FMO DATABASE

FMODB ID: G5JG1

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	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. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1028447.747112
FMO2-HF: Nuclear repulsion	976823.995432
FMO2-HF: Total energy	-51623.75168
FMO2-MP2: Total energy	-51762.243841

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.
170.448	173.541	2.662	-2.454	-3.301	-0.018

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 : 1.019 / q_NPA : 1.016

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	0.040	0.013	2.541	-16.679	-13.674	2.663	-2.449	-3.219	-0.018
4	A	4	ALA	0	0.044	0.002	4.581	2.309	2.397	-0.001	-0.005	-0.082	0.000
5	A	5	ALA	0	0.062	0.041	6.328	2.650	2.650	0.000	0.000	0.000	0.000
6	A	6	ALA	0	0.032	0.022	7.154	1.939	1.939	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.953	0.989	5.671	45.313	45.313	0.000	0.000	0.000	0.000
8	A	8	PHE	0	0.020	0.011	8.415	2.555	2.555	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.779	-0.905	11.472	-19.848	-19.848	0.000	0.000	0.000	0.000
10	A	10	ARG	1	0.797	0.860	7.659	32.995	32.995	0.000	0.000	0.000	0.000
11	A	11	GLN	0	-0.014	-0.016	10.597	1.903	1.903	0.000	0.000	0.000	0.000
12	A	12	HIS	0	-0.021	-0.011	13.511	-0.003	-0.003	0.000	0.000	0.000	0.000
13	A	13	MET	0	-0.026	0.017	16.147	1.047	1.047	0.000	0.000	0.000	0.000
14	A	14	ASP	-1	-0.761	-0.863	18.052	-14.860	-14.860	0.000	0.000	0.000	0.000
15	A	15	SER	0	-0.063	-0.040	20.891	0.476	0.476	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.063	0.037	23.255	0.075	0.075	0.000	0.000	0.000	0.000
17	A	17	ASN	0	-0.005	-0.008	26.646	0.459	0.459	0.000	0.000	0.000	0.000
18	A	18	SER	0	-0.001	0.003	29.827	0.009	0.009	0.000	0.000	0.000	0.000
19	A	19	PRO	0	-0.011	0.018	28.834	-0.058	-0.058	0.000	0.000	0.000	0.000
20	A	20	SER	0	0.019	-0.002	30.165	0.423	0.423	0.000	0.000	0.000	0.000
21	A	21	SER	0	-0.023	-0.015	30.402	-0.308	-0.308	0.000	0.000	0.000	0.000
22	A	22	SER	0	0.034	0.001	29.918	0.125	0.125	0.000	0.000	0.000	0.000
23	A	23	SER	0	0.039	0.013	30.207	-0.369	-0.369	0.000	0.000	0.000	0.000
24	A	24	ASN	0	0.043	0.034	28.626	-0.504	-0.504	0.000	0.000	0.000	0.000
25	A	25	TYR	0	-0.004	-0.013	22.746	-0.448	-0.448	0.000	0.000	0.000	0.000
26	A	26	CYS	0	-0.047	-0.017	21.214	-0.062	-0.062	0.000	0.000	0.000	0.000
27	A	27	ASN	0	0.027	0.010	22.382	-0.952	-0.952	0.000	0.000	0.000	0.000
28	A	28	LEU	0	0.038	0.035	22.895	-0.450	-0.450	0.000	0.000	0.000	0.000
29	A	29	MET	0	0.021	0.005	20.311	-0.728	-0.728	0.000	0.000	0.000	0.000
30	A	30	MET	0	-0.022	-0.006	17.265	-1.296	-1.296	0.000	0.000	0.000	0.000
31	A	31	YCM	0	0.011	0.020	17.128	-1.014	-1.014	0.000	0.000	0.000	0.000
32	A	32	YCM	0	-0.023	-0.027	16.959	-1.351	-1.351	0.000	0.000	0.000	0.000
33	A	33	ARG	1	0.773	0.877	14.908	16.910	16.910	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.864	0.934	11.896	17.276	17.276	0.000	0.000	0.000	0.000
35	A	35	MET	0	-0.075	-0.022	12.225	-2.311	-2.311	0.000	0.000	0.000	0.000
36	A	36	THR	0	0.038	0.014	14.336	0.592	0.592	0.000	0.000	0.000	0.000
37	A	37	GLN	0	0.041	0.021	11.509	1.893	1.893	0.000	0.000	0.000	0.000
38	A	38	GLY	0	0.004	0.017	13.265	-1.514	-1.514	0.000	0.000	0.000	0.000
39	A	39	LYS	1	0.918	0.946	14.481	19.144	19.144	0.000	0.000	0.000	0.000
40	A	40	CYS	0	-0.022	0.019	15.839	-0.685	-0.685	0.000	0.000	0.000	0.000
41	A	41	LYS	1	0.817	0.908	13.190	21.465	21.465	0.000	0.000	0.000	0.000
42	A	42	PRO	0	0.043	0.030	16.627	0.534	0.534	0.000	0.000	0.000	0.000
43	A	43	VAL	0	-0.003	-0.015	18.688	0.944	0.944	0.000	0.000	0.000	0.000
44	A	44	ASN	0	-0.018	-0.019	16.339	-2.292	-2.292	0.000	0.000	0.000	0.000
45	A	45	THR	0	0.018	0.001	18.697	0.799	0.799	0.000	0.000	0.000	0.000
46	A	46	PHE	0	0.013	0.011	17.330	-1.014	-1.014	0.000	0.000	0.000	0.000
47	A	47	VAL	0	0.019	0.001	20.134	0.752	0.752	0.000	0.000	0.000	0.000
48	A	48	HIS	0	-0.011	0.026	21.996	-0.267	-0.267	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.724	-0.830	24.551	-10.827	-10.827	0.000	0.000	0.000	0.000
50	A	50	SER	0	-0.004	-0.026	23.609	-0.709	-0.709	0.000	0.000	0.000	0.000
51	A	51	LEU	0	0.019	-0.010	16.875	-0.239	-0.239	0.000	0.000	0.000	0.000
52	A	52	ALA	0	0.020	0.014	20.406	-0.521	-0.521	0.000	0.000	0.000	0.000
53	A	53	ASP	-1	-0.803	-0.865	22.928	-11.940	-11.940	0.000	0.000	0.000	0.000
54	A	54	VAL	0	-0.008	-0.016	18.567	-0.071	-0.071	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.797	0.880	14.402	19.299	19.299	0.000	0.000	0.000	0.000
56	A	56	ALA	0	0.048	0.035	19.422	-0.111	-0.111	0.000	0.000	0.000	0.000
57	A	57	VAL	0	-0.004	0.006	20.687	0.512	0.512	0.000	0.000	0.000	0.000
58	A	58	CYS	0	-0.122	-0.047	14.441	-0.946	-0.946	0.000	0.000	0.000	0.000
59	A	59	SER	0	-0.063	-0.032	20.382	0.130	0.130	0.000	0.000	0.000	0.000
60	A	60	GLN	0	0.022	0.017	23.916	0.886	0.886	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.949	0.987	25.600	10.847	10.847	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.940	0.969	22.265	13.141	13.141	0.000	0.000	0.000	0.000
63	A	63	VAL	0	-0.061	-0.040	22.580	0.682	0.682	0.000	0.000	0.000	0.000
64	A	64	THR	0	-0.001	0.000	22.529	-0.455	-0.455	0.000	0.000	0.000	0.000
65	A	65	CYS	0	-0.042	0.006	17.717	-1.050	-1.050	0.000	0.000	0.000	0.000
66	A	66	LYS	1	0.891	0.914	19.558	14.751	14.751	0.000	0.000	0.000	0.000
67	A	67	ASN	0	-0.005	-0.001	14.785	1.099	1.099	0.000	0.000	0.000	0.000
68	A	68	GLY	0	0.034	0.021	18.720	-0.070	-0.070	0.000	0.000	0.000	0.000
69	A	69	GLN	0	0.001	0.016	16.214	0.515	0.515	0.000	0.000	0.000	0.000
70	A	70	THR	0	0.043	0.007	19.452	0.375	0.375	0.000	0.000	0.000	0.000
71	A	71	ASN	0	-0.031	-0.018	14.384	1.002	1.002	0.000	0.000	0.000	0.000
72	A	73	TYR	0	0.007	0.002	18.964	0.957	0.957	0.000	0.000	0.000	0.000
73	A	74	GLN	0	0.019	-0.001	21.440	-0.376	-0.376	0.000	0.000	0.000	0.000
74	A	75	SER	0	0.001	-0.001	24.291	0.143	0.143	0.000	0.000	0.000	0.000
75	A	76	LYS	1	0.960	0.974	25.807	10.809	10.809	0.000	0.000	0.000	0.000
76	A	77	SER	0	-0.006	-0.005	28.806	0.429	0.429	0.000	0.000	0.000	0.000
77	A	78	THR	0	0.022	0.021	28.584	-0.458	-0.458	0.000	0.000	0.000	0.000
78	A	79	MET	0	-0.039	-0.014	23.940	-0.299	-0.299	0.000	0.000	0.000	0.000
79	A	80	ARG	1	0.836	0.898	27.712	10.980	10.980	0.000	0.000	0.000	0.000
80	A	81	ILE	0	-0.050	-0.034	23.991	-0.592	-0.592	0.000	0.000	0.000	0.000
81	A	82	THR	0	0.011	-0.030	24.297	0.777	0.777	0.000	0.000	0.000	0.000
82	A	83	ASP	-1	-0.804	-0.858	23.329	-13.546	-13.546	0.000	0.000	0.000	0.000
83	A	85	ARG	1	0.855	0.901	22.182	11.806	11.806	0.000	0.000	0.000	0.000
84	A	86	GLU	-1	-0.814	-0.873	20.664	-14.306	-14.306	0.000	0.000	0.000	0.000
85	A	87	THR	0	-0.046	-0.026	24.281	0.486	0.486	0.000	0.000	0.000	0.000
86	A	88	GLY	0	0.020	0.001	27.338	-0.239	-0.239	0.000	0.000	0.000	0.000
87	A	89	SER	0	0.001	-0.001	29.776	0.169	0.169	0.000	0.000	0.000	0.000
88	A	90	SER	0	-0.102	-0.062	23.277	-0.021	-0.021	0.000	0.000	0.000	0.000
89	A	91	LYS	1	0.969	0.970	24.615	11.955	11.955	0.000	0.000	0.000	0.000
90	A	92	TYR	0	0.038	0.036	17.566	-0.185	-0.185	0.000	0.000	0.000	0.000
91	A	93	PRO	0	-0.026	-0.033	21.209	0.365	0.365	0.000	0.000	0.000	0.000
92	A	94	ASN	0	0.013	0.011	22.265	-0.519	-0.519	0.000	0.000	0.000	0.000
93	A	96	ALA	0	0.040	0.023	23.004	0.241	0.241	0.000	0.000	0.000	0.000
94	A	97	TYR	0	-0.018	-0.035	19.131	-0.107	-0.107	0.000	0.000	0.000	0.000
95	A	98	LYS	1	0.945	0.982	25.502	10.503	10.503	0.000	0.000	0.000	0.000
96	A	99	THR	0	0.022	-0.024	26.509	-0.642	-0.642	0.000	0.000	0.000	0.000
97	A	100	THR	0	-0.078	-0.060	27.139	0.555	0.555	0.000	0.000	0.000	0.000
98	A	101	GLN	0	0.061	0.058	27.886	-0.224	-0.224	0.000	0.000	0.000	0.000
99	A	102	VAL	0	-0.017	-0.012	28.262	0.364	0.364	0.000	0.000	0.000	0.000
100	A	103	GLU	-1	-0.864	-0.928	29.258	-10.004	-10.004	0.000	0.000	0.000	0.000
101	A	104	LYS	1	0.828	0.912	27.120	11.572	11.572	0.000	0.000	0.000	0.000
102	A	105	HIS	0	0.006	0.011	27.244	0.053	0.053	0.000	0.000	0.000	0.000
103	A	106	ILE	0	-0.008	-0.005	20.589	-0.208	-0.208	0.000	0.000	0.000	0.000
104	A	107	ILE	0	-0.012	-0.011	20.432	0.335	0.335	0.000	0.000	0.000	0.000
105	A	108	VAL	0	0.009	0.007	16.562	-0.652	-0.652	0.000	0.000	0.000	0.000
106	A	109	ALA	0	0.046	0.019	13.997	0.674	0.674	0.000	0.000	0.000	0.000
107	A	111	GLY	0	0.027	0.010	12.693	0.129	0.129	0.000	0.000	0.000	0.000
108	A	112	GLY	0	0.030	0.027	12.709	-0.193	-0.193	0.000	0.000	0.000	0.000
109	A	113	LYS	1	0.894	0.947	13.231	18.847	18.847	0.000	0.000	0.000	0.000
110	A	114	PRO	0	0.101	0.042	15.600	-0.277	-0.277	0.000	0.000	0.000	0.000
111	A	115	SER	0	-0.049	-0.017	15.573	-1.454	-1.454	0.000	0.000	0.000	0.000
112	A	116	VAL	0	0.036	0.006	12.575	0.787	0.787	0.000	0.000	0.000	0.000
113	A	117	PRO	0	0.046	0.007	13.870	-0.872	-0.872	0.000	0.000	0.000	0.000
114	A	118	VAL	0	-0.081	-0.040	9.466	-1.634	-1.634	0.000	0.000	0.000	0.000
115	A	119	HIS	0	-0.035	-0.032	9.956	-3.408	-3.408	0.000	0.000	0.000	0.000
116	A	120	PHE	0	0.018	0.020	12.612	1.399	1.399	0.000	0.000	0.000	0.000
117	A	121	ASP	-1	-0.798	-0.876	16.066	-16.529	-16.529	0.000	0.000	0.000	0.000
118	A	122	ALA	0	-0.004	-0.015	18.278	0.619	0.619	0.000	0.000	0.000	0.000
119	A	123	SER	0	0.064	0.045	21.757	-0.018	-0.018	0.000	0.000	0.000	0.000
120	A	124	VAL	0	-0.009	0.002	24.391	0.383	0.383	0.000	0.000	0.000	0.000

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