FMO DATABASE

FMODB ID: 5J83Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1222574.811066
FMO2-HF: Nuclear repulsion	1170001.027523
FMO2-HF: Total energy	-52573.783543
FMO2-MP2: Total energy	-52731.099111

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.
-11.384	-8.617	3.565	-2.847	-3.483	0.022

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 : 0.019 / q_NPA : 0.013

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	0.069	0.052	3.548	-0.948	2.070	-0.005	-1.640	-1.372	0.005
4	A	1343	HIS	0	0.012	-0.019	4.881	-0.615	-0.615	0.000	0.000	0.000	0.000
5	A	1344	THR	0	0.015	0.001	9.009	0.082	0.082	0.000	0.000	0.000	0.000
6	A	1345	ALA	0	0.004	0.015	11.046	0.010	0.010	0.000	0.000	0.000	0.000
7	A	1346	PHE	0	0.052	0.026	8.854	-0.038	-0.038	0.000	0.000	0.000	0.000
8	A	1347	LEU	0	0.023	-0.001	10.989	0.008	0.008	0.000	0.000	0.000	0.000
9	A	1348	LYS	1	0.935	0.962	13.379	0.161	0.161	0.000	0.000	0.000	0.000
10	A	1349	ALA	0	0.016	0.017	13.677	0.018	0.018	0.000	0.000	0.000	0.000
11	A	1350	MET	0	-0.070	-0.031	12.880	0.000	0.000	0.000	0.000	0.000	0.000
12	A	1351	LEU	0	-0.016	0.003	16.166	-0.016	-0.016	0.000	0.000	0.000	0.000
13	A	1352	SER	0	-0.044	-0.015	18.712	0.026	0.026	0.000	0.000	0.000	0.000
14	A	1353	THR	0	0.041	0.018	20.572	-0.008	-0.008	0.000	0.000	0.000	0.000
15	A	1354	GLY	0	-0.006	-0.007	21.730	-0.006	-0.006	0.000	0.000	0.000	0.000
16	A	1355	PHE	0	-0.002	-0.010	22.729	0.019	0.019	0.000	0.000	0.000	0.000
17	A	1356	LYS	1	0.881	0.966	18.676	-0.129	-0.129	0.000	0.000	0.000	0.000
18	A	1357	ILE	0	0.047	0.015	23.504	0.020	0.020	0.000	0.000	0.000	0.000
19	A	1358	PRO	0	-0.078	-0.029	21.506	-0.009	-0.009	0.000	0.000	0.000	0.000
20	A	1359	GLN	0	0.033	0.009	23.946	-0.011	-0.011	0.000	0.000	0.000	0.000
21	A	1360	LYS	1	0.866	0.934	23.386	-0.112	-0.112	0.000	0.000	0.000	0.000
22	A	1361	GLY	0	0.062	0.039	23.550	-0.007	-0.007	0.000	0.000	0.000	0.000
23	A	1362	ILE	0	-0.013	-0.004	22.460	0.023	0.023	0.000	0.000	0.000	0.000
24	A	1363	LEU	0	-0.039	-0.015	17.768	-0.002	-0.002	0.000	0.000	0.000	0.000
25	A	1364	ILE	0	0.020	0.002	21.595	0.021	0.021	0.000	0.000	0.000	0.000
26	A	1365	GLY	0	-0.018	-0.007	21.337	0.004	0.004	0.000	0.000	0.000	0.000
27	A	1366	ILE	0	-0.013	-0.012	22.400	0.007	0.007	0.000	0.000	0.000	0.000
28	A	1367	GLN	0	0.021	0.021	24.737	0.020	0.020	0.000	0.000	0.000	0.000
29	A	1368	GLN	0	0.055	0.025	26.343	-0.015	-0.015	0.000	0.000	0.000	0.000
30	A	1369	SER	0	0.030	0.001	29.579	-0.007	-0.007	0.000	0.000	0.000	0.000
31	A	1370	PHE	0	-0.053	-0.025	28.272	-0.012	-0.012	0.000	0.000	0.000	0.000
32	A	1371	ARG	1	0.887	0.949	29.061	-0.243	-0.243	0.000	0.000	0.000	0.000
33	A	1372	PRO	0	0.020	0.012	31.938	-0.004	-0.004	0.000	0.000	0.000	0.000
34	A	1373	ARG	1	0.882	0.925	32.348	-0.167	-0.167	0.000	0.000	0.000	0.000
35	A	1374	PHE	0	0.011	-0.005	26.445	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	1375	LEU	0	0.056	0.038	31.336	0.002	0.002	0.000	0.000	0.000	0.000
37	A	1376	GLY	0	0.044	0.027	33.798	-0.003	-0.003	0.000	0.000	0.000	0.000
38	A	1377	VAL	0	0.008	-0.003	29.138	-0.004	-0.004	0.000	0.000	0.000	0.000
39	A	1378	ALA	0	-0.046	-0.021	30.287	0.002	0.002	0.000	0.000	0.000	0.000
40	A	1379	GLU	-1	-0.903	-0.959	31.251	0.122	0.122	0.000	0.000	0.000	0.000
41	A	1380	GLN	0	0.034	0.020	33.368	0.001	0.001	0.000	0.000	0.000	0.000
42	A	1381	LEU	0	0.001	-0.005	27.188	0.000	0.000	0.000	0.000	0.000	0.000
43	A	1382	HIS	0	-0.021	-0.010	31.082	-0.009	-0.009	0.000	0.000	0.000	0.000
44	A	1383	ASN	0	-0.097	-0.060	32.723	-0.008	-0.008	0.000	0.000	0.000	0.000
45	A	1384	GLU	-1	-0.859	-0.930	32.470	0.092	0.092	0.000	0.000	0.000	0.000
46	A	1385	GLY	0	-0.059	-0.015	32.692	-0.004	-0.004	0.000	0.000	0.000	0.000
47	A	1386	PHE	0	-0.038	-0.004	25.791	0.006	0.006	0.000	0.000	0.000	0.000
48	A	1387	LYS	1	0.915	0.970	27.213	-0.171	-0.171	0.000	0.000	0.000	0.000
49	A	1388	LEU	0	0.003	0.002	26.524	0.021	0.021	0.000	0.000	0.000	0.000
50	A	1389	PHE	0	0.031	0.000	23.138	-0.010	-0.010	0.000	0.000	0.000	0.000
51	A	1390	ALA	0	0.050	0.024	24.024	0.022	0.022	0.000	0.000	0.000	0.000
52	A	1391	THR	0	-0.007	-0.003	22.077	-0.018	-0.018	0.000	0.000	0.000	0.000
53	A	1392	GLU	-1	-0.878	-0.947	24.761	0.216	0.216	0.000	0.000	0.000	0.000
54	A	1393	ALA	0	0.038	0.023	28.139	-0.011	-0.011	0.000	0.000	0.000	0.000
55	A	1394	THR	0	-0.017	-0.017	26.691	-0.019	-0.019	0.000	0.000	0.000	0.000
56	A	1395	SER	0	0.033	0.027	28.124	-0.011	-0.011	0.000	0.000	0.000	0.000
57	A	1396	ASP	-1	-0.864	-0.920	29.837	0.174	0.174	0.000	0.000	0.000	0.000
58	A	1397	TRP	0	-0.038	-0.024	30.380	-0.005	-0.005	0.000	0.000	0.000	0.000
59	A	1398	LEU	0	-0.002	0.002	28.967	-0.007	-0.007	0.000	0.000	0.000	0.000
60	A	1399	ASN	0	0.004	-0.017	32.335	-0.019	-0.019	0.000	0.000	0.000	0.000
61	A	1400	ALA	0	-0.048	-0.021	35.417	-0.010	-0.010	0.000	0.000	0.000	0.000
62	A	1401	ASN	0	-0.126	-0.080	36.534	-0.012	-0.012	0.000	0.000	0.000	0.000
63	A	1402	ASN	0	-0.009	-0.001	38.213	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	1403	VAL	0	0.041	0.032	32.449	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	1404	PRO	0	-0.013	-0.004	33.579	0.009	0.009	0.000	0.000	0.000	0.000
66	A	1405	ALA	0	-0.022	-0.010	29.109	0.010	0.010	0.000	0.000	0.000	0.000
67	A	1406	THR	0	-0.057	-0.017	27.050	-0.014	-0.014	0.000	0.000	0.000	0.000
68	A	1407	PRO	0	0.051	0.025	26.659	0.023	0.023	0.000	0.000	0.000	0.000
69	A	1408	VAL	0	-0.038	-0.025	21.404	0.000	0.000	0.000	0.000	0.000	0.000
70	A	1409	ALA	0	0.025	0.008	21.845	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	1410	TRP	0	0.009	-0.003	19.716	0.044	0.044	0.000	0.000	0.000	0.000
72	A	1411	PRO	0	-0.020	-0.021	15.135	-0.025	-0.025	0.000	0.000	0.000	0.000
73	A	1412	SER	0	-0.058	-0.070	17.284	-0.046	-0.046	0.000	0.000	0.000	0.000
74	A	1413	GLN	0	-0.016	-0.007	18.657	-0.039	-0.039	0.000	0.000	0.000	0.000
75	A	1414	GLU	-1	-0.753	-0.817	17.602	0.441	0.441	0.000	0.000	0.000	0.000
76	A	1415	GLY	0	0.033	0.018	21.254	-0.004	-0.004	0.000	0.000	0.000	0.000
77	A	1416	GLN	0	-0.018	-0.006	24.022	0.001	0.001	0.000	0.000	0.000	0.000
78	A	1417	ASN	0	-0.026	-0.017	25.272	-0.030	-0.030	0.000	0.000	0.000	0.000
79	A	1418	PRO	0	0.066	0.039	27.713	0.004	0.004	0.000	0.000	0.000	0.000
80	A	1419	SER	0	-0.034	-0.018	29.061	0.003	0.003	0.000	0.000	0.000	0.000
81	A	1420	LEU	0	-0.031	-0.011	25.027	0.010	0.010	0.000	0.000	0.000	0.000
82	A	1421	SER	0	0.027	0.019	22.613	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	1422	SER	0	-0.113	-0.091	17.456	0.025	0.025	0.000	0.000	0.000	0.000
84	A	1423	ILE	0	0.127	0.049	15.436	-0.016	-0.016	0.000	0.000	0.000	0.000
85	A	1424	ARG	1	0.859	0.904	12.467	-0.579	-0.579	0.000	0.000	0.000	0.000
86	A	1425	LYS	1	0.874	0.945	14.656	-0.361	-0.361	0.000	0.000	0.000	0.000
87	A	1426	LEU	0	0.082	0.050	17.448	-0.029	-0.029	0.000	0.000	0.000	0.000
88	A	1427	ILE	0	-0.002	0.003	13.404	-0.014	-0.014	0.000	0.000	0.000	0.000
89	A	1428	ARG	1	0.885	0.937	14.267	-0.238	-0.238	0.000	0.000	0.000	0.000
90	A	1429	ASP	-1	-0.945	-0.972	15.486	0.149	0.149	0.000	0.000	0.000	0.000
91	A	1430	GLY	0	0.022	0.021	18.247	-0.026	-0.026	0.000	0.000	0.000	0.000
92	A	1431	SER	0	-0.041	-0.027	19.946	-0.017	-0.017	0.000	0.000	0.000	0.000
93	A	1432	ILE	0	-0.086	-0.043	18.686	0.004	0.004	0.000	0.000	0.000	0.000
94	A	1433	ASP	-1	-0.781	-0.889	18.523	0.213	0.213	0.000	0.000	0.000	0.000
95	A	1434	LEU	0	0.032	0.006	19.102	0.000	0.000	0.000	0.000	0.000	0.000
96	A	1435	VAL	0	-0.042	-0.012	15.955	0.011	0.011	0.000	0.000	0.000	0.000
97	A	1436	ILE	0	0.041	0.037	18.796	0.015	0.015	0.000	0.000	0.000	0.000
98	A	1437	ASN	0	-0.012	-0.018	17.408	0.045	0.045	0.000	0.000	0.000	0.000
99	A	1438	LEU	0	0.008	0.018	19.181	0.030	0.030	0.000	0.000	0.000	0.000
100	A	1439	PRO	0	-0.039	-0.024	20.904	0.028	0.028	0.000	0.000	0.000	0.000
101	A	1440	ASN	0	0.035	-0.003	21.390	-0.055	-0.055	0.000	0.000	0.000	0.000
102	A	1441	ASN	0	-0.017	-0.005	21.915	0.038	0.038	0.000	0.000	0.000	0.000
103	A	1442	ASN	0	0.031	0.026	24.250	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	1443	THR	0	0.067	0.018	22.459	0.036	0.036	0.000	0.000	0.000	0.000
105	A	1444	LYS	1	0.896	0.964	21.735	-0.289	-0.289	0.000	0.000	0.000	0.000
106	A	1445	PHE	0	0.007	-0.007	20.392	0.006	0.006	0.000	0.000	0.000	0.000
107	A	1446	VAL	0	0.030	0.036	17.013	0.061	0.061	0.000	0.000	0.000	0.000
108	A	1447	HIS	0	0.059	0.023	11.480	0.064	0.064	0.000	0.000	0.000	0.000
109	A	1448	ASP	-1	-0.732	-0.831	14.218	0.758	0.758	0.000	0.000	0.000	0.000
110	A	1449	ASN	0	-0.009	-0.011	15.273	0.046	0.046	0.000	0.000	0.000	0.000
111	A	1450	TYR	0	-0.012	0.013	7.400	0.250	0.250	0.000	0.000	0.000	0.000
112	A	1451	VAL	0	0.022	-0.006	10.618	0.244	0.244	0.000	0.000	0.000	0.000
113	A	1452	ILE	0	-0.015	0.001	11.280	0.087	0.087	0.000	0.000	0.000	0.000
114	A	1453	ARG	1	0.857	0.905	12.335	-0.750	-0.750	0.000	0.000	0.000	0.000
115	A	1454	ARG	1	0.819	0.900	2.095	-13.767	-14.126	3.571	-1.198	-2.014	0.017
116	A	1455	THR	0	0.001	-0.015	8.063	0.178	0.178	0.000	0.000	0.000	0.000
117	A	1456	ALA	0	-0.003	0.001	9.838	-0.150	-0.150	0.000	0.000	0.000	0.000
118	A	1457	VAL	0	0.014	0.004	8.320	-0.126	-0.126	0.000	0.000	0.000	0.000
119	A	1458	ASP	-1	-0.804	-0.884	4.735	4.627	4.735	-0.001	-0.009	-0.097	0.000
120	A	1459	SER	0	-0.109	-0.064	7.332	-0.534	-0.534	0.000	0.000	0.000	0.000
121	A	1460	GLY	0	-0.020	-0.013	10.579	-0.157	-0.157	0.000	0.000	0.000	0.000
122	A	1461	ILE	0	-0.057	-0.010	12.554	-0.090	-0.090	0.000	0.000	0.000	0.000
123	A	1462	PRO	0	-0.021	0.001	14.620	0.082	0.082	0.000	0.000	0.000	0.000
124	A	1463	LEU	0	-0.007	-0.013	13.130	0.035	0.035	0.000	0.000	0.000	0.000
125	A	1464	LEU	0	0.031	0.023	16.731	-0.015	-0.015	0.000	0.000	0.000	0.000
126	A	1465	THR	0	-0.016	-0.021	16.148	-0.007	-0.007	0.000	0.000	0.000	0.000
127	A	1466	ASN	0	0.017	-0.006	19.525	-0.025	-0.025	0.000	0.000	0.000	0.000
128	A	1467	PHE	0	0.055	0.013	22.922	-0.003	-0.003	0.000	0.000	0.000	0.000
129	A	1468	GLN	0	0.057	0.039	26.271	-0.015	-0.015	0.000	0.000	0.000	0.000
130	A	1469	VAL	0	0.030	0.011	23.066	-0.009	-0.009	0.000	0.000	0.000	0.000
131	A	1470	THR	0	-0.020	-0.037	24.268	-0.003	-0.003	0.000	0.000	0.000	0.000
132	A	1471	LYN	0	-0.033	0.016	26.019	-0.005	-0.005	0.000	0.000	0.000	0.000
133	A	1472	LEU	0	0.039	0.017	29.069	-0.011	-0.011	0.000	0.000	0.000	0.000
134	A	1473	PHE	0	-0.069	-0.032	25.466	-0.006	-0.006	0.000	0.000	0.000	0.000
135	A	1474	ALA	0	0.006	0.007	28.324	-0.005	-0.005	0.000	0.000	0.000	0.000
136	A	1475	GLU	-1	-0.821	-0.915	30.976	0.116	0.116	0.000	0.000	0.000	0.000
137	A	1476	ALA	0	-0.091	-0.027	31.402	-0.010	-0.010	0.000	0.000	0.000	0.000
138	A	1477	VAL	0	-0.047	-0.028	33.512	-0.008	-0.008	0.000	0.000	0.000	0.000
139	A	1478	GLN	0	-0.020	0.001	28.489	0.005	0.005	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:SER)