FMO DATABASE

FMODB ID: G56Z1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-904754.526553
FMO2-HF: Nuclear repulsion	853098.713729
FMO2-HF: Total energy	-51655.812824
FMO2-MP2: Total energy	-51794.029338

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.
67.786	65.872	15.358	-8.116	-5.329	-0.09

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 : 0.907 / q_NPA : 0.930

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	0.070	0.045	1.703	-44.527	-46.667	15.360	-8.101	-5.119	-0.090
4	A	4	ALA	0	0.037	0.001	4.460	1.353	1.499	-0.001	-0.012	-0.133	0.000
5	A	5	ALA	0	0.025	0.023	6.214	3.231	3.231	0.000	0.000	0.000	0.000
6	A	6	ALA	0	0.083	0.042	6.590	1.774	1.774	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.904	0.966	4.781	45.698	45.778	-0.001	-0.003	-0.077	0.000
8	A	8	PHE	0	-0.007	-0.006	7.297	3.102	3.102	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.897	-0.970	10.595	-21.977	-21.977	0.000	0.000	0.000	0.000
10	A	10	ARG	1	0.833	0.880	6.771	37.547	37.547	0.000	0.000	0.000	0.000
11	A	11	GLN	0	-0.081	-0.050	9.368	-1.811	-1.811	0.000	0.000	0.000	0.000
12	A	12	HIS	0	-0.033	-0.006	12.679	2.225	2.225	0.000	0.000	0.000	0.000
13	A	13	MET	0	-0.046	-0.006	15.183	1.360	1.360	0.000	0.000	0.000	0.000
14	A	14	ASP	-1	-0.840	-0.914	16.919	-14.648	-14.648	0.000	0.000	0.000	0.000
15	A	15	SER	0	-0.024	-0.030	19.832	0.537	0.537	0.000	0.000	0.000	0.000
16	A	16	GLY	0	-0.012	0.022	21.943	0.652	0.652	0.000	0.000	0.000	0.000
17	A	17	ASN	0	-0.042	-0.038	24.326	0.391	0.391	0.000	0.000	0.000	0.000
18	A	18	SER	0	0.098	0.064	24.258	0.484	0.484	0.000	0.000	0.000	0.000
19	A	19	ALA	0	-0.047	-0.034	26.258	0.103	0.103	0.000	0.000	0.000	0.000
20	A	20	SER	0	0.024	0.008	28.793	0.457	0.457	0.000	0.000	0.000	0.000
21	A	21	SER	0	0.001	0.001	30.511	0.220	0.220	0.000	0.000	0.000	0.000
22	A	22	SER	0	-0.015	-0.014	32.434	0.340	0.340	0.000	0.000	0.000	0.000
23	A	23	SER	0	0.028	0.013	33.602	0.185	0.185	0.000	0.000	0.000	0.000
24	A	24	ASN	0	0.002	0.015	35.370	0.122	0.122	0.000	0.000	0.000	0.000
25	A	25	TYR	0	0.053	0.027	37.932	0.288	0.288	0.000	0.000	0.000	0.000
26	A	26	CYS	0	-0.023	-0.009	39.633	-0.009	-0.009	0.000	0.000	0.000	0.000
27	A	27	ASN	0	0.037	0.037	40.712	0.351	0.351	0.000	0.000	0.000	0.000
28	A	28	GLN	0	0.058	0.047	41.583	0.241	0.241	0.000	0.000	0.000	0.000
29	A	29	MET	0	-0.008	-0.006	43.265	0.214	0.214	0.000	0.000	0.000	0.000
30	A	30	MET	0	-0.023	-0.014	45.605	0.194	0.194	0.000	0.000	0.000	0.000
31	A	31	YCM	0	-0.019	-0.006	45.834	0.172	0.172	0.000	0.000	0.000	0.000
32	A	32	YCM	0	-0.013	0.000	45.555	0.250	0.250	0.000	0.000	0.000	0.000
33	A	33	ARG	1	0.879	0.935	47.395	6.754	6.754	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.964	0.975	51.289	5.757	5.757	0.000	0.000	0.000	0.000
35	A	35	MET	0	-0.029	-0.007	49.666	0.122	0.122	0.000	0.000	0.000	0.000
36	A	36	THR	0	0.052	0.024	49.480	0.011	0.011	0.000	0.000	0.000	0.000
37	A	37	GLN	0	-0.011	0.005	52.570	0.137	0.137	0.000	0.000	0.000	0.000
38	A	38	GLY	0	-0.011	-0.010	56.200	0.068	0.068	0.000	0.000	0.000	0.000
39	A	39	LYS	1	0.949	0.966	56.011	5.598	5.598	0.000	0.000	0.000	0.000
40	A	40	CYS	0	-0.028	0.013	48.858	-0.042	-0.042	0.000	0.000	0.000	0.000
41	A	41	LYS	1	0.864	0.940	51.417	6.294	6.294	0.000	0.000	0.000	0.000
42	A	42	PRO	0	0.067	0.044	49.944	-0.143	-0.143	0.000	0.000	0.000	0.000
43	A	43	VAL	0	-0.005	-0.014	47.197	-0.182	-0.182	0.000	0.000	0.000	0.000
44	A	44	ASN	0	0.003	0.004	47.010	0.324	0.324	0.000	0.000	0.000	0.000
45	A	45	THR	0	0.001	0.008	44.093	-0.127	-0.127	0.000	0.000	0.000	0.000
46	A	46	PHE	0	-0.009	-0.008	43.615	0.195	0.195	0.000	0.000	0.000	0.000
47	A	47	VAL	0	0.038	0.013	43.504	-0.149	-0.149	0.000	0.000	0.000	0.000
48	A	48	HIS	0	-0.053	-0.004	39.107	-0.041	-0.041	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.701	-0.809	40.853	-8.032	-8.032	0.000	0.000	0.000	0.000
50	A	50	SER	0	0.010	-0.013	43.742	0.071	0.071	0.000	0.000	0.000	0.000
51	A	51	LEU	0	-0.011	-0.010	46.582	0.076	0.076	0.000	0.000	0.000	0.000
52	A	52	ALA	0	-0.006	-0.005	50.010	0.110	0.110	0.000	0.000	0.000	0.000
53	A	53	ASP	-1	-0.792	-0.878	46.426	-6.772	-6.772	0.000	0.000	0.000	0.000
54	A	54	VAL	0	-0.015	-0.020	47.551	0.062	0.062	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.915	0.952	49.865	5.827	5.827	0.000	0.000	0.000	0.000
56	A	56	ALA	0	0.034	0.026	51.381	0.110	0.110	0.000	0.000	0.000	0.000
57	A	57	VAL	0	0.002	0.001	49.730	0.027	0.027	0.000	0.000	0.000	0.000
58	A	58	CYS	0	-0.106	-0.049	52.569	-0.024	-0.024	0.000	0.000	0.000	0.000
59	A	59	SER	0	-0.073	-0.040	55.425	0.164	0.164	0.000	0.000	0.000	0.000
60	A	60	GLN	0	0.031	0.038	49.962	-0.122	-0.122	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.904	0.952	52.133	6.236	6.236	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.877	0.945	54.319	5.260	5.260	0.000	0.000	0.000	0.000
63	A	63	VAL	0	-0.057	-0.039	53.519	-0.071	-0.071	0.000	0.000	0.000	0.000
64	A	64	THR	0	0.045	0.036	56.898	0.057	0.057	0.000	0.000	0.000	0.000
65	A	65	CYS	0	-0.071	-0.033	56.653	-0.147	-0.147	0.000	0.000	0.000	0.000
66	A	66	LYS	1	0.815	0.863	53.930	5.958	5.958	0.000	0.000	0.000	0.000
67	A	67	ASP	-1	-0.885	-0.935	56.664	-5.366	-5.366	0.000	0.000	0.000	0.000
68	A	68	GLY	0	0.042	0.020	60.198	0.071	0.071	0.000	0.000	0.000	0.000
69	A	69	GLN	0	-0.032	-0.016	61.737	0.083	0.083	0.000	0.000	0.000	0.000
70	A	70	THR	0	0.039	0.020	61.464	-0.099	-0.099	0.000	0.000	0.000	0.000
71	A	71	ASN	0	-0.052	-0.027	61.483	-0.022	-0.022	0.000	0.000	0.000	0.000
72	A	73	TYR	0	0.041	0.027	54.836	0.096	0.096	0.000	0.000	0.000	0.000
73	A	74	GLN	0	0.040	0.025	48.772	0.039	0.039	0.000	0.000	0.000	0.000
74	A	75	SER	0	0.010	0.003	46.150	0.057	0.057	0.000	0.000	0.000	0.000
75	A	76	LYS	1	0.934	0.954	44.871	6.960	6.960	0.000	0.000	0.000	0.000
76	A	77	SER	0	-0.020	-0.009	43.181	-0.054	-0.054	0.000	0.000	0.000	0.000
77	A	78	THR	0	0.038	0.036	39.528	0.161	0.161	0.000	0.000	0.000	0.000
78	A	79	MET	0	-0.060	-0.022	41.683	0.091	0.091	0.000	0.000	0.000	0.000
79	A	80	ARG	1	0.933	0.935	36.568	8.231	8.231	0.000	0.000	0.000	0.000
80	A	81	ILE	0	-0.059	-0.036	39.286	0.269	0.269	0.000	0.000	0.000	0.000
81	A	82	THR	0	0.008	-0.030	38.999	-0.351	-0.351	0.000	0.000	0.000	0.000
82	A	83	ASP	-1	-0.885	-0.928	40.382	-7.157	-7.157	0.000	0.000	0.000	0.000
83	A	85	ARG	1	0.903	0.934	42.897	7.351	7.351	0.000	0.000	0.000	0.000
84	A	86	GLU	-1	-0.812	-0.874	43.652	-6.628	-6.628	0.000	0.000	0.000	0.000
85	A	87	THR	0	-0.060	-0.038	41.499	-0.053	-0.053	0.000	0.000	0.000	0.000
86	A	88	GLY	0	0.032	0.004	44.180	0.143	0.143	0.000	0.000	0.000	0.000
87	A	89	SER	0	-0.002	-0.003	43.067	0.107	0.107	0.000	0.000	0.000	0.000
88	A	90	SER	0	-0.102	-0.063	45.953	0.044	0.044	0.000	0.000	0.000	0.000
89	A	91	LYS	1	0.986	0.982	47.916	6.145	6.145	0.000	0.000	0.000	0.000
90	A	92	TYR	0	0.029	0.030	51.587	-0.033	-0.033	0.000	0.000	0.000	0.000
91	A	93	PRO	0	0.000	-0.007	53.644	0.079	0.079	0.000	0.000	0.000	0.000
92	A	94	ASN	0	-0.026	-0.014	48.682	0.016	0.016	0.000	0.000	0.000	0.000
93	A	96	ALA	0	0.032	0.019	43.712	-0.109	-0.109	0.000	0.000	0.000	0.000
94	A	97	TYR	0	-0.026	-0.036	43.346	0.037	0.037	0.000	0.000	0.000	0.000
95	A	98	LYS	1	0.908	0.944	35.887	8.531	8.531	0.000	0.000	0.000	0.000
96	A	99	THR	0	0.000	-0.038	36.998	0.238	0.238	0.000	0.000	0.000	0.000
97	A	100	THR	0	-0.022	-0.012	36.506	-0.323	-0.323	0.000	0.000	0.000	0.000
98	A	101	GLN	0	0.029	0.027	33.573	0.021	0.021	0.000	0.000	0.000	0.000
99	A	102	VAL	0	-0.017	-0.006	35.398	-0.169	-0.169	0.000	0.000	0.000	0.000
100	A	103	GLU	-1	-0.878	-0.939	34.673	-8.886	-8.886	0.000	0.000	0.000	0.000
101	A	104	LYS	1	0.832	0.915	38.171	7.458	7.458	0.000	0.000	0.000	0.000
102	A	105	HIS	0	-0.021	-0.010	41.367	-0.066	-0.066	0.000	0.000	0.000	0.000
103	A	106	ILE	0	-0.016	-0.019	44.966	-0.010	-0.010	0.000	0.000	0.000	0.000
104	A	107	ILE	0	0.021	0.006	47.650	0.060	0.060	0.000	0.000	0.000	0.000
105	A	108	VAL	0	-0.005	-0.003	51.391	-0.018	-0.018	0.000	0.000	0.000	0.000
106	A	109	ALA	0	0.081	0.039	54.046	0.073	0.073	0.000	0.000	0.000	0.000
107	A	111	GLY	0	0.044	0.020	59.367	0.087	0.087	0.000	0.000	0.000	0.000
108	A	112	GLY	0	0.032	0.021	62.185	-0.058	-0.058	0.000	0.000	0.000	0.000
109	A	113	LYS	1	0.937	0.969	64.766	4.799	4.799	0.000	0.000	0.000	0.000
110	A	114	PRO	0	0.053	0.020	61.143	0.047	0.047	0.000	0.000	0.000	0.000
111	A	115	SER	0	-0.008	-0.003	59.874	0.027	0.027	0.000	0.000	0.000	0.000
112	A	116	VAL	0	-0.009	-0.004	57.698	-0.110	-0.110	0.000	0.000	0.000	0.000
113	A	117	PRO	0	0.029	-0.011	53.660	0.065	0.065	0.000	0.000	0.000	0.000
114	A	118	VAL	0	-0.053	-0.020	56.526	0.032	0.032	0.000	0.000	0.000	0.000
115	A	119	HIS	0	-0.018	-0.020	56.375	0.026	0.026	0.000	0.000	0.000	0.000
116	A	120	PHE	0	-0.001	0.005	47.048	-0.029	-0.029	0.000	0.000	0.000	0.000
117	A	121	ASP	-1	-0.783	-0.848	52.899	-5.829	-5.829	0.000	0.000	0.000	0.000
118	A	122	ALA	0	0.063	0.022	50.207	-0.007	-0.007	0.000	0.000	0.000	0.000
119	A	123	SER	0	0.015	0.003	45.469	-0.099	-0.099	0.000	0.000	0.000	0.000
120	A	124	VAL	0	0.041	0.043	42.694	-0.067	-0.067	0.000	0.000	0.000	0.000

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