FMO DATABASE

FMODB ID: 7G2JK

Calculation Name: 5TDA- -Xray330

Preferred Name:

Target Type:

Ligand Name: zinc ion

ligand 3-letter code: ZN

PDB ID: 5TDA

Chain ID:

ChEMBL ID:

UniProt ID: Q8IWV8

Base Structure: X-ray

Registration Date: 2022-07-14

Reference: Kyohei Imai, Daichi Takimoto, Ryosuke Saito, Chiduru Watanabe, Kaori Fukuzawa, Kurita Noriyuki, FMO calculations for zinc metalloprotease:Fragmentation of amino-acid residues coordinated to zinc ion, CBI J., 22, pp. 21-25, 2022.

DOI: 10.1273/cbij.22.21

IFIE MAP

IFIE Diagram

Modeling method

Optimization	AMBER18
Restraint	Optimized only hydrogen in crystal water
Protonation	tleap only crystal water
Complement	No
Water	All crystal waters in PDB.
Procedure	Manual calculation

FMO calculation

FMO method	FMO2-MP2/6-31G
Fragmentation	Manual
Number of fragment	172
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-727701.187787
FMO2-HF: Nuclear repulsion	681773.246501
FMO2-HF: Total energy	-45927.941287
FMO2-MP2: Total energy	-45999.86913

3D Structure

Snapshot

Ligand structure

MOL

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.
-627.237	-610.373	96.618	-51.172	-62.315	0.445

Interactive mode: IFIE and PIEDA for fragment #65(:74:MOL)

Summations of interaction energy for fragment #65(:74:MOL)

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.
-627.237	-610.373	96.618	-51.172	-62.315	-0.445

Interaction energy analysis for fragmet #65(:74:MOL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.557 / q_NPA : 0.845

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.	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].
4	76	merge: :LE	-2	-0.718	-0.842	1.895	-113.323	-114.542	6.991	-3.113	-2.658	-0.044
8	8	PHE	0	0.005	0.037	3.517	4.491	5.445	0.017	-0.222	-0.749	0.000
14	14	THR	0	0.040	0.049	2.542	-3.171	-2.874	0.390	-0.146	-0.541	-0.001
16	16	SER	0	0.005	0.031	4.581	-4.934	-4.920	-0.001	-0.004	-0.009	0.000
22	23	ASP	-1	-0.775	-0.850	4.342	-68.180	-67.865	0.000	-0.112	-0.203	0.000
24	25	THR	0	-0.046	0.004	2.443	-10.854	-6.735	2.209	-2.244	-4.085	-0.025
25	26	CYS	0	-0.001	0.018	2.120	-49.305	-45.079	6.202	-4.263	-6.165	-0.058
26	27	VAL	0	-0.054	-0.036	2.109	19.239	19.830	4.609	-0.854	-4.346	-0.003
27	28	LEU	0	0.002	0.015	4.699	-8.837	-8.733	-0.001	-0.021	-0.083	0.000
41	46	THR	0	-0.047	0.005	4.119	2.053	2.273	0.000	-0.029	-0.191	0.000
46	51	GLY	0	0.023	0.034	3.514	5.071	6.128	0.024	-0.286	-0.796	0.000
47	52	GLY	0	0.049	0.033	2.552	-6.184	-3.852	2.852	-2.018	-3.167	0.007
48	53	PHE	0	-0.031	-0.028	2.162	-7.599	-7.401	9.146	-1.534	-7.810	-0.012
49	55	ASP	-1	-0.730	-0.897	1.840	-207.836	-209.968	21.736	-10.056	-9.548	-0.142
51	58	ASP	-1	-0.907	-0.944	2.006	-123.920	-122.729	8.215	-4.999	-4.408	-0.088
52	59	THR	0	-0.003	-0.031	4.851	-0.770	-0.731	-0.001	-0.003	-0.036	0.000
53	60	GLU	-1	-0.867	-0.851	4.114	-36.293	-36.169	-0.001	-0.013	-0.111	0.000
54	61	ALA	0	0.025	0.014	2.783	-6.308	-5.601	0.741	-0.449	-0.999	0.002
55	62	TRP	0	-0.032	-0.025	3.955	6.548	6.772	0.013	-0.019	-0.217	0.000
87	99	WAT	0	-0.006	-0.022	2.201	-14.471	-12.172	2.920	-2.744	-2.476	-0.033
89	101	WAT	0	0.024	0.005	1.945	-20.623	-23.183	6.271	-2.163	-1.548	-0.028
92	104	WAT	0	0.008	0.026	2.691	-4.916	-3.872	1.406	-1.154	-1.297	0.011
93	105	WAT	0	0.039	0.024	2.473	-0.232	0.619	0.597	-0.787	-0.660	-0.006
96	108	WAT	0	-0.007	-0.022	2.598	-1.495	-0.849	0.603	-0.599	-0.650	-0.006
104	116	WAT	0	-0.001	-0.003	3.251	-0.319	0.496	0.050	-0.466	-0.400	-0.002
111	123	WAT	0	-0.013	-0.027	2.527	-0.576	0.429	0.661	-0.866	-0.799	-0.006
116	128	WAT	0	-0.086	-0.086	4.787	4.261	4.306	0.000	-0.002	-0.043	0.000
125	137	WAT	0	-0.005	-0.007	3.502	-3.223	-2.678	0.039	-0.321	-0.263	-0.001
128	140	WAT	0	0.013	-0.011	3.113	1.478	1.754	0.014	-0.113	-0.178	0.000
157	169	WAT	0	0.033	0.022	2.460	-3.419	-2.694	0.560	-0.552	-0.733	-0.004
168	180	WAT	0	0.017	0.002	1.683	-11.522	-13.856	10.325	-4.843	-3.148	-0.009
169	181	WAT	0	-0.018	-0.013	1.904	-19.086	-19.824	6.658	-3.871	-2.049	0.028
170	182	WAT	0	-0.023	-0.024	2.171	-11.622	-12.253	3.173	-1.392	-1.149	-0.021
171	183	WAT	0	-0.022	-0.042	3.850	-3.701	-3.187	0.056	-0.299	-0.272	0.001
172	184	WAT	0	-0.008	-0.002	2.600	-3.398	-2.397	0.144	-0.615	-0.528	-0.005
1	1	ACE	1	-1.460	-1.517	16.907	23.197	23.197	0.000	0.000	0.000	0.000
2	2	SER	-1	0.097	0.047	15.865	-22.107	-22.107	0.000	0.000	0.000	0.000
3	3	LEU	0	0.450	0.600	9.668	-0.540	-0.540	0.000	0.000	0.000	0.000
5	5	GLY	0	0.006	0.002	7.846	3.080	3.080	0.000	0.000	0.000	0.000
6	6	ARG	1	0.865	0.950	8.338	32.116	32.116	0.000	0.000	0.000	0.000
7	7	VAL	0	-0.024	-0.004	6.258	-7.216	-7.216	0.000	0.000	0.000	0.000
9	9	LYS	1	0.944	0.976	7.231	24.207	24.207	0.000	0.000	0.000	0.000
10	10	VAL	0	0.036	0.008	8.964	-0.769	-0.769	0.000	0.000	0.000	0.000
11	11	GLY	0	0.040	0.033	9.989	0.400	0.400	0.000	0.000	0.000	0.000
12	12	GLU	-1	-0.835	-0.831	8.469	-29.054	-29.054	0.000	0.000	0.000	0.000
13	13	PRO	0	-0.010	-0.014	7.868	-1.191	-1.191	0.000	0.000	0.000	0.000
15	15	TYR	0	0.026	0.005	5.681	5.017	5.017	0.000	0.000	0.000	0.000
17	77	merge: :SE	0	0.131	0.079	6.562	7.529	7.529	0.000	0.000	0.000	0.000
18	18	ARG	1	0.873	0.923	9.448	19.782	19.782	0.000	0.000	0.000	0.000
19	19	ASP	-1	-0.777	-0.888	10.564	-21.955	-21.955	0.000	0.000	0.000	0.000
20	21	ALA	0	-0.037	0.002	7.193	-2.924	-2.924	0.000	0.000	0.000	0.000
21	22	VAL	0	0.055	0.039	5.053	6.814	6.814	0.000	0.000	0.000	0.000
23	24	PRO	0	-0.047	-0.040	5.178	-5.521	-5.521	0.000	0.000	0.000	0.000
28	30	MET	0	-0.042	-0.035	8.896	1.520	1.520	0.000	0.000	0.000	0.000
29	31	GLU	-1	-0.790	-0.913	11.359	-24.191	-24.191	0.000	0.000	0.000	0.000
30	33	PHE	0	-0.023	0.002	10.266	0.845	0.845	0.000	0.000	0.000	0.000
31	34	LEU	0	0.013	-0.013	12.232	1.736	1.736	0.000	0.000	0.000	0.000
32	35	GLY	0	0.011	0.020	15.340	2.073	2.073	0.000	0.000	0.000	0.000
33	36	SER	0	-0.027	0.012	13.696	-0.355	-0.355	0.000	0.000	0.000	0.000
34	37	ILE	0	0.035	0.000	15.637	1.532	1.532	0.000	0.000	0.000	0.000
35	39	ARG	1	0.889	0.985	14.639	20.287	20.287	0.000	0.000	0.000	0.000
36	40	ASP	-1	-0.777	-0.781	15.990	-17.070	-17.070	0.000	0.000	0.000	0.000
37	42	ARG	1	0.909	0.966	13.909	21.456	21.456	0.000	0.000	0.000	0.000
38	43	TYR	0	-0.008	0.022	10.212	-1.683	-1.683	0.000	0.000	0.000	0.000
39	44	ARG	1	0.843	0.937	5.269	25.372	25.372	0.000	0.000	0.000	0.000
40	45	MET	0	0.019	0.038	6.877	-2.787	-2.787	0.000	0.000	0.000	0.000
42	47	THR	0	0.049	0.012	6.578	-1.320	-1.320	0.000	0.000	0.000	0.000
43	48	SER	0	0.002	0.034	4.862	2.622	2.622	0.000	0.000	0.000	0.000
44	49	GLY	0	0.053	-0.004	5.924	1.701	1.701	0.000	0.000	0.000	0.000
45	50	GLY	0	-0.023	0.015	5.891	2.592	2.592	0.000	0.000	0.000	0.000
50	57	GLY	0	0.045	0.003	7.360	0.310	0.310	0.000	0.000	0.000	0.000
56	63	LYS	1	0.870	0.973	7.768	33.973	33.973	0.000	0.000	0.000	0.000
57	64	GLU	-1	-0.735	-0.826	10.709	-20.264	-20.264	0.000	0.000	0.000	0.000
58	65	GLY	0	0.006	0.001	11.782	-2.193	-2.193	0.000	0.000	0.000	0.000
59	66	PRO	0	-0.006	0.006	8.916	-2.305	-2.305	0.000	0.000	0.000	0.000
60	67	TYR	0	0.046	0.039	8.695	-5.039	-5.039	0.000	0.000	0.000	0.000
61	69	GLN	0	0.056	0.055	14.105	0.145	0.145	0.000	0.000	0.000	0.000
62	70	LYS	1	0.903	0.958	15.733	22.864	22.864	0.000	0.000	0.000	0.000
63	72	GLU	-1	-0.889	-0.883	14.147	-22.545	-22.545	0.000	0.000	0.000	0.000
64	73	NME	0	-0.036	0.002	15.617	1.027	1.027	0.000	0.000	0.000	0.000
66	78	WAT	0	-0.095	-0.127	19.917	0.250	0.250	0.000	0.000	0.000	0.000
67	79	WAT	0	0.026	0.010	11.751	-0.638	-0.638	0.000	0.000	0.000	0.000
68	80	WAT	0	-0.057	-0.089	8.236	-1.168	-1.168	0.000	0.000	0.000	0.000
69	81	WAT	0	0.120	0.101	6.708	2.172	2.172	0.000	0.000	0.000	0.000
70	82	WAT	0	-0.063	-0.070	17.931	0.107	0.107	0.000	0.000	0.000	0.000
71	83	WAT	0	-0.049	-0.074	10.448	0.191	0.191	0.000	0.000	0.000	0.000
72	84	WAT	0	-0.053	-0.035	18.255	-0.296	-0.296	0.000	0.000	0.000	0.000
73	85	WAT	0	0.022	0.041	12.649	-0.451	-0.451	0.000	0.000	0.000	0.000
74	86	WAT	0	-0.021	0.000	19.422	0.069	0.069	0.000	0.000	0.000	0.000
75	87	WAT	0	-0.067	-0.061	20.581	0.034	0.034	0.000	0.000	0.000	0.000
76	88	WAT	0	0.012	-0.022	9.285	0.561	0.561	0.000	0.000	0.000	0.000
77	89	WAT	0	-0.047	-0.047	15.668	-0.473	-0.473	0.000	0.000	0.000	0.000
78	90	WAT	0	-0.002	-0.016	21.060	0.086	0.086	0.000	0.000	0.000	0.000
79	91	WAT	0	-0.057	-0.043	14.866	-1.013	-1.013	0.000	0.000	0.000	0.000
80	92	WAT	0	-0.003	-0.015	10.473	-0.205	-0.205	0.000	0.000	0.000	0.000
81	93	WAT	0	-0.020	-0.019	16.380	0.336	0.336	0.000	0.000	0.000	0.000
82	94	WAT	0	-0.041	-0.045	21.365	0.132	0.132	0.000	0.000	0.000	0.000
83	95	WAT	0	0.000	0.029	8.443	2.911	2.911	0.000	0.000	0.000	0.000
84	96	WAT	0	-0.037	-0.036	16.388	0.589	0.589	0.000	0.000	0.000	0.000
85	97	WAT	0	-0.027	-0.015	17.112	0.085	0.085	0.000	0.000	0.000	0.000
86	98	WAT	0	-0.034	-0.034	5.446	2.379	2.379	0.000	0.000	0.000	0.000
88	100	WAT	0	-0.024	-0.020	7.109	-0.051	-0.051	0.000	0.000	0.000	0.000
90	102	WAT	0	-0.042	-0.032	6.406	-0.243	-0.243	0.000	0.000	0.000	0.000
91	103	WAT	0	-0.060	-0.051	8.122	0.661	0.661	0.000	0.000	0.000	0.000
94	106	WAT	0	-0.006	-0.006	8.174	1.558	1.558	0.000	0.000	0.000	0.000
95	107	WAT	0	-0.006	-0.023	8.525	1.037	1.037	0.000	0.000	0.000	0.000
97	109	WAT	0	-0.001	-0.008	14.034	-0.114	-0.114	0.000	0.000	0.000	0.000
98	110	WAT	0	-0.018	-0.029	10.929	1.135	1.135	0.000	0.000	0.000	0.000
99	111	WAT	0	-0.002	-0.006	6.396	4.179	4.179	0.000	0.000	0.000	0.000
100	112	WAT	0	-0.031	-0.025	7.565	0.410	0.410	0.000	0.000	0.000	0.000
101	113	WAT	0	-0.028	-0.048	14.931	0.023	0.023	0.000	0.000	0.000	0.000
102	114	WAT	0	-0.002	-0.019	15.822	-0.780	-0.780	0.000	0.000	0.000	0.000
103	115	WAT	0	-0.006	-0.007	20.478	-0.538	-0.538	0.000	0.000	0.000	0.000
105	117	WAT	0	-0.063	-0.052	9.320	-0.114	-0.114	0.000	0.000	0.000	0.000
106	118	WAT	0	-0.008	0.001	9.664	0.456	0.456	0.000	0.000	0.000	0.000
107	119	WAT	0	-0.020	-0.021	12.704	-1.335	-1.335	0.000	0.000	0.000	0.000
108	120	WAT	0	-0.006	-0.018	11.089	0.428	0.428	0.000	0.000	0.000	0.000
109	121	WAT	0	0.022	-0.011	9.215	0.984	0.984	0.000	0.000	0.000	0.000
110	122	WAT	0	0.014	0.017	8.739	0.956	0.956	0.000	0.000	0.000	0.000
112	124	WAT	0	-0.032	-0.023	13.967	0.909	0.909	0.000	0.000	0.000	0.000
113	125	WAT	0	0.010	0.020	14.355	0.530	0.530	0.000	0.000	0.000	0.000
114	126	WAT	0	-0.009	0.002	17.412	0.433	0.433	0.000	0.000	0.000	0.000
115	127	WAT	0	0.018	-0.016	12.383	-1.316	-1.316	0.000	0.000	0.000	0.000
117	129	WAT	0	-0.025	-0.040	18.476	-0.535	-0.535	0.000	0.000	0.000	0.000
118	130	WAT	0	0.010	0.010	8.910	1.600	1.600	0.000	0.000	0.000	0.000
119	131	WAT	0	0.007	0.013	18.961	0.617	0.617	0.000	0.000	0.000	0.000
120	132	WAT	0	-0.008	-0.008	14.137	-0.173	-0.173	0.000	0.000	0.000	0.000
121	133	WAT	0	0.037	0.023	6.749	2.100	2.100	0.000	0.000	0.000	0.000
122	134	WAT	0	0.017	0.007	10.467	-0.896	-0.896	0.000	0.000	0.000	0.000
123	135	WAT	0	-0.034	-0.034	14.262	-0.653	-0.653	0.000	0.000	0.000	0.000
124	136	WAT	0	0.008	0.001	16.257	-0.322	-0.322	0.000	0.000	0.000	0.000
126	138	WAT	0	0.001	-0.024	18.721	-0.675	-0.675	0.000	0.000	0.000	0.000
127	139	WAT	0	0.013	0.004	8.163	-0.965	-0.965	0.000	0.000	0.000	0.000
129	141	WAT	0	-0.058	-0.034	5.866	1.979	1.979	0.000	0.000	0.000	0.000
130	142	WAT	0	0.026	0.013	7.533	-1.178	-1.178	0.000	0.000	0.000	0.000
131	143	WAT	0	0.039	0.016	11.249	-0.638	-0.638	0.000	0.000	0.000	0.000
132	144	WAT	0	-0.038	-0.025	16.598	-0.356	-0.356	0.000	0.000	0.000	0.000
133	145	WAT	0	-0.017	-0.037	19.343	0.063	0.063	0.000	0.000	0.000	0.000
134	146	WAT	0	-0.095	-0.074	13.538	-0.191	-0.191	0.000	0.000	0.000	0.000
135	147	WAT	0	-0.042	-0.042	17.937	0.092	0.092	0.000	0.000	0.000	0.000
136	148	WAT	0	0.006	-0.016	13.632	-0.017	-0.017	0.000	0.000	0.000	0.000
137	149	WAT	0	-0.039	-0.078	12.971	-0.739	-0.739	0.000	0.000	0.000	0.000
138	150	WAT	0	-0.036	-0.034	20.663	0.237	0.237	0.000	0.000	0.000	0.000
139	151	WAT	0	-0.004	-0.034	10.339	0.109	0.109	0.000	0.000	0.000	0.000
140	152	WAT	0	-0.004	0.004	12.608	0.650	0.650	0.000	0.000	0.000	0.000
141	153	WAT	0	-0.042	-0.035	18.426	0.123	0.123	0.000	0.000	0.000	0.000
142	154	WAT	0	0.037	0.079	13.590	-0.004	-0.004	0.000	0.000	0.000	0.000
143	155	WAT	0	0.027	0.018	16.924	-0.468	-0.468	0.000	0.000	0.000	0.000
144	156	WAT	0	-0.145	-0.132	8.501	-0.525	-0.525	0.000	0.000	0.000	0.000
145	157	WAT	0	-0.003	-0.025	11.182	0.254	0.254	0.000	0.000	0.000	0.000
146	158	WAT	0	0.010	0.021	16.652	-0.170	-0.170	0.000	0.000	0.000	0.000
147	159	WAT	0	0.034	0.027	10.479	-0.650	-0.650	0.000	0.000	0.000	0.000
148	160	WAT	0	-0.024	-0.013	21.521	-0.229	-0.229	0.000	0.000	0.000	0.000
149	161	WAT	0	0.041	0.046	20.948	-0.633	-0.633	0.000	0.000	0.000	0.000
150	162	WAT	0	-0.012	0.007	12.181	0.835	0.835	0.000	0.000	0.000	0.000
151	163	WAT	0	-0.027	-0.017	15.574	-0.523	-0.523	0.000	0.000	0.000	0.000
152	164	WAT	0	-0.059	-0.078	10.340	0.414	0.414	0.000	0.000	0.000	0.000
153	165	WAT	0	0.025	0.022	12.210	-0.680	-0.680	0.000	0.000	0.000	0.000
154	166	WAT	0	0.009	0.027	21.250	-0.326	-0.326	0.000	0.000	0.000	0.000
155	167	WAT	0	0.040	0.061	5.647	-6.317	-6.317	0.000	0.000	0.000	0.000
156	168	WAT	0	0.015	0.020	14.268	-0.290	-0.290	0.000	0.000	0.000	0.000
158	170	WAT	0	-0.031	-0.038	13.466	-0.563	-0.563	0.000	0.000	0.000	0.000
159	171	WAT	0	0.044	0.037	12.358	0.371	0.371	0.000	0.000	0.000	0.000
160	172	WAT	0	0.030	0.033	11.253	-0.876	-0.876	0.000	0.000	0.000	0.000
161	173	WAT	0	-0.032	-0.030	17.541	-0.038	-0.038	0.000	0.000	0.000	0.000
162	174	WAT	0	-0.037	-0.022	10.400	1.430	1.430	0.000	0.000	0.000	0.000
163	175	WAT	0	0.013	-0.023	14.068	0.152	0.152	0.000	0.000	0.000	0.000
164	176	WAT	0	-0.002	-0.016	14.503	-0.289	-0.289	0.000	0.000	0.000	0.000
165	177	WAT	0	-0.038	-0.021	23.305	0.170	0.170	0.000	0.000	0.000	0.000
166	178	WAT	0	-0.025	-0.024	21.004	0.545	0.545	0.000	0.000	0.000	0.000
167	179	WAT	0	0.014	0.006	7.161	-2.117	-2.117	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #65(:74:MOL)