FMO DATABASE

FMODB ID: 1N78Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-906091.076015
FMO2-HF: Nuclear repulsion	854435.999642
FMO2-HF: Total energy	-51655.076374
FMO2-MP2: Total energy	-51793.397611

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.
73.165	73.174	13.214	-7.764	-5.46	-0.088

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 : 0.893 / q_NPA : 0.924

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	0.087	0.048	1.754	-39.954	-40.187	13.216	-7.745	-5.239	-0.088
4	A	4	ALA	0	0.057	0.011	4.500	0.740	0.896	-0.001	-0.015	-0.140	0.000
5	A	5	ALA	0	0.031	0.017	6.083	2.887	2.887	0.000	0.000	0.000	0.000
6	A	6	ALA	0	0.084	0.038	6.427	2.115	2.115	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.882	0.957	4.605	44.827	44.913	-0.001	-0.004	-0.081	0.000
8	A	8	PHE	0	-0.011	-0.009	7.045	3.146	3.146	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.918	-0.966	10.479	-21.729	-21.729	0.000	0.000	0.000	0.000
10	A	10	ARG	1	0.808	0.862	6.007	39.274	39.274	0.000	0.000	0.000	0.000
11	A	11	GLN	0	-0.088	-0.062	9.311	-0.655	-0.655	0.000	0.000	0.000	0.000
12	A	12	HIS	0	-0.030	-0.008	12.273	2.280	2.280	0.000	0.000	0.000	0.000
13	A	13	MET	0	-0.052	-0.002	14.846	1.381	1.381	0.000	0.000	0.000	0.000
14	A	14	ASP	-1	-0.868	-0.940	16.683	-15.192	-15.192	0.000	0.000	0.000	0.000
15	A	15	SER	0	-0.049	-0.030	19.577	0.554	0.554	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.002	0.016	21.724	0.701	0.701	0.000	0.000	0.000	0.000
17	A	17	ASN	0	-0.006	-0.011	24.179	-0.067	-0.067	0.000	0.000	0.000	0.000
18	A	18	SER	0	0.088	0.064	24.314	0.371	0.371	0.000	0.000	0.000	0.000
19	A	19	ALA	0	-0.035	-0.039	26.315	0.161	0.161	0.000	0.000	0.000	0.000
20	A	20	SER	0	0.037	0.012	28.702	0.425	0.425	0.000	0.000	0.000	0.000
21	A	21	SER	0	0.003	0.006	30.080	0.322	0.322	0.000	0.000	0.000	0.000
22	A	22	SER	0	-0.016	-0.019	32.221	0.361	0.361	0.000	0.000	0.000	0.000
23	A	23	SER	0	0.011	0.014	33.119	0.144	0.144	0.000	0.000	0.000	0.000
24	A	24	ASN	0	-0.056	-0.028	34.873	0.073	0.073	0.000	0.000	0.000	0.000
25	A	25	TYR	0	0.076	0.043	37.495	0.229	0.229	0.000	0.000	0.000	0.000
26	A	26	CYS	0	-0.006	0.004	39.222	0.004	0.004	0.000	0.000	0.000	0.000
27	A	27	ASN	0	0.056	0.049	40.137	0.349	0.349	0.000	0.000	0.000	0.000
28	A	28	GLN	0	0.068	0.054	41.102	0.272	0.272	0.000	0.000	0.000	0.000
29	A	29	MET	0	-0.021	-0.019	42.712	0.216	0.216	0.000	0.000	0.000	0.000
30	A	30	MET	0	-0.035	-0.025	45.156	0.182	0.182	0.000	0.000	0.000	0.000
31	A	31	YCM	0	-0.027	-0.006	45.355	0.178	0.178	0.000	0.000	0.000	0.000
32	A	32	YCM	0	0.004	0.003	45.185	0.239	0.239	0.000	0.000	0.000	0.000
33	A	33	ARG	1	0.880	0.941	47.007	6.785	6.785	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.946	0.971	50.926	5.749	5.749	0.000	0.000	0.000	0.000
35	A	35	MET	0	-0.037	-0.015	49.240	0.124	0.124	0.000	0.000	0.000	0.000
36	A	36	THR	0	0.039	0.014	48.905	-0.014	-0.014	0.000	0.000	0.000	0.000
37	A	37	GLN	0	0.009	0.015	52.318	0.106	0.106	0.000	0.000	0.000	0.000
38	A	38	GLY	0	0.000	0.006	55.837	0.072	0.072	0.000	0.000	0.000	0.000
39	A	39	LYS	1	0.970	0.962	55.638	5.544	5.544	0.000	0.000	0.000	0.000
40	A	40	CYS	0	-0.012	0.015	48.364	-0.051	-0.051	0.000	0.000	0.000	0.000
41	A	41	LYS	1	0.870	0.945	51.235	6.279	6.279	0.000	0.000	0.000	0.000
42	A	42	PRO	0	0.068	0.049	49.847	-0.145	-0.145	0.000	0.000	0.000	0.000
43	A	43	VAL	0	0.008	-0.006	46.847	-0.177	-0.177	0.000	0.000	0.000	0.000
44	A	44	ASN	0	0.014	0.003	46.618	0.323	0.323	0.000	0.000	0.000	0.000
45	A	45	THR	0	0.004	0.009	44.097	-0.124	-0.124	0.000	0.000	0.000	0.000
46	A	46	PHE	0	-0.024	-0.013	42.969	0.169	0.169	0.000	0.000	0.000	0.000
47	A	47	VAL	0	0.052	0.030	42.914	-0.172	-0.172	0.000	0.000	0.000	0.000
48	A	48	HIS	0	-0.047	-0.004	38.757	-0.021	-0.021	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.709	-0.825	40.658	-8.021	-8.021	0.000	0.000	0.000	0.000
50	A	50	SER	0	-0.002	-0.022	43.508	0.078	0.078	0.000	0.000	0.000	0.000
51	A	51	LEU	0	0.004	0.003	46.146	0.073	0.073	0.000	0.000	0.000	0.000
52	A	52	ALA	0	-0.008	-0.013	49.659	0.061	0.061	0.000	0.000	0.000	0.000
53	A	53	ASP	-1	-0.786	-0.865	45.855	-6.840	-6.840	0.000	0.000	0.000	0.000
54	A	54	VAL	0	0.013	0.000	47.385	0.094	0.094	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.910	0.946	49.643	5.848	5.848	0.000	0.000	0.000	0.000
56	A	56	ALA	0	0.065	0.045	51.213	0.131	0.131	0.000	0.000	0.000	0.000
57	A	57	VAL	0	-0.047	-0.020	49.323	0.052	0.052	0.000	0.000	0.000	0.000
58	A	58	CYS	0	-0.132	-0.051	52.320	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	59	SER	0	-0.070	-0.040	55.239	0.150	0.150	0.000	0.000	0.000	0.000
60	A	60	GLN	0	0.007	0.027	49.686	-0.105	-0.105	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.940	0.977	52.344	6.224	6.224	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.919	0.983	54.739	5.226	5.226	0.000	0.000	0.000	0.000
63	A	63	VAL	0	-0.071	-0.042	53.591	-0.078	-0.078	0.000	0.000	0.000	0.000
64	A	64	THR	0	0.052	0.038	57.023	0.072	0.072	0.000	0.000	0.000	0.000
65	A	65	CYS	0	-0.013	-0.004	56.455	-0.133	-0.133	0.000	0.000	0.000	0.000
66	A	66	LYS	1	0.850	0.898	53.833	5.993	5.993	0.000	0.000	0.000	0.000
67	A	67	ASP	-1	-0.863	-0.919	56.510	-5.362	-5.362	0.000	0.000	0.000	0.000
68	A	68	GLY	0	0.003	-0.014	60.027	0.011	0.011	0.000	0.000	0.000	0.000
69	A	69	GLN	0	-0.058	-0.014	61.563	0.122	0.122	0.000	0.000	0.000	0.000
70	A	70	THR	0	0.042	0.006	61.541	-0.084	-0.084	0.000	0.000	0.000	0.000
71	A	71	ASN	0	-0.103	-0.071	61.467	-0.047	-0.047	0.000	0.000	0.000	0.000
72	A	73	TYR	0	-0.005	-0.010	54.855	0.101	0.101	0.000	0.000	0.000	0.000
73	A	74	GLN	0	0.005	0.014	48.349	0.040	0.040	0.000	0.000	0.000	0.000
74	A	75	SER	0	0.002	-0.004	46.198	0.045	0.045	0.000	0.000	0.000	0.000
75	A	76	LYS	1	0.969	0.958	44.932	7.007	7.007	0.000	0.000	0.000	0.000
76	A	77	SER	0	-0.012	-0.006	43.250	-0.071	-0.071	0.000	0.000	0.000	0.000
77	A	78	THR	0	0.008	0.026	39.594	0.130	0.130	0.000	0.000	0.000	0.000
78	A	79	MET	0	-0.060	-0.017	41.166	0.068	0.068	0.000	0.000	0.000	0.000
79	A	80	ARG	1	0.938	0.941	36.223	8.214	8.214	0.000	0.000	0.000	0.000
80	A	81	ILE	0	-0.049	-0.029	39.072	0.254	0.254	0.000	0.000	0.000	0.000
81	A	82	THR	0	-0.005	-0.042	38.748	-0.321	-0.321	0.000	0.000	0.000	0.000
82	A	83	ASP	-1	-0.940	-0.965	39.825	-7.240	-7.240	0.000	0.000	0.000	0.000
83	A	85	ARG	1	0.907	0.923	42.739	7.384	7.384	0.000	0.000	0.000	0.000
84	A	86	GLU	-1	-0.843	-0.880	43.531	-6.647	-6.647	0.000	0.000	0.000	0.000
85	A	87	THR	0	-0.047	-0.041	41.226	-0.049	-0.049	0.000	0.000	0.000	0.000
86	A	88	GLY	0	0.035	0.002	43.551	0.146	0.146	0.000	0.000	0.000	0.000
87	A	89	SER	0	-0.004	-0.006	43.089	0.121	0.121	0.000	0.000	0.000	0.000
88	A	90	SER	0	-0.108	-0.065	45.903	0.072	0.072	0.000	0.000	0.000	0.000
89	A	91	LYS	1	1.013	1.008	47.618	6.180	6.180	0.000	0.000	0.000	0.000
90	A	92	TYR	0	0.025	0.058	51.178	-0.034	-0.034	0.000	0.000	0.000	0.000
91	A	93	PRO	0	-0.020	-0.025	53.368	0.069	0.069	0.000	0.000	0.000	0.000
92	A	94	ASN	0	-0.037	-0.043	48.233	0.024	0.024	0.000	0.000	0.000	0.000
93	A	96	ALA	0	0.032	0.021	43.209	-0.113	-0.113	0.000	0.000	0.000	0.000
94	A	97	TYR	0	-0.031	-0.038	42.942	0.055	0.055	0.000	0.000	0.000	0.000
95	A	98	LYS	1	0.936	0.974	35.902	8.540	8.540	0.000	0.000	0.000	0.000
96	A	99	THR	0	0.011	-0.017	36.569	0.245	0.245	0.000	0.000	0.000	0.000
97	A	100	THR	0	-0.030	-0.022	35.932	-0.325	-0.325	0.000	0.000	0.000	0.000
98	A	101	GLN	0	0.042	0.041	33.183	0.065	0.065	0.000	0.000	0.000	0.000
99	A	102	VAL	0	-0.012	-0.008	35.287	-0.134	-0.134	0.000	0.000	0.000	0.000
100	A	103	GLU	-1	-0.859	-0.928	34.646	-8.952	-8.952	0.000	0.000	0.000	0.000
101	A	104	LYS	1	0.868	0.929	38.266	7.591	7.591	0.000	0.000	0.000	0.000
102	A	105	HIS	0	-0.019	0.003	41.518	-0.075	-0.075	0.000	0.000	0.000	0.000
103	A	106	ILE	0	-0.010	-0.008	45.109	-0.014	-0.014	0.000	0.000	0.000	0.000
104	A	107	ILE	0	0.018	0.004	47.617	0.062	0.062	0.000	0.000	0.000	0.000
105	A	108	VAL	0	-0.003	-0.008	51.320	0.007	0.007	0.000	0.000	0.000	0.000
106	A	109	ALA	0	0.103	0.066	53.858	0.076	0.076	0.000	0.000	0.000	0.000
107	A	111	GLY	0	0.045	0.014	59.203	0.073	0.073	0.000	0.000	0.000	0.000
108	A	112	GLY	0	0.013	0.007	62.267	-0.040	-0.040	0.000	0.000	0.000	0.000
109	A	113	LYS	1	0.949	0.992	64.136	4.741	4.741	0.000	0.000	0.000	0.000
110	A	114	PRO	0	0.060	0.007	61.003	0.051	0.051	0.000	0.000	0.000	0.000
111	A	115	SER	0	0.007	0.004	59.730	0.018	0.018	0.000	0.000	0.000	0.000
112	A	116	VAL	0	-0.011	-0.010	57.304	-0.110	-0.110	0.000	0.000	0.000	0.000
113	A	117	PRO	0	0.016	-0.016	53.206	0.066	0.066	0.000	0.000	0.000	0.000
114	A	118	VAL	0	-0.040	-0.018	56.082	0.014	0.014	0.000	0.000	0.000	0.000
115	A	119	HIS	0	-0.015	-0.017	56.191	0.048	0.048	0.000	0.000	0.000	0.000
116	A	120	PHE	0	-0.024	-0.001	46.990	-0.044	-0.044	0.000	0.000	0.000	0.000
117	A	121	ASP	-1	-0.781	-0.878	52.899	-5.842	-5.842	0.000	0.000	0.000	0.000
118	A	122	ALA	0	0.065	0.029	49.785	-0.017	-0.017	0.000	0.000	0.000	0.000
119	A	123	SER	0	-0.029	-0.014	45.254	-0.113	-0.113	0.000	0.000	0.000	0.000
120	A	124	VAL	0	0.044	0.034	43.040	0.054	0.054	0.000	0.000	0.000	0.000

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