FMO DATABASE

FMODB ID: JLJK9

Calculation Name: 1YCP-K-Xray372

Preferred Name: Fibrinogen

Target Type: PROTEIN FAMILY

Ligand Name:

ligand 3-letter code:

PDB ID: 1YCP

Chain ID: K

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	145
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1371610.150095
FMO2-HF: Nuclear repulsion	1312362.409173
FMO2-HF: Total energy	-59247.740922
FMO2-MP2: Total energy	-59421.304301

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(K:16:ILE)

Summations of interaction energy for fragment #1(K:16:ILE)

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.
-18.704	-9.926	9.743	-7.304	-11.219	-0.047

Interaction energy analysis for fragmet #1(K:16:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.016 / q_NPA : -0.008

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	K	18	GLU	-1	-0.923	-0.955	2.897	-4.899	-1.827	0.262	-1.666	-1.668	-0.006
4	K	19	GLY	0	-0.041	-0.006	2.328	-0.320	0.683	1.863	-1.444	-1.423	-0.001
5	K	20	GLN	0	-0.063	-0.032	3.079	0.684	-0.247	0.058	1.117	-0.245	0.000
6	K	21	ASP	-1	-0.823	-0.880	5.257	-1.076	-1.076	0.000	0.000	0.000	0.000
7	K	22	ALA	0	0.020	0.013	6.794	0.083	0.083	0.000	0.000	0.000	0.000
8	K	23	GLU	-1	-0.835	-0.926	8.692	-0.049	-0.049	0.000	0.000	0.000	0.000
9	K	24	VAL	0	-0.026	-0.024	11.704	0.092	0.092	0.000	0.000	0.000	0.000
10	K	25	GLY	0	0.053	0.025	13.148	-0.017	-0.017	0.000	0.000	0.000	0.000
11	K	26	LEU	0	-0.078	-0.018	8.193	0.052	0.052	0.000	0.000	0.000	0.000
12	K	27	SER	0	-0.031	-0.034	8.096	-0.002	-0.002	0.000	0.000	0.000	0.000
13	K	28	PRO	0	0.042	0.040	10.884	0.082	0.082	0.000	0.000	0.000	0.000
14	K	29	TRP	0	0.027	0.023	10.193	-0.060	-0.060	0.000	0.000	0.000	0.000
15	K	30	GLN	0	-0.034	-0.009	6.454	0.245	0.245	0.000	0.000	0.000	0.000
16	K	31	VAL	0	-0.020	-0.013	10.391	-0.126	-0.126	0.000	0.000	0.000	0.000
17	K	32	MET	0	-0.048	-0.010	9.767	0.208	0.208	0.000	0.000	0.000	0.000
18	K	33	LEU	0	-0.041	-0.017	11.166	-0.189	-0.189	0.000	0.000	0.000	0.000
19	K	34	PHE	0	0.044	0.002	12.932	0.067	0.067	0.000	0.000	0.000	0.000
20	K	35	ARG	1	0.885	0.940	15.287	-0.342	-0.342	0.000	0.000	0.000	0.000
21	K	36	LYS	1	0.785	0.884	18.516	-0.263	-0.263	0.000	0.000	0.000	0.000
22	K	36	SER	0	0.001	0.009	22.105	-0.028	-0.028	0.000	0.000	0.000	0.000
23	K	37	PRO	0	0.086	0.023	19.645	0.008	0.008	0.000	0.000	0.000	0.000
24	K	38	GLN	0	-0.015	0.000	18.643	0.039	0.039	0.000	0.000	0.000	0.000
25	K	39	GLU	-1	-0.851	-0.912	14.662	0.359	0.359	0.000	0.000	0.000	0.000
26	K	40	LEU	0	-0.045	-0.031	9.104	0.004	0.004	0.000	0.000	0.000	0.000
27	K	41	LEU	0	0.017	0.028	11.289	0.127	0.127	0.000	0.000	0.000	0.000
28	K	42	CYS	0	-0.101	-0.064	9.093	0.173	0.173	0.000	0.000	0.000	0.000
29	K	43	GLY	0	0.024	0.033	7.152	-0.033	-0.033	0.000	0.000	0.000	0.000
30	K	44	ALA	0	-0.026	-0.025	8.150	-0.145	-0.145	0.000	0.000	0.000	0.000
31	K	45	SER	0	-0.001	0.012	10.075	0.041	0.041	0.000	0.000	0.000	0.000
32	K	46	LEU	0	-0.010	0.003	12.276	-0.064	-0.064	0.000	0.000	0.000	0.000
33	K	47	ILE	0	0.023	0.002	15.797	-0.001	-0.001	0.000	0.000	0.000	0.000
34	K	48	SER	0	-0.002	-0.008	18.258	-0.035	-0.035	0.000	0.000	0.000	0.000
35	K	49	ASP	-1	-0.719	-0.852	20.210	0.270	0.270	0.000	0.000	0.000	0.000
36	K	50	ARG	1	0.838	0.902	22.629	-0.218	-0.218	0.000	0.000	0.000	0.000
37	K	51	TRP	0	-0.009	0.013	20.516	0.004	0.004	0.000	0.000	0.000	0.000
38	K	52	VAL	0	0.034	0.015	14.566	0.019	0.019	0.000	0.000	0.000	0.000
39	K	53	LEU	0	-0.003	0.005	14.425	-0.046	-0.046	0.000	0.000	0.000	0.000
40	K	54	THR	0	0.002	-0.016	11.479	0.114	0.114	0.000	0.000	0.000	0.000
41	K	55	ALA	0	0.048	0.031	11.804	-0.086	-0.086	0.000	0.000	0.000	0.000
42	K	56	ALA	0	0.019	0.014	13.564	-0.004	-0.004	0.000	0.000	0.000	0.000
43	K	57	HIS	1	0.897	0.926	10.631	-0.995	-0.995	0.000	0.000	0.000	0.000
44	K	59	LEU	0	-0.033	-0.014	14.308	-0.042	-0.042	0.000	0.000	0.000	0.000
45	K	60	LEU	0	0.021	0.012	17.957	-0.048	-0.048	0.000	0.000	0.000	0.000
46	K	60	TYR	0	-0.033	-0.031	18.203	0.042	0.042	0.000	0.000	0.000	0.000
47	K	60	PRO	0	0.057	0.024	20.361	-0.012	-0.012	0.000	0.000	0.000	0.000
48	K	60	PRO	0	-0.025	-0.003	21.900	-0.016	-0.016	0.000	0.000	0.000	0.000
49	K	60	TRP	0	-0.039	-0.014	15.154	0.022	0.022	0.000	0.000	0.000	0.000
50	K	60	ASP	-1	-0.864	-0.924	22.397	0.183	0.183	0.000	0.000	0.000	0.000
51	K	60	LYS	1	0.807	0.926	15.481	-0.538	-0.538	0.000	0.000	0.000	0.000
52	K	60	ASN	0	0.037	-0.005	21.688	0.024	0.024	0.000	0.000	0.000	0.000
53	K	60	PHE	0	-0.036	-0.001	17.461	-0.015	-0.015	0.000	0.000	0.000	0.000
54	K	60	THR	0	-0.006	-0.030	21.933	0.000	0.000	0.000	0.000	0.000	0.000
55	K	61	VAL	0	-0.043	-0.039	22.563	0.027	0.027	0.000	0.000	0.000	0.000
56	K	62	ASP	-1	-0.857	-0.925	23.817	0.225	0.225	0.000	0.000	0.000	0.000
57	K	63	ASP	-1	-0.783	-0.855	21.870	0.260	0.260	0.000	0.000	0.000	0.000
58	K	64	LEU	0	-0.040	-0.017	17.355	0.020	0.020	0.000	0.000	0.000	0.000
59	K	65	LEU	0	-0.049	-0.033	18.368	-0.049	-0.049	0.000	0.000	0.000	0.000
60	K	66	VAL	0	-0.004	0.008	16.009	0.061	0.061	0.000	0.000	0.000	0.000
61	K	67	ARG	1	0.824	0.896	14.770	-0.470	-0.470	0.000	0.000	0.000	0.000
62	K	68	ILE	0	0.023	-0.001	13.915	0.097	0.097	0.000	0.000	0.000	0.000
63	K	69	GLY	0	0.070	0.043	14.582	-0.058	-0.058	0.000	0.000	0.000	0.000
64	K	70	LYS	1	0.706	0.845	12.214	-0.415	-0.415	0.000	0.000	0.000	0.000
65	K	71	HIS	0	0.001	-0.008	10.934	0.067	0.067	0.000	0.000	0.000	0.000
66	K	72	SER	0	0.011	0.013	10.006	-0.002	-0.002	0.000	0.000	0.000	0.000
67	K	73	ARG	1	0.961	0.971	7.470	0.071	0.071	0.000	0.000	0.000	0.000
68	K	74	THR	0	-0.028	-0.020	10.361	0.027	0.027	0.000	0.000	0.000	0.000
69	K	75	ARG	1	0.915	0.963	13.627	-0.034	-0.034	0.000	0.000	0.000	0.000
70	K	76	TYR	0	0.041	0.028	15.936	0.041	0.041	0.000	0.000	0.000	0.000
71	K	77	GLU	-1	-0.745	-0.879	14.595	0.168	0.168	0.000	0.000	0.000	0.000
72	K	77	ARG	1	0.975	0.978	18.898	-0.076	-0.076	0.000	0.000	0.000	0.000
73	K	78	LYS	1	0.936	0.974	21.630	-0.078	-0.078	0.000	0.000	0.000	0.000
74	K	79	VAL	0	0.023	0.035	17.484	-0.007	-0.007	0.000	0.000	0.000	0.000
75	K	80	GLU	-1	-0.748	-0.848	17.109	0.340	0.340	0.000	0.000	0.000	0.000
76	K	81	LYS	1	0.897	0.964	18.526	-0.293	-0.293	0.000	0.000	0.000	0.000
77	K	82	ILE	0	0.029	0.007	18.358	0.042	0.042	0.000	0.000	0.000	0.000
78	K	83	SER	0	-0.053	-0.032	20.118	-0.043	-0.043	0.000	0.000	0.000	0.000
79	K	84	MET	0	0.026	0.013	20.920	0.012	0.012	0.000	0.000	0.000	0.000
80	K	85	LEU	0	0.041	0.018	19.157	0.001	0.001	0.000	0.000	0.000	0.000
81	K	86	ASP	-1	-0.843	-0.891	23.101	0.199	0.199	0.000	0.000	0.000	0.000
82	K	87	LYS	1	0.933	0.941	24.755	-0.227	-0.227	0.000	0.000	0.000	0.000
83	K	88	ILE	0	0.011	0.007	20.617	0.027	0.027	0.000	0.000	0.000	0.000
84	K	89	TYR	0	-0.013	-0.009	21.760	-0.030	-0.030	0.000	0.000	0.000	0.000
85	K	90	ILE	0	0.051	0.023	19.802	0.031	0.031	0.000	0.000	0.000	0.000
86	K	91	HIS	0	-0.002	0.008	21.036	-0.052	-0.052	0.000	0.000	0.000	0.000
87	K	92	PRO	0	0.020	-0.003	22.960	0.001	0.001	0.000	0.000	0.000	0.000
88	K	93	ARG	1	0.916	0.948	25.031	-0.225	-0.225	0.000	0.000	0.000	0.000
89	K	94	TYR	0	-0.006	-0.006	18.133	0.008	0.008	0.000	0.000	0.000	0.000
90	K	95	ASN	0	-0.017	-0.015	22.087	-0.017	-0.017	0.000	0.000	0.000	0.000
91	K	96	TRP	0	0.019	-0.014	20.176	0.002	0.002	0.000	0.000	0.000	0.000
92	K	97	LYS	1	0.909	0.963	21.249	-0.173	-0.173	0.000	0.000	0.000	0.000
93	K	97	GLU	-1	-0.863	-0.903	22.833	0.176	0.176	0.000	0.000	0.000	0.000
94	K	98	ASN	0	0.005	-0.018	20.179	0.023	0.023	0.000	0.000	0.000	0.000
95	K	99	LEU	0	-0.018	0.001	15.192	0.038	0.038	0.000	0.000	0.000	0.000
96	K	100	ASP	-1	-0.754	-0.855	17.948	0.336	0.336	0.000	0.000	0.000	0.000
97	K	101	ARG	1	0.800	0.866	19.857	-0.262	-0.262	0.000	0.000	0.000	0.000
98	K	102	ASP	-1	-0.740	-0.835	14.186	0.732	0.732	0.000	0.000	0.000	0.000
99	K	103	ILE	0	-0.072	-0.026	15.342	0.082	0.082	0.000	0.000	0.000	0.000
100	K	104	ALA	0	0.012	-0.010	16.474	-0.065	-0.065	0.000	0.000	0.000	0.000
101	K	105	LEU	0	-0.001	0.012	16.938	0.052	0.052	0.000	0.000	0.000	0.000
102	K	106	LEU	0	0.010	-0.001	16.184	-0.029	-0.029	0.000	0.000	0.000	0.000
103	K	107	LYS	1	0.841	0.932	19.826	-0.240	-0.240	0.000	0.000	0.000	0.000
104	K	108	LEU	0	0.010	-0.005	19.228	-0.003	-0.003	0.000	0.000	0.000	0.000
105	K	109	LYS	1	0.906	0.954	23.058	-0.234	-0.234	0.000	0.000	0.000	0.000
106	K	110	ARG	1	0.944	0.969	25.459	-0.215	-0.215	0.000	0.000	0.000	0.000
107	K	111	PRO	0	-0.002	-0.001	24.776	0.020	0.020	0.000	0.000	0.000	0.000
108	K	112	ILE	0	-0.081	-0.034	18.941	-0.013	-0.013	0.000	0.000	0.000	0.000
109	K	113	GLU	-1	-0.940	-0.971	23.148	0.166	0.166	0.000	0.000	0.000	0.000
110	K	114	LEU	0	-0.029	-0.022	21.295	0.021	0.021	0.000	0.000	0.000	0.000
111	K	115	SER	0	0.019	0.005	21.150	-0.023	-0.023	0.000	0.000	0.000	0.000
112	K	116	ASP	-1	-0.816	-0.889	20.430	0.160	0.160	0.000	0.000	0.000	0.000
113	K	117	TYR	0	-0.080	-0.059	16.395	0.013	0.013	0.000	0.000	0.000	0.000
114	K	118	ILE	0	-0.093	-0.046	15.965	0.067	0.067	0.000	0.000	0.000	0.000
115	K	119	HIS	0	0.067	0.022	16.776	-0.045	-0.045	0.000	0.000	0.000	0.000
116	K	120	PRO	0	-0.029	-0.018	16.425	0.048	0.048	0.000	0.000	0.000	0.000
117	K	121	VAL	0	0.012	0.014	13.432	-0.024	-0.024	0.000	0.000	0.000	0.000
118	K	122	CYS	0	-0.025	-0.017	16.462	-0.009	-0.009	0.000	0.000	0.000	0.000
119	K	123	LEU	0	0.028	0.015	17.444	0.035	0.035	0.000	0.000	0.000	0.000
120	K	124	PRO	0	-0.010	-0.009	17.487	-0.035	-0.035	0.000	0.000	0.000	0.000
121	K	125	ASP	-1	-0.738	-0.828	20.439	0.195	0.195	0.000	0.000	0.000	0.000
122	K	126	LYS	1	0.983	0.972	23.467	-0.148	-0.148	0.000	0.000	0.000	0.000
123	K	127	GLN	0	0.054	0.024	25.424	-0.014	-0.014	0.000	0.000	0.000	0.000
124	K	128	THR	0	-0.016	-0.011	20.188	-0.012	-0.012	0.000	0.000	0.000	0.000
125	K	129	ALA	0	0.021	0.002	20.576	0.000	0.000	0.000	0.000	0.000	0.000
126	K	129	ALA	0	-0.015	-0.012	21.650	-0.003	-0.003	0.000	0.000	0.000	0.000
127	K	129	LYS	1	0.818	0.887	23.454	-0.162	-0.162	0.000	0.000	0.000	0.000
128	K	129	LEU	0	0.004	0.007	17.669	-0.013	-0.013	0.000	0.000	0.000	0.000
129	K	130	LEU	0	0.000	0.009	16.830	0.008	0.008	0.000	0.000	0.000	0.000
130	K	131	HIS	1	0.834	0.919	18.679	-0.161	-0.161	0.000	0.000	0.000	0.000
131	K	132	ALA	0	0.091	0.045	18.045	0.012	0.012	0.000	0.000	0.000	0.000
132	K	133	GLY	0	0.006	0.008	17.221	-0.011	-0.011	0.000	0.000	0.000	0.000
133	K	134	PHE	0	-0.028	-0.016	16.662	-0.022	-0.022	0.000	0.000	0.000	0.000
134	K	135	LYS	1	0.956	0.976	11.565	0.108	0.108	0.000	0.000	0.000	0.000
135	K	136	GLY	0	0.034	0.019	10.934	-0.001	-0.001	0.000	0.000	0.000	0.000
136	K	137	ARG	1	0.932	0.974	6.992	-0.327	-0.327	0.000	0.000	0.000	0.000
137	K	138	VAL	0	0.030	0.016	2.622	-0.519	-0.057	0.518	-0.162	-0.819	0.001
138	K	139	THR	0	-0.005	-0.009	3.157	-1.106	-0.496	0.045	-0.149	-0.506	0.000
139	K	140	GLY	0	0.025	0.008	3.055	-0.717	0.459	0.273	-0.462	-0.986	-0.003
140	K	141	TRP	0	-0.047	-0.048	3.065	-0.983	-0.002	0.190	-0.341	-0.830	-0.004
141	K	142	GLY	0	0.025	0.017	3.364	-2.289	-1.528	0.066	-0.318	-0.509	0.002
142	K	143	ASN	0	0.009	-0.002	2.815	-4.240	-2.841	1.049	-1.027	-1.421	-0.008
143	K	144	ARG	1	0.837	0.882	2.049	-3.598	-3.511	5.417	-2.825	-2.680	-0.028
144	K	145	ARG	1	0.972	0.981	3.900	2.041	2.199	0.002	-0.027	-0.132	0.000
145	K	146	GLU	-1	-0.935	-0.953	6.388	-0.265	-0.265	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(K:16:ILE)