FMO DATABASE

FMODB ID: VQ5J1

Calculation Name: 3BCP-A-Xray372

Preferred Name: Seminal ribonuclease

Target Type: SINGLE PROTEIN

Ligand Name: s-(2-amino-2-oxoethyl)-l-cysteine

ligand 3-letter code: YCM

PDB ID: 3BCP

Chain ID: A

ChEMBL ID: CHEMBL1075179

UniProt ID: P00669

Base Structure: X-ray

Registration Date: 2023-09-21

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	120
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-905868.824121
FMO2-HF: Nuclear repulsion	854214.797395
FMO2-HF: Total energy	-51654.026725
FMO2-MP2: Total energy	-51792.450824

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(A:1:LYS)

Summations of interaction energy for fragment #1(A:1:LYS)

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.
91.382	96.875	0.779	-3.182	-3.09	-0.035

Interaction energy analysis for fragmet #1(A:1:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.932 / q_NPA : 0.954

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

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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	A	3	SER	0	0.057	0.026	2.630	-18.682	-13.281	0.780	-3.176	-3.005	-0.035
4	A	4	ALA	0	0.066	0.012	4.908	0.593	0.685	-0.001	-0.006	-0.085	0.000
5	A	5	ALA	0	0.036	0.019	6.906	2.211	2.211	0.000	0.000	0.000	0.000
6	A	6	ALA	0	0.076	0.032	6.978	1.869	1.869	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.904	0.963	5.605	44.113	44.113	0.000	0.000	0.000	0.000
8	A	8	PHE	0	-0.017	-0.012	7.427	2.555	2.555	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.937	-0.972	10.968	-20.795	-20.795	0.000	0.000	0.000	0.000
10	A	10	ARG	1	0.867	0.932	6.488	37.743	37.743	0.000	0.000	0.000	0.000
11	A	11	GLN	0	-0.099	-0.069	10.022	0.532	0.532	0.000	0.000	0.000	0.000
12	A	12	HIS	0	-0.025	-0.005	12.582	1.972	1.972	0.000	0.000	0.000	0.000
13	A	13	MET	0	-0.045	0.000	15.129	1.367	1.367	0.000	0.000	0.000	0.000
14	A	14	ASP	-1	-0.882	-0.941	16.981	-15.256	-15.256	0.000	0.000	0.000	0.000
15	A	15	SER	0	-0.046	-0.032	19.800	0.536	0.536	0.000	0.000	0.000	0.000
16	A	16	GLY	0	-0.005	0.013	22.066	0.691	0.691	0.000	0.000	0.000	0.000
17	A	17	ASN	0	-0.004	-0.015	24.415	-0.177	-0.177	0.000	0.000	0.000	0.000
18	A	18	SER	0	0.099	0.069	24.428	0.314	0.314	0.000	0.000	0.000	0.000
19	A	19	ALA	0	-0.039	-0.038	26.442	0.155	0.155	0.000	0.000	0.000	0.000
20	A	20	SER	0	0.036	0.004	28.889	0.415	0.415	0.000	0.000	0.000	0.000
21	A	21	SER	0	0.022	0.011	30.349	0.374	0.374	0.000	0.000	0.000	0.000
22	A	22	SER	0	-0.035	-0.024	32.245	0.358	0.358	0.000	0.000	0.000	0.000
23	A	23	SER	0	-0.011	0.013	33.123	0.149	0.149	0.000	0.000	0.000	0.000
24	A	24	ASN	0	-0.024	-0.009	35.006	0.072	0.072	0.000	0.000	0.000	0.000
25	A	25	TYR	0	0.084	0.042	37.734	0.232	0.232	0.000	0.000	0.000	0.000
26	A	26	CYS	0	-0.046	-0.008	39.314	-0.023	-0.023	0.000	0.000	0.000	0.000
27	A	27	ASN	0	0.060	0.049	40.579	0.325	0.325	0.000	0.000	0.000	0.000
28	A	28	GLN	0	0.085	0.060	41.043	0.327	0.327	0.000	0.000	0.000	0.000
29	A	29	MET	0	-0.022	-0.016	42.656	0.202	0.202	0.000	0.000	0.000	0.000
30	A	30	MET	0	-0.054	-0.035	45.284	0.176	0.176	0.000	0.000	0.000	0.000
31	A	31	YCM	0	-0.031	-0.006	45.190	0.210	0.210	0.000	0.000	0.000	0.000
32	A	32	YCM	0	0.004	-0.006	45.434	0.190	0.190	0.000	0.000	0.000	0.000
33	A	33	ARG	1	0.883	0.944	47.585	6.742	6.742	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.936	0.966	51.084	5.725	5.725	0.000	0.000	0.000	0.000
35	A	35	MET	0	-0.028	-0.006	49.269	0.119	0.119	0.000	0.000	0.000	0.000
36	A	36	THR	0	0.029	0.007	49.111	-0.051	-0.051	0.000	0.000	0.000	0.000
37	A	37	GLN	0	-0.010	0.007	52.437	0.100	0.100	0.000	0.000	0.000	0.000
38	A	38	GLY	0	0.018	0.013	55.932	0.070	0.070	0.000	0.000	0.000	0.000
39	A	39	LYS	1	0.957	0.951	55.897	5.495	5.495	0.000	0.000	0.000	0.000
40	A	40	CYS	0	0.002	0.016	48.546	-0.047	-0.047	0.000	0.000	0.000	0.000
41	A	41	LYS	1	0.905	0.970	51.190	6.212	6.212	0.000	0.000	0.000	0.000
42	A	42	PRO	0	0.064	0.042	50.088	-0.141	-0.141	0.000	0.000	0.000	0.000
43	A	43	VAL	0	0.022	0.005	47.471	-0.171	-0.171	0.000	0.000	0.000	0.000
44	A	44	ASN	0	-0.038	-0.039	47.045	0.298	0.298	0.000	0.000	0.000	0.000
45	A	45	THR	0	0.011	0.023	44.460	-0.123	-0.123	0.000	0.000	0.000	0.000
46	A	46	PHE	0	-0.042	-0.019	43.274	0.168	0.168	0.000	0.000	0.000	0.000
47	A	47	VAL	0	0.056	0.035	43.297	-0.168	-0.168	0.000	0.000	0.000	0.000
48	A	48	HIS	0	-0.059	0.034	38.740	-0.050	-0.050	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.757	-0.880	41.372	-7.909	-7.909	0.000	0.000	0.000	0.000
50	A	50	SER	0	0.036	0.025	43.968	0.100	0.100	0.000	0.000	0.000	0.000
51	A	51	LEU	0	0.022	0.007	46.532	0.075	0.075	0.000	0.000	0.000	0.000
52	A	52	ALA	0	-0.023	-0.026	50.055	0.064	0.064	0.000	0.000	0.000	0.000
53	A	53	ASP	-1	-0.811	-0.900	45.905	-6.794	-6.794	0.000	0.000	0.000	0.000
54	A	54	VAL	0	-0.003	-0.006	47.986	0.098	0.098	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.913	0.944	50.192	5.858	5.858	0.000	0.000	0.000	0.000
56	A	56	ALA	0	0.085	0.054	51.788	0.135	0.135	0.000	0.000	0.000	0.000
57	A	57	VAL	0	-0.033	-0.049	50.037	0.052	0.052	0.000	0.000	0.000	0.000
58	A	58	CYS	0	-0.167	-0.051	52.960	0.005	0.005	0.000	0.000	0.000	0.000
59	A	59	SER	0	-0.058	-0.036	55.888	0.146	0.146	0.000	0.000	0.000	0.000
60	A	60	GLN	0	-0.006	0.082	50.164	-0.135	-0.135	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.997	0.997	53.001	6.133	6.133	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.956	0.987	55.435	5.135	5.135	0.000	0.000	0.000	0.000
63	A	63	VAL	0	-0.088	-0.037	54.311	-0.072	-0.072	0.000	0.000	0.000	0.000
64	A	64	THR	0	0.047	0.028	57.616	0.054	0.054	0.000	0.000	0.000	0.000
65	A	65	CYS	0	-0.028	-0.014	57.122	-0.122	-0.122	0.000	0.000	0.000	0.000
66	A	66	LYS	1	0.871	0.921	53.812	5.953	5.953	0.000	0.000	0.000	0.000
67	A	67	ASP	-1	-0.917	-0.956	56.925	-5.335	-5.335	0.000	0.000	0.000	0.000
68	A	68	GLY	0	0.031	0.001	60.412	0.015	0.015	0.000	0.000	0.000	0.000
69	A	69	GLN	0	-0.071	-0.015	61.957	0.134	0.134	0.000	0.000	0.000	0.000
70	A	70	THR	0	0.060	0.006	62.048	-0.059	-0.059	0.000	0.000	0.000	0.000
71	A	71	ASN	0	-0.099	-0.052	61.593	-0.035	-0.035	0.000	0.000	0.000	0.000
72	A	73	TYR	0	-0.012	-0.017	55.368	0.090	0.090	0.000	0.000	0.000	0.000
73	A	74	GLN	0	-0.014	-0.002	49.076	0.025	0.025	0.000	0.000	0.000	0.000
74	A	75	SER	0	0.011	0.002	46.951	0.055	0.055	0.000	0.000	0.000	0.000
75	A	76	LYS	1	0.958	0.946	46.180	6.863	6.863	0.000	0.000	0.000	0.000
76	A	77	SER	0	-0.027	-0.021	43.981	-0.050	-0.050	0.000	0.000	0.000	0.000
77	A	78	THR	0	0.004	0.019	40.218	0.091	0.091	0.000	0.000	0.000	0.000
78	A	79	MET	0	-0.058	-0.019	41.702	0.067	0.067	0.000	0.000	0.000	0.000
79	A	80	ARG	1	1.017	1.012	36.775	8.060	8.060	0.000	0.000	0.000	0.000
80	A	81	ILE	0	-0.033	-0.024	39.589	0.245	0.245	0.000	0.000	0.000	0.000
81	A	82	THR	0	-0.033	-0.095	39.149	-0.302	-0.302	0.000	0.000	0.000	0.000
82	A	83	ASP	-1	-0.952	-0.977	40.089	-7.162	-7.162	0.000	0.000	0.000	0.000
83	A	85	ARG	1	0.940	0.946	42.995	7.319	7.319	0.000	0.000	0.000	0.000
84	A	86	GLU	-1	-0.830	-0.871	43.809	-6.601	-6.601	0.000	0.000	0.000	0.000
85	A	87	THR	0	-0.027	-0.029	41.479	0.006	0.006	0.000	0.000	0.000	0.000
86	A	88	GLY	0	0.024	0.000	43.904	0.143	0.143	0.000	0.000	0.000	0.000
87	A	89	SER	0	-0.008	-0.010	43.834	0.077	0.077	0.000	0.000	0.000	0.000
88	A	90	SER	0	-0.101	-0.051	46.217	0.055	0.055	0.000	0.000	0.000	0.000
89	A	91	LYS	1	1.021	1.011	47.886	6.115	6.115	0.000	0.000	0.000	0.000
90	A	92	TYR	0	0.016	0.066	51.433	-0.033	-0.033	0.000	0.000	0.000	0.000
91	A	93	PRO	0	-0.025	-0.027	53.548	0.072	0.072	0.000	0.000	0.000	0.000
92	A	94	ASN	0	-0.029	-0.039	48.332	0.031	0.031	0.000	0.000	0.000	0.000
93	A	96	ALA	0	0.014	0.010	43.380	-0.121	-0.121	0.000	0.000	0.000	0.000
94	A	97	TYR	0	-0.021	-0.041	43.154	0.067	0.067	0.000	0.000	0.000	0.000
95	A	98	LYS	1	0.966	0.992	36.135	8.449	8.449	0.000	0.000	0.000	0.000
96	A	99	THR	0	0.023	-0.029	36.679	0.187	0.187	0.000	0.000	0.000	0.000
97	A	100	THR	0	-0.022	-0.013	36.492	-0.282	-0.282	0.000	0.000	0.000	0.000
98	A	101	GLN	0	0.038	0.032	33.588	0.093	0.093	0.000	0.000	0.000	0.000
99	A	102	VAL	0	-0.024	-0.008	35.638	-0.130	-0.130	0.000	0.000	0.000	0.000
100	A	103	GLU	-1	-0.859	-0.934	35.445	-8.859	-8.859	0.000	0.000	0.000	0.000
101	A	104	LYS	1	0.824	0.898	38.793	7.450	7.450	0.000	0.000	0.000	0.000
102	A	105	HIS	0	-0.031	0.000	42.067	-0.068	-0.068	0.000	0.000	0.000	0.000
103	A	106	ILE	0	0.009	-0.005	45.687	-0.016	-0.016	0.000	0.000	0.000	0.000
104	A	107	ILE	0	0.035	0.011	48.139	0.058	0.058	0.000	0.000	0.000	0.000
105	A	108	VAL	0	-0.007	-0.007	51.833	0.006	0.006	0.000	0.000	0.000	0.000
106	A	109	ALA	0	0.105	0.060	54.356	0.078	0.078	0.000	0.000	0.000	0.000
107	A	111	GLY	0	0.033	0.006	59.730	0.075	0.075	0.000	0.000	0.000	0.000
108	A	112	GLY	0	0.012	0.006	62.805	-0.040	-0.040	0.000	0.000	0.000	0.000
109	A	113	LYS	1	0.951	0.992	64.704	4.690	4.690	0.000	0.000	0.000	0.000
110	A	114	PRO	0	0.059	0.007	61.495	0.051	0.051	0.000	0.000	0.000	0.000
111	A	115	SER	0	0.015	0.009	60.196	0.019	0.019	0.000	0.000	0.000	0.000
112	A	116	VAL	0	-0.023	-0.018	57.846	-0.110	-0.110	0.000	0.000	0.000	0.000
113	A	117	PRO	0	-0.002	-0.023	53.774	0.067	0.067	0.000	0.000	0.000	0.000
114	A	118	VAL	0	-0.033	-0.012	56.580	0.011	0.011	0.000	0.000	0.000	0.000
115	A	119	HIS	0	0.015	-0.001	56.631	0.038	0.038	0.000	0.000	0.000	0.000
116	A	120	PHE	0	-0.017	0.000	47.491	-0.043	-0.043	0.000	0.000	0.000	0.000
117	A	121	ASP	-1	-0.770	-0.868	53.337	-5.775	-5.775	0.000	0.000	0.000	0.000
118	A	122	ALA	0	0.019	-0.004	50.159	-0.021	-0.021	0.000	0.000	0.000	0.000
119	A	123	SER	0	-0.037	0.002	45.800	-0.126	-0.126	0.000	0.000	0.000	0.000
120	A	124	VAL	0	0.051	0.033	43.595	0.046	0.046	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1:LYS)