FMO DATABASE

FMODB ID: VQ9L1

Calculation Name: 1N1X-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: 1N1X

Chain ID: A

ChEMBL ID: CHEMBL1075179

UniProt ID: P00669

Base Structure: X-ray

Registration Date: 2023-09-23

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. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1027271.105165
FMO2-HF: Nuclear repulsion	975648.227133
FMO2-HF: Total energy	-51622.878032
FMO2-MP2: Total energy	-51761.450622

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.
166.697	169.602	0.786	-1.59	-2.1	-0.008

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 : 0.989 / q_NPA : 0.979

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	A	3	SER	0	0.033	0.010	2.816	-12.025	-9.186	0.787	-1.587	-2.039	-0.008
4	A	4	ALA	0	0.055	0.006	4.835	0.918	0.984	-0.001	-0.003	-0.061	0.000
5	A	5	ALA	0	0.039	0.017	6.802	2.344	2.344	0.000	0.000	0.000	0.000
6	A	6	ALA	0	0.036	0.019	7.395	1.854	1.854	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.939	0.989	5.847	43.741	43.741	0.000	0.000	0.000	0.000
8	A	8	PHE	0	0.003	-0.005	8.250	2.182	2.182	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.929	-0.970	11.671	-18.648	-18.648	0.000	0.000	0.000	0.000
10	A	10	ARG	1	0.799	0.868	7.287	32.051	32.051	0.000	0.000	0.000	0.000
11	A	11	GLN	0	-0.036	-0.041	10.704	0.806	0.806	0.000	0.000	0.000	0.000
12	A	12	HIS	0	-0.020	-0.019	13.499	-0.175	-0.175	0.000	0.000	0.000	0.000
13	A	13	MET	0	-0.006	0.046	16.100	0.930	0.930	0.000	0.000	0.000	0.000
14	A	14	ASP	-1	-0.821	-0.889	18.078	-14.071	-14.071	0.000	0.000	0.000	0.000
15	A	15	SER	0	-0.050	-0.017	20.948	0.442	0.442	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.101	0.054	23.214	0.048	0.048	0.000	0.000	0.000	0.000
17	A	17	ASN	0	-0.032	-0.033	26.590	0.346	0.346	0.000	0.000	0.000	0.000
18	A	18	SER	0	-0.002	0.002	29.771	-0.005	-0.005	0.000	0.000	0.000	0.000
19	A	19	PRO	0	0.012	0.030	28.412	-0.057	-0.057	0.000	0.000	0.000	0.000
20	A	20	SER	0	0.008	-0.004	29.775	0.421	0.421	0.000	0.000	0.000	0.000
21	A	21	SER	0	0.003	0.013	30.262	-0.404	-0.404	0.000	0.000	0.000	0.000
22	A	22	SER	0	0.041	-0.001	29.524	0.134	0.134	0.000	0.000	0.000	0.000
23	A	23	SER	0	0.046	0.020	29.855	-0.368	-0.368	0.000	0.000	0.000	0.000
24	A	24	ASN	0	0.019	0.002	28.439	-0.483	-0.483	0.000	0.000	0.000	0.000
25	A	25	TYR	0	-0.020	-0.028	22.631	-0.497	-0.497	0.000	0.000	0.000	0.000
26	A	26	CYS	0	-0.066	-0.033	20.991	0.012	0.012	0.000	0.000	0.000	0.000
27	A	27	ASN	0	0.061	0.021	22.168	-0.999	-0.999	0.000	0.000	0.000	0.000
28	A	28	LEU	0	0.023	0.032	22.598	-0.410	-0.410	0.000	0.000	0.000	0.000
29	A	29	MET	0	0.022	0.006	19.325	-0.610	-0.610	0.000	0.000	0.000	0.000
30	A	30	MET	0	-0.020	-0.004	16.792	-1.255	-1.255	0.000	0.000	0.000	0.000
31	A	31	YCM	0	0.003	0.016	16.944	-1.210	-1.210	0.000	0.000	0.000	0.000
32	A	32	YCM	0	0.001	-0.007	16.784	-1.322	-1.322	0.000	0.000	0.000	0.000
33	A	33	ARG	1	0.814	0.902	14.418	16.551	16.551	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.904	0.949	11.354	17.335	17.335	0.000	0.000	0.000	0.000
35	A	35	MET	0	-0.100	-0.021	12.218	-2.010	-2.010	0.000	0.000	0.000	0.000
36	A	36	THR	0	0.052	0.024	13.976	0.347	0.347	0.000	0.000	0.000	0.000
37	A	37	GLN	0	0.006	-0.001	10.775	2.187	2.187	0.000	0.000	0.000	0.000
38	A	38	GLY	0	-0.027	-0.009	12.441	-1.764	-1.764	0.000	0.000	0.000	0.000
39	A	39	LYS	1	0.968	0.960	13.717	20.455	20.455	0.000	0.000	0.000	0.000
40	A	40	CYS	0	-0.026	0.011	15.399	-0.664	-0.664	0.000	0.000	0.000	0.000
41	A	41	LYS	1	0.826	0.929	12.778	21.839	21.839	0.000	0.000	0.000	0.000
42	A	42	PRO	0	0.043	0.028	16.023	0.571	0.571	0.000	0.000	0.000	0.000
43	A	43	VAL	0	0.012	0.002	18.251	0.974	0.974	0.000	0.000	0.000	0.000
44	A	44	ASN	0	-0.027	-0.027	16.076	-2.238	-2.238	0.000	0.000	0.000	0.000
45	A	45	THR	0	0.023	0.014	18.466	0.673	0.673	0.000	0.000	0.000	0.000
46	A	46	PHE	0	-0.003	-0.005	17.269	-1.054	-1.054	0.000	0.000	0.000	0.000
47	A	47	VAL	0	0.021	-0.003	20.215	0.684	0.684	0.000	0.000	0.000	0.000
48	A	48	HIS	0	-0.030	0.004	21.877	-0.188	-0.188	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.751	-0.879	23.655	-10.584	-10.584	0.000	0.000	0.000	0.000
50	A	50	SER	0	0.040	0.013	23.192	-0.715	-0.715	0.000	0.000	0.000	0.000
51	A	51	LEU	0	0.082	0.020	16.944	-0.115	-0.115	0.000	0.000	0.000	0.000
52	A	52	ALA	0	-0.020	-0.012	20.828	-0.385	-0.385	0.000	0.000	0.000	0.000
53	A	53	ASP	-1	-0.847	-0.928	22.942	-11.421	-11.421	0.000	0.000	0.000	0.000
54	A	54	VAL	0	-0.031	-0.017	18.929	-0.097	-0.097	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.933	0.952	16.327	16.815	16.815	0.000	0.000	0.000	0.000
56	A	56	ALA	0	0.025	0.021	20.074	-0.113	-0.113	0.000	0.000	0.000	0.000
57	A	57	VAL	0	-0.001	-0.001	21.262	0.450	0.450	0.000	0.000	0.000	0.000
58	A	58	CYS	0	-0.134	-0.042	14.961	-0.759	-0.759	0.000	0.000	0.000	0.000
59	A	59	SER	0	-0.076	-0.020	21.090	0.129	0.129	0.000	0.000	0.000	0.000
60	A	60	GLN	0	0.018	0.011	24.372	0.646	0.646	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.973	0.995	26.346	10.500	10.500	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.949	0.990	22.253	13.008	13.008	0.000	0.000	0.000	0.000
63	A	63	VAL	0	-0.063	-0.033	23.082	0.616	0.616	0.000	0.000	0.000	0.000
64	A	64	THR	0	0.002	-0.003	22.835	-0.413	-0.413	0.000	0.000	0.000	0.000
65	A	65	CYS	0	-0.029	0.002	17.968	-1.084	-1.084	0.000	0.000	0.000	0.000
66	A	66	LYS	1	0.953	0.962	19.115	13.977	13.977	0.000	0.000	0.000	0.000
67	A	67	ASN	0	-0.002	-0.001	14.903	1.123	1.123	0.000	0.000	0.000	0.000
68	A	68	GLY	0	0.039	0.024	18.847	-0.028	-0.028	0.000	0.000	0.000	0.000
69	A	69	GLN	0	-0.012	0.007	15.799	0.459	0.459	0.000	0.000	0.000	0.000
70	A	70	THR	0	0.048	0.012	19.134	0.405	0.405	0.000	0.000	0.000	0.000
71	A	71	ASN	0	-0.080	-0.048	14.536	0.914	0.914	0.000	0.000	0.000	0.000
72	A	73	TYR	0	0.015	0.003	19.566	0.865	0.865	0.000	0.000	0.000	0.000
73	A	74	GLN	0	0.007	-0.005	21.833	-0.074	-0.074	0.000	0.000	0.000	0.000
74	A	75	SER	0	0.003	-0.015	24.609	0.141	0.141	0.000	0.000	0.000	0.000
75	A	76	LYS	1	0.974	0.983	25.995	10.448	10.448	0.000	0.000	0.000	0.000
76	A	77	SER	0	0.021	0.017	29.078	0.376	0.376	0.000	0.000	0.000	0.000
77	A	78	THR	0	-0.005	0.023	28.629	-0.427	-0.427	0.000	0.000	0.000	0.000
78	A	79	MET	0	-0.024	-0.012	24.211	-0.239	-0.239	0.000	0.000	0.000	0.000
79	A	80	ARG	1	0.907	0.966	28.004	10.776	10.776	0.000	0.000	0.000	0.000
80	A	81	ILE	0	-0.027	-0.015	24.034	-0.544	-0.544	0.000	0.000	0.000	0.000
81	A	82	THR	0	0.023	-0.018	24.112	0.759	0.759	0.000	0.000	0.000	0.000
82	A	83	ASP	-1	-0.923	-0.947	23.208	-13.540	-13.540	0.000	0.000	0.000	0.000
83	A	85	ARG	1	0.930	0.954	21.844	11.440	11.440	0.000	0.000	0.000	0.000
84	A	86	GLU	-1	-0.797	-0.868	21.346	-13.960	-13.960	0.000	0.000	0.000	0.000
85	A	87	THR	0	-0.047	-0.022	23.684	0.279	0.279	0.000	0.000	0.000	0.000
86	A	88	GLY	0	0.019	0.002	26.582	-0.229	-0.229	0.000	0.000	0.000	0.000
87	A	89	SER	0	0.006	-0.006	28.734	0.031	0.031	0.000	0.000	0.000	0.000
88	A	90	SER	0	-0.108	-0.055	22.814	-0.020	-0.020	0.000	0.000	0.000	0.000
89	A	91	LYS	1	1.003	0.992	24.127	11.806	11.806	0.000	0.000	0.000	0.000
90	A	92	TYR	0	0.029	0.055	16.864	-0.189	-0.189	0.000	0.000	0.000	0.000
91	A	93	PRO	0	-0.055	-0.044	20.532	0.303	0.303	0.000	0.000	0.000	0.000
92	A	94	ASN	0	0.010	-0.004	21.503	-0.114	-0.114	0.000	0.000	0.000	0.000
93	A	96	ALA	0	0.025	0.020	22.553	0.336	0.336	0.000	0.000	0.000	0.000
94	A	97	TYR	0	-0.019	-0.049	18.698	-0.304	-0.304	0.000	0.000	0.000	0.000
95	A	98	LYS	1	0.946	0.977	25.038	10.574	10.574	0.000	0.000	0.000	0.000
96	A	99	THR	0	0.052	0.004	26.224	-0.641	-0.641	0.000	0.000	0.000	0.000
97	A	100	THR	0	-0.087	-0.049	27.159	0.489	0.489	0.000	0.000	0.000	0.000
98	A	101	GLN	0	0.044	0.040	27.821	-0.526	-0.526	0.000	0.000	0.000	0.000
99	A	102	VAL	0	-0.045	-0.027	28.066	0.372	0.372	0.000	0.000	0.000	0.000
100	A	103	GLU	-1	-0.878	-0.935	29.268	-9.828	-9.828	0.000	0.000	0.000	0.000
101	A	104	LYS	1	0.886	0.944	27.091	11.089	11.089	0.000	0.000	0.000	0.000
102	A	105	HIS	0	-0.005	0.003	27.047	0.069	0.069	0.000	0.000	0.000	0.000
103	A	106	ILE	0	0.010	0.013	20.604	-0.216	-0.216	0.000	0.000	0.000	0.000
104	A	107	ILE	0	-0.022	-0.013	20.416	0.410	0.410	0.000	0.000	0.000	0.000
105	A	108	VAL	0	-0.009	0.002	16.736	-0.684	-0.684	0.000	0.000	0.000	0.000
106	A	109	ALA	0	0.051	0.020	13.946	0.679	0.679	0.000	0.000	0.000	0.000
107	A	111	GLY	0	0.035	0.013	13.081	0.259	0.259	0.000	0.000	0.000	0.000
108	A	112	GLY	0	0.022	0.017	12.895	-0.453	-0.453	0.000	0.000	0.000	0.000
109	A	113	LYS	1	0.928	0.983	13.518	17.462	17.462	0.000	0.000	0.000	0.000
110	A	114	PRO	0	0.068	0.012	15.642	-0.251	-0.251	0.000	0.000	0.000	0.000
111	A	115	SER	0	-0.025	-0.005	15.657	-1.164	-1.164	0.000	0.000	0.000	0.000
112	A	116	VAL	0	-0.001	-0.007	13.065	0.924	0.924	0.000	0.000	0.000	0.000
113	A	117	PRO	0	0.058	0.011	14.586	-0.780	-0.780	0.000	0.000	0.000	0.000
114	A	118	VAL	0	-0.071	-0.039	9.797	-1.328	-1.328	0.000	0.000	0.000	0.000
115	A	119	HIS	0	-0.018	-0.013	10.359	-3.530	-3.530	0.000	0.000	0.000	0.000
116	A	120	PHE	0	0.033	0.026	12.786	1.423	1.423	0.000	0.000	0.000	0.000
117	A	121	ASP	-1	-0.838	-0.937	15.996	-16.900	-16.900	0.000	0.000	0.000	0.000
118	A	122	ALA	0	-0.050	-0.032	17.977	0.387	0.387	0.000	0.000	0.000	0.000
119	A	123	SER	0	0.043	0.032	21.386	0.044	0.044	0.000	0.000	0.000	0.000
120	A	124	VAL	0	-0.028	-0.018	24.332	0.181	0.181	0.000	0.000	0.000	0.000

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