FMO DATABASE

FMODB ID: 989R2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1434779.504306
FMO2-HF: Nuclear repulsion	1375481.626484
FMO2-HF: Total energy	-59297.877821
FMO2-MP2: Total energy	-59472.119281

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.
-1.494	2.751	0.385	-1.637	-2.993	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 : 0.039 / q_NPA : 0.029

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	0.006	-0.014	2.916	-2.787	1.251	0.386	-1.621	-2.804	0.005
4	A	-1	GLN	0	-0.045	-0.006	4.297	0.234	0.393	0.000	-0.011	-0.148	0.000
5	A	0	GLY	0	0.040	0.016	5.657	0.155	0.155	0.000	0.000	0.000	0.000
6	A	1	MET	0	-0.008	0.006	6.875	0.052	0.052	0.000	0.000	0.000	0.000
7	A	2	ASP	-1	-0.771	-0.841	9.749	0.295	0.295	0.000	0.000	0.000	0.000
8	A	3	LEU	0	-0.012	-0.014	11.073	-0.026	-0.026	0.000	0.000	0.000	0.000
9	A	4	THR	0	-0.041	-0.038	13.733	0.003	0.003	0.000	0.000	0.000	0.000
10	A	5	LYS	1	0.789	0.887	12.991	-0.221	-0.221	0.000	0.000	0.000	0.000
11	A	6	GLN	0	-0.061	-0.032	12.373	-0.034	-0.034	0.000	0.000	0.000	0.000
12	A	7	PHE	0	0.022	0.016	16.759	0.013	0.013	0.000	0.000	0.000	0.000
13	A	8	PRO	0	-0.034	0.004	17.275	-0.024	-0.024	0.000	0.000	0.000	0.000
14	A	9	ARG	1	0.792	0.828	17.240	0.231	0.231	0.000	0.000	0.000	0.000
15	A	10	SER	0	0.002	-0.008	21.254	0.005	0.005	0.000	0.000	0.000	0.000
16	A	11	PRO	0	-0.012	-0.006	24.892	-0.012	-0.012	0.000	0.000	0.000	0.000
17	A	12	VAL	0	0.006	-0.009	26.192	-0.005	-0.005	0.000	0.000	0.000	0.000
18	A	13	ASP	-1	-0.851	-0.902	23.779	-0.122	-0.122	0.000	0.000	0.000	0.000
19	A	14	ARG	1	0.813	0.877	25.342	0.063	0.063	0.000	0.000	0.000	0.000
20	A	15	LEU	0	-0.007	-0.001	21.563	-0.004	-0.004	0.000	0.000	0.000	0.000
21	A	16	GLY	0	0.041	0.014	25.702	0.001	0.001	0.000	0.000	0.000	0.000
22	A	17	GLY	0	-0.022	0.000	28.072	0.006	0.006	0.000	0.000	0.000	0.000
23	A	18	MET	0	-0.029	-0.011	26.772	0.005	0.005	0.000	0.000	0.000	0.000
24	A	19	ASH	0	-0.003	-0.045	27.305	-0.007	-0.007	0.000	0.000	0.000	0.000
25	A	20	HIS	0	0.011	0.026	21.965	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	21	LEU	0	-0.003	0.003	21.095	-0.008	-0.008	0.000	0.000	0.000	0.000
27	A	22	LYS	1	0.851	0.915	20.356	0.123	0.123	0.000	0.000	0.000	0.000
28	A	23	ARG	1	0.812	0.883	19.019	0.038	0.038	0.000	0.000	0.000	0.000
29	A	24	VAL	0	0.009	-0.008	18.242	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	25	ILE	0	0.003	0.001	15.591	-0.025	-0.025	0.000	0.000	0.000	0.000
31	A	26	ASP	-1	-0.777	-0.861	14.399	-0.257	-0.257	0.000	0.000	0.000	0.000
32	A	27	LYS	1	0.834	0.912	13.393	0.044	0.044	0.000	0.000	0.000	0.000
33	A	28	ALA	0	-0.008	0.004	13.137	0.016	0.016	0.000	0.000	0.000	0.000
34	A	29	ARG	1	0.820	0.910	9.992	0.497	0.497	0.000	0.000	0.000	0.000
35	A	30	ALA	0	0.027	0.015	8.522	-0.074	-0.074	0.000	0.000	0.000	0.000
36	A	31	HIS	0	0.001	-0.008	9.182	0.143	0.143	0.000	0.000	0.000	0.000
37	A	32	VAL	0	-0.066	-0.029	5.859	0.064	0.064	0.000	0.000	0.000	0.000
38	A	33	ALA	0	-0.054	-0.034	4.577	-0.085	-0.037	-0.001	-0.005	-0.041	0.000
39	A	34	GLY	0	0.009	0.032	5.573	0.555	0.555	0.000	0.000	0.000	0.000
40	A	35	THR	0	-0.087	-0.058	7.342	0.069	0.069	0.000	0.000	0.000	0.000
41	A	36	LEU	0	0.022	0.005	10.000	-0.086	-0.086	0.000	0.000	0.000	0.000
42	A	37	GLY	0	0.016	0.002	13.301	-0.031	-0.031	0.000	0.000	0.000	0.000
43	A	38	GLU	-1	-0.935	-0.962	15.791	0.093	0.093	0.000	0.000	0.000	0.000
44	A	39	TYR	0	-0.057	-0.044	16.621	-0.022	-0.022	0.000	0.000	0.000	0.000
45	A	40	THR	0	0.016	-0.009	17.206	0.023	0.023	0.000	0.000	0.000	0.000
46	A	41	TYR	0	-0.061	-0.049	15.035	-0.032	-0.032	0.000	0.000	0.000	0.000
47	A	42	ASN	0	-0.025	-0.026	17.038	0.006	0.006	0.000	0.000	0.000	0.000
48	A	43	OCS	-1	-0.836	-0.890	19.956	-0.015	-0.015	0.000	0.000	0.000	0.000
49	A	44	PRO	0	0.066	0.012	22.406	-0.013	-0.013	0.000	0.000	0.000	0.000
50	A	45	LEU	0	0.000	0.004	24.399	-0.007	-0.007	0.000	0.000	0.000	0.000
51	A	46	ASP	-1	-0.744	-0.866	19.308	-0.089	-0.089	0.000	0.000	0.000	0.000
52	A	47	GLN	0	-0.057	-0.026	22.790	-0.011	-0.011	0.000	0.000	0.000	0.000
53	A	48	ALA	0	0.003	0.008	24.838	-0.005	-0.005	0.000	0.000	0.000	0.000
54	A	49	PHE	0	0.004	0.001	22.530	-0.004	-0.004	0.000	0.000	0.000	0.000
55	A	50	PHE	0	-0.010	-0.030	18.582	-0.007	-0.007	0.000	0.000	0.000	0.000
56	A	51	SER	0	-0.001	0.007	24.716	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	52	PHE	0	-0.016	0.002	28.081	0.000	0.000	0.000	0.000	0.000	0.000
58	A	53	PHE	0	-0.011	-0.017	26.664	0.001	0.001	0.000	0.000	0.000	0.000
59	A	54	GLY	0	0.026	0.050	28.014	-0.006	-0.006	0.000	0.000	0.000	0.000
60	A	55	LEU	0	-0.062	-0.029	22.522	-0.011	-0.011	0.000	0.000	0.000	0.000
61	A	56	ASP	-1	-0.777	-0.875	19.976	-0.127	-0.127	0.000	0.000	0.000	0.000
62	A	57	HIS	0	0.051	0.016	17.812	-0.033	-0.033	0.000	0.000	0.000	0.000
63	A	58	GLU	-1	-0.863	-0.916	15.983	-0.114	-0.114	0.000	0.000	0.000	0.000
64	A	59	LYS	1	0.865	0.908	15.319	0.090	0.090	0.000	0.000	0.000	0.000
65	A	60	PHE	0	-0.011	-0.007	16.452	-0.050	-0.050	0.000	0.000	0.000	0.000
66	A	61	ALA	0	0.007	0.002	12.408	-0.048	-0.048	0.000	0.000	0.000	0.000
67	A	62	GLU	-1	-0.818	-0.903	10.669	-0.856	-0.856	0.000	0.000	0.000	0.000
68	A	63	ALA	0	-0.042	-0.008	12.525	-0.103	-0.103	0.000	0.000	0.000	0.000
69	A	64	VAL	0	0.047	-0.011	11.443	-0.035	-0.035	0.000	0.000	0.000	0.000
70	A	65	LYS	1	0.813	0.904	7.302	0.874	0.874	0.000	0.000	0.000	0.000
71	A	66	SER	0	-0.023	-0.011	9.471	-0.108	-0.108	0.000	0.000	0.000	0.000
72	A	67	ARG	1	0.834	0.928	12.012	0.514	0.514	0.000	0.000	0.000	0.000
73	A	68	PRO	0	0.055	0.023	11.063	0.023	0.023	0.000	0.000	0.000	0.000
74	A	69	GLN	0	0.030	0.025	12.858	0.064	0.064	0.000	0.000	0.000	0.000
75	A	70	ASP	-1	-0.761	-0.872	16.364	-0.241	-0.241	0.000	0.000	0.000	0.000
76	A	71	GLN	0	0.004	-0.009	19.018	0.014	0.014	0.000	0.000	0.000	0.000
77	A	72	ASP	-1	-0.849	-0.917	17.237	-0.345	-0.345	0.000	0.000	0.000	0.000
78	A	73	MET	0	-0.042	-0.002	16.220	-0.009	-0.009	0.000	0.000	0.000	0.000
79	A	74	LEU	0	-0.026	0.002	18.996	0.022	0.022	0.000	0.000	0.000	0.000
80	A	75	ALA	0	0.018	0.008	22.177	0.018	0.018	0.000	0.000	0.000	0.000
81	A	76	TRP	0	0.007	0.003	19.632	0.009	0.009	0.000	0.000	0.000	0.000
82	A	77	VAL	0	0.064	0.035	21.677	0.018	0.018	0.000	0.000	0.000	0.000
83	A	78	HIS	0	-0.021	-0.027	23.885	0.015	0.015	0.000	0.000	0.000	0.000
84	A	79	SER	0	-0.141	-0.089	23.959	0.011	0.011	0.000	0.000	0.000	0.000
85	A	80	GLN	0	-0.049	-0.020	22.315	0.010	0.010	0.000	0.000	0.000	0.000
86	A	81	SER	0	-0.002	-0.009	25.754	0.015	0.015	0.000	0.000	0.000	0.000
87	A	82	PRO	0	0.024	0.003	28.482	0.000	0.000	0.000	0.000	0.000	0.000
88	A	83	ARG	1	0.808	0.903	31.579	0.070	0.070	0.000	0.000	0.000	0.000
89	A	84	SER	0	0.017	-0.005	28.441	0.000	0.000	0.000	0.000	0.000	0.000
90	A	85	LYS	1	0.913	0.967	30.005	0.123	0.123	0.000	0.000	0.000	0.000
91	A	86	ASN	0	-0.009	0.003	32.508	0.005	0.005	0.000	0.000	0.000	0.000
92	A	87	PRO	0	0.063	0.020	34.870	0.001	0.001	0.000	0.000	0.000	0.000
93	A	88	LYS	1	0.893	0.926	35.926	0.061	0.061	0.000	0.000	0.000	0.000
94	A	89	GLU	-1	-0.824	-0.887	34.752	-0.059	-0.059	0.000	0.000	0.000	0.000
95	A	90	VAL	0	-0.004	0.005	30.910	0.001	0.001	0.000	0.000	0.000	0.000
96	A	91	GLU	-1	-0.881	-0.924	33.125	-0.062	-0.062	0.000	0.000	0.000	0.000
97	A	92	SER	0	-0.031	-0.013	35.787	0.005	0.005	0.000	0.000	0.000	0.000
98	A	93	PHE	0	0.018	0.010	27.678	0.003	0.003	0.000	0.000	0.000	0.000
99	A	94	ASN	0	0.010	-0.008	31.069	0.000	0.000	0.000	0.000	0.000	0.000
100	A	95	ARG	1	0.957	0.986	33.026	0.042	0.042	0.000	0.000	0.000	0.000
101	A	96	GLU	-1	-0.839	-0.902	34.427	-0.037	-0.037	0.000	0.000	0.000	0.000
102	A	97	TYR	0	-0.044	-0.052	25.537	0.006	0.006	0.000	0.000	0.000	0.000
103	A	98	GLU	-1	-0.804	-0.858	32.232	-0.055	-0.055	0.000	0.000	0.000	0.000
104	A	99	SER	0	-0.100	-0.043	33.840	0.005	0.005	0.000	0.000	0.000	0.000
105	A	100	ARG	1	0.852	0.922	30.883	0.043	0.043	0.000	0.000	0.000	0.000
106	A	101	SER	0	0.030	-0.003	34.546	0.001	0.001	0.000	0.000	0.000	0.000
107	A	102	PRO	0	-0.041	-0.020	35.603	0.000	0.000	0.000	0.000	0.000	0.000
108	A	103	ASP	-1	-0.828	-0.875	35.303	0.000	0.000	0.000	0.000	0.000	0.000
109	A	104	SER	0	0.025	0.000	37.801	0.001	0.001	0.000	0.000	0.000	0.000
110	A	105	PRO	0	0.016	-0.003	39.766	0.000	0.000	0.000	0.000	0.000	0.000
111	A	106	GLU	-1	-0.883	-0.925	37.389	0.023	0.023	0.000	0.000	0.000	0.000
112	A	107	LYS	1	0.890	0.912	33.442	-0.004	-0.004	0.000	0.000	0.000	0.000
113	A	108	TRP	0	-0.034	-0.029	36.399	0.000	0.000	0.000	0.000	0.000	0.000
114	A	109	ASP	-1	-0.840	-0.909	38.857	0.013	0.013	0.000	0.000	0.000	0.000
115	A	110	TYR	0	0.001	0.004	29.127	0.000	0.000	0.000	0.000	0.000	0.000
116	A	111	PHE	0	-0.028	-0.017	33.756	0.001	0.001	0.000	0.000	0.000	0.000
117	A	112	ARG	1	0.839	0.905	35.194	-0.008	-0.008	0.000	0.000	0.000	0.000
118	A	113	SER	0	0.035	0.037	35.765	0.001	0.001	0.000	0.000	0.000	0.000
119	A	114	VAL	0	0.001	0.007	30.369	0.002	0.002	0.000	0.000	0.000	0.000
120	A	115	ARG	1	0.842	0.919	33.440	-0.002	-0.002	0.000	0.000	0.000	0.000
121	A	116	ASP	-1	-0.846	-0.918	35.183	0.008	0.008	0.000	0.000	0.000	0.000
122	A	117	SER	0	-0.090	-0.050	33.124	0.002	0.002	0.000	0.000	0.000	0.000
123	A	118	LEU	0	-0.028	0.001	29.518	0.000	0.000	0.000	0.000	0.000	0.000
124	A	119	ALA	0	-0.016	-0.033	33.528	-0.002	-0.002	0.000	0.000	0.000	0.000
125	A	120	PRO	0	0.032	0.024	36.591	-0.003	-0.003	0.000	0.000	0.000	0.000
126	A	121	GLY	0	-0.044	-0.006	39.800	-0.001	-0.001	0.000	0.000	0.000	0.000
127	A	122	ARG	1	0.759	0.829	36.611	0.012	0.012	0.000	0.000	0.000	0.000
128	A	123	THR	0	0.008	-0.007	39.544	-0.001	-0.001	0.000	0.000	0.000	0.000
129	A	124	ASP	-1	-0.801	-0.860	40.023	-0.014	-0.014	0.000	0.000	0.000	0.000
130	A	125	ILE	0	-0.038	-0.005	34.766	-0.003	-0.003	0.000	0.000	0.000	0.000
131	A	126	THR	0	0.009	-0.018	37.905	0.002	0.002	0.000	0.000	0.000	0.000
132	A	127	THR	0	-0.009	0.007	34.801	0.001	0.001	0.000	0.000	0.000	0.000
133	A	128	TRP	0	0.062	0.015	30.152	0.001	0.001	0.000	0.000	0.000	0.000
134	A	129	VAL	0	0.007	0.001	28.857	0.001	0.001	0.000	0.000	0.000	0.000
135	A	130	LYS	1	0.966	0.983	29.701	0.031	0.031	0.000	0.000	0.000	0.000
136	A	131	LEU	0	0.026	0.021	30.575	0.000	0.000	0.000	0.000	0.000	0.000
137	A	132	LEU	0	0.022	0.014	24.925	0.001	0.001	0.000	0.000	0.000	0.000
138	A	133	ASP	-1	-0.779	-0.876	26.914	-0.052	-0.052	0.000	0.000	0.000	0.000
139	A	134	LEU	0	-0.056	-0.019	28.413	0.000	0.000	0.000	0.000	0.000	0.000
140	A	135	GLU	-1	-0.912	-0.956	25.831	0.021	0.021	0.000	0.000	0.000	0.000
141	A	136	GLU	-1	-0.771	-0.816	22.438	-0.035	-0.035	0.000	0.000	0.000	0.000
142	A	137	LYS	1	0.899	0.947	25.349	-0.020	-0.020	0.000	0.000	0.000	0.000
143	A	138	ARG	1	0.806	0.888	22.339	0.051	0.051	0.000	0.000	0.000	0.000
144	A	139	PRO	0	-0.010	-0.010	28.930	0.005	0.005	0.000	0.000	0.000	0.000
145	A	140	VAL	0	0.003	0.023	31.655	-0.003	-0.003	0.000	0.000	0.000	0.000

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