FMO DATABASE

FMODB ID: 853KY

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1373044.074458
FMO2-HF: Nuclear repulsion	1313798.651866
FMO2-HF: Total energy	-59245.422592
FMO2-MP2: Total energy	-59419.198478

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.
-17.58	-11.69	14.487	-7.894	-12.483	-0.042

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 : -0.019 / 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	-0.933	-0.970	3.263	-3.233	-0.371	0.092	-1.317	-1.637	0.003
4	K	19	GLY	0	-0.030	-0.002	2.329	-0.150	0.647	1.814	-1.239	-1.372	-0.001
5	K	20	GLN	0	-0.019	-0.015	3.093	0.094	-0.751	-0.014	1.085	-0.226	-0.001
6	K	21	ASP	-1	-0.965	-0.977	5.529	-1.251	-1.251	0.000	0.000	0.000	0.000
7	K	22	ALA	0	-0.017	-0.007	6.764	0.175	0.175	0.000	0.000	0.000	0.000
8	K	23	GLU	-1	-0.893	-0.937	8.431	-0.134	-0.134	0.000	0.000	0.000	0.000
9	K	24	VAL	0	-0.007	-0.030	11.526	0.079	0.079	0.000	0.000	0.000	0.000
10	K	25	GLY	0	0.034	0.012	13.358	0.000	0.000	0.000	0.000	0.000	0.000
11	K	26	LEU	0	-0.041	0.007	8.322	0.055	0.055	0.000	0.000	0.000	0.000
12	K	27	SER	0	-0.041	-0.031	8.205	0.046	0.046	0.000	0.000	0.000	0.000
13	K	28	PRO	0	0.033	0.027	11.011	0.037	0.037	0.000	0.000	0.000	0.000
14	K	29	TRP	0	0.021	0.015	10.196	-0.048	-0.048	0.000	0.000	0.000	0.000
15	K	30	GLN	0	-0.021	-0.003	6.761	0.245	0.245	0.000	0.000	0.000	0.000
16	K	31	VAL	0	-0.007	-0.001	10.484	-0.134	-0.134	0.000	0.000	0.000	0.000
17	K	32	MET	0	-0.044	-0.005	9.910	0.150	0.150	0.000	0.000	0.000	0.000
18	K	33	LEU	0	-0.028	-0.006	11.780	-0.147	-0.147	0.000	0.000	0.000	0.000
19	K	34	PHE	0	0.006	-0.027	13.349	0.048	0.048	0.000	0.000	0.000	0.000
20	K	35	ARG	1	0.957	1.003	15.581	-0.276	-0.276	0.000	0.000	0.000	0.000
21	K	36	LYS	1	0.840	0.932	18.576	-0.231	-0.231	0.000	0.000	0.000	0.000
22	K	36	SER	0	-0.010	0.027	22.044	-0.029	-0.029	0.000	0.000	0.000	0.000
23	K	37	PRO	0	0.076	0.011	20.114	0.011	0.011	0.000	0.000	0.000	0.000
24	K	38	GLN	0	0.022	-0.016	18.254	0.016	0.016	0.000	0.000	0.000	0.000
25	K	39	GLU	-1	-0.951	-0.987	14.340	0.283	0.283	0.000	0.000	0.000	0.000
26	K	40	LEU	0	-0.026	-0.007	8.636	0.009	0.009	0.000	0.000	0.000	0.000
27	K	41	LEU	0	0.019	0.018	11.738	0.050	0.050	0.000	0.000	0.000	0.000
28	K	42	CYS	0	-0.128	-0.085	9.640	0.226	0.226	0.000	0.000	0.000	0.000
29	K	43	GLY	0	0.014	0.018	7.876	-0.012	-0.012	0.000	0.000	0.000	0.000
30	K	44	ALA	0	-0.006	-0.017	8.925	-0.096	-0.096	0.000	0.000	0.000	0.000
31	K	45	SER	0	0.019	0.005	10.517	0.036	0.036	0.000	0.000	0.000	0.000
32	K	46	LEU	0	-0.028	-0.001	12.513	-0.061	-0.061	0.000	0.000	0.000	0.000
33	K	47	ILE	0	0.007	-0.002	15.916	-0.001	-0.001	0.000	0.000	0.000	0.000
34	K	48	SER	0	0.011	0.001	18.163	-0.035	-0.035	0.000	0.000	0.000	0.000
35	K	49	ASP	-1	-0.766	-0.883	20.300	0.239	0.239	0.000	0.000	0.000	0.000
36	K	50	ARG	1	0.890	0.937	22.737	-0.211	-0.211	0.000	0.000	0.000	0.000
37	K	51	TRP	0	0.004	-0.001	20.629	0.005	0.005	0.000	0.000	0.000	0.000
38	K	52	VAL	0	0.045	0.030	14.831	0.014	0.014	0.000	0.000	0.000	0.000
39	K	53	LEU	0	-0.022	-0.007	14.420	-0.041	-0.041	0.000	0.000	0.000	0.000
40	K	54	THR	0	0.005	-0.016	12.312	0.118	0.118	0.000	0.000	0.000	0.000
41	K	55	ALA	0	0.059	0.043	11.971	-0.064	-0.064	0.000	0.000	0.000	0.000
42	K	56	ALA	0	0.056	0.025	13.886	-0.031	-0.031	0.000	0.000	0.000	0.000
43	K	57	HIS	1	0.871	0.925	11.536	-1.057	-1.057	0.000	0.000	0.000	0.000
44	K	59	LEU	0	-0.036	-0.020	14.787	-0.052	-0.052	0.000	0.000	0.000	0.000
45	K	60	LEU	0	0.000	-0.009	18.340	-0.050	-0.050	0.000	0.000	0.000	0.000
46	K	60	TYR	0	-0.021	-0.041	18.637	0.042	0.042	0.000	0.000	0.000	0.000
47	K	60	PRO	0	0.032	-0.001	20.777	-0.015	-0.015	0.000	0.000	0.000	0.000
48	K	60	PRO	0	-0.022	0.015	22.173	-0.017	-0.017	0.000	0.000	0.000	0.000
49	K	60	TRP	0	-0.038	-0.030	15.324	0.016	0.016	0.000	0.000	0.000	0.000
50	K	60	ASP	-1	-0.848	-0.904	22.282	0.169	0.169	0.000	0.000	0.000	0.000
51	K	60	LYS	1	0.808	0.931	16.658	-0.475	-0.475	0.000	0.000	0.000	0.000
52	K	60	ASN	0	0.025	0.006	22.091	0.036	0.036	0.000	0.000	0.000	0.000
53	K	60	PHE	0	-0.031	-0.009	18.391	-0.016	-0.016	0.000	0.000	0.000	0.000
54	K	60	THR	0	-0.001	-0.007	22.431	0.003	0.003	0.000	0.000	0.000	0.000
55	K	61	VAL	0	-0.026	-0.035	23.366	0.020	0.020	0.000	0.000	0.000	0.000
56	K	62	ASP	-1	-0.938	-0.954	24.298	0.198	0.198	0.000	0.000	0.000	0.000
57	K	63	ASP	-1	-0.785	-0.878	22.368	0.226	0.226	0.000	0.000	0.000	0.000
58	K	64	LEU	0	-0.053	-0.038	17.741	0.028	0.028	0.000	0.000	0.000	0.000
59	K	65	LEU	0	-0.043	-0.018	18.941	-0.037	-0.037	0.000	0.000	0.000	0.000
60	K	66	VAL	0	-0.009	0.000	16.035	0.046	0.046	0.000	0.000	0.000	0.000
61	K	67	ARG	1	0.886	0.948	14.718	-0.285	-0.285	0.000	0.000	0.000	0.000
62	K	68	ILE	0	0.008	-0.010	14.583	0.076	0.076	0.000	0.000	0.000	0.000
63	K	69	GLY	0	0.111	0.060	15.170	-0.051	-0.051	0.000	0.000	0.000	0.000
64	K	70	LYS	1	0.726	0.883	12.450	-0.224	-0.224	0.000	0.000	0.000	0.000
65	K	71	HIS	0	0.015	0.009	10.557	0.060	0.060	0.000	0.000	0.000	0.000
66	K	72	SER	0	0.008	0.011	10.497	-0.106	-0.106	0.000	0.000	0.000	0.000
67	K	73	ARG	1	1.003	0.990	8.181	0.514	0.514	0.000	0.000	0.000	0.000
68	K	74	THR	0	-0.031	-0.024	10.555	0.071	0.071	0.000	0.000	0.000	0.000
69	K	75	ARG	1	0.938	0.968	13.670	0.160	0.160	0.000	0.000	0.000	0.000
70	K	76	TYR	0	0.038	0.052	16.046	0.020	0.020	0.000	0.000	0.000	0.000
71	K	77	GLU	-1	-0.835	-0.945	15.651	-0.018	-0.018	0.000	0.000	0.000	0.000
72	K	77	ARG	1	0.954	0.963	19.673	-0.010	-0.010	0.000	0.000	0.000	0.000
73	K	78	LYS	1	0.920	0.975	22.266	-0.014	-0.014	0.000	0.000	0.000	0.000
74	K	79	VAL	0	0.060	0.038	17.202	0.001	0.001	0.000	0.000	0.000	0.000
75	K	80	GLU	-1	-0.816	-0.927	16.874	0.208	0.208	0.000	0.000	0.000	0.000
76	K	81	LYS	1	0.888	0.966	18.764	-0.211	-0.211	0.000	0.000	0.000	0.000
77	K	82	ILE	0	0.010	0.002	18.967	0.024	0.024	0.000	0.000	0.000	0.000
78	K	83	SER	0	-0.021	-0.025	20.813	-0.029	-0.029	0.000	0.000	0.000	0.000
79	K	84	MET	0	0.040	0.027	21.529	0.014	0.014	0.000	0.000	0.000	0.000
80	K	85	LEU	0	0.035	0.018	19.495	0.004	0.004	0.000	0.000	0.000	0.000
81	K	86	ASP	-1	-0.938	-0.959	23.546	0.182	0.182	0.000	0.000	0.000	0.000
82	K	87	LYS	1	0.957	0.958	25.063	-0.211	-0.211	0.000	0.000	0.000	0.000
83	K	88	ILE	0	0.044	0.034	20.735	0.025	0.025	0.000	0.000	0.000	0.000
84	K	89	TYR	0	-0.070	-0.038	21.865	-0.035	-0.035	0.000	0.000	0.000	0.000
85	K	90	ILE	0	0.068	0.041	20.178	0.037	0.037	0.000	0.000	0.000	0.000
86	K	91	HIS	0	0.006	0.000	21.402	-0.049	-0.049	0.000	0.000	0.000	0.000
87	K	92	PRO	0	0.015	0.002	23.054	-0.002	-0.002	0.000	0.000	0.000	0.000
88	K	93	ARG	1	0.951	0.958	25.903	-0.232	-0.232	0.000	0.000	0.000	0.000
89	K	94	TYR	0	0.013	0.016	18.381	0.019	0.019	0.000	0.000	0.000	0.000
90	K	95	ASN	0	-0.012	0.005	22.378	-0.017	-0.017	0.000	0.000	0.000	0.000
91	K	96	TRP	0	0.035	-0.008	20.612	0.018	0.018	0.000	0.000	0.000	0.000
92	K	97	LYS	1	0.907	0.943	21.401	-0.195	-0.195	0.000	0.000	0.000	0.000
93	K	97	GLU	-1	-0.906	-0.944	23.247	0.211	0.211	0.000	0.000	0.000	0.000
94	K	98	ASN	0	0.032	0.016	19.749	0.004	0.004	0.000	0.000	0.000	0.000
95	K	99	LEU	0	-0.034	-0.004	14.563	0.051	0.051	0.000	0.000	0.000	0.000
96	K	100	ASP	-1	-0.831	-0.895	17.726	0.399	0.399	0.000	0.000	0.000	0.000
97	K	101	ARG	1	0.833	0.899	19.683	-0.324	-0.324	0.000	0.000	0.000	0.000
98	K	102	ASP	-1	-0.727	-0.841	14.386	0.780	0.780	0.000	0.000	0.000	0.000
99	K	103	ILE	0	-0.060	-0.029	15.323	0.080	0.080	0.000	0.000	0.000	0.000
100	K	104	ALA	0	-0.009	-0.016	16.475	-0.064	-0.064	0.000	0.000	0.000	0.000
101	K	105	LEU	0	0.010	0.015	17.140	0.046	0.046	0.000	0.000	0.000	0.000
102	K	106	LEU	0	0.030	0.020	16.743	-0.024	-0.024	0.000	0.000	0.000	0.000
103	K	107	LYS	1	0.922	0.979	20.330	-0.223	-0.223	0.000	0.000	0.000	0.000
104	K	108	LEU	0	-0.017	-0.013	19.253	-0.003	-0.003	0.000	0.000	0.000	0.000
105	K	109	LYS	1	0.903	0.953	23.238	-0.201	-0.201	0.000	0.000	0.000	0.000
106	K	110	ARG	1	0.940	0.958	25.737	-0.179	-0.179	0.000	0.000	0.000	0.000
107	K	111	PRO	0	-0.084	-0.048	25.003	0.016	0.016	0.000	0.000	0.000	0.000
108	K	112	ILE	0	-0.027	-0.009	19.554	-0.019	-0.019	0.000	0.000	0.000	0.000
109	K	113	GLU	-1	-0.920	-0.963	23.583	0.129	0.129	0.000	0.000	0.000	0.000
110	K	114	LEU	0	-0.037	-0.018	21.751	0.012	0.012	0.000	0.000	0.000	0.000
111	K	115	SER	0	0.048	0.027	20.873	-0.020	-0.020	0.000	0.000	0.000	0.000
112	K	116	ASP	-1	-0.869	-0.930	20.447	0.102	0.102	0.000	0.000	0.000	0.000
113	K	117	TYR	0	-0.067	-0.050	16.230	0.002	0.002	0.000	0.000	0.000	0.000
114	K	118	ILE	0	-0.071	-0.034	16.225	0.053	0.053	0.000	0.000	0.000	0.000
115	K	119	HIS	0	0.064	0.013	16.948	-0.030	-0.030	0.000	0.000	0.000	0.000
116	K	120	PRO	0	-0.008	-0.002	16.349	0.052	0.052	0.000	0.000	0.000	0.000
117	K	121	VAL	0	0.019	0.040	13.418	-0.026	-0.026	0.000	0.000	0.000	0.000
118	K	122	CYS	0	-0.024	-0.030	16.367	-0.018	-0.018	0.000	0.000	0.000	0.000
119	K	123	LEU	0	-0.013	0.000	17.309	0.045	0.045	0.000	0.000	0.000	0.000
120	K	124	PRO	0	0.011	-0.002	17.547	-0.035	-0.035	0.000	0.000	0.000	0.000
121	K	125	ASP	-1	-0.763	-0.853	20.336	0.222	0.222	0.000	0.000	0.000	0.000
122	K	126	LYS	1	1.000	0.982	23.551	-0.174	-0.174	0.000	0.000	0.000	0.000
123	K	127	GLN	0	0.003	-0.008	24.912	-0.010	-0.010	0.000	0.000	0.000	0.000
124	K	128	THR	0	0.049	0.011	20.023	-0.009	-0.009	0.000	0.000	0.000	0.000
125	K	129	ALA	0	0.016	-0.001	20.339	0.011	0.011	0.000	0.000	0.000	0.000
126	K	129	ALA	0	-0.035	-0.029	21.374	0.001	0.001	0.000	0.000	0.000	0.000
127	K	129	LYS	1	0.862	0.941	23.381	-0.183	-0.183	0.000	0.000	0.000	0.000
128	K	129	LEU	0	0.020	0.016	16.990	-0.011	-0.011	0.000	0.000	0.000	0.000
129	K	130	LEU	0	0.003	0.000	16.445	0.007	0.007	0.000	0.000	0.000	0.000
130	K	131	HIS	1	0.833	0.932	18.339	-0.225	-0.225	0.000	0.000	0.000	0.000
131	K	132	ALA	0	0.072	0.044	17.760	0.013	0.013	0.000	0.000	0.000	0.000
132	K	133	GLY	0	0.023	0.014	16.885	-0.026	-0.026	0.000	0.000	0.000	0.000
133	K	134	PHE	0	-0.058	-0.032	16.186	-0.022	-0.022	0.000	0.000	0.000	0.000
134	K	135	LYS	1	0.976	0.986	11.325	0.040	0.040	0.000	0.000	0.000	0.000
135	K	136	GLY	0	0.018	0.009	10.589	-0.018	-0.018	0.000	0.000	0.000	0.000
136	K	137	ARG	1	0.941	0.973	6.928	-0.359	-0.359	0.000	0.000	0.000	0.000
137	K	138	VAL	0	0.031	0.020	2.210	0.128	-0.702	2.806	-0.489	-1.487	0.005
138	K	139	THR	0	-0.001	-0.004	2.967	-1.527	-0.553	0.161	-0.308	-0.827	0.000
139	K	140	GLY	0	0.026	0.007	3.143	-0.628	0.545	0.332	-0.417	-1.087	-0.004
140	K	141	TRP	0	-0.049	-0.033	2.819	-1.319	-0.185	0.517	-0.536	-1.115	-0.006
141	K	142	GLY	0	0.009	0.010	3.488	-1.782	-1.172	0.042	-0.249	-0.404	0.001
142	K	143	ASN	0	0.011	-0.004	2.548	-5.598	-4.191	1.661	-1.317	-1.750	-0.012
143	K	144	ARG	1	0.994	1.001	1.973	-3.110	-4.604	7.077	-3.093	-2.490	-0.027
144	K	145	ARG	1	0.969	0.977	4.125	1.867	1.969	-0.001	-0.014	-0.088	0.000
145	K	146	GLU	-1	-0.931	-0.946	6.256	-0.244	-0.244	0.000	0.000	0.000	0.000

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