FMO DATABASE

FMODB ID: 1NMKZ

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	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. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1027880.427505
FMO2-HF: Nuclear repulsion	976256.971605
FMO2-HF: Total energy	-51623.4559
FMO2-MP2: Total energy	-51761.987325

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.
170.247	174.033	1.887	-2.537	-3.134	-0.01

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 : 1.003 / q_NPA : 1.006

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	0.044	0.009	2.680	-14.355	-10.652	1.888	-2.533	-3.057	-0.010
4	A	4	ALA	0	0.059	0.010	4.603	0.807	0.890	-0.001	-0.004	-0.077	0.000
5	A	5	ALA	0	0.048	0.021	6.206	2.632	2.632	0.000	0.000	0.000	0.000
6	A	6	ALA	0	0.016	0.007	7.125	2.082	2.082	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.938	0.992	5.688	44.561	44.561	0.000	0.000	0.000	0.000
8	A	8	PHE	0	0.008	-0.001	8.156	2.473	2.473	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.805	-0.909	11.239	-18.823	-18.823	0.000	0.000	0.000	0.000
10	A	10	ARG	1	0.801	0.863	7.258	33.587	33.587	0.000	0.000	0.000	0.000
11	A	11	GLN	0	-0.013	-0.025	10.525	1.202	1.202	0.000	0.000	0.000	0.000
12	A	12	HIS	0	-0.019	-0.027	13.212	-0.140	-0.140	0.000	0.000	0.000	0.000
13	A	13	MET	0	0.000	0.049	16.007	0.974	0.974	0.000	0.000	0.000	0.000
14	A	14	ASP	-1	-0.786	-0.876	17.964	-14.781	-14.781	0.000	0.000	0.000	0.000
15	A	15	SER	0	-0.062	-0.038	20.830	0.469	0.469	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.106	0.047	23.059	0.033	0.033	0.000	0.000	0.000	0.000
17	A	17	ASN	0	-0.044	-0.031	26.444	0.450	0.450	0.000	0.000	0.000	0.000
18	A	18	SER	0	-0.003	0.008	29.478	0.011	0.011	0.000	0.000	0.000	0.000
19	A	19	PRO	0	0.011	0.029	28.385	-0.065	-0.065	0.000	0.000	0.000	0.000
20	A	20	SER	0	0.006	-0.008	29.743	0.446	0.446	0.000	0.000	0.000	0.000
21	A	21	SER	0	0.004	0.016	30.244	-0.420	-0.420	0.000	0.000	0.000	0.000
22	A	22	SER	0	0.047	-0.001	29.700	0.102	0.102	0.000	0.000	0.000	0.000
23	A	23	SER	0	0.037	0.019	29.857	-0.396	-0.396	0.000	0.000	0.000	0.000
24	A	24	ASN	0	0.030	0.011	28.415	-0.487	-0.487	0.000	0.000	0.000	0.000
25	A	25	TYR	0	-0.013	-0.018	22.436	-0.517	-0.517	0.000	0.000	0.000	0.000
26	A	26	CYS	0	-0.064	-0.027	20.958	0.011	0.011	0.000	0.000	0.000	0.000
27	A	27	ASN	0	0.051	0.018	22.121	-0.981	-0.981	0.000	0.000	0.000	0.000
28	A	28	LEU	0	0.029	0.031	22.587	-0.433	-0.433	0.000	0.000	0.000	0.000
29	A	29	MET	0	0.017	0.005	19.549	-0.685	-0.685	0.000	0.000	0.000	0.000
30	A	30	MET	0	-0.015	0.000	16.906	-1.341	-1.341	0.000	0.000	0.000	0.000
31	A	31	YCM	0	-0.001	0.010	16.929	-1.114	-1.114	0.000	0.000	0.000	0.000
32	A	32	YCM	0	0.005	-0.003	16.776	-1.379	-1.379	0.000	0.000	0.000	0.000
33	A	33	ARG	1	0.775	0.884	14.444	16.874	16.874	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.875	0.932	11.498	17.711	17.711	0.000	0.000	0.000	0.000
35	A	35	MET	0	-0.094	-0.021	12.246	-2.085	-2.085	0.000	0.000	0.000	0.000
36	A	36	THR	0	0.045	0.022	13.995	0.359	0.359	0.000	0.000	0.000	0.000
37	A	37	GLN	0	0.022	0.011	11.020	2.044	2.044	0.000	0.000	0.000	0.000
38	A	38	GLY	0	0.006	0.011	12.668	-1.703	-1.703	0.000	0.000	0.000	0.000
39	A	39	LYS	1	0.949	0.954	13.781	19.786	19.786	0.000	0.000	0.000	0.000
40	A	40	CYS	0	-0.033	0.009	15.586	-0.697	-0.697	0.000	0.000	0.000	0.000
41	A	41	LYS	1	0.821	0.915	12.727	22.305	22.305	0.000	0.000	0.000	0.000
42	A	42	PRO	0	0.045	0.028	16.122	0.537	0.537	0.000	0.000	0.000	0.000
43	A	43	VAL	0	-0.001	-0.009	18.287	0.965	0.965	0.000	0.000	0.000	0.000
44	A	44	ASN	0	-0.013	-0.015	15.899	-2.360	-2.360	0.000	0.000	0.000	0.000
45	A	45	THR	0	0.017	0.009	18.166	0.704	0.704	0.000	0.000	0.000	0.000
46	A	46	PHE	0	0.017	0.007	17.097	-1.086	-1.086	0.000	0.000	0.000	0.000
47	A	47	VAL	0	0.025	-0.002	19.728	0.726	0.726	0.000	0.000	0.000	0.000
48	A	48	HIS	0	-0.027	0.007	21.774	-0.252	-0.252	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.733	-0.853	23.489	-10.777	-10.777	0.000	0.000	0.000	0.000
50	A	50	SER	0	-0.023	-0.034	23.039	-0.769	-0.769	0.000	0.000	0.000	0.000
51	A	51	LEU	0	0.048	0.004	16.596	-0.157	-0.157	0.000	0.000	0.000	0.000
52	A	52	ALA	0	-0.001	0.001	20.616	-0.394	-0.394	0.000	0.000	0.000	0.000
53	A	53	ASP	-1	-0.813	-0.875	22.737	-11.826	-11.826	0.000	0.000	0.000	0.000
54	A	54	VAL	0	-0.016	-0.013	18.427	-0.065	-0.065	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.845	0.905	15.074	18.656	18.656	0.000	0.000	0.000	0.000
56	A	56	ALA	0	0.034	0.026	19.688	-0.093	-0.093	0.000	0.000	0.000	0.000
57	A	57	VAL	0	-0.006	-0.003	20.783	0.509	0.509	0.000	0.000	0.000	0.000
58	A	58	CYS	0	-0.133	-0.040	14.523	-0.816	-0.816	0.000	0.000	0.000	0.000
59	A	59	SER	0	-0.067	-0.018	20.569	0.134	0.134	0.000	0.000	0.000	0.000
60	A	60	GLN	0	0.006	0.005	23.872	0.771	0.771	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.970	0.998	25.897	10.765	10.765	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.920	0.967	22.119	13.120	13.120	0.000	0.000	0.000	0.000
63	A	63	VAL	0	-0.053	-0.030	22.752	0.654	0.654	0.000	0.000	0.000	0.000
64	A	64	THR	0	-0.003	-0.003	22.635	-0.447	-0.447	0.000	0.000	0.000	0.000
65	A	65	CYS	0	-0.040	-0.001	17.635	-1.157	-1.157	0.000	0.000	0.000	0.000
66	A	66	LYS	1	0.902	0.934	19.055	14.789	14.789	0.000	0.000	0.000	0.000
67	A	67	ASN	0	0.002	-0.006	14.826	1.080	1.080	0.000	0.000	0.000	0.000
68	A	68	GLY	0	0.038	0.025	18.879	-0.012	-0.012	0.000	0.000	0.000	0.000
69	A	69	GLN	0	-0.004	0.013	15.750	0.528	0.528	0.000	0.000	0.000	0.000
70	A	70	THR	0	0.053	0.014	19.066	0.422	0.422	0.000	0.000	0.000	0.000
71	A	71	ASN	0	-0.062	-0.035	14.242	0.906	0.906	0.000	0.000	0.000	0.000
72	A	73	TYR	0	0.017	0.004	19.142	0.900	0.900	0.000	0.000	0.000	0.000
73	A	74	GLN	0	0.008	-0.001	21.426	-0.180	-0.180	0.000	0.000	0.000	0.000
74	A	75	SER	0	0.005	-0.011	24.202	0.139	0.139	0.000	0.000	0.000	0.000
75	A	76	LYS	1	0.973	0.978	25.516	10.673	10.673	0.000	0.000	0.000	0.000
76	A	77	SER	0	0.007	0.007	28.568	0.370	0.370	0.000	0.000	0.000	0.000
77	A	78	THR	0	0.011	0.025	28.139	-0.465	-0.465	0.000	0.000	0.000	0.000
78	A	79	MET	0	-0.048	-0.025	23.926	-0.240	-0.240	0.000	0.000	0.000	0.000
79	A	80	ARG	1	0.874	0.934	27.506	11.017	11.017	0.000	0.000	0.000	0.000
80	A	81	ILE	0	-0.033	-0.019	23.489	-0.603	-0.603	0.000	0.000	0.000	0.000
81	A	82	THR	0	0.025	-0.013	23.895	0.785	0.785	0.000	0.000	0.000	0.000
82	A	83	ASP	-1	-0.862	-0.903	23.005	-13.656	-13.656	0.000	0.000	0.000	0.000
83	A	85	ARG	1	0.870	0.912	21.808	11.711	11.711	0.000	0.000	0.000	0.000
84	A	86	GLU	-1	-0.794	-0.860	20.817	-14.274	-14.274	0.000	0.000	0.000	0.000
85	A	87	THR	0	-0.060	-0.029	23.764	0.500	0.500	0.000	0.000	0.000	0.000
86	A	88	GLY	0	0.020	-0.003	26.721	-0.239	-0.239	0.000	0.000	0.000	0.000
87	A	89	SER	0	0.006	-0.002	28.919	0.080	0.080	0.000	0.000	0.000	0.000
88	A	90	SER	0	-0.096	-0.053	22.935	-0.010	-0.010	0.000	0.000	0.000	0.000
89	A	91	LYS	1	1.004	0.993	24.358	11.811	11.811	0.000	0.000	0.000	0.000
90	A	92	TYR	0	0.026	0.044	17.323	-0.207	-0.207	0.000	0.000	0.000	0.000
91	A	93	PRO	0	-0.069	-0.046	20.775	0.352	0.352	0.000	0.000	0.000	0.000
92	A	94	ASN	0	0.022	0.001	21.740	-0.267	-0.267	0.000	0.000	0.000	0.000
93	A	96	ALA	0	0.035	0.019	22.696	0.322	0.322	0.000	0.000	0.000	0.000
94	A	97	TYR	0	-0.031	-0.049	18.760	-0.269	-0.269	0.000	0.000	0.000	0.000
95	A	98	LYS	1	0.950	0.984	25.068	10.623	10.623	0.000	0.000	0.000	0.000
96	A	99	THR	0	0.017	-0.017	26.185	-0.656	-0.656	0.000	0.000	0.000	0.000
97	A	100	THR	0	-0.073	-0.050	27.057	0.536	0.536	0.000	0.000	0.000	0.000
98	A	101	GLN	0	0.052	0.045	27.630	-0.420	-0.420	0.000	0.000	0.000	0.000
99	A	102	VAL	0	-0.045	-0.029	27.647	0.374	0.374	0.000	0.000	0.000	0.000
100	A	103	GLU	-1	-0.866	-0.930	28.846	-10.041	-10.041	0.000	0.000	0.000	0.000
101	A	104	LYS	1	0.893	0.951	26.959	11.418	11.418	0.000	0.000	0.000	0.000
102	A	105	HIS	0	0.003	0.007	26.712	0.029	0.029	0.000	0.000	0.000	0.000
103	A	106	ILE	0	0.006	0.010	20.214	-0.219	-0.219	0.000	0.000	0.000	0.000
104	A	107	ILE	0	-0.007	-0.009	20.219	0.397	0.397	0.000	0.000	0.000	0.000
105	A	108	VAL	0	-0.008	0.002	16.302	-0.705	-0.705	0.000	0.000	0.000	0.000
106	A	109	ALA	0	0.054	0.021	13.652	0.716	0.716	0.000	0.000	0.000	0.000
107	A	111	GLY	0	0.036	0.016	12.675	0.311	0.311	0.000	0.000	0.000	0.000
108	A	112	GLY	0	0.018	0.016	12.757	-0.530	-0.530	0.000	0.000	0.000	0.000
109	A	113	LYS	1	0.925	0.980	13.315	17.633	17.633	0.000	0.000	0.000	0.000
110	A	114	PRO	0	0.087	0.022	15.405	-0.289	-0.289	0.000	0.000	0.000	0.000
111	A	115	SER	0	-0.027	-0.005	15.477	-1.225	-1.225	0.000	0.000	0.000	0.000
112	A	116	VAL	0	0.012	-0.004	12.749	0.892	0.892	0.000	0.000	0.000	0.000
113	A	117	PRO	0	0.054	0.006	14.043	-0.790	-0.790	0.000	0.000	0.000	0.000
114	A	118	VAL	0	-0.086	-0.046	9.394	-1.481	-1.481	0.000	0.000	0.000	0.000
115	A	119	HIS	0	-0.026	-0.017	9.952	-3.553	-3.553	0.000	0.000	0.000	0.000
116	A	120	PHE	0	0.032	0.029	12.421	1.526	1.526	0.000	0.000	0.000	0.000
117	A	121	ASP	-1	-0.819	-0.914	15.641	-16.748	-16.748	0.000	0.000	0.000	0.000
118	A	122	ALA	0	-0.024	-0.020	17.725	0.405	0.405	0.000	0.000	0.000	0.000
119	A	123	SER	0	0.049	0.031	21.124	0.032	0.032	0.000	0.000	0.000	0.000
120	A	124	VAL	0	-0.033	-0.020	24.010	0.190	0.190	0.000	0.000	0.000	0.000

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