Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: N23LQ

Calculation Name: 1LGV-B-Xray372

Preferred Name:

Target Type:

Ligand Name: pyroglutamic acid

ligand 3-letter code: PCA

PDB ID: 1LGV

Chain ID: B

ChEMBL ID:

UniProt ID: Q6PJG0

Base Structure: X-ray

Registration Date: 2023-09-26

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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2042711.021748
FMO2-HF: Nuclear repulsion 1964139.980934
FMO2-HF: Total energy -78571.040815
FMO2-MP2: Total energy -78801.403266


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
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/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(B:1:PCA)


Summations of interaction energy for fragment #1(B:1:PCA)
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.
-0.1571.898-0.014-1.069-0.9720.003
Interaction energy analysis for fragmet #1(B:1:PCA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.018 / q_NPA : -0.019
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   
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].
3B3ALA00.0020.0033.8681.0382.735-0.018-0.947-0.7320.003
4B4LEU00.0010.0126.5890.9450.9450.0000.0000.0000.000
5B5THR00.0140.0193.954-1.351-0.9930.004-0.122-0.2400.000
6B6GLN00.038-0.0105.9460.1750.1750.0000.0000.0000.000
7B7PRO0-0.0070.0197.766-0.100-0.1000.0000.0000.0000.000
8B8ALA00.0810.0499.259-0.167-0.1670.0000.0000.0000.000
9B9SER0-0.017-0.00910.604-0.115-0.1150.0000.0000.0000.000
10B10VAL0-0.040-0.01414.3150.1100.1100.0000.0000.0000.000
11B11SER0-0.022-0.03417.055-0.049-0.0490.0000.0000.0000.000
12B12GLY00.0100.01420.8860.0400.0400.0000.0000.0000.000
13B13SER00.001-0.00324.103-0.026-0.0260.0000.0000.0000.000
14B14PRO00.0320.00427.8570.0060.0060.0000.0000.0000.000
15B15GLY0-0.033-0.00730.1770.0070.0070.0000.0000.0000.000
16B16GLN00.0000.01627.2460.0070.0070.0000.0000.0000.000
17B17SER00.014-0.00326.190-0.022-0.0220.0000.0000.0000.000
18B18ILE0-0.018-0.00219.8770.0230.0230.0000.0000.0000.000
19B19THR00.0210.01418.080-0.046-0.0460.0000.0000.0000.000
20B20VAL00.0200.03714.0850.0610.0610.0000.0000.0000.000
21B21SER00.006-0.00113.650-0.026-0.0260.0000.0000.0000.000
22B22CYS0-0.063-0.01410.3540.0260.0260.0000.0000.0000.000
23B23THR0-0.023-0.0077.0310.1210.1210.0000.0000.0000.000
24B24GLY00.0630.0298.0190.1220.1220.0000.0000.0000.000
25B25VAL00.0310.0178.970-0.294-0.2940.0000.0000.0000.000
26B26SER0-0.080-0.04712.123-0.118-0.1180.0000.0000.0000.000
27B27SER0-0.067-0.0238.855-0.036-0.0360.0000.0000.0000.000
28B28ILE0-0.0080.00910.178-0.133-0.1330.0000.0000.0000.000
29B29VAL00.0520.01912.2100.1140.1140.0000.0000.0000.000
30B30GLY00.0210.01515.424-0.045-0.0450.0000.0000.0000.000
31B31SER0-0.012-0.01114.857-0.011-0.0110.0000.0000.0000.000
32B32TYR0-0.002-0.00616.9950.0240.0240.0000.0000.0000.000
33B33ASN00.0150.00019.1290.0350.0350.0000.0000.0000.000
34B34LEU00.0090.01819.5970.0100.0100.0000.0000.0000.000
35B35VAL00.001-0.01115.979-0.046-0.0460.0000.0000.0000.000
36B36SER0-0.026-0.01717.4960.0310.0310.0000.0000.0000.000
37B37TRP0-0.0220.01213.751-0.049-0.0490.0000.0000.0000.000
38B38TYR00.0260.00817.6380.0060.0060.0000.0000.0000.000
39B39GLN00.0470.02318.3860.0090.0090.0000.0000.0000.000
40B40GLN0-0.025-0.02818.476-0.045-0.0450.0000.0000.0000.000
41B41HIS00.0650.03720.882-0.013-0.0130.0000.0000.0000.000
42B42PRO00.0260.00122.704-0.026-0.0260.0000.0000.0000.000
43B43GLY00.0060.00123.4950.0210.0210.0000.0000.0000.000
44B44LYS10.8540.94224.6250.1360.1360.0000.0000.0000.000
45B45ALA00.0500.02822.999-0.031-0.0310.0000.0000.0000.000
46B46PRO0-0.018-0.01519.1390.0320.0320.0000.0000.0000.000
47B47LYS10.9050.97221.4620.0890.0890.0000.0000.0000.000
48B48LEU0-0.0110.00021.7310.0050.0050.0000.0000.0000.000
49B49LEU0-0.051-0.02821.2900.0190.0190.0000.0000.0000.000
50B50THR0-0.010-0.02621.4590.0150.0150.0000.0000.0000.000
51B51TYR00.0430.01321.754-0.029-0.0290.0000.0000.0000.000
52B52GLU-1-0.832-0.91422.822-0.011-0.0110.0000.0000.0000.000
53B53VAL0-0.048-0.00119.9220.0380.0380.0000.0000.0000.000
54B54ASN0-0.013-0.02321.783-0.008-0.0080.0000.0000.0000.000
55B55LYS10.8500.95324.7530.0100.0100.0000.0000.0000.000
56B56ARG10.9330.95825.756-0.032-0.0320.0000.0000.0000.000
57B57PRO00.0050.00626.3040.0010.0010.0000.0000.0000.000
58B58SER00.0260.00029.3910.0120.0120.0000.0000.0000.000
59B59GLY00.0090.01532.103-0.010-0.0100.0000.0000.0000.000
60B60VAL0-0.068-0.02026.2690.0020.0020.0000.0000.0000.000
61B61SER00.0140.01229.6170.0110.0110.0000.0000.0000.000
62B62ASP-1-0.858-0.95128.9010.0380.0380.0000.0000.0000.000
63B63ARG10.7630.86927.564-0.025-0.0250.0000.0000.0000.000
64B64PHE0-0.054-0.01423.3940.0160.0160.0000.0000.0000.000
65B65SER0-0.002-0.00824.241-0.001-0.0010.0000.0000.0000.000
66B66GLY00.0350.01921.3560.0100.0100.0000.0000.0000.000
67B67SER0-0.013-0.01920.3460.0130.0130.0000.0000.0000.000
68B68LYS10.9000.94116.415-0.197-0.1970.0000.0000.0000.000
69B69SER0-0.0070.00517.453-0.035-0.0350.0000.0000.0000.000
70B70GLY00.0810.04316.4530.0970.0970.0000.0000.0000.000
71B71ASN00.0350.0149.266-0.355-0.3550.0000.0000.0000.000
72B72SER00.0330.01211.7820.2130.2130.0000.0000.0000.000
73B73ALA00.008-0.00113.579-0.142-0.1420.0000.0000.0000.000
74B74SER0-0.013-0.03514.8610.1300.1300.0000.0000.0000.000
75B75LEU0-0.0030.01817.274-0.061-0.0610.0000.0000.0000.000
76B76THR0-0.031-0.02419.3360.0320.0320.0000.0000.0000.000
77B77ILE0-0.0060.00020.794-0.032-0.0320.0000.0000.0000.000
78B78SER00.007-0.00624.1720.0220.0220.0000.0000.0000.000
79B79GLY00.0480.02427.628-0.018-0.0180.0000.0000.0000.000
80B80LEU0-0.075-0.02224.136-0.014-0.0140.0000.0000.0000.000
81B81GLN00.0430.02028.0410.0020.0020.0000.0000.0000.000
82B82ALA00.0460.02027.7860.0000.0000.0000.0000.0000.000
83B83GLU-1-0.867-0.94527.588-0.020-0.0200.0000.0000.0000.000
84B84ASP-1-0.770-0.84824.4020.0060.0060.0000.0000.0000.000
85B85GLU-1-0.798-0.86122.811-0.015-0.0150.0000.0000.0000.000
86B86ALA0-0.059-0.03521.293-0.025-0.0250.0000.0000.0000.000
87B87ASP-1-0.802-0.86716.226-0.249-0.2490.0000.0000.0000.000
88B88TYR0-0.026-0.04316.003-0.001-0.0010.0000.0000.0000.000
89B89TYR0-0.0060.01312.415-0.003-0.0030.0000.0000.0000.000
90B91SER0-0.003-0.02412.968-0.161-0.1610.0000.0000.0000.000
91B92SER0-0.014-0.03313.5780.1850.1850.0000.0000.0000.000
92B93TYR0-0.0260.01015.383-0.108-0.1080.0000.0000.0000.000
93B94ASP-1-0.744-0.83013.742-0.740-0.7400.0000.0000.0000.000
94B95GLY00.0070.00915.798-0.010-0.0100.0000.0000.0000.000
95B96SER0-0.116-0.08314.040-0.023-0.0230.0000.0000.0000.000
96B97SER00.004-0.03115.000-0.002-0.0020.0000.0000.0000.000
97B98THR0-0.061-0.01917.0330.0430.0430.0000.0000.0000.000
98B99SER00.0090.00816.7110.0520.0520.0000.0000.0000.000
99B100VAL0-0.039-0.02616.1620.0360.0360.0000.0000.0000.000
100B101VAL00.0050.01610.943-0.109-0.1090.0000.0000.0000.000
101B102PHE00.033-0.01811.1680.2510.2510.0000.0000.0000.000
102B103GLY00.0040.0048.259-0.327-0.3270.0000.0000.0000.000
103B104GLY0-0.033-0.0287.232-0.052-0.0520.0000.0000.0000.000
104B105GLY00.0010.0058.1740.0700.0700.0000.0000.0000.000
105B106THR0-0.068-0.04810.5400.0870.0870.0000.0000.0000.000
106B107LYS10.8470.90213.2590.2350.2350.0000.0000.0000.000
107B108LEU0-0.032-0.00816.2690.0690.0690.0000.0000.0000.000
108B109THR0-0.060-0.05319.083-0.029-0.0290.0000.0000.0000.000
109B110VAL0-0.035-0.02822.1190.0330.0330.0000.0000.0000.000
110B111LEU0-0.050-0.04424.203-0.012-0.0120.0000.0000.0000.000
111B112GLY00.0440.02527.1490.0030.0030.0000.0000.0000.000
112B113GLN0-0.076-0.03229.4240.0000.0000.0000.0000.0000.000
113B114PRO00.024-0.00228.9800.0080.0080.0000.0000.0000.000
114B115LYS10.8310.91621.520-0.234-0.2340.0000.0000.0000.000
115B116ALA0-0.027-0.01326.1390.0030.0030.0000.0000.0000.000
116B117ALA00.0620.02924.771-0.008-0.0080.0000.0000.0000.000
117B118PRO0-0.021-0.00422.825-0.011-0.0110.0000.0000.0000.000
118B119SER00.0010.00026.0630.0120.0120.0000.0000.0000.000
119B120VAL0-0.039-0.01224.454-0.015-0.0150.0000.0000.0000.000
120B121THR0-0.030-0.01927.5530.0140.0140.0000.0000.0000.000
121B122LEU0-0.047-0.01726.858-0.011-0.0110.0000.0000.0000.000
122B123PHE0-0.0070.00129.6730.0100.0100.0000.0000.0000.000
123B124PRO00.0140.00631.106-0.009-0.0090.0000.0000.0000.000
124B125PRO00.0290.01632.188-0.002-0.0020.0000.0000.0000.000
125B126SER00.0280.02534.4040.0080.0080.0000.0000.0000.000
126B127SER00.021-0.00837.851-0.004-0.0040.0000.0000.0000.000
127B128GLU-1-0.913-0.94940.523-0.075-0.0750.0000.0000.0000.000
128B129GLU-1-0.762-0.85132.958-0.117-0.1170.0000.0000.0000.000
129B130LEU0-0.019-0.01335.662-0.004-0.0040.0000.0000.0000.000
130B131GLN0-0.029-0.00638.3870.0020.0020.0000.0000.0000.000
131B132ALA0-0.055-0.01838.5940.0000.0000.0000.0000.0000.000
132B133ASN0-0.071-0.04136.174-0.002-0.0020.0000.0000.0000.000
133B134LYS10.8720.91232.0110.1230.1230.0000.0000.0000.000
134B135ALA00.013-0.01132.1120.0120.0120.0000.0000.0000.000
135B136THR0-0.038-0.03628.166-0.016-0.0160.0000.0000.0000.000
136B137LEU0-0.0230.01427.4940.0120.0120.0000.0000.0000.000
137B138VAL00.016-0.00327.570-0.017-0.0170.0000.0000.0000.000
138B139CYS0-0.056-0.01222.4720.0040.0040.0000.0000.0000.000
139B140LEU00.0320.01825.658-0.017-0.0170.0000.0000.0000.000
140B141ILE0-0.009-0.00521.8150.0190.0190.0000.0000.0000.000
141B142SER00.0630.02025.971-0.013-0.0130.0000.0000.0000.000
142B143ASP-1-0.779-0.86828.0540.0190.0190.0000.0000.0000.000
143B144PHE00.0080.01921.4640.0120.0120.0000.0000.0000.000
144B145TYR00.0360.00524.640-0.018-0.0180.0000.0000.0000.000
145B146PRO00.0640.01920.7030.0180.0180.0000.0000.0000.000
146B147GLY00.0190.01021.8520.0050.0050.0000.0000.0000.000
147B148ALA0-0.057-0.03216.374-0.044-0.0440.0000.0000.0000.000
148B149VAL00.0010.00217.4480.0480.0480.0000.0000.0000.000
149B150THR0-0.0110.00112.370-0.046-0.0460.0000.0000.0000.000
150B151VAL0-0.012-0.01115.6910.0510.0510.0000.0000.0000.000
151B152ALA0-0.0040.01015.651-0.052-0.0520.0000.0000.0000.000
152B153TRP00.0320.00017.4710.0350.0350.0000.0000.0000.000
153B154LYS10.8140.89519.771-0.080-0.0800.0000.0000.0000.000
154B155ALA00.0540.04522.2890.0020.0020.0000.0000.0000.000
155B156ASP-1-0.760-0.87525.2810.0140.0140.0000.0000.0000.000
156B157SER0-0.092-0.06223.8150.0240.0240.0000.0000.0000.000
157B158SER0-0.0040.01821.6310.0240.0240.0000.0000.0000.000
158B159PRO0-0.012-0.01516.928-0.017-0.0170.0000.0000.0000.000
159B160VAL0-0.0120.00819.023-0.022-0.0220.0000.0000.0000.000
160B161LYS10.9450.96612.5120.5120.5120.0000.0000.0000.000
161B162ALA00.0150.00117.630-0.027-0.0270.0000.0000.0000.000
162B163GLY00.0750.03120.3470.0290.0290.0000.0000.0000.000
163B164VAL0-0.076-0.02218.5070.0210.0210.0000.0000.0000.000
164B165GLU-1-0.852-0.91719.774-0.418-0.4180.0000.0000.0000.000
165B166THR0-0.077-0.04918.6600.0510.0510.0000.0000.0000.000
166B167THR0-0.0110.01720.146-0.026-0.0260.0000.0000.0000.000
167B168LYS10.9690.97317.8230.4370.4370.0000.0000.0000.000
168B169PRO00.0000.00419.4100.0170.0170.0000.0000.0000.000
169B170SER00.0040.01222.369-0.011-0.0110.0000.0000.0000.000
170B171LYS10.8930.94625.8480.0730.0730.0000.0000.0000.000
171B172GLN00.010-0.02128.355-0.008-0.0080.0000.0000.0000.000
172B173SER00.0450.01331.4220.0030.0030.0000.0000.0000.000
173B174ASN0-0.023-0.02032.408-0.003-0.0030.0000.0000.0000.000
174B175ASN0-0.004-0.02131.2210.0040.0040.0000.0000.0000.000
175B176LYS10.8330.95828.228-0.029-0.0290.0000.0000.0000.000
176B177TYR0-0.047-0.00924.450-0.020-0.0200.0000.0000.0000.000
177B178ALA0-0.017-0.00826.3090.0160.0160.0000.0000.0000.000
178B179ALA0-0.013-0.00622.710-0.021-0.0210.0000.0000.0000.000
179B180SER0-0.004-0.00424.3670.0210.0210.0000.0000.0000.000
180B181SER00.0200.01720.565-0.022-0.0220.0000.0000.0000.000
181B182TYR0-0.001-0.01423.0670.0290.0290.0000.0000.0000.000
182B183LEU00.0170.01622.525-0.024-0.0240.0000.0000.0000.000
183B184SER0-0.028-0.01824.8660.0160.0160.0000.0000.0000.000
184B185LEU0-0.044-0.01726.102-0.017-0.0170.0000.0000.0000.000
185B186THR00.003-0.02628.3060.0060.0060.0000.0000.0000.000
186B187PRO00.0080.01031.7680.0070.0070.0000.0000.0000.000
187B188GLU-1-0.782-0.88133.681-0.092-0.0920.0000.0000.0000.000
188B189GLN00.0530.04526.2360.0040.0040.0000.0000.0000.000
189B190TRP00.0130.01730.7700.0090.0090.0000.0000.0000.000
190B191LYS10.9320.94832.1500.0600.0600.0000.0000.0000.000
191B192SER0-0.064-0.03231.1170.0070.0070.0000.0000.0000.000
192B193HIS0-0.072-0.02227.009-0.008-0.0080.0000.0000.0000.000
193B194ARG10.9200.95531.474-0.029-0.0290.0000.0000.0000.000
194B195SER0-0.049-0.04429.8030.0060.0060.0000.0000.0000.000
195B196TYR00.004-0.01625.886-0.009-0.0090.0000.0000.0000.000
196B197SER0-0.0140.00224.6070.0120.0120.0000.0000.0000.000
197B199GLN0-0.018-0.02518.9270.0170.0170.0000.0000.0000.000
198B200VAL00.030-0.00219.360-0.029-0.0290.0000.0000.0000.000
199B201THR0-0.032-0.01915.5300.0270.0270.0000.0000.0000.000
200B202HIS0-0.009-0.03318.266-0.024-0.0240.0000.0000.0000.000
201B203GLU-1-0.752-0.86018.9330.2450.2450.0000.0000.0000.000
202B204GLY0-0.0080.00917.1290.0220.0220.0000.0000.0000.000
203B205SER0-0.0030.01418.1950.0220.0220.0000.0000.0000.000
204B206THR00.012-0.00318.461-0.026-0.0260.0000.0000.0000.000
205B207VAL0-0.0260.00320.5090.0070.0070.0000.0000.0000.000
206B208GLU-1-0.799-0.89822.5780.0830.0830.0000.0000.0000.000
207B209LYS10.8740.95024.704-0.049-0.0490.0000.0000.0000.000
208B210THR00.045-0.00226.557-0.011-0.0110.0000.0000.0000.000
209B211VAL00.0030.01129.0070.0020.0020.0000.0000.0000.000
210B212ALA00.0450.01331.242-0.001-0.0010.0000.0000.0000.000
211B213PRO0-0.015-0.00133.261-0.002-0.0020.0000.0000.0000.000
212B214THR0-0.0390.00036.2880.0000.0000.0000.0000.0000.000