	0.009	0.000	0.000	0.000	0.000
15	M	164	GLU	-1	-0.811	-0.894	25.370	-0.115	-0.115	0.000	0.000	0.000	0.000
16	M	165	ARG	1	0.974	0.942	27.955	0.105	0.105	0.000	0.000	0.000	0.000
17	M	166	PRO	0	-0.049	-0.026	28.725	-0.002	-0.002	0.000	0.000	0.000	0.000
18	M	167	VAL	0	0.074	0.048	24.683	0.001	0.001	0.000	0.000	0.000	0.000
19	M	168	CYS	0	-0.021	0.014	20.954	-0.012	-0.012	0.000	0.000	0.000	0.000
20	M	169	LYS	1	0.907	0.944	24.904	0.092	0.092	0.000	0.000	0.000	0.000
21	M	170	ALA	0	0.032	0.019	26.684	-0.001	-0.001	0.000	0.000	0.000	0.000
22	M	171	SER	0	-0.039	0.001	21.161	-0.003	-0.003	0.000	0.000	0.000	0.000
23	M	172	THR	0	-0.053	-0.042	21.420	-0.005	-0.005	0.000	0.000	0.000	0.000
24	M	173	ARG	1	1.000	0.992	21.428	0.129	0.129	0.000	0.000	0.000	0.000
25	M	174	ILE	0	-0.008	0.020	20.765	0.011	0.011	0.000	0.000	0.000	0.000
26	M	175	ARG	1	0.974	0.980	24.880	0.090	0.090	0.000	0.000	0.000	0.000
27	M	176	ILE	0	0.016	0.018	23.637	0.001	0.001	0.000	0.000	0.000	0.000
28	M	177	THR	0	-0.002	-0.013	27.190	0.010	0.010	0.000	0.000	0.000	0.000
29	M	178	ASP	-1	-0.927	-0.959	28.541	-0.096	-0.096	0.000	0.000	0.000	0.000
30	M	179	ASN	0	-0.038	-0.027	28.106	0.004	0.004	0.000	0.000	0.000	0.000
31	M	180	MET	0	-0.007	0.030	23.502	-0.006	-0.006	0.000	0.000	0.000	0.000
32	M	181	PHE	0	-0.043	-0.021	22.439	0.014	0.014	0.000	0.000	0.000	0.000
33	M	183	ALA	0	0.020	0.009	19.502	0.015	0.015	0.000	0.000	0.000	0.000
34	M	184	GLY	0	0.052	0.029	18.181	-0.024	-0.024	0.000	0.000	0.000	0.000
35	M	184	TYR	0	-0.007	-0.004	17.377	0.032	0.032	0.000	0.000	0.000	0.000
36	M	185	LYS	1	0.876	0.932	19.536	0.125	0.125	0.000	0.000	0.000	0.000
37	M	186	PRO	0	0.027	-0.009	20.210	0.001	0.001	0.000	0.000	0.000	0.000
38	M	186	GLY	0	0.001	0.000	21.278	-0.001	-0.001	0.000	0.000	0.000	0.000
39	M	186	GLU	-1	-0.938	-0.967	21.886	-0.146	-0.146	0.000	0.000	0.000	0.000
40	M	186	GLY	0	-0.003	0.016	20.214	0.001	0.001	0.000	0.000	0.000	0.000
41	M	186	LYS	1	0.927	0.950	17.924	0.185	0.185	0.000	0.000	0.000	0.000
42	M	187	ARG	1	0.785	0.907	12.692	0.298	0.298	0.000	0.000	0.000	0.000
43	M	188	GLY	0	-0.009	-0.006	11.962	0.008	0.008	0.000	0.000	0.000	0.000
44	M	189	ASP	-1	-0.882	-0.924	11.026	-0.360	-0.360	0.000	0.000	0.000	0.000
45	M	190	ALA	0	-0.032	-0.004	10.916	-0.066	-0.066	0.000	0.000	0.000	0.000
46	M	191	CYS	0	0.058	0.005	6.486	-0.043	-0.043	0.000	0.000	0.000	0.000
47	M	192	GLU	-1	-0.879	-0.961	6.150	-0.627	-0.627	0.000	0.000	0.000	0.000
48	M	193	GLY	0	-0.034	-0.010	7.092	-0.190	-0.190	0.000	0.000	0.000	0.000
49	M	194	ASP	-1	-0.901	-0.934	8.944	-0.842	-0.842	0.000	0.000	0.000	0.000
50	M	195	SER	0	-0.078	-0.049	11.387	0.105	0.105	0.000	0.000	0.000	0.000
51	M	196	GLY	0	-0.019	-0.009	13.797	0.016	0.016	0.000	0.000	0.000	0.000
52	M	197	GLY	0	0.020	0.014	15.671	0.033	0.033	0.000	0.000	0.000	0.000
53	M	198	PRO	0	-0.027	-0.018	17.019	0.011	0.011	0.000	0.000	0.000	0.000
54	M	199	PHE	0	0.059	0.055	18.237	-0.019	-0.019	0.000	0.000	0.000	0.000
55	M	200	VAL	0	-0.037	-0.048	20.424	0.023	0.023	0.000	0.000	0.000	0.000
56	M	201	MET	0	0.021	0.012	23.058	-0.005	-0.005	0.000	0.000	0.000	0.000
57	M	202	LYS	1	0.915	0.988	25.817	0.102	0.102	0.000	0.000	0.000	0.000
58	M	203	SER	0	-0.021	-0.009	28.262	0.002	0.002	0.000	0.000	0.000	0.000
59	M	204	PRO	0	0.021	0.003	31.854	0.003	0.003	0.000	0.000	0.000	0.000
60	M	204	TYR	0	0.021	0.010	33.734	0.004	0.004	0.000	0.000	0.000	0.000
61	M	204	ASN	0	0.008	-0.011	34.902	0.002	0.002	0.000	0.000	0.000	0.000
62	M	205	ASN	0	0.057	0.010	31.959	-0.004	-0.004	0.000	0.000	0.000	0.000
63	M	206	ARG	1	0.965	0.999	30.774	0.066	0.066	0.000	0.000	0.000	0.000
64	M	207	TRP	0	0.023	0.007	23.402	-0.002	-0.002	0.000	0.000	0.000	0.000
65	M	208	TYR	0	-0.016	-0.007	27.688	0.007	0.007	0.000	0.000	0.000	0.000
66	M	209	GLN	0	0.045	0.020	22.581	-0.022	-0.022	0.000	0.000	0.000	0.000
67	M	210	MET	0	-0.040	-0.036	24.661	0.012	0.012	0.000	0.000	0.000	0.000
68	M	211	GLY	0	0.000	-0.022	23.131	0.010	0.010	0.000	0.000	0.000	0.000
69	M	212	ILE	0	-0.039	0.001	19.193	0.001	0.001	0.000	0.000	0.000	0.000
70	M	213	VAL	0	0.043	0.011	13.861	0.016	0.016	0.000	0.000	0.000	0.000
71	M	214	SER	0	-0.050	-0.002	17.094	0.005	0.005	0.000	0.000	0.000	0.000
72	M	215	TRP	0	0.002	-0.023	15.820	-0.011	-0.011	0.000	0.000	0.000	0.000
73	M	216	GLY	0	0.077	0.028	15.154	-0.007	-0.007	0.000	0.000	0.000	0.000
74	M	217	GLU	-1	-0.846	-0.918	15.190	-0.175	-0.175	0.000	0.000	0.000	0.000
75	M	219	GLY	0	-0.049	-0.032	11.108	0.014	0.014	0.000	0.000	0.000	0.000
76	M	221	ASP	-1	-0.842	-0.929	9.850	-0.382	-0.382	0.000	0.000	0.000	0.000
77	M	221	ARG	1	0.973	1.008	11.561	0.308	0.308	0.000	0.000	0.000	0.000
78	M	222	ASP	-1	-0.839	-0.945	13.800	-0.186	-0.186	0.000	0.000	0.000	0.000
79	M	223	GLY	0	-0.037	-0.023	17.273	0.010	0.010	0.000	0.000	0.000	0.000
80	M	224	LYS	1	0.739	0.882	16.202	0.188	0.188	0.000	0.000	0.000	0.000
81	M	225	TYR	0	0.019	-0.002	17.656	0.000	0.000	0.000	0.000	0.000	0.000
82	M	226	GLY	0	0.070	0.050	16.426	-0.005	-0.005	0.000	0.000	0.000	0.000
83	M	227	PHE	0	-0.018	-0.040	17.010	0.038	0.038	0.000	0.000	0.000	0.000
84	M	228	TYR	0	0.022	0.002	16.344	-0.021	-0.021	0.000	0.000	0.000	0.000
85	M	229	THR	0	-0.006	-0.003	20.914	0.015	0.015	0.000	0.000	0.000	0.000
86	M	230	HIS	0	0.023	0.011	23.586	-0.002	-0.002	0.000	0.000	0.000	0.000
87	M	231	VAL	0	0.042	0.017	24.851	0.011	0.011	0.000	0.000	0.000	0.000
88	M	232	PHE	0	0.005	-0.003	27.451	0.009	0.009	0.000	0.000	0.000	0.000
89	M	233	ARG	1	0.901	0.966	30.407	0.103	0.103	0.000	0.000	0.000	0.000
90	M	234	LEU	0	0.031	0.016	27.495	0.007	0.007	0.000	0.000	0.000	0.000
91	M	235	LYS	1	0.985	1.001	31.380	0.080	0.080	0.000	0.000	0.000	0.000
92	M	236	LYS	1	0.898	0.935	32.741	0.077	0.077	0.000	0.000	0.000	0.000
93	M	237	TRP	0	0.007	0.010	28.787	0.003	0.003	0.000	0.000	0.000	0.000
94	M	238	ILE	0	0.082	0.016	28.781	0.002	0.002	0.000	0.000	0.000	0.000
95	M	239	GLN	0	-0.004	0.005	32.617	0.001	0.001	0.000	0.000	0.000	0.000
96	M	240	LYS	1	0.898	0.961	36.208	0.064	0.064	0.000	0.000	0.000	0.000
97	M	241	VAL	0	-0.051	-0.026	31.781	0.003	0.003	0.000	0.000	0.000	0.000
98	M	242	ILE	0	-0.023	0.002	31.111	-0.003	-0.003	0.000	0.000	0.000	0.000
99	M	243	ASP	-1	-0.972	-0.963	34.687	-0.044	-0.044	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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