FMODB

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

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: KKNM3

Calculation Name: 2CXV-A-Xray547

Preferred Name:

Target Type:

Ligand Name: n-[(benzyloxy)carbonyl]-l-alanine

Ligand 3-letter code: BBL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2CXV

Chain ID: A

ChEMBL ID:

UniProt ID: P13901

Base Structure: X-ray

Registration Date: 2025-10-03

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 212
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2503862.33905
FMO2-HF: Nuclear repulsion 2421850.233461
FMO2-HF: Total energy -82012.105589
FMO2-MP2: Total energy -82249.593016


3D Structure Molmil
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(A:1:SER)


Summations of interaction energy for fragment #1(A:1: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.
6.60213.2248.84-6.551-8.912-0.045
Interaction energy analysis for fragmet #1(A:1:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.873 / q_NPA : 0.921
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].
3A3LEU00.0190.0192.9505.2607.4020.089-0.952-1.2790.000
4A4GLU-1-0.896-0.9412.394-43.570-41.3841.871-1.371-2.6850.007
5A5ILE0-0.0190.0013.8256.9377.3790.001-0.114-0.3310.000
181A181GLN00.0420.0113.097-7.362-6.7820.025-0.158-0.447-0.001
184A184GLN00.003-0.0084.5122.0572.103-0.001-0.004-0.0410.000
185A185ASN0-0.080-0.0482.289-39.445-38.2316.856-3.946-4.124-0.051
186A186ALA00.0370.0274.8711.7891.801-0.001-0.006-0.0050.000
6A6ALA00.0290.0076.0046.5316.5310.0000.0000.0000.000
7A7GLY00.0090.0087.2204.2934.2930.0000.0000.0000.000
8A8LEU0-0.072-0.0427.6053.9563.9560.0000.0000.0000.000
9A9VAL00.0310.01310.0232.5792.5790.0000.0000.0000.000
10A10ARG10.9720.97911.74522.74322.7430.0000.0000.0000.000
11A11LYS10.8710.94413.08820.00120.0010.0000.0000.0000.000
12A12ASN0-0.026-0.03314.6801.3011.3010.0000.0000.0000.000
13A13LEU0-0.0420.00215.6530.8540.8540.0000.0000.0000.000
14A14VAL0-0.021-0.00418.1030.3740.3740.0000.0000.0000.000
15A15GLN0-0.072-0.04421.3000.0410.0410.0000.0000.0000.000
16A16PHE00.0370.02024.5920.2710.2710.0000.0000.0000.000
17A17GLY00.027-0.00227.1210.0140.0140.0000.0000.0000.000
18A18VAL0-0.013-0.00230.7610.0330.0330.0000.0000.0000.000
19A19GLY00.0190.00734.2120.0400.0400.0000.0000.0000.000
20A20GLU-1-0.855-0.92737.755-7.418-7.4180.0000.0000.0000.000
21A21LYS10.9220.95940.3987.6597.6590.0000.0000.0000.000
22A22ASN0-0.037-0.02341.6060.0630.0630.0000.0000.0000.000
23A23GLY00.0440.04441.7650.1310.1310.0000.0000.0000.000
24A24SER0-0.033-0.02538.314-0.147-0.1470.0000.0000.0000.000
25A25VAL0-0.033-0.00832.492-0.001-0.0010.0000.0000.0000.000
26A26ARG10.9530.99133.6718.9198.9190.0000.0000.0000.000
27A27TRP00.025-0.01228.485-0.247-0.2470.0000.0000.0000.000
28A28VAL0-0.056-0.01729.1300.1090.1090.0000.0000.0000.000
29A29MET0-0.041-0.01724.514-0.213-0.2130.0000.0000.0000.000
30A30ASN00.0100.04220.375-0.178-0.1780.0000.0000.0000.000
31A31ALA00.0430.01721.9470.3780.3780.0000.0000.0000.000
32A32LEU0-0.0080.00414.597-0.535-0.5350.0000.0000.0000.000
33A33GLY00.0400.02518.8080.4840.4840.0000.0000.0000.000
34A34VAL0-0.024-0.02316.617-1.413-1.4130.0000.0000.0000.000
35A35LYS10.9370.94417.40914.12814.1280.0000.0000.0000.000
36A36ASP-1-0.845-0.90720.042-12.880-12.8800.0000.0000.0000.000
37A37ASP-1-0.786-0.87322.762-11.803-11.8030.0000.0000.0000.000
38A38TRP00.0610.03122.9710.4200.4200.0000.0000.0000.000
39A39LEU0-0.032-0.02621.355-0.865-0.8650.0000.0000.0000.000
40A40LEU0-0.0040.00817.9240.3340.3340.0000.0000.0000.000
41A41VAL00.0340.00021.734-0.356-0.3560.0000.0000.0000.000
42A42PRO0-0.010-0.00322.8110.2620.2620.0000.0000.0000.000
43A43SER00.012-0.00625.6060.4560.4560.0000.0000.0000.000
44A44HIS10.7950.87226.27611.98811.9880.0000.0000.0000.000
45A45ALA0-0.047-0.02328.2090.2600.2600.0000.0000.0000.000
46A46TYR00.0410.00429.3400.0680.0680.0000.0000.0000.000
47A47LYS10.8930.96232.5399.8089.8080.0000.0000.0000.000
48A48PHE0-0.026-0.01232.3510.1420.1420.0000.0000.0000.000
49A49GLU-1-0.813-0.89636.350-8.387-8.3870.0000.0000.0000.000
50A50LYS10.8500.91138.8417.0257.0250.0000.0000.0000.000
51A51ASP-1-0.810-0.90441.260-7.235-7.2350.0000.0000.0000.000
52A52TYR00.0610.02235.060-0.055-0.0550.0000.0000.0000.000
53A53GLU-1-0.927-0.97238.009-8.220-8.2200.0000.0000.0000.000
54A54MET0-0.026-0.01639.1920.0400.0400.0000.0000.0000.000
55A55MET0-0.074-0.00937.4690.1540.1540.0000.0000.0000.000
56A56GLU-1-0.896-0.94836.350-8.581-8.5810.0000.0000.0000.000
57A57PHE00.002-0.01731.378-0.124-0.1240.0000.0000.0000.000
58A58TYR00.005-0.01331.3090.0940.0940.0000.0000.0000.000
59A59PHE00.0280.00625.690-0.343-0.3430.0000.0000.0000.000
60A60ASN0-0.0090.00526.1450.0450.0450.0000.0000.0000.000
61A61ARG10.9970.98920.56513.50413.5040.0000.0000.0000.000
62A62GLY0-0.012-0.01122.5120.0900.0900.0000.0000.0000.000
63A63GLY00.0150.01223.1290.1310.1310.0000.0000.0000.000
64A64THR0-0.045-0.01426.2070.5060.5060.0000.0000.0000.000
65A65TYR0-0.026-0.01727.333-0.385-0.3850.0000.0000.0000.000
66A66TYR00.0210.00726.7230.0240.0240.0000.0000.0000.000
67A67SER0-0.026-0.01630.695-0.206-0.2060.0000.0000.0000.000
68A68ILE0-0.005-0.00132.019-0.051-0.0510.0000.0000.0000.000
69A69SER00.0500.04734.780-0.068-0.0680.0000.0000.0000.000
70A70ALA00.007-0.00434.864-0.164-0.1640.0000.0000.0000.000
71A71GLY00.0410.02335.693-0.142-0.1420.0000.0000.0000.000
72A72ASN0-0.086-0.03636.5440.1550.1550.0000.0000.0000.000
73A73VAL0-0.023-0.01031.023-0.233-0.2330.0000.0000.0000.000
74A74VAL0-0.015-0.00131.2530.1590.1590.0000.0000.0000.000
75A75ILE0-0.026-0.01529.679-0.449-0.4490.0000.0000.0000.000
76A76GLN00.0250.02127.6310.4850.4850.0000.0000.0000.000
77A77SER0-0.032-0.02327.695-0.315-0.3150.0000.0000.0000.000
78A78LEU0-0.012-0.02321.904-0.099-0.0990.0000.0000.0000.000
79A79ASP-1-0.863-0.92225.255-11.695-11.6950.0000.0000.0000.000
80A80VAL0-0.019-0.01427.5600.2990.2990.0000.0000.0000.000
81A81GLY00.0140.01830.424-0.178-0.1780.0000.0000.0000.000
82A82PHE0-0.020-0.01530.770-0.107-0.1070.0000.0000.0000.000
83A83GLN00.0770.00526.021-0.427-0.4270.0000.0000.0000.000
84A84ASP-1-0.759-0.83425.972-12.280-12.2800.0000.0000.0000.000
85A85VAL0-0.034-0.00721.2950.1220.1220.0000.0000.0000.000
86A86VAL0-0.0180.00424.7270.1650.1650.0000.0000.0000.000
87A87LEU00.0090.00721.650-0.720-0.7200.0000.0000.0000.000
88A88MET0-0.015-0.00925.0570.5830.5830.0000.0000.0000.000
89A89LYS10.8690.92626.02510.47510.4750.0000.0000.0000.000
90A90VAL00.012-0.00727.2420.4270.4270.0000.0000.0000.000
91A91PRO00.0170.00128.599-0.212-0.2120.0000.0000.0000.000
92A92THR0-0.023-0.00630.928-0.016-0.0160.0000.0000.0000.000
93A93ILE0-0.052-0.00924.640-0.072-0.0720.0000.0000.0000.000
94A94PRO0-0.041-0.02724.078-0.014-0.0140.0000.0000.0000.000
95A95LYS10.8740.94321.50413.37713.3770.0000.0000.0000.000
96A96PHE0-0.0120.00718.320-0.494-0.4940.0000.0000.0000.000
97A97ARG10.9020.95411.10724.64024.6400.0000.0000.0000.000
98A98ASP-1-0.775-0.85716.315-17.962-17.9620.0000.0000.0000.000
99A99ILE0-0.037-0.02312.046-1.596-1.5960.0000.0000.0000.000
100A100THR00.009-0.00312.951-1.258-1.2580.0000.0000.0000.000
101A101GLN0-0.036-0.03313.076-0.405-0.4050.0000.0000.0000.000
102A102HIS0-0.020-0.0087.738-3.554-3.5540.0000.0000.0000.000
103A103PHE00.0010.0119.624-2.134-2.1340.0000.0000.0000.000
104A104ILE0-0.0260.00312.127-0.511-0.5110.0000.0000.0000.000
105A105LYS10.9911.00612.88420.88220.8820.0000.0000.0000.000
106A106LYS10.9570.95515.92313.56813.5680.0000.0000.0000.000
107A107GLY0-0.012-0.00518.8580.3310.3310.0000.0000.0000.000
108A108ASP-1-0.845-0.93213.543-21.080-21.0800.0000.0000.0000.000
109A109VAL0-0.0060.00515.030-0.909-0.9090.0000.0000.0000.000
110A110PRO00.0560.00816.173-0.657-0.6570.0000.0000.0000.000
111A111ARG10.8430.92411.85123.23923.2390.0000.0000.0000.000
112A112ALA00.0020.00112.350-1.797-1.7970.0000.0000.0000.000
113A113LEU00.0160.02613.3390.0190.0190.0000.0000.0000.000
114A114ASN0-0.044-0.02716.1330.5010.5010.0000.0000.0000.000
115A115ARG10.8960.96111.23022.04722.0470.0000.0000.0000.000
116A116LEU00.0480.03510.8290.6930.6930.0000.0000.0000.000
117A117ALA00.0220.0279.933-2.324-2.3240.0000.0000.0000.000
118A118THR0-0.049-0.0319.402-0.142-0.1420.0000.0000.0000.000
119A119LEU00.0520.05311.266-1.285-1.2850.0000.0000.0000.000
120A120VAL0-0.041-0.0109.7410.1360.1360.0000.0000.0000.000
121A121THR00.017-0.02513.0390.9020.9020.0000.0000.0000.000
122A122THR0-0.059-0.03316.413-0.303-0.3030.0000.0000.0000.000
123A123VAL00.0480.03119.1970.3600.3600.0000.0000.0000.000
124A124ASN00.006-0.00722.7300.0430.0430.0000.0000.0000.000
125A125GLY00.0380.02421.3500.3650.3650.0000.0000.0000.000
126A126THR0-0.029-0.00520.344-0.466-0.4660.0000.0000.0000.000
127A127PRO0-0.053-0.04315.361-0.301-0.3010.0000.0000.0000.000
128A128MET0-0.034-0.01515.6390.2320.2320.0000.0000.0000.000
129A129LEU0-0.015-0.0079.068-1.175-1.1750.0000.0000.0000.000
130A130ILE00.0290.01912.7420.4980.4980.0000.0000.0000.000
131A131SER0-0.018-0.01312.888-1.490-1.4900.0000.0000.0000.000
132A132GLU-1-0.867-0.94413.441-17.385-17.3850.0000.0000.0000.000
133A133GLY0-0.022-0.02714.094-1.169-1.1690.0000.0000.0000.000
134A134PRO0-0.072-0.05515.729-0.308-0.3080.0000.0000.0000.000
135A135LEU00.0130.02813.5811.0641.0640.0000.0000.0000.000
136A136LYS10.8840.93417.07914.45214.4520.0000.0000.0000.000
137A137MET00.0110.01419.121-0.518-0.5180.0000.0000.0000.000
138A138GLU-1-0.852-0.90421.776-11.371-11.3710.0000.0000.0000.000
139A139GLU-1-0.901-0.97624.838-12.769-12.7690.0000.0000.0000.000
140A140LYS10.8690.91927.00310.18110.1810.0000.0000.0000.000
141A141ALA0-0.0050.02025.9430.0480.0480.0000.0000.0000.000
142A142THR00.009-0.01428.0690.1000.1000.0000.0000.0000.000
143A143TYR0-0.061-0.06626.681-0.266-0.2660.0000.0000.0000.000
144A144VAL00.0180.02030.2270.1390.1390.0000.0000.0000.000
145A145HIS00.0270.01431.142-0.587-0.5870.0000.0000.0000.000
146A146LYS10.8840.93732.6939.4059.4050.0000.0000.0000.000
147A147LYS10.8800.96034.3207.8137.8130.0000.0000.0000.000
148A148ASN0-0.048-0.05136.197-0.162-0.1620.0000.0000.0000.000
149A149ASP-1-0.825-0.87638.250-7.779-7.7790.0000.0000.0000.000
150A150GLY0-0.020-0.00738.7030.1550.1550.0000.0000.0000.000
151A151THR0-0.064-0.05939.365-0.090-0.0900.0000.0000.0000.000
152A152THR0-0.005-0.01936.218-0.213-0.2130.0000.0000.0000.000
153A153VAL0-0.026-0.00935.2870.2240.2240.0000.0000.0000.000
154A154ASP-1-0.888-0.94134.570-9.347-9.3470.0000.0000.0000.000
155A155LEU0-0.051-0.01630.4270.1260.1260.0000.0000.0000.000
156A156THR00.006-0.00530.908-0.080-0.0800.0000.0000.0000.000
157A157VAL0-0.0300.00625.7940.1030.1030.0000.0000.0000.000
158A158ASP-1-0.800-0.88327.462-10.518-10.5180.0000.0000.0000.000
159A159GLN00.009-0.00722.589-0.975-0.9750.0000.0000.0000.000
160A160ALA00.0100.00621.634-0.442-0.4420.0000.0000.0000.000
161A161TRP0-0.005-0.01715.6620.0430.0430.0000.0000.0000.000
162A162ARG10.8850.92419.69112.74512.7450.0000.0000.0000.000
163A163GLY00.0760.04917.681-0.433-0.4330.0000.0000.0000.000
164A164LYS10.9180.96418.65313.99213.9920.0000.0000.0000.000
165A165GLY00.0450.00718.578-1.045-1.0450.0000.0000.0000.000
166A166GLU-1-0.836-0.88719.953-12.018-12.0180.0000.0000.0000.000
167A167GLY00.010-0.01120.415-0.820-0.8200.0000.0000.0000.000
168A168LEU0-0.021-0.03022.4400.6320.6320.0000.0000.0000.000
169A169PRO00.032-0.00824.320-0.328-0.3280.0000.0000.0000.000
170A170GLY00.0250.02325.282-0.170-0.1700.0000.0000.0000.000
171A171MET0-0.0160.03119.535-0.386-0.3860.0000.0000.0000.000
172A172CYS00.0030.02120.315-0.628-0.6280.0000.0000.0000.000
173A173GLY00.0530.00520.9920.1170.1170.0000.0000.0000.000
174A174GLY0-0.0280.00217.269-0.570-0.5700.0000.0000.0000.000
175A175ALA0-0.003-0.00212.8930.5380.5380.0000.0000.0000.000
176A176LEU0-0.035-0.00312.840-1.215-1.2150.0000.0000.0000.000
177A177VAL00.0140.0046.943-0.759-0.7590.0000.0000.0000.000
178A178SER00.0670.0357.8910.6060.6060.0000.0000.0000.000
179A179SER0-0.006-0.0226.069-6.983-6.9830.0000.0000.0000.000
180A180ASN0-0.027-0.0045.760-5.569-5.5690.0000.0000.0000.000
182A182SER0-0.051-0.0405.4771.1331.1330.0000.0000.0000.000
183A183ILE0-0.0110.0047.9333.0103.0100.0000.0000.0000.000
187A187ILE0-0.013-0.0127.9440.3610.3610.0000.0000.0000.000
188A188LEU00.004-0.00510.6451.1851.1850.0000.0000.0000.000
189A189GLY00.0630.02613.3721.6881.6880.0000.0000.0000.000
190A190ILE0-0.0250.00915.480-1.224-1.2240.0000.0000.0000.000
191A191HIS00.0250.01218.2220.8190.8190.0000.0000.0000.000
192A192VAL0-0.012-0.00920.0240.4250.4250.0000.0000.0000.000
193A193ALA00.0490.01223.4150.6590.6590.0000.0000.0000.000
194A194GLY0-0.013-0.01623.347-0.742-0.7420.0000.0000.0000.000
195A195GLY00.0250.02324.7830.4720.4720.0000.0000.0000.000
196A196ASN0-0.009-0.01126.654-0.137-0.1370.0000.0000.0000.000
197A197SER0-0.026-0.02724.3710.1400.1400.0000.0000.0000.000
198A198ILE0-0.092-0.02922.600-0.541-0.5410.0000.0000.0000.000
199A199LEU0-0.028-0.00618.1860.3650.3650.0000.0000.0000.000
200A200VAL00.0320.00820.992-0.185-0.1850.0000.0000.0000.000
201A201ALA00.0220.00617.879-0.092-0.0920.0000.0000.0000.000
202A202LYS10.8330.93719.82413.48913.4890.0000.0000.0000.000
203A203LEU0-0.048-0.02217.361-0.917-0.9170.0000.0000.0000.000
204A204VAL00.002-0.00917.2360.8630.8630.0000.0000.0000.000
205A205THR0-0.022-0.04416.326-0.937-0.9370.0000.0000.0000.000
206A206GLN0-0.030-0.03412.5931.7761.7760.0000.0000.0000.000
207A207GLU-1-0.785-0.88817.212-16.013-16.0130.0000.0000.0000.000
208A208MET0-0.0100.03020.2800.5080.5080.0000.0000.0000.000
209A209PHE00.007-0.00516.3690.2890.2890.0000.0000.0000.000
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