FMO DATABASE

FMODB ID: N956Q

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1372489.049316
FMO2-HF: Nuclear repulsion	1313242.192737
FMO2-HF: Total energy	-59246.85658
FMO2-MP2: Total energy	-59420.519927

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.
-18.348	-10.799	12.383	-7.731	-12.202	-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 : -0.030 / q_NPA : -0.015

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	-0.927	-0.963	3.323	-3.038	-0.241	0.053	-1.294	-1.556	0.002
4	K	19	GLY	0	-0.027	-0.002	2.379	-0.075	0.770	1.292	-0.990	-1.147	0.000
5	K	20	GLN	0	-0.026	-0.017	3.191	-0.175	-0.709	-0.008	0.730	-0.189	0.000
6	K	21	ASP	-1	-0.848	-0.898	5.532	-1.381	-1.381	0.000	0.000	0.000	0.000
7	K	22	ALA	0	0.006	0.007	6.763	0.156	0.156	0.000	0.000	0.000	0.000
8	K	23	GLU	-1	-0.862	-0.922	8.501	-0.098	-0.098	0.000	0.000	0.000	0.000
9	K	24	VAL	0	-0.009	-0.031	11.556	0.077	0.077	0.000	0.000	0.000	0.000
10	K	25	GLY	0	0.037	0.015	13.359	-0.002	-0.002	0.000	0.000	0.000	0.000
11	K	26	LEU	0	-0.059	0.002	8.542	0.053	0.053	0.000	0.000	0.000	0.000
12	K	27	SER	0	-0.032	-0.029	8.274	0.031	0.031	0.000	0.000	0.000	0.000
13	K	28	PRO	0	0.024	0.023	10.949	0.036	0.036	0.000	0.000	0.000	0.000
14	K	29	TRP	0	0.022	0.022	10.124	-0.052	-0.052	0.000	0.000	0.000	0.000
15	K	30	GLN	0	-0.015	0.002	6.416	0.302	0.302	0.000	0.000	0.000	0.000
16	K	31	VAL	0	-0.021	-0.010	10.332	-0.129	-0.129	0.000	0.000	0.000	0.000
17	K	32	MET	0	-0.042	-0.001	10.071	0.163	0.163	0.000	0.000	0.000	0.000
18	K	33	LEU	0	-0.034	-0.005	11.509	-0.147	-0.147	0.000	0.000	0.000	0.000
19	K	34	PHE	0	0.040	-0.013	13.234	0.048	0.048	0.000	0.000	0.000	0.000
20	K	35	ARG	1	0.931	0.964	15.518	-0.256	-0.256	0.000	0.000	0.000	0.000
21	K	36	LYS	1	0.781	0.907	18.525	-0.220	-0.220	0.000	0.000	0.000	0.000
22	K	36	SER	0	-0.003	0.027	21.985	-0.029	-0.029	0.000	0.000	0.000	0.000
23	K	37	PRO	0	0.075	0.010	20.042	0.010	0.010	0.000	0.000	0.000	0.000
24	K	38	GLN	0	0.022	-0.014	18.386	0.023	0.023	0.000	0.000	0.000	0.000
25	K	39	GLU	-1	-0.880	-0.935	14.356	0.252	0.252	0.000	0.000	0.000	0.000
26	K	40	LEU	0	-0.042	-0.021	8.804	0.013	0.013	0.000	0.000	0.000	0.000
27	K	41	LEU	0	0.003	0.021	11.720	0.049	0.049	0.000	0.000	0.000	0.000
28	K	42	CYS	0	-0.129	-0.090	9.352	0.209	0.209	0.000	0.000	0.000	0.000
29	K	43	GLY	0	0.025	0.026	7.608	-0.005	-0.005	0.000	0.000	0.000	0.000
30	K	44	ALA	0	-0.013	-0.017	8.654	-0.098	-0.098	0.000	0.000	0.000	0.000
31	K	45	SER	0	0.020	0.007	10.306	0.032	0.032	0.000	0.000	0.000	0.000
32	K	46	LEU	0	-0.020	0.001	12.326	-0.063	-0.063	0.000	0.000	0.000	0.000
33	K	47	ILE	0	0.018	-0.001	15.744	0.000	0.000	0.000	0.000	0.000	0.000
34	K	48	SER	0	0.006	-0.007	18.010	-0.031	-0.031	0.000	0.000	0.000	0.000
35	K	49	ASP	-1	-0.717	-0.830	20.134	0.241	0.241	0.000	0.000	0.000	0.000
36	K	50	ARG	1	0.847	0.890	22.565	-0.207	-0.207	0.000	0.000	0.000	0.000
37	K	51	TRP	0	-0.015	-0.007	20.422	0.006	0.006	0.000	0.000	0.000	0.000
38	K	52	VAL	0	0.027	0.020	14.686	0.017	0.017	0.000	0.000	0.000	0.000
39	K	53	LEU	0	-0.013	-0.006	14.318	-0.037	-0.037	0.000	0.000	0.000	0.000
40	K	54	THR	0	-0.007	-0.018	11.895	0.112	0.112	0.000	0.000	0.000	0.000
41	K	55	ALA	0	0.053	0.036	11.716	-0.061	-0.061	0.000	0.000	0.000	0.000
42	K	56	ALA	0	0.052	0.032	13.651	-0.030	-0.030	0.000	0.000	0.000	0.000
43	K	57	HIS	1	0.893	0.931	11.123	-1.014	-1.014	0.000	0.000	0.000	0.000
44	K	59	LEU	0	-0.031	-0.017	14.522	-0.051	-0.051	0.000	0.000	0.000	0.000
45	K	60	LEU	0	0.009	-0.004	18.070	-0.048	-0.048	0.000	0.000	0.000	0.000
46	K	60	TYR	0	-0.026	-0.039	18.287	0.035	0.035	0.000	0.000	0.000	0.000
47	K	60	PRO	0	0.042	0.008	20.434	-0.015	-0.015	0.000	0.000	0.000	0.000
48	K	60	PRO	0	-0.014	0.017	21.983	-0.017	-0.017	0.000	0.000	0.000	0.000
49	K	60	TRP	0	-0.040	-0.027	15.006	0.014	0.014	0.000	0.000	0.000	0.000
50	K	60	ASP	-1	-0.858	-0.913	22.243	0.152	0.152	0.000	0.000	0.000	0.000
51	K	60	LYS	1	0.797	0.926	16.057	-0.492	-0.492	0.000	0.000	0.000	0.000
52	K	60	ASN	0	0.038	0.006	21.917	0.038	0.038	0.000	0.000	0.000	0.000
53	K	60	PHE	0	-0.035	-0.004	17.634	-0.018	-0.018	0.000	0.000	0.000	0.000
54	K	60	THR	0	-0.010	-0.020	22.152	0.004	0.004	0.000	0.000	0.000	0.000
55	K	61	VAL	0	-0.020	-0.035	23.084	0.017	0.017	0.000	0.000	0.000	0.000
56	K	62	ASP	-1	-0.883	-0.934	24.021	0.180	0.180	0.000	0.000	0.000	0.000
57	K	63	ASP	-1	-0.806	-0.873	22.163	0.208	0.208	0.000	0.000	0.000	0.000
58	K	64	LEU	0	-0.039	-0.029	17.358	0.025	0.025	0.000	0.000	0.000	0.000
59	K	65	LEU	0	-0.060	-0.017	18.758	-0.035	-0.035	0.000	0.000	0.000	0.000
60	K	66	VAL	0	-0.001	-0.003	15.869	0.046	0.046	0.000	0.000	0.000	0.000
61	K	67	ARG	1	0.813	0.895	14.634	-0.281	-0.281	0.000	0.000	0.000	0.000
62	K	68	ILE	0	0.001	-0.018	14.371	0.074	0.074	0.000	0.000	0.000	0.000
63	K	69	GLY	0	0.107	0.060	15.019	-0.051	-0.051	0.000	0.000	0.000	0.000
64	K	70	LYS	1	0.715	0.869	12.169	-0.228	-0.228	0.000	0.000	0.000	0.000
65	K	71	HIS	0	0.005	-0.012	10.703	0.061	0.061	0.000	0.000	0.000	0.000
66	K	72	SER	0	0.007	0.015	10.464	-0.114	-0.114	0.000	0.000	0.000	0.000
67	K	73	ARG	1	0.972	0.980	7.659	0.528	0.528	0.000	0.000	0.000	0.000
68	K	74	THR	0	-0.011	-0.023	10.564	0.066	0.066	0.000	0.000	0.000	0.000
69	K	75	ARG	1	0.872	0.940	13.683	0.154	0.154	0.000	0.000	0.000	0.000
70	K	76	TYR	0	0.044	0.038	15.935	0.022	0.022	0.000	0.000	0.000	0.000
71	K	77	GLU	-1	-0.762	-0.908	15.390	-0.018	-0.018	0.000	0.000	0.000	0.000
72	K	77	ARG	1	0.945	0.967	19.555	-0.011	-0.011	0.000	0.000	0.000	0.000
73	K	78	LYS	1	0.945	0.985	22.282	-0.017	-0.017	0.000	0.000	0.000	0.000
74	K	79	VAL	0	0.061	0.037	17.305	0.001	0.001	0.000	0.000	0.000	0.000
75	K	80	GLU	-1	-0.761	-0.854	17.371	0.200	0.200	0.000	0.000	0.000	0.000
76	K	81	LYS	1	0.896	0.962	18.657	-0.225	-0.225	0.000	0.000	0.000	0.000
77	K	82	ILE	0	0.009	0.001	18.862	0.025	0.025	0.000	0.000	0.000	0.000
78	K	83	SER	0	-0.020	-0.021	20.738	-0.026	-0.026	0.000	0.000	0.000	0.000
79	K	84	MET	0	0.054	0.033	21.278	0.012	0.012	0.000	0.000	0.000	0.000
80	K	85	LEU	0	0.047	0.024	19.251	0.004	0.004	0.000	0.000	0.000	0.000
81	K	86	ASP	-1	-0.896	-0.946	23.285	0.183	0.183	0.000	0.000	0.000	0.000
82	K	87	LYS	1	0.986	0.972	24.840	-0.202	-0.202	0.000	0.000	0.000	0.000
83	K	88	ILE	0	0.027	0.023	20.745	0.025	0.025	0.000	0.000	0.000	0.000
84	K	89	TYR	0	-0.049	-0.039	21.616	-0.031	-0.031	0.000	0.000	0.000	0.000
85	K	90	ILE	0	0.060	0.040	20.026	0.036	0.036	0.000	0.000	0.000	0.000
86	K	91	HIS	0	0.005	0.000	21.149	-0.044	-0.044	0.000	0.000	0.000	0.000
87	K	92	PRO	0	0.023	0.002	22.838	-0.003	-0.003	0.000	0.000	0.000	0.000
88	K	93	ARG	1	0.937	0.963	25.673	-0.228	-0.228	0.000	0.000	0.000	0.000
89	K	94	TYR	0	0.003	0.003	18.235	0.020	0.020	0.000	0.000	0.000	0.000
90	K	95	ASN	0	-0.028	-0.019	22.204	-0.021	-0.021	0.000	0.000	0.000	0.000
91	K	96	TRP	0	0.027	-0.010	20.363	0.016	0.016	0.000	0.000	0.000	0.000
92	K	97	LYS	1	0.910	0.946	21.172	-0.178	-0.178	0.000	0.000	0.000	0.000
93	K	97	GLU	-1	-0.886	-0.925	23.048	0.210	0.210	0.000	0.000	0.000	0.000
94	K	98	ASN	0	0.021	0.000	19.645	0.015	0.015	0.000	0.000	0.000	0.000
95	K	99	LEU	0	-0.023	0.003	14.798	0.051	0.051	0.000	0.000	0.000	0.000
96	K	100	ASP	-1	-0.777	-0.850	17.574	0.388	0.388	0.000	0.000	0.000	0.000
97	K	101	ARG	1	0.800	0.867	19.490	-0.312	-0.312	0.000	0.000	0.000	0.000
98	K	102	ASP	-1	-0.751	-0.847	13.911	0.783	0.783	0.000	0.000	0.000	0.000
99	K	103	ILE	0	-0.056	-0.029	15.135	0.077	0.077	0.000	0.000	0.000	0.000
100	K	104	ALA	0	-0.005	-0.011	16.254	-0.064	-0.064	0.000	0.000	0.000	0.000
101	K	105	LEU	0	-0.004	0.006	16.904	0.046	0.046	0.000	0.000	0.000	0.000
102	K	106	LEU	0	0.030	0.027	16.306	-0.024	-0.024	0.000	0.000	0.000	0.000
103	K	107	LYS	1	0.864	0.951	20.079	-0.211	-0.211	0.000	0.000	0.000	0.000
104	K	108	LEU	0	0.000	-0.002	19.129	-0.004	-0.004	0.000	0.000	0.000	0.000
105	K	109	LYS	1	0.879	0.932	22.998	-0.188	-0.188	0.000	0.000	0.000	0.000
106	K	110	ARG	1	0.951	0.969	25.528	-0.171	-0.171	0.000	0.000	0.000	0.000
107	K	111	PRO	0	-0.040	-0.024	24.799	0.016	0.016	0.000	0.000	0.000	0.000
108	K	112	ILE	0	-0.058	-0.016	19.288	-0.019	-0.019	0.000	0.000	0.000	0.000
109	K	113	GLU	-1	-0.929	-0.966	23.398	0.132	0.132	0.000	0.000	0.000	0.000
110	K	114	LEU	0	-0.039	-0.020	21.424	0.013	0.013	0.000	0.000	0.000	0.000
111	K	115	SER	0	0.036	0.012	20.824	-0.022	-0.022	0.000	0.000	0.000	0.000
112	K	116	ASP	-1	-0.823	-0.896	20.496	0.107	0.107	0.000	0.000	0.000	0.000
113	K	117	TYR	0	-0.106	-0.076	16.236	0.005	0.005	0.000	0.000	0.000	0.000
114	K	118	ILE	0	-0.075	-0.034	16.184	0.050	0.050	0.000	0.000	0.000	0.000
115	K	119	HIS	0	0.069	0.019	16.843	-0.037	-0.037	0.000	0.000	0.000	0.000
116	K	120	PRO	0	-0.015	-0.003	16.253	0.051	0.051	0.000	0.000	0.000	0.000
117	K	121	VAL	0	0.012	0.028	13.379	-0.025	-0.025	0.000	0.000	0.000	0.000
118	K	122	CYS	0	-0.025	-0.023	16.296	-0.020	-0.020	0.000	0.000	0.000	0.000
119	K	123	LEU	0	0.000	0.003	17.095	0.044	0.044	0.000	0.000	0.000	0.000
120	K	124	PRO	0	-0.001	-0.011	17.331	-0.035	-0.035	0.000	0.000	0.000	0.000
121	K	125	ASP	-1	-0.744	-0.835	20.296	0.223	0.223	0.000	0.000	0.000	0.000
122	K	126	LYS	1	0.997	0.981	23.500	-0.172	-0.172	0.000	0.000	0.000	0.000
123	K	127	GLN	0	0.091	0.061	24.875	-0.006	-0.006	0.000	0.000	0.000	0.000
124	K	128	THR	0	-0.003	-0.016	20.010	-0.007	-0.007	0.000	0.000	0.000	0.000
125	K	129	ALA	0	0.011	-0.001	20.309	0.011	0.011	0.000	0.000	0.000	0.000
126	K	129	ALA	0	-0.030	-0.027	21.359	0.002	0.002	0.000	0.000	0.000	0.000
127	K	129	LYS	1	0.801	0.883	23.432	-0.198	-0.198	0.000	0.000	0.000	0.000
128	K	129	LEU	0	0.006	0.012	17.165	-0.009	-0.009	0.000	0.000	0.000	0.000
129	K	130	LEU	0	0.005	0.001	16.292	0.009	0.009	0.000	0.000	0.000	0.000
130	K	131	HIS	1	0.839	0.927	18.368	-0.235	-0.235	0.000	0.000	0.000	0.000
131	K	132	ALA	0	0.077	0.048	17.793	0.014	0.014	0.000	0.000	0.000	0.000
132	K	133	GLY	0	0.027	0.016	16.823	-0.027	-0.027	0.000	0.000	0.000	0.000
133	K	134	PHE	0	-0.051	-0.033	16.128	-0.019	-0.019	0.000	0.000	0.000	0.000
134	K	135	LYS	1	0.967	0.986	11.594	-0.008	-0.008	0.000	0.000	0.000	0.000
135	K	136	GLY	0	0.025	0.012	10.752	-0.023	-0.023	0.000	0.000	0.000	0.000
136	K	137	ARG	1	0.941	0.977	6.755	-0.374	-0.374	0.000	0.000	0.000	0.000
137	K	138	VAL	0	0.029	0.014	2.478	-0.532	-0.240	1.096	-0.259	-1.130	0.003
138	K	139	THR	0	-0.005	-0.014	2.854	-1.459	-0.515	0.187	-0.282	-0.848	0.000
139	K	140	GLY	0	0.035	0.013	3.045	-0.856	0.457	0.529	-0.554	-1.288	-0.006
140	K	141	TRP	0	-0.056	-0.041	2.702	-1.346	-0.244	0.760	-0.553	-1.309	-0.008
141	K	142	GLY	0	0.013	0.013	3.477	-1.792	-1.177	0.042	-0.248	-0.409	0.001
142	K	143	ASN	0	-0.001	-0.008	2.540	-5.318	-3.952	1.675	-1.290	-1.751	-0.012
143	K	144	ARG	1	0.856	0.903	1.992	-3.169	-4.466	6.758	-2.974	-2.487	-0.027
144	K	145	ARG	1	0.951	0.978	4.173	1.942	2.048	-0.001	-0.017	-0.088	0.000
145	K	146	GLU	-1	-0.917	-0.949	6.265	-0.329	-0.329	0.000	0.000	0.000	0.000

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