FMO DATABASE

FMODB ID: 4J83N

Calculation Name: 2YVQ-A-Xray372

Preferred Name: Carbamoyl-phosphate synthase [ammonia], mitochondrial

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2YVQ

Chain ID: A

ChEMBL ID: CHEMBL2362990

UniProt ID: P31327

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	139
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1223012.260192
FMO2-HF: Nuclear repulsion	1170439.172137
FMO2-HF: Total energy	-52573.088055
FMO2-MP2: Total energy	-52730.546243

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:5:SER)

Summations of interaction energy for fragment #1(A:5:SER)

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.
-7.324	-5.516	3.845	-2.312	-3.341	0.013

Interaction energy analysis for fragmet #1(A:5:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.023 / q_NPA : -0.011

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	7	GLY	0	0.059	0.046	3.625	0.081	2.659	-0.005	-1.384	-1.189	0.005
4	A	1343	HIS	0	0.004	-0.020	5.020	-0.783	-0.783	0.000	0.000	0.000	0.000
5	A	1344	THR	0	0.017	0.001	9.072	0.065	0.065	0.000	0.000	0.000	0.000
6	A	1345	ALA	0	0.000	0.017	11.068	-0.011	-0.011	0.000	0.000	0.000	0.000
7	A	1346	PHE	0	0.060	0.028	8.973	-0.034	-0.034	0.000	0.000	0.000	0.000
8	A	1347	LEU	0	0.022	-0.001	11.090	-0.035	-0.035	0.000	0.000	0.000	0.000
9	A	1348	LYS	1	0.930	0.957	13.480	-0.009	-0.009	0.000	0.000	0.000	0.000
10	A	1349	ALA	0	0.023	0.021	13.811	-0.006	-0.006	0.000	0.000	0.000	0.000
11	A	1350	MET	0	-0.065	-0.032	13.124	-0.014	-0.014	0.000	0.000	0.000	0.000
12	A	1351	LEU	0	-0.021	0.005	16.156	-0.034	-0.034	0.000	0.000	0.000	0.000
13	A	1352	SER	0	-0.041	-0.011	18.825	0.008	0.008	0.000	0.000	0.000	0.000
14	A	1353	THR	0	0.059	0.024	20.644	-0.008	-0.008	0.000	0.000	0.000	0.000
15	A	1354	GLY	0	0.008	-0.026	21.337	-0.006	-0.006	0.000	0.000	0.000	0.000
16	A	1355	PHE	0	-0.001	-0.010	22.349	0.017	0.017	0.000	0.000	0.000	0.000
17	A	1356	LYS	1	0.835	0.967	18.965	-0.226	-0.226	0.000	0.000	0.000	0.000
18	A	1357	ILE	0	0.060	0.021	23.366	0.025	0.025	0.000	0.000	0.000	0.000
19	A	1358	PRO	0	-0.072	-0.026	21.660	-0.010	-0.010	0.000	0.000	0.000	0.000
20	A	1359	GLN	0	0.006	-0.005	24.035	-0.019	-0.019	0.000	0.000	0.000	0.000
21	A	1360	LYS	1	0.904	0.964	23.347	-0.176	-0.176	0.000	0.000	0.000	0.000
22	A	1361	GLY	0	0.044	0.027	23.608	-0.011	-0.011	0.000	0.000	0.000	0.000
23	A	1362	ILE	0	0.007	0.006	22.524	0.029	0.029	0.000	0.000	0.000	0.000
24	A	1363	LEU	0	-0.042	-0.019	17.915	-0.007	-0.007	0.000	0.000	0.000	0.000
25	A	1364	ILE	0	0.025	0.003	21.641	0.022	0.022	0.000	0.000	0.000	0.000
26	A	1365	GLY	0	-0.022	-0.008	21.426	0.000	0.000	0.000	0.000	0.000	0.000
27	A	1366	ILE	0	-0.005	-0.009	22.480	0.007	0.007	0.000	0.000	0.000	0.000
28	A	1367	GLN	0	0.016	0.009	24.846	0.018	0.018	0.000	0.000	0.000	0.000
29	A	1368	GLN	0	0.034	0.015	26.529	-0.012	-0.012	0.000	0.000	0.000	0.000
30	A	1369	SER	0	0.027	0.004	29.782	-0.006	-0.006	0.000	0.000	0.000	0.000
31	A	1370	PHE	0	-0.043	-0.020	28.162	-0.012	-0.012	0.000	0.000	0.000	0.000
32	A	1371	ARG	1	0.931	0.976	29.717	-0.238	-0.238	0.000	0.000	0.000	0.000
33	A	1372	PRO	0	0.015	0.009	32.032	-0.003	-0.003	0.000	0.000	0.000	0.000
34	A	1373	ARG	1	0.898	0.935	32.367	-0.182	-0.182	0.000	0.000	0.000	0.000
35	A	1374	PHE	0	0.013	0.003	26.622	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	1375	LEU	0	0.056	0.040	31.325	0.003	0.003	0.000	0.000	0.000	0.000
37	A	1376	GLY	0	0.047	0.026	33.784	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	1377	VAL	0	0.009	0.000	28.987	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	1378	ALA	0	-0.046	-0.023	30.208	0.004	0.004	0.000	0.000	0.000	0.000
40	A	1379	GLU	-1	-0.920	-0.965	31.169	0.137	0.137	0.000	0.000	0.000	0.000
41	A	1380	GLN	0	0.050	0.031	33.211	0.001	0.001	0.000	0.000	0.000	0.000
42	A	1381	LEU	0	-0.015	-0.012	27.155	0.002	0.002	0.000	0.000	0.000	0.000
43	A	1382	HIS	0	-0.021	-0.011	31.077	-0.009	-0.009	0.000	0.000	0.000	0.000
44	A	1383	ASN	0	-0.091	-0.060	32.780	-0.006	-0.006	0.000	0.000	0.000	0.000
45	A	1384	GLU	-1	-0.860	-0.927	32.379	0.118	0.118	0.000	0.000	0.000	0.000
46	A	1385	GLY	0	-0.054	-0.014	32.759	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	1386	PHE	0	-0.053	-0.005	26.241	0.009	0.009	0.000	0.000	0.000	0.000
48	A	1387	LYS	1	0.920	0.969	27.173	-0.196	-0.196	0.000	0.000	0.000	0.000
49	A	1388	LEU	0	0.007	0.002	26.569	0.024	0.024	0.000	0.000	0.000	0.000
50	A	1389	PHE	0	0.022	0.001	23.141	-0.012	-0.012	0.000	0.000	0.000	0.000
51	A	1390	ALA	0	0.047	0.022	24.036	0.023	0.023	0.000	0.000	0.000	0.000
52	A	1391	THR	0	0.003	0.005	22.227	-0.018	-0.018	0.000	0.000	0.000	0.000
53	A	1392	GLU	-1	-0.871	-0.939	24.758	0.209	0.209	0.000	0.000	0.000	0.000
54	A	1393	ALA	0	0.030	0.018	28.128	-0.011	-0.011	0.000	0.000	0.000	0.000
55	A	1394	THR	0	-0.053	-0.035	26.714	-0.020	-0.020	0.000	0.000	0.000	0.000
56	A	1395	SER	0	0.040	0.022	28.143	-0.009	-0.009	0.000	0.000	0.000	0.000
57	A	1396	ASP	-1	-0.872	-0.928	29.847	0.184	0.184	0.000	0.000	0.000	0.000
58	A	1397	TRP	0	-0.048	-0.028	30.073	-0.005	-0.005	0.000	0.000	0.000	0.000
59	A	1398	LEU	0	-0.008	0.004	28.932	-0.008	-0.008	0.000	0.000	0.000	0.000
60	A	1399	ASN	0	0.033	0.011	32.351	-0.017	-0.017	0.000	0.000	0.000	0.000
61	A	1400	ALA	0	-0.050	-0.023	35.437	-0.010	-0.010	0.000	0.000	0.000	0.000
62	A	1401	ASN	0	-0.136	-0.088	36.559	-0.014	-0.014	0.000	0.000	0.000	0.000
63	A	1402	ASN	0	0.000	0.005	38.248	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	1403	VAL	0	0.035	0.028	32.604	0.000	0.000	0.000	0.000	0.000	0.000
65	A	1404	PRO	0	-0.015	-0.011	33.662	0.009	0.009	0.000	0.000	0.000	0.000
66	A	1405	ALA	0	-0.024	-0.013	29.108	0.012	0.012	0.000	0.000	0.000	0.000
67	A	1406	THR	0	-0.050	-0.017	27.097	-0.016	-0.016	0.000	0.000	0.000	0.000
68	A	1407	PRO	0	0.044	0.024	26.671	0.025	0.025	0.000	0.000	0.000	0.000
69	A	1408	VAL	0	-0.035	-0.021	21.480	0.001	0.001	0.000	0.000	0.000	0.000
70	A	1409	ALA	0	0.024	-0.001	21.950	-0.004	-0.004	0.000	0.000	0.000	0.000
71	A	1410	TRP	0	-0.011	-0.009	19.465	0.046	0.046	0.000	0.000	0.000	0.000
72	A	1411	PRO	0	0.001	-0.023	15.191	-0.025	-0.025	0.000	0.000	0.000	0.000
73	A	1412	SER	0	-0.064	-0.054	17.359	-0.047	-0.047	0.000	0.000	0.000	0.000
74	A	1413	GLN	0	-0.058	-0.029	18.762	-0.028	-0.028	0.000	0.000	0.000	0.000
75	A	1414	GLU	-1	-0.816	-0.869	17.012	0.496	0.496	0.000	0.000	0.000	0.000
76	A	1415	GLY	0	0.030	0.015	21.353	-0.008	-0.008	0.000	0.000	0.000	0.000
77	A	1416	GLN	0	-0.015	-0.006	24.058	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	1417	ASN	0	-0.030	-0.017	25.483	-0.030	-0.030	0.000	0.000	0.000	0.000
79	A	1418	PRO	0	0.062	0.035	27.628	0.005	0.005	0.000	0.000	0.000	0.000
80	A	1419	SER	0	-0.033	-0.015	29.077	0.005	0.005	0.000	0.000	0.000	0.000
81	A	1420	LEU	0	-0.025	-0.010	25.013	0.012	0.012	0.000	0.000	0.000	0.000
82	A	1421	SER	0	0.027	0.016	22.550	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	1422	SER	0	-0.074	-0.041	17.278	0.030	0.030	0.000	0.000	0.000	0.000
84	A	1423	ILE	0	0.137	0.051	15.636	-0.013	-0.013	0.000	0.000	0.000	0.000
85	A	1424	ARG	1	0.864	0.910	12.711	-0.584	-0.584	0.000	0.000	0.000	0.000
86	A	1425	LYS	1	0.898	0.950	14.652	-0.351	-0.351	0.000	0.000	0.000	0.000
87	A	1426	LEU	0	0.091	0.055	17.441	-0.025	-0.025	0.000	0.000	0.000	0.000
88	A	1427	ILE	0	0.000	0.005	13.482	-0.012	-0.012	0.000	0.000	0.000	0.000
89	A	1428	ARG	1	0.873	0.934	13.956	-0.330	-0.330	0.000	0.000	0.000	0.000
90	A	1429	ASP	-1	-0.939	-0.954	15.510	0.208	0.208	0.000	0.000	0.000	0.000
91	A	1430	GLY	0	0.032	0.029	18.286	-0.031	-0.031	0.000	0.000	0.000	0.000
92	A	1431	SER	0	-0.055	-0.053	19.994	-0.023	-0.023	0.000	0.000	0.000	0.000
93	A	1432	ILE	0	-0.073	-0.033	18.450	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	1433	ASP	-1	-0.797	-0.899	18.579	0.295	0.295	0.000	0.000	0.000	0.000
95	A	1434	LEU	0	0.029	0.001	19.169	0.006	0.006	0.000	0.000	0.000	0.000
96	A	1435	VAL	0	-0.039	-0.008	15.995	0.003	0.003	0.000	0.000	0.000	0.000
97	A	1436	ILE	0	0.037	0.037	18.790	0.017	0.017	0.000	0.000	0.000	0.000
98	A	1437	ASN	0	-0.009	-0.016	17.432	0.034	0.034	0.000	0.000	0.000	0.000
99	A	1438	LEU	0	-0.001	0.004	19.197	0.028	0.028	0.000	0.000	0.000	0.000
100	A	1439	PRO	0	-0.043	-0.025	21.056	0.025	0.025	0.000	0.000	0.000	0.000
101	A	1440	ASN	0	0.043	0.008	21.597	-0.052	-0.052	0.000	0.000	0.000	0.000
102	A	1441	ASN	0	-0.022	-0.007	22.197	0.033	0.033	0.000	0.000	0.000	0.000
103	A	1442	ASN	0	0.031	0.025	24.421	-0.008	-0.008	0.000	0.000	0.000	0.000
104	A	1443	THR	0	0.059	0.016	22.549	0.036	0.036	0.000	0.000	0.000	0.000
105	A	1444	LYS	1	0.943	0.983	21.659	-0.266	-0.266	0.000	0.000	0.000	0.000
106	A	1445	PHE	0	-0.001	-0.008	20.358	0.003	0.003	0.000	0.000	0.000	0.000
107	A	1446	VAL	0	0.018	0.023	17.145	0.060	0.060	0.000	0.000	0.000	0.000
108	A	1447	HIS	0	0.058	0.021	11.236	0.062	0.062	0.000	0.000	0.000	0.000
109	A	1448	ASP	-1	-0.734	-0.849	14.179	0.722	0.722	0.000	0.000	0.000	0.000
110	A	1449	ASN	0	0.021	0.004	15.350	0.064	0.064	0.000	0.000	0.000	0.000
111	A	1450	TYR	0	-0.022	0.009	7.681	0.234	0.234	0.000	0.000	0.000	0.000
112	A	1451	VAL	0	0.021	-0.006	10.644	0.246	0.246	0.000	0.000	0.000	0.000
113	A	1452	ILE	0	-0.021	0.006	11.282	0.118	0.118	0.000	0.000	0.000	0.000
114	A	1453	ARG	1	0.868	0.922	12.460	-0.733	-0.733	0.000	0.000	0.000	0.000
115	A	1454	ARG	1	0.882	0.939	2.374	-11.135	-12.004	3.851	-0.923	-2.059	0.008
116	A	1455	THR	0	-0.005	-0.020	8.114	0.298	0.298	0.000	0.000	0.000	0.000
117	A	1456	ALA	0	-0.006	-0.002	9.867	-0.097	-0.097	0.000	0.000	0.000	0.000
118	A	1457	VAL	0	0.007	0.002	8.066	-0.116	-0.116	0.000	0.000	0.000	0.000
119	A	1458	ASP	-1	-0.850	-0.908	5.052	5.413	5.512	-0.001	-0.005	-0.093	0.000
120	A	1459	SER	0	-0.104	-0.067	7.417	-0.520	-0.520	0.000	0.000	0.000	0.000
121	A	1460	GLY	0	-0.021	-0.014	10.657	-0.203	-0.203	0.000	0.000	0.000	0.000
122	A	1461	ILE	0	-0.060	-0.007	12.657	-0.129	-0.129	0.000	0.000	0.000	0.000
123	A	1462	PRO	0	-0.019	0.002	14.483	0.088	0.088	0.000	0.000	0.000	0.000
124	A	1463	LEU	0	0.008	-0.007	13.145	0.024	0.024	0.000	0.000	0.000	0.000
125	A	1464	LEU	0	0.019	0.016	16.508	-0.018	-0.018	0.000	0.000	0.000	0.000
126	A	1465	THR	0	-0.012	-0.020	16.202	-0.011	-0.011	0.000	0.000	0.000	0.000
127	A	1466	ASN	0	0.019	0.000	19.448	-0.029	-0.029	0.000	0.000	0.000	0.000
128	A	1467	PHE	0	0.030	-0.006	22.828	-0.001	-0.001	0.000	0.000	0.000	0.000
129	A	1468	GLN	0	0.068	0.039	26.184	-0.015	-0.015	0.000	0.000	0.000	0.000
130	A	1469	VAL	0	0.030	0.014	22.791	-0.008	-0.008	0.000	0.000	0.000	0.000
131	A	1470	THR	0	-0.021	-0.027	23.997	-0.002	-0.002	0.000	0.000	0.000	0.000
132	A	1471	LYN	0	-0.036	0.005	25.834	-0.005	-0.005	0.000	0.000	0.000	0.000
133	A	1472	LEU	0	0.052	0.028	28.850	-0.011	-0.011	0.000	0.000	0.000	0.000
134	A	1473	PHE	0	-0.077	-0.033	25.098	-0.004	-0.004	0.000	0.000	0.000	0.000
135	A	1474	ALA	0	0.004	0.004	28.042	-0.004	-0.004	0.000	0.000	0.000	0.000
136	A	1475	GLU	-1	-0.846	-0.935	30.732	0.136	0.136	0.000	0.000	0.000	0.000
137	A	1476	ALA	0	-0.084	-0.018	31.086	-0.011	-0.011	0.000	0.000	0.000	0.000
138	A	1477	VAL	0	-0.052	-0.027	33.186	-0.007	-0.007	0.000	0.000	0.000	0.000
139	A	1478	GLN	0	-0.023	-0.009	27.947	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:5:SER)