FMO DATABASE

FMODB ID: YVJQ2

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	OptAll
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	-1225296.937519
FMO2-HF: Nuclear repulsion	1172722.741962
FMO2-HF: Total energy	-52574.195557
FMO2-MP2: Total energy	-52731.417579

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.
-14.488	-14.152	6.965	-3.44	-3.862	0.026

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 : 0.050 / q_NPA : 0.033

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	0.044	0.039	3.888	-0.697	1.673	-0.012	-1.304	-1.054	0.004
4	A	1343	HIS	0	0.015	0.002	4.940	-0.230	-0.230	0.000	0.000	0.000	0.000
5	A	1344	THR	0	0.016	-0.015	8.846	0.139	0.139	0.000	0.000	0.000	0.000
6	A	1345	ALA	0	0.014	0.036	11.070	0.040	0.040	0.000	0.000	0.000	0.000
7	A	1346	PHE	0	0.076	0.032	8.817	-0.037	-0.037	0.000	0.000	0.000	0.000
8	A	1347	LEU	0	0.021	-0.008	10.885	0.020	0.020	0.000	0.000	0.000	0.000
9	A	1348	LYS	1	0.884	0.944	13.198	0.195	0.195	0.000	0.000	0.000	0.000
10	A	1349	ALA	0	0.004	0.009	13.336	0.021	0.021	0.000	0.000	0.000	0.000
11	A	1350	MET	0	-0.053	-0.031	12.445	0.000	0.000	0.000	0.000	0.000	0.000
12	A	1351	LEU	0	-0.016	0.008	15.626	-0.015	-0.015	0.000	0.000	0.000	0.000
13	A	1352	SER	0	-0.020	0.004	18.397	0.029	0.029	0.000	0.000	0.000	0.000
14	A	1353	THR	0	0.031	0.003	20.149	0.000	0.000	0.000	0.000	0.000	0.000
15	A	1354	GLY	0	0.007	0.010	21.045	0.002	0.002	0.000	0.000	0.000	0.000
16	A	1355	PHE	0	0.024	-0.011	22.076	0.031	0.031	0.000	0.000	0.000	0.000
17	A	1356	LYS	1	0.828	0.944	19.069	-0.148	-0.148	0.000	0.000	0.000	0.000
18	A	1357	ILE	0	0.043	0.014	23.541	0.021	0.021	0.000	0.000	0.000	0.000
19	A	1358	PRO	0	-0.085	-0.033	21.139	-0.012	-0.012	0.000	0.000	0.000	0.000
20	A	1359	GLN	0	0.046	0.015	23.584	-0.013	-0.013	0.000	0.000	0.000	0.000
21	A	1360	LYS	1	0.848	0.920	23.358	-0.114	-0.114	0.000	0.000	0.000	0.000
22	A	1361	GLY	0	0.058	0.009	23.540	-0.010	-0.010	0.000	0.000	0.000	0.000
23	A	1362	ILE	0	-0.027	-0.002	22.010	0.026	0.026	0.000	0.000	0.000	0.000
24	A	1363	LEU	0	-0.027	-0.007	17.244	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	1364	ILE	0	0.010	0.006	21.100	0.019	0.019	0.000	0.000	0.000	0.000
26	A	1365	GLY	0	-0.020	-0.007	20.783	-0.003	-0.003	0.000	0.000	0.000	0.000
27	A	1366	ILE	0	-0.011	-0.014	21.833	0.015	0.015	0.000	0.000	0.000	0.000
28	A	1367	GLN	0	0.024	0.021	24.183	0.020	0.020	0.000	0.000	0.000	0.000
29	A	1368	GLN	0	0.025	0.016	25.979	-0.016	-0.016	0.000	0.000	0.000	0.000
30	A	1369	SER	0	0.029	0.004	29.155	-0.008	-0.008	0.000	0.000	0.000	0.000
31	A	1370	PHE	0	-0.025	-0.009	28.048	-0.012	-0.012	0.000	0.000	0.000	0.000
32	A	1371	ARG	1	0.883	0.946	28.286	-0.268	-0.268	0.000	0.000	0.000	0.000
33	A	1372	PRO	0	0.027	0.007	31.342	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	1373	ARG	1	0.870	0.932	32.068	-0.190	-0.190	0.000	0.000	0.000	0.000
35	A	1374	PHE	0	-0.001	-0.013	25.834	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	1375	LEU	0	0.044	0.029	30.853	0.001	0.001	0.000	0.000	0.000	0.000
37	A	1376	GLY	0	0.083	0.046	33.426	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	1377	VAL	0	-0.004	0.000	29.122	-0.004	-0.004	0.000	0.000	0.000	0.000
39	A	1378	ALA	0	-0.043	-0.024	29.574	0.002	0.002	0.000	0.000	0.000	0.000
40	A	1379	GLU	-1	-0.901	-0.957	30.510	0.133	0.133	0.000	0.000	0.000	0.000
41	A	1380	GLN	0	0.028	0.020	32.974	0.001	0.001	0.000	0.000	0.000	0.000
42	A	1381	LEU	0	0.004	-0.011	26.738	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	1382	HIS	0	-0.032	-0.019	30.570	-0.010	-0.010	0.000	0.000	0.000	0.000
44	A	1383	ASN	0	-0.053	-0.036	32.106	-0.015	-0.015	0.000	0.000	0.000	0.000
45	A	1384	GLU	-1	-0.915	-0.947	31.904	0.104	0.104	0.000	0.000	0.000	0.000
46	A	1385	GLY	0	-0.026	-0.010	32.341	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	1386	PHE	0	-0.061	-0.024	25.005	0.006	0.006	0.000	0.000	0.000	0.000
48	A	1387	LYS	1	0.936	0.980	26.667	-0.173	-0.173	0.000	0.000	0.000	0.000
49	A	1388	LEU	0	0.015	0.012	26.017	0.024	0.024	0.000	0.000	0.000	0.000
50	A	1389	PHE	0	0.012	-0.010	22.706	-0.013	-0.013	0.000	0.000	0.000	0.000
51	A	1390	ALA	0	0.043	0.014	23.738	0.026	0.026	0.000	0.000	0.000	0.000
52	A	1391	THR	0	-0.014	-0.012	21.251	-0.021	-0.021	0.000	0.000	0.000	0.000
53	A	1392	GLU	-1	-0.882	-0.950	24.183	0.228	0.228	0.000	0.000	0.000	0.000
54	A	1393	ALA	0	0.038	0.023	27.550	-0.011	-0.011	0.000	0.000	0.000	0.000
55	A	1394	THR	0	-0.040	-0.019	26.058	-0.017	-0.017	0.000	0.000	0.000	0.000
56	A	1395	SER	0	-0.004	0.009	27.769	-0.011	-0.011	0.000	0.000	0.000	0.000
57	A	1396	ASP	-1	-0.837	-0.918	29.177	0.182	0.182	0.000	0.000	0.000	0.000
58	A	1397	TRP	0	-0.023	-0.015	30.119	-0.005	-0.005	0.000	0.000	0.000	0.000
59	A	1398	LEU	0	-0.011	0.000	28.454	-0.007	-0.007	0.000	0.000	0.000	0.000
60	A	1399	ASN	0	0.018	0.000	31.693	-0.019	-0.019	0.000	0.000	0.000	0.000
61	A	1400	ALA	0	-0.028	-0.014	34.819	-0.010	-0.010	0.000	0.000	0.000	0.000
62	A	1401	ASN	0	-0.101	-0.061	35.867	-0.010	-0.010	0.000	0.000	0.000	0.000
63	A	1402	ASN	0	-0.018	-0.006	37.788	-0.006	-0.006	0.000	0.000	0.000	0.000
64	A	1403	VAL	0	0.012	0.013	32.109	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	1404	PRO	0	-0.012	-0.002	33.061	0.011	0.011	0.000	0.000	0.000	0.000
66	A	1405	ALA	0	-0.032	-0.011	28.570	0.011	0.011	0.000	0.000	0.000	0.000
67	A	1406	THR	0	-0.027	-0.010	26.129	-0.017	-0.017	0.000	0.000	0.000	0.000
68	A	1407	PRO	0	0.041	0.025	26.188	0.027	0.027	0.000	0.000	0.000	0.000
69	A	1408	VAL	0	-0.044	-0.026	21.298	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	1409	ALA	0	0.019	0.003	20.736	0.000	0.000	0.000	0.000	0.000	0.000
71	A	1410	TRP	0	0.046	0.011	19.274	0.051	0.051	0.000	0.000	0.000	0.000
72	A	1411	PRO	0	-0.032	-0.024	14.471	-0.035	-0.035	0.000	0.000	0.000	0.000
73	A	1412	SER	0	-0.054	-0.060	16.640	-0.051	-0.051	0.000	0.000	0.000	0.000
74	A	1413	GLN	0	-0.004	0.001	18.425	-0.036	-0.036	0.000	0.000	0.000	0.000
75	A	1414	GLU	-1	-0.770	-0.837	17.138	0.418	0.418	0.000	0.000	0.000	0.000
76	A	1415	GLY	0	0.040	0.011	20.562	-0.008	-0.008	0.000	0.000	0.000	0.000
77	A	1416	GLN	0	-0.033	-0.001	23.596	0.001	0.001	0.000	0.000	0.000	0.000
78	A	1417	ASN	0	-0.020	-0.016	24.619	-0.027	-0.027	0.000	0.000	0.000	0.000
79	A	1418	PRO	0	0.067	0.040	27.310	0.001	0.001	0.000	0.000	0.000	0.000
80	A	1419	SER	0	-0.038	-0.024	28.459	0.005	0.005	0.000	0.000	0.000	0.000
81	A	1420	LEU	0	-0.029	-0.011	24.457	0.008	0.008	0.000	0.000	0.000	0.000
82	A	1421	SER	0	0.033	0.028	22.598	0.003	0.003	0.000	0.000	0.000	0.000
83	A	1422	SER	0	-0.086	-0.071	17.217	0.024	0.024	0.000	0.000	0.000	0.000
84	A	1423	ILE	0	0.115	0.047	14.894	-0.013	-0.013	0.000	0.000	0.000	0.000
85	A	1424	ARG	1	0.877	0.912	11.780	-0.564	-0.564	0.000	0.000	0.000	0.000
86	A	1425	LYS	1	0.814	0.918	14.081	-0.359	-0.359	0.000	0.000	0.000	0.000
87	A	1426	LEU	0	0.078	0.035	16.839	-0.029	-0.029	0.000	0.000	0.000	0.000
88	A	1427	ILE	0	-0.017	-0.003	12.865	-0.010	-0.010	0.000	0.000	0.000	0.000
89	A	1428	ARG	1	0.897	0.953	13.629	-0.167	-0.167	0.000	0.000	0.000	0.000
90	A	1429	ASP	-1	-0.912	-0.947	15.087	0.132	0.132	0.000	0.000	0.000	0.000
91	A	1430	GLY	0	0.026	0.025	18.181	-0.028	-0.028	0.000	0.000	0.000	0.000
92	A	1431	SER	0	-0.059	-0.049	19.643	-0.011	-0.011	0.000	0.000	0.000	0.000
93	A	1432	ILE	0	-0.087	-0.036	18.491	0.010	0.010	0.000	0.000	0.000	0.000
94	A	1433	ASP	-1	-0.772	-0.871	18.407	0.205	0.205	0.000	0.000	0.000	0.000
95	A	1434	LEU	0	0.014	0.006	18.926	0.004	0.004	0.000	0.000	0.000	0.000
96	A	1435	VAL	0	-0.028	-0.013	15.380	0.008	0.008	0.000	0.000	0.000	0.000
97	A	1436	ILE	0	0.037	0.032	18.314	0.032	0.032	0.000	0.000	0.000	0.000
98	A	1437	ASN	0	-0.019	-0.025	16.860	0.071	0.071	0.000	0.000	0.000	0.000
99	A	1438	LEU	0	0.032	0.036	18.656	0.046	0.046	0.000	0.000	0.000	0.000
100	A	1439	PRO	0	-0.027	-0.021	20.555	0.039	0.039	0.000	0.000	0.000	0.000
101	A	1440	ASN	0	0.032	-0.010	21.143	-0.064	-0.064	0.000	0.000	0.000	0.000
102	A	1441	ASN	0	-0.010	-0.002	21.712	0.040	0.040	0.000	0.000	0.000	0.000
103	A	1442	ASN	0	0.019	0.018	24.077	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	1443	THR	0	0.061	0.011	22.012	0.036	0.036	0.000	0.000	0.000	0.000
105	A	1444	LYS	1	0.892	0.966	21.165	-0.306	-0.306	0.000	0.000	0.000	0.000
106	A	1445	PHE	0	0.017	0.005	19.778	0.014	0.014	0.000	0.000	0.000	0.000
107	A	1446	VAL	0	0.017	0.029	16.783	0.066	0.066	0.000	0.000	0.000	0.000
108	A	1447	HIS	0	0.052	0.024	11.477	0.093	0.093	0.000	0.000	0.000	0.000
109	A	1448	ASP	-1	-0.732	-0.843	13.903	0.790	0.790	0.000	0.000	0.000	0.000
110	A	1449	ASN	0	-0.024	-0.021	14.951	0.042	0.042	0.000	0.000	0.000	0.000
111	A	1450	TYR	0	0.012	0.019	7.141	0.270	0.270	0.000	0.000	0.000	0.000
112	A	1451	VAL	0	0.021	0.004	10.292	0.286	0.286	0.000	0.000	0.000	0.000
113	A	1452	ILE	0	-0.013	0.006	10.867	0.093	0.093	0.000	0.000	0.000	0.000
114	A	1453	ARG	1	0.859	0.906	11.805	-0.878	-0.878	0.000	0.000	0.000	0.000
115	A	1454	ARG	1	0.788	0.878	1.895	-16.934	-19.354	6.974	-1.993	-2.562	0.023
116	A	1455	THR	0	0.010	-0.018	7.453	0.133	0.133	0.000	0.000	0.000	0.000
117	A	1456	ALA	0	-0.006	0.011	9.324	-0.192	-0.192	0.000	0.000	0.000	0.000
118	A	1457	VAL	0	0.017	0.006	7.574	-0.172	-0.172	0.000	0.000	0.000	0.000
119	A	1458	ASP	-1	-0.812	-0.893	4.019	4.019	4.405	0.003	-0.143	-0.246	-0.001
120	A	1459	SER	0	-0.079	-0.052	6.659	-0.604	-0.604	0.000	0.000	0.000	0.000
121	A	1460	GLY	0	-0.034	-0.019	10.095	-0.173	-0.173	0.000	0.000	0.000	0.000
122	A	1461	ILE	0	-0.036	-0.002	11.940	-0.078	-0.078	0.000	0.000	0.000	0.000
123	A	1462	PRO	0	-0.011	0.002	14.079	0.104	0.104	0.000	0.000	0.000	0.000
124	A	1463	LEU	0	0.003	-0.007	12.609	0.026	0.026	0.000	0.000	0.000	0.000
125	A	1464	LEU	0	0.051	0.031	16.432	0.006	0.006	0.000	0.000	0.000	0.000
126	A	1465	THR	0	-0.025	-0.014	15.668	-0.024	-0.024	0.000	0.000	0.000	0.000
127	A	1466	ASN	0	0.010	-0.011	18.893	-0.038	-0.038	0.000	0.000	0.000	0.000
128	A	1467	PHE	0	0.067	0.027	22.456	-0.008	-0.008	0.000	0.000	0.000	0.000
129	A	1468	GLN	0	0.053	0.031	25.902	-0.015	-0.015	0.000	0.000	0.000	0.000
130	A	1469	VAL	0	0.013	0.006	22.808	-0.014	-0.014	0.000	0.000	0.000	0.000
131	A	1470	THR	0	-0.021	-0.034	24.014	-0.003	-0.003	0.000	0.000	0.000	0.000
132	A	1471	LYN	0	-0.035	0.003	25.932	-0.006	-0.006	0.000	0.000	0.000	0.000
133	A	1472	LEU	0	0.040	0.015	29.012	-0.012	-0.012	0.000	0.000	0.000	0.000
134	A	1473	PHE	0	-0.037	-0.012	25.335	-0.008	-0.008	0.000	0.000	0.000	0.000
135	A	1474	ALA	0	-0.001	-0.001	28.270	-0.009	-0.009	0.000	0.000	0.000	0.000
136	A	1475	GLU	-1	-0.859	-0.934	30.604	0.133	0.133	0.000	0.000	0.000	0.000
137	A	1476	ALA	0	-0.080	-0.030	30.976	-0.011	-0.011	0.000	0.000	0.000	0.000
138	A	1477	VAL	0	-0.020	-0.001	33.105	-0.008	-0.008	0.000	0.000	0.000	0.000
139	A	1478	GLN	0	-0.029	-0.003	27.883	0.006	0.006	0.000	0.000	0.000	0.000

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