FMO DATABASE

FMODB ID: LN4V9

Calculation Name: 3OMD-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name: cysteinesulfonic acid

ligand 3-letter code: OCS

PDB ID: 3OMD

Chain ID: A

ChEMBL ID:
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UniProt ID:
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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	145
LigandCharge	OCS=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1433711.722877
FMO2-HF: Nuclear repulsion	1374414.492576
FMO2-HF: Total energy	-59297.230301
FMO2-MP2: Total energy	-59471.492137

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:-4:LEU)

Summations of interaction energy for fragment #1(A:-4:LEU)

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.
-0.763	3.08	0.873	-1.409	-3.307	0.005

Interaction energy analysis for fragmet #1(A:-4:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.046 / q_NPA : 0.031

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	-2	PHE	0	0.011	-0.013	2.548	-2.543	1.085	0.873	-1.391	-3.110	0.005
4	A	-1	GLN	0	-0.056	-0.007	4.170	0.295	0.456	0.001	-0.013	-0.149	0.000
5	A	0	GLY	0	0.040	0.011	5.582	0.194	0.194	0.000	0.000	0.000	0.000
6	A	1	MET	0	-0.004	0.018	6.824	0.045	0.045	0.000	0.000	0.000	0.000
7	A	2	ASP	-1	-0.822	-0.887	9.878	0.317	0.317	0.000	0.000	0.000	0.000
8	A	3	LEU	0	-0.022	-0.023	11.110	-0.034	-0.034	0.000	0.000	0.000	0.000
9	A	4	THR	0	-0.039	-0.025	13.880	-0.001	-0.001	0.000	0.000	0.000	0.000
10	A	5	LYS	1	0.863	0.937	13.506	-0.159	-0.159	0.000	0.000	0.000	0.000
11	A	6	GLN	0	-0.060	-0.040	12.746	-0.032	-0.032	0.000	0.000	0.000	0.000
12	A	7	PHE	0	0.035	0.022	16.765	0.017	0.017	0.000	0.000	0.000	0.000
13	A	8	PRO	0	-0.029	0.008	17.365	-0.027	-0.027	0.000	0.000	0.000	0.000
14	A	9	ARG	1	0.791	0.851	17.494	0.230	0.230	0.000	0.000	0.000	0.000
15	A	10	SER	0	-0.005	-0.013	21.215	0.009	0.009	0.000	0.000	0.000	0.000
16	A	11	PRO	0	-0.002	-0.003	24.860	-0.012	-0.012	0.000	0.000	0.000	0.000
17	A	12	VAL	0	0.012	-0.006	26.177	-0.005	-0.005	0.000	0.000	0.000	0.000
18	A	13	ASP	-1	-0.867	-0.900	23.918	-0.122	-0.122	0.000	0.000	0.000	0.000
19	A	14	ARG	1	0.836	0.903	25.230	0.059	0.059	0.000	0.000	0.000	0.000
20	A	15	LEU	0	-0.009	-0.002	21.368	-0.007	-0.007	0.000	0.000	0.000	0.000
21	A	16	GLY	0	0.035	0.008	25.547	0.003	0.003	0.000	0.000	0.000	0.000
22	A	17	GLY	0	-0.011	0.006	27.887	0.007	0.007	0.000	0.000	0.000	0.000
23	A	18	MET	0	-0.038	-0.014	26.556	0.006	0.006	0.000	0.000	0.000	0.000
24	A	19	ASH	0	-0.002	-0.049	27.216	-0.010	-0.010	0.000	0.000	0.000	0.000
25	A	20	HIS	0	0.014	0.026	22.066	-0.005	-0.005	0.000	0.000	0.000	0.000
26	A	21	LEU	0	-0.007	-0.003	21.088	-0.007	-0.007	0.000	0.000	0.000	0.000
27	A	22	LYS	1	0.871	0.916	20.212	0.130	0.130	0.000	0.000	0.000	0.000
28	A	23	ARG	1	0.808	0.896	19.005	0.022	0.022	0.000	0.000	0.000	0.000
29	A	24	VAL	0	0.006	-0.010	18.230	0.000	0.000	0.000	0.000	0.000	0.000
30	A	25	ILE	0	0.008	0.001	15.450	-0.019	-0.019	0.000	0.000	0.000	0.000
31	A	26	ASP	-1	-0.786	-0.881	14.390	-0.252	-0.252	0.000	0.000	0.000	0.000
32	A	27	LYS	1	0.844	0.911	13.378	0.014	0.014	0.000	0.000	0.000	0.000
33	A	28	ALA	0	-0.006	0.003	13.133	0.031	0.031	0.000	0.000	0.000	0.000
34	A	29	ARG	1	0.822	0.894	9.989	0.539	0.539	0.000	0.000	0.000	0.000
35	A	30	ALA	0	0.031	0.014	8.513	-0.063	-0.063	0.000	0.000	0.000	0.000
36	A	31	HIS	0	-0.005	-0.012	9.175	0.173	0.173	0.000	0.000	0.000	0.000
37	A	32	VAL	0	-0.064	-0.026	5.859	0.103	0.103	0.000	0.000	0.000	0.000
38	A	33	ALA	0	-0.055	-0.036	4.575	0.044	0.098	-0.001	-0.005	-0.048	0.000
39	A	34	GLY	0	0.005	0.029	5.565	0.614	0.614	0.000	0.000	0.000	0.000
40	A	35	THR	0	-0.083	-0.060	7.465	0.046	0.046	0.000	0.000	0.000	0.000
41	A	36	LEU	0	0.020	0.005	9.981	-0.109	-0.109	0.000	0.000	0.000	0.000
42	A	37	GLY	0	0.020	0.004	13.287	-0.043	-0.043	0.000	0.000	0.000	0.000
43	A	38	GLU	-1	-0.938	-0.962	15.772	0.112	0.112	0.000	0.000	0.000	0.000
44	A	39	TYR	0	-0.067	-0.057	16.589	-0.025	-0.025	0.000	0.000	0.000	0.000
45	A	40	THR	0	0.024	-0.003	17.198	0.032	0.032	0.000	0.000	0.000	0.000
46	A	41	TYR	0	-0.073	-0.063	15.021	-0.040	-0.040	0.000	0.000	0.000	0.000
47	A	42	ASN	0	-0.018	-0.025	17.041	0.005	0.005	0.000	0.000	0.000	0.000
48	A	43	OCS	-1	-0.841	-0.891	19.965	0.023	0.023	0.000	0.000	0.000	0.000
49	A	44	PRO	0	0.050	0.003	22.410	-0.015	-0.015	0.000	0.000	0.000	0.000
50	A	45	LEU	0	0.003	-0.003	24.513	-0.009	-0.009	0.000	0.000	0.000	0.000
51	A	46	ASP	-1	-0.744	-0.848	19.373	-0.050	-0.050	0.000	0.000	0.000	0.000
52	A	47	GLN	0	-0.059	-0.026	22.793	-0.015	-0.015	0.000	0.000	0.000	0.000
53	A	48	ALA	0	-0.005	0.004	24.847	-0.006	-0.006	0.000	0.000	0.000	0.000
54	A	49	PHE	0	0.004	0.004	22.584	-0.006	-0.006	0.000	0.000	0.000	0.000
55	A	50	PHE	0	-0.004	-0.026	18.620	-0.008	-0.008	0.000	0.000	0.000	0.000
56	A	51	SER	0	-0.002	0.005	24.727	-0.005	-0.005	0.000	0.000	0.000	0.000
57	A	52	PHE	0	-0.022	0.000	28.093	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	53	PHE	0	-0.023	-0.021	26.639	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	54	GLY	0	0.026	0.042	28.019	-0.007	-0.007	0.000	0.000	0.000	0.000
60	A	55	LEU	0	-0.065	-0.031	22.505	-0.011	-0.011	0.000	0.000	0.000	0.000
61	A	56	ASP	-1	-0.783	-0.891	19.863	-0.071	-0.071	0.000	0.000	0.000	0.000
62	A	57	HIS	0	0.058	0.027	17.665	-0.038	-0.038	0.000	0.000	0.000	0.000
63	A	58	GLU	-1	-0.905	-0.933	16.046	-0.038	-0.038	0.000	0.000	0.000	0.000
64	A	59	LYS	1	0.925	0.944	15.343	0.065	0.065	0.000	0.000	0.000	0.000
65	A	60	PHE	0	-0.032	-0.012	16.483	-0.056	-0.056	0.000	0.000	0.000	0.000
66	A	61	ALA	0	0.006	0.002	12.371	-0.054	-0.054	0.000	0.000	0.000	0.000
67	A	62	GLU	-1	-0.866	-0.945	11.063	-0.736	-0.736	0.000	0.000	0.000	0.000
68	A	63	ALA	0	-0.058	-0.018	12.436	-0.116	-0.116	0.000	0.000	0.000	0.000
69	A	64	VAL	0	0.069	-0.012	11.536	-0.049	-0.049	0.000	0.000	0.000	0.000
70	A	65	LYS	1	0.850	0.949	7.395	0.684	0.684	0.000	0.000	0.000	0.000
71	A	66	SER	0	-0.023	-0.005	9.338	-0.137	-0.137	0.000	0.000	0.000	0.000
72	A	67	ARG	1	0.852	0.941	11.868	0.487	0.487	0.000	0.000	0.000	0.000
73	A	68	PRO	0	0.045	0.016	10.912	0.033	0.033	0.000	0.000	0.000	0.000
74	A	69	GLN	0	0.041	0.031	12.680	0.075	0.075	0.000	0.000	0.000	0.000
75	A	70	ASP	-1	-0.752	-0.866	16.201	-0.247	-0.247	0.000	0.000	0.000	0.000
76	A	71	GLN	0	-0.008	-0.016	18.849	0.018	0.018	0.000	0.000	0.000	0.000
77	A	72	ASP	-1	-0.858	-0.921	17.304	-0.327	-0.327	0.000	0.000	0.000	0.000
78	A	73	MET	0	-0.068	-0.002	16.143	-0.007	-0.007	0.000	0.000	0.000	0.000
79	A	74	LEU	0	-0.016	0.002	18.952	0.025	0.025	0.000	0.000	0.000	0.000
80	A	75	ALA	0	0.032	0.012	22.166	0.019	0.019	0.000	0.000	0.000	0.000
81	A	76	TRP	0	0.004	0.000	19.558	0.011	0.011	0.000	0.000	0.000	0.000
82	A	77	VAL	0	0.058	0.027	21.692	0.020	0.020	0.000	0.000	0.000	0.000
83	A	78	HIS	0	-0.021	-0.024	23.803	0.015	0.015	0.000	0.000	0.000	0.000
84	A	79	SER	0	-0.141	-0.083	23.890	0.010	0.010	0.000	0.000	0.000	0.000
85	A	80	GLN	0	-0.046	-0.019	22.265	0.016	0.016	0.000	0.000	0.000	0.000
86	A	81	SER	0	-0.002	0.001	25.682	0.015	0.015	0.000	0.000	0.000	0.000
87	A	82	PRO	0	0.022	0.004	28.424	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	83	ARG	1	0.844	0.928	31.679	0.055	0.055	0.000	0.000	0.000	0.000
89	A	84	SER	0	0.012	-0.012	28.447	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	85	LYS	1	0.921	0.970	29.965	0.112	0.112	0.000	0.000	0.000	0.000
91	A	86	ASN	0	-0.013	-0.001	32.427	0.004	0.004	0.000	0.000	0.000	0.000
92	A	87	PRO	0	0.069	0.020	34.741	0.002	0.002	0.000	0.000	0.000	0.000
93	A	88	LYS	1	1.005	1.002	35.800	0.056	0.056	0.000	0.000	0.000	0.000
94	A	89	GLU	-1	-0.850	-0.912	34.769	-0.049	-0.049	0.000	0.000	0.000	0.000
95	A	90	VAL	0	-0.003	0.005	30.916	0.002	0.002	0.000	0.000	0.000	0.000
96	A	91	GLU	-1	-0.975	-0.989	33.124	-0.062	-0.062	0.000	0.000	0.000	0.000
97	A	92	SER	0	-0.043	-0.014	35.783	0.005	0.005	0.000	0.000	0.000	0.000
98	A	93	PHE	0	0.019	0.007	27.712	0.004	0.004	0.000	0.000	0.000	0.000
99	A	94	ASN	0	0.016	-0.003	31.017	0.002	0.002	0.000	0.000	0.000	0.000
100	A	95	ARG	1	0.962	0.987	33.020	0.035	0.035	0.000	0.000	0.000	0.000
101	A	96	GLU	-1	-0.937	-0.961	34.642	-0.022	-0.022	0.000	0.000	0.000	0.000
102	A	97	TYR	0	-0.074	-0.072	25.571	0.005	0.005	0.000	0.000	0.000	0.000
103	A	98	GLU	-1	-0.812	-0.872	32.227	-0.047	-0.047	0.000	0.000	0.000	0.000
104	A	99	SER	0	-0.090	-0.034	33.830	0.004	0.004	0.000	0.000	0.000	0.000
105	A	100	ARG	1	0.949	0.982	31.156	0.025	0.025	0.000	0.000	0.000	0.000
106	A	101	SER	0	0.035	0.000	34.537	0.000	0.000	0.000	0.000	0.000	0.000
107	A	102	PRO	0	-0.053	-0.024	35.595	0.001	0.001	0.000	0.000	0.000	0.000
108	A	103	ASP	-1	-0.854	-0.913	35.801	0.014	0.014	0.000	0.000	0.000	0.000
109	A	104	SER	0	0.044	0.023	37.868	0.001	0.001	0.000	0.000	0.000	0.000
110	A	105	PRO	0	0.033	0.000	39.761	0.000	0.000	0.000	0.000	0.000	0.000
111	A	106	GLU	-1	-0.868	-0.914	37.287	0.040	0.040	0.000	0.000	0.000	0.000
112	A	107	LYS	1	0.866	0.917	33.217	-0.020	-0.020	0.000	0.000	0.000	0.000
113	A	108	TRP	0	-0.025	-0.025	36.390	0.000	0.000	0.000	0.000	0.000	0.000
114	A	109	ASP	-1	-0.852	-0.925	38.845	0.023	0.023	0.000	0.000	0.000	0.000
115	A	110	TYR	0	-0.008	0.002	29.187	0.000	0.000	0.000	0.000	0.000	0.000
116	A	111	PHE	0	-0.026	-0.014	33.790	0.001	0.001	0.000	0.000	0.000	0.000
117	A	112	ARG	1	0.842	0.908	35.181	-0.018	-0.018	0.000	0.000	0.000	0.000
118	A	113	SER	0	0.027	0.037	35.803	0.000	0.000	0.000	0.000	0.000	0.000
119	A	114	VAL	0	0.035	0.026	30.421	0.001	0.001	0.000	0.000	0.000	0.000
120	A	115	ARG	1	0.868	0.943	33.422	-0.009	-0.009	0.000	0.000	0.000	0.000
121	A	116	ASP	-1	-0.901	-0.965	35.163	0.015	0.015	0.000	0.000	0.000	0.000
122	A	117	SER	0	-0.098	-0.054	33.055	0.001	0.001	0.000	0.000	0.000	0.000
123	A	118	LEU	0	-0.030	0.001	29.486	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	119	ALA	0	-0.020	-0.035	33.571	-0.003	-0.003	0.000	0.000	0.000	0.000
125	A	120	PRO	0	0.038	0.027	36.624	-0.003	-0.003	0.000	0.000	0.000	0.000
126	A	121	GLY	0	-0.047	-0.007	39.839	-0.001	-0.001	0.000	0.000	0.000	0.000
127	A	122	ARG	1	0.765	0.846	36.609	0.008	0.008	0.000	0.000	0.000	0.000
128	A	123	THR	0	0.007	-0.004	39.522	-0.001	-0.001	0.000	0.000	0.000	0.000
129	A	124	ASP	-1	-0.798	-0.869	40.198	-0.010	-0.010	0.000	0.000	0.000	0.000
130	A	125	ILE	0	-0.035	-0.005	34.691	-0.003	-0.003	0.000	0.000	0.000	0.000
131	A	126	THR	0	-0.011	-0.021	37.888	0.003	0.003	0.000	0.000	0.000	0.000
132	A	127	THR	0	0.042	0.032	34.581	0.002	0.002	0.000	0.000	0.000	0.000
133	A	128	TRP	0	0.053	0.006	30.109	0.001	0.001	0.000	0.000	0.000	0.000
134	A	129	VAL	0	0.011	0.000	28.607	0.002	0.002	0.000	0.000	0.000	0.000
135	A	130	LYS	1	0.954	0.981	29.683	0.026	0.026	0.000	0.000	0.000	0.000
136	A	131	LEU	0	0.032	0.021	30.606	-0.001	-0.001	0.000	0.000	0.000	0.000
137	A	132	LEU	0	0.011	0.006	24.774	0.002	0.002	0.000	0.000	0.000	0.000
138	A	133	ASP	-1	-0.784	-0.882	26.925	-0.046	-0.046	0.000	0.000	0.000	0.000
139	A	134	LEU	0	-0.069	-0.027	28.409	-0.001	-0.001	0.000	0.000	0.000	0.000
140	A	135	GLU	-1	-0.903	-0.953	25.630	0.038	0.038	0.000	0.000	0.000	0.000
141	A	136	GLU	-1	-0.767	-0.821	22.474	-0.021	-0.021	0.000	0.000	0.000	0.000
142	A	137	LYS	1	0.897	0.948	25.369	-0.020	-0.020	0.000	0.000	0.000	0.000
143	A	138	ARG	1	0.819	0.902	22.354	0.047	0.047	0.000	0.000	0.000	0.000
144	A	139	PRO	0	-0.017	-0.014	28.912	0.005	0.005	0.000	0.000	0.000	0.000
145	A	140	VAL	0	0.007	0.021	31.758	-0.002	-0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-4:LEU)